Workshop on Cancer Biometrics: Identifying Biomarkers and Surrogates of Cancer in Patients

The Society for Immunotherapy of Cancer Biomarkers Task Force recommendations review

The clinical successes in cancer immunotherapy have led to a critical need for biomarkers in cancer immunotherapy. It is of the utmost importance to know who is most likely to benefit from these therapies (predictive biomarkers) but also who is starting to respond (prognostic biomarkers) and how the therapy functions in order to make rational combination choices (mechanism of action biomarkers). The Society for Immunotherapy of Cancer (SITC) Biomarkers Task Force addressed the state of the art and made a series of recommendations for the field, which is summarized here.

Preamble to the 2015 SITC immunotherapy biomarkers taskforce

The Society for Immunotherapy of Cancer (SITC) has regularly hosted workshops and working groups focused on immunologic monitoring and immune biomarkers. Due to advances in cancer immunotherapy, including positive results from clinical trials testing new agents and combinations, emerging new technologies for measuring aspects of immunity, and novel candidate biomarkers from early phase trials, the SITC Immune Biomarkers Taskforce has reconvened to review the state of the art, identify current hurdles to further success and to make recommendations to the field. Topics being addressed by individual working groups include: (1) validation of candidate biomarkers, (2) identification of the most promising technologies, (3) testing of high throughput immune signatures and (4) investigation of the pre-treatment tumor microenvironment. Resultant recommendations will be published in JITC.

SITC/iSBTc Cancer Immunotherapy Biomarkers Resource Document: online resources and useful tools - a compass in the land of biomarker discovery

Recent positive clinical results in cancer immunotherapy point to the potential of immune-based strategies to provide effective treatment of a variety of cancers. In some patients, the responses to cancer immunotherapy are durable, dramatically extending survival. Extensive research efforts are being made to identify and validate biomarkers that can help identify subsets of cancer patients that will benefit most from these novel immunotherapies. In addition to the clear advantage of such predictive biomarkers, immune biomarkers are playing an important role in the development, clinical evaluation and monitoring of cancer immunotherapies. This Cancer Immunotherapy Resource Document, prepared by the Society for Immunotherapy of Cancer (SITC, formerly the International Society for Biological Therapy of Cancer, iSBTc), provides key references and online resources relevant to the discovery, evaluation and clinical application of immune biomarkers. These key resources were identified by experts in the field who are actively pursuing research in biomarker identification and validation. This organized collection of the most useful references, online resources and tools serves as a compass to guide discovery of biomarkers essential to advancing novel cancer immunotherapies.

Functional assessment of human dendritic cells labeled for in vivo (19)F magnetic resonance imaging cell tracking

BACKGROUND AIMS

Dendritic cells (DC) are increasingly being used as cellular vaccines to treat cancer and infectious diseases. While there have been some promising results in early clinical trials using DC-based vaccines, the inability to visualize non-invasively the location, migration and fate of cells once adoptively transferred into patients is often cited as a limiting factor in the advancement of these therapies. A novel perflouropolyether (PFPE) tracer agent was used to label human DC ex vivo for the purpose of tracking the cells in vivo by (19)F magnetic resonance imaging (MRI). We provide an assessment of this technology and examine its impact on the health and function of the DC.

METHODS

Monocyte-derived DC were labeled with PFPE and then assessed. Cell viability was determined by examining cell membrane integrity and mitochondrial lipid content. Immunostaining and flow cytometry were used to measure surface antigen expression of DC maturation markers. Functional tests included bioassays for interleukin (IL)-12p70 production, T-cell stimulatory function and chemotaxis. MRI efficacy was demonstrated by inoculation of PFPE-labeled human DC into NOD-SCID mice.

RESULTS

DC were effectively labeled with PFPE without significant impact on cell viability, phenotype or function. The PFPE-labeled DC were clearly detected in vivo by (19)F MRI, with mature DC being shown to migrate selectively towards draining lymph node regions within 18 h.

