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1.
Clin Cancer Res ; 25(13): 3776-3783, 2019 07 01.
Article in English | MEDLINE | ID: mdl-30952640

ABSTRACT

PURPOSE: Pegylated liposomal doxorubicin (PLD) combined with bortezomib is an effective salvage regimen for relapsed refractory multiple myeloma (RRMM). Carfilzomib, a second-generation proteasome inhibitor, has clinical efficacy even among bortezomib-refractory patients. PATIENTS AND METHODS: We performed a phase I/II trial of carfilzomib, PLD, and dexamethasone (KDD) with the primary endpoints being safety and efficacy (NCT01246063). Twenty-three patients were enrolled in the phase I portion and the MTD of carfilzomib was determined to be 56 mg/m2 (days 1, 2, 8, 9, 15, and 16) when combined with PLD (30 mg/m2 on day 8) and dexamethasone (20 mg on days 1, 2, 8, 9, 15, and 16). Seventeen additional patients were enrolled in the phase II portion. RESULTS: KDD was determined to be well tolerated with the only common grade 3/4 nonhematologic adverse events of infection. Grade 3/4 hematologic toxicity included lymphopenia (63%), thrombocytopenia (40%), anemia (40%), and neutropenia (28%). In the cohort of patients treated at the MTD, where median prior therapies were 2% and 42% were refractory to bortezomib, the overall response rate was 83% (20/24) with 54% (13/24) having a very good partial response or better. The median progression-free survival was 13.7 months (95% CI, 5.0-21.7). CONCLUSIONS: This trial is the first to report outcomes using a triplet regimen of high-dose carfilzomib. KDD was well tolerated and appears efficacious in RRMM. Additional study is needed to more precisely determine patient outcomes with this regimen and its utility compared with other carfilzomib containing salvage regimens.


Subject(s)
Antineoplastic Combined Chemotherapy Protocols/therapeutic use , Multiple Myeloma/drug therapy , Multiple Myeloma/pathology , Aged , Antineoplastic Combined Chemotherapy Protocols/adverse effects , Dexamethasone/administration & dosage , Dexamethasone/pharmacokinetics , Doxorubicin/administration & dosage , Doxorubicin/analogs & derivatives , Doxorubicin/pharmacokinetics , Drug Monitoring , Drug Resistance, Neoplasm , Female , Humans , Male , Middle Aged , Multiple Myeloma/mortality , Neoplasm Staging , Oligopeptides/administration & dosage , Oligopeptides/pharmacokinetics , Polyethylene Glycols/administration & dosage , Polyethylene Glycols/pharmacokinetics , Prognosis , Recurrence , Retreatment , Treatment Outcome
2.
Cancer Discov ; 8(4): 428-443, 2018 04.
Article in English | MEDLINE | ID: mdl-29431699

ABSTRACT

Although BRAF inhibitor monotherapy yields response rates >50% in BRAFV600-mutant melanoma, only approximately 5% of patients with BRAFV600E colorectal cancer respond. Preclinical studies suggest that the lack of efficacy in BRAFV600E colorectal cancer is due to adaptive feedback reactivation of MAPK signaling, often mediated by EGFR. This clinical trial evaluated BRAF and EGFR inhibition with dabrafenib (D) + panitumumab (P) ± MEK inhibition with trametinib (T) to achieve greater MAPK suppression and improved efficacy in 142 patients with BRAFV600E colorectal cancer. Confirmed response rates for D+P, D+T+P, and T+P were 10%, 21%, and 0%, respectively. Pharmacodynamic analysis of paired pretreatment and on-treatment biopsies found that efficacy of D+T+P correlated with increased MAPK suppression. Serial cell-free DNA analysis revealed additional correlates of response and emergence of KRAS and NRAS mutations on disease progression. Thus, targeting adaptive feedback pathways in BRAFV600E colorectal cancer can improve efficacy, but MAPK reactivation remains an important primary and acquired resistance mechanism.Significance: This trial demonstrates that combined BRAF + EGFR + MEK inhibition is tolerable, with promising activity in patients with BRAFV600E colorectal cancer. Our findings highlight the MAPK pathway as a critical target in BRAFV600E colorectal cancer and the need to optimize strategies inhibiting this pathway to overcome both primary and acquired resistance. Cancer Discov; 8(4); 428-43. ©2018 AACR.See related commentary by Janku, p. 389See related article by Hazar-Rethinam et al., p. 417This article is highlighted in the In This Issue feature, p. 371.


