Choose Wisely. Your Biospecimen Strategy Can Make or Break Your Biomarker-Driven Cancer Research

By Anuj Kalsy, Scientific Director, Precision for Medicine

Immunotherapy is transforming the treatment of cancer, with efficacy observed across a variety of tumors. Recent advances in biomarker analysis have been critical not only for identifying those patients who are likely to achieve benefit from immuno-oncology therapeutics, but also for providing insight into the mutational variations of tumors throughout treatment and disease progression. These advancements in biomarker discovery, validation, and clinical application have hinged on one critical resource: Quality biospecimens.

Access to a consistent supply of high-quality, deeply phenotyped biospecimens is required to support ongoing biomarker discovery and validation for any novel immuno-oncology treatment, from immune checkpoint and targeted therapeutics to chimeric antigen receptor T (CAR-T) cell therapies and other precision medicines. To extract the necessary data from these biospecimens, researchers must also consider which specimen type is most appropriate for the scientific question to be answered.

Below, we discuss key considerations for developing the right biospecimen strategy to advance immuno-oncology research and development (R&D), with a focus on applications of biospecimens to support biomarker discovery.

Optimizing Program Success with a Robust Biospecimen Strategy

Sourcing and selecting the right biospecimens is make or break in the identification of de novo biomarkers or therapeutic drug targets. The use of large cohorts of quality-controlled biospecimens that contain rich disease characterization has enabled the identification of tumor associated antigens and has led to the successful development of myriad targeted therapies, including monoclonal antibodies, antibody drug conjugates (ADCs), anti-cancer vaccines, and CAR-T cell therapies.

Researchers who are unable to procure the right biospecimens to validate and guide therapeutic or diagnostic development are more likely to see their programs fail in clinic. For example, many programs falter because the drug target is expressed only by a subset of patients or is also present in healthy patients, both of which could have been discovered early on by comparing biomarker prevalence in severe versus mild disease or versus controls. If the biospecimen strategy does not include disease severity characterization or a powered control group, this type of validation is impossible.

Quality biospecimens are also critical for the identification of novel cancer resistance mechanisms and oncogenic pathways. Research has shown that biomarker expression may change throughout cancer treatment and tumor progression. Repeated biospecimen profiling over time can provide insight into mechanisms of treatment-specific resistance or immunological escape and may also be used to inform disease management. Thus, procuring specimens with longitudinal collections can help guide researchers’ treatment and study stratification plans.

Successful sourcing of these specimens requires a robust biospecimen strategy and a reliable biospecimen solutions partner. The Precision for Medicine Biospecimen Solutions team has a dedicated operation for specimen collection, processing, and logistics that supports 1,500 R&D clients globally. Their prospective collection capabilities include blood, biofluids, tissues, and cell products from almost any disease, including related scientific services.

The Critical Role of Biomarkers in Immuno-Oncology

The discovery that blocking the programmed death-1 (PD-1)/programmed death-ligand 1 (PD-L1) pathway could enhance anti-tumor T cell reactivity and promote immune control over cancer cells was a turning point in immuno-oncology. The seven PD-1 or PD-L1 immune checkpoint inhibitors approved to date have been a therapeutic breakthrough for patients with many types of cancer. However, only 20-40% of patients derive benefit from these therapies and, of those who do respond, a substantial proportion acquire resistance. Moreover, some patients whose tumor biopsies do not appear to show dysregulated expression of these biomarkers still respond to treatment. All these factors highlight the complex biological underpinnings of therapeutic response, heterogeneity and underscore the need to optimize immuno-oncology biomarkers for patient selection and treatment monitoring.[i]

Already, many immune checkpoint inhibitors use either an immunohistochemistry (IHC)-based companion or complementary diagnostics to evaluate the potential safety and effectiveness of the treatment in a particular patient, though none of these diagnostics are definitive. Other biomarkers, such as tumor mutational burden (TMB), microsatellite instability (MSI), and gene expression profile, may also be valuable for subclassifying tumor types and assessing likelihood of response. In some tumor types, immune function genes, inflammatory markers, and human leukocyte antigen (HLA) expression may provide predictive information. More recently, molecular, and spatial profiling with multiplex immunofluorescence has been used to assess the tumor microenvironment, providing insight into the extent and distribution of immune cell infiltration, which affects the activity and efficacy of immune checkpoint inhibitors. The Precision for Medicine Translational Solutions team offers specialty lab capabilities, leveraging established technologies and proprietary approaches to generate robust biomarker data from the full range of biospecimens.

