1
|
Liharska L, Charney A. Transcriptomics : Approaches to Quantifying Gene Expression and Their Application to Studying the Human Brain. Curr Top Behav Neurosci 2024. [PMID: 38972894 DOI: 10.1007/7854_2024_466] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/09/2024]
Abstract
To date, the field of transcriptomics has been characterized by rapid methods development and technological advancement, with new technologies continuously rendering older ones obsolete.This chapter traces the evolution of approaches to quantifying gene expression and provides an overall view of the current state of the field of transcriptomics, its applications to the study of the human brain, and its place in the broader emerging multiomics landscape.
Collapse
Affiliation(s)
- Lora Liharska
- Icahn School of Medicine at Mount Sinai, New York, NY, USA.
| | | |
Collapse
|
2
|
Jones EF, Howton TC, Flanary VL, Clark AD, Lasseigne BN. Long-read RNA sequencing identifies region- and sex-specific C57BL/6J mouse brain mRNA isoform expression and usage. Mol Brain 2024; 17:40. [PMID: 38902764 PMCID: PMC11188239 DOI: 10.1186/s13041-024-01112-7] [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: 01/18/2024] [Accepted: 06/08/2024] [Indexed: 06/22/2024] Open
Abstract
Alternative splicing (AS) contributes to the biological heterogeneity between species, sexes, tissues, and cell types. Many diseases are either caused by alterations in AS or by alterations to AS. Therefore, measuring AS accurately and efficiently is critical for assessing molecular phenotypes, including those associated with disease. Long-read sequencing enables more accurate quantification of differentially spliced isoform expression than short-read sequencing approaches, and third-generation platforms facilitate high-throughput experiments. To assess differences in AS across the cerebellum, cortex, hippocampus, and striatum by sex, we generated and analyzed Oxford Nanopore Technologies (ONT) long-read RNA sequencing (lrRNA-Seq) C57BL/6J mouse brain cDNA libraries. From > 85 million reads that passed quality control metrics, we calculated differential gene expression (DGE), differential transcript expression (DTE), and differential transcript usage (DTU) across brain regions and by sex. We found significant DGE, DTE, and DTU across brain regions and that the cerebellum had the most differences compared to the other three regions. Additionally, we found region-specific differential splicing between sexes, with the most sex differences in DTU in the cortex and no DTU in the hippocampus. We also report on two distinct patterns of sex DTU we observed, sex-divergent and sex-specific, that could potentially help explain sex differences in the prevalence and prognosis of various neurological and psychiatric disorders in future studies. Finally, we built a Shiny web application for researchers to explore the data further. Our study provides a resource for the community; it underscores the importance of AS in biological heterogeneity and the utility of long-read sequencing to better understand AS in the brain.
Collapse
Affiliation(s)
- Emma F Jones
- Department of Cell, Developmental and Integrative Biology, Heersink School of Medicine, The University of Alabama at Birmingham, Birmingham, AL, United States of America
| | - Timothy C Howton
- Department of Cell, Developmental and Integrative Biology, Heersink School of Medicine, The University of Alabama at Birmingham, Birmingham, AL, United States of America
| | - Victoria L Flanary
- Department of Cell, Developmental and Integrative Biology, Heersink School of Medicine, The University of Alabama at Birmingham, Birmingham, AL, United States of America
| | - Amanda D Clark
- Department of Cell, Developmental and Integrative Biology, Heersink School of Medicine, The University of Alabama at Birmingham, Birmingham, AL, United States of America
| | - Brittany N Lasseigne
- Department of Cell, Developmental and Integrative Biology, Heersink School of Medicine, The University of Alabama at Birmingham, Birmingham, AL, United States of America.
| |
Collapse
|
3
|
Anand C, Torok J, Abdelnour F, Maia PD, Raj A. Selective vulnerability and resilience to Alzheimer's disease tauopathy as a function of genes and the connectome. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.03.04.583403. [PMID: 38496606 PMCID: PMC10942335 DOI: 10.1101/2024.03.04.583403] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/19/2024]
Abstract
Brain regions in Alzheimer's (AD) exhibit distinct vulnerability to the disease's hallmark pathology, with the entorhinal cortex and hippocampus succumbing early to tau tangles while others like primary sensory cortices remain resilient. The quest to understand how local/regional genetic factors, pathogenesis, and network-mediated spread of pathology together govern this selective vulnerability (SV) or resilience (SR) is ongoing. Although many risk genes in AD are known from gene association and transgenic studies, it is still not known whether and how their baseline expression signatures confer SV or SR to brain structures. Prior analyses have yielded conflicting results, pointing to a disconnect between the location of genetic risk factors and downstream tau pathology. We hypothesize that a full accounting of genes' role in mediating SV/SR would require the modeling of network-based vulnerability, whereby tau misfolds, aggregates, and propagates along fiber projections. We therefore employed an extended network diffusion model (eNDM) and tested it on tau pathology PET data from 196 AD patients from the Alzheimer's Disease Neuroimaging Initiative (ADNI). Thus the fitted eNDM model becomes a reference process from which to assess the role of innate genetic factors. Using the residual (observed - model-predicted) tau as a novel target outcome, we obtained its association with 100 top AD risk-genes, whose baseline spatial transcriptional profiles were obtained from the Allen Human Brain Atlas (AHBA). We found that while many risk genes at baseline showed a strong association with regional tau, many more showed a stronger association with residual tau. This suggests that both direct vulnerability, related to the network, as well as network-independent vulnerability, are conferred by risk genes. We then classified risk genes into four classes: network-related SV (SV-NR), network-independent SV (SV-NI), network-related SR (SR-NR), and network-independent SR (SR-NI). Each class has a distinct spatial signature and associated vulnerability to tau. Remarkably, we found from gene-ontology analyses, that genes in these classes were enriched in distinct functional processes and encompassed different functional networks. These findings offer new insights into the factors governing innate vulnerability or resilience in AD pathophysiology and may prove helpful in identifying potential intervention targets.
