‘CLEAR’ Imaging Platform for Advanced Protein Mapping in Cells and Tissues Developed

Proteins are fundamental to nearly every biological function and serve as major targets for therapeutic interventions as well as important disease biomarkers.

Indian researchers have developed an innovative imaging platform called "Cleavable Light-Erased Antibody Reporter" (CLEAR), a breakthrough technology that could dramatically transform biomedical research, disease diagnosis, and precision medicine by enabling scientists to visualize an unprecedented number of proteins within the same biological sample using just a single fluorescent marker.

The new platform, developed by researchers at the Jawaharlal Nehru Centre for Advanced Scientific Research (JNCASR), Bengaluru — an autonomous institute under the Department of Science and Technology (DST) — represents a major advancement in high-resolution multiplexed imaging and spatial proteomics.

Scientists believe the technology could significantly improve understanding of complex diseases such as cancer, neurological disorders, and immune-related conditions by enabling highly detailed mapping of proteins within cells and tissues.

Major Challenge in Protein Mapping Addressed

Proteins are fundamental to nearly every biological function and serve as major targets for therapeutic interventions as well as important disease biomarkers.

Researchers have long sought the ability to generate comprehensive proteomic maps showing the precise identity and spatial organization of proteins within their natural biological environments.

Such detailed mapping could help scientists and clinicians:

• Diagnose cancers more accurately

• Understand neurological disorders

• Study immune responses

• Identify disease biomarkers

• Develop targeted therapies

However, existing imaging technologies have struggled to visualize large numbers of proteins simultaneously within the same biological sample while maintaining high spatial resolution.

CLEAR Enables Unlimited Protein Visualization

To overcome this limitation, the JNCASR research team developed CLEAR, an imaging platform capable of repeatedly labeling, imaging, erasing, and relabeling proteins within the same sample using a single fluorophore.

The technology introduces a light-cleavable probe system that allows multiple cycles of imaging within the same spectral window.

Unlike conventional multiplex imaging techniques that require multiple fluorescent markers and often face limitations in complexity and sample compatibility, CLEAR combines:

• High multiplexing capability

• High spatial resolution

• Faster imaging workflows

• Compatibility with delicate biological samples

• Ability to work with live cells

The system effectively redefines multiplexed imaging by enabling virtually unlimited protein visualization without requiring numerous fluorophores.

How the CLEAR System Works

Researchers describe the CLEAR system as functioning similarly to a chalkboard where written information can be erased and replaced repeatedly.

The process works through several steps:

1. Proteins inside cells are labeled using cleavable fluorescent tags.

2. Images are captured under a microscope.

3. A gentle pulse of 365 nm LED light is applied to erase the fluorescent signal.

4. A new set of proteins is then labeled and imaged within the same optical window.

5. The cycle is repeated multiple times to generate highly detailed protein maps.

By continuously repeating this process, scientists can build increasingly complex and information-rich maps of proteins across:

• Single cells

• Tissue sections

• Complex biological systems

Research Led by Prof. Sarit S. Agasti

The research team was led by Prof. Sarit S. Agasti at JNCASR.

The group designed and synthesized the CLEAR probes, developed the imaging workflow, and validated the technology across different biological systems.

The work involved:

• Experimental design

• Probe chemistry development

• Imaging analysis

• Biological validation

Researchers from the Indian Institute of Science (IISc) also collaborated on demonstrating the technology in complex immune cell systems.

Published in International Scientific Journal

The findings have been published in the internationally reputed journal Chemical Science, published by the Royal Society of Chemistry.

The publication highlights the platform's potential to become a next-generation imaging technology for biomedical and translational research.

Potential Applications in Medicine and Diagnostics

Scientists believe CLEAR could have major implications for:

• Cancer diagnosis

• Immunology research

• Neurological disease studies

• Drug development

• Clinical diagnostics

• Precision medicine

In cancer biology, for example, understanding the exact spatial organization of proteins within tumor tissues can help researchers identify disease progression patterns, immune responses, and treatment targets.

In neurological disorders, detailed protein mapping could provide new insights into cellular changes associated with diseases such as Alzheimer's, Parkinson's, and other neurodegenerative conditions.

Supports Emerging Field of Spatial Proteomics

The technology aligns closely with growing global interest in spatial proteomics, a rapidly advancing field focused on studying proteins within their spatial and functional cellular context.

Spatial proteomics is increasingly viewed as essential for understanding how cells communicate, organize, and respond to disease conditions.

Experts note that advanced imaging technologies like CLEAR may play a major role in the future of:

• Personalized medicine

• Molecular diagnostics

• Biomarker discovery

• Targeted therapeutic design

Potential Contribution to Precision Medicine

Researchers stated that in the long term, CLEAR could contribute significantly to precision medicine approaches by providing comprehensive molecular insights capable of guiding highly targeted treatments.

The platform may eventually help clinicians tailor therapies based on highly detailed molecular profiles of individual patients.

The ability to repeatedly image proteins at high resolution using minimal fluorescent resources also makes the technology potentially more scalable and cost-effective for future biomedical applications.

India's Growing Role in Frontier Scientific Research

The development of CLEAR also reflects India's expanding contribution to frontier scientific research in areas such as:

• Biotechnology

• Advanced imaging systems

• Molecular biology

• Nanoscience

• Biomedical engineering

• Precision healthcare

Institutions such as JNCASR and IISc continue to play a major role in advancing globally competitive scientific research emerging from India.

Scientists believe innovations like CLEAR strengthen India's position within the global scientific and biomedical innovation ecosystem while supporting future healthcare and diagnostic advancements.