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Schyma C, Müller R, Brünig J, Zieger M, Utz S, Grabmüller M. The muzzle to target distance -staining inside different parts of the firearm barrel. Int J Legal Med 2024; 138:1149-1156. [PMID: 38091066 PMCID: PMC11003904 DOI: 10.1007/s00414-023-03141-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2023] [Accepted: 11/21/2023] [Indexed: 04/11/2024]
Abstract
Biological traces inside firearm barrels were observed as a result of contact shots to the head. The present study was conducted to investigate the influence of the muzzle to target distance on staining inside the anterior and posterior part of firearm barrels. Ninety-nine shots were fired to so-called reference cubes (10% gelatine, 12 cm edge length, embedded paint-blood-pad) using three current handguns. Shot range was varied from contact to 50 cm distance. High-speed cameras recorded external backspatter. Endoscopic examination assessed visible staining along the barrel. Each two swabbings were gathered from the anterior and the posterior part of the barrel. The first swabs were submitted to quantitative PCR, the second ones to DNA-RNA-co-extraction. Thorough mechanical and chemical cleaning was performed to avoid any contamination which was controlled by negative zero swabs after each cleaning. In single shots up to 50 cm distance, minimal, but DNA-positive sporadic traces were detected inside the barrel in vicinity of the muzzle. Visible complex staining varying in extent was observed in the anterior barrel part for 10 cm or less distance in dependence of the calibre. The posterior part showed detectable traces only after close range shots (< 5 cm). Generally staining inside the barrel decreased from the muzzle to the rear end, which correlated with the yield of DNA. Some contact shots did not cause any staining in the posterior part of the barrel despite massive external backspatter. Blood-specific miRNA was primarily found where DNA was detected. This experience encourages to take a second swab for RNA analysis. The amount of nucleic acids in the barrel at varying muzzle to target distances is subject to large variations between individual shots and therefore appears not suitable for a reliable determination of the shot distance in a particular case on its own. Instead, shot range estimation should also take into account morphology and distribution of traces inside the barrel.
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Affiliation(s)
- Christian Schyma
- Institute of Forensic Medicine of the University of Bern, Murtenstrasse 26, 3008, Bern, Switzerland.
| | - Rolf Müller
- Criminal Investigation Service, Cantonal Police Department of Bern, Nordring 30, 3013, Bern, Switzerland
| | - Julia Brünig
- Institute of Forensic Medicine of the University of Bern, Murtenstrasse 26, 3008, Bern, Switzerland
| | - Martin Zieger
- Institute of Forensic Medicine of the University of Bern, Murtenstrasse 26, 3008, Bern, Switzerland
| | - Silvia Utz
- Institute of Forensic Medicine of the University of Bern, Murtenstrasse 26, 3008, Bern, Switzerland
| | - Melanie Grabmüller
- Institute of Legal Medicine, University Bonn, Stiftsplatz 12, 53111, Bonn, Germany
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2
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Nieto-Romero V, García-Torralba A, Molinos-Vicente A, Moya FJ, Rodríguez-Perales S, García-Escudero R, Salido E, Segovia JC, García-Bravo M. Restored glyoxylate metabolism after AGXT gene correction and direct reprogramming of primary hyperoxaluria type 1 fibroblasts. iScience 2024; 27:109530. [PMID: 38577102 PMCID: PMC10993186 DOI: 10.1016/j.isci.2024.109530] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2023] [Revised: 01/18/2024] [Accepted: 03/16/2024] [Indexed: 04/06/2024] Open
Abstract
Primary hyperoxaluria type 1 (PH1) is a rare inherited metabolic disorder characterized by oxalate overproduction in the liver, resulting in renal damage. It is caused by mutations in the AGXT gene. Combined liver and kidney transplantation is currently the only permanent curative treatment. We combined locus-specific gene correction and hepatic direct cell reprogramming to generate autologous healthy induced hepatocytes (iHeps) from PH1 patient-derived fibroblasts. First, site-specific AGXT corrected cells were obtained by homology directed repair (HDR) assisted by CRISPR-Cas9, following two different strategies: accurate point mutation (c.731T>C) correction or knockin of an enhanced version of AGXT cDNA. Then, iHeps were generated, by overexpression of hepatic transcription factors. Generated AGXT-corrected iHeps showed hepatic gene expression profile and exhibited in vitro reversion of oxalate accumulation compared to non-edited PH1-derived iHeps. This strategy set up a potential alternative cellular source for liver cell replacement therapy and a personalized PH1 in vitro disease model.
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Affiliation(s)
- Virginia Nieto-Romero
- Cell Technology Division, Biomedical Innovation Unit, CIEMAT (Centro de Investigaciones Energéticas, Medioambientales y Tecnológicas), Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER)-ISCIII, Instituto de Investigación Sanitaria Fundación Jiménez Díaz (IIS-FJD, UAM), 28040 Madrid, Spain
| | - Aida García-Torralba
- Cell Technology Division, Biomedical Innovation Unit, CIEMAT (Centro de Investigaciones Energéticas, Medioambientales y Tecnológicas), Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER)-ISCIII, Instituto de Investigación Sanitaria Fundación Jiménez Díaz (IIS-FJD, UAM), 28040 Madrid, Spain
| | - Andrea Molinos-Vicente
- Cell Technology Division, Biomedical Innovation Unit, CIEMAT (Centro de Investigaciones Energéticas, Medioambientales y Tecnológicas), Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER)-ISCIII, Instituto de Investigación Sanitaria Fundación Jiménez Díaz (IIS-FJD, UAM), 28040 Madrid, Spain
| | - Francisco José Moya
- Molecular Cytogenetics and Genome Editing Unit, Human Cancer Genetics Program, Centro Nacional de Investigaciones Oncológicas (CNIO), 28029 Madrid, Spain
| | - Sandra Rodríguez-Perales
- Molecular Cytogenetics and Genome Editing Unit, Human Cancer Genetics Program, Centro Nacional de Investigaciones Oncológicas (CNIO), 28029 Madrid, Spain
| | - Ramón García-Escudero
- Molecular Oncology Unit, CIEMAT (Centro de Investigaciones Energéticas, Medioambientales y Tecnológicas), Centro de Investigación Biomédica en Red de Cáncer (CIBERONC)-ISCIII, Research Institute Hospital 12 de Octubre (imas12)-University Hospital 12 de Octubre, 28040 Madrid, Spain
| | - Eduardo Salido
- Pathology Department, Hospital Universitario de Canarias, Universidad La Laguna, Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER)-ISCIII, 38320 Tenerife, Spain
| | - José-Carlos Segovia
- Cell Technology Division, Biomedical Innovation Unit, CIEMAT (Centro de Investigaciones Energéticas, Medioambientales y Tecnológicas), Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER)-ISCIII, Instituto de Investigación Sanitaria Fundación Jiménez Díaz (IIS-FJD, UAM), 28040 Madrid, Spain
| | - María García-Bravo
- Cell Technology Division, Biomedical Innovation Unit, CIEMAT (Centro de Investigaciones Energéticas, Medioambientales y Tecnológicas), Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER)-ISCIII, Instituto de Investigación Sanitaria Fundación Jiménez Díaz (IIS-FJD, UAM), 28040 Madrid, Spain
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3
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Poch A, Dougherty MP, Roman RA, Chorich L, Hawkins Z, Kim SH, Kim HG, Layman LC. Prevalence of pathogenic variants and digenic disease in patients diagnosed with normosmic hypogonadotropic hypogonadism/Kallmann Syndrome. Mol Cell Endocrinol 2024:112224. [PMID: 38593951 DOI: 10.1016/j.mce.2024.112224] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/02/2024] [Revised: 03/26/2024] [Accepted: 03/29/2024] [Indexed: 04/11/2024]
Abstract
BACKGROUND Hypogonadotropic hypogonadism (HH) is due to impaired gonadotropin releasing hormone (GnRH) action resulting in absent puberty and infertility. At least 44 genes have been identified to possess genetic variants in 40-50% of nHH/KS, and 2-20% have presumed digenic disease, but not all variants have been characterized in vitro. HYPOTHESIS The prevalence of pathogenic (P)/likely pathogenic (LP) variants in monogenic and digenic nHH/KS is lower than reported. DESIGN Cross-sectional study. SETTING University Research Laboratory. SUBJECTS 158 patients with nHH/KS. METHODS Exome sequencing (ES) was performed and variants were filtered for 44 known genes using Varsome and confirmed by Sanger Sequencing. MAIN OUTCOME MEASURES P/LP variants in nHH/KS genes. RESULTS ES resulted in >370,000 variants, from which variants in 44 genes were filtered. Thirty-one confirmed P/LP variants in 10 genes (ANOS1, CHD7, DUSP6, FGFR1, HS6ST1, KISS1, PROKR2, SEMA3A, SEMA3E, TACR3), sufficient to cause disease, were identified in 30/158 (19%) patients. Only 2/158 (1.2%) patients had digenic variant combinations: a male with hemizygous ANOS1 and heterozygous TACR3 variants and a male with heterozygous SEMA3A and SEMA3E variants. Two patients (1.2%) had compound heterozygous GNRHR (autosomal recessive) variants-one P and one variant of uncertain significance (VUS). Five patients (3.2%) had heterozygous P/LP variants in either GNRHR or TACR3 (both autosomal recessive), but no second variant. CONCLUSION Our prevalence of P/LP variants in nHH/KS was 19%, and digenicity was observed in 1.2%. These findings are less than those previously reported, and probably represent a more accurate estimation since VUS are not included.
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Affiliation(s)
- Alexandra Poch
- Section of Reproductive Endocrinology, Infertility, & Genetics, Department of Obstetrics & Gynecology, Medical College of Georgia at Augusta University, Augusta, GA, USA.
| | - Michael P Dougherty
- Section of Reproductive Endocrinology, Infertility, & Genetics, Department of Obstetrics & Gynecology, Medical College of Georgia at Augusta University, Augusta, GA, USA
| | - Robert A Roman
- Section of Reproductive Endocrinology, Infertility, & Genetics, Department of Obstetrics & Gynecology, Medical College of Georgia at Augusta University, Augusta, GA, USA
| | - Lynn Chorich
- Section of Reproductive Endocrinology, Infertility, & Genetics, Department of Obstetrics & Gynecology, Medical College of Georgia at Augusta University, Augusta, GA, USA
| | - Zoe Hawkins
- Section of Reproductive Endocrinology, Infertility, & Genetics, Department of Obstetrics & Gynecology, Medical College of Georgia at Augusta University, Augusta, GA, USA
| | - Soo-Hyun Kim
- Molecular and Clinical Sciences Research Institute, St. George's, University of London, Cranmer Terrace, London, SW17 0RE, United Kingdom
| | - Hyung-Goo Kim
- Neurological Disorders Research Center, Qatar Biomedical Research Center, Hamad Bin Khalifa University, Doha, Qatar; College of Health and Life Sciences, Hamad Bin Khalifa University, Doha, Qatar
| | - Lawrence C Layman
- Section of Reproductive Endocrinology, Infertility, & Genetics, Department of Obstetrics & Gynecology, Medical College of Georgia at Augusta University, Augusta, GA, USA; Department of Neuroscience and Regenerative Medicine, Medical College of Georgia at Augusta University, Augusta, GA, USA; Department of Physiology, Medical College of Georgia at Augusta University, Augusta, GA, USA
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4
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Cusack SE, Maihofer AX, Bustamante D, Amstadter AB, Duncan LE. Genetic influences on testosterone and PTSD. J Psychiatr Res 2024; 174:8-11. [PMID: 38598976 DOI: 10.1016/j.jpsychires.2024.04.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/16/2023] [Revised: 02/25/2024] [Accepted: 04/02/2024] [Indexed: 04/12/2024]
Abstract
Females are twice as likely to experience PTSD as compared to males. Although sex differences in prevalence are well-established, little is known about why such sex differences occur. Biological factors that vary with sex, including sex hormone production, may contribute to these differences. Considerable evidence links sex hormones, such as testosterone, to PTSD risk though less is known about the shared genetic underpinnings. The objective of the present study was to test for genetic relationships between testosterone and PTSD. To do so, we used summary statistics from large, publicly available genetic consortia to conduct linkage disequilibrium score regression to estimate the genetic correlations between PTSD and testosterone in males and females, and two-sample, bi-directional Mendelian randomization to examine potential causal relationships of testosterone on PTSD and the reverse. Heritability estimates of testosterone were significantly higher in males (0.17, SE = 0.02) than females (0.11, SE = 0.01; z = 2.46, p = 00.01). The correlation between testosterone and PTSD was negative in males (rg = -0.11, SE = 0.02, p = 6.7 x 10-6), but not significant in females (rg = 0.002, SE = 0.03, p = 0.95). MR analyses found no evidence of a causal effect of testosterone on PTSD or the reverse. Findings are consistent with phenotypic literature suggesting a relationship between testosterone and PTSD that may be sex-specific. This work provides early evidence of a relationship between testosterone and PTSD genotypically and suggests an avenue for future research that will enable a better understanding of disparities in PTSD.
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Affiliation(s)
- Shannon E Cusack
- Virginia Institute of Psychiatric and Behavioral Genetics, Virginia Commonwealth University, USA.
| | - Adam X Maihofer
- University of California San Diego, Department of Psychiatry, La Jolla, CA, USA; Veterans Affairs San Diego Healthcare System, Research Service, San Diego, CA, USA
| | - Daniel Bustamante
- Virginia Institute of Psychiatric and Behavioral Genetics, Virginia Commonwealth University, USA
| | - Ananda B Amstadter
- Virginia Institute of Psychiatric and Behavioral Genetics, Virginia Commonwealth University, USA
| | - Laramie E Duncan
- Stanford University, Department of Psychiatry and Behavioral Sciences, USA
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5
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Schyma C, Berthold M. New alginate-gelatine method for casting of staining inside firearm barrels. Int J Legal Med 2024:10.1007/s00414-024-03213-3. [PMID: 38519639 DOI: 10.1007/s00414-024-03213-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2023] [Accepted: 03/13/2024] [Indexed: 03/25/2024]
Abstract
Contact shots to the head often leave behind biological traces inside firearm barrels, a phenomenon of great forensic interest. Until now, the visualization and preservation of these traces presented a significant challenge, lacking a reliable method. This study addresses this gap by searching for a suitable method to extract the traces within a casting. Using alginate or gelatine as suitable materials, the results were hampered by serious adhesion issues and their extraction out of the firearm barrel was impeded. Finally, the combination of 11% gelatine with 1% alginate, introduced into the barrel around a 'central spine', succeeded to consistently produce replicable castings. Experimental contact shots displayed a distinct staining gradient from the muzzle to the rear of the barrel, as revealed through endoscopy and proved in the macroscopic casting. The technique proved effective for various common handgun barrels and successfully preserved blood and gunshot residue (GSR) patterns within the barrel. This method offers the dual benefits of visually mapping staining patterns and securing localized samples for targeted molecular genetic analysis in forensic investigations.
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Affiliation(s)
- Christian Schyma
- Institute of Forensic Medicine, University of Bern, Murtenstrasse 26, Bern, CH-3008, Switzerland.
| | - Matthias Berthold
- Institute of Forensic Medicine, University of Bern, Murtenstrasse 26, Bern, CH-3008, Switzerland
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6
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Hochman MJ, DeZern AE. SOHO State of the Art Updates and Next Questions: An Update on Higher Risk Myelodysplastic Syndromes. Clin Lymphoma Myeloma Leuk 2024:S2152-2650(24)00113-7. [PMID: 38594129 DOI: 10.1016/j.clml.2024.03.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/31/2024] [Revised: 03/13/2024] [Accepted: 03/14/2024] [Indexed: 04/11/2024]
Abstract
Higher-risk myelodysplastic syndromes (HR-MDS) are clonal myeloid neoplasms that cause life-limiting complications from severe cytopenias and leukemic transformation. Efforts to better classify, prognosticate, and assess therapeutic responses in HR-MDS have resulted in publication of new clinical tools in the last several years. Given limited current treatment options and suboptimal outcomes, HR-MDS stands to benefit from the study of investigational agents.Higher-risk myelodysplastic syndromes (HR-MDS) are a heterogenous group of clonal myeloid-lineage malignancies often characterized by high-risk genetic lesions, increased blood transfusion needs, constitutional symptoms, elevated risk of progression to acute myeloid leukemia (AML), and therapeutic need for allogeneic bone marrow transplantation. Use of blast percentage and other morphologic features to define myelodysplastic neoplasm subtypes is rapidly shifting to incorporate genetics, resulting in a subset of former HR-MDS patients now being considered as AML in presence of leukemia-defining genetic alterations. A proliferation of prognostic tools has further focused use of genetic features to drive decision making in clinical management. Recently, criteria to assess response of HR-MDS to therapy were revised to incorporate more clinically meaningful endpoints and better match AML response criteria. Basic science investigations have resulted in improved understanding of the relationship between MDS genetic lesions, bone marrow stromal changes, germline predispositions, and disease phenotype. However, therapeutic advances have been more limited. There has been import of the IDH1 inhibitor ivosidenib, initially approved for AML; the Bcl-2 inhibitor venetoclax and liposomal daunorubicin/cytarabine (CPX-351) are under active investigation as well. Unfortunately, effective treatment of TP53-mutated disease remains elusive, though preliminary evidence suggests improved outcomes with oral decitabine/cedazuridine over parenteral hypomethylating agent monotherapy. Investigational agents with novel mechanisms of action may help expand the repertoire of treatment options for HR-MDS and trials continue to offer a hopeful therapeutic avenue for suitable patients.
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Affiliation(s)
- Michael J Hochman
- Department of Hematology and Medical Oncology, Winship Cancer Institute of Emory University, Atlanta, GA
| | - Amy E DeZern
- Division of Hematological Malignancies, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University, Baltimore, MD.
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7
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Islam A, Manjarrez-González JC, Song X, Gore T, Draviam VM. Search for chromosomal instability aiding variants reveal naturally occurring kinetochore gene variants that perturb chromosome segregation. iScience 2024; 27:109007. [PMID: 38361632 PMCID: PMC10867425 DOI: 10.1016/j.isci.2024.109007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2023] [Revised: 10/15/2023] [Accepted: 01/19/2024] [Indexed: 02/17/2024] Open
Abstract
Chromosomal instability (CIN) is a hallmark of cancers, and CIN-promoting mutations are not fully understood. Here, we report 141 chromosomal instability aiding variant (CIVa) candidates by assessing the prevalence of loss-of-function (LoF) variants in 135 chromosome segregation genes from over 150,000 humans. Unexpectedly, we observe both heterozygous and homozygous CIVa in Astrin and SKA3, two evolutionarily conserved kinetochore and microtubule-associated proteins essential for chromosome segregation. To stratify harmful versus harmless variants, we combine live-cell microscopy and controlled protein expression. We find the naturally occurring Astrin p.Q1012∗ variant is harmful as it fails to localize normally and induces chromosome misalignment and missegregation, in a dominant negative manner. In contrast, the Astrin p.L7Qfs∗21 variant generates a shorter isoform that localizes and functions normally, and the SKA3 p.Q70Kfs∗7 variant allows wild-type SKA complex localisation and function, revealing distinct resilience mechanisms that render these variants harmless. Thus, we present a scalable framework to predict and stratify naturally occurring CIVa, and provide insight into resilience mechanisms that compensate for naturally occurring CIVa.
