Amplification and activating mutations of the epidermal growth factor receptor (EGFR) oncogene are molecular hallmarks of glioblastomas. We hypothesized that deletion of NFKBIA (encoding nuclear factor of κ-light polypeptide gene enhancer in B-cells inhibitor-α), an inhibitor of the EGFR-signaling pathway, promotes tumorigenesis in glioblastomas that do not have alterations of EGFR. We analyzed 790 human glioblastomas for deletions, mutations, or expression of NFKBIA and EGFR. We studied the tumor-suppressor activity of NFKBIA in tumor-cell culture. We compared the molecular results with the outcome of glioblastoma in 570 affected persons. NFKBIA is often deleted but not mutated in glioblastomas; most deletions occur in nonclassical subtypes of the disease. Deletion of NFKBIA and amplification of EGFR show a pattern of mutual exclusivity. Restoration of the expression of NFKBIA attenuated the malignant phenotype and increased the vulnerability to chemotherapy of cells cultured from tumors with NFKBIA deletion; it also reduced the viability of cells with EGFR amplification but not of cells with normal gene dosages of both NFKBIA and EGFR. Deletion and low expression of NFKBIA were associated with unfavorable outcomes. Patients who had tumors with NFKBIA deletion had outcomes that were similar to those in patients with tumors harboring EGFR amplification. These outcomes were poor as compared with the outcomes in patients with tumors that had normal gene dosages of NFKBIA and EGFR. A two-gene model that was based on expression of NFKBIA and O⁶-methylguanine DNA methyltransferase was strongly associated with the clinical course of the disease. Deletion of NFKBIA has an effect that is similar to the effect of EGFR amplification in the pathogenesis of glioblastoma and is associated with comparatively short survival.

Malignant gliomas, with disproportionately high morbidity and mortality,¹ are among the most devastating of human tumors. Particular genomic alterations are fundamental to both their formation and their malignant progression.^2,3 Although genomic instability (Box) lends a dynamic character to the human glioma genome, gliomas harbor recurrent chromosomal alterations (Box).^2,4,5 Chromosomal alterations presumably exert their tumor-promoting effect on glioma cells by modifying the expression or function of distinct genes, which map to those alterations,⁶ so as to deregulate growth factor signaling and survival pathways. For many chromosomal alterations, the biologically relevant target genes remain to be discovered.

Janus kinases (JAK) and signal transducers and activator of transcription (STAT) proteins are activated in response to many cytokines and growth factors and are well studied in the immune system. This study was conducted to examine the role of the JAK/STAT pathway in neurons in response to tumor necrosis factor-α (TNFα) and insulin-like growth factor-1 (IGF-1), which play a major role during neurodegeneration, and to study their effect on expression of suppressors of cytokine signaling 3 (SOCS-3), belonging to the novel family of feedback regulators of cytokine and growth factor activities. In this report, we showed that TNFα is inhibitory to the survival of primary cortical neurons at higher doses and that IGF-1 can rescue TNFα-stimulated cell death. We showed that the JAK/STAT pathway is involved in this rescue as tyrphostin AG490, a specific inhibitor of JAK/STAT, completely inhibits cell survival in response to IGF-1. STAT3 gets tyrosine-phosphorylated and translocated to the nucleus in response to IGF-1. Northern blot, semi-quantitative reverse transcription-PCR, and real time PCR experiments demonstrated that the JAK/STAT pathway also up-regulated SOCS-3 mainly in response to IGF-1. SOCS-3 associated with the IGF receptor and blocked further STAT3 activation. To our knowledge, this is the first report that demonstrated the importance of the JAK/STAT pathway and the role of SOCS-3 in the survival of neurons in response to IGF-1. We have subsequently shown that SOCS-3 overexpression, on one hand, leads to neuroblastoma cell death and on the other hand leads to primary cell differentiation, indicating the involvement of SOCS-3 in cell survival and differentiation.

The Bmi-1 oncogene is overexpressed in a number of malignancies including breast cancer. In addition to Bmi-1, mammalian cells also express four other polycomb group (PcG) proteins that are closely related to Bmi-1. Virtually nothing is known about the role of these PcG proteins in oncogenesis. We have recently reported that Mel-18, a Bmi-1–related PcG protein, negatively regulates Bmi-1 expression, and that its expression negatively correlates with Bmi-1 in proliferating and senescing human fibroblasts. Here, we report that the expression of Bmi-1 and Mel-18 inversely correlates in a number of breast cancer cell lines and in a significant number of breast tumor samples. Overexpression of Mel-18 results in repression of Bmi-1 and reduction of the transformed phenotype in malignant breast cancer cells. Furthermore, the repression of Bmi-1 by Mel-18 is accompanied by the reduction of Akt/protein kinase B (PKB) activity in breast cancer cells. Similarly, Bmi-1 knockdown using RNA interference approach results in down-regulation of Akt/PKB activity and reduction in transformed phenotype of MCF7 cells. Importantly, we show that overexpression of constitutively active Akt overrides tumor-suppressive effect of Mel-18 overexpression and the knockdown of Bmi-1 expression. Thus, our studies suggest that Mel-18 and Bmi-1 may regulate the Akt pathway in breast cancer cells, and that Mel-18 functions as a tumor suppressor by repressing the expression of Bmi-1 and consequently down-regulating Akt activity. [Cancer Res 2007;67(11):5083–9]

Tissue-specific alternative splicing is critical for the emergence of tissue identity during development, yet the role of this process in malignant transformation is undefined. Tissue-specific splicing involves evolutionarily conserved, alternative exons that represent only a minority of the total alternative exons identified. Many of these conserved exons have functional features that influence signaling pathways to profound biological effect. Here, we determined that lineage-specific splicing of a brain-enriched cassette exon in the membrane-binding tumor suppressor annexin A7 (ANXA7) diminishes endosomal targeting of the EGFR oncoprotein, consequently enhancing EGFR signaling during brain tumor progression. ANXA7 exon splicing was mediated by the ribonucleoprotein PTBP1, which is normally repressed during neuronal development. PTBP1 was highly expressed in glioblastomas due to loss of a brain-enriched microRNA (miR-124) and to PTBP1 amplification. The alternative ANXA7 splicing trait was present in precursor cells, suggesting that glioblastoma cells inherit the trait from a potential tumor-initiating ancestor and that these cells exploit this trait through accumulation of mutations that enhance EGFR signaling. Our data illustrate that lineage-specific splicing of a tissue-regulated alternative exon in a constituent of an oncogenic pathway eliminates tumor suppressor functions and promotes glioblastoma progression. This paradigm may offer a general model as to how tissue-specific regulatory mechanisms can reprogram normal developmental processes into oncogenic ones.

Aneuploidy—an abnormal number of chromosomes—is the most frequently identified genomic abnormality in human cancer. Cancer-specific aneuploidies often result in activation of oncogenes or loss of tumor suppressor genes.¹ Conserved aneuploidies also shape the genome of glioblastomas,² which are among the most challenging of human cancers. The most frequent form of aneuploidy in glioblastomas is monosomy of chromosome 10, ie, the presence of only 1 chromosome 10 due to loss of 1 copy. We have shown monosomy of chromosome 10 to be significantly associated with gain or amplification of the epidermal growth factor receptor gene (EGFR [HGNC 3236]) on chromosome 7p12,² the most common genetic defect in growth factor signaling in these tumors.