Selecting Fit-for-Purpose Biospecimens

Given the diversity of biospecimens, it is essential to choose the specimen type that is most appropriate for generating the required data. Formalin-fixed, paraffin-embedded (FFPE) tissues are versatile biospecimens with a range of applications. FFPE specimens are frequently used to determine tissue distribution of an antigen or biomarker of interest or to perform genomic profiling. With the development of newer transcriptomic technologies, it is also possible to perform gene expression analysis studies on FFPE tissues. In addition, FFPE samples of solid tumors can be used for molecular and spatial profiling or epigenetic profiling, an emerging approach to understanding the molecular basis of carcinogenesis.

Liquid biospecimens are valuable tools for evaluating biomarkers and identifying potential targets for further validation to shape immuno-oncology therapies. Plasma is one of the most widely used biospecimens for cancer biomarker discovery research and diagnostic or therapeutic development.[ii] The plasma proteome can provide insight into normal physiological states and cancer-induced alterations in the body; however, studying it can be challenging. The plasma proteome comprises high-abundance proteins and a wide dynamic range of protein concentrations. Recent advances in mass spectrometry workflows have made it possible to perform unbiased, hypothesis-free characterizations of the plasma proteome to screen for and validate biomarkers.,[iii] These workflows eliminate the needs for separate immunoassay-based validation, accelerating biomarker discovery.

Due to their role in the innate and adaptive immune system, peripheral blood mononuclear cells (PBMCs) have long been used to study immunological mechanisms and responses. Immuno-oncology R&D generally requires PBMCs that have been characterized by cell type, quantity, and activity, and are accompanied by phenotypic data such as patient medical history. Such in-depth characterization is vital for any study seeking to elucidate the molecular differences or drivers of various disease severities or subtype or to compare against controls.

PBMCs can be used for both in vitro and in vivo studies. Common applications for in vitro PBMC studies include cell function investigations and disease modeling. In vivo analyses may involve reconstituting immunocompromised animal models with human PBMCs to study immune response to malignant tumors. PBMCs can also be used in adoptive cell therapy for expanding patient-derived T cells.

Precision for Medicine Biospecimen Solutions has developed an infrastructure for delivering fresh PBMCs with the highest viability, purity, and cell counts. In addition, their extensive biorepository enables access to deeply characterized health and disease state PBMCs from a diversity of donors, often with matched plasma and tissue, facilitating evaluation of population differences in immunological responses.

Incorporating Advanced Liquid Biopsy Techniques into a Biospecimen Strategy

Blood- or biofluid-based biomarkers offer flexibility, as samples can be collected less invasively and more frequently than tissue biopsies. Liquid biopsies enable analysis of tumor cells or tumor cell products and, in principle, have the potential to reflect all subclones present at a single point in time for assessing tumor burden, tracking tumor evolution, or monitoring treatment response. In addition to enabling longitudinal assessments, liquid biopsies can also be used to complement tumor tissue, providing deeper molecular insights.

Currently, it is possible to analyze the genetic material of circulating tumor cells at the single cell level to evaluate both spatial and temporal dynamics. Liquid biopsy techniques have also expanded to include circulating tumor DNA (ctDNA), cell-free DNA or RNA (cfDNA or cfRNA), soluble proteins, and exosomes. The approvals of the Guardant360 CDx assay and the FoundationOne Liquid CDx test, both of which combine liquid biopsy with next generation sequencing (NGS) reflect the growing importance of genomic profiling in immuno-oncology and precision medicine. NGS has been widely adopted for genomic profiling due its massively parallel sequencing capability and its compatibility with low-quantity input DNA. It is also the preferred sequencing method when target mutations are not known, as in biomarker discovery.