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Affiliation(s)
- Asifa Islam
- School of Biological and Chemical Sciences, Queen Mary, University of London, London E1 4NS, UK
| | | | - Xinhong Song
- School of Biological and Chemical Sciences, Queen Mary, University of London, London E1 4NS, UK
| | - Trupti Gore
- School of Biological and Chemical Sciences, Queen Mary, University of London, London E1 4NS, UK
- London Interdisciplinary Doctoral Program, University College London, London, UK
| | - Viji M. Draviam
- School of Biological and Chemical Sciences, Queen Mary, University of London, London E1 4NS, UK
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8
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Hu W, Ma SL, Qiong L, Du Y, Gong LP, Pan YH, Sun LP, Wen JY, Chen JN, Guan XY, Shao CK. PPM1G promotes cell proliferation via modulating mutant GOF p53 protein expression in hepatocellular carcinoma. iScience 2024; 27:109116. [PMID: 38384839 PMCID: PMC10879691 DOI: 10.1016/j.isci.2024.109116] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2023] [Revised: 11/25/2023] [Accepted: 01/31/2024] [Indexed: 02/23/2024] Open
Abstract
The serine/threonine protein phosphatase family involves series of cellular processes, such as pre-mRNA splicing. The function of one of its members, protein phosphatase, Mg2+/Mn2+ dependent 1G (PPM1G), remains unclear in hepatocellular carcinoma (HCC). Our results demonstrated that PPM1G was significantly overexpressed in HCC cells and tumor tissues compared with the normal liver tissues at both protein and RNA levels. High PPM1G expression is associated with shorter overall survival (p < 0.0001) and disease-free survival (p = 0.004) in HCC patients. Enhanced expression of PPM1G increases the cell proliferation rate, and knockdown of PPM1G led to a significant reduction in tumor volume in vivo. Further experiments illustrated that upregulated-PPM1G expression increased the protein expression of gain-of-function (GOF) mutant p53. Besides, the immunoprecipitation analysis revealed a direct interaction between PPM1G and GOF mutant p53. Collectively, PPM1G can be a powerful prognostic predictor and potential drug-target molecule.
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Affiliation(s)
- Wen Hu
- Department of Pathology, The Third Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong 510630, China
| | - Shao-Lin Ma
- Department of Gynecological Oncology, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, Guangdong 510120, China
| | - Liang Qiong
- Department of Pathology, The Third Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong 510630, China
| | - Yu Du
- Department of Pathology, The Third Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong 510630, China
| | - Li-Ping Gong
- Department of Pathology, The Third Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong 510630, China
| | - Yu-Hang Pan
- Department of Pathology, The Third Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong 510630, China
| | - Li-Ping Sun
- Department of Pathology, The Third Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong 510630, China
| | - Jing-Yun Wen
- Department of Oncology, The Third Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong 510630, China
| | - Jian-Ning Chen
- Department of Pathology, The Third Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong 510630, China
| | - Xin-Yuan Guan
- State Key Laboratory of Oncology in South China, Sun Yat-sen University Cancer Center, Guangzhou, Guangdong 510060, China
- Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, Guangdong 510060, China
- Department of Clinical Oncology, the University of Hong Kong, Hong Kong, China
| | - Chun-Kui Shao
- Department of Pathology, The Third Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong 510630, China
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9
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Vukadin L, Park B, Mohamed M, Li H, Elkholy A, Torrelli-Diljohn A, Kim JH, Jeong K, Murphy JM, Harvey CA, Dunlap S, Gehrs L, Lee H, Kim HG, Sah JP, Lee SN, Stanford D, Barrington RA, Foote JB, Sorace AG, Welner RS, Hildreth BE, Lim STS, Ahn EYE. A mouse model of Zhu-Tokita-Takenouchi-Kim syndrome reveals indispensable SON functions in organ development and hematopoiesis. JCI Insight 2024; 9:e175053. [PMID: 38290089 DOI: 10.1172/jci.insight.175053] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2023] [Accepted: 01/25/2024] [Indexed: 02/01/2024] Open
Abstract
Rare diseases are underrepresented in biomedical research, leading to insufficient awareness. Zhu-Tokita-Takenouchi-Kim (ZTTK) syndrome is a rare disease caused by genetic alterations that result in heterozygous loss of function of SON. While patients with ZTTK syndrome live with numerous symptoms, the lack of model organisms hampers our understanding of SON and this complex syndrome. Here, we developed Son haploinsufficiency (Son+/-) mice as a model of ZTTK syndrome and identified the indispensable roles of Son in organ development and hematopoiesis. Son+/- mice recapitulated clinical symptoms of ZTTK syndrome, including growth retardation, cognitive impairment, skeletal abnormalities, and kidney agenesis. Furthermore, we identified hematopoietic abnormalities in Son+/- mice, including leukopenia and immunoglobulin deficiency, similar to those observed in human patients. Surface marker analyses and single-cell transcriptome profiling of hematopoietic stem and progenitor cells revealed that Son haploinsufficiency shifted cell fate more toward the myeloid lineage but compromised lymphoid lineage development by reducing genes required for lymphoid and B cell lineage specification. Additionally, Son haploinsufficiency caused inappropriate activation of erythroid genes and impaired erythropoiesis. These findings highlight the importance of the full gene expression of Son in multiple organs. Our model serves as an invaluable research tool for this rare disease and related disorders associated with SON dysfunction.
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Affiliation(s)
- Lana Vukadin
- Department of Pathology, Division of Molecular and Cellular Pathology, and
| | - Bohye Park
- Department of Pathology, Division of Molecular and Cellular Pathology, and
| | - Mostafa Mohamed
- Department of Pathology, Division of Molecular and Cellular Pathology, and
| | - Huashi Li
- Department of Pathology, Division of Molecular and Cellular Pathology, and
| | - Amr Elkholy
- Department of Pathology, Division of Molecular and Cellular Pathology, and
| | - Alex Torrelli-Diljohn
- Department of Neurosurgery, University of Alabama at Birmingham, Birmingham, Alabama, USA
| | - Jung-Hyun Kim
- Metastasis Branch, Division of Cancer Biology, National Cancer Center, Goyang, Gyeonggi-do, South Korea
| | - Kyuho Jeong
- Department of Medicine, College of Medicine, Dongguk University, Gyeongju, South Korea
| | - James M Murphy
- Department of Pathology, Division of Molecular and Cellular Pathology, and
| | - Caitlin A Harvey
- Department of Pathology, Division of Molecular and Cellular Pathology, and
| | - Sophia Dunlap
- Department of Pathology, Division of Molecular and Cellular Pathology, and
| | - Leah Gehrs
- Department of Pathology, Division of Molecular and Cellular Pathology, and
| | - Hanna Lee
- Department of Pathology, Division of Molecular and Cellular Pathology, and
| | - Hyung-Gyoon Kim
- Department of Pathology, Division of Molecular and Cellular Pathology, and
| | - Jay Prakash Sah
- Department of Pathology, Division of Molecular and Cellular Pathology, and
| | | | - Denise Stanford
- Department of Medicine, Cystic Fibrosis Research Center, University of Alabama at Birmingham, Birmingham, Alabama, USA
| | - Robert A Barrington
- Department of Microbiology and Immunology, College of Medicine, University of South Alabama, Mobile, Alabama, USA
| | | | - Anna G Sorace
- Department of Radiology and
- O'Neal Comprehensive Cancer Center, and
| | - Robert S Welner
- O'Neal Comprehensive Cancer Center, and
- Department of Medicine, Division of Hematology and Oncology, University of Alabama at Birmingham, Birmingham, Alabama, USA
| | - Blake E Hildreth
- Department of Pathology, Division of Molecular and Cellular Pathology, and
- O'Neal Comprehensive Cancer Center, and
| | - Ssang-Taek Steve Lim
- Department of Pathology, Division of Molecular and Cellular Pathology, and
- O'Neal Comprehensive Cancer Center, and
| | - Eun-Young Erin Ahn
- Department of Pathology, Division of Molecular and Cellular Pathology, and
- O'Neal Comprehensive Cancer Center, and
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10
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Iwasaki Y, Reyes M, Jüppner H, Bastepe M. GNAS AS2 methylation status enables mechanism-based categorization of pseudohypoparathyroidism type 1B. JCI Insight 2024; 9:e177190. [PMID: 38290008 DOI: 10.1172/jci.insight.177190] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2023] [Accepted: 01/23/2024] [Indexed: 02/01/2024] Open
Abstract
Pseudohypoparathyroidism type 1B (PHP1B) results from aberrant genomic imprinting at the GNAS gene. Defining the underlying genetic cause in new patients is challenging because various genetic alterations (e.g., deletions, insertions) within the GNAS genomic region, including the neighboring STX16 gene, can cause PHP1B, and the genotype-epigenotype correlation has not been clearly established. Here, by analyzing patients with PHP1B with a wide variety of genotypes and epigenotypes, we identified a GNAS differentially methylated region (DMR) of distinct diagnostic value. This region, GNAS AS2, was hypomethylated in patients with genetic alterations located centromeric but not telomeric of this DMR. The AS2 methylation status was captured by a single probe of the methylation-sensitive multiplex ligation-dependent probe amplification (MS-MLPA) assay utilized to diagnose PHP1B. In human embryonic stem cells, where NESP55 transcription regulates GNAS methylation status on the maternal allele, AS2 methylation depended on 2 imprinting control regions (STX16-ICR and NESP-ICR) essential for NESP55 transcription. These results suggest that the AS2 methylation status in patients with PHP1B reflects the position at which the genetic alteration affects NESP55 transcription during an early embryonic period. Therefore, AS2 methylation levels can enable mechanistic PHP1B categorization based on genotype-epigenotype correlation and, thus, help identify the underlying molecular defect in patients.
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Affiliation(s)
- Yorihiro Iwasaki
- Endocrine Unit, Department of Medicine, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts, USA
- Tazuke Kofukai Medical Research Institute, Kitano Hospital, Osaka, Japan
| | - Monica Reyes
- Endocrine Unit, Department of Medicine, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts, USA
| | - Harald Jüppner
- Endocrine Unit, Department of Medicine, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts, USA
- Pediatric Nephrology Unit, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts, USA
| | - Murat Bastepe
- Endocrine Unit, Department of Medicine, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts, USA
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11
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Folpe AL. Xanthogranulomatous Epithelial Tumors and Keratin-Positive Giant Cell Rich Tumors of Soft Tissue and Bone: Two Sides of the Same Coin. Surg Pathol Clin 2024; 17:57-64. [PMID: 38278607 DOI: 10.1016/j.path.2023.07.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2024]
Abstract
Xanthogranulomatous epithelial tumor is a recently described soft tissue tumor characterized by subcutaneous location, partial encapsulation, a xanthogranulomatous inflammatory cell infiltrate, and keratin-positive mononuclear cells. It shares some morphologic features with keratin-positive, giant cell-rich soft tissue tumors. Both have recently been shown to harbor HMGA2::NCOR2 fusions. The relationship between these tumors and their differential diagnosis with other osteoclast-containing soft tissue tumors is discussed.
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Affiliation(s)
- Andrew L Folpe
- Department of Pathology and Laboratory Medicine, Mayo Clinic, Rochester, MN 55905, USA.
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12
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Iadarola MJ, Sapio MR, Loydpierson AJ, Mervis CB, Fehrenbacher JC, Vasko MR, Maric D, Eisenberg DP, Nash TA, Kippenhan JS, Garvey MH, Mannes AJ, Gregory MD, Berman KF. Syntaxin1A overexpression and pain insensitivity in individuals with 7q11.23 duplication syndrome. JCI Insight 2024; 9:e176147. [PMID: 38261410 DOI: 10.1172/jci.insight.176147] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2023] [Accepted: 01/11/2024] [Indexed: 01/25/2024] Open
Abstract
Genetic modifications leading to pain insensitivity phenotypes, while rare, provide invaluable insights into the molecular biology of pain and reveal targets for analgesic drugs. Pain insensitivity typically results from Mendelian loss-of-function mutations in genes expressed in nociceptive (pain-sensing) dorsal root ganglion (DRG) neurons that connect the body to the spinal cord. We document a pain insensitivity mechanism arising from gene overexpression in individuals with the rare 7q11.23 duplication syndrome (Dup7), who have 3 copies of the approximately 1.5-megabase Williams syndrome (WS) critical region. Based on parental accounts and pain ratings, people with Dup7, mainly children in this study, are pain insensitive following serious injury to skin, bones, teeth, or viscera. In contrast, diploid siblings (2 copies of the WS critical region) and individuals with WS (1 copy) show standard reactions to painful events. A converging series of human assessments and cross-species cell biological and transcriptomic studies identified 1 likely candidate in the WS critical region, STX1A, as underlying the pain insensitivity phenotype. STX1A codes for the synaptic vesicle fusion protein syntaxin1A. Excess syntaxin1A was demonstrated to compromise neuropeptide exocytosis from nociceptive DRG neurons. Taken together, these data indicate a mechanism for producing "genetic analgesia" in Dup7 and offer previously untargeted routes to pain control.
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Affiliation(s)
- Michael J Iadarola
- Department of Perioperative Medicine, Clinical Center, National Institutes of Health (NIH), Bethesda, Maryland, USA
| | - Matthew R Sapio
- Department of Perioperative Medicine, Clinical Center, National Institutes of Health (NIH), Bethesda, Maryland, USA
| | - Amelia J Loydpierson
- Department of Perioperative Medicine, Clinical Center, National Institutes of Health (NIH), Bethesda, Maryland, USA
| | - Carolyn B Mervis
- Neurodevelopmental Sciences Laboratory, Department of Psychological and Brain Sciences, University of Louisville, Louisville, Kentucky, USA
| | - Jill C Fehrenbacher
- Department of Pharmacology & Toxicology, Indiana University School of Medicine, Indianapolis, Indiana, USA
| | - Michael R Vasko
- Department of Pharmacology & Toxicology, Indiana University School of Medicine, Indianapolis, Indiana, USA
| | - Dragan Maric
- Flow and Imaging Cytometry Core Facility, National Institute of Neurological Disorders and Stroke (NINDS), and
| | - Daniel P Eisenberg
- Clinical and Translational Neuroscience Branch, National Institute of Mental Health (NIMH), NIH, Bethesda, Maryland, USA
| | - Tiffany A Nash
- Clinical and Translational Neuroscience Branch, National Institute of Mental Health (NIMH), NIH, Bethesda, Maryland, USA
| | - J Shane Kippenhan
- Clinical and Translational Neuroscience Branch, National Institute of Mental Health (NIMH), NIH, Bethesda, Maryland, USA
| | - Madeline H Garvey
- Clinical and Translational Neuroscience Branch, National Institute of Mental Health (NIMH), NIH, Bethesda, Maryland, USA
| | - Andrew J Mannes
- Department of Perioperative Medicine, Clinical Center, National Institutes of Health (NIH), Bethesda, Maryland, USA
| | - Michael D Gregory
- Clinical and Translational Neuroscience Branch, National Institute of Mental Health (NIMH), NIH, Bethesda, Maryland, USA
| | - Karen F Berman
- Clinical and Translational Neuroscience Branch, National Institute of Mental Health (NIMH), NIH, Bethesda, Maryland, USA
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13
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Prakasam G, Mishra A, Christie A, Miyata J, Carrillo D, Tcheuyap VT, Ye H, Do QN, Wang Y, Reig Torras O, Butti R, Zhong H, Gagan J, Jones KB, Carroll TJ, Modrusan Z, Durinck S, Requena-Komuro MC, Williams NS, Pedrosa I, Wang T, Rakheja D, Kapur P, Brugarolas J. Comparative genomics incorporating translocation renal cell carcinoma mouse model reveals molecular mechanisms of tumorigenesis. J Clin Invest 2024; 134:e170559. [PMID: 38386415 PMCID: PMC10977987 DOI: 10.1172/jci170559] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2023] [Accepted: 02/06/2024] [Indexed: 02/24/2024] Open
Abstract
Translocation renal cell carcinoma (tRCC) most commonly involves an ASPSCR1-TFE3 fusion, but molecular mechanisms remain elusive and animal models are lacking. Here, we show that human ASPSCR1-TFE3 driven by Pax8-Cre (a credentialed clear cell RCC driver) disrupted nephrogenesis and glomerular development, causing neonatal death, while the clear cell RCC failed driver, Sglt2-Cre, induced aggressive tRCC (as well as alveolar soft part sarcoma) with complete penetrance and short latency. However, in both contexts, ASPSCR1-TFE3 led to characteristic morphological cellular changes, loss of epithelial markers, and an epithelial-mesenchymal transition. Electron microscopy of tRCC tumors showed lysosome expansion, and functional studies revealed simultaneous activation of autophagy and mTORC1 pathways. Comparative genomic analyses encompassing an institutional human tRCC cohort (including a hitherto unreported SFPQ-TFEB fusion) and a variety of tumorgraft models (ASPSCR1-TFE3, PRCC-TFE3, SFPQ-TFE3, RBM10-TFE3, and MALAT1-TFEB) disclosed significant convergence in canonical pathways (cell cycle, lysosome, and mTORC1) and less established pathways such as Myc, E2F, and inflammation (IL-6/JAK/STAT3, interferon-γ, TLR signaling, systemic lupus, etc.). Therapeutic trials (adjusted for human drug exposures) showed antitumor activity of cabozantinib. Overall, this study provides insight into MiT/TFE-driven tumorigenesis, including the cell of origin, and characterizes diverse mouse models available for research.
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Affiliation(s)
- Gopinath Prakasam
- Kidney Cancer Program, Simmons Comprehensive Cancer Center
- Hematology-Oncology Division, Department of Internal Medicine
| | - Akhilesh Mishra
- Kidney Cancer Program, Simmons Comprehensive Cancer Center
- Hematology-Oncology Division, Department of Internal Medicine
| | - Alana Christie
- Kidney Cancer Program, Simmons Comprehensive Cancer Center
- Peter O’ Donnell Jr. School of Public Health
| | - Jeffrey Miyata
- Kidney Cancer Program, Simmons Comprehensive Cancer Center
- Hematology-Oncology Division, Department of Internal Medicine
| | - Deyssy Carrillo
- Kidney Cancer Program, Simmons Comprehensive Cancer Center
- Hematology-Oncology Division, Department of Internal Medicine
| | - Vanina T. Tcheuyap
- Kidney Cancer Program, Simmons Comprehensive Cancer Center
- Hematology-Oncology Division, Department of Internal Medicine
| | - Hui Ye
- Kidney Cancer Program, Simmons Comprehensive Cancer Center
- Hematology-Oncology Division, Department of Internal Medicine
| | | | - Yunguan Wang
- Quantitative Biomedical Research Center, Department of Population and Data Sciences, The University of Texas Southwestern Medical Center, Dallas, Texas, USA
| | - Oscar Reig Torras
- Kidney Cancer Program, Simmons Comprehensive Cancer Center
- Department of Medical Oncology and Translational Genomics and Targeted Therapies in Solid Tumors, Institut d’Investigacions Biomèdiques August Pi I Sunyer (IDIBAPS), Hospital Clinic de Barcelona, Barcelona, Spain
| | - Ramesh Butti
- Kidney Cancer Program, Simmons Comprehensive Cancer Center
- Hematology-Oncology Division, Department of Internal Medicine
| | - Hua Zhong
- Kidney Cancer Program, Simmons Comprehensive Cancer Center
- Department of Pathology, The University of Texas Southwestern Medical Center, Dallas, Texas, USA
| | - Jeffrey Gagan
- Department of Pathology, The University of Texas Southwestern Medical Center, Dallas, Texas, USA
| | - Kevin B. Jones
- Department of Orthopaedics and Oncological Sciences, Huntsman Cancer Institute, University of Utah, Salt Lake City, Utah, USA
| | - Thomas J. Carroll
- Department of Molecular Biology and Department of Internal Medicine, The University of Texas Southwestern Medical Center, Dallas, Texas, USA
| | - Zora Modrusan
- Department of Microchemistry, Proteomics, Lipidomics and Next Generation Sequencing and
| | - Steffen Durinck
- Department of Oncology Bioinformatics, Genentech Inc., South San Francisco, California, USA
| | - Mai-Carmen Requena-Komuro
- Kidney Cancer Program, Simmons Comprehensive Cancer Center
- Hematology-Oncology Division, Department of Internal Medicine
| | | | - Ivan Pedrosa
- Kidney Cancer Program, Simmons Comprehensive Cancer Center
- Department of Radiology, and
- Advanced Imaging Research Center, and
- Department of Urology, The University of Texas Southwestern Medical Center, Dallas, Texas, USA
| | - Tao Wang
- Kidney Cancer Program, Simmons Comprehensive Cancer Center
- Peter O’ Donnell Jr. School of Public Health
- Quantitative Biomedical Research Center, Department of Population and Data Sciences, The University of Texas Southwestern Medical Center, Dallas, Texas, USA
| | - Dinesh Rakheja
- Department of Pathology, The University of Texas Southwestern Medical Center, Dallas, Texas, USA
| | - Payal Kapur
- Kidney Cancer Program, Simmons Comprehensive Cancer Center
- Department of Pathology, The University of Texas Southwestern Medical Center, Dallas, Texas, USA
- Department of Urology, The University of Texas Southwestern Medical Center, Dallas, Texas, USA
| | - James Brugarolas
- Kidney Cancer Program, Simmons Comprehensive Cancer Center
- Hematology-Oncology Division, Department of Internal Medicine
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14
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Maharaj AV, Cottrell E, Thanasupawat T, Joustra SD, Triggs-Raine B, Fujimoto M, Kant SG, van der Kaay D, Clement-de Boers A, Brooks AS, Aguirre GA, Martín Del Estal I, Castilla de Cortázar Larrea MI, Massoud A, van Duyvenvoorde HA, De Bruin C, Hwa V, Klonisch T, Hombach-Klonisch S, Storr HL. Characterization of HMGA2 variants expands the spectrum of Silver-Russell syndrome. JCI Insight 2024; 9:e169425. [PMID: 38516887 DOI: 10.1172/jci.insight.169425] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2023] [Accepted: 02/08/2024] [Indexed: 03/23/2024] Open
Abstract
Silver-Russell syndrome (SRS) is a heterogeneous disorder characterized by intrauterine and postnatal growth retardation. HMGA2 variants are a rare cause of SRS and its functional role in human linear growth is unclear. Patients with suspected SRS negative for 11p15LOM/mUPD7 underwent whole-exome and/or targeted-genome sequencing. Mutant HMGA2 protein expression and nuclear localization were assessed. Two Hmga2-knockin mouse models were generated. Five clinical SRS patients harbored HMGA2 variants with differing functional impacts: 2 stop-gain nonsense variants (c.49G>T, c.52C>T), c.166A>G missense variant, and 2 frameshift variants (c.144delC, c.145delA) leading to an identical, extended-length protein. Phenotypic features were highly variable. Nuclear localization was reduced/absent for all variants except c.166A>G. Homozygous knockin mice recapitulating the c.166A>G variant (Hmga2K56E) exhibited a growth-restricted phenotype. An Hmga2Ter76-knockin mouse model lacked detectable full-length Hmga2 protein, similarly to patient 3 and 5 variants. These mice were infertile, with a pygmy phenotype. We report a heterogeneous group of individuals with SRS harboring variants in HMGA2 and describe the first Hmga2 missense knockin mouse model (Hmga2K56E) to our knowledge causing a growth-restricted phenotype. In patients with clinical features of SRS but negative genetic screening, HMGA2 should be included in next-generation sequencing testing approaches.