Subject(s)
Antineoplastic Combined Chemotherapy Protocols/therapeutic use , Colorectal Neoplasms/drug therapy , MAP Kinase Signaling System , Protein Kinase Inhibitors/therapeutic use , Proto-Oncogene Proteins B-raf/antagonists & inhibitors , Colorectal Neoplasms/enzymology , Colorectal Neoplasms/metabolism , Drug Resistance, Neoplasm , ErbB Receptors/antagonists & inhibitors , ErbB Receptors/metabolism , Female , Humans , Imidazoles/therapeutic use , Male , Mitogen-Activated Protein Kinase Kinases/drug effects , Mitogen-Activated Protein Kinase Kinases/metabolism , Oximes/therapeutic use , Panitumumab/therapeutic use , Proto-Oncogene Proteins B-raf/metabolism , Pyridones/therapeutic use , Pyrimidinones/therapeutic use
3.
Mol Cancer Res ; 15(12): 1722-1732, 2017 12.
Article in English | MEDLINE | ID: mdl-28851814

ABSTRACT

Nasopharyngeal carcinoma (NPC) is an Epstein-Barr virus (EBV) associated cancer characterized by a poor prognosis and a high level of lymphocyte infiltrate. Genetic hallmarks of NPC are not completely known but include deletion of the p16 (CDKN2A) locus and mutations in NF-κB pathway components, with a relatively low total mutational load. To better understand the genetic landscape, an integrated genomic analysis was performed using a large clinical cohort of treatment-naïve NPC tumor specimens. This genomic analysis was generally concordant with previous studies; however, three subtypes of NPC were identified by differences in immune cell gene expression, prognosis, tumor cell morphology, and genetic characteristics. A gene expression signature of proliferation was poorly prognostic and associated with either higher mutation load or specific EBV gene expression patterns in a subtype-specific manner. Finally, higher levels of stromal tumor-infiltrating lymphocytes associated with good prognosis and lower expression of a WNT and TGFß pathway activation signature.Implications: This study represents the first integrated analysis of mutation, copy number, and gene expression data in NPC and suggests how tumor genetics and EBV infection influence the tumor microenvironment in this disease. These insights should be considered for guiding immunotherapy treatment strategies in this disease. Mol Cancer Res; 15(12); 1722-32. ©2017 AACR.


Subject(s)
Carcinoma/genetics , Genome, Human/genetics , Nasopharyngeal Neoplasms/genetics , Prognosis , Tumor Microenvironment/genetics , Adult , Aged , Carcinoma/pathology , Carcinoma/virology , Cell Proliferation/genetics , Cyclin-Dependent Kinase Inhibitor p16 , Cyclin-Dependent Kinase Inhibitor p18/genetics , Disease-Free Survival , Female , Gene Expression Regulation, Neoplastic , Genomics , Herpesvirus 4, Human/genetics , Herpesvirus 4, Human/pathogenicity , Humans , Lymphocytes, Tumor-Infiltrating/metabolism , Lymphocytes, Tumor-Infiltrating/pathology , Male , Middle Aged , Mutation , NF-kappa B/genetics , Nasopharyngeal Carcinoma , Nasopharyngeal Neoplasms/pathology , Nasopharyngeal Neoplasms/virology , Transforming Growth Factor beta/genetics , Wnt Signaling Pathway/genetics
4.
Cancer Discov ; 7(6): 610-619, 2017 06.
Article in English | MEDLINE | ID: mdl-28363909

ABSTRACT

Preclinical evidence suggests that concomitant BRAF and EGFR inhibition leads to sustained suppression of MAPK signaling and suppressed tumor growth in BRAFV600E colorectal cancer models. Patients with refractory BRAFV600-mutant metastatic CRC (mCRC) were treated with a selective RAF kinase inhibitor (encorafenib) plus a monoclonal antibody targeting EGFR (cetuximab), with (n = 28) or without (n = 26) a PI3Kα inhibitor (alpelisib). The primary objective was to determine the maximum tolerated dose (MTD) or a recommended phase II dose. Dose-limiting toxicities were reported in 3 patients receiving dual treatment and 2 patients receiving triple treatment. The MTD was not reached for either group and the phase II doses were selected as 200 mg encorafenib (both groups) and 300 mg alpelisib. Combinations of cetuximab and encorafenib showed promising clinical activity and tolerability in patients with BRAF-mutant mCRC; confirmed overall response rates of 19% and 18% were observed and median progression-free survival was 3.7 and 4.2 months for the dual- and triple-therapy groups, respectively.Significance: Herein, we demonstrate that dual- (encorafenib plus cetuximab) and triple- (encorafenib plus cetuximab and alpelisib) combination treatments are tolerable and provide promising clinical activity in the difficult-to-treat patient population with BRAF-mutant mCRC. Cancer Discov; 7(6); 610-9. ©2017 AACR.See related commentary by Sundar et al., p. 558This article is highlighted in the In This Issue feature, p. 539.


