Visium FFPE: Revolutionizing Spatial Transcriptomics
In the world of biomedical research, a new technology is changing how scientists study tissue samples. Visium FFPE is a platform that analyzes gene expression in tissues that have been fixed and preserved. This method is set to change how we understand diseases, leading to new discoveries in tissue analysis.
Visium FFPE solves old problems with tissue samples. There are over a billion of these samples in hospitals and biobanks. This technology lets researchers study these samples in a new way, combining gene expression with the detailed information from these samples. It’s going to help scientists make new discoveries in many areas, like cancer and developmental biology.
Visium FFPE has many exciting features. It provides detailed gene expression data and works with many types of samples. It also makes it easy for researchers to get insights into how tissues work. This could lead to better understanding of diseases and new treatments.
Key Takeaways
- Visium FFPE revolutionizes spatial transcriptomics by enabling high-resolution gene expression analysis in formalin-fixed, paraffin-embedded (FFPE) tissue samples.
- With over one billion archived FFPE tissue samples worldwide, Visium FFPE unlocks a vast trove of valuable data, combining whole transcriptome analysis with histological context.
- The technology offers a streamlined workflow, high-resolution gene expression data, and compatibility with diverse sample types, transforming biomedical research and disease understanding.
- Visium FFPE’s innovative features empower researchers to gain unprecedented insights into the complex spatial dynamics within tissues, driving advancements in disease mechanisms and more effective therapies.
- Visium FFPE is poised to accelerate discoveries across a wide range of biomedical fields, from cancer research to developmental biology, by revolutionizing spatial transcriptomics.
What is Visium FFPE?
Visium FFPE is a new way to study gene expression in tissue samples. It uses RNA sequencing and histology to look at gene activity in specific parts of tissues. This technology is a big step forward in understanding how genes work in different parts of the body.
Overview of Spatial Transcriptomics
Spatial transcriptomics is a new field that shows where genes are active in tissues. Unlike old methods, Visium FFPE maps thousands of genes to their exact spots. This gives us a clear picture of how genes work together in tissues.
Importance of FFPE Samples
FFPE tissue samples are key in medical research. They are well-preserved and help us study diseases and new treatments. With Visium FFPE, we can now study these samples in ways we couldn’t before.
Applications in Research
Visium FFPE is used in many areas, like cancer and brain research. It helps us understand diseases better and find new treatments. The detailed information it gives us is crucial for studying complex biological processes.
| Feature | Specification |
|---|---|
| Capture Window Size | 6.5×6.5mm or 11x11mm |
| Spatial Resolution | 55-micron diameter spots, 100-microns apart |
| Probe Set | Whole transcriptome |
| Applications | Cancer research, drug discovery, developmental biology |
The Visium FFPE platform is leading the way in spatial transcriptomics. It shows great promise for making new discoveries in medical research.
Key Features of Visium FFPE
Visium FFPE, a new tool from 10x Genomics, is changing how we study tissues. It lets researchers dive deep into the whole transcriptome analysis of FFPE tissues. This means they can see the tissue morphology and gene mapping in their samples like never before.
High-Resolution Gene Expression
The Visium FFPE platform lets researchers map gene activity in tissues with high detail. It uses advanced sequencing to explore the full transcriptome of FFPE samples. This opens up new insights into how cells work together.
Compatibility with Diverse Samples
Visium FFPE works well with many types of FFPE samples. It can handle samples from different species and tissues. This makes it easy for researchers to use their existing samples for new studies.
Streamlined Workflow
Visium FFPE is easy to use and makes research smoother. It comes with a ready-to-use assay kit that doesn’t need special equipment. This makes it simple to go from preparing samples to analyzing data.
With these features, Visium FFPE is leading the way in spatial transcriptomics. It lets researchers study tissue biology and disease processes with great detail and speed. This is helping to advance many fields, from cancer research to neuroscience.
Benefits of Using Visium FFPE
Visium FFPE technology from 10x Genomics changes how we study tissues. It uses formalin-fixed, paraffin-embedded (FFPE) samples. This method brings many benefits, helping researchers learn more about tissues and diseases.
Enhanced Spatial Context
Visium FFPE links gene expression to specific spots in tissues. This lets researchers see how genes work together in tissues. It helps them understand complex biological processes better.
