Breaking Boundaries in 3D Biology: The Power of Highly-Multiplexed Raman Imaging

3D biological imaging of stem cells© Prasanth - stock.adobe.com

Understanding the intricate interactions within biological systems requires advanced imaging technologies capable of high spatial resolution and multiplexing. In a leading-edge review published in Chemical Communications, researchers Yingying Li, Yuchen Sun, and Lixue Shi from Shanghai Medical College, Fudan University, reported on the transformative potential of highly-multiplexed Raman imaging in three-dimensional (3D) spatial biology (1).

The Quest for Advanced Imaging Technologies

Biological systems operate through complex interactions at various scales, necessitating rich-content, high-resolution information. Traditional imaging technologies often fall short in providing the depth and clarity needed to unravel these complexities. For instance, understanding the brain's functionality or the microenvironment of cancerous cells requires imaging technologies that can measure multiple biomarkers simultaneously in a 3D context (1,2).

Recent technological advancements in spatial omics have shown promise in decoding these systems (1,2). Multiplexed measurements on mRNA, proteins, and metabolites are key to understanding the organizational complexities of biological systems. Highly-multiplexed imaging technologies that can deliver these measurements with fine spatial resolution are therefore highly sought after (1,2).

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Challenges with Existing Technologies

While various methods achieve spatially resolved multiplexing on tissues or single cells with subcellular resolution, they face significant limitations. Imaging mass spectrometry, although capable of offering complex color imaging renditions using metal isotopes, is a destructive technique requiring expensive equipment and complex sample preparation. Fluorescence imaging, though popular, is limited by its broad spectra, restricting the number of resolvable image colors and suffering from what is known as the “color ceiling” (1).

Serial fluorescence imaging strategies, which involve multiple rounds of labeling and elution, enable highly-multiplexed imaging but struggle with technical issues when applied to high-resolution or 3D contexts. These limitations underscore the need for a more robust and versatile imaging method (1).

The Emergence of Stimulated Raman Scattering Microscopy

Raman microscopy presents an appealing alternative, particularly with the advent of stimulated Raman scattering (SRS) microscopy. Unlike traditional Raman techniques, SRS microscopy uses synchronized pulsed lasers to excite molecules, significantly enhancing Raman transitions and allowing for high-speed, high-resolution imaging (1).

SRS microscopy offers several advantages for 3D spatial biology. Its narrow spectral linewidth allows for parallel measurements of numerous targets, and it provides high spatial resolution and good optical sectioning capability. Moreover, SRS imaging is noninvasive and compatible with in vivo applications, making it suitable for functional imaging (1).

Overcoming Technical Challenges

Despite its promise, developing a highly-multiplexed SRS imaging platform involves addressing several challenges. Improving the detectability of low-abundance targets, generating a wide range of Raman imaging colors, and integrating these advancements into biological specimens are critical areas of focus (1).

Innovations in SRS spectroscopy, Raman probe development, sample engineering, and computational algorithms have made significant strides in overcoming these obstacles. These developments empower highly-multiplexed Raman imaging technologies to reveal the intricate structures and interactions within biological systems (1).

Future Prospects

The future of highly-multiplexed Raman imaging is bright, with ongoing innovations expected to enhance its multiplexing capabilities, sensitivity, imaging depth, and spatial resolution. Techniques such as double resonance and optical barcoding hold the potential to significantly increase the number of resolvable image colors. Additionally, integrating advanced computational algorithms will enable the analysis of complex 3D multivariate datasets, driving data-driven discoveries (1).

Further advancements in photocontrollable and chemically activatable Raman probes will expand the range of targetable markers, facilitating multiplexed functional imaging. These technical advances will be crucial for studying key biological areas, including oncology, neuroscience, infectious diseases, and immunology (1).

References

(1) Li, Y.; Sun, Y.; Shi, L. Viewing 3D spatial biology with highly-multiplexed Raman imaging: from spectroscopy to biotechnology. Chem. Commun., 2024, Advance Article. DOI: 10.1039/D4CC02319F

(2) Swain, R. J.; Stevens, M. M. Raman microspectroscopy for non-invasive biochemical analysis of single cells. Biochem. Soc. Trans. 2007, 35 (3), 544–549. DOI: 10.1042/BST0350544