Collapse
|
4
|
Jones EF, Howton TC, Flanary VL, Clark AD, Lasseigne BN. Long-read RNA sequencing identifies region- and sex-specific C57BL/6J mouse brain mRNA isoform expression and usage. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.01.11.575219. [PMID: 38260631 PMCID: PMC10802568 DOI: 10.1101/2024.01.11.575219] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/24/2024]
Abstract
Alternative splicing (AS) contributes to the biological heterogeneity between species, sexes, tissues, and cell types. Many diseases are either caused by alterations in AS or by alterations to AS. Therefore, measuring AS accurately and efficiently is critical for assessing molecular phenotypes, including those associated with disease. Long-read sequencing enables more accurate quantification of differentially spliced isoform expression than short-read sequencing approaches, and third-generation platforms facilitate high-throughput experiments. To assess differences in AS across the cerebellum, cortex, hippocampus, and striatum by sex, we generated and analyzed Oxford Nanopore Technologies (ONT) long-read RNA sequencing (lrRNA-Seq) C57BL/6J mouse brain cDNA libraries. From >85 million reads that passed quality control metrics, we calculated differential gene expression (DGE), differential transcript expression (DTE), and differential transcript usage (DTU) across brain regions and by sex. We found significant DGE, DTE, and DTU across brain regions and that the cerebellum had the most differences compared to the other three regions. Additionally, we found region-specific differential splicing between sexes, with the most sex differences in DTU in the cortex and no DTU in the hippocampus. We also report on two distinct patterns of sex DTU we observed, sex-divergent and sex-specific, that could potentially help explain sex differences in the prevalence and prognosis of various neurological and psychiatric disorders in future studies. Finally, we built a Shiny web application for researchers to explore the data further. Our study provides a resource for the community; it underscores the importance of AS in biological heterogeneity and the utility of long-read sequencing to better understand AS in the brain.
Collapse
Affiliation(s)
- Emma F. Jones
- Department of Cell, Developmental and Integrative Biology, Heersink School of Medicine, The University of Alabama at Birmingham, Birmingham, Alabama, United States of America
| | - Timothy C. Howton
- Department of Cell, Developmental and Integrative Biology, Heersink School of Medicine, The University of Alabama at Birmingham, Birmingham, Alabama, United States of America
| | - Victoria L. Flanary
- Department of Cell, Developmental and Integrative Biology, Heersink School of Medicine, The University of Alabama at Birmingham, Birmingham, Alabama, United States of America
| | - Amanda D. Clark
- Department of Cell, Developmental and Integrative Biology, Heersink School of Medicine, The University of Alabama at Birmingham, Birmingham, Alabama, United States of America
| | - Brittany N. Lasseigne
- Department of Cell, Developmental and Integrative Biology, Heersink School of Medicine, The University of Alabama at Birmingham, Birmingham, Alabama, United States of America
| |
Collapse
|
5
|
Cetinsoy O, Anyanwu I, Krishnanand H, Natarajan G, Ramachandran N, Thomas A, Brookes KJ. Gene Association Study of the Urokinase Plasminogen Activator and Its Receptor Gene in Alzheimer's Disease. J Alzheimers Dis 2024; 99:241-250. [PMID: 38669542 DOI: 10.3233/jad-231383] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/28/2024]
Abstract
Background The role of the innate immune system has long been associated with Alzheimer's disease (AD). There is now accumulating evidence that the soluble Urokinase Plasminogen Activator Receptor pathway, and its genes, PLAU and PLAUR may be important in AD, and yet there have been few genetic association studies to explore this. Objective This study utilizes the DNA bank of the Brains for Dementia Research cohort to investigate the genetic association of common polymorphisms across the PLAU and PLAUR genes with AD. Methods TaqMan genotyping assays were used with standard procedures followed by association analysis in PLINK. Results No association was observed between the PLAU gene and AD; however, two SNPs located in the PLAUR gene were indicative of a trend towards association but did not surpass multiple testing significance thresholds. Conclusions Further genotyping studies and exploration of the consequences of these SNPs on gene expression and alternative splicing are warranted to fully uncover the role this system may have in AD.
Collapse
Affiliation(s)
- Ozde Cetinsoy
- Biosciences, Clifton Campus, Nottingham Trent University, Nottingham, UK
| | - Ijeoma Anyanwu
- Biosciences, Clifton Campus, Nottingham Trent University, Nottingham, UK
| | | | | | | | - Alan Thomas
- Brains for Dementia Research, Faculty of Medical Sciences, Newcastle University, Newcastle, UK
| | - Keeley J Brookes
- Biosciences, Clifton Campus, Nottingham Trent University, Nottingham, UK
| |
Collapse
|
6
|
Gaunt JR, Zainolabidin N, Yip AKK, Tan JM, Low AYT, Chen AI, Ch'ng TH. Cytokine enrichment in deep cerebellar nuclei is contributed by multiple glial populations and linked to reduced amyloid plaque pathology. J Neuroinflammation 2023; 20:269. [PMID: 37978387 PMCID: PMC10656954 DOI: 10.1186/s12974-023-02913-8] [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: 04/24/2023] [Accepted: 09/28/2023] [Indexed: 11/19/2023] Open
Abstract
Alzheimer's disease (AD) pathology and amyloid-beta (Aβ) plaque deposition progress slowly in the cerebellum compared to other brain regions, while the entorhinal cortex (EC) is one of the most vulnerable regions. Using a knock-in AD mouse model (App KI), we show that within the cerebellum, the deep cerebellar nuclei (DCN) has particularly low accumulation of Aβ plaques. To identify factors that might underlie differences in the progression of AD-associated neuropathology across regions, we profiled gene expression in single nuclei (snRNAseq) across all cell types in the DCN and EC of wild-type (WT) and App KI male mice at age 7 months. We found differences in expression of genes associated with inflammatory activation, PI3K-AKT signalling, and neuron support functions between both regions and genotypes. In WT mice, the expression of interferon-response genes in microglia is higher in the DCN than the EC and this enrichment is confirmed by RNA in situ hybridisation, and measurement of inflammatory cytokines by protein array. Our analyses also revealed that multiple glial populations are responsible for establishing this cytokine-enriched niche. Furthermore, homogenates derived from the DCN induced inflammatory gene expression in BV2 microglia. We also assessed the relationship between the DCN microenvironment and Aβ pathology by depleting microglia using a CSF1R inhibitor PLX5622 and saw that, surprisingly, the expression of a subset of inflammatory cytokines was increased while plaque abundance in the DCN was further reduced. Overall, our study revealed the presence of a cytokine-enriched microenvironment unique to the DCN that when modulated, can alter plaque deposition.
