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Burrack N, Yitzhaky A, Mizrahi L, Wang M, Stern S, Hertzberg L. Altered Expression of PDE4 Genes in Schizophrenia: Insights from a Brain and Blood Sample Meta-Analysis and iPSC-Derived Neurons. Genes (Basel) 2024; 15:609. [PMID: 38790238 PMCID: PMC11121586 DOI: 10.3390/genes15050609] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2023] [Revised: 05/03/2024] [Accepted: 05/05/2024] [Indexed: 05/26/2024] Open
Abstract
Schizophrenia symptomatology includes negative symptoms and cognitive impairment. Several studies have linked schizophrenia with the PDE4 family of enzymes due to their genetic association and function in cognitive processes such as long-term potentiation. We conducted a systematic gene expression meta-analysis of four PDE4 genes (PDE4A-D) in 10 brain sample datasets (437 samples) and three blood sample datasets (300 samples). Subsequently, we measured mRNA levels in iPSC-derived hippocampal dentate gyrus neurons generated from fibroblasts of three groups: healthy controls, healthy monozygotic twins (MZ), and their MZ siblings with schizophrenia. We found downregulation of PDE4B in brain tissues, further validated by independent data of the CommonMind consortium (515 samples). Interestingly, the downregulation signal was present in a subgroup of the patients, while the others showed no differential expression or even upregulation. Notably, PDE4A, PDE4B, and PDE4D exhibited upregulation in iPSC-derived neurons compared to healthy controls, whereas in blood samples, PDE4B was found to be upregulated while PDE4A was downregulated. While the precise mechanism and direction of altered PDE4 expression necessitate further investigation, the observed multilevel differential expression across the brain, blood, and iPSC-derived neurons compellingly suggests the involvement of PDE4 genes in the pathophysiology of schizophrenia.
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Affiliation(s)
- Nitzan Burrack
- Faculty of Health Sciences, Ben-Gurion University of the Negev, Beer-Sheva 84101, Israel;
- Clinical Research Center, Soroka University Medical Center, Beer-Sheva 84101, Israel
| | - Assif Yitzhaky
- Department of Physics of Complex Systems, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Liron Mizrahi
- Sagol Department of Neurobiology, Faculty of Natural Sciences, University of Haifa, Haifa 3103301, Israel
| | - Meiyan Wang
- Laboratory of Genetics, The Salk Institute for Biological Studies, La Jolla, CA 92037, USA
| | - Shani Stern
- Sagol Department of Neurobiology, Faculty of Natural Sciences, University of Haifa, Haifa 3103301, Israel
| | - Libi Hertzberg
- Department of Physics of Complex Systems, Weizmann Institute of Science, Rehovot 76100, Israel
- Shalvata Mental Health Center, Affiliated with the Faculty of Medicine, Tel-Aviv University, 13 Aliat Hanoar St., Hod Hasharon 45100, Israel
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2
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Wen Q, Wittens MMJ, Engelborghs S, van Herwijnen MHM, Tsamou M, Roggen E, Smeets B, Krauskopf J, Briedé JJ. Beyond CSF and Neuroimaging Assessment: Evaluating Plasma miR-145-5p as a Potential Biomarker for Mild Cognitive Impairment and Alzheimer's Disease. ACS Chem Neurosci 2024; 15:1042-1054. [PMID: 38407050 PMCID: PMC10921410 DOI: 10.1021/acschemneuro.3c00740] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2023] [Revised: 02/01/2024] [Accepted: 02/06/2024] [Indexed: 02/27/2024] Open
Abstract
Alzheimer's disease (AD) is the most common cause of dementia. New strategies for the early detection of MCI and sporadic AD are crucial for developing effective treatment options. Current techniques used for diagnosis of AD are invasive and/or expensive, so they are not suitable for population screening. Cerebrospinal fluid (CSF) biomarkers such as amyloid β1-42 (Aβ1-42), total tau (T-tau), and phosphorylated tau181 (P-tau181) levels are core biomarkers for early diagnosis of AD. Several studies have proposed the use of blood-circulating microRNAs (miRNAs) as potential novel early biomarkers for AD. We therefore applied a novel approach to identify blood-circulating miRNAs associated with CSF biomarkers and explored the potential of these miRNAs as biomarkers of AD. In total, 112 subjects consisting of 28 dementia due to AD cases, 63 MCI due to AD cases, and 21 cognitively healthy controls were included. We identified seven Aβ1-42-associated plasma miRNAs, six P-tau181-associated plasma miRNAs, and nine Aβ1-42-associated serum miRNAs. These miRNAs were involved in AD-relevant biological processes, such as PI3K/AKT signaling. Based on this signaling pathway, we constructed an miRNA-gene target network, wherein miR-145-5p has been identified as a hub. Furthermore, we showed that miR-145-5p performs best in the prediction of both AD and MCI. Moreover, miR-145-5p also improved the prediction performance of the mini-mental state examination (MMSE) score. The performance of this miRNA was validated using different datasets including an RT-qPCR dataset from plasma samples of 23 MCI cases and 30 age-matched controls. These findings indicate that blood-circulating miRNAs that are associated with CSF biomarkers levels and specifically plasma miR-145-5p alone or combined with the MMSE score can potentially be used as noninvasive biomarkers for AD or MCI screening in the general population, although studies in other AD cohorts are necessary for further validation.