Improved Data Insights
Visium FFPE analyzes whole tissue sections. This reduces the chance of missing key information. It gives researchers strong, reliable data, helping them make better decisions and find new discoveries.
Versatility Across Diseases
Visium FFPE works for many diseases, from cancer to neurological disorders. It helps researchers study gene expression in different tissues. This opens up new ways to understand and treat diseases.
Visium FFPE offers better spatial context, more reliable data, and works for many diseases. It helps researchers explore tissue architecture, gene expression, and disease mechanisms like never before. This technology is changing spatial transcriptomics and speeding up scientific progress.
Comparison to Other Methods
The Visium FFPE platform has many benefits over old methods and microarrays for studying spatial transcriptomics. It gives detailed gene expression data with spatial information. This helps researchers see where genes are active in a tissue sample.
Visium FFPE is more sensitive than microarrays and can find new transcripts. This is key for finding new insights into gene expression. Also, other methods like laser capture microdissection can’t match Visium FFPE’s speed and detail.
| Feature | Visium FFPE | Traditional Techniques | Microarrays |
|---|---|---|---|
| Spatial Resolution | High | Low | Moderate |
| Sensitivity | High | Moderate | Moderate |
| Novel Transcript Detection | Yes | Limited | Limited |
| Throughput | High | Low | High |
Even though Visium FFPE has big benefits, it only works with human and mouse samples for now. Researchers need to think about their research goals and sample types. This will help them choose the best spatial transcriptomics technology.
The Role of FFPE in Biomedical Research
Formalin-fixed, paraffin-embedded (FFPE) tissue samples have been key in biomedical research for over a century. They are now crucial for understanding many diseases through spatial transcriptomics and other genomic analyses.
Historical Background of FFPE Usage
FFPE has been the top choice for preserving tissue samples for over a century. It allows for long-term storage and analysis of clinical specimens. This method has helped create large biobanks of archived samples. These biobanks support long-term studies and the study of rare tissues.
Current Trends in FFPE Research
New molecular techniques, like spatial transcriptomics, have opened up new ways to study FFPE samples. Researchers can now map gene expression in tissues, revealing how cells and molecules interact in diseases.
Collaborations with Biobanks
FFPE research is becoming more important, leading to more partnerships with biobanks. These collaborations give scientists access to large collections of tissue samples. This access allows for detailed studies of disease progression and the discovery of new biomarkers and treatments.
| Metric | Value |
|---|---|
| FFPE article accesses | 133,000 |
| FFPE article citations | 259 |
| FFPE article Altmetric score | 144 |
The use of FFPE samples and interest in spatial transcriptomics show FFPE’s vital role in research. By exploring FFPE archives, scientists can find new insights. This can lead to advances in personalized medicine, drug development, and patient care.
How Visium FFPE Works
Visium FFPE is a groundbreaking technology from 10x Genomics. It changes how we study gene expression in formalin-fixed, paraffin-embedded (FFPE) tissue samples. It uses probe hybridization, spatial barcoding, and sequencing libraries to reveal insights from tough FFPE samples.
Sample Preparation Process
The Visium FFPE process starts with preparing FFPE tissue sections. These sections are placed on Visium slides with a grid of barcoded spots. Probe pairs target specific RNA sequences, capturing spatial information.
Imaging and Data Collection
After probe hybridization, the tissue is made permeable. This lets the spatial barcodes be captured. High-resolution imaging creates a detailed tissue map. Sequencing follows, mapping gene expression data to specific tissue spots.
Analysis Techniques
The data from Visium FFPE is analyzed using advanced methods. Sophisticated algorithms and tools help understand gene expression patterns. They identify key genes and show how cells and tissues interact.
| Key Capabilities of Visium FFPE | Benefits |
|---|---|
| Probe Hybridization and Ligation | Capture spatial information and gene expression data from FFPE samples |
| Spatial Barcoding | Enables mapping of gene expression data to specific tissue locations |
| Sequencing Libraries | Comprehensive analysis of gene expression patterns and spatial relationships |
Visium FFPE’s innovative approach opens a new door for discovery. It lets researchers explore the hidden details of FFPE samples. It reveals the complex spatial dynamics of gene expression in various tissues.