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Affiliation(s)
- Avinaash V Maharaj
- Centre for Endocrinology, William Harvey Research Institute, QMUL, London, United Kingdom
| | - Emily Cottrell
- Centre for Endocrinology, William Harvey Research Institute, QMUL, London, United Kingdom
| | - Thatchawan Thanasupawat
- Department of Human Anatomy and Cell Science, University of Manitoba, Winnipeg, Manitoba, Canada
| | - Sjoerd D Joustra
- Division of Paediatric Endocrinology, Department of Paediatrics, Willem-Alexander Children's Hospital, Leiden University Medical Centre, Leiden, Netherlands
| | - Barbara Triggs-Raine
- Department of Biochemistry and Medical Genetics, University of Manitoba, Winnipeg, Manitoba, Canada
| | - Masanobu Fujimoto
- Cincinnati Center for Growth Disorders, Division of Endocrinology, Cincinnati Children's Hospital Medical Center, Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, USA
| | - Sarina G Kant
- Division of Paediatric Endocrinology, Department of Paediatrics, Willem-Alexander Children's Hospital, Leiden University Medical Centre, Leiden, Netherlands
| | - Danielle van der Kaay
- Division of Paediatric Endocrinology, Department of Paediatrics, Erasmus University Medical Centre, Sophia Children's Hospital, Rotterdam, Netherlands
| | - Agnes Clement-de Boers
- Department of Paediatrics, Juliana Children's Hospital/Haga Teaching Hospital, The Hague, Netherlands
| | - Alice S Brooks
- Department of Clinical Genetics, Erasmus MC University Medical Center, Rotterdam, Netherlands
| | | | | | | | - Ahmed Massoud
- Department of Paediatrics and Child Health, HCA Healthcare UK, London, United Kingdom
| | - Hermine A van Duyvenvoorde
- Laboratory for Diagnostic Genome analysis (LDGA), Department of Clinical Genetics, Leiden University Medical Centre, Leiden, Netherlands
| | - Christiaan De Bruin
- Division of Paediatric Endocrinology, Department of Paediatrics, Willem-Alexander Children's Hospital, Leiden University Medical Centre, Leiden, Netherlands
| | - Vivian Hwa
- Cincinnati Center for Growth Disorders, Division of Endocrinology, Cincinnati Children's Hospital Medical Center, Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, USA
| | - Thomas Klonisch
- Department of Human Anatomy and Cell Science, University of Manitoba, Winnipeg, Manitoba, Canada
- Department of Pathology, and
- Department of Medical Microbiology and Infectious Diseases, University of Manitoba, Winnipeg, Manitoba, Canada
| | - Sabine Hombach-Klonisch
- Department of Human Anatomy and Cell Science, University of Manitoba, Winnipeg, Manitoba, Canada
- Department of Pathology, and
| | - Helen L Storr
- Centre for Endocrinology, William Harvey Research Institute, QMUL, London, United Kingdom
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15
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Shan Z, Li S, Gao Y, Jian C, Ti X, Zuo H, Wang Y, Zhao G, Wang Y, Zhang Q. mtDNA extramitochondrial replication mediates mitochondrial defect effects. iScience 2024; 27:108970. [PMID: 38322987 PMCID: PMC10844862 DOI: 10.1016/j.isci.2024.108970] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2023] [Revised: 11/09/2023] [Accepted: 01/16/2024] [Indexed: 02/08/2024] Open
Abstract
A high ratio of severe mitochondrial defects causes multiple human mitochondrial diseases. However, until now, the in vivo rescue signal of such mitochondrial defect effects has not been clear. Here, we built fly mitochondrial defect models by knocking down the essential mitochondrial genes dMterf4 and dMrps23. Following genome-wide RNAi screens, we found that knockdown of Med8/Tfb4/mtSSB/PolG2/mtDNA-helicase rescued dMterf4/dMrps23 RNAi-mediated mitochondrial defect effects. Extremely surprisingly, they drove mtDNA replication outside mitochondria through the Med8/Tfb4-mtSSB/PolG2/mtDNA-helicase axis to amplify cytosolic mtDNA, leading to activation of the cGAS-Sting-like IMD pathway to partially mediate dMterf4/dMrps23 RNAi-triggered effects. Moreover, we found that the Med8/Tfb4-mtSSB/PolG2/mtDNA-helicase axis also mediated other fly mitochondrial gene defect-triggered dysfunctions and Drosophila aging. Overall, our study demarcates the Med8/Tfb4-mtSSB/PolG2/mtDNA-helicase axis as a candidate mechanism to mediate mitochondrial defect effects through driving mtDNA extramitochondrial replication; dysfunction of this axis might be used for potential treatments for many mitochondrial and age-related diseases.
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Affiliation(s)
- Zhaoliang Shan
- State Key Laboratory of Pharmaceutical Biotechnology and MOE Key Laboratory of Model Animals for Disease Study, Jiangsu Key Laboratory of Molecular Medicine, Model Animal Research Center, School of Medicine, Nanjing University, Nanjing 210061, China
| | - Shengnan Li
- State Key Laboratory of Pharmaceutical Biotechnology and MOE Key Laboratory of Model Animals for Disease Study, Jiangsu Key Laboratory of Molecular Medicine, Model Animal Research Center, School of Medicine, Nanjing University, Nanjing 210061, China
| | - Yuxue Gao
- State Key Laboratory of Pharmaceutical Biotechnology and MOE Key Laboratory of Model Animals for Disease Study, Jiangsu Key Laboratory of Molecular Medicine, Model Animal Research Center, School of Medicine, Nanjing University, Nanjing 210061, China
| | - Chunhua Jian
- State Key Laboratory of Pharmaceutical Biotechnology and MOE Key Laboratory of Model Animals for Disease Study, Jiangsu Key Laboratory of Molecular Medicine, Model Animal Research Center, School of Medicine, Nanjing University, Nanjing 210061, China
| | - Xiuxiu Ti
- State Key Laboratory of Pharmaceutical Biotechnology and MOE Key Laboratory of Model Animals for Disease Study, Jiangsu Key Laboratory of Molecular Medicine, Model Animal Research Center, School of Medicine, Nanjing University, Nanjing 210061, China
| | - Hui Zuo
- State Key Laboratory of Pharmaceutical Biotechnology and MOE Key Laboratory of Model Animals for Disease Study, Jiangsu Key Laboratory of Molecular Medicine, Model Animal Research Center, School of Medicine, Nanjing University, Nanjing 210061, China
| | - Ying Wang
- State Key Laboratory of Pharmaceutical Biotechnology and MOE Key Laboratory of Model Animals for Disease Study, Jiangsu Key Laboratory of Molecular Medicine, Model Animal Research Center, School of Medicine, Nanjing University, Nanjing 210061, China
| | - Guochun Zhao
- State Key Laboratory of Pharmaceutical Biotechnology and MOE Key Laboratory of Model Animals for Disease Study, Jiangsu Key Laboratory of Molecular Medicine, Model Animal Research Center, School of Medicine, Nanjing University, Nanjing 210061, China
| | - Yan Wang
- Department of Cardiovascular Medicine, Beijing Hospital, National Center of Gerontology, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing, China
| | - Qing Zhang
- State Key Laboratory of Pharmaceutical Biotechnology and MOE Key Laboratory of Model Animals for Disease Study, Jiangsu Key Laboratory of Molecular Medicine, Model Animal Research Center, School of Medicine, Nanjing University, Nanjing 210061, China
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16
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Lappo E, Rosenberg NA. Solving the Arizona search problem by imputation. iScience 2024; 27:108831. [PMID: 38323008 PMCID: PMC10845060 DOI: 10.1016/j.isci.2024.108831] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2023] [Revised: 11/03/2023] [Accepted: 01/03/2024] [Indexed: 02/08/2024] Open
Abstract
An "Arizona search" is an evaluation of the numbers of pairs of profiles in a forensic-genetic database that possess partial or complete genotypic matches; such a search assists in establishing the extent to which a set of loci provides unique identifications. In forensic genetics, however, the potential for performing Arizona searches is constrained by the limited availability of actual forensic profiles for research purposes. Here, we use genotype imputation to circumvent this problem. From a database of genomes, we impute genotypes of forensic short-tandem-repeat (STR) loci from neighboring single-nucleotide polymorphisms (SNPs), searching for partial STR matches using the imputed profiles. We compare the distributions of the numbers of partial matches in imputed and actual profiles, finding close agreement. Despite limited potential for performing Arizona searches with actual forensic STR profiles, the questions that such searches seek to answer can be posed with imputation-based Arizona searches in increasingly large SNP databases.
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Affiliation(s)
- Egor Lappo
- Department of Biology, Stanford University, Stanford, CA, USA
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17
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Özcan GG, Lim S, Canning T, Tirathdas L, Donnelly J, Kundu T, Rihel J. Genetic and chemical disruption of amyloid precursor protein processing impairs zebrafish sleep maintenance. iScience 2024; 27:108870. [PMID: 38318375 PMCID: PMC10839650 DOI: 10.1016/j.isci.2024.108870] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2022] [Revised: 10/12/2023] [Accepted: 01/08/2024] [Indexed: 02/07/2024] Open
Abstract
Amyloid precursor protein (APP) is a brain-rich, single pass transmembrane protein that is proteolytically processed into multiple products, including amyloid-beta (Aβ), a major driver of Alzheimer disease (AD). Although both overexpression of APP and exogenously delivered Aβ lead to changes in sleep, whether APP processing plays an endogenous role in regulating sleep is unknown. Here, we demonstrate that APP processing into Aβ40 and Aβ42 is conserved in zebrafish and then describe sleep/wake phenotypes in loss-of-function appa and appb mutants. Larvae with mutations in appa had reduced waking activity, whereas larvae that lacked appb had shortened sleep bout durations at night. Treatment with the γ-secretase inhibitor DAPT also shortened night sleep bouts, whereas the BACE-1 inhibitor lanabecestat lengthened sleep bouts. Intraventricular injection of P3 also shortened night sleep bouts, suggesting that the proper balance of Appb proteolytic processing is required for normal sleep maintenance in zebrafish.
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Affiliation(s)
- Güliz Gürel Özcan
- Department of Cell and Developmental Biology, University College London, London, UK
| | - Sumi Lim
- Department of Cell and Developmental Biology, University College London, London, UK
| | - Thomas Canning
- Department of Biostatistics and Health Informatics, Institute of Psychiatry, Psychology and Neuroscience, King’s College London, London, UK
- Social, Genetic & Developmental Psychiatry Centre, Institute of Psychiatry, Psychology & Neuroscience, King’s College London, London, UK
| | - Lavitasha Tirathdas
- Department of Cell and Developmental Biology, University College London, London, UK
| | - Joshua Donnelly
- Department of Cell and Developmental Biology, University College London, London, UK
| | - Tanushree Kundu
- Department of Cell and Developmental Biology, University College London, London, UK
| | - Jason Rihel
- Department of Cell and Developmental Biology, University College London, London, UK
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18
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Folpe AL. Vascular tumors of intermediate malignancy: An update. Hum Pathol 2024:S0046-8177(24)00014-5. [PMID: 38360216 DOI: 10.1016/j.humpath.2024.01.014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/22/2024] [Revised: 01/29/2024] [Accepted: 01/30/2024] [Indexed: 02/17/2024]
Abstract
The term "hemangioendothelioma" is used for endothelial neoplasms of intermediate malignancy and describes a group of rare neoplasms having biologic behavior falling in between that of the benign hemangiomas and fully malignant angiosarcomas. The hemangioendotheliomas fall into several specific, clinicopathologically and genetically distinct entities, specifically epithelioid hemangioendothelioma, kaposiform hemangioendothelioma, papillary intralymphatic angioendothelioma and retiform hemangioendothelioma (hobnailed hemangioendothelioma), pseudomyogenic hemangioendothelioma, composite hemangioendothelioma, and YAP1::TFE3-fused hemangioendothelioma. The clinical, morphologic, immunohistochemical, and genetic features, and the differential diagnosis of each of these rare entities are discussed in this review.
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Affiliation(s)
- Andrew L Folpe
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, 55902, United States.
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19
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Johnson JL, Sargsyan D, Neiman EM, Hart A, Stojmirovic A, Kosoy R, Irizar H, Suárez-Fariñas M, Song WM, Argmann C, Avey S, Shmuel-Galia L, Vierbuchen T, Bongers G, Sun Y, Edelstein L, Perrigoue J, Towne JE, Hall AO, Fitzgerald KA, Hoebe K. Gene coexpression networks reveal a broad role for lncRNAs in inflammatory bowel disease. JCI Insight 2024; 9:e168988. [PMID: 38329124 DOI: 10.1172/jci.insight.168988] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2023] [Accepted: 12/26/2023] [Indexed: 02/09/2024] Open
Abstract
The role of long noncoding RNAs (lncRNAs) in disease is incompletely understood, but their regulation of inflammation is increasingly appreciated. We addressed the extent of lncRNA involvement in inflammatory bowel disease (IBD) using biopsy-derived RNA-sequencing data from a large cohort of deeply phenotyped patients with IBD. Weighted gene correlation network analysis revealed gene modules of lncRNAs coexpressed with protein-coding genes enriched for biological pathways, correlated with epithelial and immune cell signatures, or correlated with distal colon expression. Correlation of modules with clinical features uncovered a module correlated with disease severity, with an enriched interferon response signature containing the hub lncRNA IRF1-AS1. Connecting genes to IBD-associated single nucleotide polymorphisms (SNPs) revealed an enrichment of SNP-adjacent lncRNAs in biologically relevant modules. Ulcerative colitis-specific SNPs were enriched in distal colon-related modules, suggesting that disease-specific mechanisms may result from altered lncRNA expression. The function of the IBD-associated SNP-adjacent lncRNA IRF1-AS1 was explored in human myeloid cells, and our results suggested IRF1-AS1 promoted optimal production of TNF-α, IL-6, and IL-23. A CRISPR/Cas9-mediated activation screen in THP-1 cells revealed several lncRNAs that modulated LPS-induced TNF-α responses. Overall, this study uncovered the expression patterns of lncRNAs in IBD that identify functional, disease-relevant lncRNAs.
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Affiliation(s)
- John L Johnson
- Johnson & Johnson Innovative Medicine, Spring House, Pennsylvania, USA
| | - Davit Sargsyan
- Johnson & Johnson Innovative Medicine, Spring House, Pennsylvania, USA
| | - Eric M Neiman
- Johnson & Johnson Innovative Medicine, Spring House, Pennsylvania, USA
| | - Amy Hart
- Johnson & Johnson Innovative Medicine, Spring House, Pennsylvania, USA
| | | | - Roman Kosoy
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, Icahn Institute for Data Science and Genomic Technology, New York, New York, USA
| | - Haritz Irizar
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, Icahn Institute for Data Science and Genomic Technology, New York, New York, USA
| | - Mayte Suárez-Fariñas
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, Icahn Institute for Data Science and Genomic Technology, New York, New York, USA
- Center for Biostatistics, Department of Population Health Science and Policy, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Won-Min Song
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, Icahn Institute for Data Science and Genomic Technology, New York, New York, USA
| | - Carmen Argmann
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, Icahn Institute for Data Science and Genomic Technology, New York, New York, USA
| | - Stefan Avey
- Johnson & Johnson Innovative Medicine, Spring House, Pennsylvania, USA
| | - Liraz Shmuel-Galia
- Program in Innate Immunity, Department of Medicine, University of Massachusetts Chan Medical School, Worcester, Massachusetts, USA
| | - Tim Vierbuchen
- Program in Innate Immunity, Department of Medicine, University of Massachusetts Chan Medical School, Worcester, Massachusetts, USA
| | - Gerold Bongers
- Johnson & Johnson Innovative Medicine, Spring House, Pennsylvania, USA
| | - Yu Sun
- Johnson & Johnson Innovative Medicine, Spring House, Pennsylvania, USA
| | - Leonard Edelstein
- Johnson & Johnson Innovative Medicine, Spring House, Pennsylvania, USA
| | | | - Jennifer E Towne
- Johnson & Johnson Innovative Medicine, Spring House, Pennsylvania, USA
| | - Aisling O'Hara Hall
- Immunology Translational Early Development, Bristol Myers Squibb, Summit, New Jersey, USA
| | - Katherine A Fitzgerald
- Program in Innate Immunity, Department of Medicine, University of Massachusetts Chan Medical School, Worcester, Massachusetts, USA
| | - Kasper Hoebe
- Johnson & Johnson Innovative Medicine, Spring House, Pennsylvania, USA
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20
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Tsuji S, Wenning G. New Horizon of Multiple System Atrophy Research. Cerebellum 2024; 23:1. [PMID: 38307991 DOI: 10.1007/s12311-024-01667-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/04/2024]
Affiliation(s)
- Shoji Tsuji
- Institute of Medical Genomics, International University of Health and Welfare, 4-3, Kozunomori, Chiba, 286-8686, Japan.