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Affiliation(s)
- Qingfeng Wen
- Department
of Toxicogenomics, Maastricht University, Universiteitssingel 50, 6229 ER Maastricht, The Netherlands
- MHeNS,
School for Mental Health and Neuroscience, Maastricht University, Universiteitssingel 50, 6229 ER Maastricht, The Netherlands
| | - Mandy Melissa Jane Wittens
- Department
of Biomedical Sciences, Institute Born-Bunge, University of Antwerp, Universiteitsplein 1, BE-2610 Antwerpen, Belgium
- Neuroprotection
and Neuromodulation (NEUR), Center for Neurosciences (C4N), Vrije Universiteit Brussel (VUB), Laarbeeklaan 103, 1090 Brussel, Belgium
- Department
of Neurology, Universitair Ziekenhuis Brussel
(UZ Brussel), Laarbeeklaan
101, 1090 Brussel, Belgium
| | - Sebastiaan Engelborghs
- Department
of Biomedical Sciences, Institute Born-Bunge, University of Antwerp, Universiteitsplein 1, BE-2610 Antwerpen, Belgium
- Neuroprotection
and Neuromodulation (NEUR), Center for Neurosciences (C4N), Vrije Universiteit Brussel (VUB), Laarbeeklaan 103, 1090 Brussel, Belgium
- Department
of Neurology, Universitair Ziekenhuis Brussel
(UZ Brussel), Laarbeeklaan
101, 1090 Brussel, Belgium
| | - Marcel H. M. van Herwijnen
- Department
of Toxicogenomics, Maastricht University, Universiteitssingel 50, 6229 ER Maastricht, The Netherlands
| | - Maria Tsamou
- ToxGenSolutions
(TGS), 6229EV Maastricht, The Netherlands
| | - Erwin Roggen
- ToxGenSolutions
(TGS), 6229EV Maastricht, The Netherlands
| | - Bert Smeets
- Department
of Toxicogenomics, Maastricht University, Universiteitssingel 50, 6229 ER Maastricht, The Netherlands
- MHeNS,
School for Mental Health and Neuroscience, Maastricht University, Universiteitssingel 50, 6229 ER Maastricht, The Netherlands
| | - Julian Krauskopf
- Department
of Toxicogenomics, Maastricht University, Universiteitssingel 50, 6229 ER Maastricht, The Netherlands
| | - Jacco Jan Briedé
- Department
of Toxicogenomics, Maastricht University, Universiteitssingel 50, 6229 ER Maastricht, The Netherlands
- MHeNS,
School for Mental Health and Neuroscience, Maastricht University, Universiteitssingel 50, 6229 ER Maastricht, The Netherlands
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3
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Pomeshchik Y, Velasquez E, Gil J, Klementieva O, Gidlöf R, Sydoff M, Bagnoli S, Nacmias B, Sorbi S, Westergren-Thorsson G, Gouras GK, Rezeli M, Roybon L. Proteomic analysis across patient iPSC-based models and human post-mortem hippocampal tissue reveals early cellular dysfunction and progression of Alzheimer's disease pathogenesis. Acta Neuropathol Commun 2023; 11:150. [PMID: 37715247 PMCID: PMC10504768 DOI: 10.1186/s40478-023-01649-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2023] [Accepted: 08/30/2023] [Indexed: 09/17/2023] Open
Abstract
The hippocampus is a primary region affected in Alzheimer's disease (AD). Because AD postmortem brain tissue is not available prior to symptomatic stage, we lack understanding of early cellular pathogenic mechanisms. To address this issue, we examined the cellular origin and progression of AD pathogenesis by comparing patient-based model systems including iPSC-derived brain cells transplanted into the mouse brain hippocampus. Proteomic analysis of the graft enabled the identification of pathways and network dysfunction in AD patient brain cells, associated with increased levels of Aβ-42 and β-sheet structures. Interestingly, the host cells surrounding the AD graft also presented alterations in cellular biological pathways. Furthermore, proteomic analysis across human iPSC-based models and human post-mortem hippocampal tissue projected coherent longitudinal cellular changes indicative of early to end stage AD cellular pathogenesis. Our data showcase patient-based models to study the cell autonomous origin and progression of AD pathogenesis.
