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Gurwitz D, Shomron N. Artificial intelligence utility for drug development: ChatGPT and beyond. Drug Dev Res 2024; 85:e22121. [PMID: 37815084 DOI: 10.1002/ddr.22121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2023] [Revised: 09/20/2023] [Accepted: 10/02/2023] [Indexed: 10/11/2023]
Affiliation(s)
- David Gurwitz
- Department of Human Molecular Genetics and Biochemistry, Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
- Sagol School of Neuroscience, Tel Aviv, Israel
| | - Noam Shomron
- Sagol School of Neuroscience, Tel Aviv, Israel
- Department of Cell and Developmental Biology, Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
- Edmond J Safra Center for Bioinformatics, Tel Aviv University, Tel Aviv, Israel
- Tel Aviv University Innovation Labs (TILabs), Tel Aviv, Israel
- Djerassi Institute of Oncology, Tel Aviv University, Tel Aviv, Israel
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Monteran L, Ershaid N, Scharff Y, Zoabi Y, Sanalla T, Ding Y, Pavlovsky A, Zait Y, Langer M, Caller T, Eldar-Boock A, Avivi C, Sonnenblick A, Satchi-Fainaro R, Barshack I, Shomron N, Zhang XHF, Erez N. Combining TIGIT blockage with MDSC inhibition hinders breast cancer bone metastasis by activating anti-tumor immunity. Cancer Discov 2024:734997. [PMID: 38427556 DOI: 10.1158/2159-8290.cd-23-0762] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2023] [Revised: 01/17/2024] [Accepted: 02/28/2024] [Indexed: 03/03/2024]
Abstract
Bone is the most common site of breast cancer metastasis. Bone metastasis are incurable and are associated with severe morbidity. Utilizing an immunocompetent mouse model of spontaneous breast cancer bone metastasis, we profiled the immune transcriptome of bone metastatic lesions and peripheral bone marrow at distinct metastatic stages, revealing dynamic changes during the metastatic process. We show that crosstalk between granulocytes and T cells is central to shaping an immunosuppressive microenvironment. Specifically, we identified the PD-1 and TIGIT signaling axes and the pro-inflammatory cytokine IL1b as central players in the interactions between granulocytes and T cells. Targeting these pathways in vivo resulted in attenuated bone metastasis and improved survival, by reactivating anti-tumor immunity. Analysis of patient samples revealed that TIGIT and IL1b are prominent in human bone metastasis. Our findings suggest that co-targeting immunosuppressive granulocytes and dysfunctional T cells may be a promising novel therapeutic strategy to inhibit bone metastasis.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | - Neta Erez
- Tel Aviv University, Tel Aviv, TA, Israel
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3
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Pelgrim TAD, Philipsen A, Young AH, Juruena M, Jimenez E, Vieta E, Jukić M, Van der Eycken E, Heilbronner U, Moldovan R, Kas MJH, Jagesar RR, Nöthen MM, Hoffmann P, Shomron N, Kilarski LL, van Amelsvoort T, Campforts B, van Westrhenen R. A New Intervention for Implementation of Pharmacogenetics in Psychiatry: A Description of the PSY-PGx Clinical Study. Pharmaceuticals (Basel) 2024; 17:151. [PMID: 38399366 PMCID: PMC10892863 DOI: 10.3390/ph17020151] [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: 12/04/2023] [Revised: 01/15/2024] [Accepted: 01/18/2024] [Indexed: 02/25/2024] Open
Abstract
(1) Background Pharmacological treatment for psychiatric disorders has shown to only be effective in about one-third of patients, as it is associated with frequent treatment failure, often because of side effects, and a long process of trial-and-error pharmacotherapy until an effective and tolerable treatment is found. This notion emphasizes the urgency for a personalized medicine approach in psychiatry. (2) Methods This prospective patient- and rater-blinded, randomized, controlled study will investigate the effect of dose-adjustment of antidepressants escitalopram and sertraline or antipsychotics risperidone and aripiprazole according to the latest state-of-the-art international dosing recommendations for CYP2C19 and CYP2D6 metabolizer status in patients with mood, anxiety, and psychotic disorders. A total sample of N = 2500 will be recruited at nine sites in seven countries (expected drop-out rate of 30%). Patients will be randomized to a pharmacogenetic group or a dosing-as-usual group and treated over a 24-week period with four study visits. The primary outcome is personal recovery using the Recovery Assessment Scale as assessed by the patient (RAS-DS), with secondary outcomes including clinical effects (response or symptomatic remission), side effects, general well-being, digital phenotyping, and psychosocial functioning. (3) Conclusions This is, to our knowledge, the first international, multi-center, non-industry-sponsored randomized controlled trial (RCT) that may provide insights into the effectiveness and utility of implementing pharmacogenetic-guided treatment of psychiatric disorders, and as such, results will be incorporated in already available dosing guidelines.
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Affiliation(s)
- Teuntje A. D. Pelgrim
- Department of Psychiatry, Parnassia Psychiatric Institute, 1062HN Amsterdam, The Netherlands
| | - Alexandra Philipsen
- Department of Psychiatry and Psychotherapy, University of Bonn, 53105 Bonn, Germany
| | - Allan H. Young
- Department of Psychological Medicine, Institute of Psychiatry, Psychology and Neuroscience, King’s College London & South London and Maudsley NHS Foundation Trust, Bethlem Royal Hospital, Monks Orchard Road Beckenham, Kent BR3 3BX, UK
| | - Mario Juruena
- Department of Psychological Medicine, Institute of Psychiatry, Psychology and Neuroscience, King’s College London & South London and Maudsley NHS Foundation Trust, Bethlem Royal Hospital, Monks Orchard Road Beckenham, Kent BR3 3BX, UK
| | - Ester Jimenez
- Bipolar and Depressive Disorders Unit, Department of Psychiatry and Psychology, Hospital Clinic & Institute of Neurosciences (UBNeuro), IDIBAPS, CIBERSAM, ISCIII, University of Barcelona, 08036 Catalonia, Spain
| | - Eduard Vieta
- Bipolar and Depressive Disorders Unit, Department of Psychiatry and Psychology, Hospital Clinic & Institute of Neurosciences (UBNeuro), IDIBAPS, CIBERSAM, ISCIII, University of Barcelona, 08036 Catalonia, Spain
| | - Marin Jukić
- Department of Physiology, Faculty of Pharmacy, University of Belgrade, 11000 Belgrade, Serbia
- Department of Physiology & Pharmacology, Karolinska Institute, 171 77 Stockholm, Sweden
| | - Erik Van der Eycken
- Global Alliance of Mental Illness Advocacy Networks-Europe (GAMIAN-Europe), 1050 Brussels, Belgium
| | - Urs Heilbronner
- Institute of Psychiatric Phenomics and Genomics (IPPG), LMU University Hospital, LMU Munich, 80336 Munich, Germany
| | - Ramona Moldovan
- Department of Psychology, Babeş-Bolyai University, 400015 Cluj-Napoca, Romania
- Division of Evolution, Infection and Genomic Sciences, School of Biological Sciences, University of Manchester, Manchester M13 9PT, UK
- Manchester Center for Genomic Medicine, St. Mary’s Hospital, Manchester University NHS Foundation Trust, Manchester M13 9WL, UK
| | - Martien J. H. Kas
- Groningen Institute for Evolutionary Life Sciences, University of Groningen, 9700CC Groningen, The Netherlands
| | - Raj R. Jagesar
- Groningen Institute for Evolutionary Life Sciences, University of Groningen, 9700CC Groningen, The Netherlands
| | - Markus M. Nöthen
- Institute of Human Genetics, University Hospital of Bonn and University of Bonn, 53127 Bonn, Germany
| | - Per Hoffmann
- Institute of Human Genetics, University Hospital of Bonn and University of Bonn, 53127 Bonn, Germany
| | - Noam Shomron
- Faculty of Medicine, Tel Aviv University, Tel Aviv 69978, Israel
| | - Laura L. Kilarski
- Department of Psychiatry and Psychotherapy, University of Bonn, 53105 Bonn, Germany
| | - Thérèse van Amelsvoort
- Department of Psychiatry and Neuropsychology, Maastricht University, 6226NB Maastricht, The Netherlands
| | - Bea Campforts
- Department of Psychiatry and Neuropsychology, Maastricht University, 6226NB Maastricht, The Netherlands
| | | | - Roos van Westrhenen
- Department of Psychiatry, Parnassia Psychiatric Institute, 1062HN Amsterdam, The Netherlands
- Department of Psychological Medicine, Institute of Psychiatry, Psychology and Neuroscience, King’s College London & South London and Maudsley NHS Foundation Trust, Bethlem Royal Hospital, Monks Orchard Road Beckenham, Kent BR3 3BX, UK
- Department of Psychiatry and Neuropsychology, Maastricht University, 6226NB Maastricht, The Netherlands
- St. John’s National Academy of Health Sciences, Bangalore 560034, India
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Tuttnauer A, Atias D, Reznik O, Shomron N, Obolski U. Opioid trends and risk factors for sustained use among children and adolescents in Israel: a retrospective cohort study. Pain 2024:00006396-990000000-00491. [PMID: 38193827 DOI: 10.1097/j.pain.0000000000003153] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2023] [Accepted: 11/17/2023] [Indexed: 01/10/2024]
Abstract
ABSTRACT Despite growing global concern over opioids, little is known about the epidemiology of opioid use in children and adolescents. This retrospective study investigated opioid use trends and identified risk factors associated with sustained opioid use among outpatient children and adolescents in Israel. Electronic health records of 110,955 children and adolescents were used to establish opioid purchase trends in outpatient settings between 2003 and 2021. Of these, data from 2012 to 2021, n = 32,956, were included in a Cox proportional hazards analysis to identify demographic, clinical, and pharmacological risk factors for sustained opioid use. An increase in opioid use was observed, with a notable rise among strong opioids, peripheral areas, and noncancer patients. Prevalence of sustained opioid users was approximately 2.5%. Risk factors with significant adjusted hazard ratios for sustained use included history of frequent doctor visits 1.82 (95% CI [1.50-2.22]) and drug purchases 1.30 (95% CI [1.07-1.58]), malignancy 1.50 (95% CI [1.07-2.09]), history of cardiovascular (1.44 (95% CI [1.04-1.98]) and pain-related conditions 1.34 (95% CI [1.14-1.58]), and different opioid substances (relative to codeine use): tramadol 2.38 (95% CI [1.73-3.27]), oxycodone 4.29 (95% CI [3.00-6.16]), and "other strong opioids" 6.05 (95% CI [3.59-10.2]). Awareness of observed increase in opioid purchases is crucial for doctors and public health practitioners. Additional monitoring and secondary prevention of children and adolescents possessing the identified risk factors should facilitate where appropriate reducing sustained opioid use when it is unnecessary.
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Affiliation(s)
- Aviv Tuttnauer
- Department of Anesthesia, Pain Treatment Service, Schneider Children's Medical Center of Israel, Petach Tikva, Israel
| | - Dor Atias
- School of Public Health, Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Orly Reznik
- School of Public Health, Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
- Data Research Center, Research Authority, Schneider Children's Medical Center of Petach Tikva, Israel, Israel
| | - Noam Shomron
- Faculty of Medicine, Edmond J Safra Center for Bioinformatics, Sagol School of Neurosceince, Djerassi Institute of Oncology, Innovaiton Labs (TILabs), Tel-Aviv University, Tel Aviv, Israel
| | - Uri Obolski
- School of Public Health, Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
- Porter School of the Environment and Earth Sciences, Faculty of Exact Sciences, Tel Aviv University, Tel Aviv, Israel
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5
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Abboud M, Merenbakh-Lamin K, Volkov H, Ben-Neriah S, Ligumsky H, Bronfeld S, Keren-Khadmy N, Giladi M, Shomron N, Wolf I, Rubinek T. Revealing the tumor suppressive sequence within KL1 domain of the hormone Klotho. Oncogene 2024; 43:354-362. [PMID: 38040805 DOI: 10.1038/s41388-023-02904-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2023] [Revised: 11/09/2023] [Accepted: 11/17/2023] [Indexed: 12/03/2023]
Abstract
Klotho, a 1012 amino acid transmembrane protein, is a potent tumor suppressor in different cancer types. Klotho is composed of two internal repeats KL1 and KL2, and the tumor suppressor activity is primarily attributed to the KL1 domain. Despite its significant role in regulating various cancer-related pathways, the precise mechanism underlying its tumor suppressor activity remains unresolved. In this study, we aimed to identify the sequence responsible for the tumor suppressor function of Klotho and gain insights into its mechanism of action. To accomplish this, we generated expression vectors of truncated KL1 at the C and N-terminal regions and evaluated their ability to inhibit the colony formation of several cancer cell lines. Our findings demonstrated that truncated KL1 1-340 (KL340) effectively inhibited colony formation similar to KL1, while truncated KL1 1-320 (KL320) lost this activity. Furthermore, this correlated with the inhibitory effect of KL1 and KL340 on the Wnt/β-catenin pathway, whereas KL320 had no effect. Transcriptomic analysis of MCF-7 cells expressing the constructs revealed enriched pathways associated with tumor suppressor activity in KL1 and KL340. Interestingly, the α-fold predictor tool highlighted distinct differences in the α and β sheets of the TIM barrel fold of the truncated Klotho constructs, adding to our understanding of their structural variations. In summary, this study identified the 340 N-terminal amino acids as the sequence that possesses Klotho's tumor suppressor activity and reveals a critical role in the 320-340 sequence for this function. It also provides a foundation for the development of Klotho-based therapeutic approaches for cancer treatment.
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Affiliation(s)
- Marana Abboud
- The Oncology Division, Tel Aviv Sourasky Medical Center, Tel Aviv, Israel.
- Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel.
| | | | - Hadas Volkov
- Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
- Edmond J. Safra Center for Bioinformatics at Tel-Aviv University, Tel Aviv, Israel
| | - Shira Ben-Neriah
- The Oncology Division, Tel Aviv Sourasky Medical Center, Tel Aviv, Israel
| | - Hagai Ligumsky
- The Oncology Division, Tel Aviv Sourasky Medical Center, Tel Aviv, Israel
| | - Sarai Bronfeld
- The Oncology Division, Tel Aviv Sourasky Medical Center, Tel Aviv, Israel
- Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Noa Keren-Khadmy
- The Oncology Division, Tel Aviv Sourasky Medical Center, Tel Aviv, Israel
| | - Moshe Giladi
- Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
- Internal Medicine Division, Tel Aviv Sourasky Medical Center, Tel Aviv, Israel
| | - Noam Shomron
- Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
- Edmond J. Safra Center for Bioinformatics at Tel-Aviv University, Tel Aviv, Israel
| | - Ido Wolf
- The Oncology Division, Tel Aviv Sourasky Medical Center, Tel Aviv, Israel
- Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Tami Rubinek
- The Oncology Division, Tel Aviv Sourasky Medical Center, Tel Aviv, Israel.
- Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel.
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Peled A, Sarig O, Mohamad J, Eskin-Schwartz M, Vodo D, Bochner R, Malchin N, Isakov O, Shomron N, Fainberg G, Bertolini M, Paus R, Sprecher E. Dominant frontonasal dysplasia with ectodermal defects results from increased activity of ALX4. Am J Med Genet A 2023; 191:2806-2812. [PMID: 37724761 DOI: 10.1002/ajmg.a.63408] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2023] [Revised: 08/18/2023] [Accepted: 09/05/2023] [Indexed: 09/21/2023]
Abstract
Frontonasal dysplasia (FND) refers to a group of rare developmental disorders characterized by abnormal morphology of the craniofacial region. We studied a family manifesting with clinical features typical for FND2 including neurobehavioral abnormalities, hypotrichosis, hypodontia, and facial dysmorphism. Whole-exome sequencing analysis identified a novel heterozygous frameshift insertion in ALX4 (c.985_986insGTGC, p.Pro329Argfs*115), encoding aristaless homeobox 4. This and a previously reported dominant FND2-causing variant are predicted to result in the formation of a similar abnormally elongated protein tail domain. Using a reporter assay, we showed that the elongated ALX4 displays increased activity. ALX4 negatively regulates the Wnt/β-catenin pathway and accordingly, patient keratinocytes showed altered expression of genes associated with the WNT/β-catenin pathway, which in turn may underlie ectodermal manifestations in FND2. In conclusion, dominant FND2 with ectodermal dysplasia results from frameshift variants in ALX4 exerting a gain-of-function effect.
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Affiliation(s)
- Alon Peled
- Division of Dermatology, Tel Aviv Sourasky Medical Center, Tel Aviv, Israel
| | - Ofer Sarig
- Division of Dermatology, Tel Aviv Sourasky Medical Center, Tel Aviv, Israel
| | - Janan Mohamad
- Division of Dermatology, Tel Aviv Sourasky Medical Center, Tel Aviv, Israel
- Department of Human Molecular Genetics and Biochemistry, Tel-Aviv University, Tel Aviv, Israel
| | - Marina Eskin-Schwartz
- Faculty of Health Sciences, Ben Gurion University of the Negev, Be'er Sheva, Israel
- Soroka University Medical Center, Genetic Institute, Be'er Sheva, Israel
| | - Dan Vodo
- Division of Dermatology, Tel Aviv Sourasky Medical Center, Tel Aviv, Israel
| | - Ron Bochner
- Division of Dermatology, Tel Aviv Sourasky Medical Center, Tel Aviv, Israel
| | - Natalya Malchin
- Division of Dermatology, Tel Aviv Sourasky Medical Center, Tel Aviv, Israel
| | - Ofer Isakov
- Rabin Medical Center, Raphael Recanati Genetic Institute, Petach Tikva, Israel
- Clalit Research Institute, Clalit Health Services, Ramat Gan, Israel
- The Ivan and Francesca Berkowitz Family Living Laboratory Collaboration at Harvard Medical School and Clalit Research Institute, Boston, Massachusetts, USA
| | - Noam Shomron
- Department of Human Molecular Genetics and Biochemistry, Tel-Aviv University, Tel Aviv, Israel
| | - Gilad Fainberg
- Department of Ophthalmology, Tel Aviv Sourasky Medical Center, Tel Aviv, Israel
| | - Marta Bertolini
- Department of Dermatology, University of Münster, Münster, Germany
- Monasterium Laboratory, Nano-Bioanalytik Zentrum, Münster, Germany
| | - Ralf Paus
- Monasterium Laboratory, Nano-Bioanalytik Zentrum, Münster, Germany
- Dr Phillip Frost Department of Dermatology & Cutaneous Surgery, University of Miami Miller School of Medicine, Florida, USA
- Centre for Dermatology Research, Institute of Inflammation and Repair, University of Manchester, Manchester, UK
| | - Eli Sprecher
- Division of Dermatology, Tel Aviv Sourasky Medical Center, Tel Aviv, Israel
- Department of Human Molecular Genetics and Biochemistry, Tel-Aviv University, Tel Aviv, Israel
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Shapira G, Volkov H, Fabian I, Mohr DW, Bettinotti M, Shomron N, Avery RK, Arav-Boger R. Genomic Markers Associated with Cytomegalovirus DNAemia in Kidney Transplant Recipients. Viruses 2023; 15:2227. [PMID: 38005904 PMCID: PMC10674338 DOI: 10.3390/v15112227] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2023] [Revised: 10/29/2023] [Accepted: 11/01/2023] [Indexed: 11/26/2023] Open
Abstract
Human cytomegalovirus (CMV) is a major pathogen after solid organ transplantation, leading to high morbidity and mortality. Transplantation from a CMV-seropositive donor to a CMV-seronegative recipient (D+/R-) is associated with high risk of CMV disease. However, that risk is not uniform, suggesting a role for host factors in immune control of CMV. To identify host genetic factors that control CMV DNAemia post transplantation, we performed a whole-exome association study in two cohorts of D+/R- kidney transplant recipients. Quantitative CMV DNA was measured for at least one year following transplantation. Several CMV-protective single-nucleotide polymorphisms (SNPs) were identified in the first cohort (72 patients) but were not reproducible in the second cohort (126 patients). A meta-analysis of both cohorts revealed several SNPs that were significantly associated with protection from CMV DNAemia. The copy number variation of several genes was significantly different between recipients with and without CMV DNAemia. Amongst patients with CMV DNAemia in the second cohort, several variants of interest (p < 5 × 10-5), the most common of which was NLRC5, were associated with peak viral load. We provide new predictive genetic markers for protection of CMV DNAemia. These markers should be validated in larger cohorts.
