Breakpoint analysis of transcriptional and genomic profiles uncovers novel gene fusions spanning multiple human cancer types.

Gene fusions, like BCR/ABL1 in chronic myelogenous leukemia, have long been recognized in hematologic and mesenchymal malignancies. The recent finding of gene fusions in prostate and lung cancers has motivated the search for pathogenic gene fusions in other malignancies. Here, we developed a "breakpoint analysis" pipeline to discover candidate gene fusions by tell-tale transcript level or genomic DNA copy number transitions occurring within genes. Mining data from 974 diverse cancer samples, we identified 198 candidate fusions involving annotated cancer genes. From these, we validated and further characterized novel gene fusions involving ROS1 tyrosine kinase in angiosarcoma (CEP85L/ROS1), SLC1A2 glutamate transporter in colon cancer (APIP/SLC1A2), RAF1 kinase in pancreatic cancer (ATG7/RAF1) and anaplastic astrocytoma (BCL6/RAF1), EWSR1 in melanoma (EWSR1/CREM), CDK6 kinase in T-cell acute lymphoblastic leukemia (FAM133B/CDK6), and CLTC in breast cancer (CLTC/VMP1). Notably, while these fusions involved known cancer genes, all occurred with novel fusion partners and in previously unreported cancer types. Moreover, several constituted druggable targets (including kinases), with therapeutic implications for their respective malignancies. Lastly, breakpoint analysis identified new cell line models for known rearrangements, including EGFRvIII and FIP1L1/PDGFRA. Taken together, we provide a robust approach for gene fusion discovery, and our results highlight a more widespread role of fusion genes in cancer pathogenesis.

Subcutaneous panniculitis-like T-cell lymphoma: Pediatric case series demonstrating heterogeneous presentation and option for watchful waiting.

Subcutaneous panniculitis-like T-cell lymphoma (SPTCL) and primary cutaneous gamma delta T-cell lymphoma (PCGD-TCL) were initially both classified as subcutaneous panniculitis-like T-cell lymphoma. In 2008, SPTCL with alpha-beta T-cell receptor subtype was separated from primary cutaneous gamma delta T-cell lymphomas (PCGD-TCL). We report four pediatric cases that demonstrate the heterogeneity of each disease and show that PCGD-TCL in children can have an indolent course, whereas SPTCL can behave aggressively. Three patients had spontaneous, durable remissions without treatment, whereas the one patient with disease progression was treated successfully. Watchful waiting may thus be appropriate for initial management of children.

WARM N COLD: malignant and benign renal tumors in children.

Although Wilms tumor is the most common renal malignancy in children, the differential diagnosis is extensive and includes both malignant and benign disorders. We present a simple mnemonic-WARM N COLD, to aid in remembering these diverse tumors. Imaging clues including age of the patient, associated disease or syndrome as well as salient imaging characteristics such as bilaterality, and type or presence of metastasis are also presented and can help differentiate between these renal tumors of childhood.

Therapeutic complications in a patient with high-risk acute lymphoblastic leukemia and undiagnosed hereditary hemochromatosis.

Hereditary hemochromatosis (HH) is an autosomal-recessive disorder of iron metabolism that most commonly manifests in the fourth or fifth decade of life. Here, we describe a 14-year-old male who presented with high-risk acute lymphoblastic leukemia and previously undiagnosed HH. His treatment course was remarkable for significant therapeutic complications, including iron overload, hepatic failure, cardiac dysfunction, and death. Postmortem testing revealed homozygosity for the C282Y mutation, confirming the diagnosis of HH. Since HH mutations occur commonly in select populations, screening patients with leukemia for HH may better inform treatment decisions regarding chemotherapy, transfusions, and/or iron chelation therapy.

Liposomal amphotericin B associated with severe hyperphosphatemia.

We report 4 patients who developed hyperphosphatemia while receiving liposomal amphotericin B to treat an invasive fungal infection. Resolution of the hyperphosphatemia occurred after transition to amphotericin B lipid complex. This phenomenon may occur more commonly in patients with mild to moderate renal insufficiency.