Search

Reports that the same DNA sequence that represses the octamer factor also mediates either positive or negative transcriptional effects.

Diffuse large B cell lymphoma (DLBCL) is the most common form of non-Hodgkin's lymphoma. Patients who receive standard of care treatment have variable responses and up to 40% relapse. Not much is known regarding differences within tumors, or intratumoral heterogeneity. Thus, our question is, what are the genotypes and phenotypes of DLBCL subclones? We hypothesize DLBCL tumors contain genetic subclones with phenotypic variation that reflects axes of B cell development. The aim is to determine the implication of tumor subclones in disease pathogenesis. This study analyzed 101 DLBCL cases with paired single nuclei RNA (snRNA) and single nuclei ATAC (snATAC) sequencing, bulk whole exome and RNA sequencing, flow cytometry, and immunohistochemistry. The majority (75%) of tumors were treatment naive. Seurat 4.2.0 was used to process snRNA data. Genetic subclones were identified by snRNA-based copy number. ArchR was 1.0.3 was utilized for snATAC. The majority (85%) of tumors contained genetic subclones (mean 2, range 1-6). We identified six clusters of gene expression signatures, or themes, that characterized subclone diversity. Three themes (memory, plasma cell, and germinal center) recapitulated B cells blocked in differentiation and accounted for most of the heterogeneity between subclones (F test p = 6E-5). Two additional themes (cell cycle, metabolic) represented overall sample activity. Next, we utilized an independent discovery dataset (n = 560) to identify genetic alterations associated with each theme. Notably, we observed REL amplification is negatively associated with expression of the memory B cell theme in the discovery dataset (t test, p = 1E-11) and validated this in the single cell subclones (t test, p = 0.03). REL amplification is a highly recurrent alteration in the germinal center B cell subtype (GCB) DLBCL. In cell line models, we showed REL amplification restricted B cells to the germinal center and prevented memory B cell differentiation, thus driving cells to a malignant GCB phenotype. This study is a comprehensive characterization of intratumoral heterogeneity. We identified genetic alterations that drive tumor subclones towards specific malignant phenotypes. This work will also provide a single cell resource to the DLBCL community. [ABSTRACT FROM AUTHOR]

Pharmacological agents that inhibit enzymes of the B-cell receptor (BCR) pathway are of increasing importance in the treatment of B-cell malignancies. These include inhibitors of Bruton tyrosine kinase (BTK), phosphatidylinositol 3-kinase (PI3K), splenic tyrosine kinase and protein kinase Cβ. Two agents are already approved in the USA and Europe: ibrutinib, a BTK inhibitor, for the treatment of chronic lymphatic leukaemia (CLL), mantle cell lymphoma (MCL) and Waldenström's macroglobulinemia; and idelalisib, a PI3Kδ inhibitor, for the treatment of CLL and follicular lymphoma. In addition, the role of these drugs in diffuse large B-cell lymphoma and marginal zone lymphoma is under investigation, as single agents and in combination with chemotherapy. In CLL, both ibrutinib and idelalisib have an established role as first-line therapy in patients with del(17p), and in MCL, ibrutinib is a standard option for patients relapsing after chemoimmunotherapy. Unexpected toxicities have been encountered when combining these potent new agents with other drugs, including chemotherapy and lenalidomide, and based on this experience the risks and benefits of novel combinations must be evaluated carefully. In this review, we summarize the efficacy and safety results with these inhibitors and discuss novel combinations that are under study and the future role of BCR inhibitors in these disorders. [ABSTRACT FROM AUTHOR]