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Affiliation(s)
- Guy Shapira
- Faculty of Medicine, Tel Aviv University, Tel Aviv 69978, Israel; (G.S.)
- Edmond J. Safra Center for Bioinformatics, Tel Aviv University, Tel Aviv 69978, Israel
| | - Hadas Volkov
- Faculty of Medicine, Tel Aviv University, Tel Aviv 69978, Israel; (G.S.)
- Edmond J. Safra Center for Bioinformatics, Tel Aviv University, Tel Aviv 69978, Israel
| | - Itai Fabian
- Faculty of Medicine, Tel Aviv University, Tel Aviv 69978, Israel; (G.S.)
| | - David W. Mohr
- Johns Hopkins Genetic Resources Core Facility, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
| | - Maria Bettinotti
- Immunogenetics Laboratory, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA;
| | - Noam Shomron
- Faculty of Medicine, Tel Aviv University, Tel Aviv 69978, Israel; (G.S.)
- Edmond J. Safra Center for Bioinformatics, Tel Aviv University, Tel Aviv 69978, Israel
| | - Robin K. Avery
- Department of Medicine, Division of Infectious Diseases, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA;
| | - Ravit Arav-Boger
- Department of Pediatrics, Division of Infectious Diseases, Medical College of Wisconsin, Milwaukee, WI 53226, USA
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Farberov L, Weissglas-Volkov D, Shapira G, Zoabi Y, Schiff C, Kloeckener-Gruissem B, Neidhardt J, Shomron N. mRNA splicing is modulated by intronic microRNAs. iScience 2023; 26:107723. [PMID: 37692287 PMCID: PMC10492213 DOI: 10.1016/j.isci.2023.107723] [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: 09/15/2022] [Revised: 08/06/2023] [Accepted: 08/22/2023] [Indexed: 09/12/2023] Open
Abstract
Splicing of transcripts is catalyzed by the spliceosome, a mega-complex consisting of hundreds of proteins and five snRNAs, which employs direct interactions. When U1 snRNA forms high-affinity binding, namely more than eight base pairs, with the 5'SS, the result is usually a suppressing effect on the splicing activity. This likely occurs due to the inefficient unwinding of U1/5'SS base-pairing or other regulatory obstructions. Here, we show in vitro and in patient-derived cell lines that pre-microRNAs can modulate the splicing reaction by interacting with U1 snRNA. This leads to reduced binding affinity to the 5'SS, and hence promotes the inclusion of exons containing 5'SS, despite sequence-based high affinity to U1. Application of the mechanism resulted in correction of the splicing defect in the disease-causing VCAN gene from an individual with Wagner syndrome. This pre-miRNA/U1 interaction can regulate the expression of alternatively spliced exons, thus extending the scope of mechanisms regulating splicing.
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Affiliation(s)
- Luba Farberov
- Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Daphna Weissglas-Volkov
- Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
- Edmond J. Safra Center for Bioinformatics, Tel Aviv University, Tel Aviv, Israel
| | - Guy Shapira
- Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
- Edmond J. Safra Center for Bioinformatics, Tel Aviv University, Tel Aviv, Israel
| | - Yazeed Zoabi
- Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
- Edmond J. Safra Center for Bioinformatics, Tel Aviv University, Tel Aviv, Israel
| | - Chen Schiff
- Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Barbara Kloeckener-Gruissem
- Institute of Medical Molecular Genetics, University of Zurich, Zurich, Switzerland
- Department of Biology, ETHZ, Zurich, Switzerland
| | - John Neidhardt
- Human Genetics, Faculty of Medicine and Health Sciences, University of Oldenburg, Germany
- Research Center Neurosensory Science, University Oldenburg, Germany
| | - Noam Shomron
- Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
- Edmond J. Safra Center for Bioinformatics, Tel Aviv University, Tel Aviv, Israel
- Sagol School of Neuroscience, Tel Aviv University, Tel Aviv, Israel
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Gozes I, Shapira G, Lobyntseva A, Shomron N. Unexpected gender differences in progressive supranuclear palsy reveal efficacy for davunetide in women. Transl Psychiatry 2023; 13:319. [PMID: 37845254 PMCID: PMC10579238 DOI: 10.1038/s41398-023-02618-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/09/2023] [Revised: 09/28/2023] [Accepted: 10/03/2023] [Indexed: 10/18/2023] Open
Abstract
Progressive supranuclear palsy (PSP) is a pure tauopathy, implicating davunetide, enhancing Tau-microtubule interaction, as an ideal drug candidate. However, pooling patient data irrespective of sex concluded no efficacy. Here, analyzing sex-dependency in a 52 week-long- PSP clinical trial (involving over 200 patients) demonstrated clear baseline differences in brain ventricular volumes, a secondary endpoint. Dramatic baseline ventricular volume-dependent/volume increase correlations were observed in 52-week-placebo-treated females (r = 0.74, P = 2.36-9), whereas davunetide-treated females (like males) revealed no such effects. Assessment of primary endpoints, by the PSP Rating Scale (PSPRS) and markedly more so by the Schwab and England Activities of Daily Living (SEADL) scale, showed significantly faster deterioration in females, starting at trial week 13 (P = 0.01, and correlating with most other endpoints by week 52). Twice daily davunetide treatments slowed female disease progression and revealed significant protection according to the SEADL scale as early as at 39 weeks (P = 0.008), as well as protection of the bulbar and limb motor domains considered by the PSPRS, including speaking and swallowing difficulties caused by brain damage, and deterioration of fine motor skills, respectably (P = 0.01), at 52 weeks. Furthermore, at 52 weeks of trial, the exploratory Geriatric Depression Scale (GDS) significantly correlated with the SEADL scale deterioration in the female placebo group and demonstrated davunetide-mediated protection of females. Female-specific davunetide-mediated protection of ventricular volume corresponded to clinical efficacy. Together with the significantly slower disease progression seen in men, the results reveal sex-based drug efficacy differences, demonstrating the neuroprotective and disease-modifying impact of davunetide treatment for female PSP patients.
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Affiliation(s)
- Illana Gozes
- Elton Laboratory for Molecular Neuroendocrinology, Department of Human Molecular Genetics and Biochemistry, Faculty of Medicine, Adams Super Center for Brain Studies and Sagol School of Neuroscience, Tel Aviv University, 69978, Tel Aviv, Israel.
| | - Guy Shapira
- Department of Cell and Developmental Biology, Faculty of Medicine, Sagol School of Neuroscience, Edmond J Safra Center for Bioinformatics, Tel Aviv University, 69978, Tel Aviv, Israel
| | - Alexandra Lobyntseva
- Elton Laboratory for Molecular Neuroendocrinology, Department of Human Molecular Genetics and Biochemistry, Faculty of Medicine, Adams Super Center for Brain Studies and Sagol School of Neuroscience, Tel Aviv University, 69978, Tel Aviv, Israel
| | - Noam Shomron
- Department of Cell and Developmental Biology, Faculty of Medicine, Sagol School of Neuroscience, Edmond J Safra Center for Bioinformatics, Tel Aviv University, 69978, Tel Aviv, Israel
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Israel-Elgali I, Pan H, Oved K, Pillar N, Levy G, Barak B, Carneiro A, Gurwitz D, Shomron N. Impaired myelin ultrastructure is reversed by citalopram treatment in a mouse model for major depressive disorder. J Psychiatr Res 2023; 166:100-114. [PMID: 37757703 DOI: 10.1016/j.jpsychires.2023.09.012] [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: 05/29/2023] [Revised: 07/24/2023] [Accepted: 09/15/2023] [Indexed: 09/29/2023]
Abstract
Major depressive disorder (MDD) is the most common and widespread mental disorder. Selective serotonin reuptake inhibitors (SSRIs) are the first-line treatment for MDD. The relation between the inhibition of serotonin reuptake in the central nervous system and remission from MDD remains controversial, as reuptake inhibition occurs rapidly, but remission from MDD takes weeks to months. Myelination-related deficits and white matter abnormalities were shown to be involved in psychiatric disorders such as MDD. This may explain the delay in remission following SSRI administration. The raphe nuclei (RN), located in the brain stem, consist of clusters of serotonergic (5-HT) neurons that project to almost all regions of the brain. Thus, the RN are an intriguing area for research of the potential effect of SSRI on myelination, and their involvement in MDD. MicroRNAs (miRNAs) regulate many biological features that might be altered by antidepressants. Two cohorts of chronic unpredictable stress (CUS) mouse model for depression underwent behavioral tests for evaluating stress, anxiety, and depression levels. Following application of the CUS protocol and treatment with the SSRI, citalopram, 48 mice of the second cohort were tested via magnetic resonance imaging and diffusion tensor imaging for differences in brain white matter tracts. RN and superior colliculus were excised from both cohorts and measured for changes in miRNAs, mRNA, and protein levels of candidate genes. Using MRI-DTI scans we found lower fractional anisotropy and axial diffusivity in brains of stressed mice. Moreover, both miR-30b-5p and miR-101a-3p were found to be downregulated in the RN following CUS, and upregulated following CUS and citalopram treatment. The direct binding of these miRNAs to Qki, and the subsequent effects on mRNA and protein levels of myelin basic protein (Mbp), indicated involvement of these miRNAs in myelination ultrastructure processes in the RN, in response to CUS followed by SSRI treatment. We suggest that SSRIs are implicated in repairing myelin deficits resulting from chronic stress that leads to depression.
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Affiliation(s)
- Ifat Israel-Elgali
- Sagol School of Neuroscience, Tel-Aviv University, Tel Aviv, Israel; Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Hope Pan
- Department of Pharmacology, Center for Molecular Neuroscience, Vanderbilt University School of Medicine, Nashville, TN, USA
| | - Keren Oved
- Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Nir Pillar
- Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Gilad Levy
- Sagol School of Neuroscience, Tel-Aviv University, Tel Aviv, Israel
| | - Boaz Barak
- Sagol School of Neuroscience, Tel-Aviv University, Tel Aviv, Israel; Faculty of Social Sciences, School of Psychological Sciences, Tel Aviv University, Tel Aviv, Israel
| | - Ana Carneiro
- Department of Pharmacology, Center for Molecular Neuroscience, Vanderbilt University School of Medicine, Nashville, TN, USA
| | - David Gurwitz
- Sagol School of Neuroscience, Tel-Aviv University, Tel Aviv, Israel; Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel.
| | - Noam Shomron
- Sagol School of Neuroscience, Tel-Aviv University, Tel Aviv, Israel; Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel; Edmond J Safra Center for Bioinformatics, Tel Aviv University, Tel Aviv, Israel; Tel Aviv University Innovation Laboratories (TILabs), Tel Aviv, Israel.
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11
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Leichner GS, Schweitzer I, Dror S, Levin L, Geva P, Golan T, Zaremba L, Shapira G, Parikh R, Shomron N, Barzilai A, Hoheisel JD, Levy C, Greenberger S. Primary Melanoma miRNA Trafficking Induces Lymphangiogenesis. J Invest Dermatol 2023; 143:1788-1798.e7. [PMID: 36934839 DOI: 10.1016/j.jid.2023.02.030] [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] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2022] [Revised: 01/29/2023] [Accepted: 02/12/2023] [Indexed: 03/19/2023]
Abstract
Melanoma, the deadliest cutaneous tumor, initiates within the epidermis; during progression, cells invade into the dermis and become metastatic through the lymphatic and blood system. Before melanoma cell invasion into the dermis, an increased density of dermal lymphatic vessels is observed, generated by a mechanism which is not fully understood. In this study, we show that, while at the primary epidermal stage (in situ), melanoma cells secrete extracellular vesicles termed melanosomes, which are uptaken by dermal lymphatic cells, leading to transcriptional and phenotypic pro-lymphangiogenic changes. Mechanistically, melanoma-derived melanosomes traffic mature let-7i to lymphatic endothelial cells, which mediate pro-lymphangiogenic phenotypic changes by the induction of type I IFN signaling. Furthermore, transcriptome analysis upon treatment with melanosomes or let-7i reveals the enhancement of IFI6 expression in lymphatic cells. Because melanoma cells metastasize primarily via lymphatic vessels, our data suggest that blocking lymphangiogenesis by repressing either melanosome release or type I IFN signaling will prevent melanoma progression to the deadly metastatic stage.
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Affiliation(s)
- Gil S Leichner
- Department of Dermatology, Sheba Medical Center, Ramat Gan, Israel
| | - Inbal Schweitzer
- Department of Dermatology, Sheba Medical Center, Ramat Gan, Israel
| | - Shani Dror
- Department of Human Genetics and Biochemistry, Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Lotan Levin
- Department of Dermatology, Sheba Medical Center, Ramat Gan, Israel
| | - Polina Geva
- Department of Dermatology, Sheba Medical Center, Ramat Gan, Israel
| | - Tamar Golan
- Department of Human Genetics and Biochemistry, Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Laureen Zaremba
- Functional Genome Analysis, Deutsches Krebsforschungszentrum, Heidelberg, Germany
| | - Guy Shapira
- Department of Cell and Development Biology, Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Roma Parikh
- Department of Human Genetics and Biochemistry, Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Noam Shomron
- Department of Cell and Development Biology, Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Aviv Barzilai
- Department of Dermatology, Sheba Medical Center, Ramat Gan, Israel; Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Jörg D Hoheisel
- Functional Genome Analysis, Deutsches Krebsforschungszentrum, Heidelberg, Germany
| | - Carmit Levy
- Department of Human Genetics and Biochemistry, Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Shoshana Greenberger
- Department of Dermatology, Sheba Medical Center, Ramat Gan, Israel; Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel.
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12
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Cohen T, Shomron N. Can RNA Affect Memory Modulation? Implications for PTSD Understanding and Treatment. Int J Mol Sci 2023; 24:12908. [PMID: 37629089 PMCID: PMC10454422 DOI: 10.3390/ijms241612908] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2023] [Revised: 08/13/2023] [Accepted: 08/16/2023] [Indexed: 08/27/2023] Open
Abstract
Memories are a central aspect of our lives, but the mechanisms underlying their formation, consolidation, retrieval, and extinction remain poorly understood. In this review, we explore the molecular mechanisms of memory modulation and investigate the effects of RNA on these processes. Specifically, we examine the effects of time and location on gene expression alterations. We then discuss the potential for harnessing these alterations to modulate memories, particularly fear memories, to alleviate post-traumatic stress disorder (PTSD) symptoms. The current state of research suggests that transcriptional changes play a major role in memory modulation and targeting them through microRNAs may hold promise as a novel approach for treating memory-related disorders such as PTSD.
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Affiliation(s)
- Tehila Cohen
- Faculty of Medicine, Tel Aviv University, Tel Aviv 6997801, Israel
| | - Noam Shomron
- Faculty of Medicine, Tel Aviv University, Tel Aviv 6997801, Israel
- Edmond J Safra Center for Bioinformatics, Tel Aviv University, Tel Aviv 6997801, Israel
- Sagol School of Neuroscience, Tel Aviv University, Tel Aviv 6997801, Israel
- Tel Aviv University Innovation Labs (TILabs), Tel Aviv 6997801, Israel
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13
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Shapira G, Israel-Elgali I, Grad M, Avnat E, Rachmany L, Sarne Y, Shomron N. Hippocampal differential expression underlying the neuroprotective effect of delta-9-tetrahydrocannabinol microdose on old mice. Front Neurosci 2023; 17:1182932. [PMID: 37534036 PMCID: PMC10393280 DOI: 10.3389/fnins.2023.1182932] [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: 03/12/2023] [Accepted: 06/14/2023] [Indexed: 08/04/2023] Open
Abstract
Delta-9-tetrahydrocannabinol (THC) is the primary psychoactive compound of the cannabis plant and an exogenous ligand of the endocannabinoid system. In previous studies, we demonstrated that a single microdose of THC (0.002 mg/kg, 3-4 orders of magnitude lower than the standard dose for rodents) exerts distinct, long-term neuroprotection in model mice subjected to acute neurological insults. When administered to old, healthy mice, the THC microdose induced remarkable long-lasting (weeks) improvement in a wide range of cognitive functions, including significant morphological and biochemical brain alterations. To elucidate the mechanisms underlying these effects, we analyzed the gene expression of hippocampal samples from the model mice. Samples taken 5 days after THC treatment showed significant differential expression of genes associated with neurogenesis and brain development. In samples taken 5 weeks after treatment, the transcriptional signature was shifted to that of neuronal differentiation and survival. This study demonstrated the use of hippocampal transcriptome profiling in uncovering the molecular basis of the atypical, anti-aging effects of THC microdose treatment in old mice.
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Affiliation(s)
- Guy Shapira
- Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
- Edmond J Safra Center for Bioinformatics, Tel Aviv University, Tel Aviv, Israel
| | - Ifat Israel-Elgali
- Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
- Sagol School of Neuroscience, Tel-Aviv University, Tel Aviv, Israel
| | - Meitar Grad
- Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Eden Avnat
- Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Lital Rachmany
- Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Yosef Sarne
- Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Noam Shomron
- Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
- Edmond J Safra Center for Bioinformatics, Tel Aviv University, Tel Aviv, Israel
- Sagol School of Neuroscience, Tel-Aviv University, Tel Aviv, Israel
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14
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Markovits E, Harush O, Baruch EN, Shulman ED, Debby A, Itzhaki O, Anafi L, Danilevsky A, Shomron N, Ben-Betzalel G, Asher N, Shapira-Frommer R, Schachter J, Barshack I, Geiger T, Elkon R, Besser MJ, Markel G. MYC Induces Immunotherapy and IFNγ Resistance Through Downregulation of JAK2. Cancer Immunol Res 2023; 11:909-924. [PMID: 37074069 DOI: 10.1158/2326-6066.cir-22-0184] [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] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2022] [Revised: 11/27/2022] [Accepted: 04/17/2023] [Indexed: 04/20/2023]
Abstract
Immunotherapy has revolutionized the treatment of advanced melanoma. Because the pathways mediating resistance to immunotherapy are largely unknown, we conducted transcriptome profiling of preimmunotherapy tumor biopsies from patients with melanoma that received PD-1 blockade or adoptive cell therapy with tumor-infiltrating lymphocytes. We identified two melanoma-intrinsic, mutually exclusive gene programs, which were controlled by IFNγ and MYC, and the association with immunotherapy outcome. MYC-overexpressing melanoma cells exhibited lower IFNγ responsiveness, which was linked with JAK2 downregulation. Luciferase activity assays, under the control of JAK2 promoter, demonstrated reduced activity in MYC-overexpressing cells, which was partly reversible upon mutagenesis of a MYC E-box binding site in the JAK2 promoter. Moreover, silencing of MYC or its cofactor MAX with siRNA increased JAK2 expression and IFNγ responsiveness of melanomas, while concomitantly enhancing the effector functions of T cells coincubated with MYC-overexpressing cells. Thus, we propose that MYC plays a pivotal role in immunotherapy resistance through downregulation of JAK2.
