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Xu K, Yang Y, Ding J, Wang J, Fang Y, Tian H. Spatially Precise Genetic Engineering at the Electrode-Tissue Interface. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2024:e2401327. [PMID: 38692704 DOI: 10.1002/adma.202401327] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/25/2024] [Revised: 04/17/2024] [Indexed: 05/03/2024]
Abstract
The interface between electrodes and neural tissues plays a pivotal role in determining the efficacy and fidelity of neural activity recording and modulation. While considerable efforts have been made to improve the electrode-tissue interface, the majority of studies have primarily concentrated on the development of biocompatible neural electrodes through abiotic materials and structural engineering. In this study, an approach is presented that seamlessly integrates abiotic and biotic engineering principles into the electrode-tissue interface. Specifically, ultraflexible neural electrodes with short hairpin RNAs (shRNAs) designed to silence the expression of endogenous genes within neural tissues are combined. The system facilitates shRNA-mediated knockdown of phosphatase and tensin homolog deleted on chromosome 10 (PTEN) and polypyrimidine tract-binding protein 1 (PTBP1), two essential genes associated in neural survival/growth and neurogenesis, within specific cell populations located at the electrode-tissue interface. Additionally, it is demonstrated that the downregulation of PTEN in neurons can result in an enlargement of neuronal cell bodies at the electrode-tissue interface. Furthermore, the system enables long-term monitoring of neuronal activities following PTEN knockdown in a mouse model of Parkinson's disease and traumatic brain injury. The system provides a versatile approach for genetically engineering the electrode-tissue interface with unparalleled precision, paving the way for the development of regenerative electronics and next-generation brain-machine interfaces.
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Affiliation(s)
- Ke Xu
- CAS Center for Excellence in Nanoscience, National Center for Nanoscience and Technology, Beijing, 100190, China
- CAS Center for Excellence in Brain Science and Intelligence Technology, Institute of Neuroscience, Chinese Academy of Sciences, Shanghai, 200031, China
- School of Nanoscience and Engineering, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Yinan Yang
- CAS Center for Excellence in Nanoscience, National Center for Nanoscience and Technology, Beijing, 100190, China
- CAS Center for Excellence in Brain Science and Intelligence Technology, Institute of Neuroscience, Chinese Academy of Sciences, Shanghai, 200031, China
- School of Nanoscience and Engineering, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Jianfei Ding
- CAS Center for Excellence in Nanoscience, National Center for Nanoscience and Technology, Beijing, 100190, China
| | - Jinfen Wang
- CAS Center for Excellence in Nanoscience, National Center for Nanoscience and Technology, Beijing, 100190, China
- Chinese Institute for Brain Research, Beijing, 102206, China
| | - Ying Fang
- CAS Center for Excellence in Nanoscience, National Center for Nanoscience and Technology, Beijing, 100190, China
- CAS Center for Excellence in Brain Science and Intelligence Technology, Institute of Neuroscience, Chinese Academy of Sciences, Shanghai, 200031, China
- School of Nanoscience and Engineering, University of Chinese Academy of Sciences, Beijing, 100049, China
- Chinese Institute for Brain Research, Beijing, 102206, China
| | - Huihui Tian
- CAS Center for Excellence in Nanoscience, National Center for Nanoscience and Technology, Beijing, 100190, China
- Chinese Institute for Brain Research, Beijing, 102206, China
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Riggins TE, Whitsitt QA, Saxena A, Hunter E, Hunt B, Thompson CH, Moore MG, Purcell EK. Gene Expression Changes in Cultured Reactive Rat Astrocyte Models and Comparison to Device-Associated Effects in the Brain. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.01.06.522870. [PMID: 36712012 PMCID: PMC9881929 DOI: 10.1101/2023.01.06.522870] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
Implanted microelectrode arrays hold immense therapeutic potential for many neurodegenerative diseases. However, a foreign body response limits long-term device performance. Recent literature supports the role of astrocytes in the response to damage to the central nervous system (CNS) and suggests that reactive astrocytes exist on a spectrum of phenotypes, from beneficial to neurotoxic. The goal of our study was to gain insight into the subtypes of reactive astrocytes responding to electrodes implanted in the brain. In this study, we tested the transcriptomic profile of two reactive astrocyte culture models (cytokine cocktail or lipopolysaccharide, LPS) utilizing RNA sequencing, which we then compared to differential gene expression surrounding devices inserted into rat motor cortex via spatial transcriptomics. We interpreted changes in the genetic expression of the culture models to that of 24 hour, 1 week and 6 week rat tissue samples at multiple distances radiating from the injury site. We found overlapping expression of up to ∼250 genes between in vitro models and in vivo effects, depending on duration of implantation. Cytokine-induced cells shared more genes in common with chronically implanted tissue (≥1 week) in comparison to LPS-exposed cells. We revealed localized expression of a subset of these intersecting genes (e.g., Serping1, Chi3l1, and Cyp7b1) in regions of device-encapsulating, glial fibrillary acidic protein (GFAP)-expressing astrocytes identified with immunohistochemistry. We applied a factorization approach to assess the strength of the relationship between reactivity markers and the spatial distribution of GFAP-expressing astrocytes in vivo . We also provide lists of hundreds of differentially expressed genes between reactive culture models and untreated controls, and we observed 311 shared genes between the cytokine induced model and the LPS-reaction induced control model. Our results show that comparisons of reactive astrocyte culture models with spatial transcriptomics data can reveal new biomarkers of the foreign body response to implantable neurotechnology. These comparisons also provide a strategy to assess the development of in vitro models of the tissue response to implanted electrodes.