Subject(s)
Antineoplastic Combined Chemotherapy Protocols/therapeutic use , Carbamates/therapeutic use , Cetuximab/therapeutic use , Colorectal Neoplasms/drug therapy , Protein Kinase Inhibitors/therapeutic use , Sulfonamides/therapeutic use , Thiazoles/therapeutic use , Adult , Aged , Aged, 80 and over , Antineoplastic Agents/administration & dosage , Antineoplastic Agents/adverse effects , Antineoplastic Agents/therapeutic use , Antineoplastic Combined Chemotherapy Protocols/administration & dosage , Antineoplastic Combined Chemotherapy Protocols/adverse effects , Carbamates/administration & dosage , Carbamates/adverse effects , Cetuximab/administration & dosage , Cetuximab/adverse effects , Colorectal Neoplasms/genetics , Disease-Free Survival , Female , Humans , Male , Maximum Tolerated Dose , Middle Aged , Mutation , Phosphoinositide-3 Kinase Inhibitors , Protein Kinase Inhibitors/administration & dosage , Protein Kinase Inhibitors/adverse effects , Proto-Oncogene Proteins B-raf/antagonists & inhibitors , Proto-Oncogene Proteins B-raf/genetics , Sulfonamides/administration & dosage , Sulfonamides/adverse effects , Thiazoles/administration & dosage , Thiazoles/adverse effects
5.
Cancer Discov ; 5(8): 850-9, 2015 Aug.
Article in English | MEDLINE | ID: mdl-25971938

ABSTRACT

UNLABELLED: Focal amplification and activating point mutation of the MET gene are well-characterized oncogenic drivers that confer susceptibility to targeted MET inhibitors. Recurrent somatic splice site alterations at MET exon 14 (METex14) that result in exon skipping and MET activation have been characterized, but their full diversity and prevalence across tumor types are unknown. Here, we report analysis of tumor genomic profiles from 38,028 patients to identify 221 cases with METex14 mutations (0.6%), including 126 distinct sequence variants. METex14 mutations are detected most frequently in lung adenocarcinoma (3%), but also frequently in other lung neoplasms (2.3%), brain glioma (0.4%), and tumors of unknown primary origin (0.4%). Further in vitro studies demonstrate sensitivity to MET inhibitors in cells harboring METex14 alterations. We also report three new patient cases with METex14 alterations in lung or histiocytic sarcoma tumors that showed durable response to two different MET-targeted therapies. The diversity of METex14 mutations indicates that diagnostic testing via comprehensive genomic profiling is necessary for detection in a clinical setting. SIGNIFICANCE: Here we report the identification of diverse exon 14 splice site alterations in MET that result in constitutive activity of this receptor and oncogenic transformation in vitro. Patients whose tumors harbored these alterations derived meaningful clinical benefit from MET inhibitors. Collectively, these data support the role of METex14 alterations as drivers of tumorigenesis, and identify a unique subset of patients likely to derive benefit from MET inhibitors.


Subject(s)
Alternative Splicing , Antineoplastic Agents/therapeutic use , Exons , Neoplasms/drug therapy , Neoplasms/genetics , Protein Kinase Inhibitors/therapeutic use , Proto-Oncogene Proteins c-met/genetics , Aged , Aged, 80 and over , Antineoplastic Agents/pharmacology , Cluster Analysis , Drug Resistance, Neoplasm/genetics , Female , Gene Expression Profiling , Genomics/methods , Humans , Immunohistochemistry , Male , Mutation , Neoplasm Staging , Neoplasms/diagnosis , Protein Kinase Inhibitors/pharmacology , Proto-Oncogene Proteins c-met/metabolism , Tomography, X-Ray Computed
6.
J Biomol Screen ; 19(5): 791-802, 2014 Jun.
Article in English | MEDLINE | ID: mdl-24518063