- Department of Neurology, The University of Tokyo Hospital, 7-3-1 Hongo, Bunkyo-Ku, Tokyo, 113-8655, Japan.
| | - Gregor Wenning
- Director Division of Clinical Neurobiology, Medical University MUI, MZA | Anichstrasse 35, Innsbruck, A-6020, Austria
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21
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Camarena V, Williams MM, Morales AA, Zafeer MF, Kilic OV, Kamiar A, Abad C, Rasmussen MA, Briski LM, Peart L, Bademci G, Barbouth DS, Smithson S, Wang G, Shehadeh LA, Walz K, Tekin M. ADAMTSL2 mutations determine the phenotypic severity in geleophysic dysplasia. JCI Insight 2024; 9:e174417. [PMID: 38300707 DOI: 10.1172/jci.insight.174417] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2023] [Accepted: 01/30/2024] [Indexed: 02/03/2024] Open
Abstract
Geleophysic dysplasia-1 (GD1) is an autosomal recessive disorder caused by ADAMTS-like 2 (ADAMTSL2) variants. It is characterized by distinctive facial features, limited joint mobility, short stature, brachydactyly, and life-threatening cardiorespiratory complications. The clinical spectrum spans from perinatal lethality to milder adult phenotypes. We developed and characterized cellular and mouse models, to replicate the genetic profile of a patient who is compound heterozygous for 2 ADAMTSL2 variants, namely p.R61H and p.A165T. The impairment of ADAMTSL2 secretion was observed in both variants, but p.A165T exhibited a more severe impact. Mice carrying different allelic combinations revealed a spectrum of phenotypic severity, from lethality in knockout homozygotes to mild growth impairment observed in adult p.R61H homozygotes. Homozygous and hemizygous p.A165T mice survived but displayed severe respiratory and cardiac dysfunction. The respiratory dysfunction mainly affected the expiration phase, and some of these animals had microscopic post-obstructive pneumonia. Echocardiograms and MRI studies revealed a significant systolic dysfunction, accompanied by a reduction of the aortic root size. Histology verified the presence of hypertrophic cardiomyopathy with myocyte hypertrophy, chondroid metaplasia, and mild interstitial fibrosis. This study revealed a substantial correlation between the degree of impaired ADAMTSL2 secretion and the severity of the observed phenotype in GD1.
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Affiliation(s)
| | - Monique M Williams
- Department of Medicine, Division of Cardiology
- Interdisciplinary Stem Cell Institute
| | - Alejo A Morales
- Dr. John T. Macdonald Foundation Department of Human Genetics
| | | | - Okan V Kilic
- Dr. John T. Macdonald Foundation Department of Human Genetics
| | | | - Clemer Abad
- Dr. John T. Macdonald Foundation Department of Human Genetics
| | | | - Laurence M Briski
- Department of Pathology and Laboratory Medicine, University of Miami Leonard M. Miller School of Medicine Miami, Florida, USA
| | - LéShon Peart
- Dr. John T. Macdonald Foundation Department of Human Genetics
| | - Guney Bademci
- Dr. John T. Macdonald Foundation Department of Human Genetics
| | | | - Sarah Smithson
- Department of Clinical Genetics, University Hospitals Bristol and Weston NHS Foundation Trust, Bristol, United Kingdom
| | - Gaofeng Wang
- Dr. John T. Macdonald Foundation Department of Human Genetics
- John P. Hussmann Institute for Human Genomics
- Sylvester Comprehensive Cancer Center, University of Miami Leonard M. Miller School of Medicine, Miami, Florida, USA
| | - Lina A Shehadeh
- Department of Medicine, Division of Cardiology
- Interdisciplinary Stem Cell Institute
| | - Katherina Walz
- Dr. John T. Macdonald Foundation Department of Human Genetics
- John P. Hussmann Institute for Human Genomics
- IQUIBICEN - CONICET, Faculty of Exact and Natural Sciences, University of Buenos Aires, Argentina
| | - Mustafa Tekin
- Dr. John T. Macdonald Foundation Department of Human Genetics
- John P. Hussmann Institute for Human Genomics
- Department of Otolaryngology and
- Department of Ophthalmology, University of Miami Leonard M. Miller School of Medicine, Miami, Florida, USA
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22
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Kuehn HS, Sakovich IS, Niemela JE, Gil Silva AA, Stoddard JL, Polyakova EA, Esteve Sole A, Aleshkevich SN, Uglova TA, Belevtsev MV, Vertelko VR, Shman TV, Kupchinskaya AN, Walter JE, Fleisher TA, Notarangelo LD, Peng XP, Delmonte OM, Sharapova SO, Rosenzweig SD. Disease-associated AIOLOS variants lead to immune deficiency/dysregulation by haploinsufficiency and redefine AIOLOS functional domains. J Clin Invest 2024; 134:e172573. [PMID: 38015619 PMCID: PMC10836806 DOI: 10.1172/jci172573] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2023] [Accepted: 11/21/2023] [Indexed: 11/30/2023] Open
Abstract
AIOLOS, also known as IKZF3, is a transcription factor that is highly expressed in the lymphoid lineage and is critical for lymphocyte differentiation and development. Here, we report on 9 individuals from 3 unrelated families carrying AIOLOS variants Q402* or E82K, which led to AIOLOS haploinsufficiency through different mechanisms of action. Nonsense mutant Q402* displayed abnormal DNA binding, pericentromeric targeting, posttranscriptional modification, and transcriptome regulation. Structurally, the mutant lacked the AIOLOS zinc finger (ZF) 5-6 dimerization domain, but was still able to homodimerize with WT AIOLOS and negatively regulate DNA binding through ZF1, a previously unrecognized function for this domain. Missense mutant E82K showed overall normal AIOLOS functions; however, by affecting a redefined AIOLOS protein stability domain, it also led to haploinsufficiency. Patients with AIOLOS haploinsufficiency showed hypogammaglobulinemia, recurrent infections, autoimmunity, and allergy, but with incomplete clinical penetrance. Altogether, these data redefine the AIOLOS structure-function relationship and expand the spectrum of AIOLOS-associated diseases.
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Affiliation(s)
- Hye Sun Kuehn
- Immunology Service, Department of Laboratory Medicine, Clinical Center, NIH, Bethesda, Maryland, USA
| | - Inga S. Sakovich
- Research Department, Belarusian Research Center for Pediatric Oncology, Hematology and Immunology, Minsk, Belarus
| | - Julie E. Niemela
- Immunology Service, Department of Laboratory Medicine, Clinical Center, NIH, Bethesda, Maryland, USA
| | - Agustin A. Gil Silva
- Immunology Service, Department of Laboratory Medicine, Clinical Center, NIH, Bethesda, Maryland, USA
| | - Jennifer L. Stoddard
- Immunology Service, Department of Laboratory Medicine, Clinical Center, NIH, Bethesda, Maryland, USA
| | - Ekaterina A. Polyakova
- Research Department, Belarusian Research Center for Pediatric Oncology, Hematology and Immunology, Minsk, Belarus
| | - Ana Esteve Sole
- Immunology Service, Department of Laboratory Medicine, Clinical Center, NIH, Bethesda, Maryland, USA
| | - Svetlana N. Aleshkevich
- Research Department, Belarusian Research Center for Pediatric Oncology, Hematology and Immunology, Minsk, Belarus
| | - Tatjana A. Uglova
- Research Department, Belarusian Research Center for Pediatric Oncology, Hematology and Immunology, Minsk, Belarus
| | - Mikhail V. Belevtsev
- Research Department, Belarusian Research Center for Pediatric Oncology, Hematology and Immunology, Minsk, Belarus
| | - Vladislav R. Vertelko
- Research Department, Belarusian Research Center for Pediatric Oncology, Hematology and Immunology, Minsk, Belarus
| | - Tatsiana V. Shman
- Research Department, Belarusian Research Center for Pediatric Oncology, Hematology and Immunology, Minsk, Belarus
| | - Aleksandra N. Kupchinskaya
- Research Department, Belarusian Research Center for Pediatric Oncology, Hematology and Immunology, Minsk, Belarus
| | - Jolan E. Walter
- Division of Allergy and Immunology, Department of Pediatrics, Morsani College of Medicine, University of South Florida, Tampa, Florida, USA
- Division of Allergy and Immunology, Department of Medicine, Johns Hopkins All Children’s Hospital, St. Petersburg, Florida, USA
- Division of Pediatric Allergy and Immunology, Massachusetts General Hospital for Children, Boston, Massachusetts, USA
| | - Thomas A. Fleisher
- Immunology Service, Department of Laboratory Medicine, Clinical Center, NIH, Bethesda, Maryland, USA
| | - Luigi D. Notarangelo
- Laboratory of Clinical Immunology and Microbiology, Division of Intramural Research, National Institute of Allergy of Infectious Diseases, NIH, Bethesda, Maryland, USA
| | - Xiao P. Peng
- Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Ottavia M. Delmonte
- Laboratory of Clinical Immunology and Microbiology, Division of Intramural Research, National Institute of Allergy of Infectious Diseases, NIH, Bethesda, Maryland, USA
| | - Svetlana O. Sharapova
- Research Department, Belarusian Research Center for Pediatric Oncology, Hematology and Immunology, Minsk, Belarus
| | - Sergio D. Rosenzweig
- Immunology Service, Department of Laboratory Medicine, Clinical Center, NIH, Bethesda, Maryland, USA
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23
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Xiong S, Yu K, Lin H, Ye X, Xiao S, Yang Y, Stanley DW, Song Q, Fang Q, Ye G. Regulatory network in heat stress response in parasitoid wasp focusing on Xap5 heat stress regulator. iScience 2024; 27:108622. [PMID: 38205256 PMCID: PMC10777071 DOI: 10.1016/j.isci.2023.108622] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2023] [Revised: 10/22/2023] [Accepted: 11/30/2023] [Indexed: 01/12/2024] Open
Abstract
Insects are susceptible to elevated temperatures, resulting in impaired fertility, and shortened lifespan. This study investigated the genetic mechanisms underlying heat stress effects. We conducted RNA sequencing on Pteromalus puparum exposed to 25°C and 35°C, revealing transcriptional signatures. Weighted Gene Co-expression Network Analysis uncovered heat stress-associated modules, forming a regulatory network of 113 genes. The network is naturally divided into two subgroups, one linked to acute heat stress, including heat shock proteins (HSPs), and the other to chronic heat stress, involving lipogenesis genes. We identified an Xap5 Heat Shock Regulator (XHSR) gene as a crucial network component, validated through RNA interference and quantitative PCR assays. XHSR knockdown reduced wasps' lifespan while directly inducing HSPs and mediating lipogenesis gene induction. CRISPR/Cas9-mediated knockout of the Drosophila XHSR homolog reduced mutants' survival, highlighting its conserved role. This research sheds light on thermal tolerance mechanisms, offering potential applications in pest control amid global warming.
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Affiliation(s)
- Shijiao Xiong
- State Key Laboratory of Rice Biology and Breeding & Ministry of Agricultural and Rural Affairs Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Institute of Insect Sciences, Zhejiang University, Hangzhou 310058, China
| | - Kaili Yu
- State Key Laboratory of Rice Biology and Breeding & Ministry of Agricultural and Rural Affairs Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Institute of Insect Sciences, Zhejiang University, Hangzhou 310058, China
| | - Haiwei Lin
- State Key Laboratory of Rice Biology and Breeding & Ministry of Agricultural and Rural Affairs Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Institute of Insect Sciences, Zhejiang University, Hangzhou 310058, China
| | - Xinhai Ye
- State Key Laboratory of Rice Biology and Breeding & Ministry of Agricultural and Rural Affairs Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Institute of Insect Sciences, Zhejiang University, Hangzhou 310058, China
| | - Shan Xiao
- State Key Laboratory of Rice Biology and Breeding & Ministry of Agricultural and Rural Affairs Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Institute of Insect Sciences, Zhejiang University, Hangzhou 310058, China
| | - Yi Yang
- State Key Laboratory of Rice Biology and Breeding & Ministry of Agricultural and Rural Affairs Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Institute of Insect Sciences, Zhejiang University, Hangzhou 310058, China
| | - David W. Stanley
- USDA/ARS Biological Control of Insects Research Laboratory, 1503 S. Providence Road, Columbia MO, USA
| | - Qisheng Song
- Division of Plant Sciences, University of Missouri, Columbia, MO, USA
| | - Qi Fang
- State Key Laboratory of Rice Biology and Breeding & Ministry of Agricultural and Rural Affairs Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Institute of Insect Sciences, Zhejiang University, Hangzhou 310058, China
| | - Gongyin Ye
- State Key Laboratory of Rice Biology and Breeding & Ministry of Agricultural and Rural Affairs Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Institute of Insect Sciences, Zhejiang University, Hangzhou 310058, China
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24
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Fan Z, Liu Y, Li C, Jiang Y, Wang N, Wang M, Li C, Diao Y, Qiu W, Zhu X, Wang G, Cai S, Yang T, Lv G. T proliferating cells derived autophagy signature associated with prognosis and immunotherapy resistance in a pan-cancer analysis. iScience 2024; 27:108701. [PMID: 38222108 PMCID: PMC10784705 DOI: 10.1016/j.isci.2023.108701] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2023] [Revised: 09/11/2023] [Accepted: 12/06/2023] [Indexed: 01/16/2024] Open
Abstract
Despite autophagy modulating tumor immunity in the tumor microenvironment (TME), the immunotherapeutic efficacy and potential mechanism of autophagy signature was not explicit. We manually curated an autophagy gene set and defined a pan-cancer autophagy signature by comparing malignant tissues and normal tissues in The Cancer Genome Atlas (TCGA) cohort. The pan-cancer autophagy signature was derived from T proliferating cells as demonstrated in multiple single-cell RNA sequencing (scRNA-seq) datasets. The pan-cancer autophagy signature could influence the cell-cell interactions in the TME and predict the responsiveness of immune checkpoint inhibitors (ICIs) in the metastatic renal cell carcinoma, non-small cell lung cancer, bladder cancer, and melanoma cohorts. Metabolism inactivation accompanied with dysregulation of autophagy was investigated with transcriptomic and proteomic data. The immunotherapeutic predictive role and mechanism regulation of the autophagy signature was validated in an in-house cohort. Our study provides valuable insights into the mechanisms of ICI resistance.
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Affiliation(s)
- Zhongqi Fan
- Department of Hepatobiliary and Pancreatic Surgery, General Surgery Center, First Hospital of Jilin University, Jilin, China
| | - Yutao Liu
- State Key Laboratory of Molecular Oncology, Department of Medical Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | | | - Yanfang Jiang
- Key Laboratory of Organ Regeneration and Transplantation of the Ministry of Education, Genetic Diagnosis Centre, The First Hospital of Jilin University, Changchun, Jilin, China
| | - Nanya Wang
- Phase I Clinical Trial Unit, First Hospital of Jilin University, Jilin, China
| | - Mingda Wang
- Department of Hepatobiliary Surgery, Eastern Hepatobiliary Surgery Hospital, Second Military Medical University (Navy Medical University), Shanghai, China
| | - Chao Li
- Department of Hepatobiliary Surgery, Eastern Hepatobiliary Surgery Hospital, Second Military Medical University (Navy Medical University), Shanghai, China
| | - Yongkang Diao
- Department of Hepatobiliary Surgery, Eastern Hepatobiliary Surgery Hospital, Second Military Medical University (Navy Medical University), Shanghai, China
| | - Wei Qiu
- Department of Hepatobiliary and Pancreatic Surgery, General Surgery Center, First Hospital of Jilin University, Jilin, China
| | - Xin Zhu
- Burning Rock Biotech, Guangdong, China
| | | | | | - Tian Yang
- Department of Hepatobiliary and Pancreatic Surgery, General Surgery Center, First Hospital of Jilin University, Jilin, China
- Department of Hepatobiliary Surgery, Eastern Hepatobiliary Surgery Hospital, Second Military Medical University (Navy Medical University), Shanghai, China
| | - Guoyue Lv
- Department of Hepatobiliary and Pancreatic Surgery, General Surgery Center, First Hospital of Jilin University, Jilin, China
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25
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Ge S, Wang X, Wang Y, Dong M, Li D, Niu K, Wang T, Liu R, Zhao C, Liu N, Zhong M. Hidden features of NAD-RNA epitranscriptome in Drosophila life cycle. iScience 2024; 27:108618. [PMID: 38197055 PMCID: PMC10775904 DOI: 10.1016/j.isci.2023.108618] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2023] [Revised: 09/26/2023] [Accepted: 11/30/2023] [Indexed: 01/11/2024] Open
Abstract
Nicotinamide adenine dinucleotide (NAD), a nucleotide-containing metabolite, can be incorporated into the RNA 5'-terminus to result in NAD-capped RNA (NAD-RNA). Since NAD has been heightened as one of the most essential metabolites in cells, its linkage to RNA represents a critical but poorly studied modification at the epitranscriptomic level. Here, we design a highly sensitive method, DO-seq, to capture NAD-RNAs. Using Drosophila, we identify thousands of previously unexplored NAD-RNAs and their dynamics in the fly life cycle, from embryo to adult. We show the evidence that chromosomal clustering might be the structural basis by which co-expression can couple with NAD capping on physically and functionally linked genes. Furthermore, we note that NAD capping of cuticle genes inversely correlates with their gene expression. Combined, we propose NAD-RNA epitranscriptome as a hidden layer of regulation that underlies biological processes. DO-seq empowers the identification of NAD-capped RNAs, facilitating functional investigation into this modification.
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Affiliation(s)
- Shuwen Ge
- Interdisciplinary Research Center on Biology and Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, 100 Hai Ke Road, Shanghai 201210, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xueting Wang
- Interdisciplinary Research Center on Biology and Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, 100 Hai Ke Road, Shanghai 201210, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yingqin Wang
- Department of Critical Care Medicine, Zhongshan Hospital, Fudan University, Shanghai, China
- Shanghai Key Laboratory of Lung Inflammation and Injury, 180 Fenglin Road, Shanghai, China
- Shanghai Institute of Infectious Disease and Biosecurity, School of Public Health, Fudan University, Shanghai, China
| | - Minghui Dong
- Department of Critical Care Medicine, Zhongshan Hospital, Fudan University, Shanghai, China
- Shanghai Key Laboratory of Lung Inflammation and Injury, 180 Fenglin Road, Shanghai, China
- Shanghai Institute of Infectious Disease and Biosecurity, School of Public Health, Fudan University, Shanghai, China
| | - Dean Li
- Interdisciplinary Research Center on Biology and Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, 100 Hai Ke Road, Shanghai 201210, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Kongyan Niu
- Interdisciplinary Research Center on Biology and Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, 100 Hai Ke Road, Shanghai 201210, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Tongyao Wang
- National Clinical Research Center for Aging and Medicine, Huashan Hospital, School of Basic Medical Sciences, Shanghai Medical College, Fudan University, 131 Dong An Road, Shanghai 200032, China
| | - Rui Liu
- Singlera Genomics, 500 Fu Rong Hua Road, Shanghai 201204, China
| | - Chao Zhao
- National Clinical Research Center for Aging and Medicine, Huashan Hospital, School of Basic Medical Sciences, Shanghai Medical College, Fudan University, 131 Dong An Road, Shanghai 200032, China
| | - Nan Liu
- Interdisciplinary Research Center on Biology and Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, 100 Hai Ke Road, Shanghai 201210, China
- National Clinical Research Center for Aging and Medicine, Huashan Hospital, School of Basic Medical Sciences, Shanghai Medical College, Fudan University, 131 Dong An Road, Shanghai 200032, China
- Shanghai Key Laboratory of Aging Studies, 100 Hai Ke Road, Shanghai 201210, China
| | - Ming Zhong
- Department of Critical Care Medicine, Zhongshan Hospital, Fudan University, Shanghai, China
- Shanghai Key Laboratory of Lung Inflammation and Injury, 180 Fenglin Road, Shanghai, China
- Shanghai Institute of Infectious Disease and Biosecurity, School of Public Health, Fudan University, Shanghai, China
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26
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Spaulding SL, Maayah M, Dinauer CA, Prasad M, Darbinyan A, Morotti R, Christison-Lagay ER. Molecular Genetics Augment Cytopathologic Evaluation and Surgical Planning of Pediatric Thyroid Nodules. J Pediatr Surg 2024:S0022-3468(24)00004-6. [PMID: 38246817 DOI: 10.1016/j.jpedsurg.2024.01.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/26/2023] [Revised: 12/27/2023] [Accepted: 01/03/2024] [Indexed: 01/23/2024]
Abstract
PURPOSE Molecular genetic testing in conjunction with cytopathology may improve prediction of malignancy in thyroid nodules, particularly those with indeterminate cytology (Bethesda III/IV). Though now commonplace in adults, pediatric data are limited. This study examines molecular genetics of pediatric nodules with correlation to cytologic and histologic classification at time of surgery and the distribution of mutations. METHODS Retrospective chart review of 164 patients <22 years who underwent surgical resection of a thyroid nodule between 2002 and 2020 with molecular testing on fine-needle aspiration biopsy (FNA) or final histopathology. RESULTS 85 (52 %) of 164 patients undergoing thyroid resection had available molecular genetic testing. BRAF V600E testing was performed on the FNA samples of 73 (86 %) patients and on 15 (18 %) surgical specimens; 31 (37 %) were positive. Of the remaining 54 patients, 21 had additional mutation/fusion testing. In 17 (81 %) cases, an alternate mutation/fusion was identified including 8 gene fusions, 3 DICER1 mutations, 4 NRAS mutations, one BRAF variant, and one unknown variant. BRAF, DICER1 mutations, and gene fusions predicted malignancy. Greater than 95 % of BRAF mutations were in Bethesda V/VI lesions and associated with classic variant PTC whereas fusions and DICER1 mutations clustered in Bethesda IV nodules. Bethesda III nodules harbored BRAF and NRAS mutations. In Bethesda IV nodules, a gene fusion or DICER mutation altered the surgical decision-making (upfront thyroidectomy rather than lobectomy) in 70 % of nodules submitted for genetic testing. CONCLUSION Expanded molecular genetic testing on FNA of pediatric thyroid nodules, particularly Bethesda III/IV, may improve prediction of malignancy and augment surgical decision-making. LEVEL OF EVIDENCE III.
