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Nedorezova DD, Dubovichenko MV, Eldeeb AA, Nur MAY, Bobkov GA, Ashmarova AI, Kalnin AJ, Kolpashchikov DM. Cleaving Folded RNA by Multifunctional DNAzyme Nanomachines. Chemistry 2024:e202401580. [PMID: 38757205 DOI: 10.1002/chem.202401580] [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: 04/22/2024] [Revised: 05/09/2024] [Accepted: 05/13/2024] [Indexed: 05/18/2024]
Abstract
Both tight and specific binding of folded biological mRNA is required for gene silencing by oligonucleotide gene therapy agents. However, this is fundamentally impossible using the conventional oligonucleotide probes according to the affinity/specificity dilemma. This study addresses this problem for cleaving folded RNA by using multicomponent agents (dubbed 'DNA nanomachine' or DNM). DNMs bind RNA by four short RNA binding arms, which ensure tight and highly selective RNA binding. Along with the improved affinity, DNM maintain the high sequence selectivity of the conventional DNAzymes. DNM enabled up to 3-fold improvement in DNAzymes catalytic efficiency (kcat/Km) by facilitating both RNA substrate binding and product release steps of the catalytic cycle. This study demonstrates that multicomponent probes organized in sophisticated structures can help to achieve the balance between affinity and selectivity in recognizing folded RNA and thus creates a foundation for applying complex DNA nanostructures derived by DNA nanotechnology in gene therapy.
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Affiliation(s)
- Daria D Nedorezova
- robotics and biosensor systems, and Frontier nucleic acid technologies in gene therapy of cancer SCAMT Institute, ITMO University, St. Petersburg, 191002, Russian Federation
| | - Mikhail V Dubovichenko
- robotics and biosensor systems, and Frontier nucleic acid technologies in gene therapy of cancer SCAMT Institute, ITMO University, St. Petersburg, 191002, Russian Federation
| | - Ahmed A Eldeeb
- robotics and biosensor systems, and Frontier nucleic acid technologies in gene therapy of cancer SCAMT Institute, ITMO University, St. Petersburg, 191002, Russian Federation
| | - Moustapha A Y Nur
- robotics and biosensor systems, and Frontier nucleic acid technologies in gene therapy of cancer SCAMT Institute, ITMO University, St. Petersburg, 191002, Russian Federation
| | - Gleb A Bobkov
- robotics and biosensor systems, and Frontier nucleic acid technologies in gene therapy of cancer SCAMT Institute, ITMO University, St. Petersburg, 191002, Russian Federation
| | - Anna I Ashmarova
- robotics and biosensor systems, and Frontier nucleic acid technologies in gene therapy of cancer SCAMT Institute, ITMO University, St. Petersburg, 191002, Russian Federation
| | - Arsenij J Kalnin
- robotics and biosensor systems, and Frontier nucleic acid technologies in gene therapy of cancer SCAMT Institute, ITMO University, St. Petersburg, 191002, Russian Federation
| | - Dmitry M Kolpashchikov
- robotics and biosensor systems, and Frontier nucleic acid technologies in gene therapy of cancer SCAMT Institute, ITMO University, St. Petersburg, 191002, Russian Federation
- Chemistry Department, University of Central Florida, Orlando, FL 32816-2366, USA
- Burnett School of Biomedical Sciences, University of Central Florida, Orlando, FL 32816
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Singh H, Das A, Khan MM, Pourmotabbed T. New insights into the therapeutic approaches for the treatment of tauopathies. Neural Regen Res 2024; 19:1020-1026. [PMID: 37862204 PMCID: PMC10749630 DOI: 10.4103/1673-5374.385288] [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: 05/02/2023] [Revised: 07/05/2023] [Accepted: 08/10/2023] [Indexed: 10/22/2023] Open
Abstract
Tauopathies are a group of neurological disorders, including Alzheimer's disease and frontotemporal dementia, which involve progressive neurodegeneration, cognitive deficits, and aberrant tau protein accumulation. The development of tauopathies cannot currently be stopped or slowed down by treatment measures. Given the significant contribution of tau burden in primary tauopathies and the strong association between pathogenic tau accumulation and cognitive deficits, there has been a lot of interest in creating therapies that can alleviate tau pathology and render neuroprotective effects. Recently, small molecules, immunotherapies, and gene therapy have been used to reduce the pathological tau burden and prevent neurodegeneration in animal models of tauopathies. However, the major pitfall of the current therapeutic approach is the difficulty of drugs and gene-targeting modalities to cross the blood-brain barrier and their unintended side effects. In this review, the current therapeutic strategies used for tauopathies including the use of oligonucleotide-based gene therapy approaches that have shown a promising result for the treatment of tauopathies and Alzheimer's disease in preclinical animal models, have been discussed.
