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Area-Gomez E, Schon EA. Towards a Unitary Hypothesis of Alzheimer's Disease Pathogenesis. J Alzheimers Dis 2024; 98:1243-1275. [PMID: 38578892 DOI: 10.3233/jad-231318] [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: 04/07/2024]
Abstract
The "amyloid cascade" hypothesis of Alzheimer's disease (AD) pathogenesis invokes the accumulation in the brain of plaques (containing the amyloid-β protein precursor [AβPP] cleavage product amyloid-β [Aβ]) and tangles (containing hyperphosphorylated tau) as drivers of pathogenesis. However, the poor track record of clinical trials based on this hypothesis suggests that the accumulation of these peptides is not the only cause of AD. Here, an alternative hypothesis is proposed in which the AβPP cleavage product C99, not Aβ, is the main culprit, via its role as a regulator of cholesterol metabolism. C99, which is a cholesterol sensor, promotes the formation of mitochondria-associated endoplasmic reticulum (ER) membranes (MAM), a cholesterol-rich lipid raft-like subdomain of the ER that communicates, both physically and biochemically, with mitochondria. We propose that in early-onset AD (EOAD), MAM-localized C99 is elevated above normal levels, resulting in increased transport of cholesterol from the plasma membrane to membranes of intracellular organelles, such as ER/endosomes, thereby upregulating MAM function and driving pathology. By the same token, late-onset AD (LOAD) is triggered by any genetic variant that increases the accumulation of intracellular cholesterol that, in turn, boosts the levels of C99 and again upregulates MAM function. Thus, the functional cause of AD is upregulated MAM function that, in turn, causes the hallmark disease phenotypes, including the plaques and tangles. Accordingly, the MAM hypothesis invokes two key interrelated elements, C99 and cholesterol, that converge at the MAM to drive AD pathogenesis. From this perspective, AD is, at bottom, a lipid disorder.
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Affiliation(s)
- Estela Area-Gomez
- Department of Neurology, Columbia University, New York, NY, USA
- Centro de Investigaciones Biológicas "Margarita Salas", Spanish National Research Council, Madrid, Spain
| | - Eric A Schon
- Department of Neurology, Columbia University, New York, NY, USA
- Department of Genetics and Development>, Columbia University, New York, NY, USA
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Yost PP, Al-Nouman A, Curtiss J. The Rap1 small GTPase affects cell fate or survival and morphogenetic patterning during Drosophila melanogaster eye development. Differentiation 2023; 133:12-24. [PMID: 37437447 PMCID: PMC10528170 DOI: 10.1016/j.diff.2023.06.001] [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: 11/15/2022] [Revised: 06/06/2023] [Accepted: 06/07/2023] [Indexed: 07/14/2023]
Abstract
The Drosophila melanogaster eye has been instrumental for determining both how cells communicate with one another to determine cell fate, as well as cell morphogenesis and patterning. Here, we describe the effects of the small GTPase Rap1 on the development of multiple cell types in the D. melanogaster eye. Although Rap1 has previously been linked to RTK-Ras-MAPK signaling in eye development, we demonstrate that manipulation of Rap1 activity is modified by increase or decrease of Delta/Notch signaling during several events of cell fate specification in eye development. In addition, we demonstrate that manipulating Rap1 function either in primary pigment cells or in interommatidial cells affects cone cell contact switching, primary pigment cell enwrapment of the ommatidial cluster, and sorting of secondary and tertiary pigment cells. These data suggest that Rap1 has roles in both ommatidial cell recruitment/survival and in ommatidial morphogenesis in the pupal stage. They lay groundwork for future experiments on the role of Rap1 in these events.
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Affiliation(s)
- Philip P Yost
- New Mexico State University, 1780 E University Ave, Las Cruces, NM, 88003, USA
| | | | - Jennifer Curtiss
- New Mexico State University, 1780 E University Ave, Las Cruces, NM, 88003, USA.