CONCLUSIONS

This study is the first application of PFPE cell labeling and MRI cell tracking using human immunotherapeutic cells. These techniques may have significant potential for tracking therapeutic cells in future clinical trials.

[Molecular pathology as an necessity: its role in diagnostic and predictive pathology]

Individualized therapeutic regimes are almost exclusively based on the rapid developments in molecular pathology. Application of (additional) molecular pathological investigations may thus offer the unique opportunity to improve the classical morphologic diagnosis as well as to routinely evaluate the parameters ("biomarkers") required for therapeutic decision making. Pathologists are thus facing the cogent necessity to perform and develop molecular pathological investigations in high quality and to establish biobanks, as well as to adjust their specialist training accordingly in order to meet these requirements.

A systematic approach to biomarker discovery; preamble to "the iSBTc-FDA taskforce on immunotherapy biomarkers"

The International Society for the Biological Therapy of Cancer (iSBTc) has initiated in collaboration with the United States Food and Drug Administration (FDA) a programmatic look at innovative avenues for the identification of relevant parameters to assist clinical and basic scientists who study the natural course of host/tumor interactions or their response to immune manipulation. The task force has two primary goals: 1) identify best practices of standardized and validated immune monitoring procedures and assays to promote inter-trial comparisons and 2) develop strategies for the identification of novel biomarkers that may enhance our understating of principles governing human cancer immune biology and, consequently, implement their clinical application. Two working groups were created that will report the developed best practices at an NCI/FDA/iSBTc sponsored workshop tied to the annual meeting of the iSBTc to be held in Washington DC in the Fall of 2009. This foreword provides an overview of the task force and invites feedback from readers that might be incorporated in the discussions and in the final document.

[Molecular pathological identification of predictive biomarkers: a new task for diagnostic pathology]

The clinical management of cancer patients is still based to a great extent on the histological staging, grading, and tumor typing performed by the pathologist. As a result part of the patients are subjected to unnecessary treatment regimens with high rates of side effects and no advantages while another part of the patients could benefit from (adjuvant) therapies they would not routinely receive based on their tumor staging/grading. This situation has led to a search for so-called predictive biomarkers, which would allow better assessment of the clinical course, probability of metastases, and the efficacy of the treatment method, thus making it possible to individualize treatment for each cancer patient.

Proteome informatics for cancer research: from molecules to clinic

Proteomics offers the most direct approach to understand disease and its molecular biomarkers. Biomarkers denote the biological states of tissues, cells, or body fluids that are useful for disease detection and classification. Clinical proteomics is used for early disease detection, molecular diagnosis of disease, identification and formulation of therapies, and disease monitoring and prognostics. Bioinformatics tools are essential for converting raw proteomics data into knowledge and subsequently into useful applications. These tools are used for the collection, processing, analysis, and interpretation of the vast amounts of proteomics data. Management, analysis, and interpretation of large quantities of raw and processed data require a combination of various informatics technologies such as databases, sequence comparison, predictive models, and statistical tools. We have demonstrated the utility of bioinformatics in clinical proteomics through the analysis of the cancer antigen survivin and its suitability as a target for cancer immunotherapy.

Nanotechnology, nanomedicine, and the development of new, effective therapies for cancer

Cancer is the leading cause of death in the United States among people younger than 85 years, and for the first time has surpassed heart disease as the number one killer. This worrisome statistic has resulted not from an increase in the incidence of cancer, but because deaths from heart disease have dropped nearly in half while the number of cancer-related deaths has remained about the same. This fact accentuates the need for a new generation of more effective therapies for cancer. In this review, the development of new therapies will be discussed in the context of advances in nanotechnologies related to cancer detection, analysis, diagnosis, and therapeutic intervention. First, several nanoanalytical methods, such as the use of quantum dots in detection and imaging of cancer, will be described. These techniques will be essential to the process of precisely describing cancer at the level of the cell and whole organism. Second, examples of how nanotechnologies can be used in the development of new therapies will be given, including methods that might allow for more efficient and accurate drug delivery and rationally designed, targeted drugs. Finally, a new initiative--the National Cancer Institute Alliance for Nanotechnology in Cancer--will be described and discussed with respect to the scientific issues, policies, and funding.