Collapse
Affiliation(s)
- Jessica R Gaunt
- Lee Kong Chian School of Medicine, Nanyang Technological University, Clinical Science Building, 11 Mandalay Road, Singapore, 308232, Singapore
| | - Norliyana Zainolabidin
- Lee Kong Chian School of Medicine, Nanyang Technological University, Clinical Science Building, 11 Mandalay Road, Singapore, 308232, Singapore
| | - Alaric K K Yip
- Lee Kong Chian School of Medicine, Nanyang Technological University, Clinical Science Building, 11 Mandalay Road, Singapore, 308232, Singapore
| | - Jia Min Tan
- Lee Kong Chian School of Medicine, Nanyang Technological University, Clinical Science Building, 11 Mandalay Road, Singapore, 308232, Singapore
| | - Aloysius Y T Low
- Department of Biology, University of Pennsylvania, Philadelphia, PA, USA
| | - Albert I Chen
- Center for Aging Research, Scintillon Institute, 6868 Nancy Ridge Drive, San Diego, CA, 92121, USA.
- Molecular Neurobiology Laboratory, Salk Institute, La Jolla, CA, 92037, USA.
| | - Toh Hean Ch'ng
- Lee Kong Chian School of Medicine, Nanyang Technological University, Clinical Science Building, 11 Mandalay Road, Singapore, 308232, Singapore.
- School of Biological Science, Nanyang Technological University, Singapore, 63755, Singapore.
| |
Collapse
|
7
|
D’Angiolini S, Basile MS, Mazzon E, Gugliandolo A. In Silico Analysis Reveals the Modulation of Ion Transmembrane Transporters in the Cerebellum of Alzheimer's Disease Patients. Int J Mol Sci 2023; 24:13924. [PMID: 37762226 PMCID: PMC10530854 DOI: 10.3390/ijms241813924] [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: 08/02/2023] [Revised: 09/01/2023] [Accepted: 09/08/2023] [Indexed: 09/29/2023] Open
Abstract
Alzheimer's disease (AD) is the most common neurodegenerative disorder. AD hallmarks are extracellular amyloid β (Aβ) plaques and intracellular neurofibrillary tangles in the brain. It is interesting to notice that Aβ plaques appear in the cerebellum only in late stages of the disease, and then it was hypothesized that it can be resistant to specific neurodegenerative mechanisms. However, the role of cerebellum in AD pathogenesis is not clear yet. In this study, we performed an in silico analysis to evaluate the transcriptional profile of cerebellum in AD patients and non-AD subjects in order to deepen the knowledge on its role in AD. The analysis evidenced that only the molecular function (MF) "active ion transmembrane transporter activity" was overrepresented. Regarding the 21 differentially expressed genes included in this MF, some of them may be involved in the ion dyshomeostasis reported in AD, while others assumed, in the cerebellum, an opposite regulation compared to those reported in other brain regions in AD patients. They might be associated to a protective phenotype, that may explain the initial resistance of cerebellum to neurodegeneration in AD. Of note, this MF was not overrepresented in prefrontal cortex and visual cortex indicating that it is a peculiarity of the cerebellum.
Collapse
Affiliation(s)
| | | | - Emanuela Mazzon
- IRCCS Centro Neurolesi “Bonino-Pulejo”, Via Provinciale Palermo, Contrada Casazza, 98124 Messina, Italy; (S.D.); (M.S.B.); (A.G.)
| | | |
Collapse
|
8
|
Brookes KJ. Evaluating the Classification Accuracy of Expression Quantitative Trait Loci Calculated Polygenic Risk Scores in Alzheimer's Disease. Int J Mol Sci 2023; 24:12799. [PMID: 37628980 PMCID: PMC10454324 DOI: 10.3390/ijms241612799] [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: 07/18/2023] [Revised: 08/09/2023] [Accepted: 08/12/2023] [Indexed: 08/27/2023] Open
Abstract
Polygenic risk scores (PRS) hold promise for the early identification of those at risk from neurodegenerative disorders such as Alzheimer's Disease (AD), allowing for intervention to occur prior to neuronal damage. The current selection of informative single nucleotide polymorphisms (SNPs) to generate the risk scores is based on the modelling of large genome-wide association data using significance thresholds. However, the biological relevance of these SNPs is largely unknown. This study, in contrast, aims to identify SNPs with biological relevance to AD and then assess them for their ability to accurately classify cases and controls. Samples selected from the Brains for Dementia Research (BDR) were used to produce gene expression data to identify potential expression quantitative trait loci (eQTLs) relevant to AD. These SNPs were then incorporated into a PRS model to classify AD and controls in the full BDR cohort. Models derived from these eQTLs demonstrate modest classification potential with an accuracy between 61% and 67%. Although the model accuracy is not as high as some values in the literature based on significance thresholds from genome-wide association studies, these models may reflect a more biologically relevant model, which may provide novel targets for therapeutic intervention.