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Affiliation(s)
- Himanshi Singh
- Department of Microbiology, Immunology and Biochemistry, University of Tennessee Health Science Center, Memphis, TN, USA
- Department of Biotechnology, Delhi Technological University, Shahbad Daulatpur, Delhi, India
- Department of Neurology, College of Medicine, University of Tennessee Health Science Center, Memphis, TN, USA
| | - Asmita Das
- Department of Biotechnology, Delhi Technological University, Shahbad Daulatpur, Delhi, India
| | - Mohammad Moshahid Khan
- Department of Neurology, College of Medicine, University of Tennessee Health Science Center, Memphis, TN, USA
- Neuroscience Institute, University of Tennessee Health Science Center, Memphis, TN, USA
- Center for Muscle, Metabolism and Neuropathology, Division of Regenerative and Rehabilitation Sciences and Department of Physical Therapy, College of Health Professions, University of Tennessee Health Science Center, Memphis, TN, USA
| | - Tayebeh Pourmotabbed
- Department of Microbiology, Immunology and Biochemistry, University of Tennessee Health Science Center, Memphis, TN, USA
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Li Y, Chen S, Rahimizadeh K, Zhang Z, Veedu RN. Inhibition of survivin by 2'- O-methyl phosphorothioate-modified steric-blocking antisense oligonucleotides. RSC Adv 2024; 14:13336-13341. [PMID: 38660533 PMCID: PMC11040434 DOI: 10.1039/d4ra01925c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2024] [Accepted: 04/15/2024] [Indexed: 04/26/2024] Open
Abstract
Chemically modified antisense oligonucleotide (ASO) has been established as a successful therapeutic strategy for treating various human diseases. To date, ten ASO drugs, which are capable of either inducing mRNA degradation via RNase H recruitment (fomivirsen, mipomersen, inotersen, volanesorsen and tofersen) or splice modulation (eteplirsen, nusinersen, golodirsen, viltolarsen and casimersen), have been approved by the regulatory agencies for market entry. Nonetheless, none of these approved drugs are prescribed as cancer therapy. Towards this, we have developed steric-blocking ASOs targeting BIRC5 - a well-validated oncogene. Initial screening was performed by transfection of HepG2 cells with seven BIRC5 exon-2 targeting, uniformly 2'-OMe-PS modified ASOs at 400 nM respectively, leading to the identification of two best-performing candidates ASO-2 and ASO-7 in reducing the production of BIRC5 mRNA. Subsequent dose-response assay was conducted via transfection of HepG2 cells by different concentrations (400, 200, 100, 50, 25 nM) of ASO-2 and ASO-7 respectively, showing that both ASOs consistently and efficiently inhibited BIRC5 mRNA expression in a dose-dependent manner. Furthermore, western blot analysis confirmed that ASO-7 could significantly repress survivin production on protein level. Based on our preliminary results, we believe that ASO-7 could be a useful BIRC5 inhibitor for both research purpose and therapeutic development.