A clinical development paradigm for cancer vaccines and related biologics

Therapeutic cancer vaccines are a heterogeneous group of complex biologics with distinctly different clinical characteristics than cytotoxic agents. The current clinical development paradigm used for oncology drug development is based on criteria developed for cytotoxic agents. More flexible and focused developmental guidelines are needed to address the unique characteristics of therapeutic cancer vaccines. Over the course of 1 year, the Cancer Vaccine Clinical Trial Working Group, representing academia and the pharmaceutical and biotechnology industries with participation from the US Food and Drug Administration, defined in a consensus process the cornerstones of a new clinical development paradigm for cancer vaccines and related biologics. Four major topics were addressed: (1) end points for clinical trials, (2) trial designs and statistical methods, (3) technical and developmental challenges, and (4) combination therapy. The proposed paradigm suggests therapeutic cancer vaccines to be investigated in 2 general types of clinical studies: proof-of-principle trials and efficacy trials. Proof-of-principle trials, which introduce a novel cancer vaccine into humans, should include a minimum of 20 or more patients in a homogenous, well-defined population in an adjuvant setting or without rapidly progressive disease in a metastatic setting to allow vaccines adequate time to induce biologic activity and should incorporate immune and molecular markers. Objectives should include initiation of a safety database, determination of dose and schedule, and demonstration of biologic activity as proof-of-principle. Biologic activity is defined as any effect of the vaccine on the target disease or host immune system using biologic markers as study end points, for example, clinical, molecular, or immune response. Immune response is demonstrated if determined in 2 separate, established and reproducible assays at 2 consecutive follow-up time points after the baseline assessment. If proof-of-principle trials show such immune response, or other biologic or clinical activity, efficacy trials may be initiated. If none of these end points is met, the clinical development plan should be reevaluated to decide if further development is warranted. Efficacy trials formally establish clinical benefit either directly or through a surrogate and are encouraged to be randomized studies. This is in contrast to single-arm phase 2 trials used for cytotoxic agents, which often use tumor response rate as the primary end point and historical controls as a comparator. Efficacy trials may use prospectively planned adaptive designs to expand from randomized phase 2 into phase 3 studies if well-defined trigger-point criteria are met, but the cost of incorporating such design elements should be carefully evaluated. Efficacy trials can also be exploratory randomized phase 2 trials or conventional phase 3 trials. In addition, conventional clinical end points can be adjusted to account for biologic features of cancer vaccines. The concept of efficacy trials allows for an early assessment of vaccine efficacy based on credible prospective data. This 2-phase developmental paradigm supports a more flexible, expeditious, and focused clinical developmental process with early and informed decision making. In addition, this report addresses clinical development challenges and issues for combination therapies.

What's next in translational medicine?

Translational medicine is the integrated application of innovative pharmacology tools, biomarkers, clinical methods, clinical technologies and study designs to improve disease understanding, confidence in human drug targets and increase confidence in drug candidates, understand the therapeutic index in humans, enhance cost-effective decision making in exploratory development and increase phase II success. Translational research is one of the most important activities of translational medicine as it supports predictions about probable drug activities across species and is especially important when compounds with unprecedented drug targets are brought to humans for the first time. Translational research has the potential to deliver many practical benefits for patients and justify the extensive investments placed by the private and public sector in biomedical research. Translational research encompasses a complexity of scientific, financial, ethical, regulatory, legislative and practical hurdles that need to be addressed at several levels to make the process efficient. Several have resisted the idea of supporting translational research because of its high costs and the fear that it may re-direct funds from other biomedical disciplines. Resistance also comes from those more familiar with traditional clinical research methods. In this review, we argue that translational research should be seen as enabled by ongoing efforts in basic and clinical research and not competing with them. Translational research provides the knowledge necessary to draw important conclusions from clinical testing regarding disease and the viability of novel drug mechanisms. Advancing translational research requires education and new sources of funding. This could be achieved through public and congressional education by a joint coalition of patients' advocacy groups, academia, drug regulatory agencies and industry.

