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Mazur A, Ayyadevara S, Mainali N, Patchett S, Uden M, Roa RI, Fahy GM, Shmookler Reis RJ. Model biological systems demonstrate the inducibility of pathways that strongly reduce cryoprotectant toxicity. Cryobiology 2024; 115:104881. [PMID: 38437899 DOI: 10.1016/j.cryobiol.2024.104881] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2023] [Revised: 02/01/2024] [Accepted: 03/01/2024] [Indexed: 03/06/2024]
Abstract
Cryoprotectant toxicity is a limiting factor for the cryopreservation of many living systems. We were moved to address this problem by the potential of organ vitrification to relieve the severe shortage of viable donor organs available for human transplantation. The M22 vitrification solution is presently the only solution that has enabled the vitrification and subsequent transplantation with survival of large mammalian organs, but its toxicity remains an obstacle to organ stockpiling for transplantation. We therefore undertook a series of exploratory studies to identify potential pretreatment interventions that might reduce the toxic effects of M22. Hormesis, in which a living system becomes more resistant to toxic stress after prior subtoxic exposure to a related stress, was investigated as a potential remedy for M22 toxicity in yeast, in the nematode worm C. elegans, and in mouse kidney slices. In yeast, heat shock pretreatment increased survival by 18-fold after exposure to formamide and by over 9-fold after exposure to M22 at 30 °C; at 0 °C and with two-step addition, treatment with 90% M22 resulted in 100% yeast survival. In nematodes, surveying a panel of pretreatment interventions revealed 3 that conferred nearly total protection from acute whole-worm M22-induced damage. One of these protective pretreatments (exposure to hydrogen peroxide) was applied to mouse kidney slices in vitro and was found to strongly protect nuclear and plasma membrane integrity in both cortical and medullary renal cells exposed to 75-100% M22 at room temperature for 40 min. These studies demonstrate for the first time that endogenous cellular defenses, conserved from yeast to mammals, can be marshalled to substantially ameliorate the toxic effects of one of the most toxic single cryoprotectants and the toxicity of the most concentrated vitrification solution so far described for whole organs.
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Affiliation(s)
- Anna Mazur
- Dept. of Geriatrics, Institute on Aging, University of Arkansas for Medical Sciences, Little Rock AR, 72205, USA
| | - Srinivas Ayyadevara
- Dept. of Geriatrics, Institute on Aging, University of Arkansas for Medical Sciences, Little Rock AR, 72205, USA; Central Arkansas Veterans Healthcare System, Little Rock AR, 72205, USA
| | - Nirjal Mainali
- Dept. of Geriatrics, Institute on Aging, University of Arkansas for Medical Sciences, Little Rock AR, 72205, USA
| | - Stephanie Patchett
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, 78712, USA
| | - Matthew Uden
- Department of Psychology, The University of Texas at Austin, Austin, TX, 78712, USA
| | - Roberto I Roa
- 21st Century Medicine, Inc., Fontana, CA, 92336, USA
| | | | - Robert J Shmookler Reis
- Dept. of Geriatrics, Institute on Aging, University of Arkansas for Medical Sciences, Little Rock AR, 72205, USA; Central Arkansas Veterans Healthcare System, Little Rock AR, 72205, USA.
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2
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Balasubramaniam M, Ganne A, Mainali N, Pahal S, Ayyadevara S, Shmookler Reis RJ. Alzheimer's-specific brain amyloid interactome: Neural-network analysis of intra-aggregate crosslinking identifies novel drug targets. iScience 2024; 27:108745. [PMID: 38274404 PMCID: PMC10809092 DOI: 10.1016/j.isci.2023.108745] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2023] [Revised: 11/15/2023] [Accepted: 12/12/2023] [Indexed: 01/27/2024] Open
Abstract
Alzheimer's disease (AD) is characterized by peri-neuronal amyloid plaque and intra-neuronal neurofibrillary tangles. These aggregates are identified by the immunodetection of "seed" proteins (Aβ1-42 and hyperphosphorylated tau, respectively), but include many other proteins incorporated nonrandomly. Using click-chemistry intra-aggregate crosslinking, we previously modeled amyloid "contactomes" in SY5Y-APPSw neuroblastoma cells, revealing that aspirin impedes aggregate growth and complexity. By an analogous strategy, we now construct amyloid-specific aggregate interactomes of AD and age-matched-control hippocampi. Comparing these interactomes reveals AD-specific interactions, from which neural-network (NN) analyses predict proteins with the highest impact on pathogenic aggregate formation and/or stability. RNAi knockdowns of implicated proteins, in C. elegans and human-cell-culture models of AD, validated those predictions. Gene-Ontology meta-analysis of AD-enriched influential proteins highlighted the involvement of mitochondrial and cytoplasmic compartments in AD-specific aggregation. This approach derives dynamic consensus models of aggregate growth and architecture, implicating highly influential proteins as new targets to disrupt amyloid accrual in the AD brain.