ABSTRACT

Gene-expression data are often used to infer pathways regulating transcriptional responses. For example, differentially expressed genes (DEGs) induced by compound treatment can help characterize hits from phenotypic screens, either by correlation with known drug signatures or by pathway enrichment. Pathway enrichment is, however, typically computed with DEGs rather than "upstream" nodes that are potentially causal of "downstream" changes. Here, we present graph-based models to predict causal targets from compound-microarray data. We test several approaches to traversing network topology, and show that a consensus minimum-rank score (SigNet) beat individual methods and could highly rank compound targets among all network nodes. In addition, larger, less canonical networks outperformed linear canonical interactions. Importantly, pathway enrichment using causal nodes rather than DEGs recovers relevant pathways more often. To further validate our approach, we used integrated data sets from the Cancer Genome Atlas to identify driving pathways in triple-negative breast cancer. Critical pathways were uncovered, including the epidermal growth factor receptor 2-phosphatidylinositide 3-kinase-AKT-MAPK growth pathway andATR-p53-BRCA DNA damage pathway, in addition to unexpected pathways, such as TGF-WNT cytoskeleton remodeling, IL12-induced interferon gamma production, and TNFR-IAP (inhibitor of apoptosis) apoptosis; the latter was validated by pooled small hairpin RNA profiling in cancer cells. Overall, our approach can bridge transcriptional profiles to compound targets and driving pathways in cancer.


Subject(s)
Drug Discovery , Gene Expression Profiling , Gene Expression Regulation, Neoplastic , Neoplasms/drug therapy , Triple Negative Breast Neoplasms/drug therapy , Female , Humans , Models, Theoretical , Neoplasms/metabolism , Neoplasms/pathology , Oligonucleotide Array Sequence Analysis , Phenotype , RNA, Messenger/metabolism , ROC Curve , Signal Transduction , Triple Negative Breast Neoplasms/metabolism
7.
Oncotarget ; 4(12): 2502-11, 2013 Dec.
Article in English | MEDLINE | ID: mdl-24318446

ABSTRACT

Cancer cells rely on aerobic glycolysis to maintain cell growth and proliferation via the Warburg effect. Phosphoglycerate dehydrogenase (PHDGH) catalyzes the first step of the serine biosynthetic pathway downstream of glycolysis, which is a metabolic gatekeeper both for macromolecular biosynthesis and serine-dependent DNA synthesis. Here, we report that PHDGH is overexpressed in many ER-negative human breast cancer cell lines. PHGDH knockdown in these cells leads to a reduction of serine synthesis and impairment of cancer cell proliferation. However, PHGDH knockdown does not affect tumor maintenance and growth in established breast cancer xenograft models, suggesting that PHGDH-dependent cancer cell growth may be context-dependent. Our findings suggest that other mechanisms or pathways may bypass exclusive dependence on PHGDH in established human breast cancer xenografts, indicating that PHGDH is dispensable for the growth and maintenance and of tumors in vivo.


Subject(s)
Breast Neoplasms/enzymology , Phosphoglycerate Dehydrogenase/metabolism , Animals , Breast Neoplasms/genetics , Breast Neoplasms/pathology , Cell Growth Processes/physiology , Cell Line, Tumor , Cell Transformation, Neoplastic , Female , Gene Knockdown Techniques , Heterografts , Humans , MCF-7 Cells , Mice , Phosphoglycerate Dehydrogenase/genetics , RNA, Small Interfering/administration & dosage , RNA, Small Interfering/genetics
8.
Oncotarget ; 4(6): 816-29, 2013 Jun.
Article in English | MEDLINE | ID: mdl-23615731

ABSTRACT

The molecular chaperone heat shock protein 90 (HSP90) facilitates the appropriate folding of various oncogenic proteins and is necessary for the survival of some cancer cells. HSP90 is therefore an attractive drug target, but the efficacy of HSP90 inhibitor may be limited by HSP90 inhibition induced feedback mechanisms. Through pooled RNA interference screens, we identified that heat shock factor 1(HSF1) is a sensitizer of HSP90 inhibitor. A striking combinational effect was observed when HSF1 knockdown plus with HSP90 inhibitors treatment in various cancer cell lines and tumor mouse models. Interestingly, HSF1 is highly expressed in hepatocellular carcinoma (HCC) patient samples and HCC is sensitive to combinational treatment, indicating a potential indication for the combinational treatment. To understand the mechanism of the combinational effect, we identified that a HSF1-target gene DEDD2 is involved in attenuating the effect of HSP90 inhibitors. Thus, the transcriptional activities of HSF1 induced by HSP90 inhibitors provide a feedback mechanism of limiting the HSP90 inhibitor's activity, and targeting HSF1 may provide a new avenue to enhance HSP90 inhibitors activity in human cancers.