Collapse
Affiliation(s)
- Keeley J Brookes
- Department of Biosciences, School of Science & Technology, Nottingham Trent University, Nottingham NG11 8NS, UK
| |
Collapse
|
9
|
Ayoub CA, Wagner CS, Kuret J. Identification of gene networks mediating regional resistance to tauopathy in late-onset Alzheimer’s disease. PLoS Genet 2023; 19:e1010681. [PMID: 36972319 PMCID: PMC10079065 DOI: 10.1371/journal.pgen.1010681] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2022] [Revised: 04/06/2023] [Accepted: 02/24/2023] [Indexed: 03/29/2023] Open
Abstract
Neurofibrillary lesions composed of tau protein aggregates are defining hallmarks of Alzheimer’s Disease. Despite tau filaments appearing to spread between networked brain regions in a prion-like manner, certain areas including cerebellum resist trans-synaptic spread of tauopathy and degeneration of their constituent neuronal cell bodies. To identify molecular correlates of resistance, we derived and implemented a ratio of ratios approach for disaggregating gene expression data on the basis of regional vulnerability to tauopathic neurodegeneration. When applied to vulnerable pre-frontal cortex as an internal reference for resistant cerebellum, the approach segregated adaptive changes in expression into two components. The first was enriched for neuron-derived transcripts associated with proteostasis including specific members of the molecular chaperone family and was unique to resistant cerebellum. When produced as purified proteins, each of the identified chaperones depressed aggregation of 2N4R tau in vitro at sub-stoichiometric concentrations, consistent with the expression polarity deduced from ratio of ratios testing. In contrast, the second component enriched for glia- and microglia-derived transcripts associated with neuroinflammation, segregating these pathways from susceptibility to tauopathy. These data support the utility of ratio of ratios testing for establishing the polarity of gene expression changes with respect to selective vulnerability. The approach has the potential to identify new targets for drug discovery predicated on their ability to promote resistance to disease in vulnerable neuron populations.
Collapse
Affiliation(s)
- Christopher A. Ayoub
- Biomedical Sciences Graduate Program, Ohio State University, Columbus, Ohio, United States of America
- Medical Scientist Training Program, Ohio State University, Columbus, Ohio, United States of America
- * E-mail: (CAA); (JK)
| | - Connor S. Wagner
- Department of Biological Chemistry & Pharmacology, Ohio State University, Columbus, Ohio, United States of America
| | - Jeff Kuret
- Department of Biological Chemistry & Pharmacology, Ohio State University, Columbus, Ohio, United States of America
- * E-mail: (CAA); (JK)
| |
Collapse
|
10
|
Tauber CV, Schwarz SC, Rösler TW, Arzberger T, Gentleman S, Windl O, Krumbiegel M, Reis A, Ruf VC, Herms J, Höglinger GU. Different MAPT haplotypes influence expression of total MAPT in postmortem brain tissue. Acta Neuropathol Commun 2023; 11:40. [PMID: 36906636 PMCID: PMC10008602 DOI: 10.1186/s40478-023-01534-9] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2023] [Accepted: 02/21/2023] [Indexed: 03/13/2023] Open
Abstract
The MAPT gene, encoding the microtubule-associated protein tau on chromosome 17q21.31, is result of an inversion polymorphism, leading to two allelic variants (H1 and H2). Homozygosity for the more common haplotype H1 is associated with an increased risk for several tauopathies, but also for the synucleinopathy Parkinson's disease (PD). In the present study, we aimed to clarify whether the MAPT haplotype influences expression of MAPT and SNCA, encoding the protein α-synuclein (α-syn), on mRNA and protein levels in postmortem brains of PD patients and controls. We also investigated mRNA expression of several other MAPT haplotype-encoded genes. Postmortem tissues from cortex of fusiform gyrus (ctx-fg) and of the cerebellar hemisphere (ctx-cbl) of neuropathologically confirmed PD patients (n = 95) and age- and sex-matched controls (n = 81) were MAPT haplotype genotyped to identify cases homozygous for either H1 or H2. Relative expression of genes was quantified using real-time qPCR; soluble and insoluble protein levels of tau and α-syn were determined by Western blotting. Homozygosity for H1 versus H2 was associated with increased total MAPT mRNA expression in ctx-fg regardless of disease state. Inversely, H2 homozygosity was associated with markedly increased expression of the corresponding antisense MAPT-AS1 in ctx-cbl. PD patients had higher levels of insoluble 0N3R and 1N4R tau isoforms regardless of the MAPT genotype. The increased presence of insoluble α-syn in PD patients in ctx-fg validated the selected postmortem brain tissue. Our findings in this small, but well controlled cohort of PD and controls support a putative biological relevance of tau in PD. However, we did not identify any link between the disease-predisposing H1/H1 associated overexpression of MAPT with PD status. Further studies are required to gain a deeper understanding of the potential regulatory role of MAPT-AS1 and its association to the disease-protective H2/H2 condition in the context of PD.