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Affiliation(s)
- Yalin Li
- School of Food and Biological Engineering, Henan University of Animal Husbandry and Economy Zhengzhou 450018 China
| | - Suxiang Chen
- Centre for Molecular Medicine and Innovative Therapeutics, Health Futures Institute, Murdoch University Murdoch 6150 Australia
- Precision Nucleic Acid Therapeutics, Perron Institute for Neurological and Translational Science Nedlands WA 6009 Australia
| | - Kamal Rahimizadeh
- Centre for Molecular Medicine and Innovative Therapeutics, Health Futures Institute, Murdoch University Murdoch 6150 Australia
- Precision Nucleic Acid Therapeutics, Perron Institute for Neurological and Translational Science Nedlands WA 6009 Australia
| | - Zhen Zhang
- School of Food and Biological Engineering, Henan University of Animal Husbandry and Economy Zhengzhou 450018 China
| | - Rakesh N Veedu
- Centre for Molecular Medicine and Innovative Therapeutics, Health Futures Institute, Murdoch University Murdoch 6150 Australia
- Precision Nucleic Acid Therapeutics, Perron Institute for Neurological and Translational Science Nedlands WA 6009 Australia
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Vemula P, Schoch KM, Miller TM. Evaluating the efficacy of purchased antisense oligonucleotides to reduce mouse and human tau in vivo. Front Mol Neurosci 2023; 16:1320182. [PMID: 38192302 PMCID: PMC10773814 DOI: 10.3389/fnmol.2023.1320182] [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: 10/12/2023] [Accepted: 11/23/2023] [Indexed: 01/10/2024] Open
Abstract
Many preclinical and clinical studies support the use of antisense oligonucleotides (ASOs) as effective therapeutic strategies. However, acquiring ASOs for research purposes may be limited by partnerships with the pharmaceutical companies. Our lab previously developed an effective ASO strategy to lower human tau and reverse pathology in aged tauopathy model mice. Testing the efficacy of purchased tau lowering ASOs would provide support for these reagents as broad research tools. Purchased mouse and human tau lowering ASOs were infused or injected intracerebroventricularly into wildtype and tau transgenic mice. Following treatment, brain tissue evaluated for ASO distribution and levels of tau mRNA, protein, and phosphorylated tau. We show that purchased ASOs enter cell types of the brain and effectively decrease mouse or human tau mRNA and protein levels. Human tau lowering ASO treatment in PS19 mice decreased phosphorylated tau and gliosis relative to saline-treated PS19 mice, consistent with our previous study using a non-commercial tau lowering ASO. The results of this study demonstrate the efficacy of purchased tau targeting ASOs in vivo to support their broad use by researchers.
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Affiliation(s)
- Pranav Vemula
- Department of Neurology, Hope Center for Neurological Disorders, Washington University in St. Louis School of Medicine, St. Louis, MO, United States
| | - Kathleen M Schoch
- Department of Neurology, Hope Center for Neurological Disorders, Washington University in St. Louis School of Medicine, St. Louis, MO, United States
| | - Timothy M Miller
- Department of Neurology, Hope Center for Neurological Disorders, Washington University in St. Louis School of Medicine, St. Louis, MO, United States
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Balachandran AA, Raguraman P, Rahimizadeh K, Veedu RN. Splice-Switching Antisense Oligonucleotides Targeting Extra- and Intracellular Domains of Epidermal Growth Factor Receptor in Cancer Cells. Biomedicines 2023; 11:3299. [PMID: 38137520 PMCID: PMC10741442 DOI: 10.3390/biomedicines11123299] [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: 10/27/2023] [Revised: 11/29/2023] [Accepted: 12/07/2023] [Indexed: 12/24/2023] Open
Abstract
Cancer is one of the leading causes of death globally. Epidermal growth factor receptor is one of the proteins involved in cancer cell proliferation, differentiation, and invasion. Antisense oligonucleotides are chemical nucleic acids that bind to target messenger ribonucleic acid and modulate its expression. Herein, we demonstrate the efficacy of splice-modulating antisense oligonucleotides to target specific exons in the extracellular (exon 3) and intracellular (exon 18, 21) domains of epidermal growth factor receptor. These antisense oligonucleotides were synthesized as 25mer 2'-O methyl phosphorothioate-modified ribonucleic acids that bind to complementary specific regions in respective exons. We found that PNAT524, PNAT525, PNAT576, and PNAT578 effectively skipped exon 3, exon 18, and exon 21 in glioblastoma, liver cancer, and breast cancer cell lines. PNAT578 treatment also skipped partial exon 19, complete exon 20, and partial exon 21 in addition to complete exon 21 skipping. We also found that a cocktail of PNAT576 and PNAT578 antisense oligonucleotides performed better than their individual counterparts. The migration potential of glioblastoma cancer cells was reduced to a greater extent after treatment with these antisense oligonucleotides. We firmly believe that using these splice-modulating antisense oligonucleotides in combination with existing EGFR-targeted therapies could improve therapeutic outcomes.
