Monitoring Anti-melanoma Vaccination with Dendritic Cells Using Microarrays

Anna K. Palucka, M.D., Ph.D.

Baylor Institute for Immunology Research

Funded in June, 2002: $300000 for 4 years
LAY SUMMARY . ABSTRACT . BIOGRAPHY . FINDINGS . SELECTED PUBLICATIONS .

LAY SUMMARY

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Can Immune Markers Indicate Melanoma Vaccine Efficacy?

Novel therapies are needed to improve the management of cancer patients. Dendritic cells (DCs) are unique cells in the body that can recognize invading agents and transmit this information to immune cells to induce a protective immune response. Immunotherapy using vaccination with DCs is safe and recent trials in cancer patients showed clinical and immune responses.

We have vaccinated patients with stage IV melanoma using DCs derived from certain stem cells. Ten weeks and four vaccines after protocol initiation, 10/18 patients showed clinical and tumor-specific immune responses. Thus, immune responses correlate with clinical responses. Furthermore, progressive patients do not mount immunity to melanoma, while they do mount immunity to control antigens. This indicates that the non-responding patients' immune systems are working, but not against their own tumors.

Blood represents both a reservoir of immune cells and a migration compartment for these cells. Therefore, white blood cells include cells that have recently been exposed to environmental stimuli such as biological and/or chemical warfare agents. Therefore the pattern of gene expression in the blood cells will reflect the status of the immune system and a status of health.

The main objective of our project is to identify patterns of gene expression "signatures" that are predictive and/or diagnostic of health or disease. The availability of clinical responders and non-responders will permit us to define "tumor regression" and "tumor progression" signatures.

ABSTRACT

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Monitoring Anti-Melanoma Vaccination with Dendritic Cells Using Microarrays

Novel therapies are needed to improve the management of cancer patients. Immunotherapy using vaccination with DCs is safe, and recent trials showed clinical and immune responses. We have vaccinated patients with stage IV melanoma using DCs derived from CD34+ hematopoietic progenitors. Ten weeks and four vaccines after protocol initiation, 10/18 patients showed clinical and tumor-specific immune responses. Thus, immune responses correlate with clinical responses and progressive patients do not mount melanoma immunity, while they do mount immunity to control antigens, thus indicating tumor-specific tolerance.

We are now engaged to address two major questions:
1) Can we identify a "Tumor regression signature"?
2) Can we identify a "Tumor progression signature"?

Affymetrix oligonucleotide microarray evaluation of PBMC from two melanoma patients showed before vaccination nearly identical gene patterns considerably different from those observed in healthy controls. Strikingly, vaccination with DC induced a considerable alteration of this pattern, which became close to that of healthy controls. Therefore, we propose now to analyze the genotype of PBMC from our 18 patients at various stages of their vaccination therapy. The availability of clinical responders and non-responders will permits us to define "tumor regression" and 'tumor progression" signatures.

INVESTIGATOR BIOGRAPHIES

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Anna K. Palucka, M.D., Ph.D.

Anna Palucka, M.D., Ph.D., completed her internal medicine and medical oncology residency program at the Maria Sklodowska-Curie Memorial Institute, Warsaw, and her Ph.D. at Karolinska Institute in Stockholm. After post-doctoral training in the laboratory of Professor J.C. Gluckman in Paris, where she had been studying the cytokine regulation of monocyte differentiation towards dendritic cells, she has joined Baylor Institute for Immunology Research at Dallas (under the direction of Jacques Banchereau, Ph.D).

Vaccines may constitute the greatest achievement of modern medicine, and there is a great hope that they also could contribute to our fight against cancer. We now know that dendritic cells represent a key element in successful vaccination. Therefore, Dr. Palucka's research program is focused on in vitro and in vivo (pre-clinical models and clinical trials) evaluation of DCs as adjuvants in cancer immunotherapy. Her laboratory is focused on the use of dendritic cells as vectors for therapy in patients with cancer.