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Affiliation(s)
- Ettai Markovits
- Ella Lemelbaum Institute for Immuno-oncology, Sheba Medical Center, Tel Hashomer, Israel
- Department of Clinical Microbiology and Immunology, The Sackler School of Medicine, Tel Aviv University, Tel-Aviv, Israel
| | - Ortal Harush
- Ella Lemelbaum Institute for Immuno-oncology, Sheba Medical Center, Tel Hashomer, Israel
- Department of Clinical Microbiology and Immunology, The Sackler School of Medicine, Tel Aviv University, Tel-Aviv, Israel
| | - Erez N Baruch
- Ella Lemelbaum Institute for Immuno-oncology, Sheba Medical Center, Tel Hashomer, Israel
- Department of Clinical Microbiology and Immunology, The Sackler School of Medicine, Tel Aviv University, Tel-Aviv, Israel
| | - Eldad D Shulman
- Department of Human Molecular Genetics and Biochemistry, The Sackler School of Medicine, Tel Aviv University, Tel-Aviv, Israel
| | - Assaf Debby
- Institute of Pathology, Sheba Medical Center, Tel Hashomer, Israel
- Department of Dermatology, Sheba Medical Center, Tel Hashomer, Israel
| | - Orit Itzhaki
- Ella Lemelbaum Institute for Immuno-oncology, Sheba Medical Center, Tel Hashomer, Israel
| | - Liat Anafi
- Institute of Pathology, Sheba Medical Center, Tel Hashomer, Israel
| | - Artem Danilevsky
- Sackler School of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Noam Shomron
- Sackler School of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Guy Ben-Betzalel
- Ella Lemelbaum Institute for Immuno-oncology, Sheba Medical Center, Tel Hashomer, Israel
| | - Nethanel Asher
- Ella Lemelbaum Institute for Immuno-oncology, Sheba Medical Center, Tel Hashomer, Israel
| | - Ronnie Shapira-Frommer
- Ella Lemelbaum Institute for Immuno-oncology, Sheba Medical Center, Tel Hashomer, Israel
| | - Jacob Schachter
- Ella Lemelbaum Institute for Immuno-oncology, Sheba Medical Center, Tel Hashomer, Israel
- Sackler School of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Iris Barshack
- Institute of Pathology, Sheba Medical Center, Tel Hashomer, Israel
- Sackler School of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Tamar Geiger
- Department of Human Molecular Genetics and Biochemistry, The Sackler School of Medicine, Tel Aviv University, Tel-Aviv, Israel
| | - Ran Elkon
- Department of Human Molecular Genetics and Biochemistry, The Sackler School of Medicine, Tel Aviv University, Tel-Aviv, Israel
| | - Michal J Besser
- Ella Lemelbaum Institute for Immuno-oncology, Sheba Medical Center, Tel Hashomer, Israel
- Department of Clinical Microbiology and Immunology, The Sackler School of Medicine, Tel Aviv University, Tel-Aviv, Israel
- Davidoff Cancer Center, Rabin Medical Center-Beilinson Hospital, Petah Tikva, Israel
- Felsenstein Medical Research Center, Rabin Medical Center-Beilinson Hospital, Petah Tikva, Israel
| | - Gal Markel
- Department of Clinical Microbiology and Immunology, The Sackler School of Medicine, Tel Aviv University, Tel-Aviv, Israel
- Davidoff Cancer Center, Rabin Medical Center-Beilinson Hospital, Petah Tikva, Israel
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15
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Sachs N, Wechsberg O, Landau YE, Krause I, Israel Elgali I, Darawshe M, Shomron N, Lidzbarsky G, Orenstein N. A novel SLC25A13 gene splice site variant causes Citrin deficiency in an infant. Gene 2023; 874:147483. [PMID: 37196891 DOI: 10.1016/j.gene.2023.147483] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2023] [Revised: 05/01/2023] [Accepted: 05/09/2023] [Indexed: 05/19/2023]
Abstract
Citrin deficiency is an autosomal recessive disorder associated with SLC25A13 gene pathogenic variants, with more than a hundred known at present. It manifests in neonates as failure to thrive and acute liver insufficiency. We herein describe a case of a 4-week-old infant who presented with insufficient weight gain and liver failure accompanied by hyperammonemia. She was diagnosed with Citrin deficiency after a thorough biochemical and molecular analysis including amino acid profile, DNA sequencing of genes of interest and RNA splice site evaluation, to reveal a yet unknown damaging variant of the SLC25A13 gene.
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Affiliation(s)
- Nimrod Sachs
- Department of Pediatrics C, Schneider Children's Medical Center of Israel, Petah Tikva, Israel; Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel.
| | - Oded Wechsberg
- Pediatric Genetics Unit, Schneider Children's Medical Center of Israel, Petah Tikva, Israel; Maccabi Healthcare Services, Tel Aviv, Israel
| | - Yuval E Landau
- Metabolic Disease Service, Schneider Children's Medical Center of Israel, Petah Tikva, Israel; Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Irit Krause
- Department of Pediatrics C, Schneider Children's Medical Center of Israel, Petah Tikva, Israel; Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Ifat Israel Elgali
- Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel; Sagol School of Neuroscience, Tel Aviv University, Tel Aviv, Israel
| | - Malak Darawshe
- Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Noam Shomron
- Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Gabriel Lidzbarsky
- The Raphael Recanati Genetic institute, Rabin Medical Center, Beilinson hospital, Petah Tikva, Israel
| | - Naama Orenstein
- Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel; Pediatric Genetics Unit, Schneider Children's Medical Center of Israel, Petah Tikva, Israel
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16
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Ofek P, Yeini E, Arad G, Danilevsky A, Pozzi S, Luna CB, Dangoor SI, Grossman R, Ram Z, Shomron N, Brem H, Hyde TM, Geiger T, Satchi-Fainaro R. Deoxyhypusine hydroxylase: A novel therapeutic target differentially expressed in short-term vs long-term survivors of glioblastoma. Int J Cancer 2023. [PMID: 37141410 DOI: 10.1002/ijc.34545] [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: 09/27/2022] [Revised: 02/13/2023] [Accepted: 03/10/2023] [Indexed: 05/06/2023]
Abstract
Glioblastoma (GB) is the most aggressive neoplasm of the brain. Poor prognosis is mainly attributed to tumor heterogeneity, invasiveness and drug resistance. Only a small fraction of GB patients survives longer than 24 months from the time of diagnosis (ie, long-term survivors [LTS]). In our study, we aimed to identify molecular markers associated with favorable GB prognosis as a basis to develop therapeutic applications to improve patients' outcome. We have recently assembled a proteogenomic dataset of 87 GB clinical samples of varying survival rates. Following RNA-seq and mass spectrometry (MS)-based proteomics analysis, we identified several differentially expressed genes and proteins, including some known cancer-related pathways and some less established that showed higher expression in short-term (<6 months) survivors (STS) compared to LTS. One such target found was deoxyhypusine hydroxylase (DOHH), which is known to be involved in the biosynthesis of hypusine, an unusual amino acid essential for the function of the eukaryotic translation initiation factor 5A (eIF5A), which promotes tumor growth. We consequently validated DOHH overexpression in STS samples by quantitative polymerase chain reaction (qPCR) and immunohistochemistry. We further showed robust inhibition of proliferation, migration and invasion of GB cells following silencing of DOHH with short hairpin RNA (shRNA) or inhibition of its activity with small molecules, ciclopirox and deferiprone. Moreover, DOHH silencing led to significant inhibition of tumor progression and prolonged survival in GB mouse models. Searching for a potential mechanism by which DOHH promotes tumor aggressiveness, we found that it supports the transition of GB cells to a more invasive phenotype via epithelial-mesenchymal transition (EMT)-related pathways.
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Affiliation(s)
- Paula Ofek
- Department of Physiology and Pharmacology, Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Eilam Yeini
- Department of Physiology and Pharmacology, Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Gali Arad
- Department of Molecular Genetics, Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Artem Danilevsky
- Department of Cell and Developmental Biology, Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
- Edmond J Safra Center for Bioinformatics, Tel Aviv University, Tel Aviv, Israel
| | - Sabina Pozzi
- Department of Physiology and Pharmacology, Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Christian Burgos Luna
- Department of Physiology and Pharmacology, Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Sahar Israeli Dangoor
- Department of Physiology and Pharmacology, Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Rachel Grossman
- Department of Neurosurgery, Tel Aviv Sourasky Medical Center, Tel Aviv, Israel
| | - Zvi Ram
- Department of Neurosurgery, Tel Aviv Sourasky Medical Center, Tel Aviv, Israel
| | - Noam Shomron
- Department of Cell and Developmental Biology, Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
- Edmond J Safra Center for Bioinformatics, Tel Aviv University, Tel Aviv, Israel
- Sagol School of Neurosciences, Tel Aviv University, Tel Aviv, Israel
| | - Henry Brem
- Department of Neurosurgery, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Thomas M Hyde
- Lieber Institute for Brain Development, Johns Hopkins Medical Campus, Baltimore, Maryland, USA
- Department of Psychiatry & Behavioral Science, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
- Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Tamar Geiger
- Department of Molecular Genetics, Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Ronit Satchi-Fainaro
- Department of Physiology and Pharmacology, Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
- Sagol School of Neurosciences, Tel Aviv University, Tel Aviv, Israel
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17
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Avnat E, Shapira G, Shoval S, Israel-Elgali I, Alkelai A, Shuldiner AR, Gonzaga-Jauregui C, Zidan J, Maray T, Shomron N, Friedman E. Comprehensive Genetic Analysis of Druze Provides Insights into Carrier Screening. Genes (Basel) 2023; 14:genes14040937. [PMID: 37107695 PMCID: PMC10137689 DOI: 10.3390/genes14040937] [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: 02/18/2023] [Revised: 03/24/2023] [Accepted: 04/14/2023] [Indexed: 04/29/2023] Open
Abstract
BACKGROUND Druze individuals, like many genetically homogeneous and isolated populations, harbor recurring pathogenic variants (PV) in autosomal recessive (AR) disorders. METHODS Variant calling of whole-genome sequencing (WGS) of 40 Druze from the Human Genome Diversity Project (HGDP) was performed (HGDP-cohort). Additionally, we performed whole exome sequencing (WES) of 118 Druze individuals: 38 trios and 2 couples, representing geographically distinct clans (WES-cohort). Rates of validated PV were compared with rates in worldwide and Middle Eastern populations, from the gnomAD and dbSNP datasets. RESULTS Overall, 34 PVs were identified: 30 PVs in genes underlying AR disorders, 3 additional PVs were associated with autosomal dominant (AD) disorders, and 1 PV with X-linked-dominant inherited disorder in the WES cohort. CONCLUSIONS The newly identified PVs associated with AR conditions should be considered for incorporation into prenatal-screening options offered to Druze individuals after an extension and validation of the results in a larger study.
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Affiliation(s)
- Eden Avnat
- Faculty of Medicine, Tel Aviv University, Tel Aviv 69978, Israel
| | - Guy Shapira
- Faculty of Medicine, Tel Aviv University, Tel Aviv 69978, Israel
- Edmond J. Safra Center for Bioinformatics, Tel Aviv University, Tel Aviv 69978, Israel
| | - Shelly Shoval
- The Susanne Levy Gertner Oncogenetics Unit, Institute of Human Genetics, Sheba Medical Center, Ramat Gan 52621, Israel
| | - Ifat Israel-Elgali
- Faculty of Medicine, Tel Aviv University, Tel Aviv 69978, Israel
- Sagol School of Neuroscience, Tel-Aviv University, Tel Aviv 69978, Israel
| | - Anna Alkelai
- Regeneron Genetics Center, Tarrytown, NY 10591, USA
| | | | - Claudia Gonzaga-Jauregui
- Regeneron Genetics Center, Tarrytown, NY 10591, USA
- International Laboratory for Human Genome Research, Laboratorio Internacional de Investigación sobre el Genoma Humano, Universidad Nacional Autónoma de México, Juriquilla 04510, Querétaro, Mexico
| | - Jamal Zidan
- The Oncology Department, Ziv Medical Center, and the Azrieli Faculty of Medicine, Bar-Ilan University, Zefat 13206, Israel
| | - Taiseer Maray
- Golan for Development, Majdal Shams 1243800, Golan Heights
| | - Noam Shomron
- Faculty of Medicine, Tel Aviv University, Tel Aviv 69978, Israel
- Edmond J. Safra Center for Bioinformatics, Tel Aviv University, Tel Aviv 69978, Israel
- Sagol School of Neuroscience, Tel-Aviv University, Tel Aviv 69978, Israel
| | - Eitan Friedman
- Faculty of Medicine, Tel Aviv University, Tel Aviv 69978, Israel
- The Meirav High Risk Clinic, Chaim Sheba Medical Center, Tel-Hashomer, Ramat Gan 52621, Israel
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18
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Shapira G, Patalon T, Gazit S, Shomron N. Immunosuppression as a Hub for SARS-CoV-2 Mutational Drift. Viruses 2023; 15:v15040855. [PMID: 37112835 PMCID: PMC10145566 DOI: 10.3390/v15040855] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2023] [Revised: 03/16/2023] [Accepted: 03/23/2023] [Indexed: 03/29/2023] Open
Abstract
The clinical course of coronavirus disease 2019 (COVID-19), caused by severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2), is largely determined by host factors, with a wide range of outcomes. Despite an extensive vaccination campaign and high rates of infection worldwide, the pandemic persists, adapting to overcome antiviral immunity acquired through prior exposure. The source of many such major adaptations is variants of concern (VOCs), novel SARS-CoV-2 variants produced by extraordinary evolutionary leaps whose origins remain mostly unknown. In this study, we tested the influence of factors on the evolutionary course of SARS-CoV-2. Electronic health records of individuals infected with SARS-CoV-2 were paired to viral whole-genome sequences to assess the effects of host clinical parameters and immunity on the intra-host evolution of SARS-CoV-2. We found slight, albeit significant, differences in SARS-CoV-2 intra-host diversity, which depended on host parameters such as vaccination status and smoking. Only one viral genome had significant alterations as a result of host parameters; it was found in an immunocompromised, chronically infected woman in her 70s. We highlight the unusual viral genome obtained from this woman, which had an accelerated mutational rate and an excess of rare mutations, including near-complete truncating of the accessory protein ORF3a. Our findings suggest that the evolutionary capacity of SARS-CoV-2 during acute infection is limited and mostly unaffected by host characteristics. Significant viral evolution is seemingly exclusive to a small subset of COVID-19 cases, which typically prolong infections in immunocompromised patients. In these rare cases, SARS-CoV-2 genomes accumulate many impactful and potentially adaptive mutations; however, the transmissibility of such viruses remains unclear.
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19
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Cha J, Lavi M, Kim J, Shomron N, Lee I. Imputation of single-cell transcriptome data enables the reconstruction of networks predictive of breast cancer metastasis. Comput Struct Biotechnol J 2023; 21:2296-2304. [PMID: 37035549 PMCID: PMC10073994 DOI: 10.1016/j.csbj.2023.03.036] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2022] [Revised: 03/21/2023] [Accepted: 03/21/2023] [Indexed: 03/30/2023] Open
Abstract
Single-cell transcriptome data provide a unique opportunity to explore the gene networks of a particular cell type. However, insufficient capture rate and high dimensionality of single-cell RNA sequencing (scRNA-seq) data challenge cell-type-specific gene network (CGN) reconstruction. Here, we demonstrated that the imputation of scRNA-seq data enables reconstruction of CGNs by effective retrieval of gene functional associations. We reconstructed CGNs for seven primary and nine metastatic breast cancer cell lines using scRNA-seq data with imputation. Key genes for primary or metastatic cell lines were prioritized based on network centrality measures and CGN hub genes that were presumed to be the major determinant of cell type characteristics. To identify novel genes in breast cancer metastasis, we used the average rank difference of centrality between the primary and metastatic cell lines. Genes predicted using CGN centrality analysis were more enriched for known breast cancer metastatic genes than those predicted using differential expression. The molecular chaperone CCT2 was identified as a novel gene for breast metastasis during knockdown assays of several candidate genes. Overall, our study demonstrated an effective CGN reconstruction technique with imputation of scRNA-seq data and the feasibility of identifying key genes for particular cell subsets using single-cell network analysis.
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Affiliation(s)
- Junha Cha
- Department of Biotechnology, College of Life Science and Biotechnology, Yonsei University, Seoul 03722, Republic of Korea
| | - Michael Lavi
- Faculty of Medicine and Edmond J Safra Center for Bioinformatics, Tel Aviv University, Tel Aviv 69978, Israel
| | - Junhan Kim
- Department of Biotechnology, College of Life Science and Biotechnology, Yonsei University, Seoul 03722, Republic of Korea
| | - Noam Shomron
- Faculty of Medicine and Edmond J Safra Center for Bioinformatics, Tel Aviv University, Tel Aviv 69978, Israel
- Corresponding author.
| | - Insuk Lee
- Department of Biotechnology, College of Life Science and Biotechnology, Yonsei University, Seoul 03722, Republic of Korea
- POSTECH Biotech Center, Pohang University of Science and Technology (POSTECH), Pohang 37673, Republic of Korea
- Corresponding author at: Department of Biotechnology, College of Life Science and Biotechnology, Yonsei University, Seoul 03722, Republic of Korea.
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20
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Hen Gabzi R, Patalon T, Shomron N, Gazit S. A Data-Driven Strategy for Identifying Individuals Resistant to SARS-CoV-2 Virus under In-Household Exposure. J Pers Med 2022; 12:jpm12121975. [PMID: 36556196 PMCID: PMC9784910 DOI: 10.3390/jpm12121975] [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: 10/29/2022] [Revised: 11/21/2022] [Accepted: 11/26/2022] [Indexed: 12/02/2022] Open
Abstract
This report describes the development of a data-driven approach for identifying individuals who tested negative to a SARS-CoV-2 infection, despite their residence with individuals who had confirmed infections. Household studies have demonstrated efficiency in evaluating exposure to SARS-CoV-2. Leveraging earlier studies based on the household unit, our analysis utilized close contacts in order to trace chains of infection and to subsequently categorize TEFLONs, an acronym for Timely Exposed to Family members Leaving One Not infected. We used over one million anonymized electronic medical records, retrieved from Maccabi Healthcare Services' centralized computerized database from March 2020 to March 2022. The analysis yielded 252 TEFLONs, who were probably at very high risk of infection and yet, demonstrated clinical resistance. The exposure extent in each household positively correlated with household size, reflecting the in-house rolling transmission event. Our approach can be easily implemented in other clinical fields and should spur further research of clinical resistance to various infections.
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Affiliation(s)
- Roni Hen Gabzi
- Faculty of Medicine, Tel Aviv University, Tel Aviv 69978, Israel
- Edmond J Safra Center for Bioinformatics, Tel Aviv University, Tel Aviv 69978, Israel
- Tel Aviv University Innovation Laboratory (TILabs), Tel Aviv University, Tel Aviv 69978, Israel
- Correspondence: (R.H.G.); (S.G.)
| | - Tal Patalon
- Kahn Sagol Maccabi (KSM) Research & Innovation Center, Maccabi Healthcare Services, Tel Aviv 69978, Israel
- Maccabitech Institute for Research and Innovation, Maccabi Healthcare Services, Tel Aviv 69978, Israel
| | - Noam Shomron
- Faculty of Medicine, Tel Aviv University, Tel Aviv 69978, Israel
- Edmond J Safra Center for Bioinformatics, Tel Aviv University, Tel Aviv 69978, Israel
- Tel Aviv University Innovation Laboratory (TILabs), Tel Aviv University, Tel Aviv 69978, Israel
| | - Sivan Gazit
- Kahn Sagol Maccabi (KSM) Research & Innovation Center, Maccabi Healthcare Services, Tel Aviv 69978, Israel
- Maccabitech Institute for Research and Innovation, Maccabi Healthcare Services, Tel Aviv 69978, Israel
- Correspondence: (R.H.G.); (S.G.)