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Rocha JJ, Jayaram SA, Stevens TJ, Muschalik N, Shah RD, Emran S, Robles C, Freeman M, Munro S. Functional unknomics: Systematic screening of conserved genes of unknown function. PLoS Biol 2023; 21:e3002222. [PMID: 37552676 PMCID: PMC10409296 DOI: 10.1371/journal.pbio.3002222] [Citation(s) in RCA: 14] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2023] [Accepted: 06/27/2023] [Indexed: 08/10/2023] Open
Abstract
The human genome encodes approximately 20,000 proteins, many still uncharacterised. It has become clear that scientific research tends to focus on well-studied proteins, leading to a concern that poorly understood genes are unjustifiably neglected. To address this, we have developed a publicly available and customisable "Unknome database" that ranks proteins based on how little is known about them. We applied RNA interference (RNAi) in Drosophila to 260 unknown genes that are conserved between flies and humans. Knockdown of some genes resulted in loss of viability, and functional screening of the rest revealed hits for fertility, development, locomotion, protein quality control, and resilience to stress. CRISPR/Cas9 gene disruption validated a component of Notch signalling and 2 genes contributing to male fertility. Our work illustrates the importance of poorly understood genes, provides a resource to accelerate future research, and highlights a need to support database curation to ensure that misannotation does not erode our awareness of our own ignorance.
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Affiliation(s)
- João J. Rocha
- MRC Laboratory of Molecular Biology, Cambridge, United Kingdom
| | | | - Tim J. Stevens
- MRC Laboratory of Molecular Biology, Cambridge, United Kingdom
| | | | - Rajen D. Shah
- Centre for Mathematical Sciences, University of Cambridge, Cambridge, United Kingdom
| | - Sahar Emran
- MRC Laboratory of Molecular Biology, Cambridge, United Kingdom
| | - Cristina Robles
- MRC Laboratory of Molecular Biology, Cambridge, United Kingdom
| | - Matthew Freeman
- MRC Laboratory of Molecular Biology, Cambridge, United Kingdom
- Sir William Dunn School of Pathology, University of Oxford, Oxford, United Kingdom
| | - Sean Munro
- MRC Laboratory of Molecular Biology, Cambridge, United Kingdom
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Yamakawa T, Yuslimatin Mujizah E, Matsuno K. Notch Signalling Under Maternal-to-Zygotic Transition. Fly (Austin) 2022; 16:347-359. [PMID: 36346359 PMCID: PMC9645253 DOI: 10.1080/19336934.2022.2139981] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Abstract
The development of all animal embryos is initially directed by the gene products supplied by their mothers. With the progression of embryogenesis, the embryo's genome is activated to command subsequent developments. This transition, which has been studied in many model animals, is referred to as the Maternal-to-Zygotic Transition (MZT). In many organisms, including flies, nematodes, and sea urchins, genes involved in Notch signaling are extensively influenced by the MZT. This signaling pathway is highly conserved across metazoans; moreover, it regulates various developmental processes. Notch signaling defects are commonly associated with various human diseases. The maternal contribution of its factors was first discovered in flies. Subsequently, several genes were identified from mutant embryos with a phenotype similar to Notch mutants only upon the removal of the maternal contributions. Studies on these maternal genes have revealed various novel steps in the cascade of Notch signal transduction. Among these genes, pecanex and almondex have been functionally characterized in recent studies. Therefore, in this review, we will focus on the roles of these two maternal genes in Notch signaling and discuss future research directions on its maternal function.