A comprehensive urinary metabolomic approach for identifying kidney cancerr

The diagnosis of cancer by examination of the urine has the potential to improve patient outcomes by means of earlier detection. Due to the fact that the urine contains metabolic signatures of many biochemical pathways, this biofluid is ideally suited for metabolomic analysis, especially involving diseases of the kidney and urinary system. In this pilot study, we test three independent analytical techniques for suitability for detection of renal cell carcinoma (RCC) in urine of affected patients. Hydrophilic interaction chromatography (HILIC-LC-MS), reversed-phase ultra performance liquid chromatography (RP-UPLC-MS), and gas chromatography time-of-flight mass spectrometry (GC-TOF-MS) all were used as complementary separation techniques. The combination of these techniques is best suited to cover a very large part of the urine metabolome by enabling the detection of both lipophilic and hydrophilic metabolites present therein. In this study, it is demonstrated that sample pretreatment with urease dramatically alters the metabolome composition apart from removal of urea. Two new freely available peak alignment methods, MZmine and XCMS, are used for peak detection and retention time alignment. The results are analyzed by a feature selection algorithm with subsequent univariate analysis of variance (ANOVA) and a multivariate partial least squares (PLS) approach. From more than 2000 mass spectral features detected in the urine, we identify several significant components that lead to discrimination between RCC patients and controls despite the relatively small sample size. A feature selection process condensed the significant features to less than 30 components in each of the data sets. In future work, these potential biomarkers will be further validated with a larger patient cohort. Such investigation will likely lead to clinically applicable assays for earlier diagnosis of RCC, as well as other malignancies, and thereby improved patient prognosis.

Rapid flow cytometric measurement of cytokine-induced phosphorylation pathways [CIPP] in human peripheral blood leukocytes

Current strategies designed to assess cells in the peripheral blood are limited to evaluation of phenotype or delayed measurement [>6 h] of function, usually quantifying cytokine production, cytolytic activity, or response to antigens. We reasoned that measurable abnormalities in signaling pathways could reflect pathological environs that cells experience in the setting of inflammatory states/cancer and could be represented in the peripheral blood. Two major pathways regulating the immune response are the JAK/STAT and MAPK/ERK pathways. These pathways are initiated by ligand-receptor binding and are rapidly propagated by subsequent protein phosphorylation cascades. We evaluated the brief application of cytokines in vitro to interrogate the early phosphorylation events of these signaling pathways in normal peripheral blood mononuclear cells (PBMC). Individual cytokine doses and time intervals of treatment were assessed to identify conditions useful in a clinical laboratory and as an initial goal to induce maximal phosphorylation. Surprisingly, all of the STAT proteins assessed and ERK1/2 are maximally phosphorylated within 15 min in human PBMC simply following addition of cytokines without preactivation of the cells. At 2 h, cells typically return to their basal phosphorylation states. For most of the cytokines tested, increased phosphorylation directly correlated with increased concentrations of the individual cytokines. These strategies will enable robust development of simple blood analyses to identify normal levels as well as impairments in STAT and MAPK/ERK signaling pathways associated with various human disease states including acute and chronic inflammatory conditions throughout clinical immunology.

MHC–peptide specificity and T-cell epitope mapping: where immunotherapy starts

The evaluation and characterization of epitope-specific human leukocyte antigen (HLA)-restricted memory T-cell reactivity is an important step for the development of preventive vaccines and peptide-based immunotherapies for viral and tumor diseases. The past decade has witnessed the use of HLA-restricted peptides as tools to activate strong immune responses of naïve or memory T cells specifically. This has fuelled an active search for methodological approaches focusing on HLA and peptide associations. Here, we outline new perspective on the emerging opportunity of evaluating HLA and peptide restriction by using novel approaches, such as quantitative real-time PCR, that can identify epitope specificities that are potentially useful in clinical settings.