Collapse
Affiliation(s)
- Christina V Tauber
- Department of Translational Neurodegeneration, German Center for Neurodegenerative Diseases (DZNE), Munich, Germany.,Department of Neurology, School of Medicine, Technical University Munich, Munich, Germany.,Department of Obstetrics and Gynecology, Ludiwgs-Maximilians University of Munich, Munich, Germany
| | - Sigrid C Schwarz
- Department of Translational Neurodegeneration, German Center for Neurodegenerative Diseases (DZNE), Munich, Germany
| | - Thomas W Rösler
- Department of Translational Neurodegeneration, German Center for Neurodegenerative Diseases (DZNE), Munich, Germany.,Department of Neurology, School of Medicine, Technical University Munich, Munich, Germany
| | - Thomas Arzberger
- Center for Neuropathology and Prion Research, Ludwig-Maximilians University of Munich, Munich, Germany.,Department of Psychiatry and Psychotherapy, University Hospital, Ludwig-Maximilians-University, Munich, Germany
| | - Steve Gentleman
- Parkinson's UK Brain Bank, Department of Brain Sciences, Imperial College London, London, UK.,Neuropathology Unit, Department of Brain Sciences, Department of Medicine, Imperial College London, London, UK
| | - Otto Windl
- Center for Neuropathology and Prion Research, Ludwig-Maximilians University of Munich, Munich, Germany
| | - Mandy Krumbiegel
- Institute of Human Genetics, Friedrich-Alexander University of Erlangen-Nuremberg, Erlangen, Germany
| | - André Reis
- Institute of Human Genetics, Friedrich-Alexander University of Erlangen-Nuremberg, Erlangen, Germany
| | - Viktoria C Ruf
- Center for Neuropathology and Prion Research, Ludwig-Maximilians University of Munich, Munich, Germany
| | - Jochen Herms
- Center for Neuropathology and Prion Research, Ludwig-Maximilians University of Munich, Munich, Germany.,Munich Cluster for Systems Neurology (SyNergy), Munich, Germany
| | - Günter U Höglinger
- Department of Translational Neurodegeneration, German Center for Neurodegenerative Diseases (DZNE), Munich, Germany. .,Munich Cluster for Systems Neurology (SyNergy), Munich, Germany. .,Department of Neurology, Ludwig-Maximilians University of Munich, Munich, Germany.
| |
Collapse
|
11
|
Age-related changes in tau and autophagy in human brain in the absence of neurodegeneration. PLoS One 2023; 18:e0262792. [PMID: 36701399 PMCID: PMC9879510 DOI: 10.1371/journal.pone.0262792] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2021] [Accepted: 08/19/2022] [Indexed: 01/27/2023] Open
Abstract
Tau becomes abnormally hyper-phosphorylated and aggregated in tauopathies like Alzheimers disease (AD). As age is the greatest risk factor for developing AD, it is important to understand how tau protein itself, and the pathways implicated in its turnover, change during aging. We investigated age-related changes in total and phosphorylated tau in brain samples from two cohorts of cognitively normal individuals spanning 19-74 years, without overt neurodegeneration. One cohort utilised resected tissue and the other used post-mortem tissue. Total soluble tau levels declined with age in both cohorts. Phosphorylated tau was undetectable in the post-mortem tissue but was clearly evident in the resected tissue and did not undergo significant age-related change. To ascertain if the decline in soluble tau was correlated with age-related changes in autophagy, three markers of autophagy were tested but only two appeared to increase with age and the third was unchanged. This implies that in individuals who do not develop neurodegeneration, there is an age-related reduction in soluble tau which could potentially be due to age-related changes in autophagy. Thus, to explore how an age-related increase in autophagy might influence tau-mediated dysfunctions in vivo, autophagy was enhanced in a Drosophila model and all age-related tau phenotypes were significantly ameliorated. These data shed light on age-related physiological changes in proteins implicated in AD and highlights the need to study pathways that may be responsible for these changes. It also demonstrates the therapeutic potential of interventions that upregulate turnover of aggregate-prone proteins during aging.
Collapse
|
12
|
Santana DA, Bedrat A, Puga RD, Turecki G, Mechawar N, Faria TC, Gigek CO, Payão SL, Smith MA, Lemos B, Chen ES. The role of H3K9 acetylation and gene expression in different brain regions of Alzheimer's disease patients. Epigenomics 2022; 14:651-670. [PMID: 35588246 DOI: 10.2217/epi-2022-0096] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Aims: To evaluate H3K9 acetylation and gene expression profiles in three brain regions of Alzheimer's disease (AD) patients and elderly controls, and to identify AD region-specific abnormalities. Methods: Brain samples of auditory cortex, hippocampus and cerebellum from AD patients and controls underwent chromatin immunoprecipitation sequencing, RNA sequencing and network analyses. Results: We found a hyperacetylation of AD cerebellum and a slight hypoacetylation of AD hippocampus. The transcriptome revealed differentially expressed genes in the hippocampus and auditory cortex. Network analysis revealed Rho GTPase-mediated mechanisms. Conclusions: These findings suggest that some crucial mechanisms, such as Rho GTPase activity and cytoskeletal organization, are differentially dysregulated in brain regions of AD patients at the epigenetic and transcriptomic levels, and might contribute toward future research on AD pathogenesis.