Subject(s)
Carcinoma, Hepatocellular/therapy , DNA-Binding Proteins/genetics , HSP90 Heat-Shock Proteins/antagonists & inhibitors , HSP90 Heat-Shock Proteins/metabolism , Liver Neoplasms/therapy , Transcription Factors/genetics , Animals , Apoptosis/physiology , Carcinoma, Hepatocellular/drug therapy , Carcinoma, Hepatocellular/genetics , Cell Line, Tumor , DNA-Binding Proteins/metabolism , Death Domain Receptor Signaling Adaptor Proteins/genetics , Doxycycline/pharmacology , Extracellular Signal-Regulated MAP Kinases/metabolism , Gene Knockdown Techniques , HCT116 Cells , HSP90 Heat-Shock Proteins/genetics , Heat Shock Transcription Factors , Humans , Liver Neoplasms/drug therapy , Liver Neoplasms/genetics , Mice , Molecular Targeted Therapy , Nuclear Proteins/genetics , RNA, Small Interfering/genetics , Transcription Factors/metabolism , Xenograft Model Antitumor Assays
9.
J Biomol Screen ; 18(4): 367-77, 2013 Apr.
Article in English | MEDLINE | ID: mdl-23204073

ABSTRACT

Screens using high-throughput, information-rich technologies such as microarrays, high-content screening (HCS), and next-generation sequencing (NGS) have become increasingly widespread. Compared with single-readout assays, these methods produce a more comprehensive picture of the effects of screened treatments. However, interpreting such multidimensional readouts is challenging. Univariate statistics such as t-tests and Z-factors cannot easily be applied to multidimensional profiles, leaving no obvious way to answer common screening questions such as "Is treatment X active in this assay?" and "Is treatment X different from (or equivalent to) treatment Y?" We have developed a simple, straightforward metric, the multidimensional perturbation value (mp-value), which can be used to answer these questions. Here, we demonstrate application of the mp-value to three data sets: a multiplexed gene expression screen of compounds and genomic reagents, a microarray-based gene expression screen of compounds, and an HCS compound screen. In all data sets, active treatments were successfully identified using the mp-value, and simulations and follow-up analyses supported the mp-value's statistical and biological validity. We believe the mp-value represents a promising way to simplify the analysis of multidimensional data while taking full advantage of its richness.


Subject(s)
High-Throughput Screening Assays/methods , Statistics as Topic , Computer Simulation , Humans , Hydroxamic Acids/pharmacology , MCF-7 Cells , Principal Component Analysis
10.
Development ; 139(6): 1164-74, 2012 Mar.
Article in English | MEDLINE | ID: mdl-22296846

ABSTRACT

A subfamily of Drosophila homeodomain (HD) transcription factors (TFs) controls the identities of individual muscle founder cells (FCs). However, the molecular mechanisms by which these TFs generate unique FC genetic programs remain unknown. To investigate this problem, we first applied genome-wide mRNA expression profiling to identify genes that are activated or repressed by the muscle HD TFs Slouch (Slou) and Muscle segment homeobox (Msh). Next, we used protein-binding microarrays to define the sequences that are bound by Slou, Msh and other HD TFs that have mesodermal expression. These studies revealed that a large class of HDs, including Slou and Msh, predominantly recognize TAAT core sequences but that each HD also binds to unique sites that deviate from this canonical motif. To understand better the regulatory specificity of an individual FC identity HD, we evaluated the functions of atypical binding sites that are preferentially bound by Slou relative to other HDs within muscle enhancers that are either activated or repressed by this TF. These studies showed that Slou regulates the activities of particular myoblast enhancers through Slou-preferred sequences, whereas swapping these sequences for sites that are capable of binding to multiple HD family members does not support the normal regulatory functions of Slou. Moreover, atypical Slou-binding sites are overrepresented in putative enhancers associated with additional Slou-responsive FC genes. Collectively, these studies provide new insights into the roles of individual HD TFs in determining cellular identity, and suggest that the diversity of HD binding preferences can confer regulatory specificity.