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21
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Levert-Levitt E, Shapira G, Sragovich S, Shomron N, Lam JCK, Li VOK, Heimesaat MM, Bereswill S, Yehuda AB, Sagi-Schwartz A, Solomon Z, Gozes I. Oral microbiota signatures in post-traumatic stress disorder (PTSD) veterans. Mol Psychiatry 2022; 27:4590-4598. [PMID: 35864319 DOI: 10.1038/s41380-022-01704-6] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/28/2022] [Revised: 07/06/2022] [Accepted: 07/06/2022] [Indexed: 12/14/2022]
Abstract
Post-traumatic stress disorder (PTSD) represents a global public health concern, affecting about 1 in 20 individuals. The symptoms of PTSD include intrusiveness (involuntary nightmares or flashbacks), avoidance of traumatic memories, negative alterations in cognition and mood (such as negative beliefs about oneself or social detachment), increased arousal and reactivity with irritable reckless behavior, concentration problems, and sleep disturbances. PTSD is also highly comorbid with anxiety, depression, and substance abuse. To advance the field from subjective, self-reported psychological measurements to objective molecular biomarkers while considering environmental influences, we examined a unique cohort of Israeli veterans who participated in the 1982 Lebanon war. Non-invasive oral 16S RNA sequencing was correlated with psychological phenotyping. Thus, a microbiota signature (i.e., decreased levels of the bacteria sp_HMT_914, 332 and 871 and Noxia) was correlated with PTSD severity, as exemplified by intrusiveness, arousal, and reactivity, as well as additional psychopathological symptoms, including anxiety, hostility, memory difficulties, and idiopathic pain. In contrast, education duration correlated with significantly increased levels of sp_HMT_871 and decreased levels of Bacteroidetes and Firmicutes, and presented an inverted correlation with adverse psychopathological measures. Air pollution was positively correlated with PTSD symptoms, psychopathological symptoms, and microbiota composition. Arousal and reactivity symptoms were correlated with reductions in transaldolase, an enzyme controlling a major cellular energy pathway, that potentially accelerates aging. In conclusion, the newly discovered bacterial signature, whether an outcome or a consequence of PTSD, could allow for objective soldier deployment and stratification according to decreases in sp_HMT_914, 332, 871, and Noxia levels, coupled with increases in Bacteroidetes levels. These findings also raise the possibility of microbiota pathway-related non-intrusive treatments for PTSD.
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Affiliation(s)
- Ella Levert-Levitt
- School of Psychological Sciences, Center for the Study of Child Development, University of Haifa, 6035 Rabin Building, Haifa, 3190501, Israel
| | - Guy Shapira
- Department of Cell and Developmental Biology, Sackler Faculty of Medicine, Sagol School of Neuroscience, Edmond J Safra Center for Bioinformatics, Tel Aviv University, Tel Aviv, 69978, Israel
| | - Shlomo Sragovich
- Elton Laboratory for Molecular Neuroendocrinology, Department of Human Molecular Genetics and Biochemistry, Sackler Faculty of Medicine, Adams Super Center for Brain Studies and Sagol School of Neuroscience, Tel Aviv University, 69978, Tel Aviv, Israel
| | - Noam Shomron
- Department of Cell and Developmental Biology, Sackler Faculty of Medicine, Sagol School of Neuroscience, Edmond J Safra Center for Bioinformatics, Tel Aviv University, Tel Aviv, 69978, Israel
| | - Jacqueline C K Lam
- Department of Electrical and Electronic Engineering, The University of Hong Kong, Hong Kong, China
| | - Victor O K Li
- Department of Electrical and Electronic Engineering, The University of Hong Kong, Hong Kong, China
| | - Markus M Heimesaat
- Institute for Microbiology, Infectious Diseases and Immunology, Charité - Universitätsmedizin Berlin, Hindenburgdamm 30, 12203, Berlin, Germany
| | - Stefan Bereswill
- Institute for Microbiology, Infectious Diseases and Immunology, Charité - Universitätsmedizin Berlin, Hindenburgdamm 30, 12203, Berlin, Germany
| | - Ariel Ben Yehuda
- Department of Health and Well-being, Medical Corps, Israel Defense Forces (IDF), Ramat Gan, Israel.,'Shalvata' Mental Health Center, Clalit Health Services, Hod Hasharon, 4534708, Israel
| | - Abraham Sagi-Schwartz
- School of Psychological Sciences, Center for the Study of Child Development, University of Haifa, 6035 Rabin Building, Haifa, 3190501, Israel
| | - Zahava Solomon
- Gershon H. Gordon Faculty of Social Sciences, Tel Aviv University, Tel Aviv, 69978, Israel
| | - Illana Gozes
- Elton Laboratory for Molecular Neuroendocrinology, Department of Human Molecular Genetics and Biochemistry, Sackler Faculty of Medicine, Adams Super Center for Brain Studies and Sagol School of Neuroscience, Tel Aviv University, 69978, Tel Aviv, Israel.
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22
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Liu W, Shomron N. Analysis of MicroRNA Regulation and Gene Expression Variability in Single Cell Data. J Pers Med 2022; 12:jpm12101750. [PMID: 36294889 PMCID: PMC9605646 DOI: 10.3390/jpm12101750] [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: 08/12/2022] [Revised: 09/29/2022] [Accepted: 10/18/2022] [Indexed: 01/24/2023] Open
Abstract
MicroRNAs (miRNAs) regulate gene expression by binding to mRNAs, and thus reduce target gene expression levels and expression variability, also known as 'noise'. Single-cell RNA sequencing (scRNA-seq) technology has been used to study miRNA and mRNA expression in single cells. To evaluate scRNA-seq as a tool for investigating miRNA regulation, we analyzed datasets with both mRNA and miRNA expression in single-cell format. We found that miRNAs slightly reduce the expression noise of target genes; however, this effect is easily masked by strong technical noise from scRNA-seq. We suggest improvements aimed at reducing technical noise, which can be implemented in experimental design and computational analysis prior to running scRNA-seq. Our study provides useful guidelines for experiments that evaluate the effect of miRNAs on mRNA expression from scRNA-seq.
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Affiliation(s)
- Wendao Liu
- Faculty of Medicine, Tel Aviv University, Tel Aviv 69978, Israel
| | - Noam Shomron
- Faculty of Medicine, Tel Aviv University, Tel Aviv 69978, Israel
- Edmond J. Safra Center for Bioinformatics, Tel Aviv University, Tel Aviv 6329302, Israel
- Correspondence: ; Tel.: +972-3-640-7387
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23
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Gutwillig A, Santana-Magal N, Farhat-Younis L, Rasoulouniriana D, Madi A, Luxenburg C, Cohen J, Padmanabhan K, Shomron N, Shapira G, Gleiberman A, Parikh R, Levy C, Feinmesser M, Hershkovitz D, Zemser-Werner V, Zlotnik O, Kroon S, Hardt WD, Debets R, Reticker-Flynn NE, Rider P, Carmi Y. Transient cell-in-cell formation underlies tumor relapse and resistance to immunotherapy. eLife 2022; 11:80315. [PMID: 36124553 PMCID: PMC9489212 DOI: 10.7554/elife.80315] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2022] [Accepted: 07/28/2022] [Indexed: 11/13/2022] Open
Abstract
Despite the remarkable successes of cancer immunotherapies, the majority of patients will experience only partial response followed by relapse of resistant tumors. While treatment resistance has frequently been attributed to clonal selection and immunoediting, comparisons of paired primary and relapsed tumors in melanoma and breast cancers indicate that they share the majority of clones. Here, we demonstrate in both mouse models and clinical human samples that tumor cells evade immunotherapy by generating unique transient cell-in-cell structures, which are resistant to killing by T cells and chemotherapies. While the outer cells in this cell-in-cell formation are often killed by reactive T cells, the inner cells remain intact and disseminate into single tumor cells once T cells are no longer present. This formation is mediated predominantly by IFNγ-activated T cells, which subsequently induce phosphorylation of the transcription factors signal transducer and activator of transcription 3 (STAT3) and early growth response-1 (EGR-1) in tumor cells. Indeed, inhibiting these factors prior to immunotherapy significantly improves its therapeutic efficacy. Overall, this work highlights a currently insurmountable limitation of immunotherapy and reveals a previously unknown resistance mechanism which enables tumor cells to survive immune-mediated killing without altering their immunogenicity. Cancer immunotherapies use the body’s own immune system to fight off cancer. But, despite some remarkable success stories, many patients only see a temporary improvement before the immunotherapy stops being effective and the tumours regrow. It is unclear why this occurs, but it may have to do with how the immune system attacks cancer cells. Immunotherapies aim to activate a special group of cells known as killer T-cells, which are responsible for the immune response to tumours. These cells can identify cancer cells and inject toxic granules through their membranes, killing them. However, killer T-cells are not always effective. This is because cancer cells are naturally good at avoiding detection, and during treatment, their genes can mutate, giving them new ways to evade the immune system. Interestingly, when scientists analysed the genes of tumour cells before and after immunotherapy, they found that many of the genes that code for proteins recognized by T-cells do not change significantly. This suggests that tumours’ resistance to immune attack may be physical, rather than genetic. To investigate this hypothesis, Gutwillig et al. developed several mouse tumour models that stop responding to immunotherapy after initial treatment. Examining cells from these tumours revealed that when the immune system attacks, they reorganise by getting inside one another. This allows some cancer cells to hide under many layers of cell membrane. At this point killer T-cells can identify and inject the outer cell with toxic granules, but it cannot reach the cells inside. This ability of cancer cells to hide within one another relies on them recognising when the immune system is attacking. This happens because the cancer cells can detect certain signals released by the killer T-cells, allowing them to hide. Gutwillig et al. identified some of these signals, and showed that blocking them stopped cancer cells from hiding inside each other, making immunotherapy more effective. This new explanation for how cancer cells escape the immune system could guide future research and lead to new cancer treatments, or approaches to boost existing treatments. Understanding the process in more detail could allow scientists to prevent it from happening, by revealing which signals to block, and when, for best results.
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Affiliation(s)
- Amit Gutwillig
- Department of Pathology, Sackler School of Medicine, Tel Aviv University
| | | | - Leen Farhat-Younis
- Department of Pathology, Sackler School of Medicine, Tel Aviv University
| | | | - Asaf Madi
- Department of Pathology, Sackler School of Medicine, Tel Aviv University
| | - Chen Luxenburg
- Cell and Developmental Biology, Sackler School of Medicine, Tel Aviv University
| | - Jonathan Cohen
- Cell and Developmental Biology, Sackler School of Medicine, Tel Aviv University
| | | | - Noam Shomron
- Cell and Developmental Biology, Sackler School of Medicine, Tel Aviv University
| | - Guy Shapira
- Cell and Developmental Biology, Sackler School of Medicine, Tel Aviv University
| | - Annette Gleiberman
- Department of Pathology, Sackler School of Medicine, Tel Aviv University
| | - Roma Parikh
- Human Molecular Genetics and Biochemistry, Sackler School of Medicine, Tel Aviv University
| | - Carmit Levy
- Human Molecular Genetics and Biochemistry, Sackler School of Medicine, Tel Aviv University
| | - Meora Feinmesser
- Department of Pathology, Sackler School of Medicine, Tel Aviv University
- Institute of Pathology, Rabin Medical Center- Beilinson Hospital
| | - Dov Hershkovitz
- Department of Pathology, Sackler School of Medicine, Tel Aviv University
- Institute of Pathology, Tel Aviv Sourasky Medical Center
| | | | - Oran Zlotnik
- Department of General Surgery, Rabin Medical Center- Beilinson Campus
| | - Sanne Kroon
- Department of Biology, Institute of Microbiology
| | | | - Reno Debets
- Department of Medical Oncology, Erasmus MC Cancer Institute
| | | | - Peleg Rider
- Department of Pathology, Sackler School of Medicine, Tel Aviv University
| | - Yaron Carmi
- Department of Pathology, Sackler School of Medicine, Tel Aviv University
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24
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Voinsky I, Zoabi Y, Shomron N, Harel M, Cassuto H, Tam J, Rose S, Scheck AC, Karim MA, Frye RE, Aran A, Gurwitz D. Blood RNA Sequencing Indicates Upregulated BATF2 and LY6E and Downregulated ISG15 and MT2A Expression in Children with Autism Spectrum Disorder. Int J Mol Sci 2022; 23:ijms23179843. [PMID: 36077244 PMCID: PMC9456089 DOI: 10.3390/ijms23179843] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2022] [Revised: 08/24/2022] [Accepted: 08/28/2022] [Indexed: 11/16/2022] Open
Abstract
Mutations in over 100 genes are implicated in autism spectrum disorder (ASD). DNA SNPs, CNVs, and epigenomic modifications also contribute to ASD. Transcriptomics analysis of blood samples may offer clues for pathways dysregulated in ASD. To expand and validate published findings of RNA-sequencing (RNA-seq) studies, we performed RNA-seq of whole blood samples from an Israeli discovery cohort of eight children with ASD compared with nine age- and sex-matched neurotypical children. This revealed 10 genes with differential expression. Using quantitative real-time PCR, we compared RNAs from whole blood samples of 73 Israeli and American children with ASD and 26 matched neurotypical children for the 10 dysregulated genes detected by RNA-seq. This revealed higher expression levels of the pro-inflammatory transcripts BATF2 and LY6E and lower expression levels of the anti-inflammatory transcripts ISG15 and MT2A in the ASD compared to neurotypical children. BATF2 was recently reported as upregulated in blood samples of Japanese adults with ASD. Our findings support an involvement of these genes in ASD phenotypes, independent of age and ethnicity. Upregulation of BATF2 and downregulation of ISG15 and MT2A were reported to reduce cancer risk. Implications of the dysregulated genes for pro-inflammatory phenotypes, immunity, and cancer risk in ASD are discussed.
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Affiliation(s)
- Irena Voinsky
- Department of Human Molecular Genetics and Biochemistry, Faculty of Medicine, Tel Aviv University, Tel Aviv 69978, Israel
| | - Yazeed Zoabi
- Department of Cell and Developmental Biology, Faculty of Medicine, Tel Aviv University, Tel Aviv 69978, Israel
- Edmond J. Safra Center for Bioinformatics, Tel Aviv University, Tel Aviv 69978, Israel
| | - Noam Shomron
- Department of Cell and Developmental Biology, Faculty of Medicine, Tel Aviv University, Tel Aviv 69978, Israel
- Edmond J. Safra Center for Bioinformatics, Tel Aviv University, Tel Aviv 69978, Israel
- Sagol School of Neuroscience, Tel Aviv University, Tel Aviv 69978, Israel
| | - Moria Harel
- Shaare Zedek Medical Center, Jerusalem 91031, Israel
| | | | - Joseph Tam
- Obesity and Metabolism Laboratory, Institute for Drug Research, School of Pharmacy, Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem 91120, Israel
| | - Shannon Rose
- Department of Pediatrics, University of Arkansas for Medical Sciences and Arkansas Children’s Research Institute, Little Rock, AR 72205, USA
| | - Adrienne C. Scheck
- Barrow Neurological Institute, Phoenix Children’s Hospital, Phoenix, AZ 85016, USA
- Department of Child Health, University of Arizona College of Medicine-Phoenix, Phoenix, AZ 85004, USA
| | - Mohammad A. Karim
- Barrow Neurological Institute, Phoenix Children’s Hospital, Phoenix, AZ 85016, USA
- Department of Child Health, University of Arizona College of Medicine-Phoenix, Phoenix, AZ 85004, USA
| | - Richard E. Frye
- Barrow Neurological Institute, Phoenix Children’s Hospital, Phoenix, AZ 85016, USA
- Department of Child Health, University of Arizona College of Medicine-Phoenix, Phoenix, AZ 85004, USA
- Rossignol Medical Center, Phoenix, AZ 85050, USA
| | - Adi Aran
- Shaare Zedek Medical Center, Jerusalem 91031, Israel
- Obesity and Metabolism Laboratory, Institute for Drug Research, School of Pharmacy, Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem 91120, Israel
- Correspondence: (A.A.); (D.G.)
| | - David Gurwitz
- Department of Human Molecular Genetics and Biochemistry, Faculty of Medicine, Tel Aviv University, Tel Aviv 69978, Israel
- Sagol School of Neuroscience, Tel Aviv University, Tel Aviv 69978, Israel
- Correspondence: (A.A.); (D.G.)
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25
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Avnat E, Shapira G, Gurwitz D, Shomron N. Elevated Expression of RGS2 May Underlie Reduced Olfaction in COVID-19 Patients. J Pers Med 2022; 12:jpm12091396. [PMID: 36143181 PMCID: PMC9504192 DOI: 10.3390/jpm12091396] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2022] [Revised: 08/15/2022] [Accepted: 08/25/2022] [Indexed: 12/03/2022] Open
Abstract
Anosmia is common in COVID-19 patients, lasting for weeks or months following recovery. The biological mechanism underlying olfactory deficiency in COVID-19 does not involve direct damage to nasal olfactory neurons, which do not express the proteins required for SARS-CoV-2 infection. A recent study suggested that anosmia results from downregulation of olfactory receptors. We hypothesized that anosmia in COVID-19 may also reflect SARS-CoV-2 infection-driven elevated expression of regulator of G protein signaling 2 (RGS2), a key regulator of odorant receptors, thereby silencing their signaling. To test our hypothesis, we analyzed gene expression of nasopharyngeal swabs from SARS-CoV-2 positive patients and non-infected controls (two published RNA-sequencing datasets, 580 individuals). Our analysis found upregulated RGS2 expression in SARS-CoV-2 positive patients (FC = 14.5, Padj = 1.69 × 10−5 and FC = 2.4; Padj = 0.001, per dataset). Additionally, RGS2 expression was strongly correlated with PTGS2, IL1B, CXCL8, NAMPT and other inflammation markers with substantial upregulation in early infection. These observations suggest that upregulated expression of RGS2 may underlie anosmia in COVID-19 patients. As a regulator of numerous G-protein coupled receptors, RGS2 may drive further neurological symptoms of COVID-19. Studies are required for clarifying the cellular mechanisms by which SARS-CoV-2 infection drives the upregulation of RGS2 and other genes implicated in inflammation. Insights on these pathway(s) may assist in understanding anosmia and additional neurological symptoms reported in COVID-19 patients.
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Affiliation(s)
- Eden Avnat
- Faculty of Medicine, Tel Aviv University, Tel Aviv 69978, Israel
| | - Guy Shapira
- Faculty of Medicine, Tel Aviv University, Tel Aviv 69978, Israel
- Edmond J Safra Center for Bioinformatics, Tel Aviv University, Tel Aviv 69978, Israel
| | - David Gurwitz
- Faculty of Medicine, Tel Aviv University, Tel Aviv 69978, Israel
- Sagol School of Neuroscience, Tel Aviv University, Tel Aviv 69978, Israel
- Correspondence: (D.G.); (N.S.); Tel.: +972-3-640-7611 (D.G.); +972-3-640-6594 (N.S.)
| | - Noam Shomron
- Faculty of Medicine, Tel Aviv University, Tel Aviv 69978, Israel
- Edmond J Safra Center for Bioinformatics, Tel Aviv University, Tel Aviv 69978, Israel
- Sagol School of Neuroscience, Tel Aviv University, Tel Aviv 69978, Israel
- Correspondence: (D.G.); (N.S.); Tel.: +972-3-640-7611 (D.G.); +972-3-640-6594 (N.S.)
