Innovative Approaches to Mapping Gene Expression in 3D Tissue Environments

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Introduction

Gene expression mapping has witnessed tremendous change, especially in recent times, owing to the new technologies that permit more analysis within incorporating tissues. For instance, gene expression studies such as bulk RNA sequencing have provided a simple but invaluable understanding of gene expression discrimination, yet they do not allow for consideration of tissue spatial geometry or investigation of single cells within their native environment. In that regard, there has been a move to create new methods in which gene expression can be studied in situ in 3D cultured ocelot tissues. Such technologies work at the interface of molecular biology and spatial biology, allowing a complete analysis of genes and how they are turned on and off within the structure of tissues. This review focuses on several novel strategies employed to determine specific sites of gene expression within three-dimensional model systems, which hold great potential to enhance our comprehension of tissue behavior and diseases as well as targeting therapies to specified sites.

3D Intact-Tissue Sequencing: A New Dimension of Transcriptomics

One of the astonishing improvements in this field is the ability to perform 3D intact-tissue sequencing, which is the integration of conventional sequencing workflows and advanced imaging. Using this technique, researchers can efficiently transcriptomically map the tissues at the single-cell level without destroying the architecture of the tissue sample. It is possible to sequence cellular RNAs from tissue by entombing them within a hydrogel matrix to fix tissue, which allows efficient even-gene transcriptome sequencing with all transcript positional information attached. The fusion of transcriptome analysis with histology is crucial when it comes to tissues that are densely packed, such as the brain, where the spatial arrangement of a cellular subpopulation is integral to that cell’s ability to perform a function.

The use of 3D intact-tissue sequencing has changed the focus of neuroscience forever. Since thousands of genes can be mapped according to specific regions of the brain where neuron subtypes are identified, specific regions of the brain can be comprehensively mapped along with myriad circuits tracing intercellular communications. This makes it possible for an ever more detailed exploration of the normal and diseased brain, imitating complex human behavior and also severe neurological diseases at the molecular level.

Spatial Transcriptomics: Linking Gene Expression to Tissue Architecture

Additionally, spatial transcriptomics is an innovative technique that has altered the way we visualize the relationship between gene expression and tissue structure. While earlier techniques disconnected the cells from their surrounding architecture, spatial transcriptomics retains and maps the positions of RNA inside tissue slices. This method consists of covering the cut tissue piecemeal with different barcodes depending on the position of interest to see the transcription of various polynucleotides within one tissue’s cross-section.

A very important application of spatial transcriptomics is the study of cancer. Tumors are rather complex structures comprising several different, often heterogeneous cells that are constantly active and interact in the tumor microenvironment. By using spatial transcriptomics, scientists can study spatial interactions of cancer cells with immune and stromal cells and their impact on tumor progression and metastasis. Such detailed data makes it possible to characterize the genes differentially regulated in distinct tumor areas that may be considered for further developing on-target therapy.

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MERFISH: High-Throughput Single-Molecular Imaging

Multiplexed Error-Robust Fluorescence In Situ Hybridization (MERFISH) is a technique perfect for the quantification and visualization of RNA molecules specifically in situ at the single-cell level. Using combinatorial labeling and sequential imaging, MERFISH can achieve the detection of thousands or more RNA species in one assay, and this allows for tracing the patterns of gene expression at molecular resolution spatially within the tissue.

MERFISH has also been particularly useful for generating cell atlases for more complex tissues, especially the brain and immune tissues. For instance, researchers have used MERFISH to map neuronal and glial cell types in the brain, revealing the diversity and spatial distribution of molecular types within these cells. Such approaches not only characterize which cellular immunotypes are present but also what functional states these cells are in and how they are localized and interact with the surrounding environment. Imaging of gene expression at this level will yield new insights into how cellular microenvironments influence normal tissue and disease functions.

DNA Microscopy: Imaging Without Optics

DNA microscopy is a cutting-edge tactic regarding the spatial distribution of gene expression. It involves imaging without any form of optical devices. Every molecule within the cited field is tagged with random nucleotides that are unique for each molecule embedded in the tested tissue. As these tagged sequences grow and link, they form a molecular map where the transcripts relate to their actual positions. Spatial information is reconstructed from algorithms that map out where the encoded sequences should have been placed in the tissues of living molecular masterpieces.

This method of forming modulation images of monocytes in culture does allow significant simplification of existing stage-by-stage approaches and incorporates the image processing function. DNA microscopy is also applied to the study of these types of tissues in cases where there is no proper optical access or large tissues need to be studied. Extensive usage of such methods will be observed in the future, not limited to fundamental research only, but will see clinical diagnostic applications and ways of personalized medicine.

STARmap: Three-Dimensional Spatial Transcriptomics

STARmap (Spatially-Resolved Transcript Amplicon Readout Mapping) is yet another new find that combines hydrogel-tissue chemistry and in situ sequencing for 3D spatial transcriptomics. This technique is designed to visualize RNA molecules in thick tissue blocks with many cells, permitting the study of the spatial arrangement of cells along with their functional genomics. Because of its fine sequencing resolution, STARmap is also effective in examining neural circuitry—comprised of heterogeneous cellular structural organizations that must be spatially aware for appropriate applications of brain functions.