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Affiliation(s)
- Sarah L Spaulding
- Pediatric Surgery, Department of Surgery, Yale School of Medicine, New Haven, CT, USA.
| | - Marah Maayah
- Pediatric Surgery, Department of Surgery, Yale School of Medicine, New Haven, CT, USA
| | - Catherine A Dinauer
- Endocrinology & Diabetes, Department of Pediatrics, Yale School of Medicine, New Haven, CT, USA
| | - Manju Prasad
- Department of Pathology, Yale School of Medicine, New Haven, CT, USA
| | - Armine Darbinyan
- Department of Pathology, Yale School of Medicine, New Haven, CT, USA
| | - Raffaella Morotti
- Department of Pathology, Yale School of Medicine, New Haven, CT, USA
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27
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Abedini A, Sánchez-Navaro A, Wu J, Klötzer KA, Ma Z, Poudel B, Doke T, Balzer MS, Frederick J, Cernecka H, Liu H, Liang X, Vitale S, Kolkhof P, Susztak K. Single-cell transcriptomics and chromatin accessibility profiling elucidate the kidney-protective mechanism of mineralocorticoid receptor antagonists. J Clin Invest 2024; 134:e157165. [PMID: 37906287 PMCID: PMC10760974 DOI: 10.1172/jci157165] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2021] [Accepted: 10/23/2023] [Indexed: 11/02/2023] Open
Abstract
Mineralocorticoid excess commonly leads to hypertension (HTN) and kidney disease. In our study, we used single-cell expression and chromatin accessibility tools to characterize the mineralocorticoid target genes and cell types. We demonstrated that mineralocorticoid effects were established through open chromatin and target gene expression, primarily in principal and connecting tubule cells and, to a lesser extent, in segments of the distal convoluted tubule cells. We examined the kidney-protective effects of steroidal and nonsteroidal mineralocorticoid antagonists (MRAs), as well as of amiloride, an epithelial sodium channel inhibitor, in a rat model of deoxycorticosterone acetate, unilateral nephrectomy, and high-salt consumption-induced HTN and cardiorenal damage. All antihypertensive therapies protected against cardiorenal damage. However, finerenone was particularly effective in reducing albuminuria and improving gene expression changes in podocytes and proximal tubule cells, even with an equivalent reduction in blood pressure. We noted a strong correlation between the accumulation of injured/profibrotic tubule cells expressing secreted posphoprotein 1 (Spp1), Il34, and platelet-derived growth factor subunit b (Pdgfb) and the degree of fibrosis in rat kidneys. This gene signature also showed a potential for classifying human kidney samples. Our multiomics approach provides fresh insights into the possible mechanisms underlying HTN-associated kidney disease, the target cell types, the protective effects of steroidal and nonsteroidal MRAs, and amiloride.
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Affiliation(s)
- Amin Abedini
- Renal, Electrolyte, and Hypertension Division, Department of Medicine
- Institute for Diabetes, Obesity, and Metabolism, and
- Department of Genetics, University of Pennsylvania, Perelman School of Medicine, Philadelphia, Pennsylvania, USA
| | - Andrea Sánchez-Navaro
- Renal, Electrolyte, and Hypertension Division, Department of Medicine
- Institute for Diabetes, Obesity, and Metabolism, and
- Department of Genetics, University of Pennsylvania, Perelman School of Medicine, Philadelphia, Pennsylvania, USA
| | - Junnan Wu
- Renal, Electrolyte, and Hypertension Division, Department of Medicine
- Institute for Diabetes, Obesity, and Metabolism, and
- Department of Genetics, University of Pennsylvania, Perelman School of Medicine, Philadelphia, Pennsylvania, USA
| | - Konstantin A. Klötzer
- Renal, Electrolyte, and Hypertension Division, Department of Medicine
- Institute for Diabetes, Obesity, and Metabolism, and
- Department of Genetics, University of Pennsylvania, Perelman School of Medicine, Philadelphia, Pennsylvania, USA
| | - Ziyuan Ma
- Renal, Electrolyte, and Hypertension Division, Department of Medicine
- Institute for Diabetes, Obesity, and Metabolism, and
- Department of Genetics, University of Pennsylvania, Perelman School of Medicine, Philadelphia, Pennsylvania, USA
| | - Bibek Poudel
- Renal, Electrolyte, and Hypertension Division, Department of Medicine
- Institute for Diabetes, Obesity, and Metabolism, and
- Department of Genetics, University of Pennsylvania, Perelman School of Medicine, Philadelphia, Pennsylvania, USA
| | - Tomohito Doke
- Renal, Electrolyte, and Hypertension Division, Department of Medicine
- Institute for Diabetes, Obesity, and Metabolism, and
- Department of Genetics, University of Pennsylvania, Perelman School of Medicine, Philadelphia, Pennsylvania, USA
| | - Michael S. Balzer
- Renal, Electrolyte, and Hypertension Division, Department of Medicine
- Institute for Diabetes, Obesity, and Metabolism, and
- Department of Genetics, University of Pennsylvania, Perelman School of Medicine, Philadelphia, Pennsylvania, USA
| | - Julia Frederick
- Renal, Electrolyte, and Hypertension Division, Department of Medicine
- Institute for Diabetes, Obesity, and Metabolism, and
- Department of Genetics, University of Pennsylvania, Perelman School of Medicine, Philadelphia, Pennsylvania, USA
| | - Hana Cernecka
- Bayer AG, Pharmaceuticals, Research and Development, Cardiovascular Research, Wuppertal, Germany
| | - Hongbo Liu
- Renal, Electrolyte, and Hypertension Division, Department of Medicine
- Institute for Diabetes, Obesity, and Metabolism, and
- Department of Genetics, University of Pennsylvania, Perelman School of Medicine, Philadelphia, Pennsylvania, USA
| | - Xiujie Liang
- Renal, Electrolyte, and Hypertension Division, Department of Medicine
- Institute for Diabetes, Obesity, and Metabolism, and
- Department of Genetics, University of Pennsylvania, Perelman School of Medicine, Philadelphia, Pennsylvania, USA
| | - Steven Vitale
- Renal, Electrolyte, and Hypertension Division, Department of Medicine
- Institute for Diabetes, Obesity, and Metabolism, and
- Department of Genetics, University of Pennsylvania, Perelman School of Medicine, Philadelphia, Pennsylvania, USA
| | - Peter Kolkhof
- Bayer AG, Pharmaceuticals, Research and Development, Cardiovascular Research, Wuppertal, Germany
| | - Katalin Susztak
- Renal, Electrolyte, and Hypertension Division, Department of Medicine
- Institute for Diabetes, Obesity, and Metabolism, and
- Department of Genetics, University of Pennsylvania, Perelman School of Medicine, Philadelphia, Pennsylvania, USA
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28
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Qijun C, Wei W, Cheng W, Dongni L. Clinicopathological features and molecular genetic changes in 17 cases of uterine tumor resembling ovarian sex cord tumor. Hum Pathol 2024; 143:33-41. [PMID: 38000680 DOI: 10.1016/j.humpath.2023.11.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/03/2023] [Revised: 11/10/2023] [Accepted: 11/17/2023] [Indexed: 11/26/2023]
Abstract
Uterine tumor resembling ovarian sex cord tumor (UTROSCT) is a rare mesenchymal neoplasm that was recently reported to exhibit recurrent NCOA1-3rearrangement with the most frequent partners ESR1 and GREB1. In this study, the clinicopathological characteristics of 17 UTROSCT cases were summarized; among them, the fusion genes of 12 cases were retrospectively analyzed by targeted RNA sequencing. The mean age of our cohort was 47 years (19-67 y). Although the majority of UTROSCTs had clear boundaries on gross examination, microscopic infiltration into the myometrium was observed in 82.4 % of cases. The tumor cells showed diffuse, trabecular, nested, reticular, pseudopapillary, hollow and solid tubular patterns, expressing sex cord, epithelial, and myogenic markers. Six fusion genes, including ESR1::NCOA3 (n = 4), ESR1::NCOA2 (n = 2), ESR1::CITED2 (n = 2), GREB1::NCOA2 (n = 2), GREB1::NCOA1 (n = 1), and GREB1::NCOA3 (n = 1), were identified. The fusion genes of the three cases with recurrence and metastasis were GREB1::NCOA2, ESR1::NCOA3, and ESR1::CITED2. All 3 cases of recurrent tumors showed infiltrative growth, with moderate to severe dysplasia of tumor cells and different degrees of rhabdomyoid differentiation. This is the first report of the ESR1::CITED2 fusion genes in UTROSCT, and one of the two patients had recurrence and metastasis. Compared with UTROSCT withESR1 rearrangement, UTROSCT with GREB1 rearrangement was more common in elderly patientsand was more likely to present with intramural masses, less sex cord differentiation, poor prognosis, and relapse and metastasis.
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Affiliation(s)
- Chen Qijun
- Department of Pathology, West China Second Hospital of Sichuan University / Key Laboratory of Birth Defects and Related Diseases of Women and Children (Sichuan University), Chengdu, 610041, Sichuan Province, China.
| | - Wang Wei
- Department of Pathology, West China Second Hospital of Sichuan University / Key Laboratory of Birth Defects and Related Diseases of Women and Children (Sichuan University), Chengdu, 610041, Sichuan Province, China.
| | - Wang Cheng
- Department of Pathology, West China Second Hospital of Sichuan University / Key Laboratory of Birth Defects and Related Diseases of Women and Children (Sichuan University), Chengdu, 610041, Sichuan Province, China.
| | - Liang Dongni
- Department of Pathology, West China Second Hospital of Sichuan University / Key Laboratory of Birth Defects and Related Diseases of Women and Children (Sichuan University), Chengdu, 610041, Sichuan Province, China.
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29
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Beal MA, Meier MJ, Dykes A, Yauk CL, Lambert IB, Marchetti F. The functional mutational landscape of the lacZ gene. iScience 2023; 26:108407. [PMID: 38058303 PMCID: PMC10696112 DOI: 10.1016/j.isci.2023.108407] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2023] [Revised: 09/23/2023] [Accepted: 11/03/2023] [Indexed: 12/08/2023] Open
Abstract
The lacZ gene of Escherichia coli encodes β-galactosidase (β-gal), a lactose metabolism enzyme of the lactose operon. Previous chemical modification or site-directed mutagenesis experiments have identified 21 amino acids that are essential for β-gal catalytic activity. We have assembled over 10,000 lacZ mutations from published studies that were collected using a positive selection assay to identify mutations in lacZ that disrupted β-gal function. We analyzed 6,465 independent lacZ mutations that resulted in 2,732 missense mutations that impaired β-gal function. Those mutations affected 492 of the 1,023 lacZ codons, including most of the 21 previously known residues critical for catalytic activity. Most missense mutations occurred near the catalytic site and in regions important for subunit tetramerization. Overall, our work provides a comprehensive and detailed map of the amino acid residues affecting the structure and catalytic activity of the β-gal enzyme.
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Affiliation(s)
- Marc A. Beal
- Environmental Health Science and Research Bureau, Healthy Environments and Consumer Safety Branch, Health Canada, Ottawa, ON K1A 0K9, Canada
| | - Matthew J. Meier
- Environmental Health Science and Research Bureau, Healthy Environments and Consumer Safety Branch, Health Canada, Ottawa, ON K1A 0K9, Canada
| | - Angela Dykes
- Environmental Health Science and Research Bureau, Healthy Environments and Consumer Safety Branch, Health Canada, Ottawa, ON K1A 0K9, Canada
- Department of Biology, Carleton University, Ottawa, ON K1S 5B6, Canada
| | - Carole L. Yauk
- Environmental Health Science and Research Bureau, Healthy Environments and Consumer Safety Branch, Health Canada, Ottawa, ON K1A 0K9, Canada
- Department of Biology, University of Ottawa, Ottawa, ON K1N 6N5, Canada
| | - Iain B. Lambert
- Department of Biology, Carleton University, Ottawa, ON K1S 5B6, Canada
| | - Francesco Marchetti
- Environmental Health Science and Research Bureau, Healthy Environments and Consumer Safety Branch, Health Canada, Ottawa, ON K1A 0K9, Canada
- Department of Biology, Carleton University, Ottawa, ON K1S 5B6, Canada
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30
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Türkyılmaz A, Kaplan AT, Öskan Yalçın S, Sağer SG, Şimşek Ş. Identification of novel variants in Turkish families with non-syndromic congenital cataracts using whole-exome sequencing. Int Ophthalmol 2023; 43:4573-4583. [PMID: 37592116 DOI: 10.1007/s10792-023-02857-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2021] [Accepted: 08/05/2023] [Indexed: 08/19/2023]
Abstract
PURPOSE The present study aimed to identify the molecular etiology of non-syndromic congenital cataract (CC) using whole-exome sequencing (WES) analysis. METHODS In the present study, ophthalmologic results and pedigree analysis of the families of 12 patients with non-syndromic CC were evaluated. WES analysis was conducted after DNA was isolated from peripheral blood samples obtained from the patients. RESULTS Twelve non-syndromic probands (10 males and 2 females) with bilateral CC were included in the study. Patient age ranged between 1 and 11 months. WES analysis showed pathogenic/likely pathogenic variant in 7 (58%) of the 12 families and variant of unknown significance (VUS) in 5 (42%) of them. All the 13 different variants detected in 9 different CC-related genes were co-segregated with the disease. Autosomal dominant inheritance was found in 7 (58%) of the families and autosomal recessive inheritance was found in 5 (42%) of them. CONCLUSION To the best of our knowledge, the present research is one of the limited numbers of studies in the Turkish population in which genetically heterogeneous non-syndromic CC was investigated using WES analysis. Novel variants that we identified in DNMBP, LSS, and WFS1 genes, which are rarely associated with the CC phenotype, have contributed to the mutation spectrum of this disease. Identifying the relevant molecular genetic etiology allows accurate genetic counseling to be provided to the families.
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Affiliation(s)
- Ayberk Türkyılmaz
- Department of Medical Genetics, Faculty of Medicine, Karadeniz Technical University, Ortahisar, Trabzon, Turkey.
| | - Ayşin Tuba Kaplan
- Department of Ophthalmology, Kartal Dr. Lütfi Kırdar City Hospital, Istanbul, Turkey
| | - Sibel Öskan Yalçın
- Department of Ophthalmology, Kartal Dr. Lütfi Kırdar City Hospital, Istanbul, Turkey
| | - Safiye Güneş Sağer
- Department of Pediatric Neurology, Kartal Dr. Lütfi Kırdar City Hospital, Istanbul, Turkey
| | - Şaban Şimşek
- Department of Ophthalmology, Kartal Dr. Lütfi Kırdar City Hospital, Istanbul, Turkey
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31
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Asa SL, Erickson LA, Rindi G. The Spectrum of Endocrine Pathology. Endocr Pathol 2023; 34:368-381. [PMID: 36933149 PMCID: PMC10024030 DOI: 10.1007/s12022-023-09758-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 03/06/2023] [Indexed: 03/19/2023]
Abstract
Endocrine pathology comprises a spectrum of disorders originating in various sites throughout the body. Some disorders affect endocrine glands, and others arise from endocrine cells that are dispersed in non-endocrine tissues. Endocrine cells can broadly be classified as neuroendocrine, steroidogenic, or thyroid follicular cells; these three families have distinct embryologic origins, morphologic structure, and biochemical hormone synthetic pathways. Lesions affecting the endocrine system include developmental abnormalities, inflammatory processes that can be infectious or autoimmune, hypofunction with atrophy or hyperfunction caused by hyperplasia secondary to pathology in other sites, and neoplasia of many types. Understanding endocrine pathology requires knowledge of both structure and function, including the biochemical signaling pathways that regulate hormone synthesis and secretion. Molecular genetics has clarified sporadic and hereditary disease that is common in this field.
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Affiliation(s)
- Sylvia L. Asa
- Department of Pathology, Institute of Pathology, University Hospitals Cleveland Medical Center, Case Western Reserve University, 11100 Euclid Avenue, Room 204, Cleveland, OH 44106 USA
| | - Lori A. Erickson
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN 55901 USA
| | - Guido Rindi
- Department of Life Sciences and Public Health, Section of Anatomic Pathology, Universita Cattolica del Sacro Cuore, Rome, Italy
- Department of Woman and Child Health Sciences and Public Health, Anatomic Pathology Unit, Fondazione Policlinico Universitario A. Gemelli – IRCCS, Largo A. Gemelli, 00168 Rome, Italy
- ENETS Center of Excellence, Rome, Italy
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32
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Zhang Z, Cui Y, Su V, Wang D, Tol MJ, Cheng L, Wu X, Kim J, Rajbhandari P, Zhang S, Li W, Tontonoz P, Villanueva CJ, Sallam T. A PPARγ/long noncoding RNA axis regulates adipose thermoneutral remodeling in mice. J Clin Invest 2023; 133:e170072. [PMID: 37909330 PMCID: PMC10617768 DOI: 10.1172/jci170072] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2023] [Accepted: 09/06/2023] [Indexed: 11/03/2023] Open
Abstract
Interplay between energy-storing white adipose cells and thermogenic beige adipocytes contributes to obesity and insulin resistance. Irrespective of specialized niche, adipocytes require the activity of the nuclear receptor PPARγ for proper function. Exposure to cold or adrenergic signaling enriches thermogenic cells though multiple pathways that act synergistically with PPARγ; however, the molecular mechanisms by which PPARγ licenses white adipose tissue to preferentially adopt a thermogenic or white adipose fate in response to dietary cues or thermoneutral conditions are not fully elucidated. Here, we show that a PPARγ/long noncoding RNA (lncRNA) axis integrates canonical and noncanonical thermogenesis to restrain white adipose tissue heat dissipation during thermoneutrality and diet-induced obesity. Pharmacologic inhibition or genetic deletion of the lncRNA Lexis enhances uncoupling protein 1-dependent (UCP1-dependent) and -independent thermogenesis. Adipose-specific deletion of Lexis counteracted diet-induced obesity, improved insulin sensitivity, and enhanced energy expenditure. Single-nuclei transcriptomics revealed that Lexis regulates a distinct population of thermogenic adipocytes. We systematically map Lexis motif preferences and show that it regulates the thermogenic program through the activity of the metabolic GWAS gene and WNT modulator TCF7L2. Collectively, our studies uncover a new mode of crosstalk between PPARγ and WNT that preserves white adipose tissue plasticity.
