1
|
Tang D, Li X, Fu Y, Wang H, Li X, Parviainen T, Kärkkäinen T. Neural correlates of emotion-label vs. emotion-laden word processing in late bilinguals: evidence from an ERP study. Cogn Emot 2024:1-18. [PMID: 38738622 DOI: 10.1080/02699931.2024.2352584] [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: 12/13/2023] [Accepted: 03/19/2024] [Indexed: 05/14/2024]
Abstract
The brain processes underlying the distinction between emotion-label words (e.g. happy, sad) and emotion-laden words (e.g. successful, failed) remain inconclusive in bilingualism research. The present study aims to directly compare the processing of these two types of emotion words in both the first language (L1) and second language (L2) by recording event-related potentials (ERP) from late Chinese-English bilinguals during a lexical decision task. The results revealed that in the early word processing stages, the N170 emotion effect emerged only for L1 negative emotion-laden words and L2 negative emotion-label words. In addition, larger early posterior negativity (EPN) was elicited by emotion-laden words than emotion-label words in both L1 and L2. In the later processing stages, the N400 emotion effect was evident for L1 emotion words, excluding positive emotion-laden words, while it was absent in L2. Notably, L1 emotion words elicited enhanced N400 and attenuated late positive complex (LPC) compared to those in L2. Taken together, these findings confirmed the engagement of emotion, and highlighted the modulation of emotion word type and valence on word processing in both early and late processing stages. Different neural mechanisms between L1 and L2 in processing written emotion words were elucidated.
Collapse
Affiliation(s)
- Dong Tang
- School of Foreign Languages, Dalian University of Technology, Dalian, People's Republic of China
- Faculty of Information Technology, University of Jyväskylä, Jyväskylä, Finland
| | - Xueqiao Li
- Centre for Interdisciplinary Brain Research, Department of Psychology, University of Jyväskylä, Jyväskylä, Finland
| | - Yang Fu
- School of International Studies, Zhejiang University, Hangzhou, People's Republic of China
| | - Huili Wang
- School of Foreign Languages, Hangzhou City University, Hangzhou, People's Republic of China
| | - Xueyan Li
- School of Foreign Languages, Dalian University of Technology, Dalian, People's Republic of China
| | - Tiina Parviainen
- Centre for Interdisciplinary Brain Research, Department of Psychology, University of Jyväskylä, Jyväskylä, Finland
| | - Tommi Kärkkäinen
- Faculty of Information Technology, University of Jyväskylä, Jyväskylä, Finland
| |
Collapse
|
2
|
Balzanelli MG, Rastmanesh R, Distratis P, Lazzaro R, Inchingolo F, Del Prete R, Pham VH, Aityan SK, Cong TT, Nguyen KCD, Isacco CG. The Role of SARS-CoV-2 Spike Protein in Long-term Damage of Tissues and Organs, the Underestimated Role of Retrotransposons and Stem Cells, a Working Hypothesis. Endocr Metab Immune Disord Drug Targets 2024; 24:EMIDDT-EPUB-139081. [PMID: 38468535 DOI: 10.2174/0118715303283480240227113401] [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: 10/30/2023] [Revised: 02/09/2024] [Accepted: 02/09/2024] [Indexed: 03/13/2024]
Abstract
Coronavirus disease-2019 (COVID-19) is a respiratory disease in which Spike protein from SARS-CoV-2 plays a key role in transferring virus genomic code into target cells. Spike protein, which is found on the surface of the SARS-CoV-2 virus, latches onto angiotensin-converting enzyme 2 receptors (ACE2r) on target cells. The RNA genome of coronaviruses, with an average length of 29 kb, is the longest among all RNA viruses and comprises six to ten open reading frames (ORFs) responsible for encoding replicase and structural proteins for the virus. Each component of the viral genome is inserted into a helical nucleocapsid surrounded by a lipid bilayer. The Spike protein is responsible for damage to several organs and tissues, even leading to severe impairments and long-term disabilities. Spike protein could also be the cause of the long-term post-infectious conditions known as Long COVID-19, characterized by a group of unresponsive idiopathic severe neuro- and cardiovascular disorders, including strokes, cardiopathies, neuralgias, fibromyalgia, and Guillaume-Barret's like-disease. In this paper, we suggest a pervasive mechanism whereby the Spike proteins either from SARS-CoV-2 mRNA or mRNA vaccines, tend to enter the mature cells, and progenitor, multipotent, and pluripotent stem cells (SCs), altering the genome integrity. This will eventually lead to the production of newly affected clones and mature cells. The hypothesis presented in this paper proposes that the mRNA integration into DNA occurs through several components of the evolutionarily genetic mechanism such as retrotransposons and retrotransposition, LINE-1 or L1 (long interspersed element-1), and ORF-1 and 2 responsible for the generation of retrogenes. Once the integration phase is concluded, somatic cells, progenitor cells, and SCs employ different silencing mechanisms. DNA methylation, followed by histone modification, begins to generate unlimited lines of affected cells and clones that form affected tissues characterized by abnormal patterns that become targets of systemic immune cells, generating uncontrolled inflammatory conditions, as observed in both Long COVID-19 syndrome and the mRNA vaccine.
Collapse
Affiliation(s)
- Mario G Balzanelli
- 118 SET, Department of Pre-hospital and Emergency, SG Giuseppe Moscati Hospital, 74120 Taranto, Italy
| | - Reza Rastmanesh
- The Nutrition Society, Boyd Orr House, 10 Cambridge Court, 210 Shepherds Bush Road, London, UK
| | - Pietro Distratis
- 118 SET, Department of Pre-hospital and Emergency, SG Giuseppe Moscati Hospital, 74120 Taranto, Ital
| | - Rita Lazzaro
- 118 SET, Department of Pre-hospital and Emergency, SG Giuseppe Moscati Hospital, 74120 Taranto, Ital
| | - Francesco Inchingolo
- Department of Interdisciplinary Medicine, Section of Microbiology and Virology, School of Medicine, University of Bari "Aldo Moro", 70124 Bari, Italy
| | - Raffaele Del Prete
- Department of Interdisciplinary Medicine, Section of Microbiology and Virology, School of Medicine, University of Bari "Aldo Moro", 70124 Bari, Italy
| | - Van H Pham
- Phan Chau Trinh University of Medicine, Quang Nam 70000, Vietnam
| | - Sergey K Aityan
- Northwestern University, Multidisciplinary Research Center; Oakland, CA 94612-USA
| | - Toai Tran Cong
- Pham Ngoc Thach University of Medicine, Ho Chi Minh City 700000, Vietnam
| | - Kieu C D Nguyen
- Department of Interdisciplinary Medicine, Section of Microbiology and Virology, School of Medicine, University of Bari "Aldo Moro", 70124 Bari, Italy
| | - Ciro Gargiulo Isacco
- 118 SET, Department of Pre-hospital and Emergency, SG Giuseppe Moscati Hospital, 74120 Taranto, Italy
- Department of Interdisciplinary Medicine, Section of Microbiology and Virology, School of Medicine, University of Bari "Aldo Moro", 70124 Bari, Italy
| |
Collapse
|
3
|
Toda T, Bedrosian TA, Schafer ST, Cuoco MS, Linker SB, Ghassemzadeh S, Mitchell L, Whiteley JT, Novaresi N, McDonald AH, Gallina IS, Yoon H, Hester ME, Pena M, Lim C, Suljic E, AlFatah Mansour A, Boulard M, Parylak SL, Gage FH. Long interspersed nuclear elements safeguard neural progenitors from precocious differentiation. Cell Rep 2024; 43:113774. [PMID: 38349791 PMCID: PMC10948021 DOI: 10.1016/j.celrep.2024.113774] [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: 11/12/2022] [Revised: 11/30/2023] [Accepted: 01/24/2024] [Indexed: 02/15/2024] Open
Abstract
Long interspersed nuclear element-1 (L1 or LINE-1) is a highly abundant mobile genetic element in both humans and mice, comprising almost 20% of each genome. L1s are silenced by several mechanisms, as their uncontrolled expression has the potential to induce genomic instability. However, L1s are paradoxically expressed at high levels in differentiating neural progenitor cells. Using in vitro and in vivo techniques to modulate L1 expression, we report that L1s play a critical role in both human and mouse brain development by regulating the rate of neural differentiation in a reverse-transcription-independent manner.
Collapse
Affiliation(s)
- Tomohisa Toda
- Laboratory of Genetics, The Salk Institute for Biological Studies, 10010 North Torrey Pines Road, La Jolla, CA 92037, USA; Laboratory of Neural Epigenomics, Institute of Medical Physics and Micro-tissue Engineering, Friedrich-Alexander-Universität Erlangen-Nürnberg, 91054 Erlangen, Germany; Nuclear Architecture in Neural Plasticity and Aging Laboratory, German Center for Neurodegenerative Diseases, 01307 Dresden, Germany.
| | - Tracy A Bedrosian
- Laboratory of Genetics, The Salk Institute for Biological Studies, 10010 North Torrey Pines Road, La Jolla, CA 92037, USA; Institute for Genomic Medicine, Nationwide Children's Hospital, Columbus, OH 43205, USA
| | - Simon T Schafer
- Laboratory of Genetics, The Salk Institute for Biological Studies, 10010 North Torrey Pines Road, La Jolla, CA 92037, USA; Department of Psychiatry and Psychotherapy, School of Medicine and Health, Technical University of Munich, Munich, Germany; TUM Center for Organoid Systems (COS), Munich Institute of Biomedical Engineering, Garching, Germany
| | - Michael S Cuoco
- Laboratory of Genetics, The Salk Institute for Biological Studies, 10010 North Torrey Pines Road, La Jolla, CA 92037, USA; Computational Neural DNA Dynamics Lab, Department of Cognitive Science, University of California, San Diego, San Diego, CA, USA; Bioinformatics and Systems Biology Graduate Program, University of California, San Diego, San Diego, CA, USA
| | - Sara B Linker
- Laboratory of Genetics, The Salk Institute for Biological Studies, 10010 North Torrey Pines Road, La Jolla, CA 92037, USA
| | - Saeed Ghassemzadeh
- Laboratory of Genetics, The Salk Institute for Biological Studies, 10010 North Torrey Pines Road, La Jolla, CA 92037, USA
| | - Lisa Mitchell
- Laboratory of Genetics, The Salk Institute for Biological Studies, 10010 North Torrey Pines Road, La Jolla, CA 92037, USA
| | - Jack T Whiteley
- Laboratory of Genetics, The Salk Institute for Biological Studies, 10010 North Torrey Pines Road, La Jolla, CA 92037, USA
| | - Nicole Novaresi
- Laboratory of Genetics, The Salk Institute for Biological Studies, 10010 North Torrey Pines Road, La Jolla, CA 92037, USA
| | - Aidan H McDonald
- Laboratory of Genetics, The Salk Institute for Biological Studies, 10010 North Torrey Pines Road, La Jolla, CA 92037, USA
| | - Iryna S Gallina
- Laboratory of Genetics, The Salk Institute for Biological Studies, 10010 North Torrey Pines Road, La Jolla, CA 92037, USA
| | - Hyojung Yoon
- Institute for Genomic Medicine, Nationwide Children's Hospital, Columbus, OH 43205, USA
| | - Mark E Hester
- Institute for Genomic Medicine, Nationwide Children's Hospital, Columbus, OH 43205, USA
| | - Monique Pena
- Laboratory of Genetics, The Salk Institute for Biological Studies, 10010 North Torrey Pines Road, La Jolla, CA 92037, USA; Department of Psychiatry and Psychotherapy, School of Medicine and Health, Technical University of Munich, Munich, Germany; TUM Center for Organoid Systems (COS), Munich Institute of Biomedical Engineering, Garching, Germany
| | - Christina Lim
- Laboratory of Genetics, The Salk Institute for Biological Studies, 10010 North Torrey Pines Road, La Jolla, CA 92037, USA
| | - Emelia Suljic
- Laboratory of Genetics, The Salk Institute for Biological Studies, 10010 North Torrey Pines Road, La Jolla, CA 92037, USA
| | - Abed AlFatah Mansour
- Laboratory of Genetics, The Salk Institute for Biological Studies, 10010 North Torrey Pines Road, La Jolla, CA 92037, USA
| | - Matthieu Boulard
- Epigenetics & Neurobiology Unit, EMBL Rome, European Molecular Biology Laboratory, Via Ramarini 32, 00015 Monterotondo, Italy
| | - Sarah L Parylak
- Laboratory of Genetics, The Salk Institute for Biological Studies, 10010 North Torrey Pines Road, La Jolla, CA 92037, USA
| | - Fred H Gage
- Laboratory of Genetics, The Salk Institute for Biological Studies, 10010 North Torrey Pines Road, La Jolla, CA 92037, USA.
| |
Collapse
|
4
|
Devine SE. Emerging Opportunities to Study Mobile Element Insertions and Their Source Elements in an Expanding Universe of Sequenced Human Genomes. Genes (Basel) 2023; 14:1923. [PMID: 37895272 PMCID: PMC10606232 DOI: 10.3390/genes14101923] [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: 09/02/2023] [Revised: 09/29/2023] [Accepted: 09/30/2023] [Indexed: 10/29/2023] Open
Abstract
Three mobile element classes, namely Alu, LINE-1 (L1), and SVA elements, remain actively mobile in human genomes and continue to produce new mobile element insertions (MEIs). Historically, MEIs have been discovered and studied using several methods, including: (1) Southern blots, (2) PCR (including PCR display), and (3) the detection of MEI copies from young subfamilies. We are now entering a new phase of MEI discovery where these methods are being replaced by whole genome sequencing and bioinformatics analysis to discover novel MEIs. We expect that the universe of sequenced human genomes will continue to expand rapidly over the next several years, both with short-read and long-read technologies. These resources will provide unprecedented opportunities to discover MEIs and study their impact on human traits and diseases. They also will allow the MEI community to discover and study the source elements that produce these new MEIs, which will facilitate our ability to study source element regulation in various tissue contexts and disease states. This, in turn, will allow us to better understand MEI mutagenesis in humans and the impact of this mutagenesis on human biology.
Collapse
Affiliation(s)
- Scott E Devine
- Institute for Genome Sciences, Department of Medicine, and Greenebaum Comprehensive Cancer Center, University of Maryland School of Medicine, Baltimore, MD 21201, USA
| |
Collapse
|
5
|
Zygouras I, Leventakou D, Pouliakis A, Panagiotou S, Tsakogiannis D, Konstantopoulos G, Logotheti E, Samaras M, Kyriakopoulou Z, Beloukas A, Pateras IS, Delides A, Psyrri A, Panayiotides IG, Yiangou M, Kottaridi C. Human Papillomavirus 16 DNA Methylation Patterns and Investigation of Integration Status in Head and Neck Cancer Cases. Int J Mol Sci 2023; 24:14593. [PMID: 37834041 PMCID: PMC10572864 DOI: 10.3390/ijms241914593] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2023] [Revised: 09/26/2023] [Accepted: 09/26/2023] [Indexed: 10/15/2023] Open
Abstract
Persistent high-risk human papillomavirus (HPV) infection is a pivotal factor in the progression of cervical cancer. In recent years, an increasing interest has emerged in comprehending the influence of HPV on head and neck squamous cell carcinoma (HNSCC). Notably, it is well established that HPV-associated HNSCC show cases with distinct molecular and clinical attributes compared to HPV-negative cases. The present study delves into the epigenetic landscape of HPV16, specifically its L1 gene and untranslated region (UTR), through pyrosequencing, while the HPV16 DNA physical status was evaluated using E2/E6 ratio analysis in HPV16-positive HNSCC FFPE biopsies. Our findings reveal substantial methylation across six sites within the HPV16 L1 gene and seven sites in the UTR. Specifically, methylation percentages of two L1 CpG sites (7136, 7145) exhibit significant associations with tumor histological grade (p < 0.01), while proving concurrent methylation across multiple sites. The HPV16 DNA physical status was not correlated with the methylation of viral genome or tumor characteristics. This is the first study that examines epigenetic modifications and the HPV16 DNA physical status in Greek HNSCC patients. Our findings suggest an orchestrated epigenetic modulation among specific sites, impacting viral gene expression and intricate virus-host interactions.