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Affiliation(s)
- Tomoko Yamakawa
- Department of Biological Sciences, Graduate School of Science, Osaka University, Osaka, Japan,CONTACT Tomoko Yamakawa Department of Biological Sciences, Graduate School of Science, Osaka University, Osaka, Japan
| | | | - Kenji Matsuno
- Department of Biological Sciences, Graduate School of Science, Osaka University, Osaka, Japan
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Insights into the use of genetically modified decellularized biomaterials for tissue engineering and regenerative medicine. Adv Drug Deliv Rev 2022; 188:114413. [PMID: 35777666 DOI: 10.1016/j.addr.2022.114413] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2022] [Revised: 04/25/2022] [Accepted: 06/25/2022] [Indexed: 11/24/2022]
Abstract
Various modifications have been performed on biomaterials to improve their applications in tissue engineering and regenerative medicine. However, the challenges of immunogenicity and biocompatibility existed since the application of biomaterials. As a method to solve this problem, the decellularization process removes most living cells from biomaterials to minimize their immunogenicity; and preserves the native structures and compositions that favour cell growth and the subsequent construction of functional tissue. On the other hand, genetic modification of biomaterials aims to achieve specific functions (low immunogenicity, osteogenesis, etc.) or analyse the genetic mechanisms underlying some diseases (cardiac dysfunction, liver fibrosis, etc.). The combination of decellularization and gene modification is highly superior to biomaterials; thus, we must obtain a deeper understanding of these novel biomaterials. In this review, we summarize the fabrication approaches and current applications of genetically modified decellularized biomaterials and then discuss their disadvantages and corresponding future perspectives.
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Yang SA, Salazar JL, Li-Kroeger D, Yamamoto S. Functional Studies of Genetic Variants Associated with Human Diseases in Notch Signaling-Related Genes Using Drosophila. Methods Mol Biol 2022; 2472:235-276. [PMID: 35674905 PMCID: PMC9396741 DOI: 10.1007/978-1-0716-2201-8_19] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Rare variants in the many genes related to Notch signaling cause diverse Mendelian diseases that affect myriad organ systems. In addition, genome- and exome-wide association studies have linked common and rare variants in Notch-related genes to common diseases and phenotypic traits. Moreover, somatic mutations in these genes have been observed in many types of cancer, some of which are classified as oncogenic and others as tumor suppressive. While functional characterization of some of these variants has been performed through experimental studies, the number of "variants of unknown significance" identified in patients with diverse conditions keeps increasing as high-throughput sequencing technologies become more commonly used in the clinic. Furthermore, as disease gene discovery efforts identify rare variants in human genes that have yet to be linked to a disease, the demand for functional characterization of variants in these "genes of unknown significance" continues to increase. In this chapter, we describe a workflow to functionally characterize a rare variant in a Notch signaling related gene that was found to be associated with late-onset Alzheimer's disease. This pipeline involves informatic analysis of the variant of interest using diverse human and model organism databases, followed by in vivo experiments in the fruit fly Drosophila melanogaster. The protocol described here can be used to study variants that affect amino acids that are not conserved between human and fly. By "humanizing" the almondex gene in Drosophila with mutant alleles and heterologous genomic rescue constructs, a missense variant in TM2D3 (TM2 Domain Containing 3) was shown to be functionally damaging. This, and similar approaches, greatly facilitate functional interpretations of genetic variants in the human genome and propel personalized medicine.
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Affiliation(s)
- Sheng-An Yang
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
- Jan and Dan Duncan Neurological Research Institute, Texas Children's Hospital, Houston, TX, USA
| | - Jose L Salazar
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
- Jan and Dan Duncan Neurological Research Institute, Texas Children's Hospital, Houston, TX, USA
| | - David Li-Kroeger
- Jan and Dan Duncan Neurological Research Institute, Texas Children's Hospital, Houston, TX, USA.
- Department of Neurology, Baylor College of Medicine, Houston, TX, USA.
| | - Shinya Yamamoto
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA.
- Jan and Dan Duncan Neurological Research Institute, Texas Children's Hospital, Houston, TX, USA.
- Department of Neuroscience, Baylor College of Medicine, Houston, TX, USA.
- Development, Disease Models and Therapeutics Graduate Program, Baylor College of Medicine, Houston, TX, USA.
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