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Affiliation(s)
| | - Akshatha Ganne
- Department of Geriatrics, Reynolds Institute on Aging, University of Arkansas for Medical Sciences, Little Rock, AR 72205, USA
| | - Nirjal Mainali
- Bioinformatics Program, University of Arkansas for Medical Sciences and University of Arkansas at Little Rock, Little Rock, AR 72205, USA
| | - Sonu Pahal
- Bioinformatics Program, University of Arkansas for Medical Sciences and University of Arkansas at Little Rock, Little Rock, AR 72205, USA
| | - Srinivas Ayyadevara
- Department of Geriatrics, Reynolds Institute on Aging, University of Arkansas for Medical Sciences, Little Rock, AR 72205, USA
- McClellan Veterans Medical Center, Central Arkansas Veterans Healthcare Service, Little Rock, AR 72205, USA
| | - Robert J. Shmookler Reis
- Department of Geriatrics, Reynolds Institute on Aging, University of Arkansas for Medical Sciences, Little Rock, AR 72205, USA
- McClellan Veterans Medical Center, Central Arkansas Veterans Healthcare Service, Little Rock, AR 72205, USA
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3
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Kakraba S, Ayyadevara S, Mainali N, Balasubramaniam M, Bowroju S, Penthala NR, Atluri R, Barger SW, Griffin ST, Crooks PA, Shmookler Reis RJ. Thiadiazolidinone (TDZD) Analogs Inhibit Aggregation-Mediated Pathology in Diverse Neurodegeneration Models, and Extend C. elegans Life- and Healthspan. Pharmaceuticals (Basel) 2023; 16:1498. [PMID: 37895969 PMCID: PMC10610358 DOI: 10.3390/ph16101498] [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: 08/25/2023] [Revised: 09/29/2023] [Accepted: 10/02/2023] [Indexed: 10/29/2023] Open
Abstract
Chronic, low-grade inflammation has been implicated in aging and age-dependent conditions, including Alzheimer's disease, cardiomyopathy, and cancer. One of the age-associated processes underlying chronic inflammation is protein aggregation, which is implicated in neuroinflammation and a broad spectrum of neurodegenerative diseases such as Alzheimer's, Huntington's, and Parkinson's diseases. We screened a panel of bioactive thiadiazolidinones (TDZDs) from our in-house library for rescue of protein aggregation in human-cell and C. elegans models of neurodegeneration. Among the tested TDZD analogs, PNR886 and PNR962 were most effective, significantly reducing both the number and intensity of Alzheimer-like tau and amyloid aggregates in human cell-culture models of pathogenic aggregation. A C. elegans strain expressing human Aβ1-42 in muscle, leading to AD-like amyloidopathy, developed fewer and smaller aggregates after PNR886 or PNR962 treatment. Moreover, age-progressive paralysis was reduced 90% by PNR886 and 75% by PNR962, and "healthspan" (the median duration of spontaneous motility) was extended 29% and 62%, respectively. These TDZD analogs also extended wild-type C. elegans lifespan by 15-30% (p < 0.001), placing them among the most effective life-extension drugs. Because the lead drug in this family, TDZD-8, inhibits GSK3β, we used molecular-dynamic tools to assess whether these analogs may also target GSK3β. In silico modeling predicted that PNR886 or PNR962 would bind to the same allosteric pocket of inactive GSK3β as TDZD-8, employing the same pharmacophore but attaching with greater avidity. PNR886 and PNR962 are thus compelling candidate drugs for treatment of tau- and amyloid-associated neurodegenerative diseases such as AD, potentially also reducing all-cause mortality.
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Affiliation(s)
- Samuel Kakraba
- Department of Geriatrics, University of Arkansas for Medical Sciences, Little Rock, AR 72205, USA; (N.M.); (M.B.); (R.A.); (S.W.B.); (S.T.G.)
| | - Srinivas Ayyadevara
- Department of Geriatrics, University of Arkansas for Medical Sciences, Little Rock, AR 72205, USA; (N.M.); (M.B.); (R.A.); (S.W.B.); (S.T.G.)
- Central Arkansas Veterans Healthcare Service, Little Rock, AR 72205, USA
| | - Nirjal Mainali
- Department of Geriatrics, University of Arkansas for Medical Sciences, Little Rock, AR 72205, USA; (N.M.); (M.B.); (R.A.); (S.W.B.); (S.T.G.)
| | - Meenakshisundaram Balasubramaniam
- Department of Geriatrics, University of Arkansas for Medical Sciences, Little Rock, AR 72205, USA; (N.M.); (M.B.); (R.A.); (S.W.B.); (S.T.G.)
| | - Suresh Bowroju
- Department of Pharmaceutical Sciences, University of Arkansas for Medical Sciences, Little Rock, AR 72205, USA; (S.B.); (N.R.P.); (P.A.C.)
| | - Narsimha Reddy Penthala
- Department of Pharmaceutical Sciences, University of Arkansas for Medical Sciences, Little Rock, AR 72205, USA; (S.B.); (N.R.P.); (P.A.C.)
| | - Ramani Atluri
- Department of Geriatrics, University of Arkansas for Medical Sciences, Little Rock, AR 72205, USA; (N.M.); (M.B.); (R.A.); (S.W.B.); (S.T.G.)
| | - Steven W. Barger
- Department of Geriatrics, University of Arkansas for Medical Sciences, Little Rock, AR 72205, USA; (N.M.); (M.B.); (R.A.); (S.W.B.); (S.T.G.)
