Discovering the Unseen in Less Time: Light-Seq’s Role in Identifying Rare Retinal Biomarkers

Discovering the Unseen in Less Time: Light-Seq’s Role in Identifying Rare Retinal Biomarkers

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Understanding cellular states is critical to pursuing effective treatments. High-throughput spatial transcriptomics offers promise in revealing spatial gene expression and cellular interactions by capturing transcriptional changes in situ. Despite its potential, existing methods sacrifice tissue integrity for further muli-omics investigations.

Light-Seq fuses together microscopy and NGS. It was introduced by Kishi et al. (2022), and uses light-induced DNA barcodes to label regions of interest precisely without damaging samples, therefore, overcoming existing limitations.

Light-Seq: Illuminating Next-Gen Sequencing with Precision

Light directed labeling of biomolecules in fixed tissues in situ, or Light-Seq,  merges microscopy with Next-Generation Sequencing by attaching spatial indices onto biomolecules in intact samples using light. This process involves using specialized light-sensitive nucleosides to create distinct spatial patterns via UV illumination. These patterns mark regions of interest (ROIs) with unique barcode sequences, followed by high throughput sequence which permits comprehensive spatially aware transcriptional profiling  of cells and tissues.

Through in situ reverse transcription and the utilization of unique barcode docking sites, Light-Seq facilitates precise spatial labeling of RNAs across multiple ROIs. Its sensitivity is comparable to single-cell RNA sequencing for the same set of genes.

A significant advantage of Light-Seq lies in its adaptability. Spatially restricting barcoding to targeted cDNAs and selectively amplifying them for library generation allows sequencing reads to be focused on the cells of interest. This approach optimizes sequencing depth and cost, which is particularly beneficial for experiments targeting very few cells.

Shedding Light on the UnseenLight-Seq Identifies New Retinal Biomarkers

Researchers employed Light-Seq to investigate rare cell types in the mouse retina. Light-Seq successfully targeted and sequenced dopaminergic amacrine cells (DACs), an extremely rare subset comprising less than 0.01% of retinal cells. Previous methods have been unable  to successfully isolate and sequence DACs due to their scarcity and interspersed distribution among various neuron types. However, Light-Seq’s combination of in situ identification, barcoding, and sequencing confirmed known markers and unveiled novel biomarkers linked to DACs, thereby offering profound insights into retinal neuron subtypes.

Lighting the Path Forward in Precision Medicine

Precision medicine incorporates genomics, histomorphology, and cellular biology. Multi-omics approaches decode tumor heterogeneity, brain atlas, developmental transcriptional regulation, and disease pathogenesis.

Light-Seq’s ability in spatial transcriptomics offers the potential to accelerate precision medicine. The non-invasive methodology preserves samples, enabling broader multi-omics studies. This technique can be used to track cancer mutations, identify microbial species in tissue samples, investigate rare diseases, and identify cell subtypes within pathology. Potentially, this could allow us to better understand the physiology and pathology of disorders involving complex cell types, which may lead to the development of more effective treatments.

Outsourcing Bioinformatics Analysis: How Bridge Informatics Can Help

BI’s data scientists prioritize studying, understanding, and reporting on the latest developments so we can advise our clients confidently. The generation, storage and analysis of biological data is faster and more accessible than ever before. From pipeline development and software engineering to deploying your existing bioinformatic tools, Bridge Informatics can help you on every step of your research journey.

As experts across data types from leading sequencing platforms, we can help you tackle the challenging computational tasks of storing, analyzing and interpreting genomic and transcriptomic data. Bridge Informatics’ bioinformaticians are trained bench biologists, so they understand the biological questions driving your computational analysis. Click here to schedule a free introductory call with a member of our team.

More information

Jocelyn Kishi, Light-Seq: light-directed in situ barcoding of biomolecules in fixed cells and tissues for spatially indexed sequencing, Nature Methods (2022). DOI: 0.1038/s41592-022-01604-1

Shahrzad Ghazisaeidi, PhD, Data Scientist, Bridge Informatics

Shahrzad specializes in high-throughput sequencing, data pre-processing, and downstream analysis of transcriptomic and epigenetic landscapes. She is particularly passionate about developing innovative tools for drug repurposing.

Prior to joining Bridge Informatics, Shahrzad served as a Postdoctoral Associate at the Hospital for Sick Children in Toronto, Canada where she researched the epigenetics of peripheral nerve injury models.

Shahrzad earned her Ph.D. in Physiology and Neuroscience from the University of Toronto. Her studies focused on the sex-dependent and independent gene regulation of peripheral nerve injury. Currently based in Toronto, Shahrzad balances her professional pursuits with personal interests by making time for yoga, martial arts, and poetry.

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