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Moore MG, Thompson CH, Reimers MA, Purcell EK. Differential Co-Expression Analysis of RNA-Seq Data Reveals Novel Potential Biomarkers of Device-Tissue Interaction. ANNUAL INTERNATIONAL CONFERENCE OF THE IEEE ENGINEERING IN MEDICINE AND BIOLOGY SOCIETY. IEEE ENGINEERING IN MEDICINE AND BIOLOGY SOCIETY. ANNUAL INTERNATIONAL CONFERENCE 2022; 2022:3072-3076. [PMID: 36085767 PMCID: PMC9724584 DOI: 10.1109/embc48229.2022.9871437] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/15/2023]
Abstract
The biological response to electrodes implanted in the brain has been a long-standing barrier to achieving a stable tissue device-interface. Understanding the mechanisms underlying this response could explain phenomena including recording instability and loss, shifting stimulation thresholds, off-target effects of neuromodulation, and stimulation-induced depression of neural excitability. Our prior work detected differential expression in hundreds of genes following device implantation. Here, we extend upon that work by providing new analyses using differential co-expression analysis, which identifies changes in the correlation structure between groups of genes detected at the interface in comparison to control tissues. We used an "eigengene" approach to identify hub genes associated with each module. Our work adds to a growing body of literature which applies new techniques in molecular biology and computational analysis to long-standing issues surrounding electrode integration with the brain.
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Shi D, Dhawan V, Cui XT. Bio-integrative design of the neural tissue-device interface. Curr Opin Biotechnol 2021; 72:54-61. [PMID: 34710753 PMCID: PMC8671324 DOI: 10.1016/j.copbio.2021.10.003] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2021] [Revised: 09/19/2021] [Accepted: 10/06/2021] [Indexed: 10/20/2022]
Abstract
Neural implants enable bidirectional communications with nervous tissue and have demonstrated tremendous potential in research and clinical applications. To obtain high fidelity and stable information exchange, we need to minimize the undesired host responses and achieve intimate neuron-device interaction. This paper highlights the key bio-integrative strategies aimed at seamless integration through intelligent device designs to minimize the immune responses, as well as incorporate bioactive elements to actively modulate cellular reactions. These approaches span from surface modification and bioactive agent delivery, to biomorphic and biohybrid designs. Many of these strategies have shown effectiveness in functional outcome measures, others are exploratory but with fascinating potentials. The combination of bio-integrative strategies may synergistically promote the next generation of neural interfaces.
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Affiliation(s)
- Delin Shi
- Department of Bioengineering, University of Pittsburgh, Pittsburgh, PA, United States; Center for Neural Basis of Cognition, Pittsburgh, PA, United States
| | - Vaishnavi Dhawan
- Department of Bioengineering, University of Pittsburgh, Pittsburgh, PA, United States; Center for Neural Basis of Cognition, Pittsburgh, PA, United States
| | - Xinyan Tracy Cui
- Department of Bioengineering, University of Pittsburgh, Pittsburgh, PA, United States; Center for Neural Basis of Cognition, Pittsburgh, PA, United States; McGowan Institute for Regenerative Medicine, Pittsburgh, PA, United States.
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Zou L, Tian H, Guan S, Ding J, Gao L, Wang J, Fang Y. Self-assembled multifunctional neural probes for precise integration of optogenetics and electrophysiology. Nat Commun 2021; 12:5871. [PMID: 34620851 PMCID: PMC8497603 DOI: 10.1038/s41467-021-26168-0] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2020] [Accepted: 09/17/2021] [Indexed: 11/12/2022] Open
Abstract
Optogenetics combined with electrical recording has emerged as a powerful tool for investigating causal relationships between neural circuit activity and function. However, the size of optogenetically manipulated tissue is typically 1-2 orders of magnitude larger than that can be electrically recorded, rendering difficulty for assigning functional roles of recorded neurons. Here we report a viral vector-delivery optrode (VVD-optrode) system for precise integration of optogenetics and electrophysiology in the brain. Our system consists of flexible microelectrode filaments and fiber optics that are simultaneously self-assembled in a nanoliter-scale, viral vector-delivery polymer carrier. The highly localized delivery and neuronal expression of opsin genes at microelectrode-tissue interfaces ensure high spatial congruence between optogenetically manipulated and electrically recorded neuronal populations. We demonstrate that this multifunctional system is capable of optogenetic manipulation and electrical recording of spatially defined neuronal populations for three months, allowing precise and long-term studies of neural circuit functions. The authors present a viral vector-delivery optrode system to integrate optogenetics and electrophysiology. The flexible microelectrode filaments and fiber optics self-assemble in a nanoliter-scale, viral vector-delivery polymer carrier for localized delivery and expression of opsin genes at microelectrode-tissue interfaces.