Collapse
Affiliation(s)
- Ioannis Zygouras
- Department of Genetics, Development and Molecular Biology, School of Biology, Aristotle University of Thessaloniki, 54124 Thessaloniki, Greece; (I.Z.); (S.P.); (G.K.); (E.L.); (M.Y.)
| | - Danai Leventakou
- 2nd Department of Pathology, University General Hospital “Attikon”, School of Medicine, National and Kapodistrian University of Athens, 12464 Athens, Greece; (D.L.); (A.P.); (M.S.); (I.S.P.); (I.G.P.)
| | - Abraham Pouliakis
- 2nd Department of Pathology, University General Hospital “Attikon”, School of Medicine, National and Kapodistrian University of Athens, 12464 Athens, Greece; (D.L.); (A.P.); (M.S.); (I.S.P.); (I.G.P.)
| | - Styliana Panagiotou
- Department of Genetics, Development and Molecular Biology, School of Biology, Aristotle University of Thessaloniki, 54124 Thessaloniki, Greece; (I.Z.); (S.P.); (G.K.); (E.L.); (M.Y.)
| | | | - Georgios Konstantopoulos
- Department of Genetics, Development and Molecular Biology, School of Biology, Aristotle University of Thessaloniki, 54124 Thessaloniki, Greece; (I.Z.); (S.P.); (G.K.); (E.L.); (M.Y.)
| | - Eirini Logotheti
- Department of Genetics, Development and Molecular Biology, School of Biology, Aristotle University of Thessaloniki, 54124 Thessaloniki, Greece; (I.Z.); (S.P.); (G.K.); (E.L.); (M.Y.)
| | - Menelaos Samaras
- 2nd Department of Pathology, University General Hospital “Attikon”, School of Medicine, National and Kapodistrian University of Athens, 12464 Athens, Greece; (D.L.); (A.P.); (M.S.); (I.S.P.); (I.G.P.)
| | - Zaharoula Kyriakopoulou
- Department of Environment, School of Technology, University of Thessaly, Gaiopolis Campus, 41500 Larissa, Greece;
| | - Apostolos Beloukas
- Department of Biomedical Sciences, University of West Attica, 12243 Athens, Greece;
- National AIDS Reference Centre of Southern Greece, School of Public Health, University of West Attica, 11521 Athens, Greece
| | - Ioannis S. Pateras
- 2nd Department of Pathology, University General Hospital “Attikon”, School of Medicine, National and Kapodistrian University of Athens, 12464 Athens, Greece; (D.L.); (A.P.); (M.S.); (I.S.P.); (I.G.P.)
| | - Alexandros Delides
- 2nd Department of Otolaryngology, University General Hospital “Attikon”, School of Medicine, National and Kapodistrian University of Athens, 12464 Athens, Greece;
| | - Amanda Psyrri
- 2nd Department of Internal Medicine-Propaedeutic, University General Hospital “Attikon”, School of Medicine, National and Kapodistrian University of Athens, 12464 Athens, Greece;
| | - Ioannis G. Panayiotides
- 2nd Department of Pathology, University General Hospital “Attikon”, School of Medicine, National and Kapodistrian University of Athens, 12464 Athens, Greece; (D.L.); (A.P.); (M.S.); (I.S.P.); (I.G.P.)
| | - Minas Yiangou
- Department of Genetics, Development and Molecular Biology, School of Biology, Aristotle University of Thessaloniki, 54124 Thessaloniki, Greece; (I.Z.); (S.P.); (G.K.); (E.L.); (M.Y.)
| | - Christine Kottaridi
- Department of Genetics, Development and Molecular Biology, School of Biology, Aristotle University of Thessaloniki, 54124 Thessaloniki, Greece; (I.Z.); (S.P.); (G.K.); (E.L.); (M.Y.)
| |
Collapse
|
6
|
Yamada K, Ishii Y, Tateda K. Diversity of blaL1-like genes in Stenotrophomonas species: insights from genome analysis of publicly available genome sequences. Antimicrob Agents Chemother 2023; 67:e0067323. [PMID: 37584548 PMCID: PMC10508171 DOI: 10.1128/aac.00673-23] [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: 05/21/2023] [Accepted: 06/26/2023] [Indexed: 08/17/2023] Open
Abstract
L1 metallo-β-lactamases produced by Stenotrophomonas maltophilia exhibit high diversity. Here, we characterized the genomes of Stenotrophomonas species harboring blaL1-like genes using publicly available genome sequences. Our findings provide evidence that Stenotrophomonas species with blaL1-like genes constitute a complex comprising many species with high genetic diversity, and similarities between blaL1-like genes are lower than those of the genome. This suggests that the diversity of blaL1-like is attributable to species diversity in Stenotrophomonas species harboring blaL1-like and the rapid evolutionary changes in blaL1-like genes.
Collapse
Affiliation(s)
- Kageto Yamada
- Department of Microbiology and Infectious Disease, Toho University School of Medicine, Tokyo, Japan
| | - Yoshikazu Ishii
- Department of Microbiology and Infectious Disease, Toho University School of Medicine, Tokyo, Japan
| | - Kazuhiro Tateda
- Department of Microbiology and Infectious Disease, Toho University School of Medicine, Tokyo, Japan
| |
Collapse
|
7
|
Saha A, Gavert N, Brabletz T, Ben-Ze’ev A. An Increase in Mucin2 Expression Is Required for Colon Cancer Progression Mediated by L1. Int J Mol Sci 2023; 24:13418. [PMID: 37686224 PMCID: PMC10488000 DOI: 10.3390/ijms241713418] [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: 07/20/2023] [Revised: 08/27/2023] [Accepted: 08/28/2023] [Indexed: 09/10/2023] Open
Abstract
An induction in the expression of the cell adhesion receptor L1, a Wnt target gene, is a characteristic feature of Wnt/β-catenin activation in colon cancer cells at later stages of the disease. We investigated the proteins secreted following L1 expression in colon cancer cells and identified Mucin2 among the most abundant secreted proteins. We found that suppressing Mucin2 expression in L1-expressing colon cancer cells inhibits cell proliferation, motility, tumorigenesis, and liver metastasis. We detected several signaling pathways involved in Mucin2 induction in L1-expressing cells. In human colon cancer tissue, Mucin2 expression was significantly reduced or lost in the adenocarcinoma tissue, while in the mucinous subtype of colon cancer tissue, Mucin2 expression was increased. An increased signature of L1/Mucin2 expression reduced the survival rate of human colon cancer patients. Thus, induction of Mucin2 expression by L1 is required during mucinous colon cancer progression and can serve as a marker for diagnosis and a target for therapy.
Collapse
Affiliation(s)
- Arka Saha
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot 7610001, Israel; (A.S.); (N.G.)
| | - Nancy Gavert
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot 7610001, Israel; (A.S.); (N.G.)
| | - Thomas Brabletz
- Department of Experimental Medicine I, Nikolaus-Feibiger-Center for Molecular Medicine, University of Erlangen-Nuernberg, 91054 Erlangen, Germany;
| | - Avri Ben-Ze’ev
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot 7610001, Israel; (A.S.); (N.G.)
| |
Collapse
|
8
|
Park S, Kim HK, Lee HJ, Choi M, Lee M, Jakovljevic M. Strategic management and organizational culture of medical device companies in relation to corporate performance. J Med Econ 2023:1-23. [PMID: 37300440 DOI: 10.1080/13696998.2023.2224168] [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: 04/28/2023] [Revised: 06/07/2023] [Accepted: 06/08/2023] [Indexed: 06/12/2023]
Abstract
AIMS Strategies focus on securing the competitiveness of medical device corporations by strengthening their organizational capabilities, which, in turn, ensure their continuous development. This study aims to investigate both management strategies and organizational culture, which may affect the performance of these companies, and analyzes the influence of education and training investment. MATERIALS AND METHODS We used data from the 3rd to 6th Human Capital Corporate Panel surveys by the Korea Research Institute for Vocational Education and Training as well as data from the Korea Information Service and 6,112 workers and 260 companies were analyzed. For the analysis, management strategy and organizational culture were set as independent variables, and corporation performance was set as the dependent variable. Additionally, investment in education and training was set as a control variable between the independent and dependent variables. Corporate performance was analyzed by dividing into organizational satisfaction and organizational commitment. RESULTS Differentiation strategy and innovative culture had a positive (+) effect on organizational satisfaction, while cost leadership strategy and hierarchical culture had a negative (-) effect. On the other hand, in the case of interaction with education and training investment, cost leadership strategy and hierarchical culture had a positive (+) effect, while differentiation strategy and innovation culture had a negative (-) effect. In organizational commitment, innovation culture had a positive (+) effect, and hierarchical culture had a negative (-) effect. In the case of interaction with investment in education and training, only the hierarchical culture had a positive (+) effect. CONCLUSIONS The innovation culture positively influenced the performance of medical device companies. Furthermore, cost leadership strategy, hierarchical culture, education and training investment improved the corporate performance of these companies. To enhance corporate performance, these companies should create an innovation culture and invest in education and training in accordance with the organizational culture.
Collapse
Affiliation(s)
- Sewon Park
- Department of Medical Science, Ajou University School of Medicine, Suwon, South Korea
| | - Han-Kyoul Kim
- Department of Rehabilitation Medicine, Seoul National University Hospital, Seoul, South Korea
- National Traffic Injury Rehabilitation Research Institute, National Traffic Injury Rehabilitation Hospital, Yang-Pyeong, South Korea
| | - Haeng-Jun Lee
- Department of Medical Science, Ajou University School of Medicine, Suwon, South Korea
| | - Mankyu Choi
- Department of Health Policy & Management, College of Health Science, Korea University, Seoul, South Korea
- BK21 FOUR R&E Center for Learning Health Systems, Korea University, Seoul, South Korea
| | - Munjae Lee
- Department of Medical Science, Ajou University School of Medicine, Suwon, South Korea
| | - Mihajlo Jakovljevic
- Institute of Advanced Manufacturing Technologies, Peter the Great St. Petersburg Polytechnic University, 195251, St Petersburg, Russia
- Institute of Comparative Economic Studies, Hosei University, Tokyo 194-0298, Japan
- Department of Global Health Economics and Policy, University of Kragujevac, 34000 Kragujevac, Serbia
| |
Collapse
|
9
|
Berzak Y, Levy R. Eye Movement Traces of Linguistic Knowledge in Native and Non-Native Reading. Open Mind (Camb) 2023; 7:179-196. [PMID: 37416079 PMCID: PMC10320821 DOI: 10.1162/opmi_a_00084] [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: 02/01/2023] [Accepted: 03/19/2023] [Indexed: 07/08/2023] Open
Abstract
The detailed study of eye movements in reading has shed considerable light into how language processing unfolds in real time. Yet eye movements in reading remain inadequately studied in non-native (L2) readers, even though much of the world's population is multilingual. Here we present a detailed analysis of the quantitative functional influences of word length, frequency, and predictability on eye movement measures in reading in a large, linguistically diverse sample of non-native English readers. We find many similar qualitative effects as in L1 readers, but crucially also a proficiency-sensitive "lexicon-context tradeoff". The most proficient L2 readers' eye movements approach an L1 pattern, but as L2 proficiency diminishes, readers' eye movements become less sensitive to a word's predictability in context and more sensitive to word frequency, which is context-invariant. This tradeoff supports a rational, experience-dependent account of how context-driven expectations are deployed in L2 language processing.
Collapse
Affiliation(s)
- Yevgeni Berzak
- Faculty of Data and Decision Sciences, Technion - Israel Institute of Technology, Haifa, Israel
- Department of Brain and Cognitive Sciences, Massachussets Institute of Technology, Cambridge, MA
| | - Roger Levy
- Department of Brain and Cognitive Sciences, Massachussets Institute of Technology, Cambridge, MA
| |
Collapse
|
10
|
Minegishi T, Kastian RF, Inagaki N. Mechanical regulation of synapse formation and plasticity. Semin Cell Dev Biol 2023; 140:82-89. [PMID: 35659473 DOI: 10.1016/j.semcdb.2022.05.017] [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] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2022] [Revised: 05/10/2022] [Accepted: 05/17/2022] [Indexed: 01/28/2023]
Abstract
Dendritic spines are small protrusions arising from dendrites and constitute the major compartment of excitatory post-synapses. They change in number, shape, and size throughout life; these changes are thought to be associated with formation and reorganization of neuronal networks underlying learning and memory. As spines in the brain are surrounded by the microenvironment including neighboring cells and the extracellular matrix, their protrusion requires generation of force to push against these structures. In turn, neighboring cells receive force from protruding spines. Recent studies have identified BAR-domain proteins as being involved in membrane deformation to initiate spine formation. In addition, forces for dendritic filopodium extension and activity-induced spine expansion are generated through cooperation between actin polymerization and clutch coupling. On the other hand, force from expanding spines affects neurotransmitter release from presynaptic terminals. Here, we review recent advances in our understanding of the physical aspects of synapse formation and plasticity, mainly focusing on spine dynamics.
Collapse
Affiliation(s)
- Takunori Minegishi
- Laboratory of Systems Neurobiology and Medicine, Division of Biological Science, Nara Institute of Science and Technology, Ikoma, Nara 630-0192, Japan
| | - Ria Fajarwati Kastian
- Laboratory of Systems Neurobiology and Medicine, Division of Biological Science, Nara Institute of Science and Technology, Ikoma, Nara 630-0192, Japan; Research Center for Genetic Engineering, National Research and Innovation Agency Republic of Indonesia, Cibinong, Bogor, Indonesia
| | - Naoyuki Inagaki
- Laboratory of Systems Neurobiology and Medicine, Division of Biological Science, Nara Institute of Science and Technology, Ikoma, Nara 630-0192, Japan.
| |
Collapse
|
11
|
Ukadike KC, Najjar R, Ni K, Laine A, Wang X, Bays A, Taylor MS, LaCava J, Mustelin T. Expression of L1 retrotransposons in granulocytes from patients with active systemic lupus erythematosus. Mob DNA 2023; 14:5. [PMID: 37165451 PMCID: PMC10170740 DOI: 10.1186/s13100-023-00293-7] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2023] [Accepted: 05/04/2023] [Indexed: 05/12/2023] Open
Abstract
BACKGROUND Patients with systemic lupus erythematosus (SLE) have autoantibodies against the L1-encoded open-reading frame 1 protein (ORF1p). Here, we report (i) which immune cells ORF1p emanates from, (ii) which L1 loci are transcriptionally active, (iii) whether the cells express L1-dependent interferon and interferon-stimulated genes, and (iv) the effect of inhibition of L1 ORF2p by reverse transcriptase inhibitors. RESULTS L1 ORF1p was detected by flow cytometry primarily in SLE CD66b+CD15+ regular and low-density granulocytes, but much less in other immune cell lineages. The amount of ORF1p was higher in neutrophils from patients with SLE disease activity index (SLEDAI) > 6 (p = 0.011) compared to patients with inactive disease, SLEDAI < 4. Patient neutrophils transcribed seven to twelve human-specific L1 loci (L1Hs), but only 3 that are full-length and with an intact ORF1. Besides serving as a source of detectable ORF1p, the most abundant transcript encoded a truncated ORF2p reverse transcriptase predicted to remain cytosolic, while the two other encoded an intact full-length ORF2p. A number of genes encoding proteins that influence L1 transcription positively or negatively were altered in patients, particularly those with active disease, compared to healthy controls. Components of nucleic acid sensing and interferon induction were also altered. SLE neutrophils also expressed type I interferon-inducible genes and interferon β, which were substantially reduced after treatment of the cells with drugs known to inhibit ORF2p reverse transcriptase activity. CONCLUSIONS We identified L1Hs loci that are transcriptionally active in SLE neutrophils, and a reduction in the epigenetic silencing mechanisms that normally counteract L1 transcription. SLE neutrophils contained L1-encoded ORF1p protein, as well as activation of the type I interferon system, which was inhibited by treatment with reverse transcriptase inhibitors. Our findings will enable a deeper analysis of L1 dysregulation and its potential role in SLE pathogenesis.
