Mapping of the Developmental Atlas of the Visual System and Research on Embryonic Neurogenesis Phenomena

This research studies how nerve cells in the human embryonic retina, visual brain regions, and brain areas responsible for higher cognitive functions grow, develop, and form interconnected functional networks.

Eye tissue, visual brain tissue, and other brain tissue linked to advanced cognitive functions will be collected from embryos whose pregnancies were terminated due to medical conditions or illnesses. High-throughput single-cell and single-nucleus sequencing will be utilized to map gene activity patterns and developmental growth pathways of retinal nerve cells.

Multiple testing tools will be combined to analyze these brain and retinal cells: Patch-seq (single-cell patch-clamp sequencing), high-density microelectrode arrays (MEA), and two-photon calcium imaging. With these tools, systematic measurements will be performed on the electrical activity, physical shape, synaptic connection patterns, and signal coding functions of neurons in the retina and visual brain regions. Multi-modal tissue maps and a public database will be constructed to store all collected research data.

Immunofluorescence staining will also be applied to compare structural differences and nerve fiber connections between visual brain regions and higher cognitive brain areas. The regenerative capacity and neuron formation process of embryonic brain stem cells, as well as the migration paths of developing neurons, will be tracked.

Overall, this study aims to fully uncover the neural foundation of visual signal processing, and identify the molecular regulatory networks that control nerve tissue development during the embryonic stage.

Study Overview

• Status: Recruiting
• Conditions: Neural Development; Embryonic Development; Retinal Anomalies
• Intervention / Treatment: Other: Tissue collection and multi-omics sequencing analysis

• Study Type: Observational
• Enrollment (Estimated): 200

Contacts and Locations

• Study Contact: Name: Sheng Liu, Doctor; Phone Number: 13622284795; Email: liush87@mail.sysu.edu.cn
• Study Contact Backup: Name: Jing Su; Phone Number: 15999937669; Email: sujing@gzzoc.com

Study Locations

• China
  • Guangdong
    • Guangzhou, Guangdong, China, 510060
      • Recruiting
      • Zhongshan Ophthalmic Center, Sun Yat-sen University
      • Contact: Sheng Liu; Phone Number: 13622284795; Email: liush87@mail.sysu.edu.cn
      • Principal Investigator: Sheng Liu

Participation Criteria

Eligibility Criteria

• Ages Eligible for Study: Child; Adult; Older Adult
• Accepts Healthy Volunteers: Yes

• Sampling Method: Non-Probability Sample

Study Population

This study recruits pregnant patients undergoing termination of pregnancy at the Third Affiliated Hospital of Sun Yat-sen University, divided into an embryonic developmental abnormality group (Abnormal group) and a normal control group (Normal group), with a planned enrollment of 100 subjects per group. The gestational age of embryos ranges from 9 to 40 weeks. Two types of samples are included: retrospective cryopreserved specimens from the hospital biobank collected between January 2025 and January 2026 (20 cases per group, with donors having signed informed consent for specimen research use); and prospective fresh specimens collected between February 2026 and June 2027 (80 cases per group). All participants sign study-specific written informed consent.

Description

Inclusion Criteria:

• Abnormal group: Embryos with clinically confirmed embryonic developmental abnormalities requiring medical termination of pregnancy; intact retinal, visual and cognitive brain tissues available for snATAC-seq, scRNA-seq, electrophysiology, proteomics and RNAscope detection.

Normal group: Embryos confirmed free of any ocular and central nervous developmental defects by prenatal examination and anatomical observation; intact embryonic ocular and brain tissues meeting all experimental detection standards.

All sample donors have signed written informed consent authorizing the use of residual embryonic tissues for scientific research, with no monetary compensation involved.

Exclusion Criteria:

• Embryonic ocular or brain tissues with severe necrosis, structural damage or microbial contamination that cannot support multi-omics and functional experiments.

Donors who withdraw or refuse the consent for tissue research use. Samples with irregular collection, transportation or cryopreservation procedures resulting in tissue degradation and failure to meet experimental requirements.

Study Plan

How is the study designed?

Number of groups / cohorts

2

Cohorts and Interventions

Group / Cohort	Intervention / Treatment
Abnormal Group; Embryos with confirmed embryonic developmental abnormalities, gestational age 9-40 weeks, from patients receiving clinically indicated termination of pregnancy. Tissue collection and multi-omics sequencing analysis will be performed on ocular and brain tissues.	Other: Tissue collection and multi-omics sequencing analysis; This observational study collects discarded human embryonic ocular and brain tissues from patients undergoing clinically indicated termination of pregnancy, with gestational age ranging from 9 to 40 weeks. We separate retinal, visual cortex and high-order cognitive cortex tissues, then perform single-cell multi-omics sequencing including transcriptome, chromatin accessibility and proteome profiling. The data is used to explore retinal neurogenesis, neuronal developmental trajectories and multi-modal cell atlas of embryonic visual system, without any clinical intervention on participants.
Normal Group; Embryonic tissues derived from normally developing embryos with gestational age of 9 to 40 weeks, collected from pregnant women who voluntarily received clinically indicated termination of pregnancy. Ocular and brain tissues will be collected and subjected to multi-omics sequencing analysis consistent with the abnormal group.	Other: Tissue collection and multi-omics sequencing analysis; This observational study collects discarded human embryonic ocular and brain tissues from patients undergoing clinically indicated termination of pregnancy, with gestational age ranging from 9 to 40 weeks. We separate retinal, visual cortex and high-order cognitive cortex tissues, then perform single-cell multi-omics sequencing including transcriptome, chromatin accessibility and proteome profiling. The data is used to explore retinal neurogenesis, neuronal developmental trajectories and multi-modal cell atlas of embryonic visual system, without any clinical intervention on participants.