Biomarker selection for detection of occult tumour cells in lymph nodes of colorectal cancer patients using real-time quantitative RT-PCR

Accurate identification of lymph node involvement is critical for successful treatment of patients with colorectal carcinoma (CRC). Real-time quantitative RT–PCR with a specific probe and RNA copy standard for biomarker mRNA has proven very powerful for detection of disseminated tumour cells. Which properties of biomarker mRNAs are important for identification of disseminated CRC cells? Seven biomarker candidates, CEA, CEACAM1-S/L, CEACAM6, CEACAM7-1/2, MUC2, MMP7 and CK20, were compared in a test-set of lymph nodes from 51 CRC patients (Dukes' A–D) and 10 controls. Normal colon epithelial cells, primary tumours, and different immune cells were also analysed. The biomarkers were ranked according to: (1) detection of haematoxylin/eosin positive nodes, (2) detection of Dukes' A and B patients, who developed metastases during a 54 months follow-up period and (3) identification of patients with Dukes' C and D tumours using the highest value of control nodes as cutoff. The following properties appear to be of importance; (a) no expression in immune cells, (b) relatively high and constant expression in tumour tissue irrespective of Dukes' stage and (c) no or weak downregulation in tumours compared to normal tissue. CEA fulfilled these criteria best, followed by CK20 and MUC2.

Impact of immune parameters on long-term survival in metastatic renal cell carcinoma

PURPOSE

The purpose of this study was to evaluate the impact of immunologic prognostic factors in combination with established clinical prognostic factors in patients with metastatic renal cell carcinoma (mRCC).

PATIENTS AND METHODS

A total of 120 consecutive patients with mRCC received interleukin-2 (IL-2) -based immunotherapy. Baseline tumor biopsies were available from 85 of these patients. Potential prognostic factors were analyzed by univariate and multivariate analyses.

RESULTS

Multivariate analysis (N = 120) identified high lactate dehydrogenase, lymph node metastases, low hemoglobin, low Karnofsky performance status, and bone metastases as independent poor prognostic clinical factors. The impact of these clinical factors has been demonstrated by others. Multivariate analysis (n = 85) also identified a high blood neutrophil count (> 6.0 x 10(9)/L; hazard ratio, 2.0; P = .015), the presence of intratumoral neutrophils (> 0 cells/mm2 tumor tissue; hazard ratio, 2.3; P = .001), and low intratumoral CD57+ natural killer cell count (< 50 cells/mm2 tumor tissue; hazard ratio, 2.1; P = .01) as independent poor prognostic immunologic factors. These three independent immunologic parameters had significant discriminatory power as supplemental risk factors in prognostic models based on the clinical risk factors, identifying subgroups within the favorable clinical group with estimated 5-year survival rates of 60%, 25%, and 0%, respectively. These findings were apparent in both our own prognostic model and in an extended Memorial Sloan-Kettering Cancer Center (New York, NY) prognostic model.

CONCLUSION

This study points on five clinical and three supplemental immunologic independent prognostic factors of survival in patients with mRCC receiving IL-2.

Successful simultaneous measurement of cell membrane and cytokine induced phosphorylation pathways [CIPP] in human peripheral blood mononuclear cells