Subject(s)
Homeodomain Proteins/genetics , Homeodomain Proteins/metabolism , Muscles/embryology , Myoblasts/physiology , Animals , Base Sequence , Binding Sites/genetics , DNA-Binding Proteins/genetics , DNA-Binding Proteins/metabolism , Drosophila Proteins/genetics , Drosophila Proteins/metabolism , Drosophila melanogaster/embryology , Drosophila melanogaster/genetics , Gene Expression Profiling , Gene Expression Regulation, Developmental , RNA, Messenger/biosynthesis , Regulatory Sequences, Nucleic Acid , Transcription Factors/genetics , Transcription Factors/metabolism
11.
Cell ; 147(6): 1233-47, 2011 Dec 09.
Article in English | MEDLINE | ID: mdl-22153071

ABSTRACT

Hepatocyte nuclear factor 4α (HNF4α) is essential for liver development and hepatocyte function. Here, we show that transient inhibition of HNF4α initiates hepatocellular transformation through a microRNA-inflammatory feedback loop circuit consisting of miR-124, IL6R, STAT3, miR-24, and miR-629. Moreover, we show that, once this circuit is activated, it maintains suppression of HNF4α and sustains oncogenesis. Systemic administration of miR-124, which modulates inflammatory signaling, prevents and suppresses hepatocellular carcinogenesis by inducing tumor-specific apoptosis without toxic side effects. As we also show that this HNF4α circuit is perturbed in human hepatocellular carcinomas, our data raise the possibility that manipulation of this microRNA feedback-inflammatory loop has therapeutic potential for treating liver cancer.


Subject(s)
Carcinoma, Hepatocellular/metabolism , Cell Transformation, Neoplastic , Hepatocyte Nuclear Factor 4/metabolism , Inflammation/metabolism , Liver Neoplasms/metabolism , MicroRNAs/metabolism , Animals , Cell Line, Tumor , Disease Models, Animal , Humans , Mice , Receptors, Interleukin-6/metabolism , STAT3 Transcription Factor/metabolism
12.
Gastroenterology ; 141(5): 1749-61.e1, 2011 Nov.
Article in English | MEDLINE | ID: mdl-21806946

ABSTRACT

BACKGROUND & AIMS: Neurotensin promotes inflammation and colon cancer via the neurotensin-1 receptor (NTR1). MicroRNAs (miR) regulate protein synthesis by degrading or preventing translation of mRNAs. We analyzed expression of 365 different microRNAs by human colonic epithelial cells (NCM460) after activation of NTR1. METHODS: We performed microarray analysis of mRNA expression by neurotensin-stimulated NCM460 cells that overexpressed NTR1. Nuclear factor-κB (NF-κB) binding sites were identified and tumorigenesis was assessed using soft agar assays and xenograft analysis of severe combined immunodeficiency mice. Targets of neurotensin-regulated microRNAs were identified via bioinformatic, real-time polymerase chain reaction, and immunoblot analyses. We analyzed RNA samples from human normal colon and tumor samples. RESULTS: Neurotensin stimulated differential expression of 38 microRNAs, including miR-21 and miR-155, which have been associated with tumor growth and contain NF-κB binding sites. Neurotensin expression increased colony formation by HCT-116 cells. Blocking miR-21 and/or miR-155 prevented colony formation (P < .001). In mice, intraperitoneal administration of neurotensin increased the growth rate of HCT-116 xenograft tumors; blocking miR-21 and/or miR-155 slowed this tumor growth. Neurotensin activated Akt in HCT-116 cells; this effect was inhibited by blocking miR-21 and/or miR-155 (P < .001). Neurotensin activated AKT through miR-155-mediated suppression of the phosphatase protein phosphatase 2A catalytic subunit alpha (PPP2CA). Levels of phosphatase and tensin homolog (PTEN) and suppressor of cytokine signaling 1 (SOCS1) mRNA, potential targets of miR-21 and miR-155, respectively, were down-regulated by these miRs. Levels of NTR1, miR-21, and miR-155 increased significantly in human colon tumor samples, compared with normal tissues, whereas PPP2CA, SOCS1, and PTEN mRNAs were reduced significantly. CONCLUSIONS: NTR1 activation stimulates expression of miR-21 and miR-155 in colonocytes, via Akt and NF-κB, to down-regulate PTEN and SOCS1 and promote growth of tumors in mice. Levels of NTR1, miR-21, and miR-155 increase in human colon tumor samples and correlate with tumor stage.