- Central Arkansas Veterans Healthcare Service, Little Rock, AR 72205, USA
| | - Sue T. Griffin
- Department of Geriatrics, University of Arkansas for Medical Sciences, Little Rock, AR 72205, USA; (N.M.); (M.B.); (R.A.); (S.W.B.); (S.T.G.)
- Central Arkansas Veterans Healthcare Service, Little Rock, AR 72205, USA
| | - Peter A. Crooks
- Department of Pharmaceutical Sciences, University of Arkansas for Medical Sciences, Little Rock, AR 72205, USA; (S.B.); (N.R.P.); (P.A.C.)
| | - Robert J. Shmookler Reis
- Department of Geriatrics, University of Arkansas for Medical Sciences, Little Rock, AR 72205, USA; (N.M.); (M.B.); (R.A.); (S.W.B.); (S.T.G.)
- Central Arkansas Veterans Healthcare Service, Little Rock, AR 72205, USA
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4
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Ganne A, Balasubramaniam M, Griffin WST, Shmookler Reis RJ, Ayyadevara S. Glial Fibrillary Acidic Protein: A Biomarker and Drug Target for Alzheimer’s Disease. Pharmaceutics 2022; 14:pharmaceutics14071354. [PMID: 35890250 PMCID: PMC9322874 DOI: 10.3390/pharmaceutics14071354] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2022] [Revised: 06/21/2022] [Accepted: 06/22/2022] [Indexed: 02/05/2023] Open
Abstract
Glial fibrillary acidic protein (GFAP) is an intermediate filament structural protein involved in cytoskeleton assembly and integrity, expressed in high abundance in activated glial cells. GFAP is neuroprotective, as knockout mice are hypersensitive to traumatic brain injury. GFAP in cerebrospinal fluid is a biomarker of Alzheimer’s disease (AD), dementia with Lewy bodies, and frontotemporal dementia (FTD). Here, we present novel evidence that GFAP is markedly overexpressed and differentially phosphorylated in AD hippocampus, especially in AD with the apolipoprotein E [ε4, ε4] genotype, relative to age-matched controls (AMCs). Kinases that phosphorylate GFAP are upregulated in AD relative to AMC. A knockdown of these kinases in SH-SY5Y-APPSw human neuroblastoma cells reduced amyloid accrual and lowered protein aggregation and associated behavioral traits in C. elegans models of polyglutamine aggregation (as observed in Huntington’s disease) and of Alzheimer’s-like amyloid formation. In silico screening of the ChemBridge structural library identified a small molecule, MSR1, with stable and specific binding to GFAP. Both MSR1 exposure and GF AP-specific RNAi knockdown reduce aggregation with remarkably high concordance of aggregate proteins depleted. These data imply that GFAP and its phosphorylation play key roles in neuropathic aggregate accrual and provide valuable new biomarkers, as well as novel therapeutic targets to alleviate, delay, or prevent AD.
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Affiliation(s)
- Akshatha Ganne
- Central Arkansas Veterans Healthcare Service, Little Rock, AR 72205, USA; (A.G.); (M.B.); (W.S.T.G.)
- Department of Geriatrics, University of Arkansas for Medical Sciences, Little Rock, AR 72205, USA
| | | | - W. Sue T. Griffin
- Central Arkansas Veterans Healthcare Service, Little Rock, AR 72205, USA; (A.G.); (M.B.); (W.S.T.G.)
- BioInformatics Program, University of Arkansas for Medical Sciences, Little Rock, AR 72205, USA
| | - Robert J. Shmookler Reis
- Central Arkansas Veterans Healthcare Service, Little Rock, AR 72205, USA; (A.G.); (M.B.); (W.S.T.G.)
- Department of Geriatrics, University of Arkansas for Medical Sciences, Little Rock, AR 72205, USA
- BioInformatics Program, University of Arkansas for Medical Sciences, Little Rock, AR 72205, USA
- Department of Biochemistry & Molecular Biology, University of Arkansas for Medical Sciences, Little Rock, AR 72205, USA
- Correspondence: (R.J.S.R.); (S.A.); Tel.: +1-501-526-5820 (R.J.S.R.); +1-501-526-7282 (S.A.)
| | - Srinivas Ayyadevara
- Central Arkansas Veterans Healthcare Service, Little Rock, AR 72205, USA; (A.G.); (M.B.); (W.S.T.G.)
- Department of Geriatrics, University of Arkansas for Medical Sciences, Little Rock, AR 72205, USA
- BioInformatics Program, University of Arkansas for Medical Sciences, Little Rock, AR 72205, USA
- Correspondence: (R.J.S.R.); (S.A.); Tel.: +1-501-526-5820 (R.J.S.R.); +1-501-526-7282 (S.A.)
