1
|
Cruchaga C, Bradley J, Western D, Wang C, Lucio Da Fonseca E, Neupane A, Kurup J, Ray NI, Jean-Francois M, Gorijala P, Bergmann K, Budde J, Martin E, Pericak-Vance M, Cuccaro M, Kunkle B, Morris J, Holtzman D, Perrin R, Naj A, Haines J, Schellenberg G, Fernandez V, Reitz C, Beecham G. Novel early-onset Alzheimer-associated genes influence risk through dysregulation of glutamate, immune activation, and intracell signaling pathways. RESEARCH SQUARE 2024:rs.3.rs-4480585. [PMID: 38883718 PMCID: PMC11177996 DOI: 10.21203/rs.3.rs-4480585/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/18/2024]
Abstract
Alzheimer Disease (AD) is a highly polygenic disease that presents with relatively earlier onset (≤70yo; EOAD) in about 5% of cases. Around 90% of these EOAD cases remain unexplained by pathogenic mutations. Using data from EOAD cases and controls, we performed a genome-wide association study (GWAS) and trans-ancestry meta-analysis on non-Hispanic Whites (NHW, NCase=6,282, NControl=13,386), African Americans (AA NCase=782, NControl=3,663) and East Asians (NCase=375, NControl=838 CO). We identified eight novel significant loci: six in the ancestry-specific analyses and two in the trans-ancestry analysis. By integrating gene-based analysis, eQTL, pQTL and functional annotations, we nominate four novel genes that are involved in microglia activation, glutamate production, and signaling pathways. These results indicate that EOAD, although sharing many genes with LOAD, harbors unique genes and pathways that could be used to create better prediction models or target identification for this type of AD.
Collapse
Affiliation(s)
| | | | - Daniel Western
- Department of Psychiatry, Washington University School of Medicine, St. Louis, MO, USA
| | | | | | | | | | | | | | | | | | | | | | | | - Michael Cuccaro
- The John P. Hussman Institute for Human Genomics, University of Miami, Miami, Florida
| | | | | | | | | | | | | | | | | | | | | |
Collapse
|
2
|
Wang H, Lakshmana MK, Fields GB. Identification of binding partners that facilitate membrane-type 5 matrix metalloproteinase (MT5-MMP) processing of amyloid precursor protein. J Cell Physiol 2024; 239:e31218. [PMID: 38345408 DOI: 10.1002/jcp.31218] [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] [Received: 08/17/2023] [Revised: 01/23/2024] [Accepted: 01/27/2024] [Indexed: 06/14/2024]
Abstract
One of the pathological hallmarks of Alzheimer's disease (AD) is the presence of extracellular deposits of amyloid beta (Aβ) peptide. In addition to Aβ as the core component of the amyloid plaque, the amyloid precursor protein (APP) processing fragment Aβ was also found accumulated around the plaque. The APPη pathway, mainly mediated by membrane-type 5 matrix metalloproteinase (MT5-MMP), represents an important factor in AD pathogenesis. The proamyloidogenic features of MT5-MMP could result from interactions with APP when trafficking between organelles, so determination of the location within the cell of APPη cleavage and interacting proteins of MT5-MMP affecting this process will be of priority in understanding the role of MT5-MMP in AD. In the present study, MT5-MMP was found to be located in the nucleus, cytosol, and cytosolic subcellular granules of CHO cells that stably expressed wild-type human APP751. MT5-MMP fusion proteins were constructed that could localize enzyme production in the Golgi apparatus, endosome, ER, mitochondria, or plasma membrane. The fusion proteins significantly increased sAPPη when directed to the endosome, Golgi apparatus, plasma membrane, or mitochondria. Since the C-terminal region of MT5-MMP is responsible for its intracellular location and trafficking, this domain was used as the bait in a yeast two-hybrid screen to identify MT5-MMP protein partners in a human brain cDNA library. Identified binding partners included N4BP2L1, TMX3, EIG121, bridging Integrator 1 (BIN1), RUFY4, HTRA1, and TMEM199. The binding of N4BP2L1, EIG121, BIN1, or TMX3 to MT5-MMP resulted in the most significant increase in sAPPη production. Thus, the action of MT5-MMP on APP occurs in multiple locations within the cell and is facilitated by site-specific binding partners.
Collapse
Affiliation(s)
- Hongjie Wang
- Department of Chemistry & Biochemistry, Institute for Human Health & Disease Intervention (I-HEALTH), Florida Atlantic University, Jupiter, Florida, USA
| | - Madepalli K Lakshmana
- Department of Immunology and Nano-Medicine, Florida International University, Miami, Florida, USA
| | - Gregg B Fields
- Department of Chemistry & Biochemistry, Institute for Human Health & Disease Intervention (I-HEALTH), Florida Atlantic University, Jupiter, Florida, USA
| |
Collapse
|
3
|
Lee CY, Riffle D, Xiong Y, Momtaz N, Lei Y, Pariser JM, Sikdar D, Hwang A, Duan Z, Zhang J. Characterizing dysregulations via cell-cell communications in Alzheimer's brains using single-cell transcriptomes. BMC Neurosci 2024; 25:24. [PMID: 38741048 PMCID: PMC11089696 DOI: 10.1186/s12868-024-00867-y] [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: 12/15/2023] [Accepted: 04/01/2024] [Indexed: 05/16/2024] Open
Abstract
BACKGROUND Alzheimer's disease (AD) is a devastating neurodegenerative disorder affecting 44 million people worldwide, leading to cognitive decline, memory loss, and significant impairment in daily functioning. The recent single-cell sequencing technology has revolutionized genetic and genomic resolution by enabling scientists to explore the diversity of gene expression patterns at the finest resolution. Most existing studies have solely focused on molecular perturbations within each cell, but cells live in microenvironments rather than in isolated entities. Here, we leveraged the large-scale and publicly available single-nucleus RNA sequencing in the human prefrontal cortex to investigate cell-to-cell communication in healthy brains and their perturbations in AD. We uniformly processed the snRNA-seq with strict QCs and labeled canonical cell types consistent with the definitions from the BRAIN Initiative Cell Census Network. From ligand and receptor gene expression, we built a high-confidence cell-to-cell communication network to investigate signaling differences between AD and healthy brains. RESULTS Specifically, we first performed broad communication pattern analyses to highlight that biologically related cell types in normal brains rely on largely overlapping signaling networks and that the AD brain exhibits the irregular inter-mixing of cell types and signaling pathways. Secondly, we performed a more focused cell-type-centric analysis and found that excitatory neurons in AD have significantly increased their communications to inhibitory neurons, while inhibitory neurons and other non-neuronal cells globally decreased theirs to all cells. Then, we delved deeper with a signaling-centric view, showing that canonical signaling pathways CSF, TGFβ, and CX3C are significantly dysregulated in their signaling to the cell type microglia/PVM and from endothelial to neuronal cells for the WNT pathway. Finally, after extracting 23 known AD risk genes, our intracellular communication analysis revealed a strong connection of extracellular ligand genes APP, APOE, and PSEN1 to intracellular AD risk genes TREM2, ABCA1, and APP in the communication from astrocytes and microglia to neurons. CONCLUSIONS In summary, with the novel advances in single-cell sequencing technologies, we show that cellular signaling is regulated in a cell-type-specific manner and that improper regulation of extracellular signaling genes is linked to intracellular risk genes, giving the mechanistic intra- and inter-cellular picture of AD.
Collapse
Affiliation(s)
- Che Yu Lee
- Department of Computer Science, University of California, Irvine, CA, USA
| | - Dylan Riffle
- Department of Computer Science, University of California, Irvine, CA, USA
| | - Yifeng Xiong
- Department of Computer Science, University of California, Irvine, CA, USA
| | - Nadia Momtaz
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD, USA
| | - Yutong Lei
- Department of Computer Science, University of California, Irvine, CA, USA
| | - Joseph M Pariser
- Department of Computer Science, University of California, Irvine, CA, USA
| | - Diptanshu Sikdar
- Department of Computer Science, University of California, Irvine, CA, USA
| | - Ahyeon Hwang
- Department of Computer Science, University of California, Irvine, CA, USA
- Mathematical, Computational and Systems Biology, University of California, Irvine, CA, USA
| | - Ziheng Duan
- Department of Computer Science, University of California, Irvine, CA, USA
| | - Jing Zhang
- Department of Computer Science, University of California, Irvine, CA, USA.
| |
Collapse
|
4
|
Westhoff M, Del Villar SG, Voelker TL, Thai PN, Spooner HC, Costa AD, Sirish P, Chiamvimonvat N, Dickson EJ, Dixon RE. BIN1 knockdown rescues systolic dysfunction in aging male mouse hearts. Nat Commun 2024; 15:3528. [PMID: 38664444 PMCID: PMC11045846 DOI: 10.1038/s41467-024-47847-8] [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: 05/02/2023] [Accepted: 04/15/2024] [Indexed: 04/28/2024] Open
Abstract
Cardiac dysfunction is a hallmark of aging in humans and mice. Here we report that a two-week treatment to restore youthful Bridging Integrator 1 (BIN1) levels in the hearts of 24-month-old mice rejuvenates cardiac function and substantially reverses the aging phenotype. Our data indicate that age-associated overexpression of BIN1 occurs alongside dysregulated endosomal recycling and disrupted trafficking of cardiac CaV1.2 and type 2 ryanodine receptors. These deficiencies affect channel function at rest and their upregulation during acute stress. In vivo echocardiography reveals reduced systolic function in old mice. BIN1 knockdown using an adeno-associated virus serotype 9 packaged shRNA-mBIN1 restores the nanoscale distribution and clustering plasticity of ryanodine receptors and recovers Ca2+ transient amplitudes and cardiac systolic function toward youthful levels. Enhanced systolic function correlates with increased phosphorylation of the myofilament protein cardiac myosin binding protein-C. These results reveal BIN1 knockdown as a novel therapeutic strategy to rejuvenate the aging myocardium.