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Affiliation(s)
- Yuriy Pomeshchik
- iPSC Laboratory for CNS Disease Modelling, Department of Experimental Medical Science, BMC D10, Lund University, 22184, Lund, Sweden.
- Strategic Research Area MultiPark, Lund University, 22184, Lund, Sweden.
- Lund Stem Cell Center, Lund University, 22184, Lund, Sweden.
| | - Erika Velasquez
- iPSC Laboratory for CNS Disease Modelling, Department of Experimental Medical Science, BMC D10, Lund University, 22184, Lund, Sweden
- Strategic Research Area MultiPark, Lund University, 22184, Lund, Sweden
- Lund Stem Cell Center, Lund University, 22184, Lund, Sweden
| | - Jeovanis Gil
- Clinical Protein Science & Imaging, Department of Biomedical Engineering, BMC D13, Lund University, 22184, Lund, Sweden
| | - Oxana Klementieva
- Strategic Research Area MultiPark, Lund University, 22184, Lund, Sweden
- Medical Micro-Spectroscopy, Department of Experimental Medical Science, BMC B10, Lund University, 22184, Lund, Sweden
| | - Ritha Gidlöf
- Lund University BioImaging Centre, Faculty of Medicine, Lund University, 22142, Lund, Sweden
| | - Marie Sydoff
- Lund University BioImaging Centre, Faculty of Medicine, Lund University, 22142, Lund, Sweden
| | - Silvia Bagnoli
- Laboratorio Di Neurogenetica, Dipartimento Di Neuroscienze, Psicologia, Area del Farmaco e Salute del Bambino- NEUROFARBA, Università degli Studi di Firenze, 50134, Florence, Italy
- IRCCS Fondazione Don Carlo Gnocchi, Florence, Italy
| | - Benedetta Nacmias
- Laboratorio Di Neurogenetica, Dipartimento Di Neuroscienze, Psicologia, Area del Farmaco e Salute del Bambino- NEUROFARBA, Università degli Studi di Firenze, 50134, Florence, Italy
- IRCCS Fondazione Don Carlo Gnocchi, Florence, Italy
| | - Sandro Sorbi
- Laboratorio Di Neurogenetica, Dipartimento Di Neuroscienze, Psicologia, Area del Farmaco e Salute del Bambino- NEUROFARBA, Università degli Studi di Firenze, 50134, Florence, Italy
- IRCCS Fondazione Don Carlo Gnocchi, Florence, Italy
| | - Gunilla Westergren-Thorsson
- Department of Experimental Medical Science, BMC C12, Faculty of Medicine, Lund University, 22142, Lund, Sweden
| | - Gunnar K Gouras
- Strategic Research Area MultiPark, Lund University, 22184, Lund, Sweden
- Experimental Dementia Research Unit, Department of Experimental Medical Science, BMC B11, Lund University, 22184, Lund, Sweden
| | - Melinda Rezeli
- Clinical Protein Science & Imaging, Department of Biomedical Engineering, BMC D13, Lund University, 22184, Lund, Sweden
- Swedish National Infrastructure for Biological Mass Spectrometry (BioMS), Lund University, 22184, Lund, Sweden
| | - Laurent Roybon
- iPSC Laboratory for CNS Disease Modelling, Department of Experimental Medical Science, BMC D10, Lund University, 22184, Lund, Sweden.