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Shmookler Reis RJ, Atluri R, Balasubramaniam M, Johnson J, Ganne A, Ayyadevara S. "Protein aggregates" contain RNA and DNA, entrapped by misfolded proteins but largely rescued by slowing translational elongation. Aging Cell 2021; 20:e13326. [PMID: 33788386 PMCID: PMC8135009 DOI: 10.1111/acel.13326] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2020] [Revised: 01/12/2021] [Accepted: 02/01/2021] [Indexed: 01/03/2023] Open
Abstract
All neurodegenerative diseases feature aggregates, which usually contain disease-specific diagnostic proteins; non-protein constituents, however, have rarely been explored. Aggregates from SY5Y-APPSw neuroblastoma, a cell model of familial Alzheimer's disease, were crosslinked and sequences of linked peptides identified. We constructed a normalized "contactome" comprising 11 subnetworks, centered on 24 high-connectivity hubs. Remarkably, all 24 are nucleic acid-binding proteins. This led us to isolate and sequence RNA and DNA from Alzheimer's and control aggregates. RNA fragments were mapped to the human genome by RNA-seq and DNA by ChIP-seq. Nearly all aggregate RNA sequences mapped to specific genes, whereas DNA fragments were predominantly intergenic. These nucleic acid mappings are all significantly nonrandom, making an artifactual origin extremely unlikely. RNA (mostly cytoplasmic) exceeded DNA (chiefly nuclear) by twofold to fivefold. RNA fragments recovered from AD tissue were ~1.5-to 2.5-fold more abundant than those recovered from control tissue, similar to the increase in protein. Aggregate abundances of specific RNA sequences were strikingly differential between cultured SY5Y-APPSw glioblastoma cells expressing APOE3 vs. APOE4, consistent with APOE4 competition for E-box/CLEAR motifs. We identified many G-quadruplex and viral sequences within RNA and DNA of aggregates, suggesting that sequestration of viral genomes may have driven the evolution of disordered nucleic acid-binding proteins. After RNA-interference knockdown of the translational-procession factor EEF2 to suppress translation in SY5Y-APPSw cells, the RNA content of aggregates declined by >90%, while reducing protein content by only 30% and altering DNA content by ≤10%. This implies that cotranslational misfolding of nascent proteins may ensnare polysomes into aggregates, accounting for most of their RNA content.
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Affiliation(s)
- Robert J. Shmookler Reis
- Central Arkansas Veterans Healthcare System Little Rock AR USA
- Department of Geriatrics University of Arkansas for Medical Sciences Little Rock AR USA
- BioInformatics Program University of Arkansas for Medical Sciences and University of Arkansas at Little Rock Little Rock AR USA
| | - Ramani Atluri
- Department of Geriatrics University of Arkansas for Medical Sciences Little Rock AR USA
| | | | - Jay Johnson
- BioInformatics Program University of Arkansas for Medical Sciences and University of Arkansas at Little Rock Little Rock AR USA
| | - Akshatha Ganne
- BioInformatics Program University of Arkansas for Medical Sciences and University of Arkansas at Little Rock Little Rock AR USA
| | - Srinivas Ayyadevara
- Central Arkansas Veterans Healthcare System Little Rock AR USA
- Department of Geriatrics University of Arkansas for Medical Sciences Little Rock AR USA
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Balasubramaniam M, Lakkaniga NR, Dera AA, Fayi MA, Abohashrh M, Ahmad I, Chandramoorthy HC, Nalini G, Rajagopalan P. FCX-146, a potent allosteric inhibitor of Akt kinase in cancer cells: Lead optimization of the second-generation arylidene indanone scaffold. Biotechnol Appl Biochem 2020; 68:82-91. [PMID: 32067263 DOI: 10.1002/bab.1896] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2019] [Accepted: 02/04/2020] [Indexed: 12/16/2022]
Abstract
Akt, a serine-threonine protein kinase, is regulated by class-I PI3K signaling. Akt regulates a wide variety of cell processes including cell proliferation, survival, and angiogenesis through serine/threonine phosphorylation of downstream targets including mTOR and glycogen-synthase-kinase-3-beta (GSK3β). Targeting cancer-specific overexpression of Akt protein could be an efficient way to control cancer-cell proliferation. However, the ATP-competitive inhibitors are challenged by the highly conserved ATP binding site, and by competition with high cellular concentrations of ATP. We previously developed an allosteric inhibitor, 2-arylidene-4, 7-dimethyl indan-1-one (FXY-1) that showed promising activity against several lung cancer models. In this work, we designed a congeneric series of molecules based on FXY-1 and optimized lead based on computational, in vitro assays. Computational screening followed by enzyme-inhibition and cell-proliferation assays identified a derivative (FCX-146) as a new lead molecule with threefold greater potency than the parent compound. FCX-146 increased apoptosis in HL-60 cells, mediated in part through decreased expression of antiapoptotic Bcl-2 protein and increased levels of Bax-2 and Caspase-3. Molecular-dynamic simulations showed stable binding of FCX-146 to an allosteric (i.e., noncatalytic) pocket in Akt. Together, we propose FCX-146 as a potent second-generation arylidene indanone compound that binds to the allosteric pocket of Akt and potently inhibits its activation.