Collapse
Affiliation(s)
- Maartje Westhoff
- Department of Physiology and Membrane Biology, University of California Davis, Davis, CA, USA
| | - Silvia G Del Villar
- Department of Physiology and Membrane Biology, University of California Davis, Davis, CA, USA
| | - Taylor L Voelker
- Department of Physiology and Membrane Biology, University of California Davis, Davis, CA, USA
| | - Phung N Thai
- Division of Cardiovascular Medicine, Department of Internal Medicine, University of California, Davis, Davis, CA, USA
| | - Heather C Spooner
- Department of Physiology and Membrane Biology, University of California Davis, Davis, CA, USA
| | - Alexandre D Costa
- Department of Physiology and Membrane Biology, University of California Davis, Davis, CA, USA
| | - Padmini Sirish
- Division of Cardiovascular Medicine, Department of Internal Medicine, University of California, Davis, Davis, CA, USA
| | - Nipavan Chiamvimonvat
- Division of Cardiovascular Medicine, Department of Internal Medicine, University of California, Davis, Davis, CA, USA
- Department of Veterans Affairs, Northern California Health Care System, Mather, CA, USA
- Department of Pharmacology, University of California Davis, Davis, CA, USA
| | - Eamonn J Dickson
- Department of Physiology and Membrane Biology, University of California Davis, Davis, CA, USA
| | - Rose E Dixon
- Department of Physiology and Membrane Biology, University of California Davis, Davis, CA, USA.
| |
Collapse
|
5
|
Mishra S, Jayadev S, Young JE. Differential effects of SORL1 deficiency on the endo-lysosomal network in human neurons and microglia. Philos Trans R Soc Lond B Biol Sci 2024; 379:20220389. [PMID: 38368935 PMCID: PMC10874699 DOI: 10.1098/rstb.2022.0389] [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: 04/17/2023] [Accepted: 08/27/2023] [Indexed: 02/20/2024] Open
Abstract
The endosomal gene SORL1 is a strong Alzheimer's disease (AD) risk gene that harbours loss-of-function variants causative for developing AD. The SORL1 protein SORL1/SORLA is an endosomal receptor that interacts with the multi-protein sorting complex retromer to traffic various cargo through the endo-lysosomal network (ELN). Impairments in endo-lysosomal trafficking are an early cellular symptom in AD and a novel therapeutic target. However, the cell types of the central nervous system are diverse and use the ELN differently. If this pathway is to be effectively therapeutically targeted, understanding how key molecules in the ELN function in various cell types and how manipulating them affects cell-type specific responses relative to AD is essential. Here, we discuss an example where deficiency of SORL1 expression in a human model leads to stress on early endosomes and recycling endosomes in neurons, but preferentially leads to stress on lysosomes in microglia. The differences observed in these organelles could relate to the unique roles of these cells in the brain as neurons are professional secretory cells and microglia are professional phagocytic cells. Experiments to untangle these differences are fundamental to advancing the understanding of cell biology in AD and elucidating important pathways for therapeutic development. Human-induced pluripotent stem cell models are a valuable platform for such experiments. This article is part of a discussion meeting issue 'Understanding the endo-lysosomal network in neurodegeneration'.
Collapse
Affiliation(s)
- Swati Mishra
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA 98109, USA
- Institute for Stem Cell and Regenerative Medicine, University of Washington, Seattle, WA 98109, USA
| | - Suman Jayadev
- Deparment of Neurology, University of Washington, Seattle, WA 98109, USA
- Institute for Stem Cell and Regenerative Medicine, University of Washington, Seattle, WA 98109, USA
| | - Jessica E. Young
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA 98109, USA
- Institute for Stem Cell and Regenerative Medicine, University of Washington, Seattle, WA 98109, USA
| |
Collapse
|
6
|
Maninger JK, Nowak K, Goberdhan S, O'Donoghue R, Connor-Robson N. Cell type-specific functions of Alzheimer's disease endocytic risk genes. Philos Trans R Soc Lond B Biol Sci 2024; 379:20220378. [PMID: 38368934 PMCID: PMC10874703 DOI: 10.1098/rstb.2022.0378] [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: 03/17/2023] [Accepted: 09/12/2023] [Indexed: 02/20/2024] Open
Abstract
Endocytosis is a key cellular pathway required for the internalization of cellular nutrients, lipids and receptor-bound cargoes. It is also critical for the recycling of cellular components, cellular trafficking and membrane dynamics. The endocytic pathway has been consistently implicated in Alzheimer's disease (AD) through repeated genome-wide association studies and the existence of rare coding mutations in endocytic genes. BIN1 and PICALM are two of the most significant late-onset AD risk genes after APOE and are both key to clathrin-mediated endocytic biology. Pathological studies also demonstrate that endocytic dysfunction is an early characteristic of late-onset AD, being seen in the prodromal phase of the disease. Different cell types of the brain have specific requirements of the endocytic pathway. Neurons require efficient recycling of synaptic vesicles and microglia use the specialized form of endocytosis-phagocytosis-for their normal function. Therefore, disease-associated changes in endocytic genes will have varied impacts across different cell types, which remains to be fully explored. Given the genetic and pathological evidence for endocytic dysfunction in AD, understanding how such changes and the related cell type-specific vulnerabilities impact normal cellular function and contribute to disease is vital and could present novel therapeutic opportunities. This article is part of a discussion meeting issue 'Understanding the endo-lysosomal network in neurodegeneration'.
Collapse
Affiliation(s)
| | - Karolina Nowak
- Cardiff University, Dementia Research Institute, Cardiff University¸ Cardiff, CF24 4HQ, UK
| | - Srilakshmi Goberdhan
- Cardiff University, Dementia Research Institute, Cardiff University¸ Cardiff, CF24 4HQ, UK
| | - Rachel O'Donoghue
- Cardiff University, Dementia Research Institute, Cardiff University¸ Cardiff, CF24 4HQ, UK
| | - Natalie Connor-Robson
- Cardiff University, Dementia Research Institute, Cardiff University¸ Cardiff, CF24 4HQ, UK
| |
Collapse
|
7
|
Garcia‐Agudo LF, Shi Z, Smith IF, Kramár EA, Tran K, Kawauchi S, Wang S, Collins S, Walker A, Shi K, Neumann J, Liang HY, Da Cunha C, Milinkeviciute G, Morabito S, Miyoshi E, Rezaie N, Gomez‐Arboledas A, Arvilla AM, Ghaemi DI, Tenner AJ, LaFerla FM, Wood MA, Mortazavi A, Swarup V, MacGregor GR, Green KN. BIN1 K358R suppresses glial response to plaques in mouse model of Alzheimer's disease. Alzheimers Dement 2024; 20:2922-2942. [PMID: 38460121 PMCID: PMC11032570 DOI: 10.1002/alz.13767] [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: 11/07/2023] [Revised: 01/16/2024] [Accepted: 01/17/2024] [Indexed: 03/11/2024]
Abstract
INTRODUCTION The BIN1 coding variant rs138047593 (K358R) is linked to Late-Onset Alzheimer's Disease (LOAD) via targeted exome sequencing. METHODS To elucidate the functional consequences of this rare coding variant on brain amyloidosis and neuroinflammation, we generated BIN1K358R knock-in mice using CRISPR/Cas9 technology. These mice were subsequently bred with 5xFAD transgenic mice, which serve as a model for Alzheimer's pathology. RESULTS The presence of the BIN1K358R variant leads to increased cerebral amyloid deposition, with a dampened response of astrocytes and oligodendrocytes, but not microglia, at both the cellular and transcriptional levels. This correlates with decreased neurofilament light chain in both plasma and brain tissue. Synaptic densities are significantly increased in both wild-type and 5xFAD backgrounds homozygous for the BIN1K358R variant. DISCUSSION The BIN1 K358R variant modulates amyloid pathology in 5xFAD mice, attenuates the astrocytic and oligodendrocytic responses to amyloid plaques, decreases damage markers, and elevates synaptic densities. HIGHLIGHTS BIN1 rs138047593 (K358R) coding variant is associated with increased risk of LOAD. BIN1 K358R variant increases amyloid plaque load in 12-month-old 5xFAD mice. BIN1 K358R variant dampens astrocytic and oligodendrocytic response to plaques. BIN1 K358R variant decreases neuronal damage in 5xFAD mice. BIN1 K358R upregulates synaptic densities and modulates synaptic transmission.