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Affiliation(s)
- Zhengyi Zhang
- Division of Cardiology, Department of Medicine
- Department of Physiology, and
- Molecular Biology Institute, UCLA, Los Angeles, California, USA
| | - Ya Cui
- Division of Computational Biomedicine, Biological Chemistry, University of California, Irvine, Irvine, California, USA
| | - Vivien Su
- Division of Cardiology, Department of Medicine
- Department of Physiology, and
- Molecular Biology Institute, UCLA, Los Angeles, California, USA
| | - Dan Wang
- Division of Cardiology, Department of Medicine
- Department of Physiology, and
- Molecular Biology Institute, UCLA, Los Angeles, California, USA
| | - Marcus J. Tol
- Molecular Biology Institute, UCLA, Los Angeles, California, USA
- Department of Pathology and Laboratory Medicine, UCLA, Los Angeles, California, USA
| | - Lijing Cheng
- Division of Cardiology, Department of Medicine
- Department of Physiology, and
- Molecular Biology Institute, UCLA, Los Angeles, California, USA
| | - Xiaohui Wu
- Division of Cardiology, Department of Medicine
- Department of Physiology, and
- Molecular Biology Institute, UCLA, Los Angeles, California, USA
| | - Jason Kim
- Division of Cardiology, Department of Medicine
- Department of Physiology, and
- Molecular Biology Institute, UCLA, Los Angeles, California, USA
| | - Prashant Rajbhandari
- Diabetes, Obesity, and Metabolism Institute, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Sicheng Zhang
- Molecular Biology Institute, UCLA, Los Angeles, California, USA
| | - Wei Li
- Division of Computational Biomedicine, Biological Chemistry, University of California, Irvine, Irvine, California, USA
| | - Peter Tontonoz
- Molecular Biology Institute, UCLA, Los Angeles, California, USA
- Department of Pathology and Laboratory Medicine, UCLA, Los Angeles, California, USA
- Department of Biological Chemistry and
| | - Claudio J. Villanueva
- Molecular Biology Institute, UCLA, Los Angeles, California, USA
- Department of Integrative Biology and Physiology, College of Life Sciences, UCLA, Los Angeles, California, USA
| | - Tamer Sallam
- Division of Cardiology, Department of Medicine
- Department of Physiology, and
- Molecular Biology Institute, UCLA, Los Angeles, California, USA
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33
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Ding J, Wang S, Liu Q, Duan Y, Cheng T, Ye Z, Cui Z, Zhang A, Liu Q, Zhang Z, Zhang N, Liu Q, An N, Zhao J, Yi D, Li Q, Wang J, Zhang Y, Ma L, Guo S, Wang J, Liang C, Zhou J, Cen S, Li X. Schlafen-5 inhibits LINE-1 retrotransposition. iScience 2023; 26:107968. [PMID: 37810251 PMCID: PMC10551903 DOI: 10.1016/j.isci.2023.107968] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2022] [Revised: 07/20/2023] [Accepted: 09/15/2023] [Indexed: 10/10/2023] Open
Abstract
Long interspersed element 1 (LINE-1) is the only currently known active autonomous transposon in humans, and its retrotransposition may cause deleterious effects on the structure and function of host cell genomes and result in sporadic genetic diseases. Host cells therefore developed defense strategies to restrict LINE-1 mobilization. In this study, we demonstrated that IFN-inducible Schlafen5 (SLFN5) inhibits LINE-1 retrotransposition. Mechanistic studies revealed that SLFN5 interrupts LINE-1 ribonucleoprotein particle (RNP) formation, thus diminishing nuclear entry of the LINE-1 RNA template and subsequent LINE-1 cDNA production. The ability of SLFN5 to bind to LINE-1 RNA and the involvement of the helicase domain of SLFN5 in its inhibitory activity suggest a mechanism that SLFN5 binds to LINE-1 RNA followed by dissociation of ORF1p through its helicase activity, resulting in impaired RNP formation. These data highlight a new mechanism of host cells to restrict LINE-1 mobilization.
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Affiliation(s)
- Jiwei Ding
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Shujie Wang
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Qipeng Liu
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Yuqing Duan
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Tingting Cheng
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Zhongjie Ye
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Zhanding Cui
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Ao Zhang
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Qiuyu Liu
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Zixiong Zhang
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Ning Zhang
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Qian Liu
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Ni An
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Jianyuan Zhao
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Dongrong Yi
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Quanjie Li
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Jing Wang
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Yongxin Zhang
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Ling Ma
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Saisai Guo
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Jinhui Wang
- Peking Union Medical College Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Chen Liang
- The Lady Davis Institute-Jewish General Hospital, Montreal, QC H3T 1E2, Canada
| | - Jinming Zhou
- Key Laboratory of the Ministry of Education for Advanced Catalysis Materials, Department of Chemistry, Zhejiang Normal University, 688 Yingbin Road, Jinhua 321004, China
| | - Shan Cen
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Xiaoyu Li
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
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34
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Reyes EA, Castillo-Azofeifa D, Rispal J, Wald T, Zwick RK, Palikuqi B, Mujukian A, Rabizadeh S, Gupta AR, Gardner JM, Boffelli D, Gartner ZJ, Klein OD. Epithelial TNF controls cell differentiation and CFTR activity to maintain intestinal mucin homeostasis. J Clin Invest 2023; 133:e163591. [PMID: 37643009 PMCID: PMC10575728 DOI: 10.1172/jci163591] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2022] [Accepted: 08/22/2023] [Indexed: 08/31/2023] Open
Abstract
The gastrointestinal tract relies on the production, maturation, and transit of mucin to protect against pathogens and to lubricate the epithelial lining. Although the molecular and cellular mechanisms that regulate mucin production and movement are beginning to be understood, the upstream epithelial signals that contribute to mucin regulation remain unclear. Here, we report that the inflammatory cytokine tumor necrosis factor (TNF), generated by the epithelium, contributes to mucin homeostasis by regulating both cell differentiation and cystic fibrosis transmembrane conductance regulator (CFTR) activity. We used genetic mouse models and noninflamed samples from patients with inflammatory bowel disease (IBD) undergoing anti-TNF therapy to assess the effect of in vivo perturbation of TNF. We found that inhibition of epithelial TNF promotes the differentiation of secretory progenitor cells into mucus-producing goblet cells. Furthermore, TNF treatment and CFTR inhibition in intestinal organoids demonstrated that TNF promotes ion transport and luminal flow via CFTR. The absence of TNF led to slower gut transit times, which we propose results from increased mucus accumulation coupled with decreased luminal fluid pumping. These findings point to a TNF/CFTR signaling axis in the adult intestine and identify epithelial cell-derived TNF as an upstream regulator of mucin homeostasis.
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Affiliation(s)
- Efren A. Reyes
- Department of Orofacial Sciences and Program in Craniofacial Biology, and
- Department of Pharmaceutical Chemistry and TETRAD Program, UCSF, San Francisco, California, USA
| | - David Castillo-Azofeifa
- Department of Orofacial Sciences and Program in Craniofacial Biology, and
- Department of Regenerative Medicine, Genentech, Inc., South San Francisco, California, USA
| | - Jérémie Rispal
- Department of Orofacial Sciences and Program in Craniofacial Biology, and
| | - Tomas Wald
- Department of Orofacial Sciences and Program in Craniofacial Biology, and
| | - Rachel K. Zwick
- Department of Orofacial Sciences and Program in Craniofacial Biology, and
| | - Brisa Palikuqi
- Department of Orofacial Sciences and Program in Craniofacial Biology, and
| | - Angela Mujukian
- F. Widjaja Foundation Inflammatory Bowel and Immunobiology Research Institute, Cedars-Sinai Medical Center, Los Angeles, California, USA
| | - Shervin Rabizadeh
- F. Widjaja Foundation Inflammatory Bowel and Immunobiology Research Institute, Cedars-Sinai Medical Center, Los Angeles, California, USA
- Department of Pediatrics, Cedars-Sinai Guerin Children’s, Los Angeles, California, USA
| | | | - James M. Gardner
- Department of Surgery, and
- Diabetes Center, UCSF, San Francisco, California, USA
- Chan-Zuckerberg Biohub, San Francisco, California, USA
- The Center for Cellular Construction, San Francisco, California, USA
| | - Dario Boffelli
- Department of Pediatrics, Cedars-Sinai Guerin Children’s, Los Angeles, California, USA
| | - Zev J. Gartner
- Department of Pharmaceutical Chemistry and TETRAD Program, UCSF, San Francisco, California, USA
| | - Ophir D. Klein
- Department of Orofacial Sciences and Program in Craniofacial Biology, and
- Department of Pediatrics, Cedars-Sinai Guerin Children’s, Los Angeles, California, USA
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35
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Guo M, Xiong Y. Sex-biased genome-editing effects of CRISPR-Cas9 across cancer cells dependent on p53 status. iScience 2023; 26:107529. [PMID: 37636042 PMCID: PMC10448110 DOI: 10.1016/j.isci.2023.107529] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2022] [Revised: 06/12/2023] [Accepted: 07/28/2023] [Indexed: 08/29/2023] Open
Abstract
The CRISPR-Cas9 system has emerged as the dominant technology for gene editing and clinical applications. One major concern is its off-target effect after the introduction of exogenous CRISPR-Cas9 into cells. Several previous studies have investigated either Cas9 alone or CRISPR-Cas9 interactions with p53. Here, we reanalyzed previously reported data of p53-associated Cas9 activities and observed large significant sex differences between p53-wildtype and p53-mutant cells. To expand the impact of this finding, we further examined all protein-coding genes for sex-specific dependencies in a large-scale CRISPR-Cas9 screening dataset from the DepMap project. We highlighted the p53-dependent sex bias of gene knockouts (including MYC, PIK3CA, KAT2B, KDM4E, SUV39H1, FANCB, TLR7, and APC2) across cancer types and potential mechanisms (mediated by transcriptional factors, including SOX9, FOXO4, LEF1, and RYBP) underlying this phenomenon. Our results suggest that the p53-dependent sex bias may need to be considered in future clinical applications of CRISPR-Cas9, especially in cancer.
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Affiliation(s)
- Mengbiao Guo
- Key Laboratory of Gene Engineering of the Ministry of Education, Institute of Healthy Aging Research, School of Life Sciences, Sun Yat-sen University, Guangzhou 510006, China
| | - Yuanyan Xiong
- Key Laboratory of Gene Engineering of the Ministry of Education, Institute of Healthy Aging Research, School of Life Sciences, Sun Yat-sen University, Guangzhou 510006, China
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Hu Y, Hou Y, Zhou S, Wang Y, Shen C, Mu L, Su D, Zhang R. Mechanism of assembly of snRNP cores assisted by ICln and the SMN complex in fission yeast. iScience 2023; 26:107604. [PMID: 37664592 PMCID: PMC10470402 DOI: 10.1016/j.isci.2023.107604] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2023] [Revised: 07/11/2023] [Accepted: 08/08/2023] [Indexed: 09/05/2023] Open
Abstract
The spliceosomal snRNP cores, each comprised of a snRNA and a seven-membered Sm ring (D1/D2/F/E/G/D3/B), are assembled by twelve chaperoning proteins in human. However, only six assembly-assisting proteins, ICln and the SMN complex (SMN/Gemin2/Gemin6-8), have been found in Schizosaccharomyces pombe (Sp). Here, we used recombinant proteins to reconstitute the chaperone machinery and investigated the roles of these proteins systematically. We found that, like the human system, the assembly in S. pombe requires ICln and the SMN complex sequentially. However, there are several significant differences. For instance, h_F/E/G forms heterohexamers and heterotrimers, while Sp_F/E/G only forms heterohexamers; h_Gemin2 alone can bind D1/D2/F/E/G, but Sp_Gemin2 cannot. Moreover, we found that Sp_Gemin2 is essential using genetic approaches. These mechanistic studies reveal that these six proteins are necessary and sufficient for Sm core assembly at the molecular level, and enrich our understanding of the chaperone systems in species variation and evolution.
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Affiliation(s)
- Yan Hu
- Department of Ophthalmology, West China Hospital, Sichuan University and Collaborative Innovation Center for Biotherapy, Chengdu 610041, P.R. China
- State Key Laboratory of Biotherapy, West China Hospital, Sichuan University and Collaborative Innovation Center for Biotherapy, Chengdu 610041, P.R. China
| | - Yan Hou
- Department of Ophthalmology, West China Hospital, Sichuan University and Collaborative Innovation Center for Biotherapy, Chengdu 610041, P.R. China
- State Key Laboratory of Biotherapy, West China Hospital, Sichuan University and Collaborative Innovation Center for Biotherapy, Chengdu 610041, P.R. China
| | - Shijie Zhou
- Department of Ophthalmology, West China Hospital, Sichuan University and Collaborative Innovation Center for Biotherapy, Chengdu 610041, P.R. China
- State Key Laboratory of Biotherapy, West China Hospital, Sichuan University and Collaborative Innovation Center for Biotherapy, Chengdu 610041, P.R. China
| | - Yingzhi Wang
- Department of Ophthalmology, West China Hospital, Sichuan University and Collaborative Innovation Center for Biotherapy, Chengdu 610041, P.R. China
- State Key Laboratory of Biotherapy, West China Hospital, Sichuan University and Collaborative Innovation Center for Biotherapy, Chengdu 610041, P.R. China
| | - Congcong Shen
- Department of Ophthalmology, West China Hospital, Sichuan University and Collaborative Innovation Center for Biotherapy, Chengdu 610041, P.R. China
- State Key Laboratory of Biotherapy, West China Hospital, Sichuan University and Collaborative Innovation Center for Biotherapy, Chengdu 610041, P.R. China
| | - Li Mu
- Department of Ophthalmology, West China Hospital, Sichuan University and Collaborative Innovation Center for Biotherapy, Chengdu 610041, P.R. China
- State Key Laboratory of Biotherapy, West China Hospital, Sichuan University and Collaborative Innovation Center for Biotherapy, Chengdu 610041, P.R. China
| | - Dan Su
- State Key Laboratory of Biotherapy, West China Hospital, Sichuan University and Collaborative Innovation Center for Biotherapy, Chengdu 610041, P.R. China
| | - Rundong Zhang
- Department of Ophthalmology, West China Hospital, Sichuan University and Collaborative Innovation Center for Biotherapy, Chengdu 610041, P.R. China
- State Key Laboratory of Biotherapy, West China Hospital, Sichuan University and Collaborative Innovation Center for Biotherapy, Chengdu 610041, P.R. China
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Ruijmbeek CW, Housley F, Idrees H, Housley MP, Pestel J, Keller L, Lai JK, van der Linde HC, Willemsen R, Piesker J, Al-Hassnan ZN, Almesned A, Dalinghaus M, van den Bersselaar LM, van Slegtenhorst MA, Tessadori F, Bakkers J, van Ham TJ, Stainier DY, Verhagen JM, Reischauer S. Biallelic variants in FLII cause pediatric cardiomyopathy by disrupting cardiomyocyte cell adhesion and myofibril organization. JCI Insight 2023; 8:e168247. [PMID: 37561591 PMCID: PMC10544232 DOI: 10.1172/jci.insight.168247] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2022] [Accepted: 07/20/2023] [Indexed: 08/12/2023] Open
Abstract
Pediatric cardiomyopathy (CM) represents a group of rare, severe disorders that affect the myocardium. To date, the etiology and mechanisms underlying pediatric CM are incompletely understood, hampering accurate diagnosis and individualized therapy development. Here, we identified biallelic variants in the highly conserved flightless-I (FLII) gene in 3 families with idiopathic, early-onset dilated CM. We demonstrated that patient-specific FLII variants, when brought into the zebrafish genome using CRISPR/Cas9 genome editing, resulted in the manifestation of key aspects of morphological and functional abnormalities of the heart, as observed in our patients. Importantly, using these genetic animal models, complemented with in-depth loss-of-function studies, we provided insights into the function of Flii during ventricular chamber morphogenesis in vivo, including myofibril organization and cardiomyocyte cell adhesion, as well as trabeculation. In addition, we identified Flii function to be important for the regulation of Notch and Hippo signaling, crucial pathways associated with cardiac morphogenesis and function. Taken together, our data provide experimental evidence for a role for FLII in the pathogenesis of pediatric CM and report biallelic variants as a genetic cause of pediatric CM.
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Affiliation(s)
- Claudine W.B. Ruijmbeek
- Department of Clinical Genetics, Erasmus MC, University Medical Center Rotterdam, Rotterdam, Netherlands
| | - Filomena Housley
- Department of Developmental Genetics, Max Planck Institute for Heart and Lung Research, Bad Nauheim, Germany
| | - Hafiza Idrees
- Medical Clinic I (Cardiology/Angiology) and Campus Kerckhoff, Justus-Liebig-University Giessen, Giessen, Germany
- Excellence Cluster Cardio-Pulmonary Institute (CPI), Giessen/Bad Nauheim, Germany
| | - Michael P. Housley
- Department of Developmental Genetics, Max Planck Institute for Heart and Lung Research, Bad Nauheim, Germany
| | - Jenny Pestel
- Department of Developmental Genetics, Max Planck Institute for Heart and Lung Research, Bad Nauheim, Germany
| | - Leonie Keller
- Department of Developmental Genetics, Max Planck Institute for Heart and Lung Research, Bad Nauheim, Germany
| | - Jason K.H. Lai
- Department of Developmental Genetics, Max Planck Institute for Heart and Lung Research, Bad Nauheim, Germany
| | - Herma C. van der Linde
- Department of Clinical Genetics, Erasmus MC, University Medical Center Rotterdam, Rotterdam, Netherlands
| | - Rob Willemsen
- Department of Clinical Genetics, Erasmus MC, University Medical Center Rotterdam, Rotterdam, Netherlands
| | - Janett Piesker
- Scientific Service Group Microscopy, Max Planck Institute for Heart and Lung Research, Bad Nauheim, Germany
| | - Zuhair N. Al-Hassnan
- Department of Medical Genetics, and
- Cardiovascular Genetics Program, King Faisal Specialist Hospital & Research Center, Riyadh, Saudi Arabia
| | | | - Michiel Dalinghaus
- Department of Pediatric Cardiology, Erasmus MC, University Medical Center Rotterdam, Rotterdam, Netherlands
| | - Lisa M. van den Bersselaar
- Department of Clinical Genetics, Erasmus MC, University Medical Center Rotterdam, Rotterdam, Netherlands
| | - Marjon A. van Slegtenhorst
- Department of Clinical Genetics, Erasmus MC, University Medical Center Rotterdam, Rotterdam, Netherlands
| | - Federico Tessadori
- Hubrecht Institute-KNAW and University Medical Center Utrecht, Utrecht, Netherlands
| | - Jeroen Bakkers
- Hubrecht Institute-KNAW and University Medical Center Utrecht, Utrecht, Netherlands
- Department of Pediatric Cardiology, University Medical Center Utrecht, Utrecht, Netherlands
| | - Tjakko J. van Ham
- Department of Clinical Genetics, Erasmus MC, University Medical Center Rotterdam, Rotterdam, Netherlands
| | - Didier Y.R. Stainier
- Department of Developmental Genetics, Max Planck Institute for Heart and Lung Research, Bad Nauheim, Germany
- Excellence Cluster Cardio-Pulmonary Institute (CPI), Giessen/Bad Nauheim, Germany
- German Centre for Cardiovascular Research (DZHK), RheinMain partner site, Bad Nauheim, Germany
| | - Judith M.A. Verhagen
- Department of Clinical Genetics, Erasmus MC, University Medical Center Rotterdam, Rotterdam, Netherlands
| | - Sven Reischauer
- Department of Developmental Genetics, Max Planck Institute for Heart and Lung Research, Bad Nauheim, Germany
- Medical Clinic I (Cardiology/Angiology) and Campus Kerckhoff, Justus-Liebig-University Giessen, Giessen, Germany
- Excellence Cluster Cardio-Pulmonary Institute (CPI), Giessen/Bad Nauheim, Germany
- German Centre for Cardiovascular Research (DZHK), RheinMain partner site, Bad Nauheim, Germany
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Alhalabi OT, Sahm F, Unterberg AW, Jakobs M. The molecular diagnostic yield of frame-based stereotactic biopsies in the age of precision neuro-oncology: a cross-sectional study. Acta Neurochir (Wien) 2023; 165:2479-2487. [PMID: 37553446 PMCID: PMC10477138 DOI: 10.1007/s00701-023-05742-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2023] [Accepted: 07/23/2023] [Indexed: 08/10/2023]
Abstract
PURPOSE With the increasing role of molecular genetics in the diagnostics of intracranial tumors, delivering sufficient representative tissue for such analyses is of paramount importance. This study explored the rate of successful diagnosis after frame-based stereotactic biopsies of intracranial lesions. METHODS Consecutive patients undergoing frame-based stereotactic biopsies in 2020 and 2021 were included in this retrospective analysis. Cases were classified into three groups: conclusive, diagnosis with missing molecular genetics (MG) data, and inconclusive neuropathological diagnosis. RESULTS Of 145 patients, a conclusive diagnosis was possible in n = 137 cases (94.5%). For 3 cases (2.0%), diagnosis was established with missing MG data. In 5 cases (3.5%), an inconclusive (tumor) diagnosis was met. Diagnoses comprised mainly WHO 4 glioblastomas (n = 73, 56%), CNS lymphomas (n = 23, 16%), inflammatory diseases (n = 14, 10%), and metastases (n = 5, 3%). Methylomics were applied in 49% (n = 44) of tumor cases (panel sequencing in n = 28, 30% of tumors). The average number of specimens used for MG diagnostics was 5, while the average number of specimens provided was 15. In a univariate analysis, insufficient DNA was associated with an inconclusive diagnosis or a diagnosis with missing MG data (p < 0.001). Analyses of planned and implemented trajectories of cases with diagnosis with missing MG data or inconclusive diagnosis (n = 8) revealed that regions of interest were reached in almost all cases (n = 7). CONCLUSION Although stereotactic frame-based biopsies deliver a limited amount of tissue, they bear high histopathological and molecular genetic diagnostic yields. Given the proven surgical precision of the planned biopsy trajectories, optimizing surveyed lesion regions could help improve the rate of conclusive diagnoses.
