Use of Magnetic Resonance Imaging and Biopsy Data to Guide Sampling Procedures for Prostate Cancer Biobanking
October 10th, 2019
This method involves utilization of clinical diagnostic data for prostate cancer patients in order to guide sampling procedures, when biobanking tissue following radical prostatectomy. This overcomes issues with previously published methods around efficiency and availability of fresh tissue for a wider range of downstream applications.
The significance of this protocol over previous prostate sampling methods is that it gives us a higher confidence of targeting fresh tumor tissue for research. Therefore, we can take the fresh tissue straight back to the lab and use it for culture or imaging because we have a high confidence of which samples are tumor and which are benign. My key advice when learning the technique is to work with your local pathologist so that final tissue diagnosis and report are not compromised.
To target the tumor location, review the MRI images to measure the location above the tumor and find the sequence at which the tumor is most visible in the axial plane. Scroll through the axial images to identify the image in which the tumor is the largest and print the image for reference. In the corresponding coronal image, measure the distance from the base of the prostate to the selected axial position and measure the full length of the prostate from the apex to the base in millimeters.
Then print these measurements and mark the locations of the tumor for reference. After the specimen has been collected, sterilize the laminar flow hood and prostate slicing apparatus with 70%ethanol and weigh the prostate on a standard scale in grams. Then paint the right side with blue ink and the left side of the specimen with black ink covering the full capsule and seminal vesicles with ink to allow discrimination of the surgical margins.
To slice the prostate, place the tissue with the base and apex facing opposite walls of the apparatus with the posterior side down and the anterior side up. Place gold pins around the tissue specimen pushing the prostate inward slightly if necessary to achieve a snug fit and measure the prostate length from the base to the apex to compare this measurement to the prostate length that is measured by MRI. If the prostate has shrunk, adjust the anticipated slicing position by the appropriate percentage of the reduction.
Next, measure from the base to the desired transverse slice and select the pin that sits closest to this measurement to slice around. Wearing chainmail gloves to prevent injury, place the blades of the slicing device on either side of the identified pin and use the spacer to keep the blades five millimeters apart. To acquire the slice, use long strokes to slowly but firmly move the blades downward, forward, and backward confirming by feel that a full slice has been separated before disassembling the apparatus.
Then remove the walls and pins and use gloves to carefully transfer the slice onto a sterile piece of corkboard. After acquiring the specimen, visually inspect the transverse slice for comparison with the axial MRI image. In some cases, the tumor area may appear paler than the surrounding tissue.
Palpate the transverse slice gently. The tumor may feel firmer than the surrounding tissue. Using the axial MRI image as a guide, select one or more areas for sampling and use a six millimeter punch to push down on the tissue area of interest.
Twist the tissue punch on the spot and down against the cork to ensure a full separation using a sharp scalpel to separate the biopsy sample from the specimen as necessary. When the sample has been acquired, remove the punch and use the plunger to eject the sample into the appropriate container for the subsequent downstream analysis. Then ink the holes where the punches were taken in red and note the location of each punch along with the weight of the prostate and any observations about the tissue color and firmness.
Pin the prostate capsule to the cork to prevent bilging during fixation. Submerge the prostate and cork into fixative ensuring the sample is fully submerged. In this representative analysis, of the first 92 cases sampled as demonstrated, 64%of the specimens contained at least 40%tumor and were submitted to the 100, 000 Genomes Project without microdissection.
DNA was extracted and was of sufficient yield and quality in all of the cases and an initial subset of 59 of these samples has been published for comparison with an earlier specimen sampling method. Following this procedure, the fresh tumor samples can be used for either live imaging or culture allowing us to test new biomarkers, drugs, and find out more about tumor biology. Now that we use this method routinely, I've been able to bring forward a project using this tissue for ex vivo culture to look at new combinations of preclinical therapies for prostate cancer.
Overview
This protocol enhances the efficiency of prostate cancer tissue sampling by utilizing clinical diagnostic data to guide the sampling process. It allows for the collection of fresh tumor tissue, which can be directly used for various downstream applications.