Collapse
Affiliation(s)
| | - Zechuan Shi
- Department of Neurobiology and BehaviorUniversity of CaliforniaIrvineCaliforniaUSA
| | - Ian F. Smith
- Department of Neurobiology and BehaviorUniversity of CaliforniaIrvineCaliforniaUSA
| | - Enikö A. Kramár
- Department of Neurobiology and BehaviorUniversity of CaliforniaIrvineCaliforniaUSA
| | - Katelynn Tran
- Institute for Memory Impairments and Neurological Disorders, University of CaliforniaIrvineCaliforniaUSA
| | - Shimako Kawauchi
- Institute for Memory Impairments and Neurological Disorders, University of CaliforniaIrvineCaliforniaUSA
- Transgenic Mouse Facility, ULAR, Office of Research, University of CaliforniaIrvineCaliforniaUSA
| | - Shuling Wang
- Transgenic Mouse Facility, ULAR, Office of Research, University of CaliforniaIrvineCaliforniaUSA
| | - Sherilyn Collins
- Transgenic Mouse Facility, ULAR, Office of Research, University of CaliforniaIrvineCaliforniaUSA
| | - Amber Walker
- Transgenic Mouse Facility, ULAR, Office of Research, University of CaliforniaIrvineCaliforniaUSA
| | - Kai‐Xuan Shi
- Transgenic Mouse Facility, ULAR, Office of Research, University of CaliforniaIrvineCaliforniaUSA
| | - Jonathan Neumann
- Transgenic Mouse Facility, ULAR, Office of Research, University of CaliforniaIrvineCaliforniaUSA
| | - Heidi Yahan Liang
- Department of Developmental and Cell BiologyUniversity of CaliforniaIrvineCaliforniaUSA
- Center for Complex Biological Systems, University of CaliforniaIrvineCaliforniaUSA
| | - Celia Da Cunha
- Institute for Memory Impairments and Neurological Disorders, University of CaliforniaIrvineCaliforniaUSA
| | - Giedre Milinkeviciute
- Institute for Memory Impairments and Neurological Disorders, University of CaliforniaIrvineCaliforniaUSA
| | - Samuel Morabito
- Department of Neurobiology and BehaviorUniversity of CaliforniaIrvineCaliforniaUSA
| | - Emily Miyoshi
- Department of Neurobiology and BehaviorUniversity of CaliforniaIrvineCaliforniaUSA
| | - Narges Rezaie
- Department of Developmental and Cell BiologyUniversity of CaliforniaIrvineCaliforniaUSA
- Center for Complex Biological Systems, University of CaliforniaIrvineCaliforniaUSA
| | - Angela Gomez‐Arboledas
- Institute for Memory Impairments and Neurological Disorders, University of CaliforniaIrvineCaliforniaUSA
| | - Adrian Mendoza Arvilla
- Institute for Memory Impairments and Neurological Disorders, University of CaliforniaIrvineCaliforniaUSA
| | - Daryan Iman Ghaemi
- Department of Neurobiology and BehaviorUniversity of CaliforniaIrvineCaliforniaUSA
| | - Andrea J. Tenner
- Department of Neurobiology and BehaviorUniversity of CaliforniaIrvineCaliforniaUSA
- Institute for Memory Impairments and Neurological Disorders, University of CaliforniaIrvineCaliforniaUSA
- Department of Molecular Biology & BiochemistryUniversity of CaliforniaIrvineCaliforniaUSA
- Department of Pathology and Laboratory MedicineUniversity of CaliforniaIrvineCaliforniaUSA
| | - Frank M. LaFerla
- Department of Neurobiology and BehaviorUniversity of CaliforniaIrvineCaliforniaUSA
- Institute for Memory Impairments and Neurological Disorders, University of CaliforniaIrvineCaliforniaUSA
| | - Marcelo A. Wood
- Department of Neurobiology and BehaviorUniversity of CaliforniaIrvineCaliforniaUSA
- Institute for Memory Impairments and Neurological Disorders, University of CaliforniaIrvineCaliforniaUSA
| | - Ali Mortazavi
- Department of Developmental and Cell BiologyUniversity of CaliforniaIrvineCaliforniaUSA
- Center for Complex Biological Systems, University of CaliforniaIrvineCaliforniaUSA
| | - Vivek Swarup
- Department of Neurobiology and BehaviorUniversity of CaliforniaIrvineCaliforniaUSA
- Institute for Memory Impairments and Neurological Disorders, University of CaliforniaIrvineCaliforniaUSA
- Center for Complex Biological Systems, University of CaliforniaIrvineCaliforniaUSA
| | - Grant R. MacGregor
- Transgenic Mouse Facility, ULAR, Office of Research, University of CaliforniaIrvineCaliforniaUSA
- Department of Developmental and Cell BiologyUniversity of CaliforniaIrvineCaliforniaUSA
| | - Kim N. Green
- Department of Neurobiology and BehaviorUniversity of CaliforniaIrvineCaliforniaUSA
- Institute for Memory Impairments and Neurological Disorders, University of CaliforniaIrvineCaliforniaUSA
| |
Collapse
|
8
|
Saha O, Melo de Farias AR, Pelletier A, Siedlecki-Wullich D, Landeira BS, Gadaut J, Carrier A, Vreulx AC, Guyot K, Shen Y, Bonnefond A, Amouyel P, Tcw J, Kilinc D, Queiroz CM, Delahaye F, Lambert JC, Costa MR. The Alzheimer's disease risk gene BIN1 regulates activity-dependent gene expression in human-induced glutamatergic neurons. Mol Psychiatry 2024:10.1038/s41380-024-02502-y. [PMID: 38514804 DOI: 10.1038/s41380-024-02502-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/03/2023] [Revised: 02/22/2024] [Accepted: 02/27/2024] [Indexed: 03/23/2024]
Abstract
Bridging Integrator 1 (BIN1) is the second most important Alzheimer's disease (AD) risk gene, but its physiological roles in neurons and its contribution to brain pathology remain largely elusive. In this work, we show that BIN1 plays a critical role in the regulation of calcium homeostasis, electrical activity, and gene expression of glutamatergic neurons. Using single-cell RNA-sequencing on cerebral organoids generated from isogenic BIN1 wild type (WT), heterozygous (HET) and homozygous knockout (KO) human-induced pluripotent stem cells (hiPSCs), we show that BIN1 is mainly expressed by oligodendrocytes and glutamatergic neurons, like in the human brain. Both BIN1 HET and KO cerebral organoids show specific transcriptional alterations, mainly associated with ion transport and synapses in glutamatergic neurons. We then demonstrate that BIN1 cell-autonomously regulates gene expression in glutamatergic neurons by using a novel protocol to generate pure culture of hiPSC-derived induced neurons (hiNs). Using this system, we also show that BIN1 plays a key role in the regulation of neuronal calcium transients and electrical activity via its interaction with the L-type voltage-gated calcium channel Cav1.2. BIN1 KO hiNs show reduced activity-dependent internalization and higher Cav1.2 expression compared to WT hiNs. Pharmacological blocking of this channel with clinically relevant doses of nifedipine, a calcium channel blocker, partly rescues electrical and gene expression alterations in BIN1 KO glutamatergic neurons. Further, we show that transcriptional alterations in BIN1 KO hiNs that affect biological processes related to calcium homeostasis are also present in glutamatergic neurons of the human brain at late stages of AD pathology. Together, these findings suggest that BIN1-dependent alterations in neuronal properties could contribute to AD pathophysiology and that treatment with low doses of clinically approved calcium blockers should be considered as an option to slow disease-onset and progression.
Collapse
Affiliation(s)
- Orthis Saha
- Univ. Lille, Inserm, CHU Lille, Institut Pasteur de Lille, U1167-RID-AGE facteurs de risque et déterminants moléculaires des maladies liées au vieillissement, DISTALZ, 1 rue du Professeur Calmette, 59019, Lille, France
| | - Ana Raquel Melo de Farias
- Univ. Lille, Inserm, CHU Lille, Institut Pasteur de Lille, U1167-RID-AGE facteurs de risque et déterminants moléculaires des maladies liées au vieillissement, DISTALZ, 1 rue du Professeur Calmette, 59019, Lille, France
- Brain Institute, Federal University of Rio Grande do Norte, Av. Senador Salgado Filho, 3000, Campus Universitário, Lagoa, Nova, 59078-970, Natal, Brazil
| | - Alexandre Pelletier
- Univ. Lille, Inserm, CNRS, CHU Lille, Institut Pasteur de Lille, U1283-UMR 8199 EGID, Pôle Recherche, 1 Place de Verdun, 59045, Lille, Cedex, France
- Department of Pharmacology, Physiology & Biophysics, Boston University, Chobanian & Avedisian School of Medicine, Boston, MA, 02118, USA
| | - Dolores Siedlecki-Wullich
- Univ. Lille, Inserm, CHU Lille, Institut Pasteur de Lille, U1167-RID-AGE facteurs de risque et déterminants moléculaires des maladies liées au vieillissement, DISTALZ, 1 rue du Professeur Calmette, 59019, Lille, France
| | - Bruna Soares Landeira
- Univ. Lille, Inserm, CHU Lille, Institut Pasteur de Lille, U1167-RID-AGE facteurs de risque et déterminants moléculaires des maladies liées au vieillissement, DISTALZ, 1 rue du Professeur Calmette, 59019, Lille, France
| | - Johanna Gadaut
- Univ. Lille, Inserm, CHU Lille, Institut Pasteur de Lille, U1167-RID-AGE facteurs de risque et déterminants moléculaires des maladies liées au vieillissement, DISTALZ, 1 rue du Professeur Calmette, 59019, Lille, France
| | - Arnaud Carrier
- Univ. Lille, Inserm, CNRS, CHU Lille, Institut Pasteur de Lille, U1283-UMR 8199 EGID, Pôle Recherche, 1 Place de Verdun, 59045, Lille, Cedex, France
| | - Anaïs-Camille Vreulx
- Univ. Lille, Inserm, CHU Lille, Institut Pasteur de Lille, U1167-RID-AGE facteurs de risque et déterminants moléculaires des maladies liées au vieillissement, DISTALZ, 1 rue du Professeur Calmette, 59019, Lille, France
| | - Karine Guyot
- Univ. Lille, Inserm, CHU Lille, Institut Pasteur de Lille, U1167-RID-AGE facteurs de risque et déterminants moléculaires des maladies liées au vieillissement, DISTALZ, 1 rue du Professeur Calmette, 59019, Lille, France
| | - Yun Shen
- Department of Pharmacology, Physiology & Biophysics, Boston University, Chobanian & Avedisian School of Medicine, Boston, MA, 02118, USA
| | - Amelie Bonnefond
- Univ. Lille, Inserm, CNRS, CHU Lille, Institut Pasteur de Lille, U1283-UMR 8199 EGID, Pôle Recherche, 1 Place de Verdun, 59045, Lille, Cedex, France
| | - Philippe Amouyel
- Univ. Lille, Inserm, CHU Lille, Institut Pasteur de Lille, U1167-RID-AGE facteurs de risque et déterminants moléculaires des maladies liées au vieillissement, DISTALZ, 1 rue du Professeur Calmette, 59019, Lille, France
| | - Julia Tcw
- Department of Pharmacology, Physiology & Biophysics, Boston University, Chobanian & Avedisian School of Medicine, Boston, MA, 02118, USA
- Bioinformatics Program, Faculty of Computing & Data Sciences, Boston University, Boston, MA, 02115, USA
| | - Devrim Kilinc
- Univ. Lille, Inserm, CHU Lille, Institut Pasteur de Lille, U1167-RID-AGE facteurs de risque et déterminants moléculaires des maladies liées au vieillissement, DISTALZ, 1 rue du Professeur Calmette, 59019, Lille, France
| | - Claudio Marcos Queiroz
- Brain Institute, Federal University of Rio Grande do Norte, Av. Senador Salgado Filho, 3000, Campus Universitário, Lagoa, Nova, 59078-970, Natal, Brazil
| | - Fabien Delahaye
- Univ. Lille, Inserm, CNRS, CHU Lille, Institut Pasteur de Lille, U1283-UMR 8199 EGID, Pôle Recherche, 1 Place de Verdun, 59045, Lille, Cedex, France
| | - Jean-Charles Lambert
- Univ. Lille, Inserm, CHU Lille, Institut Pasteur de Lille, U1167-RID-AGE facteurs de risque et déterminants moléculaires des maladies liées au vieillissement, DISTALZ, 1 rue du Professeur Calmette, 59019, Lille, France
| | - Marcos R Costa
- Univ. Lille, Inserm, CHU Lille, Institut Pasteur de Lille, U1167-RID-AGE facteurs de risque et déterminants moléculaires des maladies liées au vieillissement, DISTALZ, 1 rue du Professeur Calmette, 59019, Lille, France.