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Affiliation(s)
| | - Naga Rajiv Lakkaniga
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Arkansas for Medical Sciences, Little Rock, AR, USA
| | - Ayed A Dera
- Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, King Khalid University, Abha, Saudi Arabia
- Central Research Laboratory, College of Applied Medical Sciences, King Khalid University, Abha, Saudi Arabia
| | - Majed Al Fayi
- Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, King Khalid University, Abha, Saudi Arabia
- Central Research Laboratory, College of Applied Medical Sciences, King Khalid University, Abha, Saudi Arabia
| | - Mohammed Abohashrh
- Department of Basic Medical Sciences, College of Applied Medical Sciences, King Khalid University, Abha, Saudi Arabia
| | - Irfan Ahmad
- Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, King Khalid University, Abha, Saudi Arabia
- Central Research Laboratory, College of Applied Medical Sciences, King Khalid University, Abha, Saudi Arabia
| | - Harish C Chandramoorthy
- Center for Stem Cell Research and Department of Microbiology & Clinical Parasitology College of Medicine, King Khalid University, Abha, Saudi Arabia
| | - Ganesan Nalini
- Department of Chemistry, Pachaiyappas College, Chennai, Tamil Nadu, India
| | - Prasanna Rajagopalan
- Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, King Khalid University, Abha, Saudi Arabia
- Central Research Laboratory, College of Applied Medical Sciences, King Khalid University, Abha, Saudi Arabia
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Kakraba S, Ayyadevara S, Penthala NR, Balasubramaniam M, Ganne A, Liu L, Alla R, Bommagani SB, Barger SW, Griffin WST, Crooks PA, Shmookler Reis RJ. A Novel Microtubule-Binding Drug Attenuates and Reverses Protein Aggregation in Animal Models of Alzheimer's Disease. Front Mol Neurosci 2020; 12:310. [PMID: 31920540 PMCID: PMC6920216 DOI: 10.3389/fnmol.2019.00310] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2019] [Accepted: 11/29/2019] [Indexed: 11/14/2022] Open
Abstract
Age-progressive neurodegenerative pathologies, including Alzheimer’s disease (AD), are distinguished and diagnosed by disease-specific components of intra- or extra-cellular aggregates. Increasing evidence suggests that neuroinflammation promotes protein aggregation, and is involved in the etiology of neurological diseases. We synthesized and tested analogs of the naturally occurring tubulin-binding compound, combretastatin A-4. One such analog, PNR502, markedly reduced the quantity of Alzheimer-associated amyloid aggregates in the BRI-Aβ1–42 mouse model of AD, while blunting the ability of the pro-inflammatory cytokine IL-1β to raise levels of amyloid plaque and its protein precursors in a neuronal cell-culture model. In transgenic Caenorhabditis elegans (C. elegans) strains that express human Aβ1–42 in muscle or neurons, PNR502 rescued Aβ-induced disruption of motility (3.8-fold, P < 0.0001) or chemotaxis (1.8-fold, P < 0.05), respectively. Moreover, in C. elegans with neuronal expression of Aβ1–42, a single day of PNR502 exposure reverses the chemotaxis deficit by 54% (P < 0.01), actually exceeding the protection from longer exposure. Moreover, continuous PNR502 treatment extends nematode lifespan 23% (P ≤ 0.001). Given that PNR502 can slow, prevent, or reverse Alzheimer-like protein aggregation in human-cell-culture and animal models, and that its principal predicted and observed binding targets are proteins previously implicated in Alzheimer’s, we propose that PNR502 has therapeutic potential to inhibit cerebral Aβ1–42 aggregation and prevent or reverse neurodegeneration.
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Affiliation(s)
- Samuel Kakraba
- BioInformatics Program, University of Arkansas for Medical Sciences and University of Arkansas at Little Rock, Little Rock, AR, United States
| | - Srinivas Ayyadevara
- Central Arkansas Veterans Healthcare Service, Little Rock, AR, United States.,Department of Geriatrics, University of Arkansas for Medical Sciences, Little Rock, AR, United States
| | - Narsimha Reddy Penthala
- Department of Pharmaceutical Sciences, University of Arkansas for Medical Sciences, Little Rock, AR, United States
| | | | - Akshatha Ganne
- BioInformatics Program, University of Arkansas for Medical Sciences and University of Arkansas at Little Rock, Little Rock, AR, United States
| | - Ling Liu
- Department of Geriatrics, University of Arkansas for Medical Sciences, Little Rock, AR, United States
| | - Ramani Alla
- Central Arkansas Veterans Healthcare Service, Little Rock, AR, United States.,Department of Geriatrics, University of Arkansas for Medical Sciences, Little Rock, AR, United States
| | - Shoban Babu Bommagani
- Department of Pharmaceutical Sciences, University of Arkansas for Medical Sciences, Little Rock, AR, United States
| | - Steven W Barger
- Central Arkansas Veterans Healthcare Service, Little Rock, AR, United States.,Department of Geriatrics, University of Arkansas for Medical Sciences, Little Rock, AR, United States
| | - W Sue T Griffin
- Central Arkansas Veterans Healthcare Service, Little Rock, AR, United States.,Department of Geriatrics, University of Arkansas for Medical Sciences, Little Rock, AR, United States
| | - Peter A Crooks
- Department of Pharmaceutical Sciences, University of Arkansas for Medical Sciences, Little Rock, AR, United States
| | - Robert J Shmookler Reis
- BioInformatics Program, University of Arkansas for Medical Sciences and University of Arkansas at Little Rock, Little Rock, AR, United States.,Central Arkansas Veterans Healthcare Service, Little Rock, AR, United States.,Department of Geriatrics, University of Arkansas for Medical Sciences, Little Rock, AR, United States