Subject(s)
Cell Proliferation , Colorectal Neoplasms/metabolism , Colorectal Neoplasms/pathology , MicroRNAs/metabolism , Neurotensin/metabolism , Proto-Oncogene Proteins c-akt/metabolism , Signal Transduction/physiology , Adenocarcinoma/metabolism , Adenocarcinoma/pathology , Animals , Cell Line, Tumor , Disease Models, Animal , Humans , Mice , Mice, Nude , NF-kappa B/metabolism , PTEN Phosphohydrolase/metabolism , Protein Phosphatase 2/metabolism , Receptors, Neurotensin/metabolism , Suppressor of Cytokine Signaling 1 Protein , Suppressor of Cytokine Signaling Proteins/metabolism , Transplantation, Heterologous
13.
Mol Cell ; 39(4): 493-506, 2010 Aug 27.
Article in English | MEDLINE | ID: mdl-20797623

ABSTRACT

A transient inflammatory signal can initiate an epigenetic switch from nontransformed to cancer cells via a positive feedback loop involving NF-kappaB, Lin28, let-7, and IL-6. We identify differentially regulated microRNAs important for this switch and putative transcription factor binding sites in their promoters. STAT3, a transcription factor activated by IL-6, directly activates miR-21 and miR-181b-1. Remarkably, transient expression of either microRNA induces the epigenetic switch. MiR-21 and miR-181b-1, respectively, inhibit PTEN and CYLD tumor suppressors, leading to increased NF-kappaB activity required to maintain the transformed state. These STAT3-mediated regulatory circuits are required for the transformed state in diverse cell lines and tumor growth in xenografts, and their transcriptional signatures are observed in colon adenocarcinomas. Thus, STAT3 is not only a downstream target of IL-6 but, with miR-21, miR-181b-1, PTEN, and CYLD, is part of the positive feedback loop that underlies the epigenetic switch that links inflammation to cancer.


Subject(s)
Breast Neoplasms/metabolism , Cell Transformation, Neoplastic/metabolism , Epigenesis, Genetic , Inflammation/metabolism , Mammary Glands, Human/metabolism , MicroRNAs/metabolism , PTEN Phosphohydrolase/metabolism , STAT3 Transcription Factor/metabolism , Tumor Suppressor Proteins/metabolism , Adenocarcinoma/genetics , Adenocarcinoma/metabolism , Adenocarcinoma/therapy , Algorithms , Animals , Binding Sites , Breast Neoplasms/genetics , Breast Neoplasms/pathology , Cell Movement , Cell Proliferation , Cell Transformation, Neoplastic/genetics , Cell Transformation, Neoplastic/pathology , Colonic Neoplasms/genetics , Colonic Neoplasms/metabolism , Colonic Neoplasms/therapy , Computational Biology , Deubiquitinating Enzyme CYLD , Female , Gene Expression Regulation, Neoplastic , Genes, src , HCT116 Cells , HT29 Cells , Humans , Inflammation/genetics , Inflammation Mediators/metabolism , Kinetics , Mammary Glands, Human/pathology , Mice , Mice, Nude , NF-kappa B/metabolism , Neoplasm Invasiveness , Promoter Regions, Genetic , Proto-Oncogene Proteins c-akt/metabolism , Proto-Oncogene Proteins c-myc/genetics , Proto-Oncogene Proteins c-myc/metabolism , RNA Interference , Receptors, Estrogen/genetics , Signal Transduction , Transcriptional Activation , Transfection , Tumor Burden , Tumor Suppressor Proteins/genetics , Xenograft Model Antitumor Assays
14.
Cancer Cell ; 17(4): 348-61, 2010 Apr 13.
Article in English | MEDLINE | ID: mdl-20385360

ABSTRACT

Transcriptional profiling of two isogenic models of transformation identifies a gene signature linking cancer with inflammatory and metabolic diseases. In accord with this common transcriptional program, many drugs used for treatment of diabetes and cardiovascular diseases inhibit transformation and tumor growth. Unexpectedly, lipid metabolism genes are important for transformation and are upregulated in cancer tissues. As in atherosclerosis, oxidized LDL and its receptor OLR1 activate the inflammatory pathway through NF-kappaB, leading to transformation. OLR1 is important for maintaining the transformed state in developmentally diverse cancer cell lines and for tumor growth, suggesting a molecular connection between cancer and atherosclerosis. We suggest that the interplay between this common transcriptional program and cell-type-specific factors gives rise to phenotypically disparate human diseases.