- Strategic Research Area MultiPark, Lund University, 22184, Lund, Sweden.
- Lund Stem Cell Center, Lund University, 22184, Lund, Sweden.
- Department of Neurodegenerative Science, The MiND Program, Van Andel Institute, Grand Rapids, MI, USA.
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4
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Flannagan K, Stopperan JA, Hauger BM, Troutwine BR, Lysaker CR, Strope TA, Csikos Drummond V, Gilmore CA, Swerdlow NA, Draper JM, Gouvion CM, Vivian JL, Haeri M, Swerdlow RH, Wilkins HM. Cell type and sex specific mitochondrial phenotypes in iPSC derived models of Alzheimer's disease. Front Mol Neurosci 2023; 16:1201015. [PMID: 37614699 PMCID: PMC10442646 DOI: 10.3389/fnmol.2023.1201015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2023] [Accepted: 07/26/2023] [Indexed: 08/25/2023] Open
Abstract
Introduction Mitochondrial dysfunction is observed in Alzheimer's disease (AD). Altered mitochondrial respiration, cytochrome oxidase (COX) Vmax, and mitophagy are observed in human subjects and animal models of AD. Models derived from induced pluripotent stem cells (iPSCs) may not recapitulate these phenotypes after reprogramming from differentiated adult cells. Methods We examined mitochondrial function across iPSC derived models including cerebral organoids, forebrain neurons, and astrocytes. iPSCs were reprogrammed from fibroblasts either from the University of Kansas Alzheimer's Disease Research Center (KU ADRC) cohort or purchased from WiCell. A total of four non-demented and four sporadic AD iPSC lines were examined. Models were subjected to mitochondrial respiration analysis using Seahorse XF technology, spectrophotometric cytochrome oxidase (COX) Vmax assays, fluorescent assays to determine mitochondrial mass, mitochondrial membrane potential, calcium, mitochondrial dynamics, and mitophagy levels. AD pathological hallmarks were also measured. Results iPSC derived neurons and cerebral organoids showed reduced COX Vmax in AD subjects with more profound defects in the female cohort. These results were not observed in astrocytes. iPSC derived neurons and astrocytes from AD subjects had reduced mitochondrial respiration parameters with increased glycolytic flux. iPSC derived neurons and astrocytes from AD subjects showed sex dependent effects on mitochondrial membrane potential, mitochondrial superoxide production, and mitochondrial calcium. iPSC derived neurons from AD subjects had reduced mitochondrial localization in lysosomes with sex dependent effects on mitochondrial mass, while iPSC derived astrocytes from female AD subjects had increased mitochondrial localization to lysosomes. Both iPSC derived neurons and astrocytes from AD subjects showed altered mitochondrial dynamics. iPSC derived neurons had increased secreted Aβ, and sex dependent effects on total APP protein expression. iPSC derived astrocytes showed sex dependent changes in GFAP expression in AD derived cells. Conclusion Overall, iPSC derived models from AD subjects show mitochondrial phenotypes and AD pathological hallmarks in a cell type and sex dependent manner. These results highlight the importance of sex as a biological variable in cell culture studies.