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Balasubramaniam M, Ayyadevara S, Ganne A, Kakraba S, Penthala NR, Du X, Crooks PA, Griffin ST, Shmookler Reis RJ. Aggregate Interactome Based on Protein Cross-linking Interfaces Predicts Drug Targets to Limit Aggregation in Neurodegenerative Diseases. iScience 2019; 20:248-264. [PMID: 31593839 PMCID: PMC6817627 DOI: 10.1016/j.isci.2019.09.026] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2019] [Revised: 06/20/2019] [Accepted: 09/17/2019] [Indexed: 01/02/2023] Open
Abstract
Diagnosis of neurodegenerative diseases hinges on “seed” proteins detected in disease-specific aggregates. These inclusions contain diverse constituents, adhering through aberrant interactions that our prior data indicate are nonrandom. To define preferential protein-protein contacts mediating aggregate coalescence, we created click-chemistry reagents that cross-link neighboring proteins within human, APPSw-driven, neuroblastoma-cell aggregates. These reagents incorporate a biotinyl group to efficiently recover linked tryptic-peptide pairs. Mass-spectroscopy outputs were screened for all possible peptide pairs in the aggregate proteome. These empirical linkages, ranked by abundance, implicate a protein-adherence network termed the “aggregate contactome.” Critical hubs and hub-hub interactions were assessed by RNAi-mediated rescue of chemotaxis in aging nematodes, and aggregation-driving properties were inferred by multivariate regression and neural-network approaches. Aspirin, while disrupting aggregation, greatly simplified the aggregate contactome. This approach, and the dynamic model of aggregate accrual it implies, reveals the architecture of insoluble-aggregate networks and may reveal targets susceptible to interventions to ameliorate protein-aggregation diseases. Cross-link data support a preferred hierarchy of protein accrual into aggregates Contact networks can predict proteins that contribute functionally to aggregation RNAi knockdowns of key hubs and hub connectors imply functional roles in accrual Aspirin opposes protein aggregation by reducing contactome interactions >5-fold
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Affiliation(s)
- Meenakshisundaram Balasubramaniam
- McClellan Veterans Medical Ctr., Central Arkansas Veterans Healthcare Service, Little Rock, AR 72205, USA; Department of Geriatrics, Reynolds Institute on Aging, University of Arkansas for Medical Sciences, Little Rock, AR 72205, USA.
| | - Srinivas Ayyadevara
- McClellan Veterans Medical Ctr., Central Arkansas Veterans Healthcare Service, Little Rock, AR 72205, USA; Department of Geriatrics, Reynolds Institute on Aging, University of Arkansas for Medical Sciences, Little Rock, AR 72205, USA.
| | - Akshatha Ganne
- Bioinformatics Program, University of Arkansas for Medical Sciences, University of Arkansas at Little Rock, Little Rock, AR 72205, USA
| | - Samuel Kakraba
- Bioinformatics Program, University of Arkansas for Medical Sciences, University of Arkansas at Little Rock, Little Rock, AR 72205, USA
| | - Narsimha Reddy Penthala
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Arkansas for Medical Sciences, Little Rock, AR 72205, USA
| | - Xiuxia Du
- Department of Bioinformatics & Genomics, University of North Carolina at Charlotte, Charlotte, NC 28223, USA
| | - Peter A Crooks
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Arkansas for Medical Sciences, Little Rock, AR 72205, USA
| | - Sue T Griffin
- McClellan Veterans Medical Ctr., Central Arkansas Veterans Healthcare Service, Little Rock, AR 72205, USA; Department of Geriatrics, Reynolds Institute on Aging, University of Arkansas for Medical Sciences, Little Rock, AR 72205, USA
| | - Robert J Shmookler Reis
- McClellan Veterans Medical Ctr., Central Arkansas Veterans Healthcare Service, Little Rock, AR 72205, USA; Department of Geriatrics, Reynolds Institute on Aging, University of Arkansas for Medical Sciences, Little Rock, AR 72205, USA.
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Zhang W, Zhou Q, Wei Y, Da M, Zhang C, Zhong J, Liu J, Shen J. The exosome-mediated PI3k/Akt/mTOR signaling pathway in cervical cancer. INTERNATIONAL JOURNAL OF CLINICAL AND EXPERIMENTAL PATHOLOGY 2019; 12:2474-2484. [PMID: 31934074 PMCID: PMC6949546] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 03/27/2019] [Accepted: 05/23/2019] [Indexed: 06/10/2023]
Abstract
BACKGROUND Cervical cancer is the second most common cancer and one of the leading causes of cancer deaths among women worldwide. OBJECTIVE To evaluate the clinical significance of the PI3k/Akt/mTOR signaling pathway in cancer tissues and exosomes extracted from vaginal secretions. METHODS Immunohistochemical staining was used to detect the protein expression of PI3k, Akt, and mTOR in tissue samples from the control group, the CIN (cervical intraepithelial neoplasia) group, and the cervical cancer group. qPCR (quantitative PCR) was used to detect the expressions of PI3k, Akt, and mTOR in cervical cancer tissues, the corresponding adjacent tissues, and exosomes extracted from vaginal secretions. RESULTS Compared with those of healthy people and CIN, the PI3k/Akt/mTOR protein levels in extracts from tissues were higher in the cervical cancer patients. The PI3k/Akt/mTOR gene and protein levels increased in the cervical cancer tissues with the increase in the degree of malignancy of the cancer. There was no significant difference in PI3k/Akt/mTOR gene expression between the cervical cancer tissues and the exosomes extracted from vaginal secretions, but both were significantly higher than the expressions of the corresponding adjacent tissues. CONCLUSIONS The PI3k/Akt/mTOR signaling pathway mediated by exosomes extracted from vaginal secretions may provide candidate diagnostic biomarkers or potential therapeutic targets.
