Spatial Gene Expression is a next-generation molecular profiling tool that uses total mRNA to classify tissue. Map the entire transcriptome in FFPE or fresh frozen tissues with morphological context to get new insights into normal development, disease pathology, and clinical translational research. The study of transcriptional genomics in its spatial setting is referred to as spatial gene expression. Two-dimensional or three-dimensional space within a tissue, cell, or at subcellular resolution can be referred to as spatial context.
Cells exist in three-dimensional space within an organism. The social and geographical surroundings of a cell are frequently crucial for proper functioning. As a result, assessing gene expression in context is critical for gaining a more comprehensive understanding of molecular cell biology.
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Scientists can assess spatially resolved gene expression by combining immunofluorescence and gene sequencing, two conventional molecular biology techniques. For example, using fluorescently tagged antibodies or probes to detect proteins or RNAs, researchers can generate spatial gene expression.
The main reason that scientists are interested in SGE is that they believe that scientists will be able to develop treatments that target these disease-specific spatial gene expression patterns. The idea is that there will be a way to treat specific diseases with targeted surgery. For example, surgeons would be able to target one part of someone’s body and repair the damage from a disease in that area by cutting out a tissue from another area, perhaps where there is no damage. The recipient would then receive the cells needed for regeneration after surgery. With these advances, the pharmaceutical industry hopes to use genetic testing to create customized drugs for specific diseases based on SGE research.
5 Reasons Spatial Gene Expression is Important in Healthcare
1. Spatial Gene Expression Patterns Correlate with Diseases
While discovering the role of genes is an ongoing process, scientists have been able to observe the spatial gene expression related to certain diseases. For instance, scientists were able to identify that lung cancer is correlated with a particular spatial gene expression pattern, which helps them understand why this disease occurs and how it can be treated. “The tissue specificity of gene expression has been shown to play important roles in development and disease.” This correlation with diseases is one of the strengths of SGE.
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For example, scientists have been able to identify that lung cancer is correlated with a particular spatial gene expression pattern, which helps them understand why this disease occurs and how it can be treated. “The tissue specificity of gene expression has been shown to play important roles in development and disease.”
2. Spatial Gene Expression Patterns Can be Used as Early Indicators
With these patterns, tissue-specific markers could be present even earlier than they are now. As noted by researchers at Georgetown University Medical Center, “The spatial expression pattern of a particular gene (i.e., the gene distribution pattern across all the different organs and tissues) can provide a strong foundation for the development of new disease markers because most of these patterns are tissue-specific and can emerge much earlier than clinical symptoms.”Individuals with cancer have different gene expressions than normal cells, which indicates that a person has cancer. This can be observed by looking at the spatial gene expression patterns in the patient’s tumor. As noted by researchers at Georgetown University Medical Center, “Cancer is one of the diseases where understanding of the spatially resolved genome becomes critical to diagnose and treat this disease.”
3. Understanding Disease Causes is Key to Developing Treatments
By understanding the correlations between diseases and spatial gene expression, researchers believe they will be able to understand why certain diseases occur. This could help with research regarding early detection, diagnosis, or treatment.
As noted by researchers at Johns Hopkins School of Medicine, “Understanding the underlying causes of a disease is the best way to develop new treatments. By learning how a particular disease arises, it becomes feasible to find ways to stop or slow the process.”
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Developing treatments to eliminate the cause of a disease is not always possible, but if researchers can begin to understand the causes of a disease, then they will be able to develop preventative treatments. “Understanding the underlying causes of a disease is the best way to develop new treatments. By learning how a particular disease arises, it becomes feasible to find ways to stop or slow the process.”
4. Spatial Gene Expression Patterns Could be Used to Make Customized Drugs
Genetic testing is already being used for personalized medicine. This advanced method of testing could make it even easier for pharmaceutical companies to create drugs for specific patients based on their SGE signatures.
This could help to reduce the risks associated with using broad-spectrum drugs on healthy people, which include overprescription, dosage errors, and side effects. Customized drugs may also be more effective than typical pharmaceuticals by targeting the specific gene expression needed in each patient instead of affecting all cells, whether they need treatment or not.
Ultimately, these new methods will create an entirely new set of pharmaceuticals that will treat diseases based on their gene expression spatial patterns. These are expected to be much more targeted and effective than conventional pharmaceuticals.
5. Spatial Gene Expression Patterns could Provide Insight into Genetic Diseases
While understanding SGE is important to the pharmaceutical industry, it can also be useful for many other areas of science. For example, researchers at Johns Hopkins School of Medicine are interested in learning how SGE works for certain genetic diseases like cystic fibrosis and sickle cell disease.
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Researchers are hoping to gain insight into how these particular diseases occur by studying the spatial gene expression patterns related to these diseases. In this recent study, researchers analyzed spatial gene expression patterns in heart muscle tissue to learn more about how development is affected by tissue-specific gene expression patterns. Results showed that this process occurs as a result of developmental dysfunctions in cardiac muscle cells, which may account for some of the causes of heart diseases.
In this research study, scientists examined how spatial gene expression was affected by two different genetic disorders related to the development of heart diseases.
How Does the Spatial Expression of Genes Affect Development?
A question related to spatial gene expression is: what happens in tissues with different spatial gene expression patterns? The relation between the process of development and the spatial expression pattern of genes has not been thoroughly investigated. Some recent studies provide insights into this process, showing the importance of tissue-specificity for normal development.
For example, the right deployment of regulatory genes for cell differentiation that leads to tissue patterning and organ creation in a developing embryo is reliant on the location, time, and level of gene expression. Understanding the process of organogenesis requires dissecting these complicated gene regulatory networks spatially. Another advantage of spatial gene expression is that it can be quantified, which helps us understand gene regulation even further.
Spatial gene expression patterns have been observed in various tissues, including the heart, brain, blood cells, skeletal muscle, liver, and pancreas. It has recently been discovered that spatial gene expression patterns also occur in human embryonic stem cells (hESCs) and mouse ESCs that are dividing for cell differentiation.
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For example, a recent study using morphological analysis found that tissues with different SGE show distinct cell types with different shapes and sizes. This study showed that a particular cell type is formed in response to the presence or absence of a specific set of genes. This finding also means that cells with the same structural identity can be found in different organs and tissues, while cells with different spatial gene expression patterns can have the same shape and size.
In conclusion, the spatial gene expression pattern is one of the most valuable resources for understanding the molecular basis of development. The discovery of spatial gene expression patterns will help scientists to find novel methods for adult stem cell therapy, better understand how and why genetic diseases occur, and provide new insights into how cells change their shape and size during normal development.
Conclusion
Currently, there are four notable methods that can be used to study spatial gene expression patterns: high-throughput in situ hybridization (HTIS), single-cell RNA sequencing (scRNA-Seq), chromosome conformation capture (3C), and chromosomal contact analysis (3C). Spatial transcriptomics is a technique that allows researchers to spatially locate and quantify gene expression in the form of mRNA transcripts within native cells or tissues. Spatial transcriptomics provides an unbiased analysis of quantifiable mRNA transcripts in situ.
All cells in a multicellular creature share the same genome; nevertheless, the expression pattern of the genome dictates the cell’s physiological fate. This fluctuating gene expression pattern causes cellular diversification, and tracking gene expressions with positional context is now achievable thanks to spatial transcriptomics.
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The results from these methods show that spatial gene expression patterns are tissue-specific and cell-type-specific. With a complete map of the spatial gene expression pattern, we can learn more about how different tissues develop and what genes may play a role in their development. The future of this research will be in finding new treatments for diseases related to improper spatial gene expressions, such as cancer and heart disease.
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