Collapse
Affiliation(s)
- Daliléia A Santana
- Department of Morphology & Genetics, Universidade Federal de São Paulo (UNIFESP), São Paulo,SP, 04023-062, Brazil
| | - Amina Bedrat
- Department of Environmental Health & Molecular & Integrative Physiological Sciences Program, Harvard TH Chan School of Public Health, Boston, MA 02115-5810, USA
| | - Renato D Puga
- Hermes Pardini Institute, São Paulo, SP, 04038-030, Brazil
| | - Gustavo Turecki
- Department of Psychiatry, Douglas Hospital Research Center, McGill University, Montreal, QC, H4H1R3, Canada
| | - Naguib Mechawar
- Department of Psychiatry, Douglas Hospital Research Center, McGill University, Montreal, QC, H4H1R3, Canada
| | - Tathyane C Faria
- Department of Morphology & Genetics, Universidade Federal de São Paulo (UNIFESP), São Paulo,SP, 04023-062, Brazil
| | - Carolina O Gigek
- Department of Pathology, Universidade Federal de São Paulo (UNIFESP), São Paulo, SP, 04023-062, Brazil
| | - Spencer Lm Payão
- Department of Genetics, Blood Center, Faculdade de Medicina de Marília (FAMEMA), Marília, SP, 17519-050, Brazil
| | - Marília Ac Smith
- Department of Morphology & Genetics, Universidade Federal de São Paulo (UNIFESP), São Paulo,SP, 04023-062, Brazil
| | - Bernardo Lemos
- Department of Environmental Health & Molecular & Integrative Physiological Sciences Program, Harvard TH Chan School of Public Health, Boston, MA 02115-5810, USA
| | - Elizabeth S Chen
- Department of Morphology & Genetics, Universidade Federal de São Paulo (UNIFESP), São Paulo,SP, 04023-062, Brazil.,Department of Environmental Health & Molecular & Integrative Physiological Sciences Program, Harvard TH Chan School of Public Health, Boston, MA 02115-5810, USA
| |
Collapse
|
13
|
Kakouri AC, Votsi C, Oulas A, Nicolaou P, Aureli M, Lunghi G, Samarani M, Compagnoni GM, Salani S, Di Fonzo A, Christophides T, Tanteles GA, Zamba-Papanicolaou E, Pantzaris M, Spyrou GM, Christodoulou K. Transcriptomic characterization of tissues from patients and subsequent pathway analyses reveal biological pathways that are implicated in spastic ataxia. Cell Biosci 2022; 12:29. [PMID: 35277195 PMCID: PMC8917697 DOI: 10.1186/s13578-022-00754-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2021] [Accepted: 02/04/2022] [Indexed: 11/25/2022] Open
Abstract
BACKGROUND Spastic ataxias (SAs) encompass a group of rare and severe neurodegenerative diseases, characterized by an overlap between ataxia and spastic paraplegia clinical features. They have been associated with pathogenic variants in a number of genes, including GBA2. This gene codes for the non-lysososomal β-glucosylceramidase, which is involved in sphingolipid metabolism through its catalytic role in the degradation of glucosylceramide. However, the mechanism by which GBA2 variants lead to the development of SA is still unclear. METHODS In this work, we perform next-generation RNA-sequencing (RNA-seq), in an attempt to discover differentially expressed genes (DEGs) in lymphoblastoid, fibroblast cell lines and induced pluripotent stem cell-derived neurons derived from patients with SA, homozygous for the GBA2 c.1780G > C missense variant. We further exploit DEGs in pathway analyses in order to elucidate candidate molecular mechanisms that are implicated in the development of the GBA2 gene-associated SA. RESULTS Our data reveal a total of 5217 genes with significantly altered expression between patient and control tested tissues. Furthermore, the most significant extracted pathways are presented and discussed for their possible role in the pathogenesis of the disease. Among them are the oxidative stress, neuroinflammation, sphingolipid signaling and metabolism, PI3K-Akt and MAPK signaling pathways. CONCLUSIONS Overall, our work examines for the first time the transcriptome profiles of GBA2-associated SA patients and suggests pathways and pathway synergies that could possibly have a role in SA pathogenesis. Lastly, it provides a list of DEGs and pathways that could be further validated towards the discovery of disease biomarkers.
Collapse
Affiliation(s)
- Andrea C. Kakouri
- Department of Neurogenetics, The Cyprus Institute of Neurology and Genetics, 2370 Nicosia, Cyprus
- Department of Bioinformatics, The Cyprus Institute of Neurology and Genetics, 2370 Nicosia, Cyprus
- The Cyprus School of Molecular Medicine, The Cyprus Institute of Neurology and Genetics, 2370 Nicosia, Cyprus
| | - Christina Votsi
- Department of Neurogenetics, The Cyprus Institute of Neurology and Genetics, 2370 Nicosia, Cyprus
- The Cyprus School of Molecular Medicine, The Cyprus Institute of Neurology and Genetics, 2370 Nicosia, Cyprus
| | - Anastasis Oulas
- Department of Bioinformatics, The Cyprus Institute of Neurology and Genetics, 2370 Nicosia, Cyprus
- The Cyprus School of Molecular Medicine, The Cyprus Institute of Neurology and Genetics, 2370 Nicosia, Cyprus
| | - Paschalis Nicolaou
- Department of Neurogenetics, The Cyprus Institute of Neurology and Genetics, 2370 Nicosia, Cyprus
- The Cyprus School of Molecular Medicine, The Cyprus Institute of Neurology and Genetics, 2370 Nicosia, Cyprus
| | - Massimo Aureli
- Department of Medical Biotechnology and Translational Medicine, University of Milan, 20090 Milano, Italy
| | - Giulia Lunghi
- Department of Medical Biotechnology and Translational Medicine, University of Milan, 20090 Milano, Italy
| | - Maura Samarani
- Unité de Trafic Membranaire ét PathogénèseDépartement de Biologie Cellulaire et Infection, Institut Pasteur, 75015 Paris, France
| | - Giacomo M. Compagnoni
- Neurology Unit, Foundation IRCCS Ca’ Granda Ospedale Maggiore Policlinico, 20122 Milan, Italy
- School of Medicine and Surgery, University of Milano-Bicocca, 20126 Monza, Milan Italy
| | - Sabrina Salani