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Affiliation(s)
- Kaitlin Flannagan
- University of Kansas Alzheimer's Disease Research Center, University of Kansas Medical Center, Kansas City, KS, United States
| | - Julia A. Stopperan
- University of Kansas Alzheimer's Disease Research Center, University of Kansas Medical Center, Kansas City, KS, United States
| | - Brittany M. Hauger
- University of Kansas Alzheimer's Disease Research Center, University of Kansas Medical Center, Kansas City, KS, United States
| | - Benjamin R. Troutwine
- University of Kansas Alzheimer's Disease Research Center, University of Kansas Medical Center, Kansas City, KS, United States
| | - Colton R. Lysaker
- University of Kansas Alzheimer's Disease Research Center, University of Kansas Medical Center, Kansas City, KS, United States
- Department of Biochemistry and Molecular Biology, University of Kansas Medical Center, Kansas City, KS, United States
| | - Taylor A. Strope
- University of Kansas Alzheimer's Disease Research Center, University of Kansas Medical Center, Kansas City, KS, United States
- Department of Biochemistry and Molecular Biology, University of Kansas Medical Center, Kansas City, KS, United States
| | - Vivien Csikos Drummond
- University of Kansas Alzheimer's Disease Research Center, University of Kansas Medical Center, Kansas City, KS, United States
- Department of Biochemistry and Molecular Biology, University of Kansas Medical Center, Kansas City, KS, United States
| | - Caleb A. Gilmore
- University of Kansas Alzheimer's Disease Research Center, University of Kansas Medical Center, Kansas City, KS, United States
| | - Natalie A. Swerdlow
- University of Kansas Alzheimer's Disease Research Center, University of Kansas Medical Center, Kansas City, KS, United States
| | - Julia M. Draper
- Transgenic and Gene Targeting Facility, University of Kansas Medical Center, Kansas City, KS, United States
| | - Cynthia M. Gouvion
- University of Kansas Alzheimer's Disease Research Center, University of Kansas Medical Center, Kansas City, KS, United States
| | - Jay L. Vivian
- Transgenic and Gene Targeting Facility, University of Kansas Medical Center, Kansas City, KS, United States
- Department of Pediatrics, University of Kansas Missouri-Kansas City School of Medicine, Kansas City, KS, United States
- Institute for Reproduction and Perinatal Research, University of Kansas Medical Center, Kansas City, KS, United States
- Department of Pathology & Laboratory Medicine, University of Kansas Medical Center, Kansas City, KS, United States
| | - Mohammad Haeri
- University of Kansas Alzheimer's Disease Research Center, University of Kansas Medical Center, Kansas City, KS, United States
- Department of Pathology & Laboratory Medicine, University of Kansas Medical Center, Kansas City, KS, United States
| | - Russell H. Swerdlow
- University of Kansas Alzheimer's Disease Research Center, University of Kansas Medical Center, Kansas City, KS, United States
- Department of Biochemistry and Molecular Biology, University of Kansas Medical Center, Kansas City, KS, United States
- Department of Molecular and Integrative Physiology, University of Kansas Medical Center, Kansas City, KS, United States
- Department of Neurology, University of Kansas Medical Center, Kansas City, KS, United States
| | - Heather M. Wilkins
- University of Kansas Alzheimer's Disease Research Center, University of Kansas Medical Center, Kansas City, KS, United States
- Department of Biochemistry and Molecular Biology, University of Kansas Medical Center, Kansas City, KS, United States
- Department of Neurology, University of Kansas Medical Center, Kansas City, KS, United States
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5
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Grünblatt E, Homolak J, Babic Perhoc A, Davor V, Knezovic A, Osmanovic Barilar J, Riederer P, Walitza S, Tackenberg C, Salkovic-Petrisic M. From attention-deficit hyperactivity disorder to sporadic Alzheimer's disease-Wnt/mTOR pathways hypothesis. Front Neurosci 2023; 17:1104985. [PMID: 36875654 PMCID: PMC9978448 DOI: 10.3389/fnins.2023.1104985] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2022] [Accepted: 01/31/2023] [Indexed: 02/18/2023] Open
Abstract
Alzheimer's disease (AD) is the most common neurodegenerative disorder with the majority of patients classified as sporadic AD (sAD), in which etiopathogenesis remains unresolved. Though sAD is argued to be a polygenic disorder, apolipoprotein E (APOE) ε4, was found three decades ago to pose the strongest genetic risk for sAD. Currently, the only clinically approved disease-modifying drugs for AD are aducanumab (Aduhelm) and lecanemab (Leqembi). All other AD treatment options are purely symptomatic with modest benefits. Similarly, attention-deficit hyperactivity disorder (ADHD), is one of the most common neurodevelopmental mental disorders in children and adolescents, acknowledged to persist in adulthood in over 60% of the patients. Moreover, for ADHD whose etiopathogenesis is not completely understood, a large proportion of patients respond well to treatment (first-line psychostimulants, e.g., methylphenidate/MPH), however, no disease-modifying therapy exists. Interestingly, cognitive impairments, executive, and memory deficits seem to be common in ADHD, but also in early stages of mild cognitive impairment (MCI), and dementia, including sAD. Therefore, one of many hypotheses is that ADHD and sAD might have similar origins or that they intercalate with one another, as shown recently that ADHD may be considered a risk factor for sAD. Intriguingly, several overlaps have been shown between the two disorders, e.g., inflammatory activation, oxidative stress, glucose and insulin pathways, wingless-INT/mammalian target of rapamycin (Wnt/mTOR) signaling, and altered lipid metabolism. Indeed, Wnt/mTOR activities were found to be modified by MPH in several ADHD studies. Wnt/mTOR was also found to play a role in sAD and in animal models of the disorder. Moreover, MPH treatment in the MCI phase was shown to be successful for apathy including some improvement in cognition, according to a recent meta-analysis. In several AD animal models, ADHD-like behavioral phenotypes have been observed indicating a possible interconnection between ADHD and AD. In this concept paper, we will discuss the various evidence in human and animal models supporting the hypothesis in which ADHD might increase the risk for sAD, with common involvement of the Wnt/mTOR-pathway leading to lifespan alteration at the neuronal levels.