To identify novel signaling pathways necessary for rhabdomyosarcoma (RMS) survival, we performed a loss-of-function screen using an inducible small hairpin RNA (shRNA) library in an alveolar and an embryonal RMS cell line. This screen identified CRKL expression as necessary for growth of alveolar RMS and embryonal RMS both in vitro and in vivo. We also found that CRKL was uniformly highly expressed in both RMS cell lines and tumor tissue. As CRKL is a member of the CRK adapter protein family that contains an SH2 and two SH3 domains and is involved in signal transduction from multiple tyrosine kinase receptors, we evaluated CRKL interaction with multiple tyrosine kinase receptor signaling pathways in RMS cells. While we saw no interaction of CRKL with IGFIR, MET or PI3KAKT/mTOR pathways, we determined that CRKL signaling was associated with SRC family kinase (SFK) signaling, specifically with YES kinase. Inhibition of SFK signaling with dasatinib or another SFK inhibitor, sarcatinib, suppressed RMS cell growth in vitro and in vivo. These data identify CRKL as a novel critical component of RMS growth. This study also demonstrates the use of functional screening to identify a potentially novel therapeutic target and treatment approach for these highly aggressive pediatric cancers. [ABSTRACT FROM AUTHOR]

The median survival of patients with mantle cell lymphoma (MCL) ranges from 3 to 5 years with current chemotherapeutic regimens. A common secondary genomic alteration detected in MCL is chromosome 13q31-q32 gain/amplification, which targets a microRNA (miRNA) cluster, miR-17∼92. On the basis of gene expression profiling, we found that high level expression of C13orf25, the primary transcript from which these miRNAs are processed, was associated with poorer survival in patients with MCL (P=0.021). We demonstrated that the protein phosphatase PHLPP2, an important negative regulator of the PI3K/AKT pathway, was a direct target of miR-17∼92 miRNAs, in addition to PTEN and BIM. These proteins were down-modulated in MCL cells with overexpression of the miR-17∼92 cluster. Overexpression of miR-17∼92 activated the PI3K/AKT pathway and inhibited chemotherapy-induced apoptosis in MCL cell lines. Conversely, inhibition of miR-17∼92 expression suppressed the PI3K/AKT pathway and inhibited tumor growth in a xenograft MCL mouse model. Targeting the miR-17∼92 cluster may therefore provide a novel therapeutic approach for patients with MCL. [ABSTRACT FROM AUTHOR]

The median survival of patients with mantle cell lymphoma (MCL) ranges from 3 to 5 years with current chemotherapeutic regimens. A common secondary genomic alteration detected in MCL is chromosome 13q31-q32 gain/amplification, which targets a microRNA (miRNA) cluster, miR-17∼92. On the basis of gene expression profiling, we found that high level expression of C13orf25, the primary transcript from which these miRNAs are processed, was associated with poorer survival in patients with MCL (P=0.021). We demonstrated that the protein phosphatase PHLPP2, an important negative regulator of the PI3K/AKT pathway, was a direct target of miR-17∼92 miRNAs, in addition to PTEN and BIM. These proteins were down-modulated in MCL cells with overexpression of the miR-17∼92 cluster. Overexpression of miR-17∼92 activated the PI3K/AKT pathway and inhibited chemotherapy-induced apoptosis in MCL cell lines. Conversely, inhibition of miR-17∼92 expression suppressed the PI3K/AKT pathway and inhibited tumor growth in a xenograft MCL mouse model. Targeting the miR-17∼92 cluster may therefore provide a novel therapeutic approach for patients with MCL. [ABSTRACT FROM AUTHOR]

Activating mutations in the KRAS gene are among the most prevalent genetic changes in human cancers. To identify synthetic lethal interactions in cancer cells harbouring mutant KRAS, we performed a large-scale screen in isogenic paired colon cancer cell lines that differ by a single allele of mutant KRAS using an inducible short hairpin RNA interference library. Snail2, a zinc finger transcriptional repressor encoded by the SNAI2 gene, was found to be selectively required for the long-term survival of cancer cells with mutant KRAS that have undergone epithelial–mesenchymal transition (EMT), a transdifferentiation event that is frequently seen in advanced tumours and is promoted by RAS activation. Snail2 expression is regulated by the RAS pathway and is required for EMT. Our findings support Snail2 as a possible target for the treatment of the broad spectrum of human cancers of epithelial origin with mutant RAS that have undergone EMT and are characterized by a high degree of chemoresistance and radioresistance. [ABSTRACT FROM AUTHOR]

Presents a letter to the editor of the journal "Leukemia," describing a study which found a novel mechanism of SOCS1 inactivation by biallelic chromosome deletion in the Karpas 1106 cell line.