- Neurology Unit, Foundation IRCCS Ca’ Granda Ospedale Maggiore Policlinico, 20122 Milan, Italy
| | - Alessio Di Fonzo
- Neurology Unit, Foundation IRCCS Ca’ Granda Ospedale Maggiore Policlinico, 20122 Milan, Italy
| | | | - George A. Tanteles
- The Cyprus School of Molecular Medicine, The Cyprus Institute of Neurology and Genetics, 2370 Nicosia, Cyprus
- Department of Clinical Genetics and Genomics, The Cyprus Institute of Neurology and Genetics, 2370 Nicosia, Cyprus
| | - Eleni Zamba-Papanicolaou
- The Cyprus School of Molecular Medicine, The Cyprus Institute of Neurology and Genetics, 2370 Nicosia, Cyprus
- Neurology Clinic D, The Cyprus Institute of Neurology and Genetics, 2370 Nicosia, Cyprus
| | - Marios Pantzaris
- The Cyprus School of Molecular Medicine, The Cyprus Institute of Neurology and Genetics, 2370 Nicosia, Cyprus
- Neurology Clinic C, The Cyprus Institute of Neurology and Genetics, 2370 Nicosia, Cyprus
| | - George M. Spyrou
- Department of Bioinformatics, The Cyprus Institute of Neurology and Genetics, 2370 Nicosia, Cyprus
- The Cyprus School of Molecular Medicine, The Cyprus Institute of Neurology and Genetics, 2370 Nicosia, Cyprus
| | - Kyproula Christodoulou
- Department of Neurogenetics, The Cyprus Institute of Neurology and Genetics, 2370 Nicosia, Cyprus
- The Cyprus School of Molecular Medicine, The Cyprus Institute of Neurology and Genetics, 2370 Nicosia, Cyprus
| |
Collapse
|
14
|
Mendes MS, Majewska AK. An overview of microglia ontogeny and maturation in the homeostatic and pathological brain. Eur J Neurosci 2021; 53:3525-3547. [PMID: 33835613 PMCID: PMC8225243 DOI: 10.1111/ejn.15225] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2020] [Revised: 03/17/2021] [Accepted: 04/01/2021] [Indexed: 12/21/2022]
Abstract
Microglia are the resident immune cells of the central nervous system (CNS) and are increasingly recognized as critical players in development, brain homeostasis, and disease pathogenesis. The lifespan, maintenance, proliferation, and turnover of microglia are important factors that regulate microglial behavior and affect their roles in the CNS. However, emerging evidence suggests that microglia are morphologically and phenotypically distinct in different brain areas, at different ages, and during disease. Ongoing research focuses on understanding how microglia acquire specific phenotypes in response to extrinsic cues in the environment and how phenotypes are specified by intrinsic properties of different populations of microglia. With the development of pharmacological and genetic tools that allow the investigation of microglia in vivo, there have been considerable advances in understanding molecular signatures of both homeostatic microglia and those reacting to injury and disease. Here, we review the master gene regulators that define microglia as well as discuss the evidence that microglia are heterogeneous and fall into distinct clusters that display specific intrinsic properties and perform unique tasks in different settings. Taken together, the information presented supports the idea that microglia morphology and transcriptional heterogeneity should be considered when studying the complex nature of microglia and their roles in brain health and disease.
Collapse
Affiliation(s)
- Monique S Mendes
- Department of Neuroscience, University of Rochester Medical Center, Rochester, NY, USA
| | - Ania K Majewska
- Department of Neuroscience, University of Rochester Medical Center, Rochester, NY, USA
- Center for Visual Science, University of Rochester, Rochester, NY, USA
| |
Collapse
|
15
|
Vavougios GD, Nday C, Pelidou SH, Zarogiannis SG, Gourgoulianis KI, Stamoulis G, Doskas T. Double hit viral parasitism, polymicrobial CNS residency and perturbed proteostasis in Alzheimer's disease: A data driven, in silico analysis of gene expression data. Mol Immunol 2020; 127:124-135. [PMID: 32971399 DOI: 10.1016/j.molimm.2020.08.021] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2020] [Revised: 07/25/2020] [Accepted: 08/30/2020] [Indexed: 01/04/2023]
Abstract
The aim of this study was to determine the interaction of peripheral immunity vs. the CNS in the setting of AD pathogenesis at the transcriptomic level in a data driven manner. For this purpose, publicly available gene expression data from the GEO Datasets repository. We performed differential gene expression and functional enrichment analyses were performed on the five retrieved studies: (a) three hippocampal cortex (HC) studies (b) one study of peripheral blood mononuclear cells (PBMC) and (c) one involving neurofibrillary tangle - containing neurons of the entorhinal cortex (NFT EC). Subsequently, BLAST was used to determine protein conservation between human proteins vs. microbial, whereas putative protein / oligopeptide antigenicity were determined via RANKPep. Gene ontology and pathway analyses revealed significantly enriched viral parasitism pathways in both PBMC and NFT - EC datasets, mediated by ribosomal protein families and epigenetic regulators. Among these, a salient viral pathway referred to Influenza A infection. NFT - EC annotations included leukocyte chemotaxis and immune response pathways. All datasets were significantly enriched for infectious pathways, as well as pathways involved in impaired proteostasis and non - phagocytic cell phagosomal cascades. In conclusion, our in silico analysis outlined an ad hoc model of AD pathophysiology in which double hit (PBMC and NFT-EC) viral parasitism is mediated by eukaryotic translational hijacking, and may be further implicated by impaired immune responses. Overall, our results overlap with the antimicrobial protection hypothesis of AD pathogenesis and support the notion of a pathogen - driven etiology.