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Affiliation(s)
- Edna Grünblatt
- Department of Child and Adolescent Psychiatry and Psychotherapy, Psychiatric University Hospital Zurich (PUK), University of Zurich, Zurich, Switzerland.,Neuroscience Center Zurich, University of Zurich and the Swiss Federal Institute of Technology (ETH) Zurich, Zurich, Switzerland.,Zurich Center for Integrative Human Physiology, University of Zurich, Zurich, Switzerland
| | - Jan Homolak
- Department of Pharmacology and Croatian Institute for Brain Research, University of Zagreb School of Medicine, Zagreb, Croatia
| | - Ana Babic Perhoc
- Department of Pharmacology and Croatian Institute for Brain Research, University of Zagreb School of Medicine, Zagreb, Croatia
| | - Virag Davor
- Department of Pharmacology and Croatian Institute for Brain Research, University of Zagreb School of Medicine, Zagreb, Croatia
| | - Ana Knezovic
- Department of Pharmacology and Croatian Institute for Brain Research, University of Zagreb School of Medicine, Zagreb, Croatia
| | - Jelena Osmanovic Barilar
- Department of Pharmacology and Croatian Institute for Brain Research, University of Zagreb School of Medicine, Zagreb, Croatia
| | - Peter Riederer
- Department of Psychiatry, Psychosomatics and Psychotherapy, Center of Mental Health, University Hospital Würzburg, Würzburg, Germany.,Department and Research Unit of Psychiatry, Institute of Clinical Research, University of Southern Denmark, Odense, Denmark
| | - Susanne Walitza
- Department of Child and Adolescent Psychiatry and Psychotherapy, Psychiatric University Hospital Zurich (PUK), University of Zurich, Zurich, Switzerland.,Neuroscience Center Zurich, University of Zurich and the Swiss Federal Institute of Technology (ETH) Zurich, Zurich, Switzerland.,Zurich Center for Integrative Human Physiology, University of Zurich, Zurich, Switzerland
| | - Christian Tackenberg
- Neuroscience Center Zurich, University of Zurich and the Swiss Federal Institute of Technology (ETH) Zurich, Zurich, Switzerland.,Institute for Regenerative Medicine (IREM), University of Zurich, Schlieren, Switzerland
| | - Melita Salkovic-Petrisic
- Department of Pharmacology and Croatian Institute for Brain Research, University of Zagreb School of Medicine, Zagreb, Croatia
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6
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Nazzari M, Hauser D, van Herwijnen M, Romitti M, Carvalho DJ, Kip AM, Caiment F. CODA: a combo-Seq data analysis workflow. Brief Bioinform 2022; 24:6955042. [PMID: 36545800 PMCID: PMC9851309 DOI: 10.1093/bib/bbac582] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2022] [Revised: 11/23/2022] [Accepted: 11/28/2022] [Indexed: 12/24/2022] Open
Abstract
The analysis of the combined mRNA and miRNA content of a biological sample can be of interest for answering several research questions, like biomarkers discovery, or mRNA-miRNA interactions. However, the process is costly and time-consuming, separate libraries need to be prepared and sequenced on different flowcells. Combo-Seq is a library prep kit that allows us to prepare combined mRNA-miRNA libraries starting from very low total RNA. To date, no dedicated bioinformatics method exists for the processing of Combo-Seq data. In this paper, we describe CODA (Combo-seq Data Analysis), a workflow specifically developed for the processing of Combo-Seq data that employs existing free-to-use tools. We compare CODA with exceRpt, the pipeline suggested by the kit manufacturer for this purpose. We also evaluate how Combo-Seq libraries analysed with CODA perform compared with conventional poly(A) and small RNA libraries prepared from the same samples. We show that using CODA more successfully trimmed reads are recovered compared with exceRpt, and the difference is more dramatic with short sequencing reads. We demonstrate how Combo-Seq identifies as many genes and fewer miRNAs compared to the standard libraries, and how miRNA validation favours conventional small RNA libraries over Combo-Seq. The CODA code is available at https://github.com/marta-nazzari/CODA.