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26
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Pertzov B, Shapira G, Abushkara S, Cohen S, Turjeman A, Kramer MR, Gurwitz D, Shomron N. Lower serum alpha 1 antitrypsin levels in patients with severe COVID-19 compared with patients hospitalized due to non-COVID-19 pneumonia. Infect Dis (Lond) 2022; 54:846-851. [PMID: 35975662 DOI: 10.1080/23744235.2022.2111464] [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] [Indexed: 11/05/2022] Open
Abstract
INTRODUCTION Alpha 1 antitrypsin (A1AT) is the major human blood serine protease inhibitor. Transmembrane serine protease 2 (TMPRSS2), which is crucial for SARS-CoV-2 cell entry, is inhibited by A1AT. Therefore, we hypothesized that individuals with diminished levels of A1AT may be more prone to SARS-CoV-2 infection and severe COVID-19 disease. Our aim in this study was to evaluate the level of A1AT in hospitalized COVID-19 patients in comparison to hospitalized patients with non-COVID-19 pneumonia. METHODS We conducted an observational prospective study between October 2020 and April 2021 in Rabin Medical Centre in Israel. A1AT levels were measured from the routine serum samples of hospitalized patients with COVID-19 and non-COVID-19 pneumonia (control group). The primary outcome was A1AT level, secondary outcomes were clinical outcomes and predictors of morality. RESULTS Overall, 145 patients were included in the study, 98 in the COVID-19 group and 47 in the control group. The median A1AT level was 222 mg/dL (interquartile range (IQR) 188-269) and 258 mg/dL (IQR 210-281) in the COVID-19 and control groups, respectively (p = .045). Multivariate analysis for independent risk factors for mortality among COVID-19 patients showed that diabetes mellitus (p = .02), older age (p = .04), and high A1AT levels (p = .04) were all associated with increased mortality. CONCLUSION Patients admitted due to severe COVID-19 had lower A1AT levels in comparison to patients admitted due to non-COVID pneumonia. This observation may suggest an association between mildly diminished A1AT and higher risk of SARS-CoV-2 infection with severe COVID-19 disease.
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Affiliation(s)
- Barak Pertzov
- Pulmonary institute, Rabin Medical Center, Petach Tikva, Israel.,Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Guy Shapira
- Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel.,Edmond J Safra Center for Bioinformatics, Tel Aviv University, Tel Aviv, Israel
| | - Simon Abushkara
- Pulmonary institute, Rabin Medical Center, Petach Tikva, Israel
| | - Sharon Cohen
- Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel.,Biochemistry and Pharmacology Laboratory, Rabin Medical Center, Petach Tikva, Israel
| | - Adi Turjeman
- Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel.,Department of Medicine E, Rabin Medical Center, Petach Tikva, Israel
| | - Mordechai R Kramer
- Pulmonary institute, Rabin Medical Center, Petach Tikva, Israel.,Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - David Gurwitz
- Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Noam Shomron
- Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel.,Edmond J Safra Center for Bioinformatics, Tel Aviv University, Tel Aviv, Israel
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27
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Kuznitsov-Yanovsky L, Shapira G, Gildin L, Shomron N, Ben-Yosef D. Transcriptomic Analysis of Human Fragile X Syndrome Neurons Reveals Neurite Outgrowth Modulation by the TGFβ/BMP Pathway. Int J Mol Sci 2022; 23:ijms23169278. [PMID: 36012539 PMCID: PMC9409179 DOI: 10.3390/ijms23169278] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2022] [Revised: 08/11/2022] [Accepted: 08/14/2022] [Indexed: 11/25/2022] Open
Abstract
Fragile X Syndrome (FXS) is the main genetic reason for intellectual disability and is caused by the silencing of fragile X mental retardation protein (FMRP), an RNA-binding protein regulating the translation of many neuronal mRNAs. Neural differentiation of FX human embryonic stem cells (hESC) mimics the neurodevelopment of FXS fetuses and thus serves as a good model to explore the mechanisms underlining the development of FXS. Isogenic hESC clones with and without the FX mutation that share the same genetic background were in vitro differentiated into neurons, and their transcriptome was analyzed by RNA sequencing. FX neurons inactivating FMR1 expression presented delayed neuronal development and maturation, concomitant with dysregulation of the TGFβ/BMP signaling pathway, and genes related to the extracellular matrix. Migration assay showed decreased neurite outgrowth in FX neurons that was rescued by inhibition of the TGFβ/BMP signaling pathway. Our results provide new insights into the molecular pathway by which loss of FMRP affects neuronal network development. In FX neurons, the lack of FMRP dysregulates members of the BMP signaling pathway associated with ECM organization which, in a yet unknown mechanism, reduces the guidance of axonal growth cones, probably leading to the aberrant neuronal network function seen in FXS.
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Affiliation(s)
- Liron Kuznitsov-Yanovsky
- Wolfe PGD Stem Cell Lab, Racine IVF Unit, Lis Maternity Hospital Tel-Aviv Sourasky Medical Center, Tel Aviv 64239, Israel
- Department of Cell and Developmental Biology, Sackler Faculty of Medicine, Tel-Aviv University, Tel Aviv 69978, Israel
| | - Guy Shapira
- Department of Cell and Developmental Biology, Sackler Faculty of Medicine, Tel-Aviv University, Tel Aviv 69978, Israel
| | - Lital Gildin
- Wolfe PGD Stem Cell Lab, Racine IVF Unit, Lis Maternity Hospital Tel-Aviv Sourasky Medical Center, Tel Aviv 64239, Israel
- Department of Cell and Developmental Biology, Sackler Faculty of Medicine, Tel-Aviv University, Tel Aviv 69978, Israel
| | - Noam Shomron
- Department of Cell and Developmental Biology, Sackler Faculty of Medicine, Tel-Aviv University, Tel Aviv 69978, Israel
- Sagol School of Neuroscience, Tel-Aviv University, Tel Aviv 69978, Israel
| | - Dalit Ben-Yosef
- Wolfe PGD Stem Cell Lab, Racine IVF Unit, Lis Maternity Hospital Tel-Aviv Sourasky Medical Center, Tel Aviv 64239, Israel
- Department of Cell and Developmental Biology, Sackler Faculty of Medicine, Tel-Aviv University, Tel Aviv 69978, Israel
- Sagol School of Neuroscience, Tel-Aviv University, Tel Aviv 69978, Israel
- Correspondence:
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28
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Abstract
Metabolomics describes a high-throughput approach for measuring a repertoire of metabolites and small molecules in biological samples. One utility of untargeted metabolomics, unbiased global analysis of the metabolome, is to detect key metabolites as contributors to, or readouts of, human health and disease. In this perspective, we discuss how artificial intelligence (AI) and machine learning (ML) have promoted major advances in untargeted metabolomics workflows and facilitated pivotal findings in the areas of disease screening and diagnosis. We contextualize applications of AI and ML to the emerging field of high-resolution mass spectrometry (HRMS) exposomics, which unbiasedly detects endogenous metabolites and exogenous chemicals in human tissue to characterize exposure linked with disease outcomes. We discuss the state of the science and suggest potential opportunities for using AI and ML to improve data quality, rigor, detection, and chemical identification in untargeted metabolomics and exposomics studies.
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Affiliation(s)
- Lauren M. Petrick
- The Bert Strassburger Metabolic Center, Sheba Medical Center, Tel-Hashomer, Israel
- Department of Environmental Medicine and Public Health, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Institute for Exposomics Research, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Noam Shomron
- Faculty of Medicine, Edmond J. Safra Center for Bioinformatics, Sagol School of Neuroscience, Center for Nanoscience and Nanotechnology, Center for Innovation Laboratories (TILabs), Tel Aviv University, Tel Aviv, Israel
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29
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Danilevsky A, Polsky AL, Shomron N. Adaptive sequencing using nanopores and deep learning of mitochondrial DNA. Brief Bioinform 2022; 23:6634223. [PMID: 35804265 DOI: 10.1093/bib/bbac251] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [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: 11/16/2021] [Revised: 05/13/2022] [Accepted: 05/30/2022] [Indexed: 12/24/2022] Open
Abstract
Nanopore sequencing is an emerging technology that reads DNA by utilizing a unique method of detecting nucleic acid sequences and identifies the various chemical modifications they carry. Deep learning has increased in popularity as a useful technique to solve many complex computational tasks. 'Adaptive sequencing' is an implementation of selective sequencing, intended for use on the nanopore sequencing platform. In this study, we demonstrated an alternative method of software-based selective sequencing that is performed in real time by combining nanopore sequencing and deep learning. Our results showed the feasibility of using deep learning for classifying signals from only the first 200 nucleotides in a raw nanopore sequencing signal format. This was further demonstrated by comparing the accuracy of our deep learning classification model across data from several human cell lines and other eukaryotic organisms. We used custom deep learning models and a script that utilizes a 'Read Until' framework to target mitochondrial molecules in real time from a human cell line sample. This achieved a significant separation and enrichment ability of 2.3-fold. In a series of very short sequencing experiments (10, 30 and 120 min), we identified genomic and mitochondrial reads with accuracy above 90%, although mitochondrial DNA comprised only 0.1% of the total input material. The uniqueness of our method is the ability to distinguish two groups of DNA even without a labeled reference. This contrasts with studies that required a well-defined reference, whether of a DNA sequence or of another type of representation. Additionally, our method showed higher correlation to the theoretically possible enrichment factor, compared with other published methods. We believe that our results will lay the foundation for rapid and selective sequencing using nanopore technology and will pave the approach for clinical applications that use nanopore sequencing data.
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Affiliation(s)
- Artem Danilevsky
- Faculty of Medicine and Edmond J Safra Center for Bioinformatics, Tel Aviv University, Tel Aviv 69978, Israel
| | - Avital Luba Polsky
- Faculty of Medicine and Edmond J Safra Center for Bioinformatics, Tel Aviv University, Tel Aviv 69978, Israel
| | - Noam Shomron
- Faculty of Medicine and Edmond J Safra Center for Bioinformatics, Tel Aviv University, Tel Aviv 69978, Israel
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30
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Karmon G, Sragovich S, Hacohen-Kleiman G, Ben-Horin-Hazak I, Kasparek P, Schuster B, Sedlacek R, Pasmanik-Chor M, Theotokis P, Touloumi O, Zoidou S, Huang L, Wu PY, Shi R, Kapitansky O, Lobyntseva A, Giladi E, Shapira G, Shomron N, Bereswill S, Heimesaat MM, Grigoriadis N, McKinney RA, Rubinstein M, Gozes I. Novel ADNP Syndrome Mice Reveal Dramatic Sex-Specific Peripheral Gene Expression With Brain Synaptic and Tau Pathologies. Biol Psychiatry 2022; 92:81-95. [PMID: 34865853 DOI: 10.1016/j.biopsych.2021.09.018] [Citation(s) in RCA: 28] [Impact Index Per Article: 14.0] [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: 04/19/2021] [Revised: 08/19/2021] [Accepted: 09/17/2021] [Indexed: 01/18/2023]
Abstract
BACKGROUND ADNP is essential for embryonic development. As such, de novo ADNP mutations lead to an intractable autism/intellectual disability syndrome requiring investigation. METHODS Mimicking humans, CRISPR (clustered regularly interspaced short palindromic repeats)-Cas9 editing produced mice carrying heterozygous Adnp p.Tyr718∗ (Tyr), a paralog of the most common ADNP syndrome mutation. Phenotypic rescue was validated by treatment with the microtubule/autophagy-protective ADNP fragment NAPVSIPQ (NAP). RESULTS RNA sequencing of spleens, representing a peripheral biomarker source, revealed Tyr-specific sex differences (e.g., cell cycle), accentuated in females (with significant effects on antigen processing and cellular senescence) and corrected by NAP. Differentially expressed, NAP-correctable transcripts, including the autophagy and microbiome resilience-linked FOXO3, were also deregulated in human patient-derived ADNP-mutated lymphoblastoid cells. There were also Tyr sex-specific microbiota signatures. Phenotypically, Tyr mice, similar to patients with ADNP syndrome, exhibited delayed development coupled with sex-dependent gait defects. Speech acquisition delays paralleled sex-specific mouse syntax abnormalities. Anatomically, dendritic spine densities/morphologies were decreased with NAP amelioration. These findings were replicated in the Adnp+/- mouse, including Foxo3 deregulation, required for dendritic spine formation. Grooming duration and nociception threshold (autistic traits) were significantly affected only in males. Early-onset tauopathy was accentuated in males (hippocampus and visual cortex), mimicking humans, and was paralleled by impaired visual evoked potentials and correction by acute NAP treatment. CONCLUSIONS Tyr mice model ADNP syndrome pathology. The newly discovered ADNP/NAP target FOXO3 controls the autophagy initiator LC3 (microtubule-associated protein 1 light chain 3), with known ADNP binding to LC3 augmented by NAP, protecting against tauopathy. NAP amelioration attests to specificity, with potential for drug development targeting accessible biomarkers.
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Affiliation(s)
- Gidon Karmon
- Elton Laboratory for Molecular Neuroendocrinology, Department of Human Molecular Genetics and Biochemistry, Sackler Faculty of Medicine, Sagol School of Neuroscience and Adams Super Center for Brain Studies, Tel Aviv University, Tel Aviv, Israel
| | - Shlomo Sragovich
- Elton Laboratory for Molecular Neuroendocrinology, Department of Human Molecular Genetics and Biochemistry, Sackler Faculty of Medicine, Sagol School of Neuroscience and Adams Super Center for Brain Studies, Tel Aviv University, Tel Aviv, Israel
| | - Gal Hacohen-Kleiman
- Elton Laboratory for Molecular Neuroendocrinology, Department of Human Molecular Genetics and Biochemistry, Sackler Faculty of Medicine, Sagol School of Neuroscience and Adams Super Center for Brain Studies, Tel Aviv University, Tel Aviv, Israel
| | - Inbar Ben-Horin-Hazak
- Elton Laboratory for Molecular Neuroendocrinology, Department of Human Molecular Genetics and Biochemistry, Sackler Faculty of Medicine, Sagol School of Neuroscience and Adams Super Center for Brain Studies, Tel Aviv University, Tel Aviv, Israel
| | - Petr Kasparek
- Department of Transgenic Models of Diseases and Czech Centre for Phenogenomics, Institute of Molecular Genetics of the Czech Academy of Sciences, Vestec, Czech Republic
| | - Björn Schuster
- Department of Transgenic Models of Diseases and Czech Centre for Phenogenomics, Institute of Molecular Genetics of the Czech Academy of Sciences, Vestec, Czech Republic
| | - Radislav Sedlacek
- Department of Transgenic Models of Diseases and Czech Centre for Phenogenomics, Institute of Molecular Genetics of the Czech Academy of Sciences, Vestec, Czech Republic
| | - Metsada Pasmanik-Chor
- Bioinformatics Unit, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv, Israel
| | - Paschalis Theotokis
- Department of Neurology, Laboratory of Experimental Neurology, AHEPA University Hospital, Aristotle University of Thessaloniki, Thessaloniki, Greece
| | - Olga Touloumi
- Department of Neurology, Laboratory of Experimental Neurology, AHEPA University Hospital, Aristotle University of Thessaloniki, Thessaloniki, Greece
| | - Sofia Zoidou
- Department of Neurology, Laboratory of Experimental Neurology, AHEPA University Hospital, Aristotle University of Thessaloniki, Thessaloniki, Greece
| | - Linxuan Huang
- Department of Pharmacology and Therapeutics, McGill University, Montreal, Quebec, Canada
| | - Pei You Wu
- Department of Pharmacology and Therapeutics, McGill University, Montreal, Quebec, Canada
| | - Roy Shi
- Department of Pharmacology and Therapeutics, McGill University, Montreal, Quebec, Canada
| | - Oxana Kapitansky
- Elton Laboratory for Molecular Neuroendocrinology, Department of Human Molecular Genetics and Biochemistry, Sackler Faculty of Medicine, Sagol School of Neuroscience and Adams Super Center for Brain Studies, Tel Aviv University, Tel Aviv, Israel
| | - Alexandra Lobyntseva
- Elton Laboratory for Molecular Neuroendocrinology, Department of Human Molecular Genetics and Biochemistry, Sackler Faculty of Medicine, Sagol School of Neuroscience and Adams Super Center for Brain Studies, Tel Aviv University, Tel Aviv, Israel
| | - Eliezer Giladi
- Elton Laboratory for Molecular Neuroendocrinology, Department of Human Molecular Genetics and Biochemistry, Sackler Faculty of Medicine, Sagol School of Neuroscience and Adams Super Center for Brain Studies, Tel Aviv University, Tel Aviv, Israel
| | - Guy Shapira
- Department of Cell and Developmental Biology and Edmond J. Safra Center for Bioinformatics, Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Noam Shomron
- Department of Cell and Developmental Biology and Edmond J. Safra Center for Bioinformatics, Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Stefan Bereswill
- Gastrointestinal Microbiology Research Group, Institute for Microbiology, Infectious Diseases and Immunology, Charité-University Medicine Berlin, Berlin, Germany
| | - Markus M Heimesaat
- Gastrointestinal Microbiology Research Group, Institute for Microbiology, Infectious Diseases and Immunology, Charité-University Medicine Berlin, Berlin, Germany
| | - Nikolaos Grigoriadis
- Department of Neurology, Laboratory of Experimental Neurology, AHEPA University Hospital, Aristotle University of Thessaloniki, Thessaloniki, Greece
| | - R Anne McKinney
- Department of Pharmacology and Therapeutics, McGill University, Montreal, Quebec, Canada
| | - Moran Rubinstein
- Elton Laboratory for Molecular Neuroendocrinology, Department of Human Molecular Genetics and Biochemistry, Sackler Faculty of Medicine, Sagol School of Neuroscience and Adams Super Center for Brain Studies, Tel Aviv University, Tel Aviv, Israel; Goldschleger Eye Research Institute, Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Illana Gozes
- Elton Laboratory for Molecular Neuroendocrinology, Department of Human Molecular Genetics and Biochemistry, Sackler Faculty of Medicine, Sagol School of Neuroscience and Adams Super Center for Brain Studies, Tel Aviv University, Tel Aviv, Israel.
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31
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Admoni-Elisha L, Elbaz T, Chopra A, Shapira G, Bedford M, Fry C, Shomron N, Biggar K, Feldman M, Levy D. TWIST1 methylation by SETD6 selectively antagonizes LINC-PINT expression in glioma. Nucleic Acids Res 2022; 50:6903-6918. [PMID: 35694846 PMCID: PMC9262621 DOI: 10.1093/nar/gkac485] [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] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2021] [Revised: 05/16/2022] [Accepted: 05/30/2022] [Indexed: 12/24/2022] Open
Abstract
Gliomas are one of the most common and lethal brain tumors among adults. One process that contributes to glioma progression and recurrence is the epithelial to mesenchymal transition (EMT). EMT is regulated by a set of defined transcription factors which tightly regulate this process, among them is the basic helix-loop-helix family member, TWIST1. Here we show that TWIST1 is methylated on lysine-33 at chromatin by SETD6, a methyltransferase with expression levels correlating with poor survival in glioma patients. RNA-seq analysis in U251 glioma cells suggested that both SETD6 and TWIST1 regulate cell adhesion and migration processes. We further show that TWIST1 methylation attenuates the expression of the long-non-coding RNA, LINC-PINT, thereby promoting EMT in glioma. Mechanistically, TWIST1 methylation represses the transcription of LINC-PINT by increasing the occupancy of EZH2 and the catalysis of the repressive H3K27me3 mark at the LINC-PINT locus. Under un-methylated conditions, TWIST1 dissociates from the LINC-PINT locus, allowing the expression of LINC-PINT which leads to increased cell adhesion and decreased cell migration. Together, our findings unravel a new mechanistic dimension for selective expression of LINC-PINT mediated by TWIST1 methylation.