Supporting New Biomarker Discovery and Development

Clinically meaningful, actionable mutations occur at extremely low frequencies and finding biospecimens with those specific mutations is a challenge for researchers and diagnostic or therapeutic developers. To help create a library of deeply characterized biospecimens that can be leveraged for immuno-oncology R&D, Precision for Medicine Biospecimen Solutions launched the Precision Oncology Sequencing Initiative (Project P.O.S.I.) Project P.O.S.I. is a large-scale, two phase NGS initiative to screen biospecimens for key biomarkers across cancer indications, designed to generate data from real clinical samples rather than contrived specimens. The screening panels used include the Oncomine Precision Assay, which detects 2,768 unique cancer variants across 50 genes, and the Illumina TSO500 assay, which includes pan-cancer biomarker content for a variety of solid tumor types and can also measure TMB and MSI.

The first phase of this undertaking, which is ongoing, focuses on NGS screening of thousands of FFPE tumor tissues from our extensive biorepository. The second phase of Project P.O.S.I. involves mass screening of liquid biopsies. From our global clinical network comprising over 55 countries, Precision for Medicine is prospectively collecting cfDNA from liquid biopsies obtained from patients with cancer. NGS data from these cfDNA samples is combined with clinical information and liquid biopsy metadata and then interrogated using QuartzBioSM, our proprietary multi-omics data processing engine.

Key Takeaway

Precision for Medicine is dedicated to accelerating the discovery of clinically meaningful biomarkers to support the development of immuno-oncology therapeutics and diagnostics. With our extensive biospecimen repository, large specialty lab network, logistics capabilities, and full-service clinical research organization solutions, we are helping researchers and developers deliver on the promise of precision oncology.

Anuj Kalsy, Scientific Director, Precision for Medicine (Insert Anuj’s headshot here)

[Anuj Kalsy is an advanced-career pharma professional & leader amassing over two decades of specialized scientific experience in academia & industry, patents, and several high-impact factor publications. He uses his scientific, leadership & translational drug discovery research skills as a biomedical leader to contribute effectively to the Pharma & Clinical R&D niche. Anuj also serves as a subject management expert in oncology, angiogenesis, immuno-oncology, targeted therapies, immunology & vaccine design, and development. Anuj Kalsy’s translational focus is on development of antibody drug conjugates, high content imaging, primary patient-derived tumor cell line engineering, patient-derived tumor xenografts tumor model development, in vitro & in vivo target validation, cell-based assays & biomarker discovery.]


[1] Doroshow DB, et al. PD-L1 as a biomarker of response to immune-checkpoint inhibitors. Nat Rev Clin Oncol. 2021;18(6):345-362.

[1] Kumar V, Ray S, Ghantasala S, Srivastava S. An integrated quantitative proteomics workflow for cancer biomarker discovery and validation in plasma. Front Oncol. 2020;10:543997.

[1] Geyer PE, Holdt LM, Teupser D, Mann M. Revisiting biomarker discovery by plasma proteomics. Mol Syst Biol. 2017;13(9);942.

[i] Doroshow DB, et al. PD-L1 as a biomarker of response to immune-checkpoint inhibitors. Nat Rev Clin Oncol. 2021;18(6):345-362.

[ii] Kumar V, Ray S, Ghantasala S, Srivastava S. An integrated quantitative proteomics workflow for cancer biomarker discovery and validation in plasma. Front Oncol. 2020;10:543997.

[iii] Geyer PE, Holdt LM, Teupser D, Mann M. Revisiting biomarker discovery by plasma proteomics. Mol Syst Biol. 2017;13(9);942.