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Affiliation(s)
- Obada T Alhalabi
- Department of Neurosurgery, Heidelberg University Hospital, Im Neuenheimer Feld 400, 69121, Heidelberg, Germany
| | - Felix Sahm
- Department of Neuropathology, Heidelberg University Hospital, Heidelberg, Germany
| | - Andreas W Unterberg
- Department of Neurosurgery, Heidelberg University Hospital, Im Neuenheimer Feld 400, 69121, Heidelberg, Germany
| | - Martin Jakobs
- Department of Neurosurgery, Heidelberg University Hospital, Im Neuenheimer Feld 400, 69121, Heidelberg, Germany.
- Division of Stereotactic Neurosurgery, Department of Neurosurgery, Heidelberg University Hospital, Heidelberg, Germany.
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Tatman PD, Kao DP, Chatfield KC, Carroll IA, Wagner JA, Jonas ER, Sucharov CC, Port JD, Lowes BD, Minobe WA, Huebler SP, Karimpour-Fard A, Rodriguez EM, Liggett SB, Bristow MR. An extensive β1-adrenergic receptor gene signaling network regulates molecular remodeling in dilated cardiomyopathies. JCI Insight 2023; 8:e169720. [PMID: 37606047 PMCID: PMC10543724 DOI: 10.1172/jci.insight.169720] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2023] [Accepted: 07/11/2023] [Indexed: 08/23/2023] Open
Abstract
We investigated the extent, biologic characterization, phenotypic specificity, and possible regulation of a β1-adrenergic receptor-linked (β1-AR-linked) gene signaling network (β1-GSN) involved in left ventricular (LV) eccentric pathologic remodeling. A 430-member β1-GSN was identified by mRNA expression in transgenic mice overexpressing human β1-ARs or from literature curation, which exhibited opposite directional behavior in interventricular septum endomyocardial biopsies taken from patients with beta-blocker-treated, reverse remodeled dilated cardiomyopathies. With reverse remodeling, the major biologic categories and percentage of the dominant directional change were as follows: metabolic (19.3%, 81% upregulated); gene regulation (14.9%, 78% upregulated); extracellular matrix/fibrosis (9.1%, 92% downregulated); and cell homeostasis (13.3%, 60% upregulated). Regarding the comparison of β1-GSN categories with expression from 19,243 nonnetwork genes, phenotypic selection for major β1-GSN categories was exhibited for LV end systolic volume (contractility measure), ejection fraction (remodeling index), and pulmonary wedge pressure (wall tension surrogate), beginning at 3 months and persisting to study completion at 12 months. In addition, 121 lncRNAs were identified as possibly involved in cis-acting regulation of β1-GSN members. We conclude that an extensive 430-member gene network downstream from the β1-AR is involved in pathologic ventricular remodeling, with metabolic genes as the most prevalent category.
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Affiliation(s)
| | - David P. Kao
- Division of Cardiology, Department of Medicine, and
- Colorado Center for Personalized Medicine University of Colorado School of Medicine, Aurora, Colorado, USA
| | - Kathryn C. Chatfield
- Division of Cardiology, Department of Medicine, and
- Department of Pediatric Cardiology, Children’s Hospital Colorado, Aurora, Colorado, USA
| | - Ian A. Carroll
- Division of Cardiology, Department of Medicine, and
- ARCA biopharma, Westminster, Colorado, USA
| | | | | | | | | | - Brian D. Lowes
- Division of Cardiovascular Medicine, University of Nebraska Medical Center, Omaha, Nebraska, USA
| | | | | | - Anis Karimpour-Fard
- Department of Biomedical Informatics, University of Colorado School of Medicine, Aurora, Colorado, USA
| | | | - Stephen B. Liggett
- Departments of Medicine and Molecular Pharmacology and Physiology, Morsani College of Medicine, University of South Florida, Tampa, Florida, USA
| | - Michael R. Bristow
- Division of Cardiology, Department of Medicine, and
- ARCA biopharma, Westminster, Colorado, USA
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Han R, Lin C, Zhang C, Kang J, Lu C, Zhang Y, Wang Y, Hu C, He Y. The potential therapeutic regimen for overcoming resistance to osimertinib due to rare mutations in NSCLC. iScience 2023; 26:107105. [PMID: 37416479 PMCID: PMC10320197 DOI: 10.1016/j.isci.2023.107105] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2022] [Revised: 05/07/2023] [Accepted: 06/08/2023] [Indexed: 07/08/2023] Open
Abstract
The mechanisms of osimertinib resistance have not been well characterized. We conducted next-generation sequencing to recognize novel resistance mechanism and used cell line-derived xenograft (CDX) and patient-derived xenograft (PDX) models to evaluate the anti-proliferative effects of aspirin in vivo and in vitro. We observed that PIK3CG mutations led to acquired resistance to osimertinib in a patient and further confirmed that both PIK3CG and PIK3CA mutations caused osimertinib resistance. Mechanistically, the expression of PI3Kγ or PI3Kα was up-regulated after PIK3CG or PIK3CA lentivirus transfection, respectively, and which can be effectively suppressed by aspirin. Lastly, our results from in vivo studies indicate that aspirin can reverse osimertinib resistance caused by PIK3CG or PIK3CA mutations in both CDX and PDX models. Herein, we first confirmed that mutations in PIK3CG can lead to resistance to osimertinib, and the combined therapy may be a strategy to reverse PIK3CG/PIK3CA mutation-induced osimertinib resistance.
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Affiliation(s)
- Rui Han
- Department of Respiratory Disease, Daping Hospital, Army Medical University, Chongqing, China
| | - Caiyu Lin
- Department of Respiratory Disease, Daping Hospital, Army Medical University, Chongqing, China
| | - Chong Zhang
- Department of Ultrasound, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Jun Kang
- Department of Respiratory Disease, Daping Hospital, Army Medical University, Chongqing, China
| | - Conghua Lu
- Department of Respiratory Disease, Daping Hospital, Army Medical University, Chongqing, China
| | - Yiming Zhang
- Department of Respiratory Disease, Daping Hospital, Army Medical University, Chongqing, China
| | - Yubo Wang
- Department of Respiratory Disease, Daping Hospital, Army Medical University, Chongqing, China
| | - Chen Hu
- Department of Respiratory Disease, Daping Hospital, Army Medical University, Chongqing, China
| | - Yong He
- Department of Respiratory Disease, Daping Hospital, Army Medical University, Chongqing, China
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Sirohi VK, Medrano TI, Kannan A, Bagchi IC, Cooke PS. Uterine-specific Ezh2 deletion enhances stromal cell senescence and impairs placentation, resulting in pregnancy loss. iScience 2023; 26:107028. [PMID: 37360688 PMCID: PMC10285549 DOI: 10.1016/j.isci.2023.107028] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2023] [Revised: 05/10/2023] [Accepted: 05/30/2023] [Indexed: 06/28/2023] Open
Abstract
Maternal uterine remodeling facilitates embryo implantation, stromal cell decidualization and placentation, and perturbation of these processes may cause pregnancy loss. Enhancer of zeste homolog 2 (EZH2) is a histone methyltransferase that epigenetically represses gene transcription; loss of uterine EZH2 affects endometrial physiology and induces infertility. We utilized a uterine Ezh2 conditional knockout (cKO) mouse to determine EZH2's role in pregnancy progression. Despite normal fertilization and implantation, embryo resorption occurred mid-gestation in Ezh2cKO mice, accompanied by compromised decidualization and placentation. Western blot analysis revealed Ezh2-deficient stromal cells have reduced amounts of the histone methylation mark H3K27me3, causing upregulation of senescence markers p21 and p16 and indicating that enhanced stromal cell senescence likely impairs decidualization. Placentas from Ezh2cKO dams on gestation day (GD) 12 show architectural defects, including mislocalization of spongiotrophoblasts and reduced vascularization. In summary, uterine Ezh2 loss impairs decidualization, increases decidual senescence, and alters trophoblast differentiation, leading to pregnancy loss.
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Affiliation(s)
- Vijay K. Sirohi
- Department of Physiological Sciences, University of Florida, Gainesville, FL, USA
| | - Theresa I. Medrano
- Department of Physiological Sciences, University of Florida, Gainesville, FL, USA
| | - Athilakshmi Kannan
- Department of Comparative Biosciences, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Indrani C. Bagchi
- Department of Comparative Biosciences, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Paul S. Cooke
- Department of Physiological Sciences, University of Florida, Gainesville, FL, USA
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42
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Hägerling R. [Genetics, diagnostics and clinical presentation of primary lymphoedema]. Dermatologie (Heidelb) 2023:10.1007/s00105-023-05183-w. [PMID: 37402871 DOI: 10.1007/s00105-023-05183-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Accepted: 05/30/2023] [Indexed: 07/06/2023]
Abstract
Primary lymphoedema is a hereditary genetic disorder of the lymphatic system. These genetic disorders can result in malformation or dysfunction of the lymphatic system, which leads to an accumulation of fluid in the tissue and, thus to the formation of oedema. The most common form is peripheral lymphoedema of the lower limbs, but systemic manifestations such as intestinal lymphangiectasia, ascites, chylothorax or hydrops fetalis may also occur. The clinical presentation and the degree of lymphoedema varies depending on the causative gene and the specific gene alteration. Primary lymphoedema is divided into five categories: (1) disorders with somatic mosaicism and segmental growth abnormality, (2a) syndromal disorders, (2b) disorders with systemic involvement, (2c) congenital lymphoedema and (2d) disorders that occur after the first year of life (late onset lymphoedema). Targeted genetic diagnosis is based on the patient's clinical presentation and classification into one of the five categories. In general, the diagnosis usually starts with basic diagnostics, which include cytogenetic and molecular genetic testing. Subsequently, a molecular genetic diagnosis is made by performing single-gene analyses, gene panel examinations, exome sequencing or whole genome sequencing. This allows the identification of genetic variants or mutations that are considered to be causative for the presenting symptoms. Combined with human genetic counselling, the genetic diagnosis allows for conclusions about inheritance, the risk of recurrence and potential concomitant symptoms. In many cases, only this approach allows the definite form of primary lymphoedema to be described.
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Affiliation(s)
- René Hägerling
- Lymphovaskuläre Medizin und Translationale 3D-Histopathologie, Institut für Medizinische Genetik und Humangenetik, Charité - Universitätsmedizin Berlin, Augustenburger Platz 1, 13353, Berlin, Deutschland.
- BIH Center für Regenerative Therapien, Berlin Institute of Health der Charité - Universitätsmedizin Berlin, Augustenburger Platz 1, 13353, Berlin, Deutschland.
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Göder A, Quinlan A, Rainey MD, Bennett D, Shamavu D, Corso J, Santocanale C. PTBP1 enforces ATR-CHK1 signaling determining the potency of CDC7 inhibitors. iScience 2023; 26:106951. [PMID: 37378325 PMCID: PMC10291475 DOI: 10.1016/j.isci.2023.106951] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2023] [Revised: 04/27/2023] [Accepted: 05/22/2023] [Indexed: 06/29/2023] Open
Abstract
CDC7 kinase is crucial for DNA replication initiation and fork processing. CDC7 inhibition mildly activates the ATR pathway, which further limits origin firing; however, to date the relationship between CDC7 and ATR remains controversial. We show that CDC7 and ATR inhibitors are either synergistic or antagonistic depending on the degree of inhibition of each individual kinase. We find that Polypyrimidine Tract Binding Protein 1 (PTBP1) is important for ATR activity in response to CDC7 inhibition and genotoxic agents. Compromised PTBP1 expression makes cells defective in RPA recruitment, genomically unstable, and resistant to CDC7 inhibitors. PTBP1 deficiency affects the expression and splicing of many genes indicating a multifactorial impact on drug response. We find that an exon skipping event in RAD51AP1 contributes to checkpoint deficiency in PTBP1-deficient cells. These results identify PTBP1 as a key factor in replication stress response and define how ATR activity modulates the activity of CDC7 inhibitors.
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Affiliation(s)
- Anja Göder
- Centre for Chromosome Biology, School of Biological and Chemical Sciences, University of Galway, Galway H91W2TY, Ireland
| | - Aisling Quinlan
- Centre for Chromosome Biology, School of Biological and Chemical Sciences, University of Galway, Galway H91W2TY, Ireland
| | - Michael D. Rainey
- Centre for Chromosome Biology, School of Biological and Chemical Sciences, University of Galway, Galway H91W2TY, Ireland
| | - Declan Bennett
- School of Mathematical & Statistical Sciences, University of Galway, Galway H91TK33, Ireland
| | - Daniel Shamavu
- Centre for Chromosome Biology, School of Biological and Chemical Sciences, University of Galway, Galway H91W2TY, Ireland
| | - Jacqueline Corso
- Centre for Chromosome Biology, School of Biological and Chemical Sciences, University of Galway, Galway H91W2TY, Ireland
| | - Corrado Santocanale
- Centre for Chromosome Biology, School of Biological and Chemical Sciences, University of Galway, Galway H91W2TY, Ireland
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44
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García-Diéguez L, Diaz-Tang G, Marin Meneses E, Cruise V, Barraza I, Craddock TJ, Smith RP. Periodically disturbing biofilms reduces expression of quorum sensing-regulated virulence factors in Pseudomonas aeruginosa. iScience 2023; 26:106843. [PMID: 37255658 PMCID: PMC10225924 DOI: 10.1016/j.isci.2023.106843] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2023] [Revised: 04/26/2023] [Accepted: 05/04/2023] [Indexed: 06/01/2023] Open
Abstract
Pseudomonas aeruginosa uses quorum sensing to regulate the expression of virulence factors. In static environments, spatial structures, such as biofilms, can increase the expression of these virulence factors. However, in natural settings, biofilms are exposed to physical forces that disrupt spatial structure, which may affect the expression of virulence factors regulated by quorum sensing. We show that periodically disturbing biofilms composed of P. aeruginosa using a physical force reduces the expression of quorum sensing-regulated virulence factors. At an intermediate disturbance frequency, the expression of virulence factors in the las, rhl, and pqs regulons is reduced. Mathematical modeling suggests that perturbation of the pqsR receptor is critical for this reduction. Removing the lasR receptor enhances the reduction in the expression of virulence factors as a result of disturbance. Our results allow identification of environments where virulence is reduced and implicate the lasR receptor as having a buffering role against disturbance.
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Affiliation(s)
- Laura García-Diéguez
- Department of Biological Sciences, Halmos College of Arts and Science, Nova Southeastern University, Fort Lauderdale FL 33314, USA
| | - Gabriela Diaz-Tang
- Department of Biological Sciences, Halmos College of Arts and Science, Nova Southeastern University, Fort Lauderdale FL 33314, USA
| | - Estefania Marin Meneses
- Department of Biological Sciences, Halmos College of Arts and Science, Nova Southeastern University, Fort Lauderdale FL 33314, USA
| | - Vanessa Cruise
- Department of Biological Sciences, Halmos College of Arts and Science, Nova Southeastern University, Fort Lauderdale FL 33314, USA
| | - Ivana Barraza
- Department of Biological Sciences, Halmos College of Arts and Science, Nova Southeastern University, Fort Lauderdale FL 33314, USA
| | - Travis J.A. Craddock
- Clinical Systems Biology Group, Institute for Neuro-Immune Medicine, Nova Southeastern University, Fort Lauderdale FL 33314, USA
- Department of Psychology & Neuroscience, College of Psychology, Nova Southeastern University, Fort Lauderdale FL 33314, USA
- Department of Computer Science, College of Engineering and Computing, Nova Southeastern University, Fort Lauderdale FL 33314, USA
- Department of Clinical Immunology, College of Osteopathic Medicine, Nova Southeastern University, Fort Lauderdale FL 33314, USA
| | - Robert P. Smith
- Department of Biological Sciences, Halmos College of Arts and Science, Nova Southeastern University, Fort Lauderdale FL 33314, USA
- Cell Therapy Institute, Kiran Patel College of Allopathic Medicine, Nova Southeastern University, Fort Lauderdale FL 33314, USA
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45
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Oftedal BE, Assing K, Baris S, Safgren SL, Johansen IS, Jakobsen MA, Babovic-Vuksanovic D, Agre K, Klee EW, Majcic E, Ferré EM, Schmitt MM, DiMaggio T, Rosen LB, Rahman MO, Chrysis D, Giannakopoulos A, Garcia MT, González-Granado LI, Stanley K, Galant-Swafford J, Suwannarat P, Meyts I, Lionakis MS, Husebye ES. Dominant-negative heterozygous mutations in AIRE confer diverse autoimmune phenotypes. iScience 2023; 26:106818. [PMID: 37235056 PMCID: PMC10206195 DOI: 10.1016/j.isci.2023.106818] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2022] [Revised: 03/20/2023] [Accepted: 05/02/2023] [Indexed: 05/28/2023] Open
Abstract
Autoimmune polyendocrine syndrome type 1 (APS-1) is an autosomal recessive disease characterized by severe and childhood onset organ-specific autoimmunity caused by mutations in the autoimmune regulator (AIRE) gene. More recently, dominant-negative mutations within the PHD1, PHD2, and SAND domains have been associated with an incompletely penetrant milder phenotype with later onset familial clustering, often masquerading as organ-specific autoimmunity. Patients with immunodeficiencies or autoimmunity where genetic analyses revealed heterozygous AIRE mutations were included in the study and the dominant-negative effects of the AIRE mutations were functionally assessed in vitro. We here report additional families with phenotypes ranging from immunodeficiency, enteropathy, and vitiligo to asymptomatic carrier status. APS-1-specific autoantibodies can hint to the presence of these pathogenic AIRE variants although their absence does not rule out their presence. Our findings suggest functional studies of heterozygous AIRE variants and close follow-up of identified individuals and their families.