Collapse
Affiliation(s)
- Kennedy C Ukadike
- Department of Medicine, Division of Rheumatology, University of Washington, 750 Republican Street, Room E507, Seattle, WA, 99108, USA
- Department of Internal Medicine, Renown Rheumatology, Renown Health - University of Nevada, Reno School of Medicine, 75 Pringle Way, Suite 701, Reno, NV, 89502, USA
| | - Rayan Najjar
- Department of Medicine, Division of Rheumatology, University of Washington, 750 Republican Street, Room E507, Seattle, WA, 99108, USA
| | - Kathryn Ni
- Department of Medicine, Division of Rheumatology, University of Washington, 750 Republican Street, Room E507, Seattle, WA, 99108, USA
| | - Amanda Laine
- Department of Medicine, Division of Rheumatology, University of Washington, 750 Republican Street, Room E507, Seattle, WA, 99108, USA
| | - Xiaoxing Wang
- Department of Medicine, Division of Rheumatology, University of Washington, 750 Republican Street, Room E507, Seattle, WA, 99108, USA
| | - Alison Bays
- Department of Medicine, Division of Rheumatology, University of Washington, 750 Republican Street, Room E507, Seattle, WA, 99108, USA
| | - Martin S Taylor
- Department of Pathology, Massachusetts General Hospital, Boston, MA, USA
| | - John LaCava
- Laboratory of Cellular and Structural Biology, The Rockefeller University, New York, NY, USA
- European Research Institute for the Biology of Ageing, University Medical Center Groningen, Groningen, The Netherlands
| | - Tomas Mustelin
- Department of Medicine, Division of Rheumatology, University of Washington, 750 Republican Street, Room E507, Seattle, WA, 99108, USA.
| |
Collapse
|
12
|
Shah R, Shah A, Badawy SM. An evaluation of deferiprone as twice-a-day tablets or in combination therapy for the treatment of transfusional iron overload in thalassemia syndromes. Expert Rev Hematol 2023; 16:81-94. [PMID: 36755516 PMCID: PMC9992344 DOI: 10.1080/17474086.2023.2178409] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [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: 10/14/2022] [Accepted: 02/06/2023] [Indexed: 02/10/2023]
Abstract
INTRODUCTION Regular blood transfusions in patients with thalassemia syndromes can cause iron overload resulting in complications including cirrhosis, heart problems, or endocrine abnormalities. To prevent iron overload toxicity in these patients, three iron chelators are currently FDA-approved for use: deferoxamine, deferasirox, and deferiprone. In the United States, deferiprone has been approved for three times daily dosing since 2011 and has recently gained approval for twice-daily administration. AREAS COVERED A PubMed literature search was performed with the keywords 'deferiprone' and 'thalassemia.' Relevant original research studying deferiprone's effects on transfusional iron overload in patients with thalassemia syndromes was included. Exclusion criteria included case reports and review papers. Deferiprone is effective at reducing serum ferritin levels in patients with iron overload. Twice-daily administration provides a similar level of iron chelation as three times daily dosing with a comparable side effect profile and increased patient acceptability. EXPERT OPINION New studies are highlighting deferiprone's potential for combination therapy with either deferoxamine or deferasirox to improve iron chelation. Deferiprone's ability to significantly decrease cardiac and liver iron content can be utilized in other transfusion-dependent hematologic conditions, as evidenced by its recent approval for use in the United States for sickle cell disease or other anemias.
Collapse
Affiliation(s)
- Richa Shah
- Division of Hematology, Oncology, and Stem Cell Transplant, Lurie Children’s Hospital of Chicago, Chicago, IL, 60611, USA
| | - Aashaka Shah
- University of Illinois College of Medicine, Chicago, IL, 60612, USA
| | - Sherif M. Badawy
- Division of Hematology, Oncology, and Stem Cell Transplant, Lurie Children’s Hospital of Chicago, Chicago, IL, 60611, USA
- Department of Pediatrics, Northwestern University Feinberg School of Medicine, Chicago, IL, 60611, USA
| |
Collapse
|
13
|
Przybylski M, Pruski D, Millert-Kalińska S, Krzyżaniak M, de Mezer M, Frydrychowicz M, Jach R, Żurawski J. Expression of E4 Protein and HPV Major Capsid Protein ( L1) as A Novel Combination in Squamous Intraepithelial Lesions. Biomedicines 2023; 11:biomedicines11010225. [PMID: 36672733 PMCID: PMC9855969 DOI: 10.3390/biomedicines11010225] [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: 11/30/2022] [Revised: 01/11/2023] [Accepted: 01/13/2023] [Indexed: 01/18/2023] Open
Abstract
We aim to describe the relationship between the immunohistochemical expression patterns of HPV E4 markers and the presence of HPV major capsid protein (L1) in cervical tissues obtained by biopsy of patients with abnormal liquid-based cytology (LBC) results, HR HPV infections, or clinically suspicious cervix. A novel HPV-encoded marker, SILgrade-E4 (XR-E4-1), and an HPV (clone K1H8) antibody were used to demonstrate the expression in terminally differentiated epithelial cells with a productive HPV infection in the material. A semiquantitative analysis was performed based on light microscope images. The level of E4 protein decreased with the disease severity. Patients with LSIL-CIN 1 and HSIL-CIN 2 diagnoses had significantly lower levels of HPV major capsid protein (L1) than those without confirmed cervical lesions. Our analysis confirms a higher incidence of L1 in patients with molecularly diagnosed HPV infections and excluded lesions of LSIL-CIN 1 and HSIL-CIN 2. Further studies on the novel biomarkers might help assess the chances of the remission of lesions such as LSIL-CIN 1 and HSIL-CIN 2. Higher levels of E4 protein and L1 may confirm a greater probability of the remission of lesions and incidental infections. In the cytological verification or HPV-dependent screening model, testing for E4 protein and L1 expression may indicate a group with a lower risk of progression of histopathologically diagnosed lesions.
Collapse
Affiliation(s)
- Marcin Przybylski
- Gynecology Specialised Practise, 60-682 Poznań, Poland
- Department of Obstetrics and Gynecology, District Public Hospital in Poznan, 60-479 Poznań, Poland
| | - Dominik Pruski
- Department of Obstetrics and Gynecology, District Public Hospital in Poznan, 60-479 Poznań, Poland
- Gynecology Specialised Practise, 60-408 Poznań, Poland
- Correspondence:
| | - Sonja Millert-Kalińska
- Department of Obstetrics and Gynecology, District Public Hospital in Poznan, 60-479 Poznań, Poland
- Doctoral School, Poznan University of Medical Sciences, 61-701 Poznań, Poland
| | - Monika Krzyżaniak
- Department of Pathology, Hospital of Lord’s Transfiguration, Poznan University of Medical Sciences, 61-848 Poznań, Poland
| | - Mateusz de Mezer
- Department of Immunobiology, Poznan University of Medical Sciences, 60-806 Poznań, Poland
| | | | - Robert Jach
- Department of Gynecological Endocrinology, Jagiellonian University Medical College, 31-008 Cracow, Poland
| | - Jakub Żurawski
- Department of Immunobiology, Poznan University of Medical Sciences, 60-806 Poznań, Poland
| |
Collapse
|
14
|
Weber VM, Doucet AJ, Cristofari G. Precise and Scarless Insertion of Transposable Elements by Cas9-Mediated Genome Engineering. Methods Mol Biol 2023; 2607:329-353. [PMID: 36449169 DOI: 10.1007/978-1-0716-2883-6_15] [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: 06/17/2023]
Abstract
Transposable element insertions can have broad effects on gene expression, ranging from new regulatory functions to pathogenic consequences by transplanting new cis-regulating elements or perturbing existing ones. Genetic manipulation of such DNA sequences can help decipher their mechanism of action. Here, we describe a CRISPR-Cas9-mediated two-step approach to precisely insert transposable elements into into the genome of cultured human cells, without scar or reporter gene. First, a double-selection cassette is inserted into the desired target locus. Once a clone containing a single copy of this cassette has been isolated, a second editing step is performed to exchange the double-selection cassette with a markerless transposable element sequence. More generally, this method can be used for knocking in any large insert without genetic markers.
Collapse
|
15
|
Abstract
By silencing L1 retrotransposons, DNA methylation protects mammalian genomes from potent endogenous mutagens. However, some loci can escape this repressive mechanism and become active, particularly in carcinomas. Alterations of L1 DNA methylation can also locally influence gene expression. Comprehensive measurement of L1 DNA methylation at the locus level remains challenging. Here, we present bs-ATLAS-seq, a genome-wide approach to locate full-length L1 elements in the human genome, and assess their methylation levels at single-base and single-locus resolutions. This strategy targets the youngest, and only retrotransposition-competent family, L1HS, but also detects a significant fraction of older elements (L1PA2 to L1PA8). Bs-ATLAS-seq evaluates methylation at the first 15 CpGs of L1 5' UTR, which corresponds to the first half of the sense promoter. It relies on random fragmentation of the genomic DNA, adapter ligation, bisulfite treatment and suppression PCR, and ends by asymmetrical paired-end sequencing. A dedicated pipeline provides the location of L1 elements and their methylation status, including for non-reference loci, as well as their single-molecule DNA profiles.
Collapse
|
16
|
Abstract
Long Interspersed Element-1 (LINE-1, L1) is a retrotransposon that has the ability to amplify its copy in the genome autonomously. L1Hs is a human-specific active subtype of L1 reported to amplify its copy in neural progenitor cells causing genomic mosaicism. This chapter describes a new method named NECO-seq (Novel Elements Concentrated-sequence) to identify the genomic locus of L1Hs insertions at the single-cell level. This protocol contains the steps of (1) preparation of neuronal cell nuclei from a postmortem human brain, (2) whole genome amplification from single neural nuclei (snWGA), (3) single nucleotide polymorphisms (SNPs) genotyping for quality control of snWGA products, (4) library preparation for next-generation sequencing to enrich the genomic locus of L1Hs insertions, and (5) bioinformatic analysis to detect novel somatic L1Hs insertions. This method can detect approximately 97% of L1Hs originally existing in reference human genome and approximately 10-20 newly inserted L1Hs copies in a neuronal cell of a postmortem human brain.
Collapse
Affiliation(s)
- Miki Bundo
- Department of Molecular Brain Science, Graduate School of Medical Sciences, Kumamoto University, Kumamoto, Japan.
| | - Kazuya Iwamoto
- Department of Molecular Brain Science, Graduate School of Medical Sciences, Kumamoto University, Kumamoto, Japan
| |
Collapse
|
17
|
Garcia-Cañadas M, Sanchez-Luque FJ, Sanchez L, Rojas J, Garcia Perez JL. LINE-1 Retrotransposition Assays in Embryonic Stem Cells. Methods Mol Biol 2023; 2607:257-309. [PMID: 36449167 DOI: 10.1007/978-1-0716-2883-6_13] [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: 06/17/2023]
Abstract
The ongoing mobilization of active non-long terminal repeat (LTR) retrotransposons continues to impact the genomes of most mammals, including humans and rodents. Non-LTR retrotransposons mobilize using an intermediary RNA and a copy-and-paste mechanism termed retrotransposition. Non-LTR retrotransposons are subdivided into long and short interspersed elements (LINEs and SINEs, respectively), depending on their size and autonomy; while active class 1 LINEs (LINE-1s or L1s) encode the enzymatic machinery required to mobilize in cis, active SINEs use the enzymatic machinery of active LINE-1s to mobilize in trans. The mobilization mechanism used by LINE-1s/SINEs was exploited to develop ingenious plasmid-based retrotransposition assays in cultured cells, which typically exploit a reporter gene that can only be activated after a round of retrotransposition. Retrotransposition assays, in cis or in trans, are instrumental tools to study the biology of mammalian LINE-1s and SINEs. In fact, these and other biochemical/genetic assays were used to uncover that endogenous mammalian LINE-1s/SINEs naturally retrotranspose during early embryonic development. However, embryonic stem cells (ESCs) are typically used as a cellular model in these and other studies interrogating LINE-1/SINE expression/regulation during early embryogenesis. Thus, human and mouse ESCs represent an excellent model to understand how active retrotransposons are regulated and how their activity impacts the germline. Here, we describe robust and quantitative protocols to study human/mouse LINE-1 (in cis) and SINE (in trans) retrotransposition using (human and mice) ESCs. These protocols are designed to study the mobilization of active non-LTR retrotransposons in a cellular physiologically relevant context.
Collapse
Affiliation(s)
- Marta Garcia-Cañadas
- Pfizer-University of Granada-Andalusian Government Centre for Genomics and Oncological Research (GENYO), PTS Granada, Granada, Spain.
| | - Francisco J Sanchez-Luque
- Institute of Parasitology and Biomedicine "Lopez-Neyra" (IPBLN), Spanish National Research Council (CSIC), PTS Granada, Granada, Spain
| | - Laura Sanchez
- Pfizer-University of Granada-Andalusian Government Centre for Genomics and Oncological Research (GENYO), PTS Granada, Granada, Spain
| | - Johana Rojas
- Pfizer-University of Granada-Andalusian Government Centre for Genomics and Oncological Research (GENYO), PTS Granada, Granada, Spain
| | - Jose L Garcia Perez
- Pfizer-University of Granada-Andalusian Government Centre for Genomics and Oncological Research (GENYO), PTS Granada, Granada, Spain.
- MRC Human Genetics Unit, Institute of Genetics and Cancer (IGC)/University of Edinburgh, Western General Hospital Campus, Edinburgh, UK.
| |
Collapse
|
18
|
McKerrow W. Quantification of LINE-1 RNA Expression from Bulk RNA-seq Using L1EM. Methods Mol Biol 2023; 2607:115-126. [PMID: 36449161 DOI: 10.1007/978-1-0716-2883-6_7] [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: 06/17/2023]
Abstract
LINE-1 retrotransposons have the potential to cause DNA damage, contribute to genome instability, and induce an interferon response. Thus, accurate measurements of their expression, especially in disease contexts where genome instability and the interferon response are relevant, are of particular importance. Illumina-based bulk RNA sequencing remains the most abundant datatype for measuring gene expression. However, "active" expression from its own internal promoter is only one source of LINE-1 aligning reads in an RNA-seq experiment. With about half a million LINE-1 sequences scattered throughout the genome, many are incorporated into other transcripts that have nothing to do with LINE-1 activity. We call this "passive" co-transcription. Here we will describe how to use L1EM, a computational method that separates active from passive LINE-1 expression at the locus-specific level.
Collapse
Affiliation(s)
- Wilson McKerrow
- Institute for Systems Genetics, NYU Langone Health, New York, NY, USA.
| |
Collapse
|
19
|
Pardi MB, Schroeder A, Letzkus JJ. Probing top-down information in neocortical layer 1. Trends Neurosci 2023; 46:20-31. [PMID: 36428192 DOI: 10.1016/j.tins.2022.11.001] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2022] [Revised: 10/26/2022] [Accepted: 11/01/2022] [Indexed: 11/23/2022]
Abstract
Accurate perception of the environment is a constructive process that requires integration of external bottom-up sensory signals with internally generated top-down information. Decades of work have elucidated how sensory neocortex processes physical stimulus features. By contrast, examining how top-down information is encoded and integrated with bottom-up signals has been challenging using traditional neuroscience methods. Recent technological advances in functional imaging of brain-wide afferents in behaving mice have enabled the direct measurement of top-down information. Here, we review the emerging literature on encoding of these internally generated signals by different projection systems enriched in neocortical layer 1 during defined brain functions, including memory, attention, and predictive coding. Moreover, we identify gaps in current knowledge and highlight future directions for this rapidly advancing field.
Collapse
|
20
|
Tsakogiannis D, Nikolaidis M, Zagouri F, Zografos E, Kottaridi C, Kyriakopoulou Z, Tzioga L, Markoulatos P, Amoutzias GD, Bletsa G. Mutation Profile of HPV16 L1 and L2 Genes in Different Geographic Areas. Viruses 2022; 15:141. [PMID: 36680181 PMCID: PMC9867070 DOI: 10.3390/v15010141] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2022] [Revised: 12/16/2022] [Accepted: 12/19/2022] [Indexed: 01/03/2023] Open
Abstract
The causal relationship between HPV and cervical cancer in association with the high prevalence of high risk HPV genotypes led to the design of HPV vaccines based on the major capsid L1 protein. In recent years, capsid protein L2 has also become a focal point in the field of vaccine research. The present review focuses on the variability of HPV16 L1 and L2 genes, emphasizing the distribution of specific amino acid changes in the epitopes of capsid proteins. Moreover, a substantial bioinformatics analysis was conducted to describe the worldwide distribution of amino acid substitutions throughout HPV16 L1, L2 proteins. Five amino acid changes (T176N, N181T; EF loop), (T266A; FG loop), (T353P, T389S; HI loop) are frequently observed in the L1 hypervariable surface loops, while two amino acid substitutions (D43E, S122P) are adjacent to L2 specific epitopes. These changes have a high prevalence in certain geographic regions. The present review suggests that the extensive analysis of the amino acid substitutions in the HPV16 L1 immunodominant loops may provide insights concerning the ability of the virus in evading host immune response in certain populations. The genetic variability of the HPV16 L1 and L2 epitopes should be extensively analyzed in a given population.