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Affiliation(s)
- Lee Admoni-Elisha
- The Shraga Segal Department of Microbiology, Immunology and Genetics, Faculty of Health Sciences, Ben-Gurion University of the Negev, 84105 Be'er-Sheva, Israel,National Institute for Biotechnology in the Negev, Ben-Gurion University of the Negev, P.O.B. 653, Be’er-Sheva 84105, Israel
| | - Tzofit Elbaz
- The Shraga Segal Department of Microbiology, Immunology and Genetics, Faculty of Health Sciences, Ben-Gurion University of the Negev, 84105 Be'er-Sheva, Israel,National Institute for Biotechnology in the Negev, Ben-Gurion University of the Negev, P.O.B. 653, Be’er-Sheva 84105, Israel
| | - Anand Chopra
- Carleton University, 1125 Colonel By Drive, Ottawa, Ontario K1S 5B6, Canada
| | - Guy Shapira
- Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel,Edmond J. Safra Center for Bioinformatics, Tel Aviv University, Tel Aviv, Israel
| | - Mark T Bedford
- Department of Carcinogenesis, M.D. Anderson Cancer Center, Houston, TX, USA
| | | | - Noam Shomron
- Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel,Edmond J. Safra Center for Bioinformatics, Tel Aviv University, Tel Aviv, Israel
| | - Kyle Biggar
- Carleton University, 1125 Colonel By Drive, Ottawa, Ontario K1S 5B6, Canada
| | - Michal Feldman
- The Shraga Segal Department of Microbiology, Immunology and Genetics, Faculty of Health Sciences, Ben-Gurion University of the Negev, 84105 Be'er-Sheva, Israel,National Institute for Biotechnology in the Negev, Ben-Gurion University of the Negev, P.O.B. 653, Be’er-Sheva 84105, Israel
| | - Dan Levy
- To whom correspondence should be addressed. Tel: +972 8 647 7251;
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32
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Elisha L, Abaev-Schneiderman E, Cohn O, Shapira G, Shomron N, Feldman M, Levy D. Structure-function conservation between the methyltransferases SETD3 and SETD6. Biochimie 2022; 200:27-35. [PMID: 35550916 DOI: 10.1016/j.biochi.2022.05.003] [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: 03/30/2022] [Revised: 05/04/2022] [Accepted: 05/05/2022] [Indexed: 11/16/2022]
Abstract
Among the protein lysine methyltransferases family members, it appears that SETD6 is highly similar and closely related to SETD3. The two methyltransferases show high similarity in their structure, which raised the hypothesis that they share cellular functions. Using a proteomic screen, we identified 52 shared interacting-proteins. Gene Ontology (GO) analysis of the shared proteins revealed significant enrichment of proteins involved in transcription. Our RNA-seq data of SETD6 KO and SETD3 KO HeLa cells identified ∼100 up-regulated and down-regulated shared genes. We have also identified a substantial number of genes that changed dramatically in the double KO cells but did not significantly change in the single KO cells. GO analysis of these genes revealed enrichment of apoptotic genes. Accordingly, we show that the double KO cells displayed high apoptotic levels, suggesting that SETD6 and SETD3 inhibit apoptosis. Collectively, our data strongly suggest a functional link between SETD6 and SETD3 in the regulation of apoptosis.
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Affiliation(s)
- Lee Elisha
- The Shraga Segal Department of Microbiology, Immunology and Genetics, Israel; The National Institute for Biotechnology in the Negev, Ben-Gurion University of the Negev, P.O.B. 653, Be'er-Sheva, 84105, Israel
| | - Elina Abaev-Schneiderman
- The Shraga Segal Department of Microbiology, Immunology and Genetics, Israel; The National Institute for Biotechnology in the Negev, Ben-Gurion University of the Negev, P.O.B. 653, Be'er-Sheva, 84105, Israel
| | - Ofir Cohn
- The Shraga Segal Department of Microbiology, Immunology and Genetics, Israel; The National Institute for Biotechnology in the Negev, Ben-Gurion University of the Negev, P.O.B. 653, Be'er-Sheva, 84105, Israel
| | - Guy Shapira
- Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel; Edmond J. Safra Center for Bioinformatics, Tel Aviv University, Tel Aviv, Israel
| | - Noam Shomron
- Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel; Edmond J. Safra Center for Bioinformatics, Tel Aviv University, Tel Aviv, Israel
| | - Michal Feldman
- The Shraga Segal Department of Microbiology, Immunology and Genetics, Israel; The National Institute for Biotechnology in the Negev, Ben-Gurion University of the Negev, P.O.B. 653, Be'er-Sheva, 84105, Israel
| | - Dan Levy
- The Shraga Segal Department of Microbiology, Immunology and Genetics, Israel; The National Institute for Biotechnology in the Negev, Ben-Gurion University of the Negev, P.O.B. 653, Be'er-Sheva, 84105, Israel.
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33
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Shmerling M, Chalik M, Smorodinsky NI, Meeker A, Roy S, Sagi-Assif O, Meshel T, Danilevsky A, Shomron N, Levinger S, Nishry B, Baruchi D, Shargorodsky A, Ziv R, Sarusi-Portuguez A, Lahav M, Ehrlich M, Braschi B, Bruford E, Witz IP, Wreschner DH. LY6S, a New IFN-Inducible Human Member of the Ly6a Subfamily Expressed by Spleen Cells and Associated with Inflammation and Viral Resistance. Immunohorizons 2022; 6:253-272. [PMID: 35440514 PMCID: PMC9574348 DOI: 10.4049/immunohorizons.2200018] [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] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2022] [Accepted: 03/10/2022] [Indexed: 11/19/2022] Open
Abstract
Syntenic genomic loci on human chromosome 8 and mouse chromosome 15 (mChr15) code for LY6/Ly6 (lymphocyte Ag 6) family proteins. The 23 murine Ly6 family genes include eight genes that are flanked by the murine Ly6e and Ly6l genes and form an Ly6 subgroup referred to in this article as the Ly6a subfamily gene cluster. Ly6a, also known as Stem Cell Ag-1 and T cell–activating protein, is a member of the Ly6a subfamily gene cluster. No LY6 genes have been annotated within the syntenic LY6E to LY6L human locus. We report in this article on LY6S, a solitary human LY6 gene that is syntenic with the murine Ly6a subfamily gene cluster, and with which it shares a common ancestry. LY6S codes for the IFN-inducible GPI-linked LY6S-iso1 protein that contains only 9 of the 10 consensus LY6 cysteine residues and is most highly expressed in a nonclassical spleen cell population. Its expression leads to distinct shifts in patterns of gene expression, particularly of genes coding for inflammatory and immune response proteins, and LY6S-iso1–expressing cells show increased resistance to viral infection. Our findings reveal the presence of a previously unannotated human IFN-stimulated gene, LY6S, which has a 1:8 ortholog relationship with the genes of the Ly6a subfamily gene cluster, is most highly expressed in spleen cells of a nonclassical cell lineage, and whose expression induces viral resistance and is associated with an inflammatory phenotype and with the activation of genes that regulate immune responses.
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Affiliation(s)
- Moriya Shmerling
- Shmunis School of Biomedicine and Cancer Research, Tel Aviv University, Ramat Aviv, Israel
| | - Michael Chalik
- Shmunis School of Biomedicine and Cancer Research, Tel Aviv University, Ramat Aviv, Israel
| | - Nechama I Smorodinsky
- Shmunis School of Biomedicine and Cancer Research, Tel Aviv University, Ramat Aviv, Israel
| | - Alan Meeker
- The Johns Hopkins University School of Medicine, Baltimore, MD
| | - Sujayita Roy
- The Johns Hopkins University School of Medicine, Baltimore, MD
| | - Orit Sagi-Assif
- Shmunis School of Biomedicine and Cancer Research, Tel Aviv University, Ramat Aviv, Israel
| | - Tsipi Meshel
- Shmunis School of Biomedicine and Cancer Research, Tel Aviv University, Ramat Aviv, Israel
| | - Artem Danilevsky
- Faculty of Medicine and Edmond J. Safra Center for Bioinformatics, Tel Aviv University, Ramat Aviv, Israel
| | - Noam Shomron
- Faculty of Medicine and Edmond J. Safra Center for Bioinformatics, Tel Aviv University, Ramat Aviv, Israel
| | - Shmuel Levinger
- Shmunis School of Biomedicine and Cancer Research, Tel Aviv University, Ramat Aviv, Israel
| | - Bar Nishry
- Shmunis School of Biomedicine and Cancer Research, Tel Aviv University, Ramat Aviv, Israel
| | - David Baruchi
- Shmunis School of Biomedicine and Cancer Research, Tel Aviv University, Ramat Aviv, Israel
| | - Avital Shargorodsky
- Shmunis School of Biomedicine and Cancer Research, Tel Aviv University, Ramat Aviv, Israel
| | - Ravit Ziv
- Shmunis School of Biomedicine and Cancer Research, Tel Aviv University, Ramat Aviv, Israel
| | - Avital Sarusi-Portuguez
- Nancy and Stephen Grand Israel National Center for Personalized Medicine, Weizmann Institute of Science, Rehovot, Israel
| | - Maoz Lahav
- Shmunis School of Biomedicine and Cancer Research, Tel Aviv University, Ramat Aviv, Israel
| | - Marcelo Ehrlich
- Shmunis School of Biomedicine and Cancer Research, Tel Aviv University, Ramat Aviv, Israel
| | - Bryony Braschi
- HUGO Gene Nomenclature Committee, European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridgeshire, United Kingdom; and
| | - Elspeth Bruford
- HUGO Gene Nomenclature Committee, European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridgeshire, United Kingdom; and.,Department of Haematology, University of Cambridge School of Clinical Medicine, Cambridge Biomedical Campus, Cambridge, United Kingdom
| | - Isaac P Witz
- Shmunis School of Biomedicine and Cancer Research, Tel Aviv University, Ramat Aviv, Israel;
| | - Daniel H Wreschner
- Shmunis School of Biomedicine and Cancer Research, Tel Aviv University, Ramat Aviv, Israel;
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Michelson M, Lidzbarsky G, Nishri D, Israel-Elgali I, Berger R, Gafner M, Shomron N, Lev D, Goldberg Y. Microdeletion of 16q24.1-q24.2-A unique etiology of Lymphedema-Distichiasis syndrome and neurodevelopmental disorder. Am J Med Genet A 2022; 188:1990-1996. [PMID: 35312147 PMCID: PMC9314700 DOI: 10.1002/ajmg.a.62730] [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] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2021] [Revised: 12/09/2021] [Accepted: 01/28/2022] [Indexed: 01/15/2023]
Abstract
Interstitial deletions of 16q24.1–q24.2 are associated with alveolar capillary dysplasia, congenital renal malformations, neurodevelopmental disorders, and congenital abnormalities. Lymphedema–Distichiasis syndrome (LDS; OMIM # 153400) is a dominant condition caused by heterozygous pathogenic variants in FOXC2. Usually, lymphedema and distichiasis occur in puberty or later on, and affected individuals typically achieve normal developmental milestones. Here, we describe a boy with congenital lymphedema, distichiasis, bilateral hydronephrosis, and global developmental delay, with a de novo microdeletion of 894 kb at 16q24.1–q24.2. This report extends the phenotype of both 16q24.1–q24.2 microdeletion syndrome and of LDS. Interestingly, the deletion involves only the 3′‐UTR part of FOXC2.
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Affiliation(s)
- Marina Michelson
- Institute of Medical Genetics, Wolfson Medical Center, Holon, Israel.,The Genetic Institute of Maccabi Health Medicinal Organization, Tel-Aviv, Israel.,Sackler School of Medicine, Tel-Aviv University, Tel-Aviv, Israel
| | - Gabriel Lidzbarsky
- Raphael Recanati Genetic Institute, Rabin Medical Center-Beilinson Hospital, Petach Tikva, Israel
| | - Daniella Nishri
- Child Developmental Center of Maccabi Health Medicinal Organization, Tel-Aviv, Israel
| | - Ifat Israel-Elgali
- Sackler School of Medicine, Tel-Aviv University, Tel-Aviv, Israel.,Sagol School of Neuroscience, Tel-Aviv University, Tel-Aviv, Israel
| | - Rachel Berger
- The Genetic Institute of Maccabi Health Medicinal Organization, Tel-Aviv, Israel
| | - Michal Gafner
- Sackler School of Medicine, Tel-Aviv University, Tel-Aviv, Israel
| | - Noam Shomron
- Sackler School of Medicine, Tel-Aviv University, Tel-Aviv, Israel.,Sagol School of Neuroscience, Tel-Aviv University, Tel-Aviv, Israel
| | - Dorit Lev
- Institute of Medical Genetics, Wolfson Medical Center, Holon, Israel.,The Genetic Institute of Maccabi Health Medicinal Organization, Tel-Aviv, Israel.,Sackler School of Medicine, Tel-Aviv University, Tel-Aviv, Israel
| | - Yael Goldberg
- The Genetic Institute of Maccabi Health Medicinal Organization, Tel-Aviv, Israel.,Sackler School of Medicine, Tel-Aviv University, Tel-Aviv, Israel.,Raphael Recanati Genetic Institute, Rabin Medical Center-Beilinson Hospital, Petach Tikva, Israel
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35
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Shapira G, Abu Hamad R, Weiner C, Rainy N, Sorek-Abramovich R, Benveniste-Levkovitz P, Rock R, Avnat E, Levtzion-Korach O, Bar Chaim A, Shomron N. Population differences in antibody response to SARS-CoV-2 infection and BNT162b2 vaccination. FASEB J 2022; 36:e22223. [PMID: 35239233 PMCID: PMC9111330 DOI: 10.1096/fj.202101492r] [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] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2021] [Revised: 01/24/2022] [Accepted: 02/10/2022] [Indexed: 12/14/2022]
Abstract
The concentration of SARS‐CoV‐2‐specific serum antibodies, elicited by vaccination or infection, is a primary determinant of anti‐viral immunity, which correlates with protection against infection and COVID‐19. Serum samples were obtained from 25 897 participants and assayed for anti‐SARS‐CoV‐2 spike protein RBD IgG antibodies. The cohort was composed of newly vaccinated BNT162b2 recipients, in the first month or 6 months after vaccination, COVID‐19 patients and a general sample of the Israeli population. Antibody levels of BNT162b2 vaccine recipients were negatively correlated with age, with a prominent decrease in recipients over 55 years old, which was most significant in males. This trend was observable within the first month and 6 months after vaccination, while younger participants were more likely to maintain stable levels of serum antibodies. The antibody concentration of participants previously infected with SARS‐CoV‐2 was lower than the vaccinated and had a more complex, non‐linear relation to age, sex and COVID‐19 symptoms. Taken together, our data supports age and sex as primary determining factors for both the magnitude and durability of humoral response to SARS‐CoV‐2 infection and the COVID‐19 vaccine. Our results could inform vaccination policies, prioritizing the most susceptible populations for repeated vaccination.
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Affiliation(s)
- Guy Shapira
- Department of Cell and Developmental Biology, Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel.,Edmond J. Safra Center for Bioinformatics, Tel Aviv University, Tel Aviv, Israel
| | | | - Chen Weiner
- Department of Cell and Developmental Biology, Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel.,Shamir Medical Center, Be'er Yaacov, Israel
| | - Nir Rainy
- Shamir Medical Center, Be'er Yaacov, Israel
| | | | | | | | - Eden Avnat
- Department of Cell and Developmental Biology, Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | | | | | - Noam Shomron
- Department of Cell and Developmental Biology, Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel.,Edmond J. Safra Center for Bioinformatics, Tel Aviv University, Tel Aviv, Israel
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36
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Sergeeva OV, Shcherbinina EY, Shomron N, Zatsepin TS. Modulation of RNA Splicing by Oligonucleotides: Mechanisms of Action and Therapeutic Implications. Nucleic Acid Ther 2022; 32:123-138. [PMID: 35166605 DOI: 10.1089/nat.2021.0067] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [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: 12/18/2022] Open
Abstract
Dysregulation of RNA splicing causes many diseases and disorders. Several therapeutic approaches have been developed to correct aberrant alternative splicing events for the treatment of cancers and hereditary diseases, including gene therapy and redirecting splicing, using small molecules or splice switching oligonucleotides (SSO). Significant advances in the chemistry and pharmacology of nucleic acid have led to the development of clinically approved SSO drugs for the treatment of spinal muscular dystrophy and Duchenne muscular dystrophy (DMD). In this review, we discuss the mechanisms of SSO action with emphasis on "less common" approaches to modulate alternative splicing, including bipartite and bifunctional SSO, oligonucleotide decoys for splice factors and SSO-mediated mRNA degradation via AS-NMD and NGD pathways. We briefly discuss the current progress and future perspectives of SSO therapy for rare and ultrarare diseases.
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Affiliation(s)
- Olga V Sergeeva
- Center of Life Sciences, Skolkovo Institute of Science and Technology, Moscow, Russia
| | | | - Noam Shomron
- Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Timofei S Zatsepin
- Center of Life Sciences, Skolkovo Institute of Science and Technology, Moscow, Russia.,Department of Chemistry, Moscow State University, Moscow, Russia
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37
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Orenstein N, Gofin Y, Shomron N, Ruhrman-Shahar N, Magal N, Hagari O, Azulay N, Bazak L, Goldberg Y, Basel-Salmon L. DYRK1B haploinsufficiency in a family with metabolic syndrome and abnormal cognition. Clin Genet 2022; 101:265-266. [PMID: 34786696 DOI: 10.1111/cge.14084] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2021] [Revised: 10/29/2021] [Accepted: 10/30/2021] [Indexed: 11/29/2022]
Abstract
A family with DYRK1B LOF variant offering to expand the phenotype beyond the metabolic syndrome.
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Affiliation(s)
- Naama Orenstein
- Pediatric Genetics Clinic, Schneider Children's Medical Center of Israel, Petach Tikva, Israel
| | - Yoel Gofin
- Pediatric Genetics Clinic, Schneider Children's Medical Center of Israel, Petach Tikva, Israel
| | - Noam Shomron
- Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Noa Ruhrman-Shahar
- Raphael Recanati Genetic Institute, Rabin Medical Center, Beilinson Hospital, Petach Tikva, Israel
| | - Nurit Magal
- Raphael Recanati Genetic Institute, Rabin Medical Center, Beilinson Hospital, Petach Tikva, Israel
| | - Ofir Hagari
- Raphael Recanati Genetic Institute, Rabin Medical Center, Beilinson Hospital, Petach Tikva, Israel
| | - Noy Azulay
- Raphael Recanati Genetic Institute, Rabin Medical Center, Beilinson Hospital, Petach Tikva, Israel
| | - Lily Bazak
- Raphael Recanati Genetic Institute, Rabin Medical Center, Beilinson Hospital, Petach Tikva, Israel
| | - Yael Goldberg
- Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
- Raphael Recanati Genetic Institute, Rabin Medical Center, Beilinson Hospital, Petach Tikva, Israel
| | - Lina Basel-Salmon
- Pediatric Genetics Clinic, Schneider Children's Medical Center of Israel, Petach Tikva, Israel
- Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
- Raphael Recanati Genetic Institute, Rabin Medical Center, Beilinson Hospital, Petach Tikva, Israel
- Felsenstein Medical Research Center, Petach Tikva, Israel
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38
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Grad M, Nir A, Levy G, Trangle SS, Shapira G, Shomron N, Assaf Y, Barak B. Altered White Matter and microRNA Expression in a Murine Model Related to Williams Syndrome Suggests That miR-34b/c Affects Brain Development via Ptpru and Dcx Modulation. Cells 2022; 11:cells11010158. [PMID: 35011720 PMCID: PMC8750756 DOI: 10.3390/cells11010158] [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: 11/09/2021] [Revised: 12/15/2021] [Accepted: 12/28/2021] [Indexed: 11/16/2022] Open
Abstract
Williams syndrome (WS) is a multisystem neurodevelopmental disorder caused by a de novo hemizygous deletion of ~26 genes from chromosome 7q11.23, among them the general transcription factor II-I (GTF2I). By studying a novel murine model for the hypersociability phenotype associated with WS, we previously revealed surprising aberrations in myelination and cell differentiation properties in the cortices of mutant mice compared to controls. These mutant mice had selective deletion of Gtf2i in the excitatory neurons of the forebrain. Here, we applied diffusion magnetic resonance imaging and fiber tracking, which showed a reduction in the number of streamlines in limbic outputs such as the fimbria/fornix fibers and the stria terminalis, as well as the corpus callosum of these mutant mice compared to controls. Furthermore, we utilized next-generation sequencing (NGS) analysis of cortical small RNAs' expression (RNA-Seq) levels to identify altered expression of microRNAs (miRNAs), including two from the miR-34 cluster, known to be involved in prominent processes in the developing nervous system. Luciferase reporter assay confirmed the direct binding of miR-34c-5p to the 3'UTR of PTPRU-a gene involved in neural development that was elevated in the cortices of mutant mice relative to controls. Moreover, we found an age-dependent variation in the expression levels of doublecortin (Dcx)-a verified miR-34 target. Thus, we demonstrate the substantial effect a single gene deletion can exert on miRNA regulation and brain structure, and advance our understanding and, hopefully, treatment of WS.