FINDINGS

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Lay Results:
Microarrays can generate gene expression data for tens of thousands of genes. The problem is to translate these vast amounts of data into meaningful information. We developed two novel approaches to address this issue for patient-based studies. They have allowed us to identify gene expression patterns that are "signatures" of individual diseases. Our clinical findings have also identified similar immunosuppressive signatures in patients with advanced melanoma and transplant recipients who are receiving immunosuppressive drugs. We are now studying these signatures to determine if they can be used in the early diagnosis of diseases, especially diseases that are historically difficult to diagnose. We are also examining to what extent these signatures measure how well patients with specific diseases are responding to treatments.

Scientific Results:
Microarrays can generate transcriptional profiles on a genome wide scale. The problem is to translate these vast amounts of data into meaningful information. We developed two novel approaches to microarray data analysis in the context of patient-based studies: 1) The analysis of patterns of significance generated by hierarchical clustering of P-values across multiple diseases serves as a premise for the identification of disease-specific and ubiquitous sentinel signatures. 2) The characterization of transcriptional modules in patients’ blood led to the development of a radically different microarray data mining approach, with the generation of disease specific vectors that constitute clinically-relevant biomarkers and modular mapping of transcriptional profiles that provides a conceptual framework to better understand disease pathogenesis.

Modular decomposition of transcriptional profiles obtained from the blood of patients with metastatic melanoma identified a signature that was common to liver transplant recipients under immunosuppressive treatment. The analysis of significance patterns across eight different diseases demonstrated that this signature was not only common but also specific to these two groups of patients. We subsequently found a remarkable functional convergence among the genes forming this signature. It includes genes encoding molecules that display various aspects of immunoregulatory activity. These include inhibitors of the NF-kB pathway, such as TNFAIP3 and CIAS1/Cryopyrin. Also, DSIPI, a leucine zipper protein, is known to mediate the immunosuppressive effects of glucocorticoids and IL-10. Also included are inhibitors of the MAP kinase pathway, such as dual specificity phosphatases 2, 5 and 10 which interfere with the MAP kinases, ERK1/2. Inhibitors of IL2 production (e.g. CREM, FOXK2 and TCF8 that can contribute to the repression of IL-2 production in anergic T cells) and inhibitors of cell proliferation (e.g. BTG2, TOB1, AREG, SUI1 and RNF139) were also identified.

Our findings point toward a functional convergence between immunosuppressive mechanisms operating in patients with advanced melanoma and pharmacologically-treated transplant recipients. The fact that the transcripts specifically induced in immunosuppressed patients included glucocorticoid-inducible genes (e.g. DSIPI, CXCR4, JUN) and hormone nuclear receptors thought to play key roles in the development and effector functions of T lymphocytes (NR4A2 and RORA) suggests a possible role for steroid hormones in melanoma-mediated immunosuppression.

SELECTED PUBLICATIONS

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Chaussabel D., Quinn C., Shen J., Patel P., Glaser C., Baldwin N., Stichweh D., Blankenship D., Li L., Munagala I., Bennett L., Allantaz F., Mejias A., Ardura M., Kaizer E., Monnet L., Allman W., Randall H., Johnson D., Lanier A., Punaro M., Wittkowski K.M., White P., Fay J., Klintmalm G., Ramilo O., Palucka A.K., Banchereau J., and Pascual V.   A modular analysis framework for blood genomics studies: application to systemic lupus erythematosus.   Immunity. 2008 Jul;29(1):150-64.

Chaussabel D., Allman W., Mejias A., Chung W., Bennett L., Ramilo O., Pascual V., Palucka A.K., and Banchereau J.   Analysis of significance patterns identifies ubiquitous and disease-specific gene-expression signatures in patient peripheral blood leukocytes. Ann N Y Acad Sci. 2005 Dec;1062:146-54.