Collapse
Affiliation(s)
| | - Marios Nikolaidis
- Bioinformatics Laboratory, Department of Biochemistry and Biotechnology, University of Thessaly, 41500 Larissa, Greece
| | - Flora Zagouri
- Department of Clinical Therapeutics, Alexandra Hospital, National and Kapodistrian University of Athens School of Medicine, 11528 Athens, Greece
| | - Eleni Zografos
- Department of Clinical Therapeutics, Alexandra Hospital, National and Kapodistrian University of Athens School of Medicine, 11528 Athens, Greece
| | - Christine Kottaridi
- Department of Genetics, Development and Molecular Biology, School of Biology, Aristotle University of Thessaloniki, 54124 Thessaloniki, Greece
| | - Zaharoula Kyriakopoulou
- Department of Environment, School of Technology, University of Thessaly, Gaiopolis, 41500 Larissa, Greece
| | - Lamprini Tzioga
- Research Center, Hellenic Anticancer Institute, 10680 Athens, Greece
| | | | - Grigoris D. Amoutzias
- Bioinformatics Laboratory, Department of Biochemistry and Biotechnology, University of Thessaly, 41500 Larissa, Greece
| | - Garyfalia Bletsa
- Research Center, Hellenic Anticancer Institute, 10680 Athens, Greece
| |
Collapse
|
21
|
Navarro-López JD, Contreras A, Touyarot K, Herrero AI, Venero C, Cambon K, Gruart A, Delgado-García JM, Sandi C, Jiménez-Díaz L. Acquisition-dependent modulation of hippocampal neural cell adhesion molecules by associative motor learning. Front Neuroanat 2022; 16:1082701. [PMID: 36620194 PMCID: PMC9811386 DOI: 10.3389/fnana.2022.1082701] [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: 10/28/2022] [Accepted: 12/07/2022] [Indexed: 12/24/2022] Open
Abstract
It is widely accepted that some types of learning involve structural and functional changes of hippocampal synapses. Cell adhesion molecules neural cell adhesion molecule (NCAM), its polysialylated form polysialic acid to NCAM (PSA-NCAM), and L1 are prominent modulators of those changes. On the other hand, trace eyeblink conditioning, an associative motor learning task, requires the active participation of hippocampal circuits. However, the involvement of NCAM, PSA-NCAM, and L1 in this type of learning is not fully known. Here, we aimed to investigate the possible time sequence modifications of such neural cell adhesion molecules in the hippocampus during the acquisition of a trace eyeblink conditioning. To do so, the hippocampal expression of NCAM, PSA-NCAM, and L1 was assessed at three different time points during conditioning: after one (initial acquisition), three (partial acquisition), and six (complete acquisition) sessions of the conditioning paradigm. The conditioned stimulus (CS) was a weak electrical pulse separated by a 250-ms time interval from the unconditioned stimuli (US, a strong electrical pulse). An acquisition-dependent regulation of these adhesion molecules was found in the hippocampus. During the initial acquisition of the conditioning eyeblink paradigm (12 h after 1 and 3 days of training), synaptic expression of L1 and PSA-NCAM was transiently increased in the contralateral hippocampus to the paired CS-US presentations, whereas, when the associative learning was completed, such increase disappeared, but a marked and bilateral upregulation of NCAM was found. In conclusion, our findings show a specific temporal pattern of hippocampal CAMs expression during the acquisition process, highlighting the relevance of NCAM, PSA-NCAM, and L1 as learning-modulated molecules critically involved in remodeling processes underlying associative motor-memories formation.
Collapse
Affiliation(s)
- Juan D. Navarro-López
- Laboratory of Neurophysiology and Behavior, Facultad de Medicina de Ciudad Real, Universidad de Castilla-La Mancha, Ciudad Real, Spain
| | - Ana Contreras
- Laboratory of Neurophysiology and Behavior, Facultad de Medicina de Ciudad Real, Universidad de Castilla-La Mancha, Ciudad Real, Spain
| | - Katia Touyarot
- INRAE, Bordeaux INP, NutriNeuro, University of Bordeaux, Bordeaux, France
| | - Ana I. Herrero
- Department of Psychobiology, Universidad Nacional de Educación a Distancia, Madrid, Spain
| | - César Venero
- Department of Psychobiology, Universidad Nacional de Educación a Distancia, Madrid, Spain
| | - Karine Cambon
- Direction de la Recherche Fondamentale (DRF), Institut François Jacob, MIRCen, Commissariat à l’Energie Atomique et aux Energies Alternatives (CEA), Fontenay-aux-Roses, France
| | - Agnés Gruart
- Division of Neurosciences, Pablo de Olavide University, Seville, Spain
| | | | - Carmen Sandi
- Laboratory of Behavioral Genetics, Brain Mind Institute, School of Life Sciences, École Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
| | - Lydia Jiménez-Díaz
- Laboratory of Neurophysiology and Behavior, Facultad de Medicina de Ciudad Real, Universidad de Castilla-La Mancha, Ciudad Real, Spain,*Correspondence: Lydia Jiménez-Díaz,
| |
Collapse
|
22
|
Iglesias P, Tendobi C, Carlos S, Lozano MD, Barquín D, Chiva L, Reina G. Characterization of Human Papillomavirus 16 from Kinshasa (Democratic Republic of the Congo)-Implications for Pathogenicity and Vaccine Effectiveness. Microorganisms 2022; 10:microorganisms10122492. [PMID: 36557745 PMCID: PMC9782055 DOI: 10.3390/microorganisms10122492] [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: 10/31/2022] [Revised: 11/24/2022] [Accepted: 12/06/2022] [Indexed: 12/23/2022] Open
Abstract
Human Papillomavirus (HPV) type 16 is the main etiological agent of cervical cancer worldwide. Mutations within the virus genome may lead to an increased risk of cancer development and decreased vaccine response, but there is a lack of information about strains circulating in Sub-Saharan Africa. Endocervical cytology samples were collected from 480 women attending a voluntary cervical cancer screening program at Monkole Hospital and four outpatient centers in Kinshasa, Democratic Republic of the Congo (DRC). The prevalence of HPV infection was 18.8% and the most prevalent high-risk types were HPV16 (12.2%) followed by HPV52 (8.8%) and HPV33/HPV35 (7.8% each). HPV16 strains were characterized: 57.1% were classified as C lineage; two samples (28.6%) as A1 and one sample belonged to B1 lineage. HPV33, HPV35, HPV16, and HPV58 were the most frequent types associated with low-grade intraepithelial lesion while high-grade squamous intraepithelial lesions were predominantly associated with HPV16. Several L1 mutations (T266A, S282P, T353P, and N181T) were common in Kinshasa, and their potential effect on vaccine-induced neutralization, especially the presence of S282P, should be further investigated. Long control region (LCR) variability was high with frequent mutations like G7193T, G7521A, and G145T that could promote malignancy of these HPV16 strains. This study provides a helpful basis for understanding HPV16 variants circulating in Kinshasa and the potential association between mutations of LCR region and malignancy and of L1 and vaccine activity.
Collapse
Affiliation(s)
- Paula Iglesias
- Microbiology Department, Clínica Universidad de Navarra, 31008 Pamplona, Spain
| | - Celine Tendobi
- Department of Obstetrics and Gynecology, Centre Hospitalier Mère-Enfant (CHME), Ngafani, Kinshasa 4484, Democratic Republic of the Congo
| | - Silvia Carlos
- Department of Preventive Medicine and Public Health, Universidad de Navarra, 31008 Pamplona, Spain
- IdiSNA, Navarra Institute for Health Research, 31008 Pamplona, Spain
- ISTUN, Institute of Tropical Health, Universidad de Navarra, 31008 Pamplona, Spain
- Correspondence: ; Tel.: +34-948425600 (ext. 826636)
| | - Maria D. Lozano
- IdiSNA, Navarra Institute for Health Research, 31008 Pamplona, Spain
- Department of Pathology, Clínica Universidad de Navarra, 31008 Pamplona, Spain
| | - David Barquín
- Microbiology Department, Clínica Universidad de Navarra, 31008 Pamplona, Spain
| | - Luis Chiva
- IdiSNA, Navarra Institute for Health Research, 31008 Pamplona, Spain
- Department of Obstetrics and Gynecology, Clínica Universidad de Navarra, 28027 Madrid, Spain
| | - Gabriel Reina
- Microbiology Department, Clínica Universidad de Navarra, 31008 Pamplona, Spain
- IdiSNA, Navarra Institute for Health Research, 31008 Pamplona, Spain
- ISTUN, Institute of Tropical Health, Universidad de Navarra, 31008 Pamplona, Spain
| |
Collapse
|
23
|
Fekete CD, Nishiyama A. Presentation and integration of multiple signals that modulate oligodendrocyte lineage progression and myelination. Front Cell Neurosci 2022; 16:1041853. [PMID: 36451655 PMCID: PMC9701731 DOI: 10.3389/fncel.2022.1041853] [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: 09/11/2022] [Accepted: 10/17/2022] [Indexed: 11/15/2022] Open
Abstract
Myelination is critical for fast saltatory conduction of action potentials. Recent studies have revealed that myelin is not a static structure as previously considered but continues to be made and remodeled throughout adulthood in tune with the network requirement. Synthesis of new myelin requires turning on the switch in oligodendrocytes (OL) to initiate the myelination program that includes synthesis and transport of macromolecules needed for myelin production as well as the metabolic and other cellular functions needed to support this process. A significant amount of information is available regarding the individual intrinsic and extrinsic signals that promote OL commitment, expansion, terminal differentiation, and myelination. However, it is less clear how these signals are made available to OL lineage cells when needed, and how multiple signals are integrated to generate the correct amount of myelin that is needed in a given neural network state. Here we review the pleiotropic effects of some of the extracellular signals that affect myelination and discuss the cellular processes used by the source cells that contribute to the variation in the temporal and spatial availability of the signals, and how the recipient OL lineage cells might integrate the multiple signals presented to them in a manner dialed to the strength of the input.
Collapse
|
24
|
Stoyanova II, Lutz D. Functional Diversity of Neuronal Cell Adhesion and Recognition Molecule L1CAM through Proteolytic Cleavage. Cells 2022; 11:cells11193085. [PMID: 36231047 PMCID: PMC9562852 DOI: 10.3390/cells11193085] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2022] [Revised: 09/26/2022] [Accepted: 09/29/2022] [Indexed: 11/16/2022] Open
Abstract
The neuronal cell adhesion and recognition molecule L1 does not only 'keep cells together' by way of homophilic and heterophilic interactions, but can also promote cell motility when cleaved into fragments by several proteases. It has largely been thought that such fragments are signs of degradation. Now, it is clear that proteolysis contributes to the pronounced functional diversity of L1, which we have reviewed in this work. L1 fragments generated at the plasma membrane are released into the extracellular space, whereas other membrane-bound fragments are internalised and enter the nucleus, thus conveying extracellular signals to the cell interior. Post-translational modifications on L1 determine the sequence of cleavage by proteases and the subcellular localisation of the generated fragments. Inside the neuronal cells, L1 fragments interact with various binding partners to facilitate morphogenic events, as well as regenerative processes. The stimulation of L1 proteolysis via injection of L1 peptides or proteases active on L1 or L1 mimetics is a promising tool for therapy of injured nervous systems. The collective findings gathered over the years not only shed light on the great functional diversity of L1 and its fragments, but also provide novel mechanistic insights into the adhesion molecule proteolysis that is active in the developing and diseased nervous system.
Collapse
Affiliation(s)
- Irina I. Stoyanova
- Department of Anatomy and Cell Biology, Faculty of Medicine, Medical University, 9002 Varna, Bulgaria
- Department of Brain Ischemia Mechanisms, Research Institute, Medical University, 9002 Varna, Bulgaria
- Correspondence: (I.I.S.); (D.L.)
| | - David Lutz
- Department of Neuroanatomy and Molecular Brain Research, Ruhr University Bochum,
44801 Bochum, Germany
- Correspondence: (I.I.S.); (D.L.)
| |
Collapse
|
25
|
Osburn SC, Mesquita P, Neal FK, Rumbley M, Holmes MT, Ruple BA, Mobley CB, Brown MD, McCullough DJ, Kavazis AN, Roberts MD. Long-term voluntary wheel running effects on markers of Long Interspersed Nuclear Element-1 in skeletal muscle, liver, and brain tissue of female rats. Am J Physiol Cell Physiol 2022; 323:C907-C919. [PMID: 35938680 DOI: 10.1152/ajpcell.00234.2022] [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] [Indexed: 11/22/2022]
Abstract
We sought to determine the effects of long-term voluntary wheel running on markers of Long Interspersed Nuclear Element-1 (L1) in skeletal muscle, liver, and the hippocampus of female rats. Additionally, markers of the cGAS-STING DNA sensing pathway that results in inflammation were interrogated. Female Lewis rats (n=34) were separated into one of three groups including a 6-month-old group to serve as a young comparator group (CTL, n=10), a group that had access to a running wheel for voluntary wheel running (EX, n=12), and an age-matched group that did not (SED, n=12). Both SED and EX groups were carried out from 6 months to 15 months of age. There were no significant differences in L1 mRNA expression for any of the tissues between groups. Methylation of the L1 promoter in the soleus and hippocampus was significantly higher in SED and EX compared to CTL (p<0.05). ORF1p expression was higher in older SED and EX rats compared to CTL for every tissue (p<0.05). There were no differences between groups for L1 mRNA or cGAS-STING pathway markers. Our results suggest there is an increased ORF1 protein expression across tissues with aging that is not mitigated by voluntary wheel running. Additionally, while previous data imply that L1 methylation changes may play a role in acute exercise for L1 RNA expression, this does not seem to occur during extended periods of voluntary wheel running.
Collapse
Affiliation(s)
- Shelby C Osburn
- School of Kinesiology, Auburn University, Auburn, AL, United States
| | - Paulo Mesquita
- School of Kinesiology, Auburn University, Auburn, AL, United States
| | - Frances K Neal
- School of Kinesiology, Auburn University, Auburn, AL, United States
| | - Melissa Rumbley
- School of Kinesiology, Auburn University, Auburn, AL, United States
| | - Matthew T Holmes
- School of Kinesiology, Auburn University, Auburn, AL, United States
| | - Bradley A Ruple
- School of Kinesiology, Auburn University, Auburn, AL, United States
| | - C Brooks Mobley
- School of Kinesiology, Auburn University, Auburn, AL, United States
| | - Michael D Brown
- School of Public Health, University of Maryland, College Park, MD, United States
| | - Danielle J McCullough
- School of Kinesiology, Auburn University, Auburn, AL, United States.,Edward Via College of Osteopathic Medicine, Auburn, AL, United States
| | | | - Michael D Roberts
- School of Kinesiology, Auburn University, Auburn, AL, United States.,Edward Via College of Osteopathic Medicine, Auburn, AL, United States
| |
Collapse
|
26
|
Olczak P, Matsui K, Wong M, Alvarez J, Lambert P, Christensen ND, Hu J, Huber B, Kirnbauer R, Wang JW, Roden RBS. RG2-VLP: a Vaccine Designed to Broadly Protect against Anogenital and Skin Human Papillomaviruses Causing Human Cancer. J Virol 2022; 96:e0056622. [PMID: 35703545 PMCID: PMC9278150 DOI: 10.1128/jvi.00566-22] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [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: 04/05/2022] [Accepted: 05/20/2022] [Indexed: 12/20/2022] Open
Abstract
The family of human papillomaviruses (HPV) includes over 400 genotypes. Genus α genotypes generally infect the anogenital mucosa, and a subset of these HPV are a necessary, but not sufficient, cause of cervical cancer. Of the 13 high-risk (HR) and 11 intermediate-risk (IR) HPV associated with cervical cancer, genotypes 16 and 18 cause 50% and 20% of cases, respectively, whereas HPV16 dominates in other anogenital and oropharyngeal cancers. A plethora of βHPVs are associated with cutaneous squamous cell carcinoma (CSCC), especially in sun-exposed skin sites of epidermodysplasia verruciformis (EV), AIDS, and immunosuppressed patients. Licensed L1 virus-like particle (VLP) vaccines, such as Gardasil 9, target a subset of αHPV but no βHPV. To comprehensively target both α- and βHPVs, we developed a two-component VLP vaccine, RG2-VLP, in which L2 protective epitopes derived from a conserved αHPV epitope (amino acids 17 to 36 of HPV16 L2) and a consensus βHPV sequence in the same region are displayed within the DE loop of HPV16 and HPV18 L1 VLP, respectively. Unlike vaccination with Gardasil 9, vaccination of wild-type and EV model mice (Tmc6Δ/Δ or Tmc8Δ/Δ) with RG2-VLP induced robust L2-specific antibody titers and protected against β-type HPV5. RG2-VLP protected rabbits against 17 αHPV, including those not covered by Gardasil 9. HPV16- and HPV18-specific neutralizing antibody responses were similar between RG2-VLP- and Gardasil 9-vaccinated animals. However, only transfer of RG2-VLP antiserum effectively protected naive mice from challenge with all βHPVs tested. Taken together, these observations suggest RG2-VLP's potential as a broad-spectrum vaccine to prevent αHPV-driven anogenital, oropharyngeal, and βHPV-associated cutaneous cancers. IMPORTANCE Licensed preventive HPV vaccines are composed of VLPs derived by expression of major capsid protein L1. They confer protection generally restricted to infection by the αHPVs targeted by the up-to-9-valent vaccine, and their associated anogenital cancers and genital warts, but do not target βHPV that are associated with CSCC in EV and immunocompromised patients. We describe the development of a two-antigen vaccine protective in animal models against known oncogenic αHPVs as well as diverse βHPVs by incorporation into HPV16 and HPV18 L1 VLP of 20-amino-acid conserved protective epitopes derived from minor capsid protein L2.