Case Studies Demonstrating Impact
Visium FFPE has led to major breakthroughs in many areas of biomedical research. It has helped us understand tumor heterogeneity and how genes work together in cancer. It has also helped us learn more about neurodegenerative diseases by mapping genes in brain tissues.
Cancer Research Breakthroughs
In cancer research, Visium FFPE has given us new insights. It shows how different cells in a tumor work together. This helps us find better treatments.
Neurological Studies
Visium FFPE has changed neuroscience too. It lets us see how genes are expressed in brain tissues. This has helped us understand neurodegenerative diseases better.
Developmental Biology Insights
In studying how embryos develop, Visium FFPE has been very helpful. It shows how genes change during development. This helps us understand how living things grow and develop.
These examples show how spatial transcriptomics is changing research. It helps us understand diseases, tissue structure, and how we develop.
“Visium FFPE has revolutionized the way we approach biomedical research, providing unprecedented insights into the spatial and temporal dynamics of gene expression across diverse disease states and developmental processes.”
Future of Spatial Transcriptomics
The future of spatial transcriptomics, like Visium FFPE, is full of new ideas. Scientists are working hard to make this technology even better. They aim to improve single-cell resolution, advance precision medicine, and make multi-omics integration easier.
Innovations on the Horizon
The Visium HD platform is an exciting new development. It promises to offer even better spatial resolution at the single-cell level. This will help researchers understand tissue biology in new ways, revealing more about how cells talk to each other and how they work.
Potential for Clinical Applications
There’s a lot of hope for using spatial transcriptomics in medicine. It could lead to better diagnostics and personalized medicine. Doctors could use this data to create more precise treatment plans, which could greatly improve patient care and life quality.
Integration with Other Technologies
Researchers are also looking to combine spatial transcriptomics with other advanced technologies. This includes proteomics and epigenomics. By doing this, they hope to get a fuller picture of tissue biology. This could help them find new ways to fight diseases and create better treatments.
“Spatially resolved transcriptomics was named as the ‘Method of the Year 2020’ by Nature Methods, reflecting the transformative impact of this technology on the scientific community.”
As spatial transcriptomics keeps growing, everyone is looking forward to what’s next. It has the power to change how we understand tissue biology and improve healthcare. The future of this technology looks very promising for both research and medical care.
Challenges with FFPE Samples
FFPE samples are great for spatial transcriptomics studies but come with challenges. The main issues are RNA quality, handling and storage, and the need for standard protocols.
RNA Degradation and Chemical Modifications
The formalin fixation process can damage RNA and change its chemical makeup. These changes can make it hard to get reliable gene expression data. It’s important to tackle RNA degradation and sample variability to get accurate results.
Handling and Storage Limitations
FFPE samples can degrade over time, especially if not stored properly. Temperature, humidity, and light exposure can all affect them. It’s key to develop strong protocol optimization for keeping FFPE samples in good condition.
Standardization Challenges
FFPE samples are used a lot in research and clinics, but there’s no one way to process them. Different methods can lead to inconsistent data. Setting clear guidelines is vital for solving these standardization issues and making spatial transcriptomics studies reliable.
Overcoming these challenges is essential for making the most of Visium FFPE technology. It will help researchers use the vast amount of valuable FFPE samples in tissue banks and pathology archives worldwide.
Best Practices for Using Visium FFPE
Visium FFPE is a powerful tool for studying spatial transcriptomics. It requires careful attention to ensure high-quality data. From choosing samples to designing experiments and solving problems, following the right steps is key.
Sample Selection Guidelines
When using Visium FFPE, tissue quality is crucial. Samples should have a DV200 of 30% or more for FFPE, and 50% or more for frozen tissues. For fresh frozen samples, a RNA Integrity Number (RIN) of 4 or higher is best. Proper fixation and processing are also vital to keep spatial and transcriptome information intact.
Experiment Design Tips
- Use technical replicates as controls to ensure reliable and reproducible data.
- Adjust tissue permeabilization conditions for better probe hybridization and mRNA capture.
- Choose the right number of tissue sections and capture areas per slide to balance data and cost.