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Affiliation(s)
- Bergithe E. Oftedal
- Department of Clinical Science, University of Bergen and Department of Medicine, Haukeland University Hospital, Bergen, Norway
| | - Kristian Assing
- Department of Clinical Immunology, Odense University Hospital, Odense, Denmark
| | - Safa Baris
- Marmara University, Faculty of Medicine, Pediatric Allergy and Immunology, Istanbul, Turkey
- Istanbul Jeffrey Modell Diagnostic and Research Center for Primary Immunodeficiencies, Istanbul, Turkey
| | - Stephanie L. Safgren
- Center for Individualized Medicine, Department of Quantitative Health Sciences, Mayo Clinic, Rochester, MN, USA
| | - Isik S. Johansen
- Department of Infectious Diseases, Odense University Hospital, Odense, Denmark
| | | | | | | | - Eric W. Klee
- Mayo Clinic, Department of Quantitative Health Sciences, Rochester, MN, USA
| | - Emina Majcic
- Department of Clinical Science, University of Bergen and Department of Medicine, Haukeland University Hospital, Bergen, Norway
| | - Elise M.N. Ferré
- Laboratory of Clinical Immunology & Microbiology, National Institute of Allergy & Infectious Diseases (NIAID), National Institutes of Health (NIH), Bethesda, MD, USA
| | - Monica M. Schmitt
- Laboratory of Clinical Immunology & Microbiology, National Institute of Allergy & Infectious Diseases (NIAID), National Institutes of Health (NIH), Bethesda, MD, USA
| | - Tom DiMaggio
- Laboratory of Clinical Immunology & Microbiology, National Institute of Allergy & Infectious Diseases (NIAID), National Institutes of Health (NIH), Bethesda, MD, USA
| | - Lindsey B. Rosen
- Laboratory of Clinical Immunology & Microbiology, National Institute of Allergy & Infectious Diseases (NIAID), National Institutes of Health (NIH), Bethesda, MD, USA
| | - Muhammad Obaidur Rahman
- Department of Clinical Science, University of Bergen and Department of Medicine, Haukeland University Hospital, Bergen, Norway
| | - Dionisios Chrysis
- Department of Pediatrics, Division of Pediatric Endocrinology, Medical School, University of Patras, Rion, Greece
| | - Aristeidis Giannakopoulos
- Department of Pediatrics, Division of Pediatric Endocrinology, Medical School, University of Patras, Rion, Greece
| | - Maria Tallon Garcia
- Pediatric Hematology and Oncology Department, Hospital Álvaro Cunqueiro, Vigo, Spain
| | - Luis Ignacio González-Granado
- Unidad de Inmunodeficiencias, Pediatría, Instituto de Investigación Hospital 12 de Octubre, Facultad de Medicina, Universidad Complutense, Madrid, Spain
| | - Katherine Stanley
- Mid-Atlantic Permanente Medical Group, Kaiser Permanente MidAtlantic, Rockville, MD, USA
| | | | - Pim Suwannarat
- Mid-Atlantic Permanente Medical Group, Kaiser Permanente MidAtlantic, Rockville, MD, USA
| | - Isabelle Meyts
- Department of Pediatrics, University Hospital Leuven, Laboratory for Inborn Errors of Immunity, Department of Microbiology Immunology and Transplantation, KU Leuven, Leuven, Belgium
| | - Michail S. Lionakis
- Laboratory of Clinical Immunology & Microbiology, National Institute of Allergy & Infectious Diseases (NIAID), National Institutes of Health (NIH), Bethesda, MD, USA
| | - Eystein S. Husebye
- Department of Clinical Science, University of Bergen and Department of Medicine, Haukeland University Hospital, Bergen, Norway
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46
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Weichert-Leahey N, Shi H, Tao T, Oldridge DA, Durbin AD, Abraham BJ, Zimmerman MW, Zhu S, Wood AC, Reyon D, Joung JK, Young RA, Diskin SJ, Maris JM, Look AT. Genetic predisposition to neuroblastoma results from a regulatory polymorphism that promotes the adrenergic cell state. J Clin Invest 2023; 133:e166919. [PMID: 37183825 PMCID: PMC10178836 DOI: 10.1172/jci166919] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2022] [Accepted: 03/14/2023] [Indexed: 05/16/2023] Open
Abstract
Childhood neuroblastomas exhibit plasticity between an undifferentiated neural crest-like mesenchymal cell state and a more differentiated sympathetic adrenergic cell state. These cell states are governed by autoregulatory transcriptional loops called core regulatory circuitries (CRCs), which drive the early development of sympathetic neuronal progenitors from migratory neural crest cells during embryogenesis. The adrenergic cell identity of neuroblastoma requires LMO1 as a transcriptional cofactor. Both LMO1 expression levels and the risk of developing neuroblastoma in children are associated with a single nucleotide polymorphism, G/T, that affects a GATA motif in the first intron of LMO1. Here, we showed that WT zebrafish with the GATA genotype developed adrenergic neuroblastoma, while knock-in of the protective TATA allele at this locus reduced the penetrance of MYCN-driven tumors, which were restricted to the mesenchymal cell state. Whole genome sequencing of childhood neuroblastomas demonstrated that TATA/TATA tumors also exhibited a mesenchymal cell state and were low risk at diagnosis. Thus, conversion of the regulatory GATA to a TATA allele in the first intron of LMO1 reduced the neuroblastoma-initiation rate by preventing formation of the adrenergic cell state. This mechanism was conserved over 400 million years of evolution, separating zebrafish and humans.
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Affiliation(s)
- Nina Weichert-Leahey
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts, USA
- Division of Pediatric Hematology/Oncology, Boston Children’s Hospital, Boston, Massachusetts, USA
| | - Hui Shi
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts, USA
- College of Animal Sciences, Zhejiang University, Hangzhou, Zhejiang, China
| | - Ting Tao
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts, USA
- National Clinical Research Center for Child Health, National Children’s Regional Medical Center, Children’s Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
- Cancer Center, Zhejiang University, Hangzhou, Zhejiang, China
| | - Derek A. Oldridge
- Department of Pathology and Laboratory Medicine, Children’s Hospital of Philadelphia, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Adam D. Durbin
- Department of Oncology and Comprehensive Cancer Center, St. Jude Children’s Research Hospital, Memphis, Tennessee, USA
| | - Brian J. Abraham
- Whitehead Institute for Biomedical Research, Cambridge, Massachusetts, USA
- Department of Computational Biology, St. Jude Children’s Research Hospital, Memphis, Tennessee, USA
| | - Mark W. Zimmerman
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts, USA
| | - Shizhen Zhu
- Department of Biochemistry and Molecular Biology, Mayo Clinic College of Medicine, Mayo Clinic Cancer Center, Rochester, Minnesota, USA
| | - Andrew C. Wood
- Department of Molecular Medicine and Pathology, Faculty of Medical and Health Science, University of Auckland, Auckland, New Zealand
| | - Deepak Reyon
- Molecular Pathology Unit, Center for Computational and Integrative Biology, and Center for Cancer Research, Massachusetts General Hospital, Charlestown, Massachusetts, USA
- Department of Pathology, Harvard Medical School, Boston, Massachusetts, USA
| | - J. Keith Joung
- Molecular Pathology Unit, Center for Computational and Integrative Biology, and Center for Cancer Research, Massachusetts General Hospital, Charlestown, Massachusetts, USA
- Department of Pathology, Harvard Medical School, Boston, Massachusetts, USA
| | - Richard A. Young
- Whitehead Institute for Biomedical Research, Cambridge, Massachusetts, USA
- The Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
- Biology Department, MIT, Cambridge, Massachusetts, USA
| | - Sharon J. Diskin
- Division of Oncology and Center for Childhood Cancer Research, Children’s Hospital of Philadelphia and Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - John M. Maris
- Division of Oncology and Center for Childhood Cancer Research, Children’s Hospital of Philadelphia and Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - A. Thomas Look
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts, USA
- Division of Pediatric Hematology/Oncology, Boston Children’s Hospital, Boston, Massachusetts, USA
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47
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Sheppard SE, March ME, Seiler C, Matsuoka LS, Kim SE, Kao C, Rubin AI, Battig MR, Khalek N, Schindewolf E, O'Connor N, Pinto E, Priestley JR, Sanders VR, Niazi R, Ganguly A, Hou C, Slater D, Frieden IJ, Huynh T, Shieh JT, Krantz ID, Guerrero JC, Surrey LF, Biko DM, Laje P, Castelo-Soccio L, Nakano TA, Snyder K, Smith CL, Li D, Dori Y, Hakonarson H. Lymphatic disorders caused by mosaic, activating KRAS variants respond to MEK inhibition. JCI Insight 2023; 8:155888. [PMID: 37154160 DOI: 10.1172/jci.insight.155888] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2021] [Accepted: 03/17/2023] [Indexed: 05/10/2023] Open
Abstract
Central conducting lymphatic anomaly (CCLA) due to congenital maldevelopment of the lymphatics can result in debilitating and life-threatening disease with limited treatment options. We identified 4 individuals with CCLA, lymphedema, and microcystic lymphatic malformation due to pathogenic, mosaic variants in KRAS. To determine the functional impact of these variants and identify a targeted therapy for these individuals, we used primary human dermal lymphatic endothelial cells (HDLECs) and zebrafish larvae to model the lymphatic dysplasia. Expression of the p.Gly12Asp and p.Gly13Asp variants in HDLECs in a 2‑dimensional (2D) model and 3D organoid model led to increased ERK phosphorylation, demonstrating these variants activate the RAS/MAPK pathway. Expression of activating KRAS variants in the venous and lymphatic endothelium in zebrafish resulted in lymphatic dysplasia and edema similar to the individuals in the study. Treatment with MEK inhibition significantly reduced the phenotypes in both the organoid and the zebrafish model systems. In conclusion, we present the molecular characterization of the observed lymphatic anomalies due to pathogenic, somatic, activating KRAS variants in humans. Our preclinical studies suggest that MEK inhibition should be studied in future clinical trials for CCLA due to activating KRAS pathogenic variants.
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Affiliation(s)
| | | | - Christoph Seiler
- Zebrafish Core, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | | | | | | | - Adam I Rubin
- Department of Dermatology, Perelman School of Medicine at the University of Pennsylvania, Hospital of the University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | | | - Nahla Khalek
- Richard D. Wood Jr. Center for Fetal Diagnosis and Treatment and
| | | | | | - Erin Pinto
- Jill and Mark Fishman Center for Lymphatic Disorders, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | | | | | - Rojeen Niazi
- Genetic Diagnostic Laboratory, Department of Genetics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Arupa Ganguly
- Genetic Diagnostic Laboratory, Department of Genetics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | | | | | | | | | - Joseph T Shieh
- Division of Medical Genetics, Department of Pediatrics, University of California, San Francisco, San Francisco, California, USA
| | - Ian D Krantz
- Division of Human Genetics, and
- Roberts Individualized Medical Genetics Center, Division of Human Genetics
| | | | | | | | | | - Leslie Castelo-Soccio
- Dermatology Section, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - Taizo A Nakano
- Center for Cancer and Blood Disorders, Children's Hospital Colorado, Aurora, Colorado, USA
| | - Kristen Snyder
- Division of Oncology, Cancer Center, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - Christopher L Smith
- Jill and Mark Fishman Center for Lymphatic Disorders, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | | | - Yoav Dori
- Jill and Mark Fishman Center for Lymphatic Disorders, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
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48
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Tucker MH, Yu W, Menden HL, Xia S, Schreck CF, Gibson MI, Louiselle DA, Pastinen T, Raje N, Sampath V. IRF7 and UNC93B1 variants in an infant with recurrent herpes simplex virus infection. J Clin Invest 2023:154016. [PMID: 37097753 DOI: 10.1172/jci154016] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/26/2023] Open
Abstract
Neonatal herpes simplex virus (HSV) infection is a devastating disease with substantial morbidity and mortality. The genetic basis of susceptibility to HSV in neonates remains undefined. We investigated a male infant with neonatal skin/eye/mouth (SEM) HSV1 disease who had complete recovery after acyclovir but developed HSV1 encephalitis at 1 year of age. Immune work up showed an anergic peripheral blood monocyte cytokine (PBMC) response to TLR3 stimulation but no other TLRs. Exome sequencing identified rare missense variants in IRF7 and UNC93B1. PBMC single cell RNA sequencing done during childhood revealed decreased expression of several innate immune genes and a repressed TLR3 pathway signature at baseline in several immune cell populations, including CD14 monocytes. Functional studies in fibroblasts and THP-1 showed that both variants individually suppressed TLR3-driven IRF3 promoter activity and type I interferon response in vitro. Furthermore, fibroblasts expressing the IRF7 and UNC93B1 variants had higher intracellular viral titers with blunting of the type I interferon response upon HSV1 challenge. This study reports an infant with recurrent HSV1 disease complicated by encephalitis associated with deleterious variants in IRF7 and UNC93B1 genes. Our results suggest that TLR3 pathway mutations may predispose neonates to recurrent severe HSV.
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Affiliation(s)
- Megan H Tucker
- Division of Neonatology, Children's Mercy Kansas City, Kansas City, United States of America
| | - Wei Yu
- Division of Neonatology, Children's Mercy Kansas City, Kansas City, United States of America
| | - Heather L Menden
- Division of Neonatology, Children's Mercy Kansas City, Kansas City, United States of America
| | - Sheng Xia
- Division of Neonatology, Children's Mercy Kansas City, Kansas City, United States of America
| | - Carl F Schreck
- Department of Pediatrics, Genomic Medicine Center, Children's Mercy Kansas City, Kansas City, United States of America
| | - Margaret I Gibson
- Department of Pediatrics, Genomic Medicine Center, Children's Mercy Kansas City, Kansas City, United States of America
| | - Daniel A Louiselle
- Department of Pediatrics, Genomic Medicine Center, Children's Mercy Kansas City, Kansas City, United States of America
| | - Tomi Pastinen
- Department of Pediatrics, Genomic Medicine Center, Children's Mercy Kansas City, Kansas City, United States of America
| | - Nikita Raje
- Department of Pediatrics, Division of Allergy and Immunology, Children's Mercy Kansas City, Kansas City, United States of America
| | - Venkatesh Sampath
- Division of Neonatology, Children's Mercy Kansas City, Kansas City, United States of America
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49
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Iyengar P, Gandhi AY, Granados J, Guo T, Gupta A, Yu J, Llano EM, Zhang F, Gao A, Kandathil A, Williams D, Gao B, Girard L, Malladi VS, Shelton JM, Evers BM, Hannan R, Ahn C, Minna JD, Infante RE. Tumor loss-of-function mutations in STK11/LKB1 induce cachexia. JCI Insight 2023; 8:e165419. [PMID: 37092555 PMCID: PMC10243820 DOI: 10.1172/jci.insight.165419] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2022] [Accepted: 02/23/2023] [Indexed: 04/25/2023] Open
Abstract
Cancer cachexia (CC), a wasting syndrome of muscle and adipose tissue resulting in weight loss, is observed in 50% of patients with solid tumors. Management of CC is limited by the absence of biomarkers and knowledge of molecules that drive its phenotype. To identify such molecules, we injected 54 human non-small cell lung cancer (NSCLC) lines into immunodeficient mice, 17 of which produced an unambiguous phenotype of cachexia or non-cachexia. Whole-exome sequencing revealed that 8 of 10 cachexia lines, but none of the non-cachexia lines, possessed mutations in serine/threonine kinase 11 (STK11/LKB1), a regulator of nutrient sensor AMPK. Silencing of STK11/LKB1 in human NSCLC and murine colorectal carcinoma lines conferred a cachexia phenotype after cell transplantation into immunodeficient (human NSCLC) and immunocompetent (murine colorectal carcinoma) models. This host wasting was associated with an alteration in the immune cell repertoire of the tumor microenvironments that led to increases in local mRNA expression and serum levels of CC-associated cytokines. Mutational analysis of circulating tumor DNA from patients with NSCLC identified 89% concordance between STK11/LKB1 mutations and weight loss at cancer diagnosis. The current data provide evidence that tumor STK11/LKB1 loss of function is a driver of CC, simultaneously serving as a genetic biomarker for this wasting syndrome.
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Affiliation(s)
- Puneeth Iyengar
- Center for Human Nutrition
- Department of Radiation Oncology
- Harold C. Simmons Comprehensive Cancer Center
| | - Aakash Y. Gandhi
- Center for Human Nutrition
- Harold C. Simmons Comprehensive Cancer Center
| | | | | | - Arun Gupta
- Center for Human Nutrition
- Department of Radiation Oncology
| | - Jinhai Yu
- Center for Human Nutrition
- Harold C. Simmons Comprehensive Cancer Center
- Department of Internal Medicine
| | | | - Faya Zhang
- Department of Radiation Oncology
- Harold C. Simmons Comprehensive Cancer Center
| | - Ang Gao
- Harold C. Simmons Comprehensive Cancer Center
- Department of Population and Data Sciences
| | | | | | - Boning Gao
- Harold C. Simmons Comprehensive Cancer Center
- Department of Pharmacology
- Hamon Center for Therapeutic Oncology Research
| | - Luc Girard
- Harold C. Simmons Comprehensive Cancer Center
- Department of Pharmacology
- Hamon Center for Therapeutic Oncology Research
| | | | | | | | - Raquibul Hannan
- Department of Radiation Oncology
- Harold C. Simmons Comprehensive Cancer Center
| | - Chul Ahn
- Harold C. Simmons Comprehensive Cancer Center
- Department of Population and Data Sciences
| | - John D. Minna
- Harold C. Simmons Comprehensive Cancer Center
- Department of Internal Medicine
- Department of Pharmacology
- Hamon Center for Therapeutic Oncology Research
| | - Rodney E. Infante
- Center for Human Nutrition
- Harold C. Simmons Comprehensive Cancer Center
- Department of Internal Medicine
- Department of Molecular Genetics, University of Texas Southwestern Medical Center, Dallas, Texas, USA
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50
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Faber S, Mercey O, Junger K, Garanto A, Ueffing M, Collin RW, Boldt K, Guichard P, Hamel V, Roepman R. Gene augmentation of LCA5-Leber congenital amaurosis ameliorates bulge region defects of the photoreceptor ciliary axoneme. JCI Insight 2023; 8:169162. [PMID: 37071472 DOI: 10.1172/jci.insight.169162] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2023] [Accepted: 04/05/2023] [Indexed: 04/19/2023] Open
Abstract
Leber congenital amaurosis (LCA) is a group of inherited retinal diseases (IRDs) characterized by the early onset and rapid loss of photoreceptor cells. Despite the discovery of a growing number of genes associated with this disease, the molecular mechanisms of photoreceptor cell degeneration of most LCA subtypes remain poorly understood. Here, using retina-specific affinity proteomics combined with ultrastructure expansion microscopy (U-ExM), we reveal the structural and molecular defects underlying LCA type 5 (LCA5) with nanoscale resolution. We show that LCA5-encoded lebercilin, together with retinitis pigmentosa 1 protein (RP1) and the intraflagellar transport (IFT) proteins IFT81 and IFT88, localize at the bulge region of the photoreceptor outer segment (OS), a region crucial for OS membrane disc formation. Next, we demonstrate that mutant mice deficient for lebercilin exhibit early axonemal defects at the bulge region and the distal OS, accompanied by reduced levels of RP1 and IFT proteins, affecting membrane disc formation and presumably leading to photoreceptor death. Finally, AAV-based LCA5 gene augmentation partially restores the bulge region, preserves OS axoneme structure and membrane disc formation, and results in photoreceptor cell survival. Our approach thus provides a next level of assessment of retinal (gene) therapy efficacy at the molecular level.
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Affiliation(s)
- Siebren Faber
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, Netherlands
| | - Olivier Mercey
- Department of Molecular and Cellular Biology, University of Geneva, Geneva, Switzerland
| | - Katrin Junger
- Division of Experimental Ophthalmology and Medical Proteome Center, University of Tuebingen, Tuebingen, Germany
| | - Alejandro Garanto
- Department of Pediatrics, Radboud University Medical Center, Nijmegen, Netherlands
| | - Marius Ueffing
- Division of Experimental Ophthalmology and Medical Proteome Center, University of Tuebingen, Tuebingen, Germany
| | - Rob Wj Collin
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, Netherlands
| | - Karsten Boldt
- Division of Experimental Ophthalmology and Medical Proteome Center, University of Tuebingen, Tuebingen, Germany
| | - Paul Guichard
- Department of Molecular and Cellular Biology, University of Geneva, Geneva, Switzerland
| | - Virginie Hamel
- Department of Molecular and Cellular Biology, University of Geneva, Geneva, Switzerland
| | - Ronald Roepman
- Department of Human Genetics, Radboud University Medical Center Nijmegen, Nijmegen, Netherlands
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