Collapse
Affiliation(s)
- Pola Olczak
- Department of Pathology, Johns Hopkins University, Baltimore, Maryland, USA
| | | | - Margaret Wong
- Department of Pathology, Johns Hopkins University, Baltimore, Maryland, USA
| | - Jade Alvarez
- Department of Pathology, Johns Hopkins University, Baltimore, Maryland, USA
| | - Paul Lambert
- McArdle Laboratory for Cancer Research, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Neil D. Christensen
- The Jake Gittlen Laboratories for Cancer Research, Pennsylvania State University, College of Medicine, Hershey, Pennsylvania, USA
- Department of Pathology, Pennsylvania State University, College of Medicine, Hershey, Pennsylvania, USA
| | - Jiafen Hu
- The Jake Gittlen Laboratories for Cancer Research, Pennsylvania State University, College of Medicine, Hershey, Pennsylvania, USA
- Department of Pathology, Pennsylvania State University, College of Medicine, Hershey, Pennsylvania, USA
| | - Bettina Huber
- Department of Dermatology, Medical University of Vienna, Vienna, Austria
| | - Reinhard Kirnbauer
- Department of Dermatology, Medical University of Vienna, Vienna, Austria
| | | | | |
Collapse
|
27
|
Firdaus MER, Mustopa AZ, Triratna L, Syahputra G, Nurfatwa M. Dissection of Capsid Protein HPV 52 to Rationalize Vaccine Designs Using Computational Approaches Immunoinformatics and Molecular Docking. Asian Pac J Cancer Prev 2022; 23:2243-2253. [PMID: 35901328 DOI: 10.31557/apjcp.2022.23.7.2243] [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: 04/28/2021] [Indexed: 11/25/2022]
Abstract
BACKGROUND Human Papillomavirus type 52 (HPV 52) is considered one of the threatening HPV types inducing cervical cancer worldwide. This study was conducted to address strategies of an effective vaccine against cervical cancer using computational approaches immuno-informatics and molecular docking. METHODS Major capsid protein L1 and L2 HPV 52 (L1 and L2 HPV 52) sequences were investigated by multiple analyses including B and T cell epitope, toxicity, allergenicity, Immunogenicity, epitope conservancy, population coverage, and molecular docking. RESULTS L1 and L2 HPV 52 showed a conserved sequence among amino acid levels. Q307K, S383D/N, and D473E are found as major mutations in L1, while mutations in L2 are S122T, Q247H, L247S, and E365D. Multiple epitopes were identified and elicited strong immune responses against cross types of HPV in various HLA populations. To enhance vaccine effectiveness that allows having cross-protection over HPV types, N terminus HPV L2 was analyzed suggesting multi-candidates chimeric L1/L2 vaccine design. CONCLUSION This study shed a light on a useful pipeline with robust analysis for effective vaccine production.
Collapse
Affiliation(s)
- Moh Egy Rahman Firdaus
- Research Center for Genetic Engineering, National Research and Innovation Agency (BRIN), Bogor, 16911, West Java, Indonesia.,Present address: The International Institute of Molecular Mechanisms and Machines, Polish Academy of Sciences, Warsaw, Poland
| | - Apon Zaenal Mustopa
- Research Center for Genetic Engineering, National Research and Innovation Agency (BRIN), Bogor, 16911, West Java, Indonesia
| | - Lita Triratna
- Research Center for Applied Zoology, National Research and Innovation Agency (BRIN), Bogor, 16911, West Java, Indonesia
| | - Gita Syahputra
- Research Center for Vaccine and Drug, National Research and Innovation Agency (BRIN), Bogor, 16911, West Java, Indonesia
| | - Maritsa Nurfatwa
- Research Center for Genetic Engineering, National Research and Innovation Agency (BRIN), Bogor, 16911, West Java, Indonesia
| |
Collapse
|
28
|
Chiapponi C, Alakus H, Schmidt M, Faust M, Bruns CJ, Büttner R, Eich ML, Schultheis AM. Lymphatic Vessel Invasion in Routine Pathology Reports of Papillary Thyroid Cancer. Front Med (Lausanne) 2022; 9:841550. [PMID: 35265646 PMCID: PMC8899077 DOI: 10.3389/fmed.2022.841550] [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: 12/22/2021] [Accepted: 01/20/2022] [Indexed: 11/29/2022] Open
Abstract
Purpose It is not mandatory to report lymphatic vessel invasion in pathology reports of papillary thyroid cancer (PTC) according to the current Union for International Cancer Control (UICC) TNM (tumor, nodes, and metastases) classification. However, there is some evidence for its correlation with lymph node metastasis (LNM) and prognosis. The aim of this study was to explore the clinical implication of lymphatic vessel invasion documentation of PTC because pathology reports play a pivotal role in postsurgical clinical decision-making in endocrine tumor boards. Methods Patients undergoing postoperative radioiodine treatment for PTC at the University Hospital of Cologne, Germany between December 2015 and March 2020 were identified. Pathology reports were screened for documentation of lymphatic vessel invasion. Demographics and clinicopathologic data of patients documented, including lymphatic vessel invasion and lymph nodal involvement were analyzed. Results A total of 578 patients were identified and included. Lymphatic vessel invasion was reported in pathology reports of 366 (63.3%) and omitted in 112 (36.7%) patients. Positive lymphatic vessel invasion (L1) was diagnosed in 67 (18.3%) of 366 patients and was documented as absent (L0) in 299 (81.7%) patients. Lymph nodal (N) status was positive (N+) in 126 (45.6%) and negative (N0) in 150 (54.3%) of these patients. In 54 (80.6%) L1 cases N+ status and in 137 (65.6%) L0 cases N0 status was diagnosed. In 13 (19.4%) cases with L1 status, there were no LNMs (L1 N0). In total, 72 (34.4%) patients had LNM despite L0 status (L0 N+). The sensitivity and specificity of LVI reporting for LNM were 0.42 and 0.91, respectively. Conclusion In routine pathology reports of PTC used for indication to postoperative radioiodine treatment by a German endocrine tumor board, lymphatic vessel invasion was found to be reported inconsistently and mostly as L0. L1 diagnoses, however, reliably correlated with reported LNM and might, thus, be relevant for clinical decision-making. For this reason, we advocate for standardized pathologic reassessment of lymphatic vessel invasion, in particular for cases where lymph nodes are not included in the pathologic specimen and if L0 is documented.
Collapse
Affiliation(s)
- Costanza Chiapponi
- Department of General, Visceral, Cancer and Transplant Surgery, University Clinic of Cologne, Cologne, Germany
| | - Hakan Alakus
- Department of General, Visceral, Cancer and Transplant Surgery, University Clinic of Cologne, Cologne, Germany
| | - Matthias Schmidt
- Department for Nuclear Medicine, University Clinic of Cologne, Cologne, Germany
| | - Michael Faust
- Policlinic for Endocrinology, Diabetes and Prevention Medicine, University Clinic of Cologne, Cologne, Germany
| | - Christiane J Bruns
- Department of General, Visceral, Cancer and Transplant Surgery, University Clinic of Cologne, Cologne, Germany
| | - Reinhard Büttner
- Institute for Pathology, University Clinic of Cologne, Cologne, Germany
| | - Marie-Lisa Eich
- Institute for Pathology, University Clinic of Cologne, Cologne, Germany
| | - Anne M Schultheis
- Institute for Pathology, University Clinic of Cologne, Cologne, Germany
| |
Collapse
|
29
|
Creamer KM, Larsen EC, Lawrence JB. ZNF146/OZF and ZNF507 target LINE-1 sequences. G3 (Bethesda) 2022; 12:jkac002. [PMID: 35100360 PMCID: PMC8896011 DOI: 10.1093/g3journal/jkac002] [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] [Figures] [Subscribe] [Scholar Register] [Received: 06/03/2021] [Accepted: 12/03/2021] [Indexed: 06/14/2023]
Abstract
Repetitive sequences including transposable elements and transposon-derived fragments account for nearly half of the human genome. While transposition-competent transposable elements must be repressed to maintain genomic stability, mutated and fragmented transposable elements comprising the bulk of repetitive sequences can also contribute to regulation of host gene expression and broader genome organization. Here, we analyzed published ChIP-seq data sets to identify proteins broadly enriched on transposable elements in the human genome. We show 2 of the proteins identified, C2H2 zinc finger-containing proteins ZNF146 (also known as OZF) and ZNF507, are targeted to distinct sites within LINE-1 ORF2 at thousands of locations in the genome. ZNF146 binding sites are found at old and young LINE-1 elements. In contrast, ZNF507 preferentially binds at young LINE-1 sequences correlated to sequence changes in LINE-1 elements at ZNF507's binding site. To gain further insight into ZNF146 and ZNF507 function, we disrupt their expression in HEK293 cells using CRISPR/Cas9 and perform RNA sequencing, finding modest gene expression changes in cells where ZNF507 has been disrupted. We further identify a physical interaction between ZNF507 and PRMT5, suggesting ZNF507 may target arginine methylation activity to LINE-1 sequences.
Collapse
Affiliation(s)
- Kevin M Creamer
- Department of Neurology and Pediatrics, University of Massachusetts Medical School, Worcester, MA 01655, USA
| | - Eric C Larsen
- Department of Neurology and Pediatrics, University of Massachusetts Medical School, Worcester, MA 01655, USA
| | - Jeanne B Lawrence
- Department of Neurology and Pediatrics, University of Massachusetts Medical School, Worcester, MA 01655, USA
| |
Collapse
|
30
|
Brendle S, Cladel N, Balogh K, Alam S, Christensen N, Meyers C, Hu J. A Comparative Study on Delivery of Externally Attached DNA by Papillomavirus VLPs and Pseudoviruses. Vaccines (Basel) 2021; 9:vaccines9121501. [PMID: 34960247 PMCID: PMC8709278 DOI: 10.3390/vaccines9121501] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2021] [Revised: 12/10/2021] [Accepted: 12/14/2021] [Indexed: 01/07/2023] Open
Abstract
Human papillomavirus (HPV) 16 capsids have been chosen as a DNA delivery vehicle in many studies. Our preliminary studies suggest that HPV58 capsids could be better vehicles than HPV16 capsids to deliver encapsidated DNA in vitro and in vivo. In the current study, we compared HPV16, HPV58, and the cottontail rabbit papillomavirus (CRPV) capsids either as L1/L2 VLPs or pseudoviruses (PSVs) to deliver externally attached GFP-expressing DNA. Both rabbit and human cells were used to test whether there was a species-specific effect. DNA delivery efficiency was determined by quantifying either GFP-expressing cell populations or mean fluorescent intensities (MFI) by flow cytometry. Interestingly, CRPV and 58-VLPs and PSVs were significantly more efficient at delivering attached DNA when compared to 16-VLPs and PSVs. A capsid/DNA ratio of 2:1 showed the highest efficiency for delivering external DNA. The PSVs with papillomavirus DNA genomes also showed higher efficiency than those with irrelevant plasmid DNA. HPV16L1/58L2 hybrid VLPs displayed increased efficiency compared to HPV58L1/16L2 VLPs, suggesting that L2 may play a critical role in the delivery of attached DNA. Additionally, we demonstrated that VLPs increased in vivo infectivity of CRPV DNA in rabbits. We conclude that choosing CRPV or 58 capsids to deliver external DNA could improve DNA uptake in in vitro and in vivo models.
Collapse
Affiliation(s)
- Sarah Brendle
- Jake Gittlen Laboratories for Cancer Research, Pennsylvania State University College of Medicine, Hershey, PA 17033, USA; (S.B.); (N.C.); (K.B.); (N.C.)
- Department of Pathology and Laboratory Medicine, Pennsylvania State University College of Medicine, Hershey, PA 17033, USA
| | - Nancy Cladel
- Jake Gittlen Laboratories for Cancer Research, Pennsylvania State University College of Medicine, Hershey, PA 17033, USA; (S.B.); (N.C.); (K.B.); (N.C.)
- Department of Pathology and Laboratory Medicine, Pennsylvania State University College of Medicine, Hershey, PA 17033, USA
| | - Karla Balogh
- Jake Gittlen Laboratories for Cancer Research, Pennsylvania State University College of Medicine, Hershey, PA 17033, USA; (S.B.); (N.C.); (K.B.); (N.C.)
- Department of Pathology and Laboratory Medicine, Pennsylvania State University College of Medicine, Hershey, PA 17033, USA
| | - Samina Alam
- Department of Microbiology and Immunology, Pennsylvania State University College of Medicine, Hershey, PA 17033, USA; (S.A.); (C.M.)
| | - Neil Christensen
- Jake Gittlen Laboratories for Cancer Research, Pennsylvania State University College of Medicine, Hershey, PA 17033, USA; (S.B.); (N.C.); (K.B.); (N.C.)
- Department of Pathology and Laboratory Medicine, Pennsylvania State University College of Medicine, Hershey, PA 17033, USA
- Department of Microbiology and Immunology, Pennsylvania State University College of Medicine, Hershey, PA 17033, USA; (S.A.); (C.M.)
| | - Craig Meyers
- Department of Microbiology and Immunology, Pennsylvania State University College of Medicine, Hershey, PA 17033, USA; (S.A.); (C.M.)
| | - Jiafen Hu
- Jake Gittlen Laboratories for Cancer Research, Pennsylvania State University College of Medicine, Hershey, PA 17033, USA; (S.B.); (N.C.); (K.B.); (N.C.)
- Department of Pathology and Laboratory Medicine, Pennsylvania State University College of Medicine, Hershey, PA 17033, USA
- Correspondence:
| |
Collapse
|
31
|
Abstract
During initial infection, human papillomaviruses (HPV) take an unusual trafficking pathway through their host cell. It begins with a long period on the cell surface, during which the capsid is primed and a virus entry platform is formed. A specific type of clathrin-independent endocytosis and subsequent retrograde trafficking to the trans-Golgi network follow this. Cellular reorganization processes, which take place during mitosis, enable further virus transport and the establishment of infection while evading intrinsic cellular immune defenses. First, the fragmentation of the Golgi allows the release of membrane-encased virions, which are partially protected from cytoplasmic restriction factors. Second, the nuclear envelope breakdown opens the gate for these virus–vesicles to the cell nucleus. Third, the dis- and re-assembly of the PML nuclear bodies leads to the formation of modified virus-associated PML subnuclear structures, enabling viral transcription and replication. While remnants of the major capsid protein L1 and the viral DNA remain in a transport vesicle, the viral capsid protein L2 plays a crucial role during virus entry, as it adopts a membrane-spanning conformation for interaction with various cellular proteins to establish a successful infection. In this review, we follow the oncogenic HPV type 16 during its long journey into the nucleus, and contrast pro- and antiviral processes.
Collapse
|
32
|
Grandi N, Tramontano E, Berkhout B. Integration of SARS-CoV-2 RNA in infected human cells by retrotransposons: an unlikely hypothesis and old viral relationships. Retrovirology 2021; 18:34. [PMID: 34715873 PMCID: PMC8554740 DOI: 10.1186/s12977-021-00578-w] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Accepted: 10/19/2021] [Indexed: 11/22/2022] Open
Abstract
Zhang et al. (Proc Natl Acad Sci 118:e2105968118, 2021) recently reported that SARS-CoV-2 RNA can be retrotranscribed and integrated into the DNA of human cells by the L1 retrotransposon machinery. This phenomenon could cause persistence of viral sequences in patients and may explain the prolonged PCR-positivity of SARS-CoV-2 infected patients, even long after the phase of active virus replication has ended. This commentary does critically review the available data on this topic and discusses them in the context of findings made for other exogenous viruses and ancestral endogenous retroviral elements.