Troubleshooting Common Issues
Even with careful planning, problems can still occur. Issues like poor tissue permeabilization, bad probe hybridization, and data normalization problems are common. Tweaking parameters like incubation times, probe amounts, and computational methods can help solve these issues.
| Tissue Quality Assessment | Experimental Controls | Data Normalization |
|---|---|---|
| DV200 ≥ 30% for FFPE DV200 ≥ 50% for Fixed Frozen RIN ≥ 4 for Fresh Frozen |
Technical replicates Positive and negative controls |
Mitochondrial and ribosomal gene exclusion Normalization against total reads per spot |
By sticking to these best practices, researchers can get the most out of Visium FFPE. This leads to better insights and moves science forward.
The Future of Visium FFPE Technology
Researchers are excited about the future of Visium FFPE technology. This tool helps get detailed genetic information from fixed tissue samples. It’s set to become even more powerful for scientists in many fields.
Planned Upgrades and Enhancements
One big goal is to improve the technology’s spatial resolution. This means capturing more detailed information from tissue samples. Also, adding data like epigenomics and proteomics is a priority. This will give a deeper look into how biological processes work.
Feedback from Researchers
Scientists have already shown a lot of interest in Visium FFPE. Their feedback has made the technology better. Now, analyzing data is easier and more straightforward. Work is also being done to automate analysis, making it simpler to understand the data.
Vision for Broader Use Cases
The future of Visium FFPE is bright, with plans to use it on more species. This will help compare different biological systems. Also, combining different types of data from the same tissue is expected. This will give a fuller picture of how tissues work.
The future of Visium FFPE is full of promise. With upgrades, feedback from scientists, and plans for wider use, it will drive the field of spatial transcriptomics forward. As shown in the [study], it has the power to open new doors in understanding complex biological systems.
| Key Features | Current Capabilities | Future Enhancements |
|---|---|---|
| Spatial Resolution | 55 μm (~1–10 cells) | Higher resolution for increased detail |
| Multi-Omics Integration | Transcriptome profiling | Integration of epigenomic and proteomic data |
| Data Analysis | Manual data interpretation | Automated analysis pipelines for streamlined insights |
| Sample Compatibility | FFPE samples | Expansion to additional species and sample types |
Collaboration Opportunities
The Visium FFPE technology from 10x Genomics opens up new chances for working together in science. By teaming up with schools, 10x Genomics is helping to grow this advanced spatial transcriptomics tool. This teamwork lets top scientists explore new ways to use this technology.
In the business world, 10x Genomics works with many groups to use Visium FFPE for finding new biomarkers. These partnerships combine 10x Genomics’ skills with those of other companies. Together, they find new ways to understand diseases and make progress in research.
Building a strong community of Visium FFPE users is key for 10x Genomics. They hold meetings, start online forums, and more to share ideas and solve problems. This helps scientists learn from each other and move forward in their work.
10x Genomics wants to speed up progress in translational research and technology development. They also aim to create a place where people can share knowledge. These efforts are important for making the most of spatial transcriptomics and advancing medical research.
Training and Support Resources
Spatial transcriptomics with the Visium FFPE platform from 10x Genomics is a powerful tool for researchers. But, it can be challenging to use. Luckily, 10x Genomics offers a lot of training and support to help users succeed.
Workshops and Webinars
10x Genomics hosts workshops and webinars on key topics like experimental design, sample preparation, and data analysis. These sessions are interactive and hands-on. They offer guidance from experts, helping users improve their protocol optimization and understand the technology better.
Online Documentation
The 10x Genomics website has a huge library of online documentation. It includes protocols, troubleshooting guides, and tutorials for the Visium FFPE workflow. These resources are very helpful, allowing users to handle technical support and data analysis tutorials on their own.
User Community Forums
10x Genomics also has a strong user community. Online forums let researchers connect, share, and work together on projects. This community is great for exchanging tips and staying current with new protocol optimization and data analysis tutorials.
With the help of 10x Genomics’ training and support, Visium FFPE users can fully explore spatial transcriptomics. This can lead to major breakthroughs in their research.
Real-World Applications of Visium FFPE
Visium FFPE is a tool used in many fields. It helps in understanding gene expression in tissue samples. This is key in drug development, personalized medicine, and research.
Product Development in the Pharma Industry
In the pharmaceutical world, Visium FFPE helps in drug discovery and finding the right targets. It shows where genes are active in tissues. This helps in making new drugs and improving old ones.