What is the study measuring?

Primary Outcome Measures

Outcome Measure	Measure Description	Time Frame
Single-cell transcriptomic atlas and developmental trajectory of embryonic retinal and visual cortical neurons	Perform single-cell RNA sequencing on human embryonic eye and brain tissues from abnormal developmental group and normal control group. Identify all cell subtypes in retina and visual-associated cognitive cortex, reconstruct continuous developmental trajectory of retinal neurogenesis and visual cortical neurons, and compare neuronal subtype distribution differences between the two groups.	Day 1 of tissue collection
Genome-wide chromatin open regions in embryonic visual tissues	Genome-wide chromatin open regions are detected via snATAC-seq on embryonic ocular and brain tissues from case and control groups.	Day 1 of tissue collection
Differential chromatin accessibility between normal and malformed embryonic visual tissues	Differential chromatin accessibility signals are identified via integrated analysis of snATAC-seq and scRNA-seq data from embryonic ocular and brain tissues.	Day 1 of tissue collection
Candidate pathogenic genes underlying embryonic visual developmental abnormalities	Genes linked to abnormal embryonic visual development are screened based on differential chromatin and transcriptomic profiles.	Day 1 of tissue collection

Secondary Outcome Measures

Outcome Measure	Measure Description	Time Frame
Action potential firing patterns of embryonic visual neurons	Action potential firing patterns are recorded via combined Patch-seq and MEA on primary cultured retinal and visual cortical neurons from case and control embryonic tissues.	Day 1 of tissue collection
Synchronous electrical activity of embryonic neuronal networks	Neuronal network synchronous electrical activity is recorded via combined Patch-seq and MEA on primary cultured retinal and visual cortical neurons from case and control embryonic tissues.	Day 1 of tissue collection
Spatial expression localization of key visual development genes detected by RNAscope	RNAscope in situ hybridization is conducted on embryonic retinal and brain tissue slices to visualize the spatial distribution and quantitative expression levels of candidate pathogenic genes screened from multi-omics data. Compare the spatial gene expression differences between normal embryonic visual tissues and tissues with ocular developmental defects.	The day 1 of embryonic tissue collection after clinical termination of pregnancy
Differentially expressed proteins identified via global proteome sequencing	Global proteome sequencing is performed on embryonic ocular and brain tissues to generate lists of differentially expressed proteins linked to retinal neurogenesis and visual cortical development.	Day 1 of tissue collection
Spatial localization and expression abundance of proteins via immunohistochemistry	Immunohistochemistry staining is applied on embryonic tissue sections to detect spatial localization and expression abundance of core differentially expressed proteins.	Day 1 of tissue collection

Collaborators and Investigators

• Sponsor: Sheng Liu
• Collaborators: Third Affiliated Hospital, Sun Yat-Sen University

Publications and helpful links

General Publications

• Huang W, Xu Q, Liu F, Su J, Xiao D, Tang L, Hao ZZ, Liu R, Xiang K, Bi Y, Miao Z, Liu X, Liu Y, Liu S. Identification of TPBG-Expressing Amacrine Cells in DAT-tdTomato Mouse. Invest Ophthalmol Vis Sci. 2022 May 2;63(5):13. doi: 10.1167/iovs.63.5.13.
• Huang W, Xu Q, Su J, Tang L, Hao ZZ, Xu C, Liu R, Shen Y, Sang X, Xu N, Tie X, Miao Z, Liu X, Xu Y, Liu F, Liu Y, Liu S. Linking transcriptomes with morphological and functional phenotypes in mammalian retinal ganglion cells. Cell Rep. 2022 Sep 13;40(11):111322. doi: 10.1016/j.celrep.2022.111322.
• Chen X, Huang Y, Huang L, Huang Z, Hao ZZ, Xu L, Xu N, Li Z, Mou Y, Ye M, You R, Zhang X, Liu S, Miao Z. A brain cell atlas integrating single-cell transcriptomes across human brain regions. Nat Med. 2024 Sep;30(9):2679-2691. doi: 10.1038/s41591-024-03150-z. Epub 2024 Aug 2.
• Wei JR, Xiao D, Tang L, Xu N, Liu R, Shen Y, Xu Z, Sang X, Ge J, Xiang M, Liu S. Neural cell isolation from adult macaques for high-throughput analyses and neurosphere cultures. Nat Protoc. 2023 Jun;18(6):1930-1957. doi: 10.1038/s41596-023-00820-z. Epub 2023 Apr 12.

Study record dates

Study Major Dates

• Study Start (Actual): January 16, 2026
• Primary Completion (Estimated): June 1, 2027
• Study Completion (Estimated): June 1, 2027

Study Registration Dates

• First Submitted: June 23, 2026
• First Submitted That Met QC Criteria: July 6, 2026
• First Posted (Actual): July 7, 2026

Study Record Updates

• Last Update Posted (Actual): July 7, 2026
• Last Update Submitted That Met QC Criteria: July 6, 2026
• Last Verified: June 1, 2026

More Information

Terms related to this study

• Keywords: retina; visual cortex; neurogenesis; cognitive cortex
• Additional Relevant MeSH Terms: Health Care Facilities Workforce and Services; Biological Specimen Banks; Health Facilities; Tissue Banks
• Other Study ID Numbers: IIT2025136

Plan for Individual participant data (IPD)

• Plan to Share Individual Participant Data (IPD)?: NO
• IPD Plan Description: The raw individual-level data contains identifiable embryonic genomic information. To protect participants' privacy and comply with domestic biomedical research ethics and data security laws, we cannot share the original IPD with external researchers. Processed analytical results including cell atlas, differential genes and regulatory networks will be released together with related publications.