Collapse
Affiliation(s)
- Nicole Grandi
- Laboratory of Molecular Virology, Department of Life and Environmental Sciences, University of Cagliari - Cittadella Universitaria di Monserrato, SS554, Monserrato (Cagliari), Italy.
| | - Enzo Tramontano
- Laboratory of Molecular Virology, Department of Life and Environmental Sciences, University of Cagliari - Cittadella Universitaria di Monserrato, SS554, Monserrato (Cagliari), Italy.,Istituto di Ricerca Genetica e Biomedica (IRGB), CNR - SS554, Monserrato (Cagliari), Italy
| | - Ben Berkhout
- Laboratory of Experimental Virology, Department of Medical Microbiology, Amsterdam Medical Centers, Meibergdreef 15, 1105 AZ, Amsterdam, The Netherlands.
| |
Collapse
|
33
|
Zhang WJ, Huang YQ, Fu A, Chen KZ, Li SJ, Zhang Q, Zou GJ, Liu Y, Su JZ, Zhou SF, Liu JW, Li F, Bi FF, Li CQ. The Retrotransposition of L1 is Involved in the Reconsolidation of Contextual Fear Memory in Mice. CNS Neurol Disord Drug Targets 2021; 20:273-284. [PMID: 32787766 DOI: 10.2174/1871527319666200812225509] [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: 01/09/2020] [Revised: 02/25/2020] [Accepted: 04/27/2020] [Indexed: 11/22/2022]
Abstract
BACKGROUND The long interspersed element-1 (L1) participates in memory formation, and DNA methylation patterns of L1 may suggest resilience or vulnerability factors for Post-Traumatic Stress Disorder (PTSD), of which the principal manifestation is a pathological exacerbation of fear memory. However, the unique roles of L1 in the reconsolidation of fear memory remain poorly understood. OBJECTIVE The study aimed to investigate the role of L1 in the reconsolidation of context-dependent fear memory. METHODS Mice underwent fear conditioning and fear recall in the observation chambers. Fear memory was assessed by calculating the percentage of time spent freezing in 5 min. The medial prefrontal cortex (mPFC) and hippocampus were removed for further analysis. Open Reading Frame 1 (ORF1) mRNA and ORF2 mRNA of L1 were analyzed by real-time quantitative polymerase chain reaction. After reactivation of fear memory, lamivudine was administered and its effects on fear memory reconsolidation were observed. RESULTS ORF1 and ORF2 mRNA expressions in the mPFC and hippocampus after recent (24 h) and remote (14 days) fear memory recall exhibited augmentation via different temporal and spatial patterns. Reconsolidation of fear memory was markedly inhibited in mice treated with lamivudine, which could block L1. DNA methyltransferase mRNA expression declined following lamivudine treatment in remote fear memory recall. CONCLUSION The retrotransposition of L1 participated in the reconsolidation of fear memory after reactivation of fear memory, and with lamivudine treatment, spontaneous recovery decreased with time after recent and remote fear memory recall, providing clues for understanding the roles of L1 in fear memory.
Collapse
Affiliation(s)
- Wen-Juan Zhang
- Department of Anatomy and Neurobiology, School of Basic Medical Science, Central South University, Changsha 410013, China
| | - Yan-Qing Huang
- Department of Anatomy and Neurobiology, School of Basic Medical Science, Central South University, Changsha 410013, China
| | - Ao Fu
- Clinic Medicine of 5-year Program, Xiangya School of Medicine, Central South University, Changsha 410013, China
| | - Kang-Zhi Chen
- Clinic Medicine of 8-year Program, Xiangya School of Medicine, Central South University, Changsha 410013, China
| | - Song-Ji Li
- Department of Anatomy and Neurobiology, School of Basic Medical Science, Central South University, Changsha 410013, China
| | - Qi Zhang
- Department of Anatomy and Neurobiology, School of Basic Medical Science, Central South University, Changsha 410013, China
| | - Guang-Jing Zou
- Department of Anatomy and Neurobiology, School of Basic Medical Science, Central South University, Changsha 410013, China
| | - Yu Liu
- Department of Anatomy and Neurobiology, School of Basic Medical Science, Central South University, Changsha 410013, China
| | - Jing-Zhi Su
- Department of Anatomy and Neurobiology, School of Basic Medical Science, Central South University, Changsha 410013, China
| | - Shi-Fen Zhou
- Department of Anatomy and Neurobiology, School of Basic Medical Science, Central South University, Changsha 410013, China
| | - Jun-Wen Liu
- Department of Histology and Embryology, School of Basic Medical Sciences, Central South University, Changsha 410013, China
| | - Fang Li
- Department of Anatomy and Neurobiology, School of Basic Medical Science, Central South University, Changsha 410013, China
| | - Fang-Fang Bi
- Department of Neurology, XiangYa Hospital, Central South University, Changsha 410008, Hunan, China
| | - Chang-Qi Li
- Department of Anatomy and Neurobiology, School of Basic Medical Science, Central South University, Changsha 410013, China
| |
Collapse
|
34
|
Sudhindar PD, Wainwright D, Saha S, Howarth R, McCain M, Bury Y, Saha SS, McPherson S, Reeves H, Patel AH, Faulkner GJ, Lunec J, Shukla R. HCV Activates Somatic L1 Retrotransposition-A Potential Hepatocarcinogenesis Pathway. Cancers (Basel) 2021; 13:5079. [PMID: 34680227 PMCID: PMC8533982 DOI: 10.3390/cancers13205079] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2021] [Revised: 09/29/2021] [Accepted: 10/07/2021] [Indexed: 12/24/2022] Open
Abstract
Hepatitis C virus (HCV) is a common cause of hepatocellular carcinoma (HCC). The activation and mutagenic consequences of L1 retrotransposons in virus-associated-HCC have been documented. However, the direct influence of HCV upon L1 elements is unclear, and is the focus of the present study. L1 transcript expression was evaluated in a publicly available liver tissue RNA-seq dataset from patients with chronic HCV hepatitis (CHC), as well as healthy controls. L1 transcript expression was significantly higher in CHC than in controls. L1orf1p (a L1 encoded protein) expression was observed in six out of 11 CHC livers by immunohistochemistry. To evaluate the influence of HCV on retrotransposition efficiency, in vitro engineered-L1 retrotransposition assays were employed in Huh7 cells in the presence and absence of an HCV replicon. An increased retrotransposition rate was observed in the presence of replicating HCV RNA, and persisted in cells after viral clearance due to sofosbuvir (PSI7977) treatment. Increased retrotransposition could be due to dysregulation of the DNA-damage repair response, including homologous recombination, due to HCV infection. Altogether these data suggest that L1 expression can be activated before oncogenic transformation in CHC patients, with HCV-upregulated retrotransposition potentially contributing to HCC genomic instability and a risk of transformation that persists post-viral clearance.
Collapse
Affiliation(s)
- Praveen D. Sudhindar
- Newcastle University Centre for Cancer, Biosciences Institute, Faculty of Medical Sciences, The Medical School, Newcastle University, Newcastle upon Tyne NE2 4HH, UK; (P.D.S.); (D.W.); (R.H.); (J.L.)
| | - Daniel Wainwright
- Newcastle University Centre for Cancer, Biosciences Institute, Faculty of Medical Sciences, The Medical School, Newcastle University, Newcastle upon Tyne NE2 4HH, UK; (P.D.S.); (D.W.); (R.H.); (J.L.)
| | - Santu Saha
- Newcastle University Centre for Cancer, Translational and Clinical Research Institute, Faculty of Medical Sciences, The Medical School, Newcastle University, Newcastle upon Tyne NE2 4HH, UK; (S.S.); (M.M.); (S.S.S.); (H.R.)
| | - Rachel Howarth
- Newcastle University Centre for Cancer, Biosciences Institute, Faculty of Medical Sciences, The Medical School, Newcastle University, Newcastle upon Tyne NE2 4HH, UK; (P.D.S.); (D.W.); (R.H.); (J.L.)
| | - Misti McCain
- Newcastle University Centre for Cancer, Translational and Clinical Research Institute, Faculty of Medical Sciences, The Medical School, Newcastle University, Newcastle upon Tyne NE2 4HH, UK; (S.S.); (M.M.); (S.S.S.); (H.R.)
| | - Yvonne Bury
- Department of Cellular Pathology, Royal Victoria Infirmary, Newcastle upon Tyne Hospitals NHS Foundation Trust, Newcastle upon Tyne NE1 4LP, UK;
| | - Sweta S. Saha
- Newcastle University Centre for Cancer, Translational and Clinical Research Institute, Faculty of Medical Sciences, The Medical School, Newcastle University, Newcastle upon Tyne NE2 4HH, UK; (S.S.); (M.M.); (S.S.S.); (H.R.)
| | - Stuart McPherson
- The Liver Unit, Freeman Hospital, Newcastle upon Tyne Hospitals NHS Foundation Trust, Heaton NE7 7DN, UK;
| | - Helen Reeves
- Newcastle University Centre for Cancer, Translational and Clinical Research Institute, Faculty of Medical Sciences, The Medical School, Newcastle University, Newcastle upon Tyne NE2 4HH, UK; (S.S.); (M.M.); (S.S.S.); (H.R.)
- The Liver Unit, Freeman Hospital, Newcastle upon Tyne Hospitals NHS Foundation Trust, Heaton NE7 7DN, UK;
| | - Arvind H. Patel
- MRC-University of Glasgow Centre for Virus Research, University of Glasgow, Glasgow G61 1QH, UK;
| | - Geoffrey J. Faulkner
- Mater Research Institute, University of Queensland, Woolloongabba, QLD 4102, Australia;
- Queensland Brain Institute, University of Queensland, Brisbane, QLD 4072, Australia
| | - John Lunec
- Newcastle University Centre for Cancer, Biosciences Institute, Faculty of Medical Sciences, The Medical School, Newcastle University, Newcastle upon Tyne NE2 4HH, UK; (P.D.S.); (D.W.); (R.H.); (J.L.)
| | - Ruchi Shukla
- Newcastle University Centre for Cancer, Biosciences Institute, Faculty of Medical Sciences, The Medical School, Newcastle University, Newcastle upon Tyne NE2 4HH, UK; (P.D.S.); (D.W.); (R.H.); (J.L.)
| |
Collapse
|
35
|
Bychkov I, Baydakova G, Filatova A, Migiaev O, Marakhonov A, Pechatnikova N, Pomerantseva E, Konovalov F, Ampleeva M, Kaimonov V, Skoblov M, Zakharova E. Complex Transposon Insertion as a Novel Cause of Pompe Disease. Int J Mol Sci 2021; 22:ijms221910887. [PMID: 34639227 PMCID: PMC8509548 DOI: 10.3390/ijms221910887] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2021] [Revised: 10/03/2021] [Accepted: 10/06/2021] [Indexed: 11/22/2022] Open
Abstract
Pompe disease (OMIM#232300) is an autosomal recessive lysosomal storage disorder caused by mutations in the GAA gene. According to public mutation databases, more than 679 pathogenic variants have been described in GAA, none of which are associated with mobile genetic elements. In this article, we report a novel molecular genetic cause of Pompe disease, which could be hardly detected using routine molecular genetic analysis. Whole genome sequencing followed by comprehensive functional analysis allowed us to discover and characterize a complex mobile genetic element insertion deep in the intron 15 of the GAA gene in a patient with infantile onset Pompe disease.
Collapse
Affiliation(s)
- Igor Bychkov
- Research Centre for Medical Genetics, 115478 Moscow, Russia; (G.B.); (A.F.); (O.M.); (A.M.); (M.S.); (E.Z.)
- Correspondence:
| | - Galina Baydakova
- Research Centre for Medical Genetics, 115478 Moscow, Russia; (G.B.); (A.F.); (O.M.); (A.M.); (M.S.); (E.Z.)
| | - Alexandra Filatova
- Research Centre for Medical Genetics, 115478 Moscow, Russia; (G.B.); (A.F.); (O.M.); (A.M.); (M.S.); (E.Z.)
| | - Ochir Migiaev
- Research Centre for Medical Genetics, 115478 Moscow, Russia; (G.B.); (A.F.); (O.M.); (A.M.); (M.S.); (E.Z.)
| | - Andrey Marakhonov
- Research Centre for Medical Genetics, 115478 Moscow, Russia; (G.B.); (A.F.); (O.M.); (A.M.); (M.S.); (E.Z.)
| | | | - Ekaterina Pomerantseva
- Center of Genetics and Reproductive Medicine GENETICO, JSC, 119333 Moscow, Russia; (E.P.); (V.K.)
| | - Fedor Konovalov
- Independent Clinical Bioinformatics Laboratory, 123181 Moscow, Russia; (F.K.); (M.A.)
| | - Maria Ampleeva
- Independent Clinical Bioinformatics Laboratory, 123181 Moscow, Russia; (F.K.); (M.A.)
| | - Vladimir Kaimonov
- Center of Genetics and Reproductive Medicine GENETICO, JSC, 119333 Moscow, Russia; (E.P.); (V.K.)
| | - Mikhail Skoblov
- Research Centre for Medical Genetics, 115478 Moscow, Russia; (G.B.); (A.F.); (O.M.); (A.M.); (M.S.); (E.Z.)
| | - Ekaterina Zakharova
- Research Centre for Medical Genetics, 115478 Moscow, Russia; (G.B.); (A.F.); (O.M.); (A.M.); (M.S.); (E.Z.)
| |
Collapse
|
36
|
Keiffer TR, Soorya S, Sapp MJ. Recent Advances in Our Understanding of the Infectious Entry Pathway of Human Papillomavirus Type 16. Microorganisms 2021; 9:2076. [PMID: 34683397 DOI: 10.3390/microorganisms9102076] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2021] [Accepted: 09/27/2021] [Indexed: 12/31/2022] Open
Abstract
Papillomaviruses are a diverse viral species, but several types such as HPV16 are given special attention due to their contribution towards the pathogenesis of several major cancers. In this review, we will summarize how the knowledge of HPV16 entry has expanded since the last comprehensive HPV16 entry review our lab published in 2017.
Collapse
|
37
|
Smits N, Rasmussen J, Bodea GO, Amarilla AA, Gerdes P, Sanchez-Luque FJ, Ajjikuttira P, Modhiran N, Liang B, Faivre J, Deveson IW, Khromykh AA, Watterson D, Ewing AD, Faulkner GJ. No evidence of human genome integration of SARS-CoV-2 found by long-read DNA sequencing. Cell Rep 2021; 36:109530. [PMID: 34380018 PMCID: PMC8316065 DOI: 10.1016/j.celrep.2021.109530] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2021] [Revised: 07/21/2021] [Accepted: 07/22/2021] [Indexed: 01/28/2023] Open
Abstract
A recent study proposed that severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) hijacks the LINE-1 (L1) retrotransposition machinery to integrate into the DNA of infected cells. If confirmed, this finding could have significant clinical implications. Here, we apply deep (>50×) long-read Oxford Nanopore Technologies (ONT) sequencing to HEK293T cells infected with SARS-CoV-2 and do not find the virus integrated into the genome. By examining ONT data from separate HEK293T cultivars, we completely resolve 78 L1 insertions arising in vitro in the absence of L1 overexpression systems. ONT sequencing applied to hepatitis B virus (HBV)-positive liver cancer tissues located a single HBV insertion. These experiments demonstrate reliable resolution of retrotransposon and exogenous virus insertions by ONT sequencing. That we find no evidence of SARS-CoV-2 integration suggests that such events are, at most, extremely rare in vivo and therefore are unlikely to drive oncogenesis or explain post-recovery detection of the virus.