Fragmented cellular RNAs are hybridized to spherical and specific probes, which are further trapped within a hydrogel, and STARmap encapsulates the tissue. The method permits the localization and imaging of all concurrently expressed genes to the number of hundreds or even thousands, thus surveying and elucidating spatial patterns of genomic expression. In a comparable vein, while targeting the enhancer region of specific promoters, STARmap has been employed to study the identity and localization of neuronal subtypes and the mapping of functional circuit states within the organism.

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Applications in Cancer, Neuroscience, and Beyond

The capacity to visualize gene expression in three dimensions will bring forward new developments in many areas of biology and medicine. For example, in cancer studies, the assessment of gene expression profiling at a high resolution helps to address the molecular order of the cellular landscape in which cancer cells reside, including how cancer cells escape the immune defense and eventually become resistant to therapy. This could help develop novel therapeutic ideas that interfere with selective cellular communications within the tumor.

In line, how 3D gene expression mapping is helping in all aspects of neuroscience is also illustrating large gaps in our understanding of the brain. In particular, when the spatial arrangement of gene expression within neural networks is presented, it becomes possible to evaluate the impact of genetics and the environment on the development of neural disorders. This information is essential in designing therapies that will not only try to manage the symptoms but also change aberrant molecular processes in disease states, including Alzheimer’s, autism, and schizophrenia.

In addition, the combination of 3D gene expression profiling techniques with single-cell RNA sequencing and other imaging tools enhances modern tissue engineering approaches. Such a comprehensive perspective enables relating cellular activity to its spatial localization, which will enhance disease modeling and cellular therapies.

Challenges and Future Directions

The rising popularity of 3D mapping of gene expression patterns raises several concerns. Particular research challenges are the resolution of spatial information, efficiency, and adequacy of sequencing techniques. Further, advanced computational tools and analytical frameworks must be employed due to the complexity of these high-dimensional data sets.

Further improvements in this area would involve making these techniques faster and more precise to be able to use them in more tissues and diseases. The integration of 3D gene expression maps with other omics, such as proteomics and metabolomics, will provide a better understanding of tissue functions and pathologies at molecular levels.

Conclusion

New technologies that allow for 3D ultrasound reconstruction of gene expression are reshaping the biological landscape. By maintaining the spatial aspect, these technologies furnish a perspective on individual cell behavior within the cell’s environment, which is vital for the progress of fundamental science and for finding alternative means of therapy. Furthermore, as these procedures advance even further, there is a possibility that they will change the way complex biological pathways are studied and how the molecular processes responsible for maintaining health and, pathologically, disease can be understood more comprehensively.

References

  1. Wang, X., Allen, W.E., Wright, M.A., Sylwestrak, E.L., Samusik, N., Vesuna, S., Evans, K., Liu, C., Ramakrishnan, C., Liu, J. and Nolan, G.P., 2018. Three-dimensional intact-tissue sequencing of single-cell transcriptional states. Science, 361(6400), p.eaat5691.
  2. Moffitt, J.R., Bambah-Mukku, D., Eichhorn, S.W., Vaughn, E., Shekhar, K., Perez, J.D., Rubinstein, N.D., Hao, J., Regev, A., Dulac, C. and Zhuang, X., 2018. Molecular, spatial, and functional single-cell profiling of the hypothalamic preoptic region. Science, 362(6416), p.eaau5324.
  3. Gut, G., Herrmann, M.D. and Pelkmans, L., 2018. Multiplexed protein maps link subcellular organization to cellular states. Science, 361(6401), p.eaar7042.
  4. Weinstein, J.A., Regev, A. and Zhang, F., 2019. DNA microscopy: optics-free spatio-genetic imaging by a stand-alone chemical reaction. Cell, 178(1), pp.229-241.
  5. Lin, J.R., Izar, B., Wang, S., Yapp, C., Mei, S., Shah, P.M., Santagata, S. and Sorger, P.K., 2018. Highly multiplexed immunofluorescence imaging of human tissues and tumors using t-CyCIF and conventional optical microscopes. elife, 7, p.e31657.
  6. Chen, K.H., Boettiger, A.N., Moffitt, J.R., Wang, S. and Zhuang, X., 2015. Spatially resolved, highly multiplexed RNA profiling in single cells. Science, 348(6233), p.aaa6090.
  7. Wang, Y., Woehrstein, J.B., Donoghue, N., Dai, M., Avendaño, M.S., Schackmann, R.C., Zoeller, J.J., Wang, S.S.H., Tillberg, P.W., Park, D. and Lapan, S.W., 2017. Rapid sequential in situ multiplexing with DNA-Exchange-Imaging. bioRxiv, p.112227.

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