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Affiliation(s)
- Liang Zou
- CAS Center for Excellence in Nanoscience, National Center for Nanoscience and Technology, Beijing, 100190, China.,CAS Center for Excellence in Brain Science and Intelligence Technology, Institute of Neuroscience, Chinese Academy of Sciences, Shanghai, 200031, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Huihui Tian
- CAS Center for Excellence in Nanoscience, National Center for Nanoscience and Technology, Beijing, 100190, China
| | - Shouliang Guan
- CAS Center for Excellence in Nanoscience, National Center for Nanoscience and Technology, Beijing, 100190, China.,CAS Center for Excellence in Brain Science and Intelligence Technology, Institute of Neuroscience, Chinese Academy of Sciences, Shanghai, 200031, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Jianfei Ding
- CAS Center for Excellence in Nanoscience, National Center for Nanoscience and Technology, Beijing, 100190, China
| | - Lei Gao
- CAS Center for Excellence in Nanoscience, National Center for Nanoscience and Technology, Beijing, 100190, China.,CAS Center for Excellence in Brain Science and Intelligence Technology, Institute of Neuroscience, Chinese Academy of Sciences, Shanghai, 200031, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Jinfen Wang
- CAS Center for Excellence in Nanoscience, National Center for Nanoscience and Technology, Beijing, 100190, China
| | - Ying Fang
- CAS Center for Excellence in Nanoscience, National Center for Nanoscience and Technology, Beijing, 100190, China. .,CAS Center for Excellence in Brain Science and Intelligence Technology, Institute of Neuroscience, Chinese Academy of Sciences, Shanghai, 200031, China. .,University of Chinese Academy of Sciences, Beijing, 100049, China.
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Intracortical Microelectrode Array Unit Yield under Chronic Conditions: A Comparative Evaluation. MICROMACHINES 2021; 12:mi12080972. [PMID: 34442594 PMCID: PMC8400387 DOI: 10.3390/mi12080972] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/21/2021] [Revised: 08/10/2021] [Accepted: 08/12/2021] [Indexed: 01/01/2023]
Abstract
While microelectrode arrays (MEAs) offer the promise of elucidating functional neural circuitry and serve as the basis for a cortical neuroprosthesis, the challenge of designing and demonstrating chronically reliable technology remains. Numerous studies report “chronic” data but the actual time spans and performance measures corresponding to the experimental work vary. In this study, we reviewed the experimental durations that constitute chronic studies across a range of MEA types and animal species to gain an understanding of the widespread variability in reported study duration. For rodents, which are the most commonly used animal model in chronic studies, we examined active electrode yield (AEY) for different array types as a means to contextualize the study duration variance, as well as investigate and interpret the performance of custom devices in comparison to conventional MEAs. We observed wide-spread variance within species for the chronic implantation period and an AEY that decayed linearly in rodent models that implanted commercially-available devices. These observations provide a benchmark for comparing the performance of new technologies and highlight the need for consistency in chronic MEA studies. Additionally, to fully derive performance under chronic conditions, the duration of abiotic failure modes, biological processes induced by indwelling probes, and intended application of the device are key determinants.
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Pancrazio JJ, Cogan SF. Editorial for the Special Issue on Neural Electrodes: Design and Applications. MICROMACHINES 2019; 10:mi10070466. [PMID: 31336980 PMCID: PMC6680485 DOI: 10.3390/mi10070466] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 07/09/2019] [Accepted: 07/09/2019] [Indexed: 12/14/2022]
Affiliation(s)
- Joseph J Pancrazio
- Department of Bioengineering, The University of Texas at Dallas, 800 W. Campbell Road, BSB 13.633, Richardson, TX 75080, USA.
| | - Stuart F Cogan
- Department of Bioengineering, The University of Texas at Dallas, 800 W. Campbell Road, BSB 13.633, Richardson, TX 75080, USA.
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Cabrera L, Sadle C, Purcell E. Neuroethical considerations of high-density electrode arrays. Nat Biomed Eng 2019; 3:586-589. [DOI: 10.1038/s41551-019-0407-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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