DNA microarrays for comparison of gene expression profiles between diagnosis and relapse in precursor-B acute lymphoblastic leukemia: choice of technique and purification influence the identification of potential diagnostic markers

• Published in: Leukemia Vol. 17; no. 7; pp. 1324 - 1332
• Main Authors: STAAL, F. J. T, VAN DER BURG, M, VAN DONGEN, J. I. M, WESSELS, L. F. A, BARENDREGT, B. H, BAERT, M. R. M, VAN DEN BURG, C. M. M, VAN HUFFEL, C, LANGERAK, A. W, VAN DER VELDEN, V. H. I, REINDERS, M. I. T
• Format: Journal Article
• Language: English
• Published: London Nature Publishing 01.07.2003; Nature Publishing Group
• Subjects: Acute lymphoblastic leukemia; Amplification; Biological and medical sciences; Biomarkers; Cell Division - genetics; Cell proliferation; Cell survival; Cell Survival - genetics; Child; Child, Preschool; Diagnosis; Disease Progression; DNA chips; DNA microarrays; Drug resistance; Drug Resistance, Neoplasm - genetics; Gene expression; Gene Expression Profiling - methods; Gene Expression Profiling - standards; Genes; Hematologic and hematopoietic diseases; Humans; Infant; Leukemia; Leukemias. Malignant lymphomas. Malignant reticulosis. Myelofibrosis; Lymphatic leukemia; Lymphocytes; Lymphocytes T; Lymphoma; Male; Medical diagnosis; Medical prognosis; Medical sciences; Myeloid cells; Oligonucleotide Array Sequence Analysis - instrumentation; Oligonucleotide Array Sequence Analysis - methods; Precursor B-Cell Lymphoblastic Leukemia-Lymphoma - diagnosis; Precursor B-Cell Lymphoblastic Leukemia-Lymphoma - genetics; Precursor B-Cell Lymphoblastic Leukemia-Lymphoma - mortality; Precursor Cell Lymphoblastic Leukemia-Lymphoma - diagnosis; Precursor Cell Lymphoblastic Leukemia-Lymphoma - genetics; Precursor Cell Lymphoblastic Leukemia-Lymphoma - mortality; Precursors; Recurrence; Ribonucleic acid; RNA; Transcription factors; Tumors; Human; Relapse; Acute; Precursor cell; DNA chip; Biological marker; Exploration; Malignant hemopathy; B-Lymphocyte; Gene expression; DNA microarray; Lymphoproliferative syndrome; Diagnosis; Acute lymphocytic leukemia; Technique; gene expression profiling; Comparative study; precursor- B-ALL
• ISSN: 0887-6924; 1476-5551
• DOI: 10.1038/sj.leu.2402974

Microarrays for gene expression profiling are rapidly becoming important research tools for the identification of novel markers, for example, for novel classification of leukemias and lymphomas. Here, we review the considerations and infrastructure for microarray experiments. These considerations are illustrated via a microarray-based comparison of gene expression profiles of paired diagnosis-relapse samples from patients with precursor-B acute lymphoblastic leukemia (ALL), who relapsed during therapy or after completion of treatment. Initial experiments showed that several seemingly differentially expressed genes were actually derived from contaminating non-leukemic cells, particularly myeloid cells and T-lymphocytes. Therefore, we purified the ALL cells of the diagnosis and relapse samples if their frequency was lower than 95%. Furthermore, we observed in earlier studies that extra RNA amplification leads to skewing of particular gene transcripts. Sufficient (non-amplified) RNA of purified and paired diagnosis-relapse samples was obtained from only seven cases. The gene expression profiles were evaluated with Affymetrix U95A chips containing 12 600 human genes. These diagnosis-relapse comparisons revealed only a small number of genes (n=6) that differed significantly in expression: mostly signaling molecules and transcription factors involved in cell proliferation and cell survival were highly upregulated at relapse, but we did not observe any increase in drug-resistance markers. This finding fits with the observation that tumors with a high proliferation index have a poor prognosis. The genes that changed between diagnosis and relapse are currently not in use as diagnostic or disease progression markers, but represent potential new markers for such applications. Leukemia (2003) 17, 1324-1332. doi:10.1038/sj.leu.2402974