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Affiliation(s)
- Marta Nazzari
- Department of Toxicogenomics, GROW School for Oncology and Developmental Biology, Maastricht University, 6229 ER Maastricht, The Netherlands
| | - Duncan Hauser
- Department of Toxicogenomics, GROW School for Oncology and Developmental Biology, Maastricht University, 6229 ER Maastricht, The Netherlands
| | - Marcel van Herwijnen
- Department of Toxicogenomics, GROW School for Oncology and Developmental Biology, Maastricht University, 6229 ER Maastricht, The Netherlands
| | - Mírian Romitti
- Institute of Interdisciplinary Research in Molecular Human Biology (IRIBHM), Université Libre de Bruxelles, 808 route de Lennik, 1070 Brussels, Belgium
| | - Daniel J Carvalho
- Department of Instructive Biomaterials Engineering, MERLN Institute for Technology-Inspired Regenerative Medicine, Maastricht University, 6229 ER Maastricht, The Netherlands
| | - Anna M Kip
- Department of Complex Tissue Regeneration, MERLN Institute for Technology-Inspired Regenerative Medicine, Maastricht University, 6229 ER Maastricht, The Netherlands
| | - Florian Caiment
- Corresponding author: Florian Caiment, Tel.: +31433881218; E-mail:
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7
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Wen Q, Verheijen M, Wittens MMJ, Czuryło J, Engelborghs S, Hauser D, van Herwijnen MHM, Lundh T, Bergdahl IA, Kyrtopoulos SA, de Kok TM, Smeets HJM, Briedé JJ, Krauskopf J. Lead-exposure associated miRNAs in humans and Alzheimer’s disease as potential biomarkers of the disease and disease processes. Sci Rep 2022; 12:15966. [PMID: 36153426 PMCID: PMC9509380 DOI: 10.1038/s41598-022-20305-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2022] [Accepted: 09/12/2022] [Indexed: 11/23/2022] Open
Abstract
Alzheimer’s disease (AD) is a neurodegenerative disease that eventually affects memory and behavior. The identification of biomarkers based on risk factors for AD provides insight into the disease since the exact cause of AD remains unknown. Several studies have proposed microRNAs (miRNAs) in blood as potential biomarkers for AD. Exposure to heavy metals is a potential risk factor for onset and development of AD. Blood cells of subjects that are exposed to lead detected in the circulatory system, potentially reflect molecular responses to this exposure that are similar to the response of neurons. In this study we analyzed blood cell-derived miRNAs derived from a general population as proxies of potentially AD-related mechanisms triggered by lead exposure. Subsequently, we analyzed these mechanisms in the brain tissue of AD subjects and controls. A total of four miRNAs were identified as lead exposure-associated with hsa-miR-3651, hsa-miR-150-5p and hsa-miR-664b-3p being negatively and hsa-miR-627 positively associated. In human brain derived from AD and AD control subjects all four miRNAs were detected. Moreover, two miRNAs (miR-3651, miR-664b-3p) showed significant differential expression in AD brains versus controls, in accordance with the change direction of lead exposure. The miRNAs’ gene targets were validated for expression in the human brain and were found enriched in AD-relevant pathways such as axon guidance. Moreover, we identified several AD relevant transcription factors such as CREB1 associated with the identified miRNAs. These findings suggest that the identified miRNAs are involved in the development of AD and might be useful in the development of new, less invasive biomarkers for monitoring of novel therapies or of processes involved in AD development.
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