- Brain Institute, Federal University of Rio Grande do Norte, Av. Senador Salgado Filho, 3000, Campus Universitário, Lagoa, Nova, 59078-970, Natal, Brazil.
| |
Collapse
|
9
|
Ifediora N, Canoll P, Hargus G. Human stem cell transplantation models of Alzheimer's disease. Front Aging Neurosci 2024; 16:1354164. [PMID: 38450383 PMCID: PMC10915253 DOI: 10.3389/fnagi.2024.1354164] [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: 12/12/2023] [Accepted: 02/06/2024] [Indexed: 03/08/2024] Open
Abstract
Alzheimer's disease (AD) is the most frequent form of dementia. It is characterized by pronounced neuronal degeneration with formation of neurofibrillary tangles and deposition of amyloid β throughout the central nervous system. Animal models have provided important insights into the pathogenesis of AD and they have shown that different brain cell types including neurons, astrocytes and microglia have important functions in the pathogenesis of AD. However, there are difficulties in translating promising therapeutic observations in mice into clinical application in patients. Alternative models using human cells such as human induced pluripotent stem cells (iPSCs) may provide significant advantages, since they have successfully been used to model disease mechanisms in neurons and in glial cells in neurodegenerative diseases in vitro and in vivo. In this review, we summarize recent studies that describe the transplantation of human iPSC-derived neurons, astrocytes and microglial cells into the forebrain of mice to generate chimeric transplantation models of AD. We also discuss opportunities, challenges and limitations in using differentiated human iPSCs for in vivo disease modeling and their application for biomedical research.
Collapse
Affiliation(s)
- Nkechime Ifediora
- Department of Pathology and Cell Biology, Columbia University, New York, NY, United States
| | - Peter Canoll
- Department of Pathology and Cell Biology, Columbia University, New York, NY, United States
| | - Gunnar Hargus
- Department of Pathology and Cell Biology, Columbia University, New York, NY, United States
- Taub Institute for Research on Alzheimer’s Disease and the Aging Brain, Columbia University, New York, NY, United States
| |
Collapse
|
10
|
Firdaus Z, Li X. Unraveling the Genetic Landscape of Neurological Disorders: Insights into Pathogenesis, Techniques for Variant Identification, and Therapeutic Approaches. Int J Mol Sci 2024; 25:2320. [PMID: 38396996 PMCID: PMC10889342 DOI: 10.3390/ijms25042320] [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] [Revised: 02/09/2024] [Accepted: 02/13/2024] [Indexed: 02/25/2024] Open
Abstract
Genetic abnormalities play a crucial role in the development of neurodegenerative disorders (NDDs). Genetic exploration has indeed contributed to unraveling the molecular complexities responsible for the etiology and progression of various NDDs. The intricate nature of rare and common variants in NDDs contributes to a limited understanding of the genetic risk factors associated with them. Advancements in next-generation sequencing have made whole-genome sequencing and whole-exome sequencing possible, allowing the identification of rare variants with substantial effects, and improving the understanding of both Mendelian and complex neurological conditions. The resurgence of gene therapy holds the promise of targeting the etiology of diseases and ensuring a sustained correction. This approach is particularly enticing for neurodegenerative diseases, where traditional pharmacological methods have fallen short. In the context of our exploration of the genetic epidemiology of the three most prevalent NDDs-amyotrophic lateral sclerosis, Alzheimer's disease, and Parkinson's disease, our primary goal is to underscore the progress made in the development of next-generation sequencing. This progress aims to enhance our understanding of the disease mechanisms and explore gene-based therapies for NDDs. Throughout this review, we focus on genetic variations, methodologies for their identification, the associated pathophysiology, and the promising potential of gene therapy. Ultimately, our objective is to provide a comprehensive and forward-looking perspective on the emerging research arena of NDDs.
Collapse
Affiliation(s)
- Zeba Firdaus
- Department of Internal Medicine, Mayo Clinic, Rochester, MN 55905, USA;
- Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, MN 55905, USA
| | - Xiaogang Li
- Department of Internal Medicine, Mayo Clinic, Rochester, MN 55905, USA;
- Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, MN 55905, USA
| |
Collapse
|
11
|
Vuic B, Milos T, Tudor L, Nikolac Perkovic M, Konjevod M, Nedic Erjavec G, Farkas V, Uzun S, Mimica N, Svob Strac D. Pharmacogenomics of Dementia: Personalizing the Treatment of Cognitive and Neuropsychiatric Symptoms. Genes (Basel) 2023; 14:2048. [PMID: 38002991 PMCID: PMC10671071 DOI: 10.3390/genes14112048] [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: 10/10/2023] [Revised: 10/30/2023] [Accepted: 11/02/2023] [Indexed: 11/26/2023] Open
Abstract
Dementia is a syndrome of global and progressive deterioration of cognitive skills, especially memory, learning, abstract thinking, and orientation, usually affecting the elderly. The most common forms are Alzheimer's disease, vascular dementia, and other (frontotemporal, Lewy body disease) dementias. The etiology of these multifactorial disorders involves complex interactions of various environmental and (epi)genetic factors and requires multiple forms of pharmacological intervention, including anti-dementia drugs for cognitive impairment, antidepressants, antipsychotics, anxiolytics and sedatives for behavioral and psychological symptoms of dementia, and other drugs for comorbid disorders. The pharmacotherapy of dementia patients has been characterized by a significant interindividual variability in drug response and the development of adverse drug effects. The therapeutic response to currently available drugs is partially effective in only some individuals, with side effects, drug interactions, intolerance, and non-compliance occurring in the majority of dementia patients. Therefore, understanding the genetic basis of a patient's response to pharmacotherapy might help clinicians select the most effective treatment for dementia while minimizing the likelihood of adverse reactions and drug interactions. Recent advances in pharmacogenomics may contribute to the individualization and optimization of dementia pharmacotherapy by increasing its efficacy and safety via a prediction of clinical outcomes. Thus, it can significantly improve the quality of life in dementia patients.
Collapse
Affiliation(s)
- Barbara Vuic
- Laboratory for Molecular Neuropsychiatry, Division of Molecular Medicine, Rudjer Boskovic Institute, 10000 Zagreb, Croatia; (B.V.); (T.M.); (L.T.); (M.N.P.); (M.K.); (G.N.E.); (V.F.)
| | - Tina Milos
- Laboratory for Molecular Neuropsychiatry, Division of Molecular Medicine, Rudjer Boskovic Institute, 10000 Zagreb, Croatia; (B.V.); (T.M.); (L.T.); (M.N.P.); (M.K.); (G.N.E.); (V.F.)
| | - Lucija Tudor
- Laboratory for Molecular Neuropsychiatry, Division of Molecular Medicine, Rudjer Boskovic Institute, 10000 Zagreb, Croatia; (B.V.); (T.M.); (L.T.); (M.N.P.); (M.K.); (G.N.E.); (V.F.)
| | - Matea Nikolac Perkovic
- Laboratory for Molecular Neuropsychiatry, Division of Molecular Medicine, Rudjer Boskovic Institute, 10000 Zagreb, Croatia; (B.V.); (T.M.); (L.T.); (M.N.P.); (M.K.); (G.N.E.); (V.F.)
| | - Marcela Konjevod
- Laboratory for Molecular Neuropsychiatry, Division of Molecular Medicine, Rudjer Boskovic Institute, 10000 Zagreb, Croatia; (B.V.); (T.M.); (L.T.); (M.N.P.); (M.K.); (G.N.E.); (V.F.)
| | - Gordana Nedic Erjavec
- Laboratory for Molecular Neuropsychiatry, Division of Molecular Medicine, Rudjer Boskovic Institute, 10000 Zagreb, Croatia; (B.V.); (T.M.); (L.T.); (M.N.P.); (M.K.); (G.N.E.); (V.F.)
| | - Vladimir Farkas
- Laboratory for Molecular Neuropsychiatry, Division of Molecular Medicine, Rudjer Boskovic Institute, 10000 Zagreb, Croatia; (B.V.); (T.M.); (L.T.); (M.N.P.); (M.K.); (G.N.E.); (V.F.)
| | - Suzana Uzun
- Department for Biological Psychiatry and Psychogeriatry, University Hospital Vrapce, 10000 Zagreb, Croatia; (S.U.); (N.M.)