Phenotyping and simple enumeration of peripheral blood mononuclear cells (PBMC) is of limited value for the assessment of many clinical states. As a preferred alternative, cell surface phenotyping may be combined with functional assays for enhanced assessment of altered cells circulating in patients. One simple, yet informative and rapid approach is to examine signaling within individual cells following brief periods of stimulation via flow cytometry. Although monocytes and lymphoid cells can be distinguished based on size, current permeabilization strategies necessary for identifying intracellular phosphorylated signaling molecules largely compromise the labeling of cell surface proteins used to distinguish individual cellular subsets. We have successfully developed conditions that allow for simultaneous detection of cell surface proteins and intracellular phosphorylated proteins in human PBMC following rapid in vitro cytokine stimulation. We analyzed permeabilized CD4, CD8, CD14, CD19, and CD56 expressing cells together with intracellular pSTAT1, pSTAT3, pSTAT5, pSTAT6, pp38 MAPK, or pERK1/2 within total PBMC. Of the permeabilizing conditions tested, 75% methanol enabled superior simultaneous detection of both cell surface and intracellular epitopes. This method enables the rapid functional analysis of subsets within complex cell mixtures and provides an opportunity for assessing abnormalities arising in the setting of acute or chronic inflammatory states.

Circulating tumor cells: the 'leukemic phase' of solid cancers

It is well known that malignant cells circulate in the bloodstream of patients with solid tumors. However, the biological significance of circulating tumor cells (CTCs) and the clinical relevance of their detection are still debated. Besides technical issues regarding CTC-detection methods, discontinuous shedding of CTCs from established cancer deposits, genomic instability and metastatic inefficiency might underlie the conflicting results currently available. Nevertheless, technological advances and recent clinical findings are prompting researchers to dissect CTC biology further. Here, we review these recent findings, and discuss the prospects for the identification and molecular characterization of the CTC subset that is responsible for metastasis development. This would provide a formidable tool for prognosis evaluation, anticancer-drug development and, ultimately, cancer-therapy personalization.

Detection and quantification of mutations in the plasma of patients with colorectal tumors

The early detection of cancers through analysis of circulating DNA could have a substantial impact on morbidity and mortality. To achieve this goal, it is essential to determine the number of mutant molecules present in the circulation of cancer patients and to develop methods that are sufficiently sensitive to detect these mutations. Using a modified version of a recently developed assay for this purpose, we found that patients with advanced colorectal cancers consistently contained mutant adenomatous polyposis coli (APC) DNA molecules in their plasma. The median number of APC DNA fragments in such patients was 47,800 per ml of plasma, of which 8% were mutant. Mutant APC molecules were also detected in >60% of patients with early, presumably curable colorectal cancers, at levels ranging from 0.01% to 1.7% of the total APC molecules. These results have implications for the mechanisms through which tumor DNA is released into the circulation and for diagnostic tests based on this phenomenon.

Advancing cancer biotherapy with proteomics

Proteomics is becoming increasingly important for cancer biotherapy. The development of high-throughput platforms now allows the analysis of multiple proteins from small quantities of material. While these techniques are being used to discover new biomarkers, they are particularly important for assessing complex biologic processes such as immunotherapy for cancer. Recent advances in this field are reviewed, as well as the use of proteomics to assess the effectiveness and toxicities of high-dose IL-2 cancer therapy. Proteomics is becoming useful in assessing cancer biotherapies and in unraveling their mechanisms of action. High-throughput proteomic technologies have now advanced to a stage where they have the potential to become effective discovery tools for biomarkers/predictors of disease, disease recurrence, and response to therapy.

Gene profiling of immune responses against tumors

Clinical trials of tumor-antigen-specific immunization have clearly shown that immune-mediated tumor rejection requires more than simple T cell-target cell interactions. In vivo generation of tumor-specific T cells is one of a series of steps necessary for the induction of clinically relevant immune responses. In recent years, high-throughput functional genomics exposed the complexity of tumor immune biology, which underlies the kaleidoscopic array of variables associated with cancer instability and immunogenetic variability in humans. In the quest to understand immune rejection, hypothesis-driven approaches have failed to take into account the intricacy of human pathology by relying mostly on hypotheses derived from experimental models rather than direct clinical observation. Future investigations should reframe scientific thinking when applied to humans, utilizing descriptive tools to generate novel hypotheses relevant to human disease.

The challenge of implementing high-throughput technologies in clinical trials

One of the pillars on which modern translational medicine is founded lies in the search/choice of appropriate biomarkers.