Advancements in Personalized Medicine
Visium FFPE also helps in personalized medicine. It lets doctors tailor treatments based on each patient’s genes. This leads to better healthcare for everyone.
Insights from Translational Research
Visium FFPE gives insights in research. It helps connect basic science to real-world use. It’s used in many areas like cancer, brain diseases, and immune system studies.
| Application | Key Findings | Impact |
|---|---|---|
| Mapping Tumor-Immune Composition in Early-Stage Lung Cancer | Identified immune cell types and gene expression signatures in the tumor microenvironment | Revealed insights into the complex interplay between tumor cells and the immune system, informing potential therapeutic strategies |
| Tracking Cleft Palate Development | Identified cell types and genes involved in palate fusion, including three novel genes related to cilia function | Improved understanding of the underlying mechanisms of cleft palate formation, potentially leading to better preventive and interventional approaches |
| Analyzing Heterogeneous Breast Cancer Samples | Identified a small triple-positive tumor region missed by pathological annotation and defined cell composition and gene markers for different tumor regions | Provided a more comprehensive and precise characterization of tumor heterogeneity, which can inform personalized treatment strategies |
As spatial transcriptomics grows, so will Visium FFPE’s uses. It will change drug making, personalized care, and research in many diseases.
Conclusion
The Visium FFPE technology is a big step forward in understanding how genes work in tissues. It gives us new views into how genes are active in different parts of tissues. This technology is getting better and will help us learn more about many diseases.
It’s changing how we do research in many areas of medicine. You can learn more about it here: https://openworks.mdanderson.org/cgi/viewcontent.cgi?article=1049&context=sumexp21.
Summary of Key Takeaways
Visium FFPE lets us see where genes are active in tissues very clearly. It works with many types of tissue samples and makes research easier. This helps us understand how different cells work together in tissues.
It has already helped us learn a lot about cancer, brain diseases, and how bodies grow. This technology is very useful and has already led to big discoveries.
The Path Forward for Spatial Transcriptomics
As we keep improving spatial transcriptomics, Visium FFPE will be key. It will help us find new ways to understand and treat diseases. Researchers should use this technology to make new discoveries.
This will help us learn more about how our bodies work. It will also help us find new ways to fight diseases.
Call to Action for Researchers
Researchers from all fields should try Visium FFPE. It can open up new ways to study diseases. By using this technology, they can make new discoveries and help people.
Using Visium FFPE can lead to big breakthroughs. It can help us understand and treat diseases better. This will improve our health and well-being.
Q: What is Visium FFPE?
A: Visium FFPE is a new tech for studying genes in old tissue samples. It lets scientists use over a billion stored samples. This tech combines gene study with tissue details.
Q: What are the key features of Visium FFPE?
A: Visium FFPE gives detailed gene data, works with many samples, and makes research easier. It changes how we understand diseases.
Q: What are the benefits of using Visium FFPE?
A: It links gene data to specific tissue spots, giving better insights. It works well for many diseases and biological processes.
Q: How does Visium FFPE compare to other methods?
A: Visium FFPE beats old methods with its detailed gene data and high sensitivity. It finds new genes and solves old problems.
Q: What is the role of FFPE in biomedical research?
A: FFPE has preserved tissues for over 100 years. Now, it’s used for studying old samples. Researchers and biobanks work together to unlock these samples.
Q: How does the Visium FFPE technology work?
A: It uses special slides with barcodes. Tissue samples are placed on these slides. Then, imaging and sequencing map gene data to tissue spots.
Q: What are the challenges with using FFPE samples?
A: FFPE samples face issues like RNA damage and storage problems. Fixing these is key for using Visium FFPE fully.
Q: What are the best practices for using Visium FFPE?
A: Choose the right samples and design experiments well. Troubleshoot by improving tissue prep and data analysis.
Q: What is the future of Visium FFPE technology?
A: Future upgrades include better resolution and more data types. Automated tools and community help will make it easier to use.
Q: How can researchers get support and training for Visium FFPE?
A: 10x Genomics offers training and support. This includes workshops, webinars, and online help. It helps researchers share knowledge and solve problems.
Q: What are the real-world applications of Visium FFPE?
A: It’s used in drug discovery and personalized medicine. It helps in many fields, like cancer and brain studies.
