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Maximizing the Scientific Value of Tissue Biomarker Analysis: Case Studies in Immuno-Oncology and Dermatology

Tissue Biomarker Analysis

Complex diseases and target organ structures often require detailed interrogation of tissue to provide insight into disease biology or to investigate drug efficacy and safety. While tissue biopsies can be invasive, they do enable localized analysis of protein biomarkers and topographic investigation of disease-and drug-related changes. Over recent years, spatial analysis of multiple tissue biomarkers has become a routinely used method of generating supporting or exploratory data during clinical development, especially in conditions with a core immune component such as cancer and inflammatory and autoimmune skin diseases.

In this era of precision medicine, tissue biomarker data has applications in every stage of development. Thus, it is critical for researchers to develop and implement a strong biomarker strategy that generates the actionable data needed to drive both preclinical and clinical decision-making. In this article, we explore approaches for maximizing the scientific value of tissue samples in immuno-oncology and dermatology.

Approaches to Tissue-Based Analysis

Precision medicine-based approaches are focused on getting the right drug to the right patient at the right dose and time. Arguably, the most impactful use of biomarkers in precision medicine is for patient selection—identifying which patients are going to respond to a particular therapy. A classic example of this application is a validated singleplex immunohistochemistry (IHC) assay for PD-L1 expression, which can be used to screen patients with non-small cell lung cancer (NSCLC) for eligibility for pembrolizumab (Keytruda®), a PD-1 inhibitor (see Figure 1).


Figure 1. Determining eligibility for pembrolizumab in NSCLC using PD-L1 expression
[TPS: tumor proportion score]

Multiplex immunofluorescent IHC (mIF) approaches have the advantage of providing additional knowledge about the patient or the disease by generating high-content data from a single sample. This allows researchers to not only assess trial or treatment eligibility, but also take a deeper dive into the biology of that individual tumor by enumerating immune cell populations and investigating spatial relationships among cells. With the Akoya Opal system, researchers can run up to eight markers per panel plus a DAPI counterstain. This approach is often used to support exploratory biomarker analysis, especially in immuno-oncology. Panels can be designed to best investigate the relevant biology for a particular disease.

Whether an assay is used to support enrollment or exploratory investigative analyses, it must be appropriately qualified or validated. The level of validation required depends on how the assay will be applied and how the resulting data will be used and becomes more rigorous when moving from pre-clinical working assay protocols to fully validated, CLIA-regulated assays.

Application of IHC and mIF in Immuno-Oncology

Case Study 1: Developing a P-cadherin IHC assay for patient selection [1]

Client wanted to develop a validated custom IHC assay, reagent kit, and scoring index (SI) for assessing P-cadherin, a cellular adhesion protein that contributes to oncogenesis. The SI was based on the tumor area stained multiplied by the staining intensity, with a scale from 0 to 9. This assay was rolled out to three global Phase 1 sites and study eligibility required an SI of greater than or equal to 4. Each site ran the IHC assays independently and used their own pathologists to do the analysis. The laboratory served as a central site, performing independent mass analysis of site results and finding almost 92% concordance in the results. This case study demonstrated the feasibility of developing and fully validating an IHC assay at a single center and running that assay at multiple sites across the globe to support patient selection.

Case Study 2: Assessing the level of immune suppression in tumors

Spatial analyses play an important role in evaluating the tumor microenvironment and distinguishing between immunologically hot and cold tumors. Immunologically hot tumors, which account for 10-30% of solid tumors, display homing of T cells to the tumor, abundant immune cell infiltration, and high tumor mutational burden (TMB). In contrast, immunologically cold tumors demonstrate no T cell homing or immune cell infiltration, and low TMB. Understanding the level of immune suppression in tumors is critical to the success of certain immuno-oncology therapies, such as checkpoint inhibitors, which rely on a hot tumor phenotype.

Precision for Medicine used mIF approaches to examine and classify the spatial orientation, distribution, and activation status of immune cells in a tumor sample, as seen in Figure 2, which shows a PD-L1 positive tumor where the type, location, and density of immune cells confirms an immunologically hot tumor.


Figure 2. Identifying and characterizing an immunologically hot PD-L1 positive tumor

Application of IHC and mIF in Dermatology

Skin is a large, complex, peripheral lymphoid organ that provides both a mechanical and immunological defense to disease. Immune homeostasis of the skin requires a finely-regulated equilibrium among myriad cellular components and the associated skin microbiome. Dysregulation of this balance contributes to the pathogenesis of many severe, chronic inflammatory and autoimmune skin diseases, which can be extremely painful and debilitating for patients.

Scientists developing dermatology therapeutics may require detailed interrogations of the skin to establish mechanism of action or early proof of concept, or to explore issues related to drug safety. With such a broad range of often biologically distinct, inflammatory skin diseases, successful assay and clinical development depends upon reliable access to relevant, high-quality disease tissues that are representative of the target clinical population. It may also be useful to work with specialist dermatopathologists who can assist in tissue selection, sample pathology, and immunohistochemical data review and scoring.

MIF approaches help to maximize the scientific value of skin samples, which are typically obtained by invasive punch biopsy. Over the years, Precision for Medicine has developed and validated many IHC assays for targets that are relevant for dermatology research and development, including:

  • A broad panel of immune cell markers
  • Structural skin proteins, such as cytokeratins, collagens, and elastin
  • Inflammatory signaling receptors, such as prostanoid receptors and IL-36 receptor
  • Markers of barrier protein biology, such as involucrin and transglutaminase

Custom panels can also be designed and developed to interrogate the relevant biology in different disease indications (see Figure 3).


Figure 3. Sample mIF panels for common dermatology indications

Case Study 3: Maximizing samples with RNAlater

To further maximize the value of skin punch biopsy samples, Precision for Medicine explored methods to collect these samples in a manner that would enable multiple downstream evaluations performed at different timepoints or even different facilities. Skin punch biopsies were collected and placed into RNAlater® to maximize their suitability for genomic analyses. Each sample was divided into thirds and then:

  1. Formalin-fixed paraffin-embedded (FFPE) blocks were prepared and resulting sections were evaluated by H&E staining and IHC
  2. Messenger RNA (mRNA) was analyzed with RNAseq or Nanostring
  3. Immune cells were quantified using Precision for Medicine’s proprietary PCR-based epigenetic immunophenotyping platform, Epiontis ID®

We found that the skin punch biopsy samples yielded sufficient material for all three downstream evaluations and RNAlater storage had no detrimental effect on either sample utility or data quality (see Figure 4).


Figure 4. Comparison of H&E staining and mIF on immediate and RNAlater-preserved FFPE samples


The analysis of tissue biomarkers in complex diseases such as cancer and inflammatory and autoimmune skin conditions requires early planning. Success is driven by selecting fit-for-purpose biomarkers, sourcing high-quality, cohort-relevant biospecimens for assay development and validation, and securing strong specialty lab and pathology support. Working with a partner who has proven experience in custom assay development and tissue-based analyses can help researchers and developers maximize the data derived from each precious patient sample.

To learn more about how Precision for Medicine helps life science companies maximize insights into patient biology and accelerate the pace of scientific discovery and approval in complex diseases, view our on-demand webinar.


1. Davis DW, et al. “Prospective Real-Time Analysis of P-cadherin Expression to Select Patients into a Phase I Oncology Trial.” EORTC-NCI-AACR, 2009.