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Affiliation(s)
- Meitar Grad
- Sagol School of Neuroscience, Tel Aviv University, Tel Aviv 6997801, Israel; (M.G.); (A.N.); (G.L.); (N.S.); (Y.A.)
| | - Ariel Nir
- Sagol School of Neuroscience, Tel Aviv University, Tel Aviv 6997801, Israel; (M.G.); (A.N.); (G.L.); (N.S.); (Y.A.)
| | - Gilad Levy
- Sagol School of Neuroscience, Tel Aviv University, Tel Aviv 6997801, Israel; (M.G.); (A.N.); (G.L.); (N.S.); (Y.A.)
| | - Sari Schokoroy Trangle
- Faculty of Social Sciences, School of Psychological Sciences, Tel Aviv University, Tel Aviv 6997801, Israel;
| | - Guy Shapira
- Department of Cell and Developmental Biology, Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv 6997801, Israel;
- Edmond J. Safra Center for Bioinformatics, Tel Aviv University, Tel Aviv 6997801, Israel
| | - Noam Shomron
- Sagol School of Neuroscience, Tel Aviv University, Tel Aviv 6997801, Israel; (M.G.); (A.N.); (G.L.); (N.S.); (Y.A.)
- Department of Cell and Developmental Biology, Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv 6997801, Israel;
- Edmond J. Safra Center for Bioinformatics, Tel Aviv University, Tel Aviv 6997801, Israel
| | - Yaniv Assaf
- Sagol School of Neuroscience, Tel Aviv University, Tel Aviv 6997801, Israel; (M.G.); (A.N.); (G.L.); (N.S.); (Y.A.)
- Faculty of Life Sciences, School of Neurobiology, Biochemistry & Biophysics, Tel Aviv University, Tel Aviv 6997801, Israel
| | - Boaz Barak
- Sagol School of Neuroscience, Tel Aviv University, Tel Aviv 6997801, Israel; (M.G.); (A.N.); (G.L.); (N.S.); (Y.A.)
- Faculty of Social Sciences, School of Psychological Sciences, Tel Aviv University, Tel Aviv 6997801, Israel;
- Correspondence:
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39
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Dolitzky A, Shapira G, Grisaru-Tal S, Hazut I, Avlas S, Gordon Y, Itan M, Shomron N, Munitz A. Transcriptional Profiling of Mouse Eosinophils Identifies Distinct Gene Signatures Following Cellular Activation. Front Immunol 2022; 12:802839. [PMID: 34970274 PMCID: PMC8712732 DOI: 10.3389/fimmu.2021.802839] [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] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2021] [Accepted: 11/22/2021] [Indexed: 01/21/2023] Open
Abstract
Eosinophils are multifunctional, evolutionary conserved leukocytes that are involved in a plethora of responses ranging from regulation of tissue homeostasis to host defense and cancer. Eosinophils have been studied mostly in the context of Type 2 inflammatory responses such as those found in allergy. Nonetheless, it is now evident that they participate in Type 1 inflammatory responses and can respond to Type 1 cytokines such as IFN-γ. Recent data suggest that the pleotropic roles of eosinophils are due to heterogeneous responses to environmental cues. Despite this, the activation profile of eosinophils, in response to various stimuli is yet to be defined. To better understand the transcriptional spectrum of eosinophil activation, we exposed eosinophils to Type 1 (e.g. IFN-γ, E. coli) vs. Type 2 (e.g. IL-4) conditions and subjected them to global RNA sequencing. Our analyses show that IL-4, IFN-γ, E. coli and IFN-γ in the presence of E. coli (IFN-γ/E. coli)-stimulated eosinophils acquire distinct transcriptional profiles, which polarize them towards what we termed Type 1 and Type 2 eosinophils. Bioinformatics analyses using Gene Ontology based on biological processes revealed that different stimuli induced distinct pathways in eosinophils. These pathways were confirmed using functional assays by assessing cytokine/chemokine release (i.e. CXCL9, CCL24, TNF-α and IL-6) from eosinophils following activation. In addition, analysis of cell surface markers highlighted CD101 and CD274 as potential cell surface markers that distinguish between Type 1 and Type 2 eosinophils, respectively. Finally, the transcriptome signature of Type 1 eosinophils resembled that of eosinophils that were obtained from mice with experimental colitis whereas the transcriptome signature of Type 2 eosinophils resembled that of eosinophils from experimental asthma. Our data demonstrate that eosinophils are polarized to distinct “Type 1” and “Type 2” phenotypes following distinct stimulations. These findings provide fundamental knowledge regarding the heterogeneity of eosinophils and support the presence of transcriptional differences between Type 1 and Type 2 cells that are likely reflected by their pleotropic activities in diverse disease settings.
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Affiliation(s)
- Avishay Dolitzky
- Department of Clinical Microbiology and Immunology, Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Guy Shapira
- Department of Cell and Developmental Biology, Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Sharon Grisaru-Tal
- Department of Clinical Microbiology and Immunology, Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Inbal Hazut
- Department of Clinical Microbiology and Immunology, Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Shmulik Avlas
- Department of Clinical Microbiology and Immunology, Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Yaara Gordon
- Department of Clinical Microbiology and Immunology, Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Micahl Itan
- Department of Clinical Microbiology and Immunology, Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Noam Shomron
- Department of Cell and Developmental Biology, Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Ariel Munitz
- Department of Clinical Microbiology and Immunology, Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
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40
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Hollestein LM, Lo SN, Leonardi-Bee J, Rosset S, Shomron N, Couturier DL, Gran S. MULTIPLE ways to correct for MULTIPLE comparisons in MULTIPLE types of studies. Br J Dermatol 2021; 185:1081-1083. [PMID: 34919266 DOI: 10.1111/bjd.20600] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2021] [Revised: 06/15/2021] [Accepted: 06/16/2021] [Indexed: 11/28/2022]
Affiliation(s)
- L M Hollestein
- Department of Dermatology, Erasmus MC University Medical Center, Rotterdam, the Netherlands.,Department of Research, Netherlands Comprehensive Cancer Organization (IKNL), Utrecht, the Netherlands
| | - S N Lo
- Melanoma Institute Australia, The University of Sydney, Sydney, NSW, Australia.,Faculty of Medicine and Health, The University of Sydney, Sydney, NSW, Australia.,Institute for Research and Medical Consultations (IRMC), Imam Abdulrahman Bin Faisal University, Dammam, Saudi Arabia
| | - J Leonardi-Bee
- Centre for Evidence Based Healthcare, Division of Epidemiology and Public Health, University of Nottingham, Nottingham, UK
| | - S Rosset
- Department of Statistics and Operations Research, Tel Aviv University, Tel Aviv, Israel.,Edmond J. Safra Center for Bioinformatics, Tel Aviv University, Tel Aviv, Israel
| | - N Shomron
- Edmond J. Safra Center for Bioinformatics, Tel Aviv University, Tel Aviv, Israel.,Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - D-L Couturier
- Medical Research Council (MRC) Biostatistics Unit, University of Cambridge, Cambridge, UK.,Cancer Research UK - Cambridge Institute, University of Cambridge, Cambridge, UK
| | - S Gran
- Center for Evidence-Based Dermatology, School of Medicine, University of Nottingham, Nottingham, UK
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41
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Yoffe L, Kuperman AA, Isakov O, Haguel D, Polsky AL, Farberov L, Pillar N, Gurevich V, Haviv I, Shomron N. Assessing the involvement of the placental microbiome and virome in preeclampsia using non coding RNA sequencing. J Perinat Med 2021; 49:1071-1083. [PMID: 34114389 DOI: 10.1515/jpm-2021-0006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/09/2021] [Accepted: 04/29/2021] [Indexed: 11/15/2022]
Abstract
OBJECTIVES Preeclampsia is a dangerous pregnancy complication. The source of preeclampsia is unknown, though the placenta is believed to have a central role in its pathogenesis. An association between maternal infection and preeclampsia has been demonstrated, yet the involvement of the placental microbiome in the etiology of preeclampsia has not been determined. In this study, we examined whether preeclampsia is associated with an imbalanced microorganism composition in the placenta. METHODS To this end, we developed a novel method for the identification of bacteria/viruses based on sequencing of small non-coding RNA, which increases the microorganism-to-host ratio, this being a major challenge in microbiome methods. We validated the method on various infected tissues and demonstrated its efficiency in detecting microorganisms in samples with extremely low bacterial/viral biomass. We then applied the method to placenta specimens from preeclamptic and healthy pregnancies. Since the placenta is a remarkably large and heterogeneous organ, we explored the bacterial and viral RNA at each of 15 distinct locations. RESULTS Bacterial RNA was detected at all locations and was consistent with previous studies of the placental microbiome, though without significant differences between the preeclampsia and control groups. Nevertheless, the bacterial RNA composition differed significantly between various areas of the placenta. Viral RNA was detected in extremely low quantities, below the threshold of significance, thus viral abundance could not be determined. CONCLUSIONS Our results suggest that the bacterial and viral abundance in the placenta may have only limited involvement in the pathogenesis of preeclampsia. The evidence of a heterogenic bacterial RNA composition in the various placental locations warrants further investigation to capture the true nature of the placental microbiome.
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Affiliation(s)
- Liron Yoffe
- Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Amir A Kuperman
- Blood Coagulation Service and Pediatric Hematology Clinic, Galilee Medical Center, Nahariya, Israel
- Azrieli Faculty of Medicine, Bar-Ilan University, Safed, Israel
| | - Ofer Isakov
- Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
- Department of Internal Medicine "T", Tel Aviv Medical Center, Tel Aviv, Israel
| | | | | | - Luba Farberov
- Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Nir Pillar
- Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | | | - Izhak Haviv
- Azrieli Faculty of Medicine, Bar-Ilan University, Safed, Israel
| | - Noam Shomron
- Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
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42
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Altman T, Ionescu A, Ibraheem A, Priesmann D, Gradus-Pery T, Farberov L, Alexandra G, Shelestovich N, Dafinca R, Shomron N, Rage F, Talbot K, Ward ME, Dori A, Krüger M, Perlson E. Axonal TDP-43 condensates drive neuromuscular junction disruption through inhibition of local synthesis of nuclear encoded mitochondrial proteins. Nat Commun 2021; 12:6914. [PMID: 34824257 PMCID: PMC8617040 DOI: 10.1038/s41467-021-27221-8] [Citation(s) in RCA: 57] [Impact Index Per Article: 19.0] [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: 02/28/2021] [Accepted: 11/08/2021] [Indexed: 01/02/2023] Open
Abstract
Mislocalization of the predominantly nuclear RNA/DNA binding protein, TDP-43, occurs in motor neurons of ~95% of amyotrophic lateral sclerosis (ALS) patients, but the contribution of axonal TDP-43 to this neurodegenerative disease is unclear. Here, we show TDP-43 accumulation in intra-muscular nerves from ALS patients and in axons of human iPSC-derived motor neurons of ALS patient, as well as in motor neurons and neuromuscular junctions (NMJs) of a TDP-43 mislocalization mouse model. In axons, TDP-43 is hyper-phosphorylated and promotes G3BP1-positive ribonucleoprotein (RNP) condensate assembly, consequently inhibiting local protein synthesis in distal axons and NMJs. Specifically, the axonal and synaptic levels of nuclear-encoded mitochondrial proteins are reduced. Clearance of axonal TDP-43 or dissociation of G3BP1 condensates restored local translation and resolved TDP-43-derived toxicity in both axons and NMJs. These findings support an axonal gain of function of TDP-43 in ALS, which can be targeted for therapeutic development.
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Affiliation(s)
- Topaz Altman
- Sackler Faculty of Medicine, Tel-Aviv University, Tel-Aviv, Israel
| | - Ariel Ionescu
- Sackler Faculty of Medicine, Tel-Aviv University, Tel-Aviv, Israel
| | - Amjad Ibraheem
- Sackler Faculty of Medicine, Tel-Aviv University, Tel-Aviv, Israel
| | - Dominik Priesmann
- CECAD Research Center and Center for Molecular Medicine (CMMC), University of Cologne, 50931, Cologne, Germany
| | - Tal Gradus-Pery
- Sackler Faculty of Medicine, Tel-Aviv University, Tel-Aviv, Israel
| | - Luba Farberov
- Sackler Faculty of Medicine, Tel-Aviv University, Tel-Aviv, Israel
| | - Gayster Alexandra
- Pathology Institute, Sheba Medical Center, Tel Hashomer, Ramat Gan, Israel
| | | | - Ruxandra Dafinca
- Nuffield Department of Clinical Neurosciences, University of Oxford, Oxford, UK
| | - Noam Shomron
- Sackler Faculty of Medicine, Tel-Aviv University, Tel-Aviv, Israel
- Sagol School of Neuroscience, Tel-Aviv University, Tel-Aviv, Israel
| | - Florence Rage
- Institut de Génétique Moléculaire de Montpellier, IGMM UMR535, Montpellier, France
| | - Kevin Talbot
- Nuffield Department of Clinical Neurosciences, University of Oxford, Oxford, UK
| | - Michael E Ward
- National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, USA
| | - Amir Dori
- Department of Neurology, Sheba Medical Center, Tel Hashomer and Sackler Faculty of Medicine, Tel Aviv University, Ramat Gan, Israel
| | - Marcus Krüger
- CECAD Research Center and Center for Molecular Medicine (CMMC), University of Cologne, 50931, Cologne, Germany
| | - Eran Perlson
- Sackler Faculty of Medicine, Tel-Aviv University, Tel-Aviv, Israel.
- Sagol School of Neuroscience, Tel-Aviv University, Tel-Aviv, Israel.
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43
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Poleg S, Kourieh E, Ruban A, Shapira G, Shomron N, Barak B, Offen D. Behavioral aspects and neurobiological properties underlying medical cannabis treatment in Shank3 mouse model of autism spectrum disorder. Transl Psychiatry 2021; 11:524. [PMID: 34645786 PMCID: PMC8514476 DOI: 10.1038/s41398-021-01612-3] [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] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/30/2020] [Revised: 07/16/2021] [Accepted: 08/04/2021] [Indexed: 12/27/2022] Open
Abstract
Autism spectrum disorder (ASD) is a neurodevelopmental disease with a wide spectrum of manifestation. The core symptoms of ASD are persistent deficits in social communication, and restricted and repetitive patterns of behavior, interests, or activities. These are often accompanied by intellectual disabilities. At present, there is no designated effective treatment for the core symptoms and co-morbidities of ASD. Recently, interest is rising in medical cannabis as a treatment for ASD, with promising clinical data. However, there is a notable absence of basic pre-clinical research in this field. In this study, we investigate the behavioral and biochemical effects of long-term oral treatment with CBD-enriched medical cannabis oil in a human mutation-based Shank3 mouse model of ASD. Our findings show that this treatment alleviates anxiety and decreases repetitive grooming behavior by over 70% in treated mutant mice compared to non-treated mutant mice. Furthermore, we were able to uncover the involvement of CB1 receptor (CB1R) signaling in the Avidekel oil mechanism, alongside a mitigation of cerebrospinal fluid (CSF) glutamate concentrations. Subsequently, RNA sequencing (RNA seq) of cerebellar brain samples revealed changes in mRNA expression of several neurotransmission-related genes post-treatment. Finally, our results question the relevancy of CBD enrichment of medical cannabis for treating the core symptoms of ASD, and emphasize the importance of the THC component for alleviating deficits in repetitive and social behaviors in ASD.
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Affiliation(s)
- Shani Poleg
- Sackler Faculty of Medicine, Human Molecular Genetics & Biochemistry, Felsenstein Medical Research Center, Tel-Aviv University, Tel Aviv, Israel
| | - Emad Kourieh
- The George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv, Israel
- Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Angela Ruban
- Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Guy Shapira
- Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Noam Shomron
- Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Boaz Barak
- Sagol School of Neuroscience, Tel-Aviv University, Tel Aviv, Israel
- The School of Psychological Sciences, Faculty of Social Sciences, Tel Aviv University, Tel Aviv, Israel
| | - Daniel Offen
- Sackler Faculty of Medicine, Human Molecular Genetics & Biochemistry, Felsenstein Medical Research Center, Tel-Aviv University, Tel Aviv, Israel.
- Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel.
- Sagol School of Neuroscience, Tel-Aviv University, Tel Aviv, Israel.
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44
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Nachman D, Eisenkraft A, Maor Y, Constantini K, Goldstein G, Levy R, Halberthal M, Horowitz NA, Golan R, Rosenberg E, Lavon E, Cohen O, Shapira G, Shomron N, Gepner Y. Continuous monitoring of advanced hemodynamic parameters shows early cardiovascular changes in a cohort of 492 COVID-19 hospitalized patients. Eur Heart J 2021. [DOI: 10.1093/eurheartj/ehab724.3090] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Abstract
Background
COVID-19 exerts deleterious cardiopulmonary effects, leading to worse prognosis in the most effected.
Purpose
The aim of this retrospective multi-center observational cohort study was to analyze the trajectories of key advanced hemodynamic parameters amongst hospitalized COVID-19 patients according to different risk populations using a chest-patch wearable providing continuous remote patient monitoring.
Methods
The study was conducted in five COVID-19 isolation units. Patients admitted to the units were connected to a photoplethysmography based noninvasive remote advanced hemodynamic monitor after completing a basic risk factor survey. Physiological parameters were measured every 15 minutes during the hospitalization, including cardiac output (CO), cardiac index (CI), systemic vascular resistance (SVR), heart rate, blood pressure (BP), respiratory rate, blood oxygen saturation (SpO2), and body temperature.
Results
492 COVID-19 patients (179 females, average age 58.7 years) were included in the final analysis, with more than 3 million measurements collected during an average of 75.3 hours. Overall, within the first five days of hospitalizations we found a significant increase in SVR, and a significant decrease in SpO2, DBP, CO and CI (p<0.01 for all). The changes were more prominent in high risk populations- males, older age and obesity and had a temporal correspondence to changes in respiratory parameters.
Conclusions
This is the first comprehensive continuous advanced hemodynamic profiling of COVID-19 patients. Worse hemodynamic status was prominent in high risk populations.
Funding Acknowledgement
Type of funding sources: None.
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Affiliation(s)
- D Nachman
- Hadassah - Hebrew University Medical Center Jerusalem, Jerusalem, Israel
| | - A Eisenkraft
- The Hebrew University Faculty of Medicine, Jerusalem, Israel, and the Israel Defense Force Medical, Institute for Research in Military Medicine, Jerusalem, Israel
| | - Y Maor
- The Edith Wolfson Medical Center, Holon, Israel
| | - K Constantini
- Tel Aviv University, Department of Epidemiology, Preventive Medicine, School of Public Health, Sylvan Adams Sports center, Tel Aviv, Israel
| | - G Goldstein
- Tel Aviv University, Department of Epidemiology, Preventive Medicine, School of Public Health, Sylvan Adams Sports center, Tel Aviv, Israel
| | - R Levy
- Maccabi Healthcare Services, Tel Aviv, Israel
| | | | | | - R Golan
- Baruch Padeh Medical Center, The Faculty of Medicine in Galilee, Bar Ilan University, Tiberias, Israel
| | - E Rosenberg
- Soroka University Medical Center, Beer Sheva, Israel
| | - E Lavon
- Kaplan Medical Center, Rehovot, Israel
| | - O Cohen
- The Edith Wolfson Medical Center, Holon, Israel
| | - G Shapira
- Tel Aviv University, Tel Aviv, Israel
| | - N Shomron
- Tel Aviv University, Tel Aviv, Israel
| | - Y Gepner
- Tel Aviv University, Department of Epidemiology, Preventive Medicine, School of Public Health, Sylvan Adams Sports center, Tel Aviv, Israel
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45
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Zoabi Y, Kehat O, Lahav D, Weiss-Meilik A, Adler A, Shomron N. Predicting bloodstream infection outcome using machine learning. Sci Rep 2021; 11:20101. [PMID: 34635696 PMCID: PMC8505419 DOI: 10.1038/s41598-021-99105-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2021] [Accepted: 09/20/2021] [Indexed: 11/13/2022] Open
Abstract
Bloodstream infections (BSI) are a main cause of infectious disease morbidity and mortality worldwide. Early prediction of BSI patients at high risk of poor outcomes is important for earlier decision making and effective patient stratification. We developed electronic medical record-based machine learning models that predict patient outcomes of BSI. The area under the receiver-operating characteristics curve was 0.82 for a full featured inclusive model, and 0.81 for a compact model using only 25 features. Our models were trained using electronic medical records that include demographics, blood tests, and the medical and diagnosis history of 7889 hospitalized patients diagnosed with BSI. Among the implications of this work is implementation of the models as a basis for selective rapid microbiological identification, toward earlier administration of appropriate antibiotic therapy. Additionally, our models may help reduce the development of BSI and its associated adverse health outcomes and complications.