Collapse
Affiliation(s)
- Nathan Smits
- Mater Research Institute, University of Queensland, TRI Building, Woolloongabba, QLD 4102, Australia
| | - Jay Rasmussen
- Queensland Brain Institute, University of Queensland, Brisbane, QLD 4072, Australia
| | - Gabriela O Bodea
- Mater Research Institute, University of Queensland, TRI Building, Woolloongabba, QLD 4102, Australia; Queensland Brain Institute, University of Queensland, Brisbane, QLD 4072, Australia
| | - Alberto A Amarilla
- School of Chemistry and Molecular Biosciences, University of Queensland, Brisbane, QLD 4072, Australia
| | - Patricia Gerdes
- Mater Research Institute, University of Queensland, TRI Building, Woolloongabba, QLD 4102, Australia
| | - Francisco J Sanchez-Luque
- GENYO, Pfizer-University of Granada-Andalusian Government Centre for Genomics and Oncological Research, PTS Granada 18016, Spain; MRC Human Genetics Unit, Institute of Genetics and Cancer (IGC), University of Edinburgh, Western General Hospital, Edinburgh EH4 2XU, UK
| | - Prabha Ajjikuttira
- Queensland Brain Institute, University of Queensland, Brisbane, QLD 4072, Australia
| | - Naphak Modhiran
- School of Chemistry and Molecular Biosciences, University of Queensland, Brisbane, QLD 4072, Australia
| | - Benjamin Liang
- School of Chemistry and Molecular Biosciences, University of Queensland, Brisbane, QLD 4072, Australia
| | - Jamila Faivre
- INSERM, U1193, Paul-Brousse University Hospital, Hepatobiliary Centre, Villejuif 94800, France
| | - Ira W Deveson
- Kinghorn Centre for Clinical Genomics, Garvan Institute of Medical Research, Sydney, NSW 2010, Australia; St Vincent's Clinical School, Faculty of Medicine, University of New South Wales, Sydney, NSW 2052, Australia
| | - Alexander A Khromykh
- School of Chemistry and Molecular Biosciences, University of Queensland, Brisbane, QLD 4072, Australia; Australian Infectious Diseases Research Centre, Global Virus Network Centre of Excellence, Brisbane, QLD 4072, Australia
| | - Daniel Watterson
- School of Chemistry and Molecular Biosciences, University of Queensland, Brisbane, QLD 4072, Australia; Australian Infectious Diseases Research Centre, Global Virus Network Centre of Excellence, Brisbane, QLD 4072, Australia
| | - Adam D Ewing
- Mater Research Institute, University of Queensland, TRI Building, Woolloongabba, QLD 4102, Australia
| | - Geoffrey J Faulkner
- Mater Research Institute, University of Queensland, TRI Building, Woolloongabba, QLD 4102, Australia; Queensland Brain Institute, University of Queensland, Brisbane, QLD 4072, Australia.
| |
Collapse
|
38
|
Curty G, Menezes AN, Brant AC, de Mulder Rougvie M, Moreira MÂM, Soares MA. Expression of Retroelements in Cervical Cancer and Their Interplay with HPV Infection and Host Gene Expression. Cancers (Basel) 2021; 13:3513. [PMID: 34298727 DOI: 10.3390/cancers13143513] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2021] [Revised: 07/02/2021] [Accepted: 07/02/2021] [Indexed: 12/11/2022] Open
Abstract
Retroelements are expressed in diverse types of cancer and are related to tumorigenesis and to cancer progression. We characterized the expression of retroelements in cervical cancer and explored their interplay with HPV infection and their association with expression of neighboring genes. Forty biopsies of invasive cervical carcinoma (squamous cell carcinomas and adenocarcinomas) with genotyped HPV were selected and analyzed for human endogenous retrovirus (HERV) and long interspersed nuclear element 1 (L1) expression through RNA-seq data. We found 8060 retroelements expressed in the samples and a negative correlation of DNA methyltransferase 1 expression with the two most expressed L1 elements. A total of 103 retroelements were found differentially expressed between tumor histological types and between HPV types, including several HERV families (HERV-K, HERV-H, HERV-E, HERV-I and HERV-L). The comparison between HPV mono- and co-infections showed the highest proportion of differentially expressed L1 elements. The location of retroelements affected neighboring gene expression, such as shown for the interleukin-20 gene family. Three HERVs and seven L1 were located close to this gene family and two L1 showed a positive association with IL20RB expression. This study describes the expression of retroelements in cervical cancer and shows their association with HPV status and host gene expression.
Collapse
|
39
|
Dräger O, Metz K, Busch M, Dünker N. Role of L1CAM in retinoblastoma tumorigenesis: identification of novel therapeutic targets. Mol Oncol 2021; 16:957-981. [PMID: 34228897 PMCID: PMC8847994 DOI: 10.1002/1878-0261.13054] [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: 03/11/2021] [Revised: 05/11/2021] [Accepted: 07/05/2021] [Indexed: 11/08/2022] Open
Abstract
The study presented focuses on the role of the neuronal cell adhesion molecule L1 cell adhesion molecule (L1CAM) in retinoblastoma (RB), the most common malignant intraocular childhood tumor. L1CAM is differentially expressed in a variety of human cancers and has been suggested as a promising therapeutic target. We likewise observed differential expression patterns for L1CAM in RB cell lines and patient samples. The two proteases involved in ectodomain shedding of L1CAM (L1CAM sheddases: ADAM10 and ADAM17) were likewise differentially expressed in the RB cell lines investigated, and an involvement in L1CAM processing in RB cells could be verified. We also identified ezrin, galectin-3, and fibroblast growth factor basic as L1CAM signaling target genes in RB cells. Lentiviral L1CAM knockdown induced apoptosis and reduced cell viability, proliferation, growth, and colony formation capacity of RB cells, whereas L1CAM-overexpressing RB cells displayed the opposite effects. Chicken chorioallantoic membrane assays revealed that L1CAM depletion decreases the tumorigenic and migration potential of RB cells in vivo. Moreover, L1CAM depletion decreased viability and tumor growth of etoposide-resistant RB cell lines upon etoposide treatment in vitro and in vivo. Thus, L1CAM and its processing sheddases are potential novel targets for future therapeutic RB approaches.
Collapse
Affiliation(s)
- Oliver Dräger
- Institute of Anatomy II, Department of Neuroanatomy, University of Duisburg-Essen, Medical Faculty, Germany
| | - Klaus Metz
- Institute of Pathology, University of Duisburg-Essen, Medical Faculty, Germany
| | - Maike Busch
- Institute of Anatomy II, Department of Neuroanatomy, University of Duisburg-Essen, Medical Faculty, Germany
| | - Nicole Dünker
- Institute of Anatomy II, Department of Neuroanatomy, University of Duisburg-Essen, Medical Faculty, Germany
| |
Collapse
|
40
|
Desse VE, Blanchette CR, Nadour M, Perrat P, Rivollet L, Khandekar A, Bénard CY. Neuronal post-developmentally acting SAX-7S/L1CAM can function as cleaved fragments to maintain neuronal architecture in C. elegans. Genetics 2021; 218:6296841. [PMID: 34115111 DOI: 10.1093/genetics/iyab086] [Citation(s) in RCA: 3] [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: 01/24/2021] [Accepted: 05/24/2021] [Indexed: 01/09/2023] Open
Abstract
Whereas remarkable advances have uncovered mechanisms that drive nervous system assembly, the processes responsible for the lifelong maintenance of nervous system architecture remain poorly understood. Subsequent to its establishment during embryogenesis, neuronal architecture is maintained throughout life in the face of the animal's growth, maturation processes, the addition of new neurons, body movements, and aging. The C. elegans protein SAX-7, homologous to the vertebrate L1 protein family of neural adhesion molecules, is required for maintaining the organization of neuronal ganglia and fascicles after their successful initial embryonic development. To dissect the function of sax-7 in neuronal maintenance, we generated a null allele and sax-7S-isoform-specific alleles. We find that the null sax-7(qv30) is, in some contexts, more severe than previously described mutant alleles, and that the loss of sax-7S largely phenocopies the null, consistent with sax-7S being the key isoform in neuronal maintenance. Using a sfGFP::SAX-7S knock-in, we observe sax-7S to be predominantly expressed across the nervous system, from embryogenesis to adulthood. Yet, its role in maintaining neuronal organization is ensured by post-developmentally acting SAX-7S, as larval transgenic sax-7S(+) expression alone is sufficient to profoundly rescue the null mutants' neuronal maintenance defects. Moreover, the majority of the protein SAX-7 appears to be cleaved, and we show that these cleaved SAX-7S fragments together, not individually, can fully support neuronal maintenance. These findings contribute to our understanding of the role of the conserved protein SAX-7/L1CAM in long-term neuronal maintenance, and may help decipher processes that go awry in some neurodegenerative conditions.
Collapse
Affiliation(s)
- Virginie E Desse
- Department of Biological Sciences, CERMO-FC Research Center, Université du Québec à Montréal, Montréal, QC H2X 1Y4, Canada
| | - Cassandra R Blanchette
- Department of Neurobiology, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - Malika Nadour
- Department of Biological Sciences, CERMO-FC Research Center, Université du Québec à Montréal, Montréal, QC H2X 1Y4, Canada
| | - Paola Perrat
- Department of Neurobiology, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - Lise Rivollet
- Department of Biological Sciences, CERMO-FC Research Center, Université du Québec à Montréal, Montréal, QC H2X 1Y4, Canada
| | - Anagha Khandekar
- Department of Neurobiology, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - Claire Y Bénard
- Department of Biological Sciences, CERMO-FC Research Center, Université du Québec à Montréal, Montréal, QC H2X 1Y4, Canada
- Department of Neurobiology, University of Massachusetts Medical School, Worcester, MA 01605, USA
| |
Collapse
|
41
|
Jiang JC, Rothnagel JA, Upton KR. Widespread Exaptation of L1 Transposons for Transcription Factor Binding in Breast Cancer. Int J Mol Sci 2021; 22:5625. [PMID: 34070697 PMCID: PMC8199441 DOI: 10.3390/ijms22115625] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2021] [Revised: 05/18/2021] [Accepted: 05/20/2021] [Indexed: 12/29/2022] Open
Abstract
L1 transposons occupy 17% of the human genome and are widely exapted for the regulation of human genes, particularly in breast cancer, where we have previously shown abundant cancer-specific transcription factor (TF) binding sites within the L1PA2 subfamily. In the current study, we performed a comprehensive analysis of TF binding activities in primate-specific L1 subfamilies and identified pervasive exaptation events amongst these evolutionarily related L1 transposons. By motif scanning, we predicted diverse and abundant TF binding potentials within the L1 transposons. We confirmed substantial TF binding activities in the L1 subfamilies using TF binding sites consolidated from an extensive collection of publicly available ChIP-seq datasets. Young L1 subfamilies (L1HS, L1PA2 and L1PA3) contributed abundant TF binding sites in MCF7 cells, primarily via their 5' UTR. This is expected as the L1 5' UTR hosts cis-regulatory elements that are crucial for L1 replication and mobilisation. Interestingly, the ancient L1 subfamilies, where 5' truncation was common, displayed comparable TF binding capacity through their 3' ends, suggesting an alternative exaptation mechanism in L1 transposons that was previously unnoticed. Overall, primate-specific L1 transposons were extensively exapted for TF binding in MCF7 breast cancer cells and are likely prominent genetic players modulating breast cancer transcriptional regulation.
Collapse
Affiliation(s)
| | | | - Kyle R. Upton
- School of Chemistry and Molecular Biosciences, The University of Queensland, St. Lucia, QLD 4072, Australia; (J.-C.J.); (J.A.R.)
| |
Collapse
|
42
|
Xi Z, Duan PG, Mummaneni PV, Liu J, Guinn JMV, Wang M, Li B, Wu HH, Rivera J, Burch S, Berven SH, Chou D. Posterior Displacement of L1 May be a Risk Factor for Proximal Junctional Kyphosis After Adult Spinal Deformity Correction. Global Spine J 2021; 13:1042-1048. [PMID: 33998302 DOI: 10.1177/21925682211015651] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [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] [Indexed: 11/16/2022] Open
Abstract
STUDY DESIGN Retrospective cohort study. OBJECTIVE Overcorrection in adult spinal deformity (ASD) surgery may lead to proximal junctional kyphosis (PJK) because of posterior spinal displacement. The aim of this paper is to determine if the L1 position relative to the gravity line (GL) is associated with PJK. METHODS ASD patients fused from the lower thoracic spine to sacrum by 4 spine surgeons at our hospital were retrospectively studied. Lumbar-only and upper thoracic spine fusions were excluded. Spinopelvic parameters, the L1 plumb line (L1PL), L1 distance to the GL (L1-GL), and Roussouly type were measured. RESULTS One hundred fourteen patients met inclusion criteria (63 patients with PJK, 51 without). Mean age and follow up was 65.51 and 3.39 years, respectively. There was no difference between the PJK and the non-PJK groups in baseline demographics, pre-operative and immediate post-operative pelvic incidence-lumbar lordosis mismatch, sagittal vertical axis, or coronal Cobb. The immediate postoperative L1-GL was -7.24 cm in PJK and -3.45 cm in non-PJK (P < 0.001), L1PL was 1.71 cm in PJK and 3.07 cm in non-PJK (P = 0.004), and PT (23.76° vs 18.90°, P = 0.026) and TK (40.56° vs 31.39°, P < 0.001) were larger in PJK than in non-PJK. After univariate and multivariate analyses, immediate postoperative TK and immediate postoperative L1-GL were independent risk factors for PJK without collinearity. CONCLUSIONS A dorsally displaced L1 relative to the GL was associated with an increased risk of PJK after ASD surgery. The postoperative L1-GL distance may be a factor to consider during ASD surgery.
Collapse
Affiliation(s)
- Zhuo Xi
- Department of Neurosurgery, University of California San Francisco, USA.,Department of Neurosurgery, Shengjing Hospital of China Medical University, Liaoning, China
| | - Ping-Guo Duan
- Department of Neurosurgery, University of California San Francisco, USA
| | | | - Jinping Liu
- Department of Neurosurgery, University of California San Francisco, USA
| | - Jeremy M V Guinn
- Department of Neurosurgery, University of California San Francisco, USA
| | - Minghao Wang
- Department of Neurosurgery, University of California San Francisco, USA
| | - Bo Li
- Department of Neurosurgery, University of California San Francisco, USA
| | - Hao-Hua Wu
- Department of Orthopedic Surgery, University of California San Francisco, USA
| | - Joshua Rivera
- Department of Neurosurgery, University of California San Francisco, USA
| | - Shane Burch
- Department of Orthopedic Surgery, University of California San Francisco, USA
| | - Sigurd H Berven
- Department of Orthopedic Surgery, University of California San Francisco, USA
| | - Dean Chou
- Department of Neurosurgery, University of California San Francisco, USA
| |
Collapse
|
43
|
Doyle GA, Reiner BC, Crist RC, Rao AM, Ojeah NS, Arauco-Shapiro G, Levinson RN, Shah LD, Sperling MR, Ferraro TN, Buono RJ, Berrettini WH. Investigation of long interspersed element-1 retrotransposons as potential risk factors for idiopathic temporal lobe epilepsy. Epilepsia 2021; 62:1329-1342. [PMID: 33826137 DOI: 10.1111/epi.16897] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [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: 07/09/2020] [Revised: 03/19/2021] [Accepted: 03/19/2021] [Indexed: 11/29/2022]
Abstract
OBJECTIVE To determine if long interspersed element-1 (L1) retrotransposons convey risk for idiopathic temporal lobe epilepsy (TLE). METHODS Surgically resected temporal cortex from individuals with TLE (N = 33) and postmortem temporal cortex from individuals with no known neurological disease (N = 33) were analyzed for L1 content by Restriction Enzyme Based Enriched L1Hs sequencing (REBELseq). Expression of three KCNIP4 splice variants was assessed by droplet digital PCR (ddPCR). Protein ANalysis THrough Evolutionary Relationships (PANTHER) was used to determine ontologies and pathways for lists of genes harboring L1 insertions. RESULTS We identified novel L1 insertions specific to individuals with TLE, and others specific to controls. Although there were no statistically significant differences between cases and controls in the numbers of known and novel L1 insertions, PANTHER analyses of intragenic L1 insertions showed statistically significant enrichments for epilepsy-relevant gene ontologies in both cases and controls. Gene ontologies "neuron projection development" and "calcium ion transmembrane transport" were among those found only in individuals with TLE. We confirmed novel L1 insertions in several genes associated with seizures/epilepsy, including a de novo somatic L1 retrotransposition in KCNIP4 that occurred after neural crest formation in one patient. However, ddPCR results suggest this de novo L1 did not alter KCNIP4 mRNA expression. SIGNIFICANCE Given current data from this small cohort, we conclude that L1 elements, either rare heritable germline insertions or de novo somatic retrotranspositions, may contribute only minimally to overall genetic risk for idiopathic TLE. We suggest that further studies in additional patients and additional brain regions are warranted.
