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Acquired resistance through genetic mutations is a common phenomenon in several cancer therapies using molecularly targeted drugs, best exemplified by the BCR-ABL inhibitor imatinib in treating chronic myelogenous leukemia (CML). Overcoming acquired resistance is a daunting therapeutic challenge, and little is known about how these mutations evolve. To facilitate understanding the resistance mechanisms, we developed a novel culture model for CML acquired resistance in which the CML cell line KCL-22, following initial response to imatinib, develops resistant T315I BCR-ABL mutation. We demonstrate that the emergence of BCR-ABL mutations do not require preexisting BCR-ABL mutations derived from the original patient as the subclones of KCL-22 cells can form various BCR-ABL mutations upon imatinib treatment. BCR-ABL mutation rates vary from cell clone to clone and passages, in contrast to the relatively stable mutation rate of the hypoxanthine-guanine phosphoribosyltransferase gene. Strikingly, development of BCR-ABL mutations depends on its gene expression because BCR-ABL knockdown completely blocks KCL-22 cell relapse on imatinib and acquisition of mutations. We further show that the endogenous BCR-ABL locus has significantly higher mutagenesis potential than the transduced randomly integrated BCR-ABL cDNA. Our study suggests important roles of BCR-ABL gene expression and its native chromosomal locus for acquisition of BCR-ABL mutations and provides a new tool for further studying resistance mechanisms.Chronic myelogenous leukemia results from malignant transformation of a primitive hematopoietic cell by an oncogenic fusion gene BCR-ABL. Treatment with the potent ABL tyrosine kinase inhibitor imatinib mesylate (Gleevec, STI-571, imatinib) results in complete cytogenetic responses in most chronic phase patients with infrequent relapse, but the treatment has poor responses and high frequency of relapse in advanced phases of the disease (1). Clinical resistance to imatinib is mediated primarily by genetic mutations of the BCR-ABL kinase domain and, to a lesser extent, by amplification of BCR-ABL gene (2). Numerous BCR-ABL mutations have been identified in relapsed CML 3 patients, which confer various degrees of resistance to imatinib (2-4). Among them, the T315I mutation is the most resistant in that it does not respond to treatment with the more potent second generation of kinase inhibitors such as nilotinib (5, 6) and dasatinib (7).In contrast to in vivo resistance, nearly all CML cell lines derived from blast crisis CML are sensitive to imatinib treatment in culture (8). Several resistant CML cell lines have been generated by exposing cells to gradually increasing concentrations of imatinib; however, the resulting resistant cells harbor BCR-ABL gene amplification but not mutations (9), in contrast to what is seen in patients. By expressing BCR-ABL cDNA in non-CML cell lines and/or random mutagenesis, multiple studies have demonstrated clinically relevant or novel BCR-ABL mutations that render resistance to imatinib...

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Piwi-interacting RNAs (piRNAs) are a distinct group of small noncoding RNAs (sncRNAs) that silence transposable genetic elements to protect genome integrity. Because of their limited expression in gonads and sequence diversity, piRNAs remain the most mysterious class of small RNAs. Studies have shown piRNAs are present in somatic cells and dysregulated in gastric, breast and liver cancers. By deep sequencing 24 frozen benign kidney and clear cell renal cell carcinoma (ccRCC) specimens and using the publically available piRNA database, we found 26,991 piRNAs present in human kidney tissue. Among 920 piRNAs that had at least two copies in one specimen, 19 were differentially expressed in benign kidney and ccRCC tissues, and 46 were associated with metastasis. Among the metastasis-related piRNAs, we found three piRNAs (piR-32051, piR-39894 and piR-43607) to be derived from the same piRNA cluster at chromosome 17. We confirmed the three selected piRNAs not to be miRNAs or miRNA-like sncRNAs. We further validated the aberrant expression of the three piRNAs in a 68-case formalin-fixed and paraffin-embedded (FFPE) ccRCC tissue cohort and showed the upregulation of the three piRNAs to be highly associated with ccRCC metastasis, late clinical stage and poor cancer-specific survival.