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Affiliation(s)
- Yazeed Zoabi
- Sackler Faculty of Medicine, Tel Aviv University, 6997801, Tel Aviv, Israel.,Edmond J Safra Center for Bioinformatics, Tel Aviv University, 6997801, Tel Aviv, Israel
| | - Orli Kehat
- I-Medata AI Center, Tel-Aviv Sourasky Medical Center, 6423906, Tel Aviv, Israel
| | - Dan Lahav
- Sackler Faculty of Medicine, Tel Aviv University, 6997801, Tel Aviv, Israel.,Edmond J Safra Center for Bioinformatics, Tel Aviv University, 6997801, Tel Aviv, Israel.,The Blavatnik School of Computer Science, Tel Aviv University, 6997801, Tel Aviv, Israel
| | - Ahuva Weiss-Meilik
- I-Medata AI Center, Tel-Aviv Sourasky Medical Center, 6423906, Tel Aviv, Israel.
| | - Amos Adler
- Sackler Faculty of Medicine, Tel Aviv University, 6997801, Tel Aviv, Israel. .,Clinical Microbiology Laboratory, Tel Aviv Sourasky Medical Center, 6423906, Tel Aviv, Israel.
| | - Noam Shomron
- Sackler Faculty of Medicine, Tel Aviv University, 6997801, Tel Aviv, Israel. .,Edmond J Safra Center for Bioinformatics, Tel Aviv University, 6997801, Tel Aviv, Israel.
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46
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Mohamad J, Sarig O, Malki L, Rabinowitz T, Assaf S, Malovitski K, Pavlovsky M, Shomron N, Samuelov L, Sprecher E. 162 Loss-of-function variants in SERPINA12 underlie autosomal recessive palmoplantar keratoderma. J Invest Dermatol 2021. [DOI: 10.1016/j.jid.2021.08.166] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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47
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Weiner C, Hecht I, Kotlyar A, Shoshany N, Zadok D, Elbaz U, Segev F, Maytal A, Hachmo Y, Michiels C, De Backer O, Shomron N, Einan-Lifshitz A, Pras E. Association of Variants in TMEM45A With Keratoglobus. JAMA Ophthalmol 2021; 139:1089-1095. [PMID: 34410316 DOI: 10.1001/jamaophthalmol.2021.3172] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
Abstract
Importance Keratoglobus is a rare corneal disorder characterized by generalized thinning and globular protrusion of the cornea. Affected individuals typically have significantly decreased vision and are at risk of corneal perforation. The genetic basis and inheritance pattern of isolated congenital keratoglobus are currently unknown. Objective To identify the genetic basis of isolated congenital keratoglobus. Design, Setting, and Participants This case series and molecular analysis studied 3 unrelated nonconsanguineous families with keratoglobus at a medical center in Israel. Data were collected from June 2019 to March 2021 and analyzed during the same period. Exposures Whole-exome sequencing and direct Sanger sequencing, expression analysis by real-time polymerase chain reaction, splice-site variant analysis, immunohistochemical staining, and histological evaluation of a knockout mouse model. Main Outcomes and Measure Molecular characteristics associated with keratoglobus. Results Four pediatric patients (3 male individuals) from 3 families had clinical findings consistent with keratoglobus. These included globular protrusion, corneal thinning more prominent at the periphery, and high astigmatism. Truncating and splice site variants were identified in the TMEM45A gene, which fully segregate with the disorder. All affected individuals were homozygous or compound heterozygous for variants in the TMEM45A gene, while unaffected family members were heterozygous carriers. Expression analysis in healthy controls showed that TMEM45A was expressed 23 times higher in the human cornea compared with peripheral blood. Immunohistochemical staining of the TMEM45A protein in normal corneas confirmed its expression in the corneal stroma and epithelium. A TMEM45A knockout mouse model showed structural features consistent with keratoglobus. Conclusions and Relevance Expression of TMEM45A has been previously shown to result in upregulation of extracellular matrix components and fibrosis. These results suggest that isolated congenital keratoglobus is an autosomal recessively inherited disorder associated with variants in the TMEM45A gene.
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Affiliation(s)
- Chen Weiner
- Matlow's Ophthalmo-genetic Laboratory, Department of Ophthalmology, Shamir Medical Center, Zerifin, Israel.,Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Idan Hecht
- Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel.,Department of Ophthalmology, Shamir Medical Center, Zerifin, Israel
| | - Alina Kotlyar
- Matlow's Ophthalmo-genetic Laboratory, Department of Ophthalmology, Shamir Medical Center, Zerifin, Israel
| | - Nadav Shoshany
- Matlow's Ophthalmo-genetic Laboratory, Department of Ophthalmology, Shamir Medical Center, Zerifin, Israel.,Department of Ophthalmology, Shamir Medical Center, Zerifin, Israel
| | - David Zadok
- Department of Ophthalmology, Shaare Zedek Medical Center Affiliated with the Hebrew University-Hadassah School of Medicine, Jerusalem, Israel
| | - Uri Elbaz
- Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel.,Department of Ophthalmology, Rabin Medical Center, Schneider Hospital, Petah Tikva, Israel
| | - Fani Segev
- Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel.,Goldschleger Eye Institute, Sheba Medical Center, Tel Hashomer, Israel
| | - Anat Maytal
- Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel.,Department of Ophthalmology, Meir Medical Center, Kfar Saba, Israel
| | - Yafit Hachmo
- Research and Development unit, Shamir Medical Center, Zerifin, Israel
| | | | | | - Noam Shomron
- Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Adi Einan-Lifshitz
- Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel.,Department of Ophthalmology, Shamir Medical Center, Zerifin, Israel
| | - Eran Pras
- Matlow's Ophthalmo-genetic Laboratory, Department of Ophthalmology, Shamir Medical Center, Zerifin, Israel.,Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel.,Department of Ophthalmology, Shamir Medical Center, Zerifin, Israel
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48
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Eisenkraft A, Maor Y, Constantini K, Goldstein N, Nachman D, Levy R, Halberthal M, Horowitz NA, Golan R, Rosenberg E, Lavon E, Cohen O, Shapira G, Shomron N, Ishay AB, Sand E, Merin R, Fons M, Littman R, Gepner Y. Continuous Remote Patient Monitoring Shows Early Cardiovascular Changes in COVID-19 Patients. J Clin Med 2021; 10:4218. [PMID: 34575328 PMCID: PMC8468944 DOI: 10.3390/jcm10184218] [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] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2021] [Revised: 09/14/2021] [Accepted: 09/15/2021] [Indexed: 12/23/2022] Open
Abstract
COVID-19 exerts deleterious cardiopulmonary effects, leading to a worse prognosis in the most affected. This retrospective multi-center observational cohort study aimed to analyze the trajectories of key vitals amongst hospitalized COVID-19 patients using a chest-patch wearable providing continuous remote patient monitoring of numerous vital signs. The study was conducted in five COVID-19 isolation units. A total of 492 COVID-19 patients were included in the final analysis. Physiological parameters were measured every 15 min. More than 3 million measurements were collected including heart rate, systolic and diastolic blood pressure, cardiac output, cardiac index, systemic vascular resistance, respiratory rate, blood oxygen saturation, and body temperature. Cardiovascular deterioration appeared early after admission and in parallel with changes in the respiratory parameters, showing a significant difference in trajectories within sub-populations at high risk. Early detection of cardiovascular deterioration of COVID-19 patients is achievable when using frequent remote patient monitoring.
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Affiliation(s)
- Arik Eisenkraft
- Institute for Research in Military Medicine, The Hebrew University Faculty of Medicine, P.O. Box 12272, Jerusalem 9112102, Israel;
- The Israel Defense Force Medical Corps, P.O. Box 12272, Jerusalem 9112102, Israel
- Biobeat Technologies Ltd., 22 Efal St., Petah Tikva 4951122, Israel; (A.B.I.); (E.S.); (R.M.); (M.F.); (R.L.)
| | - Yasmin Maor
- Wolfson Medical Center, 62 Ha-Lokhamim St. 62, Holon 58100, Israel; (Y.M.); (O.C.)
- The Sackler Faculty of Medicine, Tel Aviv University, P.O. Box 39040, Tel Aviv 6997801, Israel; (G.S.); (N.S.)
| | - Keren Constantini
- Department of Epidemiology and Preventive Medicine, School of Public Health, Sackler Faculty of Medicine and Sylvan Adams Sports Institute, Tel Aviv University, P.O. Box 39040, Tel Aviv 6997801, Israel; (K.C.); (N.G.); (Y.G.)
| | - Nir Goldstein
- Department of Epidemiology and Preventive Medicine, School of Public Health, Sackler Faculty of Medicine and Sylvan Adams Sports Institute, Tel Aviv University, P.O. Box 39040, Tel Aviv 6997801, Israel; (K.C.); (N.G.); (Y.G.)
| | - Dean Nachman
- Institute for Research in Military Medicine, The Hebrew University Faculty of Medicine, P.O. Box 12272, Jerusalem 9112102, Israel;
- The Israel Defense Force Medical Corps, P.O. Box 12272, Jerusalem 9112102, Israel
- Heart Institute, Hadassah Ein Kerem Medical Center, P.O. Box 911201, Jerusalem 9112102, Israel
| | - Ran Levy
- Maccabi Healthcare Services, P.O. Box 50493, Tel Aviv 68125, Israel;
| | - Michael Halberthal
- General Directorate Rambam Health Care Campus, P.O. Box 9602, Haifa 3109601, Israel; (M.H.); (N.A.H.)
- The Bruce Rappaport Faculty of Medicine, Technion, P.O. Box 9649, Haifa 3525433, Israel
| | - Netanel A. Horowitz
- General Directorate Rambam Health Care Campus, P.O. Box 9602, Haifa 3109601, Israel; (M.H.); (N.A.H.)
- The Bruce Rappaport Faculty of Medicine, Technion, P.O. Box 9649, Haifa 3525433, Israel
| | - Ron Golan
- The Baruch Padeh Medical Center Poriya, The Faculty of Medicine in Galilee, Bar Ilan University, Upper Galilee, Poria 1528001, Israel;
| | - Elli Rosenberg
- Internal Medicine A, The Soroka University Medical Center, Ben-Gurion University of the Negev, P.O. Box 151, Be’er Sheva 84101, Israel;
| | - Eitan Lavon
- The Kaplan Medical Center, The Hebrew University Faculty of Medicine, P.O. Box 1, Rehovot 76100, Israel;
| | - Ornit Cohen
- Wolfson Medical Center, 62 Ha-Lokhamim St. 62, Holon 58100, Israel; (Y.M.); (O.C.)
- The Sackler Faculty of Medicine, Tel Aviv University, P.O. Box 39040, Tel Aviv 6997801, Israel; (G.S.); (N.S.)
- Faculty of Health Science, Ben-Gurion University of the Negev, P.O. Box 653, Be’er Sheva 8410501, Israel
| | - Guy Shapira
- The Sackler Faculty of Medicine, Tel Aviv University, P.O. Box 39040, Tel Aviv 6997801, Israel; (G.S.); (N.S.)
| | - Noam Shomron
- The Sackler Faculty of Medicine, Tel Aviv University, P.O. Box 39040, Tel Aviv 6997801, Israel; (G.S.); (N.S.)
| | - Arik Ben Ishay
- Biobeat Technologies Ltd., 22 Efal St., Petah Tikva 4951122, Israel; (A.B.I.); (E.S.); (R.M.); (M.F.); (R.L.)
| | - Efrat Sand
- Biobeat Technologies Ltd., 22 Efal St., Petah Tikva 4951122, Israel; (A.B.I.); (E.S.); (R.M.); (M.F.); (R.L.)
| | - Roei Merin
- Biobeat Technologies Ltd., 22 Efal St., Petah Tikva 4951122, Israel; (A.B.I.); (E.S.); (R.M.); (M.F.); (R.L.)
| | - Meir Fons
- Biobeat Technologies Ltd., 22 Efal St., Petah Tikva 4951122, Israel; (A.B.I.); (E.S.); (R.M.); (M.F.); (R.L.)
| | - Romi Littman
- Biobeat Technologies Ltd., 22 Efal St., Petah Tikva 4951122, Israel; (A.B.I.); (E.S.); (R.M.); (M.F.); (R.L.)
| | - Yftach Gepner
- Department of Epidemiology and Preventive Medicine, School of Public Health, Sackler Faculty of Medicine and Sylvan Adams Sports Institute, Tel Aviv University, P.O. Box 39040, Tel Aviv 6997801, Israel; (K.C.); (N.G.); (Y.G.)
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49
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Israel-Elgali I, Hertzberg L, Shapira G, Segev A, Krieger I, Nitzan U, Bloch Y, Pillar N, Mayer O, Weizman A, Gurwitz D, Shomron N. Blood transcriptional response to treatment-resistant depression during electroconvulsive therapy. J Psychiatr Res 2021; 141:92-103. [PMID: 34182381 DOI: 10.1016/j.jpsychires.2021.06.039] [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] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/16/2021] [Revised: 05/17/2021] [Accepted: 06/20/2021] [Indexed: 12/13/2022]
Abstract
Selective serotonin reuptake inhibitors (SSRIs) are currently the first-line antidepressant drug treatment for major depressive disorder (MDD). Treatment-resistant depression (TRD), defined as failure to achieve remission despite adequate treatment, affects ~30% of persons with MDD. The current recommended treatment for TRD is electroconvulsive therapy (ECT), while ketamine is an experimentally suggested treatment. This study aimed to elucidate the transcriptional differences in peripheral blood mononuclear cells (PBMC) between individuals with TRD and a control group without a psychiatric illness; and between patients with TRD, treated with either standard antidepressant drugs alone, or in combination with ECT or ketamine. Additionally, PBMC transcriptomics were compared between treatment responders, following completion of their treatment protocols. Total RNA was extracted from PBMC of the TRD group at two time points, and RNA and miRNA expression were profiled. Multiple mRNAs and miRNAs were found to be modified, with two protein coding genes, FKBP5 and ITGA2B, which are up- and downregulated, respectively; and several miRNAs have shown changes following successful ECT treatment. Further analysis demonstrated the direct functional regulation of ITGA2B by miR-24-3p. Our findings suggest that PBMC expression levels of FKBP5, ITGA2B, and miR-24-3p should be further explored as tentative ECT response biomarkers.
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Affiliation(s)
- Ifat Israel-Elgali
- Sagol School of Neuroscience, Tel-Aviv University, Tel Aviv, Israel; Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Libi Hertzberg
- Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel; Shalvata Mental Health Center, Hod Hasharon, Israel; Department of Physics of Complex Systems, Weizmann Institute of Science, Rehovot, Israel
| | - Guy Shapira
- Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Aviv Segev
- Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel; Shalvata Mental Health Center, Hod Hasharon, Israel
| | - Israel Krieger
- Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel; Shalvata Mental Health Center, Hod Hasharon, Israel
| | - Uri Nitzan
- Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel; Shalvata Mental Health Center, Hod Hasharon, Israel
| | - Yuval Bloch
- Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel; Shalvata Mental Health Center, Hod Hasharon, Israel
| | - Nir Pillar
- Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Ori Mayer
- Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Abraham Weizman
- Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel; Geha Mental Health Center, Petah Tiqva, Israel
| | - David Gurwitz
- Sagol School of Neuroscience, Tel-Aviv University, Tel Aviv, Israel; Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel.
| | - Noam Shomron
- Sagol School of Neuroscience, Tel-Aviv University, Tel Aviv, Israel; Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel.
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50
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Vanniya S P, Chandru J, Jeffrey JM, Rabinowitz T, Brownstein Z, Krishnamoorthy M, Avraham KB, Cheng L, Shomron N, Srisailapathy CRS. PNPT1, MYO15A, PTPRQ, and SLC12A2-associated genetic and phenotypic heterogeneity among hearing impaired assortative mating families in Southern India. Ann Hum Genet 2021; 86:1-13. [PMID: 34374074 DOI: 10.1111/ahg.12442] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2021] [Revised: 07/15/2021] [Accepted: 07/19/2021] [Indexed: 12/24/2022]
Abstract
The study was conducted between 2018 and 2020. From a cohort of 113 hearing impaired (HI), five non-DFNB12 probands identified with heterozygous CDH23 variants were subjected to exome analysis. This resolved the etiology of hearing loss (HL) in four South Indian assortative mating families. Six variants, including three novel ones, were identified in four genes: PNPT1 p.(Ala46Gly) and p.(Asn540Ser), MYO15A p.(Leu1485Pro) and p.(Tyr1891Ter), PTPRQ p.(Gln1336Ter), and SLC12A2 p.(Pro988Ser). Compound heterozygous PNPT1 variants were associated with DFNB70 causing prelingual profound sensorineural hearing loss (SNHL), vestibular dysfunction, and unilateral progressive vision loss in one family. In the second family, MYO15A variants in the myosin motor domain, including a novel variant, causing DFNB3, were found to be associated with prelingual profound SNHL. A novel PTPRQ variant was associated with postlingual progressive sensorineural/mixed HL and vestibular dysfunction in the third family with DFNB84A. In the fourth family, the SLC12A2 novel variant was found to segregate with severe-to-profound HL causing DFNA78, across three generations. Our results suggest a high level of allelic, genotypic, and phenotypic heterogeneity of HL in these families. This study is the first to report the association of PNPT1, PTPRQ, and SLC12A2 variants with HL in the Indian population.
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Affiliation(s)
- Paridhy Vanniya S
- Department of Genetics, Dr. ALM PG Institute of Basic Medical Sciences, University of Madras, Chennai, India
| | - Jayasankaran Chandru
- Department of Genetics, Dr. ALM PG Institute of Basic Medical Sciences, University of Madras, Chennai, India.,LifeBytes India Pvt. Ltd., Bengaluru, India
| | - Justin Margret Jeffrey
- Department of Genetics, Dr. ALM PG Institute of Basic Medical Sciences, University of Madras, Chennai, India
| | - Tom Rabinowitz
- Department of Cell and Developmental Biology, Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Zippora Brownstein
- Department of Human Molecular Genetics and Biochemistry, Faculty of Medicine and Sagol School of Neuroscience, Tel Aviv University, Tel Aviv, Israel
| | - Mathuravalli Krishnamoorthy
- Department of Genetics, Dr. ALM PG Institute of Basic Medical Sciences, University of Madras, Chennai, India
| | - Karen B Avraham
- Department of Human Molecular Genetics and Biochemistry, Faculty of Medicine and Sagol School of Neuroscience, Tel Aviv University, Tel Aviv, Israel
| | - Le Cheng
- BGI Genomics, Shenzhen, P. R. China
| | - Noam Shomron
- Department of Cell and Developmental Biology, Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - C R Srikumari Srisailapathy
- Department of Genetics, Dr. ALM PG Institute of Basic Medical Sciences, University of Madras, Chennai, India
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