- School of Medicine, University of Zagreb, 10000 Zagreb, Croatia
| | - Ninoslav Mimica
- Department for Biological Psychiatry and Psychogeriatry, University Hospital Vrapce, 10000 Zagreb, Croatia; (S.U.); (N.M.)
- School of Medicine, University of Zagreb, 10000 Zagreb, Croatia
| | - Dubravka Svob Strac
- Laboratory for Molecular Neuropsychiatry, Division of Molecular Medicine, Rudjer Boskovic Institute, 10000 Zagreb, Croatia; (B.V.); (T.M.); (L.T.); (M.N.P.); (M.K.); (G.N.E.); (V.F.)
| |
Collapse
|
12
|
Qin H, Zhou L, Haque FT, Martin-Jimenez C, Trang A, Benveniste EN, Wang Q. Diverse signaling mechanisms and heterogeneity of astrocyte reactivity in Alzheimer's disease. J Neurochem 2023. [PMID: 37932959 DOI: 10.1111/jnc.16002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2023] [Revised: 10/10/2023] [Accepted: 10/11/2023] [Indexed: 11/08/2023]
Abstract
Alzheimer's disease (AD) affects various brain cell types, including astrocytes, which are the most abundant cell types in the central nervous system (CNS). Astrocytes not only provide homeostatic support to neurons but also actively regulate synaptic signaling and functions and become reactive in response to CNS insults through diverse signaling pathways including the JAK/STAT, NF-κB, and GPCR-elicited pathways. The advent of new technology for transcriptomic profiling at the single-cell level has led to increasing recognition of the highly versatile nature of reactive astrocytes and the context-dependent specificity of astrocyte reactivity. In AD, reactive astrocytes have long been observed in senile plaques and have recently been suggested to play a role in AD pathogenesis and progression. However, the precise contributions of reactive astrocytes to AD remain elusive, and targeting this complex cell population for AD treatment poses significant challenges. In this review, we summarize the current understanding of astrocyte reactivity and its role in AD, with a particular focus on the signaling pathways that promote astrocyte reactivity and the heterogeneity of reactive astrocytes. Furthermore, we explore potential implications for the development of therapeutics for AD. Our objective is to shed light on the complex involvement of astrocytes in AD and offer insights into potential therapeutic targets and strategies for treating and managing this devastating neurodegenerative disorder.
Collapse
Affiliation(s)
- Hongwei Qin
- Department of Cell, Developmental and Integrative Biology, University of Alabama at Birmingham, Birmingham, Alabama, USA
| | - Lianna Zhou
- Department of Cell, Developmental and Integrative Biology, University of Alabama at Birmingham, Birmingham, Alabama, USA
| | - Faris T Haque
- Department of Cell, Developmental and Integrative Biology, University of Alabama at Birmingham, Birmingham, Alabama, USA
| | - Cynthia Martin-Jimenez
- Department of Neuroscience and Regenerative Medicine, Medical College of Georgia at Augusta University, Augusta, Georgia, USA
| | - Amy Trang
- Department of Neuroscience and Regenerative Medicine, Medical College of Georgia at Augusta University, Augusta, Georgia, USA
| | - Etty N Benveniste
- Department of Cell, Developmental and Integrative Biology, University of Alabama at Birmingham, Birmingham, Alabama, USA
| | - Qin Wang
- Department of Neuroscience and Regenerative Medicine, Medical College of Georgia at Augusta University, Augusta, Georgia, USA
| |
Collapse
|
13
|
Yeo S, Jang J, Jung HJ, Lee H, Choe Y. Primary cilia-mediated regulation of microglial secretion in Alzheimer's disease. Front Mol Biosci 2023; 10:1250335. [PMID: 37942288 PMCID: PMC10627801 DOI: 10.3389/fmolb.2023.1250335] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2023] [Accepted: 09/28/2023] [Indexed: 11/10/2023] Open
Abstract
Alzheimer's disease (AD) is a brain disorder manifested by a gradual decline in cognitive function due to the accumulation of extracellular amyloid plaques, disruptions in neuronal substance transport, and the degeneration of neurons. In affected neurons, incomplete clearance of toxic proteins by neighboring microglia leads to irreversible brain inflammation, for which cellular signaling is poorly understood. Through single-cell transcriptomic analysis, we discovered distinct regional differences in the ability of microglia to clear damaged neurites. Specifically, microglia in the septal region of wild type mice exhibited a transcriptomic signature resembling disease-associated microglia (DAM). These lateral septum (LS)-enriched microglia were associated with dense axonal bundles originating from the hippocampus. Further transcriptomic and proteomic approaches revealed that primary cilia, small hair-like structures found on cells, played a role in the regulation of microglial secretory function. Notably, primary cilia were transiently observed in microglia, and their presence was significantly reduced in microglia from AD mice. We observed significant changes in the secretion and proteomic profiles of the secretome after inhibiting the primary cilia gene intraflagellar transport particle 88 (Ift88) in microglia. Intriguingly, inhibiting primary cilia in the septal microglia of AD mice resulted in the expansion of extracellular amyloid plaques and damage to adjacent neurites. These results indicate that DAM-like microglia are present in the LS, a critical target region for hippocampal nerve bundles, and that the primary ciliary signaling system regulates microglial secretion, affecting extracellular proteostasis. Age-related primary ciliopathy probably contributes to the selective sensitivity of microglia, thereby exacerbating AD. Targeting the primary ciliary signaling system could therefore be a viable strategy for modulating neuroimmune responses in AD treatments.
Collapse
Affiliation(s)
- Seungeun Yeo
- Korea Brain Research Institute, Daegu, Republic of Korea
| | - Jaemyung Jang
- Korea Brain Research Institute, Daegu, Republic of Korea
| | - Hyun Jin Jung
- Korea Brain Research Institute, Daegu, Republic of Korea
| | - Hyeyoung Lee
- Division of Applied Bioengineering, Dong-eui University, Busan, Republic of Korea
| | - Youngshik Choe
- Korea Brain Research Institute, Daegu, Republic of Korea
| |
Collapse
|
14
|
Gamache J, Gingerich D, Shwab EK, Barrera J, Garrett ME, Hume C, Crawford GE, Ashley-Koch AE, Chiba-Falek O. Integrative single-nucleus multi-omics analysis prioritizes candidate cis and trans regulatory networks and their target genes in Alzheimer's disease brains. Cell Biosci 2023; 13:185. [PMID: 37789374 PMCID: PMC10546724 DOI: 10.1186/s13578-023-01120-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2023] [Accepted: 08/30/2023] [Indexed: 10/05/2023] Open
Abstract
BACKGROUND The genetic underpinnings of late-onset Alzheimer's disease (LOAD) are yet to be fully elucidated. Although numerous LOAD-associated loci have been discovered, the causal variants and their target genes remain largely unknown. Since the brain is composed of heterogenous cell subtypes, it is imperative to study the brain on a cell subtype specific level to explore the biological processes underlying LOAD. METHODS Here, we present the largest parallel single-nucleus (sn) multi-omics study to simultaneously profile gene expression (snRNA-seq) and chromatin accessibility (snATAC-seq) to date, using nuclei from 12 normal and 12 LOAD brains. We identified cell subtype clusters based on gene expression and chromatin accessibility profiles and characterized cell subtype-specific LOAD-associated differentially expressed genes (DEGs), differentially accessible peaks (DAPs) and cis co-accessibility networks (CCANs). RESULTS Integrative analysis defined disease-relevant CCANs in multiple cell subtypes and discovered LOAD-associated cell subtype-specific candidate cis regulatory elements (cCREs), their candidate target genes, and trans-interacting transcription factors (TFs), some of which, including ELK1, JUN, and SMAD4 in excitatory neurons, were also LOAD-DEGs. Finally, we focused on a subset of cell subtype-specific CCANs that overlap known LOAD-GWAS regions and catalogued putative functional SNPs changing the affinities of TF motifs within LOAD-cCREs linked to LOAD-DEGs, including APOE and MYO1E in a specific subtype of microglia and BIN1 in a subpopulation of oligodendrocytes. CONCLUSIONS To our knowledge, this study represents the most comprehensive systematic interrogation to date of regulatory networks and the impact of genetic variants on gene dysregulation in LOAD at a cell subtype resolution. Our findings reveal crosstalk between epigenetic, genomic, and transcriptomic determinants of LOAD pathogenesis and define catalogues of candidate genes, cCREs, and variants involved in LOAD genetic etiology and the cell subtypes in which they act to exert their pathogenic effects. Overall, these results suggest that cell subtype-specific cis-trans interactions between regulatory elements and TFs, and the genes dysregulated by these networks contribute to the development of LOAD.
Collapse
Affiliation(s)
- Julia Gamache
- Division of Translational Brain Sciences, Department of Neurology, Duke University Medical Center, DUMC Box 2900, Durham, NC, 27710, USA
- Center for Genomic and Computational Biology, Duke University Medical Center, Durham, NC, 27708, USA
| | - Daniel Gingerich
- Division of Translational Brain Sciences, Department of Neurology, Duke University Medical Center, DUMC Box 2900, Durham, NC, 27710, USA
- Center for Genomic and Computational Biology, Duke University Medical Center, Durham, NC, 27708, USA
| | - E Keats Shwab
- Division of Translational Brain Sciences, Department of Neurology, Duke University Medical Center, DUMC Box 2900, Durham, NC, 27710, USA
- Center for Genomic and Computational Biology, Duke University Medical Center, Durham, NC, 27708, USA
| | - Julio Barrera
- Division of Translational Brain Sciences, Department of Neurology, Duke University Medical Center, DUMC Box 2900, Durham, NC, 27710, USA
- Center for Genomic and Computational Biology, Duke University Medical Center, Durham, NC, 27708, USA
| | - Melanie E Garrett
- Duke Molecular Physiology Institute, Duke University Medical Center, DUMC Box 104775, Durham, NC, 27701, USA
| | - Cordelia Hume
- Division of Translational Brain Sciences, Department of Neurology, Duke University Medical Center, DUMC Box 2900, Durham, NC, 27710, USA
- Center for Genomic and Computational Biology, Duke University Medical Center, Durham, NC, 27708, USA
| | - Gregory E Crawford
- Center for Genomic and Computational Biology, Duke University Medical Center, Durham, NC, 27708, USA.