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Affiliation(s)
- Wenyuan Zhang
- Department of Gynaecology, Huzhou Central HospitalHuzhou, Zhejiang Province, China
| | - Qing Zhou
- Department of Nursing, Huzhou Central HospitalHuzhou, Zhejiang Province, China
| | - Yunhai Wei
- Department of Surgery, Huzhou Central HospitalHuzhou, Zhejiang Province, China
| | - Miao Da
- Medical College of Nursing, Huzhou UniversityHuzhou, Zhejiang Province, China
| | - Chun Zhang
- Infectious Disease, Huzhou Central HospitalHuzhou, Zhejiang Province, China
| | - Jing Zhong
- Central Laboratory, Huzhou Central HospitalHuzhou, Zhejiang Province, China
| | - Jin Liu
- Department of Pathology, Huzhou Central HospitalHuzhou, Zhejiang Province, China
| | - Junjun Shen
- Department of Medical Oncology, Huzhou Central HospitalHuzhou, Zhejiang Province, China
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10
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Ayyadevara S, Ganne A, Hendrix RD, Balasubramaniam M, Shmookler Reis RJ, Barger SW. Functional assessments through novel proteomics approaches: Application to insulin/IGF signaling in neurodegenerative disease'. J Neurosci Methods 2018; 319:40-46. [PMID: 30412730 DOI: 10.1016/j.jneumeth.2018.11.005] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2018] [Revised: 11/04/2018] [Accepted: 11/05/2018] [Indexed: 11/26/2022]
Abstract
BACKGROUND Events that instigate disease may involve biochemical events distinct from changes in the steady-state levels of proteins. Even chronic degenerative disorders appear to involve changes such as post-translational modifications. NEW METHOD We have begun a series of proteomics analyses on proteins that have been fractionated by functional status. Because Alzheimer's disease (AD) is associated with metabolic perturbations such as Type-2 diabetes, fractionation hinged on binding to phosphatidylinositol trisphosphate (PIP3), key to insulin/insulin-like growth factor signaling. We compared mice on normal chow to counterparts subjected to diet-induced obesity (DIO) or to mice expressing human Aβ1-42 from a transgene. RESULTS The prevailing phenotypic finding in either experimental group was loss of PIP3 binding. Of the 1228 proteins that showed valid PIP3 binding in any group of mice, 55% exhibited a significant quantitative difference in the number of spectral counts as a function of DIO, 63% as function of the Aβ transgene, and 79% as a function of either variable. There was remarkable overlap among the proteins altered in the two experimental groups, and pathway analysis indicated effects on proteostasis, apoptosis, and synaptic vesicles. COMPARISON WITH EXISTING METHODS Most proteomics approaches only identify differences in the steady-state levels of proteins. Our overlay of a functional distinction permits new levels of discovery that may achieve novel insights into physiology in an unbiased and inclusive manner. CONCLUSIONS Proteomics analyses have revolutionized the discovery phase of biomedical research but are conventionally limited in scope. The creative use of fractionation prior to proteomic discovery is likely to provide important insights into AD and related disorders.
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Affiliation(s)
- Srinivas Ayyadevara
- Central Arkansas Veterans Healthcare System, Little Rock, AR, 72205, United States; Department of Geriatrics, University of Arkansas for Medical Sciences, Little Rock, AR 72205, United States.
| | - Akshatha Ganne
- Department of Geriatrics, University of Arkansas for Medical Sciences, Little Rock, AR 72205, United States; BioInformatics Program, University of Arkansas for Medical Sciences, Little Rock, AR 72205, United States
| | - Rachel D Hendrix
- Department of Neurobiology & Developmental Sciences, University of Arkansas for Medical Sciences, Little Rock, AR, 72205, United States
| | | | - Robert J Shmookler Reis
- Central Arkansas Veterans Healthcare System, Little Rock, AR, 72205, United States; Department of Geriatrics, University of Arkansas for Medical Sciences, Little Rock, AR 72205, United States; BioInformatics Program, University of Arkansas for Medical Sciences, Little Rock, AR 72205, United States; Department of Biochemistry & Molecular Biology, University of Arkansas for Medical Sciences, Little Rock, AR, 72205, United States
| | - Steven W Barger
- Central Arkansas Veterans Healthcare System, Little Rock, AR, 72205, United States; Department of Geriatrics, University of Arkansas for Medical Sciences, Little Rock, AR 72205, United States; Department of Neurobiology & Developmental Sciences, University of Arkansas for Medical Sciences, Little Rock, AR, 72205, United States.