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Affiliation(s)
- Akilandeswari Ashwini Balachandran
- Centre for Molecular Medicine and Innovative Therapeutics, Murdoch University, Murdoch, WA 6150, Australia
- Perron Institute for Neurological and Translational Science, Perth, WA 6009, Australia
| | - Prithi Raguraman
- Centre for Molecular Medicine and Innovative Therapeutics, Murdoch University, Murdoch, WA 6150, Australia
- Perron Institute for Neurological and Translational Science, Perth, WA 6009, Australia
| | - Kamal Rahimizadeh
- Centre for Molecular Medicine and Innovative Therapeutics, Murdoch University, Murdoch, WA 6150, Australia
- Perron Institute for Neurological and Translational Science, Perth, WA 6009, Australia
| | - Rakesh N. Veedu
- Centre for Molecular Medicine and Innovative Therapeutics, Murdoch University, Murdoch, WA 6150, Australia
- Perron Institute for Neurological and Translational Science, Perth, WA 6009, Australia
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Mohammed MR, El-Bahkery AM, Shedid SM. The Influence of Different γ-Irradiation Patterns on Factors that May Affect Cell Cycle Progression in Male Rats. Dose Response 2022; 20:15593258221117898. [PMID: 35982824 PMCID: PMC9379971 DOI: 10.1177/15593258221117898] [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: 11/16/2022]
Abstract
Most studies of the biological effects of ionizing radiation have been done on a
single acute dose, while clinically and environmentally exposures occur under
chronic/repetitive conditions. It is important to study effects of different
patterns of ionizing radiation. In this study, a rat model was used to compare
the effects of repetitive and acute exposure. Groups: (I) control, (II, III)
were exposed to fractionated doses (1.5 GyX4) and (2 GyX4), respectively/24h
interval, and (IV, V) were exposed to 6 Gy and 8 Gy of whole-body gamma
irradiation, respectively. The gene expression of MAPT and tau phosphorylation
increased in all irradiated groups but the gene expression of PKN not affected.
TGFβ% increased at dose of 2 GyX4 only. In addition, the cell cycle was arrested
in S phase. Micronucleus (MN) increased and cell proliferation decreased. In
conclusion, the dose and pattern of ionizing radiation do not affect the MAPT
and PKN gene expression, but TGF-β, p-tau, MN assay and cell proliferation are
significantly affected. The dose of 2 GyX4 showed distinctive effect. Repetitive
exposure may increase TGF-β%, which causes radio-resistance and, G2/M delay.
Thus, the cell cycle could be regulated in a different manner according to the
dose and pattern of irradiation.
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Zhang Y, Wu KM, Yang L, Dong Q, Yu JT. Tauopathies: new perspectives and challenges. Mol Neurodegener 2022; 17:28. [PMID: 35392986 PMCID: PMC8991707 DOI: 10.1186/s13024-022-00533-z] [Citation(s) in RCA: 91] [Impact Index Per Article: 45.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2021] [Accepted: 03/23/2022] [Indexed: 12/13/2022] Open
Abstract
BACKGROUND Tauopathies are a class of neurodegenerative disorders characterized by neuronal and/or glial tau-positive inclusions. MAIN BODY Clinically, tauopathies can present with a range of phenotypes that include cognitive/behavioral-disorders, movement disorders, language disorders and non-specific amnestic symptoms in advanced age. Pathologically, tauopathies can be classified based on the predominant tau isoforms that are present in the inclusion bodies (i.e., 3R, 4R or equal 3R:4R ratio). Imaging, cerebrospinal fluid (CSF) and blood-based tau biomarkers have the potential to be used as a routine diagnostic strategy and in the evaluation of patients with tauopathies. As tauopathies are strongly linked neuropathologically and genetically to tau protein abnormalities, there is a growing interest in pursuing of tau-directed therapeutics for the disorders. Here we synthesize emerging lessons on tauopathies from clinical, pathological, genetic, and experimental studies toward a unified concept of these disorders that may accelerate the therapeutics. CONCLUSIONS Since tauopathies are still untreatable diseases, efforts have been made to depict clinical and pathological characteristics, identify biomarkers, elucidate underlying pathogenesis to achieve early diagnosis and develop disease-modifying therapies.