- Department of Pediatrics, Division of Medical Genetics, Duke University Medical Center, DUMC Box 3382, Durham, NC, 27708, USA.
- Center for Advanced Genomic Technologies, Duke University Medical Center, Durham, NC, 27708, USA.
| | - Allison E Ashley-Koch
- Duke Molecular Physiology Institute, Duke University Medical Center, DUMC Box 104775, Durham, NC, 27701, USA.
- Department of Medicine, Duke University Medical Center, Durham, NC, 27708, USA.
| | - Ornit Chiba-Falek
- Division of Translational Brain Sciences, Department of Neurology, Duke University Medical Center, DUMC Box 2900, Durham, NC, 27710, USA.
- Center for Genomic and Computational Biology, Duke University Medical Center, Durham, NC, 27708, USA.
| |
Collapse
|
15
|
Latina V, Atlante A, Malerba F, La Regina F, Balzamino BO, Micera A, Pignataro A, Stigliano E, Cavallaro S, Calissano P, Amadoro G. The Cleavage-Specific Tau 12A12mAb Exerts an Anti-Amyloidogenic Action by Modulating the Endocytic and Bioenergetic Pathways in Alzheimer's Disease Mouse Model. Int J Mol Sci 2023; 24:ijms24119683. [PMID: 37298634 DOI: 10.3390/ijms24119683] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2023] [Revised: 05/27/2023] [Accepted: 05/31/2023] [Indexed: 06/12/2023] Open
Abstract
Beyond deficits in hippocampal-dependent episodic memory, Alzheimer's Disease (AD) features sensory impairment in visual cognition consistent with extensive neuropathology in the retina. 12A12 is a monoclonal cleavage specific antibody (mAb) that in vivo selectively neutralizes the AD-relevant, harmful N-terminal 20-22 kDa tau fragment(s) (i.e., NH2htau) without affecting the full-length normal protein. When systemically injected into the Tg2576 mouse model overexpressing a mutant form of Amyloid Precursor Protein (APP), APPK670/671L linked to early onset familial AD, this conformation-specific tau mAb successfully reduces the NH2htau accumulating both in their brain and retina and, thus, markedly alleviates the phenotype-associated signs. By means of a combined biochemical and metabolic experimental approach, we report that 12A12mAb downregulates the steady state expression levels of APP and Beta-Secretase 1 (BACE-1) and, thus, limits the Amyloid beta (Aβ) production both in the hippocampus and retina from this AD animal model. The local, antibody-mediated anti-amyloidogenic action is paralleled in vivo by coordinated modulation of the endocytic (BIN1, RIN3) and bioenergetic (glycolysis and L-Lactate) pathways. These findings indicate for the first time that similar molecular and metabolic retino-cerebral pathways are modulated in a coordinated fashion in response to 12A12mAb treatment to tackle the neurosensorial Aβ accumulation in AD neurodegeneration.
Collapse
Affiliation(s)
- Valentina Latina
- European Brain Research Institute (EBRI), Viale Regina Elena 295, 00161 Rome, Italy
| | - Anna Atlante
- Institute of Biomembranes, Bioenergetics and Molecular Biotechnologies (IBIOM), National Research Council (CNR), Via Amendola 122/O, 70126 Bari, Italy
| | - Francesca Malerba
- European Brain Research Institute (EBRI), Viale Regina Elena 295, 00161 Rome, Italy
| | - Federico La Regina
- European Brain Research Institute (EBRI), Viale Regina Elena 295, 00161 Rome, Italy
| | - Bijorn Omar Balzamino
- Research Laboratories in Ophthalmology, IRCCS-Fondazione Bietti, Via Santo Stefano Rotondo 6, 00184 Rome, Italy
| | - Alessandra Micera
- Research Laboratories in Ophthalmology, IRCCS-Fondazione Bietti, Via Santo Stefano Rotondo 6, 00184 Rome, Italy
| | - Annabella Pignataro
- Institute of Translational Pharmacology (IFT), National Research Council (CNR), Via Fosso del Cavaliere 100, 00133 Rome, Italy
| | - Egidio Stigliano
- Area of Pathology, Department of Woman and Child Health and Public Health, Fondazione Policlinico Universitario A. Gemelli IRCCS, Istituto di Anatomia Patologica, Università Cattolica del Sacro Cuore, Largo Francesco Vito 1, 00168 Rome, Italy
| | - Sebastiano Cavallaro
- Institute for Biomedical Research and Innovation (IRIB), National Research Council (CNR), Via P. Gaifami 18, 95126 Catania, Italy
| | - Pietro Calissano
- European Brain Research Institute (EBRI), Viale Regina Elena 295, 00161 Rome, Italy
| | - Giuseppina Amadoro
- European Brain Research Institute (EBRI), Viale Regina Elena 295, 00161 Rome, Italy
- Institute of Translational Pharmacology (IFT), National Research Council (CNR), Via Fosso del Cavaliere 100, 00133 Rome, Italy
| |
Collapse
|
16
|
Young-Pearse TL, Lee H, Hsieh YC, Chou V, Selkoe DJ. Moving beyond amyloid and tau to capture the biological heterogeneity of Alzheimer's disease. Trends Neurosci 2023; 46:426-444. [PMID: 37019812 PMCID: PMC10192069 DOI: 10.1016/j.tins.2023.03.005] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2023] [Revised: 02/28/2023] [Accepted: 03/09/2023] [Indexed: 04/05/2023]
Abstract
Alzheimer's disease (AD) manifests along a spectrum of cognitive deficits and levels of neuropathology. Genetic studies support a heterogeneous disease mechanism, with around 70 associated loci to date, implicating several biological processes that mediate risk for AD. Despite this heterogeneity, most experimental systems for testing new therapeutics are not designed to capture the genetically complex drivers of AD risk. In this review, we first provide an overview of those aspects of AD that are largely stereotyped and those that are heterogeneous, and we review the evidence supporting the concept that different subtypes of AD are important to consider in the design of agents for the prevention and treatment of the disease. We then dive into the multifaceted biological domains implicated to date in AD risk, highlighting studies of the diverse genetic drivers of disease. Finally, we explore recent efforts to identify biological subtypes of AD, with an emphasis on the experimental systems and data sets available to support progress in this area.
Collapse
Affiliation(s)
- Tracy L Young-Pearse
- Ann Romney Center for Neurologic Diseases, Department of Neurology, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA.
| | - Hyo Lee
- Ann Romney Center for Neurologic Diseases, Department of Neurology, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Yi-Chen Hsieh
- Ann Romney Center for Neurologic Diseases, Department of Neurology, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Vicky Chou
- Ann Romney Center for Neurologic Diseases, Department of Neurology, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Dennis J Selkoe
- Ann Romney Center for Neurologic Diseases, Department of Neurology, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA.
| |
Collapse
|
17
|
Andrade-Guerrero J, Santiago-Balmaseda A, Jeronimo-Aguilar P, Vargas-Rodríguez I, Cadena-Suárez AR, Sánchez-Garibay C, Pozo-Molina G, Méndez-Catalá CF, Cardenas-Aguayo MDC, Diaz-Cintra S, Pacheco-Herrero M, Luna-Muñoz J, Soto-Rojas LO. Alzheimer's Disease: An Updated Overview of Its Genetics. Int J Mol Sci 2023; 24:ijms24043754. [PMID: 36835161 PMCID: PMC9966419 DOI: 10.3390/ijms24043754] [Citation(s) in RCA: 60] [Impact Index Per Article: 60.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2022] [Revised: 01/31/2023] [Accepted: 02/06/2023] [Indexed: 02/16/2023] Open
Abstract
Alzheimer's disease (AD) is the most common neurodegenerative disease in the world. It is classified as familial and sporadic. The dominant familial or autosomal presentation represents 1-5% of the total number of cases. It is categorized as early onset (EOAD; <65 years of age) and presents genetic mutations in presenilin 1 (PSEN1), presenilin 2 (PSEN2), or the Amyloid precursor protein (APP). Sporadic AD represents 95% of the cases and is categorized as late-onset (LOAD), occurring in patients older than 65 years of age. Several risk factors have been identified in sporadic AD; aging is the main one. Nonetheless, multiple genes have been associated with the different neuropathological events involved in LOAD, such as the pathological processing of Amyloid beta (Aβ) peptide and Tau protein, as well as synaptic and mitochondrial dysfunctions, neurovascular alterations, oxidative stress, and neuroinflammation, among others. Interestingly, using genome-wide association study (GWAS) technology, many polymorphisms associated with LOAD have been identified. This review aims to analyze the new genetic findings that are closely related to the pathophysiology of AD. Likewise, it analyzes the multiple mutations identified to date through GWAS that are associated with a high or low risk of developing this neurodegeneration. Understanding genetic variability will allow for the identification of early biomarkers and opportune therapeutic targets for AD.