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11
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Perni M, Flagmeier P, Limbocker R, Cascella R, Aprile FA, Galvagnion C, Heller GT, Meisl G, Chen SW, Kumita JR, Challa PK, Kirkegaard JB, Cohen SIA, Mannini B, Barbut D, Nollen EAA, Cecchi C, Cremades N, Knowles TPJ, Chiti F, Zasloff M, Vendruscolo M, Dobson CM. Multistep Inhibition of α-Synuclein Aggregation and Toxicity in Vitro and in Vivo by Trodusquemine. ACS Chem Biol 2018; 13:2308-2319. [PMID: 29953201 DOI: 10.1021/acschembio.8b00466] [Citation(s) in RCA: 77] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The aggregation of α-synuclein, an intrinsically disordered protein that is highly abundant in neurons, is closely associated with the onset and progression of Parkinson's disease. We have shown previously that the aminosterol squalamine can inhibit the lipid induced initiation process in the aggregation of α-synuclein, and we report here that the related compound trodusquemine is capable of inhibiting not only this process but also the fibril-dependent secondary pathways in the aggregation reaction. We further demonstrate that trodusquemine can effectively suppress the toxicity of α-synuclein oligomers in neuronal cells, and that its administration, even after the initial growth phase, leads to a dramatic reduction in the number of α-synuclein inclusions in a Caenorhabditis elegans model of Parkinson's disease, eliminates the related muscle paralysis, and increases lifespan. On the basis of these findings, we show that trodusquemine is able to inhibit multiple events in the aggregation process of α-synuclein and hence to provide important information about the link between such events and neurodegeneration, as it is initiated and progresses. Particularly in the light of the previously reported ability of trodusquemine to cross the blood-brain barrier and to promote tissue regeneration, the present results suggest that this compound has the potential to be an important therapeutic candidate for Parkinson's disease and related disorders.
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Affiliation(s)
- Michele Perni
- Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, United Kingdom
- Centre for Misfolding Diseases, Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, United Kingdom
| | - Patrick Flagmeier
- Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, United Kingdom
- Centre for Misfolding Diseases, Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, United Kingdom
| | - Ryan Limbocker
- Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, United Kingdom
- Centre for Misfolding Diseases, Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, United Kingdom
| | - Roberta Cascella
- Department of Experimental and Clinical Biomedical Sciences, University of Florence, Florence 50134, Italy
| | - Francesco A. Aprile
- Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, United Kingdom
- Centre for Misfolding Diseases, Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, United Kingdom
| | - Céline Galvagnion
- Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, United Kingdom
- German Centre for Neurodegenerative Diseases, DZNE, Sigmund-Freud-Strasse. 27, 53127, Bonn, Germany
| | - Gabriella T. Heller
- Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, United Kingdom
- Centre for Misfolding Diseases, Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, United Kingdom
| | - Georg Meisl
- Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, United Kingdom
- Centre for Misfolding Diseases, Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, United Kingdom
| | - Serene W. Chen
- Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, United Kingdom
- Centre for Misfolding Diseases, Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, United Kingdom
| | - Janet R. Kumita
- Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, United Kingdom
- Centre for Misfolding Diseases, Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, United Kingdom
| | - Pavan K. Challa
- Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, United Kingdom
- Centre for Misfolding Diseases, Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, United Kingdom
| | - Julius B. Kirkegaard
- Department of Applied Mathematics and Theoretical Physics, University of Cambridge, Cambridge CB3 0WA, United Kingdom
| | - Samuel I. A. Cohen
- Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, United Kingdom
- Centre for Misfolding Diseases, Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, United Kingdom
| | - Benedetta Mannini
- Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, United Kingdom
- Centre for Misfolding Diseases, Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, United Kingdom
| | - Denise Barbut
- Enterin Inc., 3624 Market Street, Philadelphia, Pennsylvania 19104, United States
| | - Ellen A. A. Nollen
- University Medical Centre Groningen, European Research Institute for the Biology of Aging, University of Groningen, Groningen 9713 AV, The Netherlands
| | - Cristina Cecchi
- Department of Experimental and Clinical Biomedical Sciences, University of Florence, Florence 50134, Italy
| | - Nunilo Cremades
- Institute for Biocomputation and Physics of Complex Systems (BIFI)-Joint Unit BIFI-IQFR (CSIC), University of Zaragoza, 50018 Zaragoza, Spain
| | - Tuomas P. J. Knowles
- Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, United Kingdom
- Centre for Misfolding Diseases, Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, United Kingdom
- Department of Physics, Cavendish Laboratory, University of Cambridge, Cambridge CB3 0HE, United Kingdom
| | - Fabrizio Chiti
- Department of Experimental and Clinical Biomedical Sciences, University of Florence, Florence 50134, Italy
| | - Michael Zasloff
- Enterin Inc., 3624 Market Street, Philadelphia, Pennsylvania 19104, United States
- MedStar-Georgetown Transplant Institute, Georgetown University School of Medicine, Washington, DC 20010, United States
| | - Michele Vendruscolo
- Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, United Kingdom
- Centre for Misfolding Diseases, Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, United Kingdom
| | - Christopher M. Dobson
- Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, United Kingdom
- Centre for Misfolding Diseases, Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, United Kingdom
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