Key Study Components
Area of Science
- Oncology
- Pathology
- Biobanking
Background
- Previous methods for prostate tissue sampling lacked efficiency and reliability.
- Fresh tissue is crucial for accurate research and analysis.
- Utilizing MRI imaging improves targeting of tumor locations.
- Collaboration with pathologists is essential for accurate diagnosis.
Purpose of Study
- To improve the accuracy of tumor tissue sampling in prostate cancer patients.
- To facilitate the use of fresh tissue for research applications.
- To establish a reliable protocol for biobanking prostate tissue.
Methods Used
- Reviewing MRI images to locate tumors accurately.
- Measuring and marking tumor locations on prostate specimens.
- Using a slicing apparatus to obtain transverse slices of the prostate.
- Sampling tumor areas with a tissue punch for downstream analysis.
Main Results
- 64% of specimens contained at least 40% tumor tissue.
- DNA extracted from samples was of sufficient yield and quality.
- Fresh tumor samples were successfully used for live imaging and culture.
- Initial comparisons with earlier sampling methods showed improved outcomes.
Conclusions
- The protocol significantly enhances the reliability of prostate tissue sampling.
- Fresh tissue can be effectively utilized for research on prostate cancer.
- Collaboration with pathologists is crucial for successful implementation.
Frequently Asked Questions
Executive Industry Relevance
Targeted prostate tissue sampling using MRI and biopsy data addresses a critical need for high-confidence tumor identification in biobanking workflows. This approach enhances predictive confidence for downstream applications, enabling more reliable translational research and preclinical model development. By increasing the proportion of tumor-rich samples, the method supports robust portfolio decision-making and risk-adjusted advancement in oncology R&D.
Strategic Applications in Biopharma R&D
Early Discovery & Target Validation
- Enables precise interrogation of tumor biology by isolating regions with high tumor content.
- Improves functional target validation by ensuring sample relevance and minimizing benign tissue contamination.
- Supports predictive confidence in biomarker and mechanistic studies through accurate tissue selection.
Screening & Assay Development
- Facilitates preparation of validated tumor samples for genomics, proteomics, and histological assays.
- Enhances assay reproducibility and standardization by reducing sampling variability.
- Enables reliable evaluation of compounds in ex vivo culture and live tissue imaging platforms.
Translational & Preclinical Research
- Aligns biobanking outputs with disease-relevant systems for translational biomarker discovery.
- Provides continuity from tissue acquisition to preclinical validation by supporting fresh tissue applications.
- De-risks preclinical studies by ensuring tumor content and sample quality for functional assays.
Pipeline & Workflow Integration
This MRI- and biopsy-guided sampling method integrates at the interface of tissue acquisition and downstream molecular analysis, bridging early discovery with translational and preclinical research.
- Discovery Biology: Supports hypothesis testing and pathway clarification by providing tumor-enriched samples.
- Screening: Delivers assay-ready tissue with high reproducibility and quantitative tumor content.
- Analytics: Enables robust measurement of molecular and cellular endpoints for comparative studies.
- Translational Research: Connects biobanking to biomarker and drug response studies using fresh, disease-relevant tissue.
- Enterprise Reuse: Establishes a standardized, scalable protocol for repeated use across oncology research programs.
Operational & Enterprise Impact
- Scientific Value: Increases predictive confidence and reduces mechanistic ambiguity in tissue-based studies.
- Operational Value: Standardizes sampling, improves reproducibility, and supports scalable biobanking operations.
- Strategic Value: Enables informed go/no-go decisions and reduces late-stage biological risk in oncology portfolios.
- Portfolio Impact: Supports risk-adjusted prioritization and advancement of translational and preclinical assets.
Implementation Considerations
- Requires expertise in MRI interpretation and close collaboration with pathology teams.
- Needs access to specialized slicing devices and sterile biobanking infrastructure.
- Demands rigorous cross-team standardization to maintain diagnostic integrity.
- May require adaptation for different prostate sizes or tumor locations.
- Dependent on quality of imaging and biopsy data for optimal targeting.
