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Wan T, Fu C, Peng J, Lu J, Li P, Zhuo J. Repairing the in situ hybridization missing data in the hippocampus region by using a 3D residual U-Net model. BIOMEDICAL OPTICS EXPRESS 2024; 15:3541-3554. [PMID: 38867784 PMCID: PMC11166418 DOI: 10.1364/boe.522078] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/21/2024] [Revised: 03/31/2024] [Accepted: 04/22/2024] [Indexed: 06/14/2024]
Abstract
The hippocampus is a critical brain region. Transcriptome data provides valuable insights into the structure and function of the hippocampus at the gene level. However, transcriptome data is often incomplete. To address this issue, we use the convolutional neural network model to repair the missing voxels in the hippocampus region, based on Allen institute coronal slices in situ hybridization (ISH) dataset. Moreover, we analyze the gene expression correlation between coronal and sagittal dataset in the hippocampus region. The results demonstrated that the trend of gene expression correlation between the coronal and sagittal datasets remained consistent following the repair of missing data in the coronal ISH dataset. In the last, we use repaired ISH dataset to identify novel genes specific to hippocampal subregions. Our findings demonstrate the accuracy and effectiveness of using deep learning method to repair ISH missing data. After being repaired, ISH has the potential to improve our comprehension of the hippocampus's structure and function.
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Affiliation(s)
- Tong Wan
- State Key Laboratory of Digital Medical Engineering, School of Biomedical Engineering, Hainan University, Sanya 572025, China
- Key Laboratory of Biomedical Engineering of Hainan Province, One Health Institute, Hainan University, Sanya 572025, China
| | - Changping Fu
- State Key Laboratory of Digital Medical Engineering, School of Biomedical Engineering, Hainan University, Sanya 572025, China
- Key Laboratory of Biomedical Engineering of Hainan Province, One Health Institute, Hainan University, Sanya 572025, China
| | - Jiinbo Peng
- State Key Laboratory of Digital Medical Engineering, School of Biomedical Engineering, Hainan University, Sanya 572025, China
- Key Laboratory of Biomedical Engineering of Hainan Province, One Health Institute, Hainan University, Sanya 572025, China
| | - Jinling Lu
- State Key Laboratory of Digital Medical Engineering, School of Biomedical Engineering, Hainan University, Sanya 572025, China
- Key Laboratory of Biomedical Engineering of Hainan Province, One Health Institute, Hainan University, Sanya 572025, China
- Britton Chance Center for Biomedical Photonics and MoE Key Laboratory for Biomedical Photonics, Wuhan National Laboratory for Optoelectronics-Huazhong University of Science and Technology, Wuhan, Hubei 430074, China
- Research Unit of Multimodal Cross Scale Neural Signal Detection and Imaging, Chinese Academy of Medical Science, HUST-Suzhou Institute for Brainsmatics, JITRI, Suzhou 215100, China
| | - Pengcheng Li
- State Key Laboratory of Digital Medical Engineering, School of Biomedical Engineering, Hainan University, Sanya 572025, China
- Key Laboratory of Biomedical Engineering of Hainan Province, One Health Institute, Hainan University, Sanya 572025, China
- Britton Chance Center for Biomedical Photonics and MoE Key Laboratory for Biomedical Photonics, Wuhan National Laboratory for Optoelectronics-Huazhong University of Science and Technology, Wuhan, Hubei 430074, China
- Research Unit of Multimodal Cross Scale Neural Signal Detection and Imaging, Chinese Academy of Medical Science, HUST-Suzhou Institute for Brainsmatics, JITRI, Suzhou 215100, China
| | - JunJie Zhuo
- State Key Laboratory of Digital Medical Engineering, School of Biomedical Engineering, Hainan University, Sanya 572025, China
- Key Laboratory of Biomedical Engineering of Hainan Province, One Health Institute, Hainan University, Sanya 572025, China
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Lan F, Roquet D, Dalton MA, El-Omar H, Ahmed RM, Piguet O, Irish M. Exploring graded profiles of hippocampal atrophy along the anterior-posterior axis in semantic dementia and Alzheimer's disease. Neurobiol Aging 2024; 135:70-78. [PMID: 38232501 DOI: 10.1016/j.neurobiolaging.2024.01.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2023] [Revised: 01/07/2024] [Accepted: 01/09/2024] [Indexed: 01/19/2024]
Abstract
Mounting evidence indicates marked hippocampal degeneration in semantic dementia (SD) however, the spatial distribution of hippocampal atrophy profiles in this syndrome remains unclear. Using a recently developed parcellation approach, we extracted hippocampal volumes from four distinct subregions running from anterior to posterior along the longitudinal axis (anterior, intermediate rostral, intermediate caudal, and posterior). Volumetric differences in hippocampal subregions were compared between 21 SD, 24 matched Alzheimer's disease (AD), and 27 healthy older Control participants. Despite comparable overall hippocampal volume loss, SD and AD groups diverged in terms of the magnitude of atrophy along the anterior-posterior axis of the hippocampus. Global hippocampal atrophy was observed in AD, with no discernible gradation or lateralisation. In contrast, SD patients displayed graded bilateral hippocampal atrophy, most pronounced on the left-hand side, and concentrated in anterior relative to posterior subregions. Finally, we found preliminary evidence that disease-specific vulnerability along the anterior-posterior axis of the hippocampus was associated with canonical clinical features of these syndromes.
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Affiliation(s)
- Fang Lan
- The University of Sydney, Brain and Mind Centre, Sydney, New South Wales, Australia; The University of Sydney, School of Psychology, Sydney, New South Wales, Australia
| | - Daniel Roquet
- The University of Sydney, Brain and Mind Centre, Sydney, New South Wales, Australia; The University of Sydney, School of Psychology, Sydney, New South Wales, Australia
| | - Marshall A Dalton
- The University of Sydney, Brain and Mind Centre, Sydney, New South Wales, Australia; The University of Sydney, School of Psychology, Sydney, New South Wales, Australia
| | - Hashim El-Omar
- The University of Sydney, Brain and Mind Centre, Sydney, New South Wales, Australia
| | - Rebekah M Ahmed
- The University of Sydney, Brain and Mind Centre, Sydney, New South Wales, Australia; Memory and Cognition Clinic, Department of Clinical Neurosciences, Royal Prince Alfred Hospital, Sydney, New South Wales, Australia
| | - Olivier Piguet
- The University of Sydney, Brain and Mind Centre, Sydney, New South Wales, Australia; The University of Sydney, School of Psychology, Sydney, New South Wales, Australia
| | - Muireann Irish
- The University of Sydney, Brain and Mind Centre, Sydney, New South Wales, Australia; The University of Sydney, School of Psychology, Sydney, New South Wales, Australia.
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