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Affiliation(s)
- Yi Zhang
- Department of Neurology and Institute of Neurology, Huashan Hospital, State Key Laboratory of Medical Neurobiology and MOE Frontiers Center for Brain Science, Shanghai Medical College, Fudan University, National Center for Neurological Disorders, 12th Wulumuqi Zhong Road, Shanghai, 200040 China
| | - Kai-Min Wu
- Department of Neurology and Institute of Neurology, Huashan Hospital, State Key Laboratory of Medical Neurobiology and MOE Frontiers Center for Brain Science, Shanghai Medical College, Fudan University, National Center for Neurological Disorders, 12th Wulumuqi Zhong Road, Shanghai, 200040 China
| | - Liu Yang
- Department of Neurology and Institute of Neurology, Huashan Hospital, State Key Laboratory of Medical Neurobiology and MOE Frontiers Center for Brain Science, Shanghai Medical College, Fudan University, National Center for Neurological Disorders, 12th Wulumuqi Zhong Road, Shanghai, 200040 China
| | - Qiang Dong
- Department of Neurology and Institute of Neurology, Huashan Hospital, State Key Laboratory of Medical Neurobiology and MOE Frontiers Center for Brain Science, Shanghai Medical College, Fudan University, National Center for Neurological Disorders, 12th Wulumuqi Zhong Road, Shanghai, 200040 China
| | - Jin-Tai Yu
- Department of Neurology and Institute of Neurology, Huashan Hospital, State Key Laboratory of Medical Neurobiology and MOE Frontiers Center for Brain Science, Shanghai Medical College, Fudan University, National Center for Neurological Disorders, 12th Wulumuqi Zhong Road, Shanghai, 200040 China
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Eldamaty HS, Elbasiouny H, Elmoslemany AM, Abd El-Maoula LM, El-Desoky OI, Rehan M, Abd El Moneim D, Zedan A. Protective Effect of Wheat and Barley Grass Against the Acute Toxicological Effects of the Concurrent Administration of Excessive Heavy Metals in Drinking Water on the Rats Liver and Brain. APPLIED SCIENCES 2021; 11:5059. [DOI: 10.3390/app11115059] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/01/2023]
Abstract
Heavy metal contaminated water is a great concern because of its high toxiciy, non-biodegradability, and bioaccumulation. Therefore, non-contaminated water is fundamental for a healthy life. Special attention is paid to the health-promoting ingredients of germinated whole cereal products. This study aimed to (1) examine the potentially harmful effects of Cu, Mn, and Zn on rat livers and brains, and (2) the potentially protective action of wheat and barley grasses against the expected harmful effects of these metals. The rats were treated with water contaminated by heavy metals (HMs) and germinated wheat and barley for 60 days. The rat liver functions and histopathological examinations were analyzed. Comet assay was evaluated to assess the damage in the DNA of rat livers and brains. The results indicated a significant alteration in liver functions in rats exposed to HMs; however, wheat and barley grasses at high doses decreased the harmful effects. An insignificant difference was noticed in total protein, albumin, and globulin of rats treated with HMs compared with the control. A significant increase in the serum and liver levels of HMs was recorded; however, they were reduced by wheat and barley grasses. Rat livers treated with HMs exhibited severe histological effects. The groups treated with wheat and barley grasses showed a normal liver architecture. A significant increase in DNA damage in the livers and brains was observed in rats treated with HMs, which was reduced when treated with wheat and barley grasses. Thus, using germinated seeds is promising to avoid damaging of HMs.
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Forloni G. Alzheimer's disease: from basic science to precision medicine approach. BMJ Neurol Open 2020; 2:e000079. [PMID: 33681801 PMCID: PMC7903168 DOI: 10.1136/bmjno-2020-000079] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2020] [Revised: 08/24/2020] [Accepted: 10/16/2020] [Indexed: 12/14/2022] Open
Abstract
Alzheimer’s disease (AD) is the most common form of dementia in the elderly. Together with cerebral amyloid accumulation, several factors contribute to AD pathology including vascular alterations, systemic inflammation, genetic/epigenetic status and mitochondrial dysfunction. Much is now being devoted to neuroinflammation. However, anti-inflammatory drugs as numerous other therapies, mainly targeted on β-amyloid, have failed to show efficacious effects in AD. Timing, proper selection of patients, and the need for a multitarget approach appear to be the main weak points of current therapeutic efforts. The efficacy of a treatment could be better evaluate if efficient biomarkers are available. We propose here the application of precision medicine principles in AD to simultaneously verify the efficacy of a treatment and the reliability of specific biomarkers according to individually tailored biomarker-guided targeted therapies. People at risk of developing AD or in the very early phase of the disease should be stratified according to: (1) neuropsychological tests; (2) apolipoprotein E (ApoE) genotyping; (3) biochemical analysis of plasma and cerebrospinal fluid (CSF); (4) MRI and positron emission tomography and (5) assessment of their inflammatory profile by an integration of various genetic and biochemical parameters in plasma, CSF and an analysis of microbiota composition. The selected population should be treated with antiamyloidogenic and anti-inflammatory drugs in randomised, longitudinal, placebo-controlled studies using ad hoc profiles (eg, vascular profile, mitochondrial profile, etc…) If these criteria are adopted widely and the results shared, it may be possible to rapidly develop innovative and personalised drug treatment protocols with more realistic chances of being efficacious.
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Affiliation(s)
- Gianluigi Forloni
- Neuroscience, Istituto di Ricerche Farmacologiche Mario Negri, Milano, Lombardia, Italy
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