Collapse
Affiliation(s)
- Jesús Andrade-Guerrero
- Laboratorio de Patogénesis Molecular, Laboratorio 4, Edificio A4, Carrera Médico Cirujano, Facultad de Estudios Superiores Iztacala, Universidad Nacional Autónoma de México, Tlalnepantla 54090, Edomex, Mexico
- Departamento de Neurobiología del Desarrollo y Neurofisiología, Instituto de Neurobiología, Universidad Nacional Autónoma de México, Juriquilla 76230, Querétaro, Mexico
| | - Alberto Santiago-Balmaseda
- Laboratorio de Patogénesis Molecular, Laboratorio 4, Edificio A4, Carrera Médico Cirujano, Facultad de Estudios Superiores Iztacala, Universidad Nacional Autónoma de México, Tlalnepantla 54090, Edomex, Mexico
- Red MEDICI, Carrera Médico Cirujano, Facultad de Estudios Superiores Iztacala, Universidad Nacional Autónoma de México, Tlalnepantla 54090, Edomex, Mexico
| | - Paola Jeronimo-Aguilar
- Laboratorio de Patogénesis Molecular, Laboratorio 4, Edificio A4, Carrera Médico Cirujano, Facultad de Estudios Superiores Iztacala, Universidad Nacional Autónoma de México, Tlalnepantla 54090, Edomex, Mexico
- Red MEDICI, Carrera Médico Cirujano, Facultad de Estudios Superiores Iztacala, Universidad Nacional Autónoma de México, Tlalnepantla 54090, Edomex, Mexico
- Sección de Estudios de Posgrado e Investigación, Escuela Superior de Medicina, Instituto Politécnico Nacional, Ciudad de México 11340, Mexico
| | - Isaac Vargas-Rodríguez
- Departamento de Neurobiología del Desarrollo y Neurofisiología, Instituto de Neurobiología, Universidad Nacional Autónoma de México, Juriquilla 76230, Querétaro, Mexico
| | - Ana Ruth Cadena-Suárez
- National Dementia BioBank, Ciencias Biológicas, Facultad de Estudios Superiores Cuautitlán, Universidad-Nacional Autónoma de México, Cuatitlan 53150, Edomex, Mexico
| | - Carlos Sánchez-Garibay
- Departamento de Neuropatología, Instituto Nacional de Neurología y Neurocirugía Manuel Velasco Suárez, Ciudad de México 14269, Mexico
| | - Glustein Pozo-Molina
- Laboratorio de Genética y Oncología Molecular, Laboratorio 5, Edificio A4, Carrera Médico Cirujano, Facultad de Estudios Superiores Iztacala, Universidad Nacional Autónoma de México, Tlalnepantla 54090, Edomex, Mexico
| | - Claudia Fabiola Méndez-Catalá
- Laboratorio de Genética y Oncología Molecular, Laboratorio 5, Edificio A4, Carrera Médico Cirujano, Facultad de Estudios Superiores Iztacala, Universidad Nacional Autónoma de México, Tlalnepantla 54090, Edomex, Mexico
- División de Investigación y Posgrado, Facultad de Estudios Superiores Iztacala, Universidad Nacional Autónoma de Mexico, Tlalnepantla 54090, Edomex, Mexico
| | - Maria-del-Carmen Cardenas-Aguayo
- Laboratory of Cellular Reprogramming, Departamento de Fisiología, Facultad de Medicina, Universidad Nacional Autónoma de México, Ciudad de México 04510, Mexico
| | - Sofía Diaz-Cintra
- Departamento de Neurobiología del Desarrollo y Neurofisiología, Instituto de Neurobiología, Universidad Nacional Autónoma de México, Juriquilla 76230, Querétaro, Mexico
| | - Mar Pacheco-Herrero
- Neuroscience Research Laboratory, Faculty of Health Sciences, Pontificia Universidad Católica Madre y Maestra, Santiago de los Caballeros 51000, Dominican Republic
| | - José Luna-Muñoz
- National Dementia BioBank, Ciencias Biológicas, Facultad de Estudios Superiores Cuautitlán, Universidad-Nacional Autónoma de México, Cuatitlan 53150, Edomex, Mexico
- National Brain Bank-UNPHU, Universidad Nacional Pedro Henríquez Ureña, Santo Domingo 1423, Dominican Republic
- Correspondence: (J.L.-M.); (L.O.S.-R.); Tel.: +52-55-45-23-41-20 (J.L.-M.); +52-55-39-37-94-30 (L.O.S.-R.)
| | - Luis O. Soto-Rojas
- Laboratorio de Patogénesis Molecular, Laboratorio 4, Edificio A4, Carrera Médico Cirujano, Facultad de Estudios Superiores Iztacala, Universidad Nacional Autónoma de México, Tlalnepantla 54090, Edomex, Mexico
- Red MEDICI, Carrera Médico Cirujano, Facultad de Estudios Superiores Iztacala, Universidad Nacional Autónoma de México, Tlalnepantla 54090, Edomex, Mexico
- Correspondence: (J.L.-M.); (L.O.S.-R.); Tel.: +52-55-45-23-41-20 (J.L.-M.); +52-55-39-37-94-30 (L.O.S.-R.)
| |
Collapse
|
18
|
Lang AL, Eulalio T, Fox E, Yakabi K, Bukhari SA, Kawas CH, Corrada MM, Montgomery SB, Heppner FL, Capper D, Nachun D, Montine TJ. Methylation differences in Alzheimer's disease neuropathologic change in the aged human brain. Acta Neuropathol Commun 2022; 10:174. [PMID: 36447297 PMCID: PMC9710143 DOI: 10.1186/s40478-022-01470-0] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2022] [Accepted: 10/24/2022] [Indexed: 12/05/2022] Open
Abstract
Alzheimer's disease (AD) is the most common cause of dementia with advancing age as its strongest risk factor. AD neuropathologic change (ADNC) is known to be associated with numerous DNA methylation changes in the human brain, but the oldest old (> 90 years) have so far been underrepresented in epigenetic studies of ADNC. Our study participants were individuals aged over 90 years (n = 47) from The 90+ Study. We analyzed DNA methylation from bulk samples in eight precisely dissected regions of the human brain: middle frontal gyrus, cingulate gyrus, entorhinal cortex, dentate gyrus, CA1, substantia nigra, locus coeruleus and cerebellar cortex. We deconvolved our bulk data into cell-type-specific (CTS) signals using computational methods. CTS methylation differences were analyzed across different levels of ADNC. The highest amount of ADNC related methylation differences was found in the dentate gyrus, a region that has so far been underrepresented in large scale multi-omic studies. In neurons of the dentate gyrus, DNA methylation significantly differed with increased burden of amyloid beta (Aβ) plaques at 5897 promoter regions of protein-coding genes. Amongst these, higher Aβ plaque burden was associated with promoter hypomethylation of the Presenilin enhancer 2 (PEN-2) gene, one of the rate limiting genes in the formation of gamma-secretase, a multicomponent complex that is responsible in part for the endoproteolytic cleavage of amyloid precursor protein into Aβ peptides. In addition to novel ADNC related DNA methylation changes, we present the most detailed array-based methylation survey of the old aged human brain to date. Our open-sourced dataset can serve as a brain region reference panel for future studies and help advance research in aging and neurodegenerative diseases.
Collapse
Affiliation(s)
- Anna-Lena Lang
- Department of Neuropathology, Charité–Universitätsmedizin Berlin, Corporate member of Freie Universität Berlin and Humboldt-Universität Zu Berlin, Charitéplatz 1, 10117 Berlin, Germany
| | - Tiffany Eulalio
- Department of Biomedical Data Science, Stanford University, Stanford, CA 94305 USA
| | - Eddie Fox
- Department of Pathology, Stanford University, 300 Pasteur Drive, Stanford, CA 94305 USA
| | - Koya Yakabi
- Department of Pathology, Stanford University, 300 Pasteur Drive, Stanford, CA 94305 USA
| | - Syed A. Bukhari
- Department of Pathology, Stanford University, 300 Pasteur Drive, Stanford, CA 94305 USA
| | - Claudia H. Kawas
- Department of Neurology, University of California Irvine, Orange, CA 92868-4280 USA
- Department of Neurobiology and Behavior, University of California, Irvine, CA 92697 USA
| | - Maria M. Corrada
- Department of Neurology, University of California Irvine, Orange, CA 92868-4280 USA
- Department of Epidemiology, University of California, Irvine, CA 92617 USA
| | - Stephen B. Montgomery
- Department of Pathology, Stanford University, 300 Pasteur Drive, Stanford, CA 94305 USA
- Department of Genetics, Stanford University, Stanford, CA 94305 USA
- Department of Biomedical Data Science, Stanford University, Stanford, CA 94305 USA
| | - Frank L. Heppner
- Department of Neuropathology, Charité–Universitätsmedizin Berlin, Corporate member of Freie Universität Berlin and Humboldt-Universität Zu Berlin, Charitéplatz 1, 10117 Berlin, Germany
- German Center for Neurodegenerative Diseases (DZNE), 10117 Berlin, Germany
- Cluster of Excellence, NeuroCure, 10117 Berlin, Germany
| | - David Capper
- Department of Neuropathology, Charité–Universitätsmedizin Berlin, Corporate member of Freie Universität Berlin and Humboldt-Universität Zu Berlin, Charitéplatz 1, 10117 Berlin, Germany
| | - Daniel Nachun
- Department of Genetics, Stanford University, Stanford, CA 94305 USA
| | - Thomas J. Montine
- Department of Pathology, Stanford University, 300 Pasteur Drive, Stanford, CA 94305 USA
| |
Collapse
|
19
|
Limone A, Veneruso I, D'Argenio V, Sarnataro D. Endosomal trafficking and related genetic underpinnings as a hub in Alzheimer's disease. J Cell Physiol 2022; 237:3803-3815. [PMID: 35994714 DOI: 10.1002/jcp.30864] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2022] [Revised: 07/13/2022] [Accepted: 08/08/2022] [Indexed: 01/07/2023]
Abstract
Genetic studies support the amyloid cascade as the leading hypothesis for the pathogenesis of Alzheimer's disease (AD). Although significant efforts have been made in untangling the amyloid and other pathological events in AD, ongoing interventions for AD have not been revealed efficacious for slowing down disease progression. Recent advances in the field of genetics have shed light on the etiology of AD, identifying numerous risk genes associated with late-onset AD, including genes related to intracellular endosomal trafficking. Some of the bases for the development of AD may be explained by the recently emerging AD genetic "hubs," which include the processing pathway of amyloid precursor protein and the endocytic pathway. The endosomal genetic hub may represent a common pathway through which many pathological effects can be mediated and novel, alternative biological targets could be identified for therapeutic interventions. The aim of this review is to focus on the genetic and biological aspects of the endosomal compartments related to AD progression. We report recent studies which describe how changes in endosomal genetics impact on functional events, such as the amyloidogenic and non-amyloidogenic processing, degradative pathways, and the importance of receptors related to endocytic trafficking, including the 37/67 kDa laminin-1 receptor ribosomal protein SA, and their implications for neurodegenerative diseases.