Collapse
Affiliation(s)
- Glenn A Doyle
- Department of Psychiatry, Center for Neurobiology and Behavior, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Benjamin C Reiner
- Department of Psychiatry, Center for Neurobiology and Behavior, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Richard C Crist
- Department of Psychiatry, Center for Neurobiology and Behavior, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Aditya M Rao
- Department of Psychiatry, Center for Neurobiology and Behavior, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Nkechi S Ojeah
- Department of Psychiatry, Center for Neurobiology and Behavior, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA.,Lincoln University of School of Natural Sciences and Mathematics, Lincoln University, Lincoln, PA, USA
| | - Gabriella Arauco-Shapiro
- Department of Psychiatry, Center for Neurobiology and Behavior, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Rachel N Levinson
- Department of Psychiatry, Center for Neurobiology and Behavior, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Lokesh D Shah
- Department of Psychiatry, Center for Neurobiology and Behavior, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Michael R Sperling
- Department of Neurology, Comprehensive Epilepsy Center, Thomas Jefferson University, Philadelphia, PA, USA
| | - Thomas N Ferraro
- Department of Psychiatry, Center for Neurobiology and Behavior, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA.,Department of Biomedical Sciences, Cooper Medical School of Rowan University, Camden, NJ, USA
| | - Russell J Buono
- Department of Neurology, Comprehensive Epilepsy Center, Thomas Jefferson University, Philadelphia, PA, USA.,Department of Biomedical Sciences, Cooper Medical School of Rowan University, Camden, NJ, USA
| | - Wade H Berrettini
- Department of Psychiatry, Center for Neurobiology and Behavior, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| |
Collapse
|
44
|
Cheriyamundath S, Kumar A, Gavert N, Brabletz T, Ben-Ze’ev A. The Collagen-Modifying Enzyme PLOD2 Is Induced and Required during L1-Mediated Colon Cancer Progression. Int J Mol Sci 2021; 22:3552. [PMID: 33805564 PMCID: PMC8038063 DOI: 10.3390/ijms22073552] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2021] [Revised: 03/22/2021] [Accepted: 03/26/2021] [Indexed: 11/17/2022] Open
Abstract
The overactivation of Wnt/β-catenin signaling is a hallmark of colorectal cancer (CRC) development. We identified the cell adhesion molecule L1CAM (L1) as a target of β-catenin-TCF transactivation in CRC cells. The overexpression of L1 in CRC cells confers enhanced proliferation, motility, tumorigenesis and liver metastasis, and L1 is exclusively localized in the invasive areas of human CRC tissue. A number of genes are induced after L1 transfection into CRC cells by a mechanism involving the cytoskeletal protein ezrin and the NF-κB pathway. When studying the changes in gene expression in CRC cells overexpressing L1 in which ezrin levels were suppressed by shRNA to ezrin, we discovered the collagen-modifying enzyme lysyl hydroxylase 2 (PLOD2) among these genes. We found that increased PLOD2 expression was required for the cellular processes conferred by L1, including enhanced proliferation, motility, tumorigenesis and liver metastasis, since the suppression of endogenous PLOD2 expression, or its enzymatic activity, blocked the enhanced tumorigenic properties conferred by L1. The mechanism involved in increased PLOD2 expression by L1 involves ezrin signaling and PLOD2 that affect the SMAD2/3 pathway. We found that PLOD2 is localized in the colonic crypts in the stem cell compartment of the normal mucosa and is found at increased levels in invasive areas of the tumor and, in some cases, throughout the tumor tissue. The therapeutic strategies to target PLOD2 expression might provide a useful approach for CRC treatment.
Collapse
Affiliation(s)
- Sanith Cheriyamundath
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot 7610001, Israel; (S.C.); (A.K.); (N.G.)
| | - Anmol Kumar
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot 7610001, Israel; (S.C.); (A.K.); (N.G.)
| | - Nancy Gavert
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot 7610001, Israel; (S.C.); (A.K.); (N.G.)
| | - Thomas Brabletz
- Experimental Medicine I, Nikolaus-Feibiger-Center for Molecular Medicine, University of Erlangen-Nuernberg, 91054 Erlangen, Germany;
| | - Avri Ben-Ze’ev
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot 7610001, Israel; (S.C.); (A.K.); (N.G.)
| |
Collapse
|
45
|
Jung J, Lee E, Shim H, Park JH, Eom HS, Lee H. Prediction of clinical outcomes through assessment of sarcopenia and adipopenia using computed tomography in adult patients with acute myeloid leukemia. Int J Hematol 2021; 114:44-52. [PMID: 33694061 DOI: 10.1007/s12185-021-03122-w] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [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: 01/02/2021] [Revised: 03/02/2021] [Accepted: 03/04/2021] [Indexed: 12/20/2022]
Abstract
Sarcopenia and adipopenia have prognostic significance in cancer. Analysis of a single abdominal computed tomography (CT) section at the third lumbar vertebra has been widely adopted for this purpose. The approach using a single section at the first lumbar vertebra level (L1) may extend clinical viability. We evaluated the prognostic value of sarcopenia and adipopenia assessed using a CT section at L1 in acute myeloid leukemia (AML). Data from 96 patients with available imaging were retrospectively reviewed. Patients with sarcopenia (37.5%) had significantly worse overall survival (OS) (median 17.8 months vs. not reached, p = 0.038) and treatment-related mortality (TRM) (22.2% vs. 3.0%, p = 0.0019) than those without. Subcutaneous adipopenia (51.0%) was significantly associated with inferior OS (median 17.9 months vs. not reached, p = 0.0011), progression-free survival (PFS) (median 6.2 months vs. not reached, p = 0.004), and TRM (16.3% vs. 4%, p = 0.024). Visceral adipopenia (30.2%) was associated with poor OS (12.7 vs. 31.7 months, p = 0.0055) and PFS (3.7 vs. 31.7 months, p = 0.003). Multivariable analyses found sarcopenia, subcutaneous adipopenia and visceral adipopenia were significant negative prognostic factors for OS. Sarcopenia and adipopenia assessed using a single CT section at the L1 level are useful in predicting the prognosis of AML.
Collapse
Affiliation(s)
- Jongheon Jung
- Center for Hematologic Malignancy, National Cancer Center, 323 Ilsan-ro, Ilsandong-gu, Goyang, Geyonggi, 410-769, Republic of Korea
| | - Eunyoung Lee
- Center for Hematologic Malignancy, National Cancer Center, 323 Ilsan-ro, Ilsandong-gu, Goyang, Geyonggi, 410-769, Republic of Korea
| | - Hyoeun Shim
- Department of Laboratory Medicine, National Cancer Center, Goyang, Korea
| | - Ju-Hyun Park
- Department of Statistics, Dongguk University, Seoul, Korea
| | - Hyeon-Seok Eom
- Center for Hematologic Malignancy, National Cancer Center, 323 Ilsan-ro, Ilsandong-gu, Goyang, Geyonggi, 410-769, Republic of Korea
| | - Hyewon Lee
- Center for Hematologic Malignancy, National Cancer Center, 323 Ilsan-ro, Ilsandong-gu, Goyang, Geyonggi, 410-769, Republic of Korea.
| |
Collapse
|
46
|
Ukadike KC, Mustelin T. Implications of Endogenous Retroelements in the Etiopathogenesis of Systemic Lupus Erythematosus. J Clin Med 2021; 10:856. [PMID: 33669709 PMCID: PMC7922054 DOI: 10.3390/jcm10040856] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2020] [Revised: 02/09/2021] [Accepted: 02/13/2021] [Indexed: 12/12/2022] Open
Abstract
Systemic lupus erythematosus (SLE) is a heterogeneous autoimmune disease. While its etiology remains elusive, current understanding suggests a multifactorial process with contributions by genetic, immunologic, hormonal, and environmental factors. A hypothesis that combines several of these factors proposes that genomic elements, the L1 retrotransposons, are instrumental in SLE pathogenesis. L1 retroelements are transcriptionally activated in SLE and produce two proteins, ORF1p and ORF2p, which are immunogenic and can drive type I interferon (IFN) production by producing DNA species that activate cytosolic DNA sensors. In addition, these two proteins reside in RNA-rich macromolecular assemblies that also contain well-known SLE autoantigens like Ro60. We surmise that cells expressing L1 will exhibit all the hallmarks of cells infected by a virus, resulting in a cellular and humoral immune response similar to those in chronic viral infections. However, unlike exogenous viruses, L1 retroelements cannot be eliminated from the host genome. Hence, dysregulated L1 will cause a chronic, but perhaps episodic, challenge for the immune system. The clinical and immunological features of SLE can be at least partly explained by this model. Here we review the support for, and the gaps in, this hypothesis of SLE and its potential for new diagnostic, prognostic, and therapeutic options in SLE.
Collapse
Affiliation(s)
| | - Tomas Mustelin
- Division of Rheumatology, Department of Medicine, University of Washington School of Medicine, 750 Republican Street, Seattle, WA 98109, USA;
| |
Collapse
|
47
|
Abstract
AIM The pharmaceutical or drug supply chain is the means through which prescription medicines are manufactured, stocked, and delivered to consumers. How the complexity and fragmentation of this supply chain shape or reshape the decisions and courses of action as well as risk aversions of its actors (stakeholders) is the question we address in reviewing recent literature presented at the 2021 AEA-ASSA economics convention. In doing so, we identify key aspects or dimensions of the supply chain that remain unexplored or under-explored in the empirical literature. APPROACH All original research relevant to the pharmaceutical supply chain were selected from the AEA-ASSA convention panel sessions. Empirical evidence was thematically identified, and the theoretical and practical implications of findings on firm and stakeholder decision-making were analyzed. FINDINGS Stakeholder choices and risks in the action steps or stages of the supply chain are conditioned or framed by variables that are less prominent and seldom documented in the empirical literature. These include firm ownership and marketing, the provider's IT system, pricing and discounts negotiated by pharmacy benefit managers (PBMs), health insurance coverage, employer plan sponsorship, and hassle costs of drug prescribing and monitoring. On the other hand, prominent and well documented policy initiatives, like international reference pricing and renationalization or "decoupling" from global value chains, can have unintended effects on supply chain actors and end-users, including reverse redistribution. The continuing and changing multi-dimensional character of the supply chain adds to its complexity and fragmentation. CONCLUSIONS Organizational, operational, and value-adding measures to overhaul the drug supply chain and make it perform better have been proposed in the surveyed literature and elsewhere. Yet, aspects of the supply chain that bear a direct impact on firm short-term financial success typically assume precedence in evaluations of performance and effectiveness. Whether and to what extent the drug supply chain will change to cope and adapt to the major challenges and upheavals it currently faces are lingering questions.
Collapse
Affiliation(s)
- Roger Lee Mendoza
- College of Business and Economics, California State University-Los Angeles, Los Angeles, CA, USA
| |
Collapse
|
48
|
Hampson IN, Oliver AW, Hampson L. Potential Effects of Human Papillomavirus Type Substitution, Superinfection Exclusion and Latency on the Efficacy of the Current L1 Prophylactic Vaccines. Viruses 2020; 13:v13010022. [PMID: 33374445 PMCID: PMC7823767 DOI: 10.3390/v13010022] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2020] [Revised: 12/22/2020] [Accepted: 12/22/2020] [Indexed: 12/16/2022] Open
Abstract
There are >200 different types of human papilloma virus (HPV) of which >51 infect genital epithelium, with ~14 of these classed as high-risk being more commonly associated with cervical cancer. During development of the disease, high-risk types have an increased tendency to develop a truncated non-replicative life cycle, whereas low-risk, non-cancer-associated HPV types are either asymptomatic or cause benign lesions completing their full replicative life cycle. HPVs can also be present as non-replicative so-called “latent” infections and they can also show superinfection exclusion, where cells with pre-existing infections with one type cannot be infected with a different HPV type. Thus, the HPV repertoire and replication status present in an individual can form a complex dynamic meta-community which changes with respect to both time and exposure to different HPV types. In light of these considerations, it is not clear how current prophylactic HPV vaccines will affect this system and the potential for iatrogenic outcomes is discussed in light of recent outcome data.
Collapse
|
49
|
Cheriyamundath S, Ben-Ze’ev A. Wnt/β-Catenin Target Genes in Colon Cancer Metastasis: The Special Case of L1CAM. Cancers (Basel) 2020; 12:cancers12113444. [PMID: 33228199 PMCID: PMC7699470 DOI: 10.3390/cancers12113444] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [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: 10/05/2020] [Revised: 11/01/2020] [Accepted: 11/17/2020] [Indexed: 12/12/2022] Open
Abstract
Simple Summary The Wnt/β-catenin cell–cell signaling pathway is one of the most basic and highly conserved pathways for intercellular communications regulating key steps during development, differentiation, and cancer. In colorectal cancer (CRC), in particular, aberrant activation of the Wnt/β-catenin pathway is believed to be responsible for perpetuating the disease from the very early stages of cancer development. A large number of downstream target genes of β-catenin-T-cell factor (TCF), including oncogenes, were detected as regulators of CRC development. In this review, we will summarize studies mainly on one such target gene, the L1CAM (L1) cell adhesion receptor, that is selectively induced in invasive and metastatic CRC cells and in regenerating cells of the intestine following injury. We will describe studies on the genes activated when the levels of L1 are increased in CRC cells and their effectiveness in propagating CRC development. These downstream targets of L1-signaling can serve in diagnosis and may provide additional targets for CRC therapy. Abstract Cell adhesion to neighboring cells is a fundamental biological process in multicellular organisms that is required for tissue morphogenesis. A tight coordination between cell–cell adhesion, signaling, and gene expression is a characteristic feature of normal tissues. Changes, and often disruption of this coordination, are common during invasive and metastatic cancer development. The Wnt/β-catenin signaling pathway is an excellent model for studying the role of adhesion-mediated signaling in colorectal cancer (CRC) invasion and metastasis, because β-catenin has a dual role in the cell; it is a major adhesion linker of cadherin transmembrane receptors to the cytoskeleton and, in addition, it is also a key transducer of Wnt signaling to the nucleus, where it acts as a co-transcriptional activator of Wnt target genes. Hyperactivation of Wnt/β-catenin signaling is a common feature in the majority of CRC patients. We found that the neural cell adhesion receptor L1CAM (L1) is a target gene of β-catenin signaling and is induced in carcinoma cells of CRC patients, where it plays an important role in CRC metastasis. In this review, we will discuss studies on β-catenin target genes activated during CRC development (in particular, L1), the signaling pathways affected by L1, and the role of downstream target genes activated by L1 overexpression, especially those that are also part of the intestinal stem cell gene signature. As intestinal stem cells are highly regulated by Wnt signaling and are believed to also play major roles in CRC progression, unravelling the mechanisms underlying the regulation of these genes will shed light on both normal intestinal homeostasis and the development of invasive and metastatic CRC.
Collapse
|
50
|
Biagi M, Lamm D, Meyer K, Vialichka A, Jurkovic M, Patel S, Mendes RE, Bulman ZP, Wenzler E. Activity of Aztreonam in Combination with Avibactam, Clavulanate, Relebactam, and Vaborbactam against Multidrug-Resistant Stenotrophomonas maltophilia. Antimicrob Agents Chemother 2020; 64:e00297-20. [PMID: 32928733 DOI: 10.1128/AAC.00297-20] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2020] [Accepted: 09/04/2020] [Indexed: 12/26/2022] Open
Abstract
The intrinsic L1 metallo- and L2 serine-β-lactamases in Stenotrophomonas maltophilia make it naturally multidrug resistant and difficult to treat. There is a need to identify novel treatment strategies for this pathogen, especially against isolates resistant to first-line agents. Aztreonam in combination with avibactam has demonstrated potential, although data on other aztreonam-β-lactamase inhibitor (BLI) combinations are lacking. Additionally, molecular mechanisms for reduced susceptibility to these combinations have not been explored. The objectives of this study were to evaluate and compare the in vitro activities and to understand the mechanisms of resistance to aztreonam in combination with avibactam, clavulanate, relebactam, and vaborbactam against S. maltophilia A panel of 47 clinical S. maltophilia strains nonsusceptible to levofloxacin and/or trimethoprim-sulfamethoxazole were tested against each aztreonam-BLI combination via broth microdilution, and 6 isolates were then evaluated in time-kill analyses. Three isolates with various aztreonam-BLI MICs were subjected to whole-genome sequencing and quantitative reverse transcriptase PCR. Avibactam restored aztreonam susceptibility in 98% of aztreonam-resistant isolates, compared to 61, 71, and 15% with clavulanate, relebactam, and vaborbactam, respectively. The addition of avibactam to aztreonam resulted in a ≥2-log10-CFU/ml decrease at 24 h versus aztreonam alone against 5/6 isolates compared to 1/6 with clavulanate, 4/6 with relebactam, and 2/6 with vaborbactam. Molecular analyses revealed that decreased susceptibility to aztreonam-avibactam was associated with increased expression of genes encoding L1 and L2, as well as the efflux pump (smeABC). Aztreonam-avibactam is the most promising BLI-combination against multidrug-resistant S. maltophilia Decreased susceptibility may be due to the combination of overexpressed β-lactamases and efflux pumps. Further studies evaluating this combination against S. maltophilia are warranted.
Collapse
|