Collapse
Affiliation(s)
- George D Vavougios
- Department of Neurology, Athens Naval Hospital, P.C. 115 21, Athens, Greece; Department of Respiratory Medicine, Faculty of Medicine, University of Thessaly, Biopolis, P.C, 41500, Larissa, Greece; Department of Computer Science and Telecommunications, University of Thessaly, Papasiopoulou 2 - 4, P.C. 35 131 Galaneika, Lamia, Greece.
| | - Christiane Nday
- Laboratory of Medical Physics, Faculty of Health Sciences, School of Medicine, Aristotle University of Thessaloniki, P.C. 5414, Thessaloniki, Greece
| | | | - Sotirios G Zarogiannis
- Department of Physiology, Faculty of Medicine, School of Health Sciences, University of Thessaly, BIOPOLIS, Larissa, 41500, Greece
| | - Konstantinos I Gourgoulianis
- Department of Respiratory Medicine, Faculty of Medicine, University of Thessaly, Biopolis, P.C, 41500, Larissa, Greece
| | - George Stamoulis
- Department of Electrical and Computer Engineering, University of Thessaly, 37 Glavani - 28th October Str, Deligiorgi Building, 4th floor, P.C. 382 21, Volos, Greece
| | | |
Collapse
|
16
|
Faria TC, Maldonado HL, Santos LC, DeLabio R, Payao SLM, Turecki G, Mechawar N, Santana DA, Gigek CO, Lemos B, Smith MAC, Chen ES. Characterization of Cerebellum-Specific Ribosomal DNA Epigenetic Modifications in Alzheimer's Disease: Should the Cerebellum Serve as a Control Tissue After All? Mol Neurobiol 2020; 57:2563-2571. [PMID: 32232768 DOI: 10.1007/s12035-020-01902-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2019] [Accepted: 03/09/2020] [Indexed: 11/26/2022]
Abstract
Alzheimer's disease (AD) is a neurodegenerative disease, known as the most common form of dementia. In AD onset, abnormal rRNA expression has been reported to be linked in pathogenesis. Although region-specific expression patterns have previously been reported in AD, it is not until recently that the cerebellum has come under the spotlight. Specifically, it is unclear whether DNA methylation is the mechanism involved in rRNA expression regulation in AD. Hence, we sought to explore the rDNA methylation pattern of two different brain regions - auditory cortex and cerebellum - from AD and age-/sex-matched controls. Our results showed differential hypermethylation at an upstream CpG region to the rDNA promoter when comparing cerebellum controls to auditory cortex controls. This suggests a possible regulatory region from rDNA expression regulation. Moreover, when comparing between AD and control cerebellum samples, we observed hypermethylation of the rDNA promoter region as well as an increase in rDNA content. In addition, we also observed increased rRNA levels in AD compared to control cerebellum. Although still considered a pathology-free brain region, there are growing findings that continue to suggest otherwise. Indeed, cerebellum from AD has been recently described as affected by the disease, presenting a unique pattern of molecular alterations. Given that we observed that increased rDNA promoter methylation did not silence rDNA gene expression, we suggest that rDNA promoter hypermethylation is playing a protective role in rDNA genomic stability and, therefore, increasing rRNA levels in AD cerebellum.
Collapse
Affiliation(s)
- Tathyane C Faria
- Departamento de Morfologia e Genética, Programa de Pós-Graduação em Biologia Estrutural e Funcional da UNIFESP/EPM, Disciplina de Genética, Universidade Federal de São Paulo (UNIFESP/EPM), São Paulo, SP, Brazil
| | - Héctor L Maldonado
- Department of Environmental Health, Program in Molecular and Integrative Physiological Sciences, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Leonardo C Santos
- Departamento de Morfologia e Genética, Programa de Pós-Graduação em Biologia Estrutural e Funcional da UNIFESP/EPM, Disciplina de Genética, Universidade Federal de São Paulo (UNIFESP/EPM), São Paulo, SP, Brazil
| | - Roger DeLabio
- Faculdade de Medicina de Marília (FAMEMA), Marília, SP, Brazil
| | | | - Gustavo Turecki
- Department of Psychiatry, Douglas Hospital Research Center, McGill University, Montreal, QC, Canada
| | - Naguib Mechawar
- Department of Psychiatry, Douglas Hospital Research Center, McGill University, Montreal, QC, Canada
| | - Dalileia A Santana
- Departamento de Morfologia e Genética, Programa de Pós-Graduação em Biologia Estrutural e Funcional da UNIFESP/EPM, Disciplina de Genética, Universidade Federal de São Paulo (UNIFESP/EPM), São Paulo, SP, Brazil
| | - Carolina O Gigek
- Departamento de Morfologia e Genética, Programa de Pós-Graduação em Biologia Estrutural e Funcional da UNIFESP/EPM, Disciplina de Genética, Universidade Federal de São Paulo (UNIFESP/EPM), São Paulo, SP, Brazil
| | - Bernardo Lemos
- Department of Environmental Health, Program in Molecular and Integrative Physiological Sciences, Harvard T.H. Chan School of Public Health, Boston, MA, USA
- Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Marilia A C Smith
- Departamento de Morfologia e Genética, Programa de Pós-Graduação em Biologia Estrutural e Funcional da UNIFESP/EPM, Disciplina de Genética, Universidade Federal de São Paulo (UNIFESP/EPM), São Paulo, SP, Brazil
| | - Elizabeth S Chen
- Departamento de Morfologia e Genética, Programa de Pós-Graduação em Biologia Estrutural e Funcional da UNIFESP/EPM, Disciplina de Genética, Universidade Federal de São Paulo (UNIFESP/EPM), São Paulo, SP, Brazil.
- Department of Environmental Health, Program in Molecular and Integrative Physiological Sciences, Harvard T.H. Chan School of Public Health, Boston, MA, USA.
| |
Collapse
|