Collapse
Affiliation(s)
- Adriana Limone
- Department of Molecular Medicine and Medical Biotechnology, Federico II University, Napoli, Italy
| | - Iolanda Veneruso
- Department of Molecular Medicine and Medical Biotechnology, Federico II University, Napoli, Italy.,CEINGE-Biotecnologie Avanzate, Napoli, Italy
| | - Valeria D'Argenio
- CEINGE-Biotecnologie Avanzate, Napoli, Italy.,Department of Human Sciences and Quality of Life Promotion, San Raffaele Open University, Roma, Italy
| | - Daniela Sarnataro
- Department of Molecular Medicine and Medical Biotechnology, Federico II University, Napoli, Italy
| |
Collapse
|
20
|
Sen T, Thummer RP. CRISPR and iPSCs: Recent Developments and Future Perspectives in Neurodegenerative Disease Modelling, Research, and Therapeutics. Neurotox Res 2022; 40:1597-1623. [PMID: 36044181 PMCID: PMC9428373 DOI: 10.1007/s12640-022-00564-w] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2022] [Revised: 06/17/2022] [Accepted: 08/19/2022] [Indexed: 11/15/2022]
Abstract
Neurodegenerative diseases are prominent causes of pain, suffering, and death worldwide. Traditional approaches modelling neurodegenerative diseases are deficient, and therefore, improved strategies that effectively recapitulate the pathophysiological conditions of neurodegenerative diseases are the need of the hour. The generation of human-induced pluripotent stem cells (iPSCs) has transformed our ability to model neurodegenerative diseases in vitro and provide an unlimited source of cells (including desired neuronal cell types) for cell replacement therapy. Recently, CRISPR/Cas9-based genome editing has also been gaining popularity because of the flexibility they provide to generate and ablate disease phenotypes. In addition, the recent advancements in CRISPR/Cas9 technology enables researchers to seamlessly target and introduce precise modifications in the genomic DNA of different human cell lines, including iPSCs. CRISPR-iPSC-based disease modelling, therefore, allows scientists to recapitulate the pathological aspects of most neurodegenerative processes and investigate the role of pathological gene variants in healthy non-patient cell lines. This review outlines how iPSCs, CRISPR/Cas9, and CRISPR-iPSC-based approaches accelerate research on neurodegenerative diseases and take us closer to a cure for neurodegenerative diseases such as Alzheimer’s disease, Parkinson’s disease, Huntington’s disease, Amyotrophic Lateral Sclerosis, and so forth.
Collapse
Affiliation(s)
- Tirthankar Sen
- Laboratory for Stem Cell Engineering and Regenerative Medicine, Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Guwahati - 781039, Assam, India
| | - Rajkumar P Thummer
- Laboratory for Stem Cell Engineering and Regenerative Medicine, Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Guwahati - 781039, Assam, India.
| |
Collapse
|
21
|
Human Brain Organoid: A Versatile Tool for Modeling Neurodegeneration Diseases and for Drug Screening. Stem Cells Int 2022; 2022:2150680. [PMID: 36061149 PMCID: PMC9436613 DOI: 10.1155/2022/2150680] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2021] [Revised: 05/28/2022] [Accepted: 06/18/2022] [Indexed: 11/17/2022] Open
Abstract
Clinical trials serve as the fundamental prerequisite for clinical therapy of human disease, which is primarily based on biomedical studies in animal models. Undoubtedly, animal models have made a significant contribution to gaining insight into the developmental and pathophysiological understanding of human diseases. However, none of the existing animal models could efficiently simulate the development of human organs and systems due to a lack of spatial information; the discrepancy in genetic, anatomic, and physiological basis between animals and humans limits detailed investigation. Therefore, the translational efficiency of the research outcomes in clinical applications was significantly weakened, especially for some complex, chronic, and intractable diseases. For example, the clinical trials for human fragile X syndrome (FXS) solely based on animal models have failed such as mGluR5 antagonists. To mimic the development of human organs more faithfully and efficiently translate in vitro biomedical studies to clinical trials, extensive attention to organoids derived from stem cells contributes to a deeper understanding of this research. The organoids are a miniaturized version of an organ generated in vitro, partially recapitulating key features of human organ development. As such, the organoids open a novel avenue for in vitro models of human disease, advantageous over the existing animal models. The invention of organoids has brought an innovative breakthrough in regeneration medicine. The organoid-derived human tissues or organs could potentially function as invaluable platforms for biomedical studies, pathological investigation of human diseases, and drug screening. Importantly, the study of regeneration medicine and the development of therapeutic strategies for human diseases could be conducted in a dish, facilitating in vitro analysis and experimentation. Thus far, the pilot breakthrough has been made in the generation of numerous types of organoids representing different human organs. Most of these human organoids have been employed for in vitro biomedical study and drug screening. However, the efficiency and quality of the organoids in recapitulating the development of human organs have been hindered by engineering and conceptual challenges. The efficiency and quality of the organoids are essential for downstream applications. In this article, we highlight the application in the modeling of human neurodegenerative diseases (NDDs) such as FXS, Alzheimer's disease (AD), Parkinson's disease (PD), and autistic spectrum disorders (ASD), and organoid-based drug screening. Additionally, challenges and weaknesses especially for limits of the brain organoid models in modeling late onset NDDs such as AD and PD., and future perspectives regarding human brain organoids are addressed.
Collapse
|
22
|
Kaltschmidt B, Helweg LP, Greiner JFW, Kaltschmidt C. NF-κB in neurodegenerative diseases: Recent evidence from human genetics. Front Mol Neurosci 2022; 15:954541. [PMID: 35983068 PMCID: PMC9380593 DOI: 10.3389/fnmol.2022.954541] [Citation(s) in RCA: 22] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2022] [Accepted: 07/11/2022] [Indexed: 11/13/2022] Open
Abstract
The transcription factor NF-κB is commonly known to drive inflammation and cancer progression, but is also a crucial regulator of a broad range of cellular processes within the mammalian nervous system. In the present review, we provide an overview on the role of NF-κB in the nervous system particularly including its constitutive activity within cortical and hippocampal regions, neuroprotection as well as learning and memory. Our discussion further emphasizes the increasing role of human genetics in neurodegenerative disorders, namely, germline mutations leading to defects in NF-κB-signaling. In particular, we propose that loss of function mutations upstream of NF-κB such as ADAM17, SHARPIN, HOIL, or OTULIN affect NF-κB-activity in Alzheimer’s disease (AD) patients, in turn driving anatomical defects such as shrinkage of entorhinal cortex and the limbic system in early AD. Similarly, E3 type ubiquitin ligase PARKIN is positively involved in NF-κB signaling. PARKIN loss of function mutations are most frequently observed in Parkinson’s disease patients. In contrast to AD, relying on germline mutations of week alleles and a disease development over decades, somatic mutations affecting NF-κB activation are commonly observed in cells derived from glioblastoma multiforme (GBM), the most common malignant primary brain tumor. Here, our present review particularly sheds light on the mutual exclusion of either the deletion of NFKBIA or amplification of epidermal growth factor receptor (EGFR) in GBM, both resulting in constitutive NF-κB-activity driving tumorigenesis. We also discuss emerging roles of long non-coding RNAs such as HOTAIR in suppressing phosphorylation of IκBα in the context of GBM. In summary, the recent progress in the genetic analysis of patients, particularly those suffering from AD, harbors the potential to open up new vistas for research and therapy based on TNFα/NF-κB pathway and neuroprotection.
Collapse
Affiliation(s)
- Barbara Kaltschmidt
- Department of Molecular Neurobiology, Bielefeld University, Bielefeld, Germany
- Forschungsverbund BioMedizin Bielefeld, Ostwestfalen-Lippe (OWL) (FBMB E.V.), Bielefeld, Germany
- Department of Cell Biology, Biological Faculty, University of Bielefeld, Bielefeld, Germany
- *Correspondence: Barbara Kaltschmidt,
| | - Laureen P. Helweg
- Forschungsverbund BioMedizin Bielefeld, Ostwestfalen-Lippe (OWL) (FBMB E.V.), Bielefeld, Germany
- Department of Cell Biology, Biological Faculty, University of Bielefeld, Bielefeld, Germany
| | - Johannes F. W. Greiner
- Forschungsverbund BioMedizin Bielefeld, Ostwestfalen-Lippe (OWL) (FBMB E.V.), Bielefeld, Germany
- Department of Cell Biology, Biological Faculty, University of Bielefeld, Bielefeld, Germany
| | - Christian Kaltschmidt
- Forschungsverbund BioMedizin Bielefeld, Ostwestfalen-Lippe (OWL) (FBMB E.V.), Bielefeld, Germany
- Department of Cell Biology, Biological Faculty, University of Bielefeld, Bielefeld, Germany
| |
Collapse
|