Interdisciplinary team collaboration brings new TMA resource to researchers

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The National Cancer Institute Patient-Derived Models Repository (NCI-PDMR) recently released its first publicly available tissue microarray panel from patient-derived xenografts (PDX) of pancreatic adenocarcinoma.

A team of scientists at the Frederick National Laboratory for Cancer Research collaborated to help curate and develop this new resource for the National Cancer Institute and the greater cancer research community.

“Everyone has been very excited with the public launch of the tissue microarrays for research use as part of the NCI-PDMR offerings, and we will continue to expand the ‘menu’ of tissue microarrays available,” said Yvonne A. Evrard, Ph.D., research manager for the repository at the Frederick National Laboratory.

To launch this inaugural panel, scientific teams across the national laboratory partnered to provide key support for the project, showcasing a different side of their expertise along the way.

“The Molecular Characterization Laboratory is known for providing genomic support for NCI-sponsored studies, but we are more than that,” said Chris Karlovich, Ph.D., head of the Molecular Characterization Laboratory. “We have a CLIA histopathology laboratory with wide-ranging capabilities, which has been providing support for the PDMR project since the beginning.”

The NCI-PDMR is one of the largest repositories for patient-derived models. To launch into this new venture with tissue microarray panels, the team first needed to know the types and features that would be most valuable for researchers.

Selecting the models

Cindy R. Timme, Ph.D., a scientist in the Applied and Developmental Research Directorate, oversees distribution for the repository and is the project manager for creating these tissue microarray panels. 

She selected the PDXs to use in the panel after working with National Cancer Institute clinicians to curate pancreatic models with clinically relevant features.

"The selection of PDX models was my most challenging aspect of the project as it required collating a lot of data,” she said.

She created documents to track all the patient and genomics data, parsing individual datasets and ensuring each model had its corresponding data.

Once she selected the models for the panel, Timme sent the finalized list of 60 PDXs to Lindsay Dutko and her team in the Molecular Characterization Laboratory.

Creating the panels

Dutko is the Clinical Laboratory Improvement Amendments (CLIA) manager for the Molecular Characterization Laboratory’s histopathology team, which houses all the formalin-fixed, paraffin-embedded (FFPE) blocks for the PDMR project, dating back to 2013.

Dutko and her team prepared the FFPE blocks and annotated stained slides and digital images, which a subcontractor used to create tissue microarray blocks.

The annotations shared which area of the tumor to remove the tissue cores from for the tissue microarray blocks. Each block contained 120 tissue cores–two cores from each of the 60 PDX models plus additional control tissue cores.

Dutko and her team then took the tissue microarray blocks and sectioned slide sets, which went through routine staining and testing.

Sayak Ghatak, a pathologist in the Molecular Characterization Laboratory, used his expertise in digital pathology to develop an algorithm to score cores from these tissue microarrays.

A pass/fail threshold is set for the slide set, so that slides distributed to requesting investigators have 75% of the PDX models represented on each slide with at least 500 viable human tumor cells present.

“The project was a large undertaking by our lab,” Dutko said. “With each tissue microarray panel that we create, we are learning how to be more efficient in our efforts without compromising quality.”

A ‘significant milestone’ with more to come

The total time from start to finish, from selecting the models to making the panel publicly available, took about two years. Timme said they anticipate the second panel, which will be the first of four colorectal panels, will take less time as the team has identified and worked through early hurdles and established processes for the tissue microarray creation pipeline.

“We have received a lot of inquiries from the research community on the availability of unstained tumor tissue slides for our PDX models,” Timme said.  “The launch of our tissue microarrays addresses this need in the research community.”   

Dutko said this tissue microarray panel is a significant milestone for the PDMR project, allowing investigators to interrogate 60 different PDX models against a biomarker of interest on one slide.

“I am most proud of the potential impact this work will have on the cancer research community,” Dutko said. “This tissue microarray panel will provide investigators with a valuable resource to further advance their contribution to cancer research.”