SLACS technology represents a significant advancement in RNA research, offering a set of unique benefit that overcome the limitations of traditional methods. This technology integrates the spatial arrangement of cells with high-precision molecular analysis, which is particularly beneficial in understanding the spatial organisation of gene expression.
The highlighted advantages of SLACS technology in RNA research are:
Unprecedented Spatial Resolution: SLACS achieves unmatched precision in isolating individual cells by their spatial locations within tissues, surpassing traditional methods like FACS that can lose spatial context during bulk sorting. This enables a more nuanced understanding of how gene expression is organised spatially, enriching insights into biological processes.
Full-length RNA Sequencing: SLACS allows for the analysis of full-length RNA transcripts, uncovering comprehensive details such as novel splice isoforms and post-transcriptional modifications. This capability provides a more complete view of gene expression and regulatory mechanisms.
Enhanced Data Interpretation: By integrating spatial and molecular data, SLACS facilitates a deeper and more contextual interpretation of RNA expression. This approach helps identify specific active genes and pathways in particular tissue regions or cell types, offering profound insights into underlying biological processes.
In Sum, SLACS technology propels RNA research forward, seamlessly uniting detailed anatomical mapping with the intricacies of transcriptomics to unveil the multifaceted layers of cellular dynamics and their influence on organismal health and disease.
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SLACS Validation – Cell lines
SLACS technology has been validated across various applications, demonstrating its capacity to analyse gene expression in cell lines and decipher the spatial organisation of genes within complex tissues. Validation experiments involving three human cell lines (n=152) revealed that SLACS offers reliable and accurate single-cell RNA-seq analysis. The data showed a strong correlation with bulk RNA-seq results, especially for laser-isolated, PFA-fixed cells (R=0.83) compared to methanol-fixed cells (R=0.74), indicating that PFA fixation preserves RNA integrity more effectively. Furthermore, comparison of FPKM values between unfixed/unstained and PFA-fixed/stained cells showed minimal variations, suggesting the fixation and staining processes have little impact on the accuracy of full-length transcriptome data generated by SLACS.
*Lee, Amos C., et al. "Spatial epitranscriptomics reveals A-to-I editome specific to cancer stem cell microniches." Nature Communications 13.1 (2022): 2540.
SLACS Validation – Tissue
SLACS has been effectively validated for use in complex tissue samples, broadening its utility across diverse biological studies. This technology has shown exceptional accuracy and reliability in tissue analysis, offering profound insights into the spatial organisation and gene expression within specific biological contexts. By targeting regions within tissues marked for critical characteristics, such as CD44 and ALDH1 in triple-negative breast cancer studies, SLACS facilitates a granular examination of tumour behaviour and heterogeneity. It enables the detection of cancer stem cell-like properties, immunosuppressive gene expressions, and extensive RNA diversity, including alternative splicing and editing events. The in-depth analysis provided by SLACS unveils the complex molecular dynamics within cancer microniches, enhancing our understanding of tumorigenesis.
*Lee, Amos C., et al. "Spatial epitranscriptomics reveals A-to-I editome specific to cancer stem cell microniches." Nature Communications 13.1 (2022): 2540.
Application: Therapeutic target discovery
By examining specific regions, our researchers identified crucial A-to-I RNA editing events in GPX4 transcripts, associated with ferroptosis, across cancer stem cell-like microniches, offering new insights into TNBC's progression. These discoveries enrich our comprehension of TNBC's intricate molecular framework and open avenues for innovative therapeutic approaches. Targeting these specific RNA modifications within the microniches could lead to strategies that interrupt the tumour's ecosystem, offering hope for halting disease advancement. The study's meticulous methods and comprehensive analysis set a foundation for future inquiries into cancer's epitranscriptomic processes and their potential impact on treatment paradigms. This work signifies a significant step towards understanding and potentially manipulating the molecular mechanisms underlying cancer progression and treatment resistance.
*Lee, Amos C., et al. "Spatial epitranscriptomics reveals A-to-I editome specific to cancer stem cell microniches." Nature Communications 13.1 (2022): 2540.