Subject(s)
Atherosclerosis/genetics , Gene Expression Profiling , Genetic Diseases, Inborn/genetics , Neoplasms/genetics , Transcription, Genetic , Cell Transformation, Neoplastic/genetics , Diabetes Mellitus/genetics , Genetic Linkage , Genetic Variation , Humans , Inflammation/genetics , Metabolic Syndrome/genetics , Obesity/genetics , Scavenger Receptors, Class E/genetics
15.
Genomics ; 95(4): 185-95, 2010 Apr.
Article in English | MEDLINE | ID: mdl-20079828

ABSTRACT

Sequence-specific binding by transcription factors (TFs) interprets regulatory information encoded in the genome. Using recently published universal protein binding microarray (PBM) data on the in vitro DNA binding preferences of these proteins for all possible 8-base-pair sequences, we examined the evolutionary conservation and enrichment within putative regulatory regions of the binding sequences of a diverse library of 104 nonredundant mouse TFs spanning 22 different DNA-binding domain structural classes. We found that not only high affinity binding sites, but also numerous moderate and low affinity binding sites, are under negative selection in the mouse genome. These 8-mers occur preferentially in putative regulatory regions of the mouse genome, including CpG islands and non-exonic ultraconserved elements (UCEs). Of TFs whose PBM "bound" 8-mers are enriched within sets of tissue-specific UCEs, many are expressed in the same tissue(s) as the UCE-driven gene expression. Phylogenetically conserved motif occurrences of various TFs were also enriched in the noncoding sequence surrounding numerous gene sets corresponding to Gene Ontology categories and tissue-specific gene expression clusters, suggesting involvement in transcriptional regulation of those genes. Altogether, our results indicate that many of the sequences bound by these proteins in vitro, including lower affinity DNA sequences, are likely to be functionally important in vivo. This study not only provides an initial analysis of the potential regulatory associations of 104 mouse TFs, but also presents an approach for the functional analysis of TFs from any other metazoan genome as their DNA binding preferences are determined by PBMs or other technologies.


Subject(s)
Gene Expression Regulation , Transcription Factors/metabolism , Animals , Base Sequence/genetics , Binding Sites/genetics , CpG Islands/genetics , Humans , Mice , Promoter Regions, Genetic/genetics , Protein Array Analysis , Regulatory Sequences, Nucleic Acid/genetics , Sequence Analysis, DNA
16.
Science ; 324(5935): 1720-3, 2009 Jun 26.
Article in English | MEDLINE | ID: mdl-19443739

ABSTRACT

Sequence preferences of DNA binding proteins are a primary mechanism by which cells interpret the genome. Despite the central importance of these proteins in physiology, development, and evolution, comprehensive DNA binding specificities have been determined experimentally for only a few proteins. Here, we used microarrays containing all 10-base pair sequences to examine the binding specificities of 104 distinct mouse DNA binding proteins representing 22 structural classes. Our results reveal a complex landscape of binding, with virtually every protein analyzed possessing unique preferences. Roughly half of the proteins each recognized multiple distinctly different sequence motifs, challenging our molecular understanding of how proteins interact with their DNA binding sites. This complexity in DNA recognition may be important in gene regulation and in the evolution of transcriptional regulatory networks.


Subject(s)
DNA/metabolism , Transcription Factors/chemistry , Transcription Factors/metabolism , Amino Acid Motifs , Amino Acid Sequence , Animals , Base Sequence , Binding Sites , DNA/chemistry , Electrophoretic Mobility Shift Assay , Gene Expression Regulation , Gene Regulatory Networks , Humans , Mice , Protein Array Analysis , Protein Binding , Protein Structure, Tertiary , Recombinant Fusion Proteins/chemistry , Recombinant Fusion Proteins/metabolism
17.
Cell ; 133(7): 1266-76, 2008 Jun 27.
Article in English | MEDLINE | ID: mdl-18585359

ABSTRACT

Most homeodomains are unique within a genome, yet many are highly conserved across vast evolutionary distances, implying strong selection on their precise DNA-binding specificities. We determined the binding preferences of the majority (168) of mouse homeodomains to all possible 8-base sequences, revealing rich and complex patterns of sequence specificity and showing that there are at least 65 distinct homeodomain DNA-binding activities. We developed a computational system that successfully predicts binding sites for homeodomain proteins as distant from mouse as Drosophila and C. elegans, and we infer full 8-mer binding profiles for the majority of known animal homeodomains. Our results provide an unprecedented level of resolution in the analysis of this simple domain structure and suggest that variation in sequence recognition may be a factor in its functional diversity and evolutionary success.


Subject(s)
DNA/chemistry , Homeodomain Proteins/chemistry , Animals , Base Sequence , Computational Biology , Conserved Sequence , DNA/metabolism , Evolution, Molecular , Homeodomain Proteins/metabolism , Mice , Models, Molecular , Protein Binding , Transcription Factors/chemistry , Transcription Factors/metabolism
18.
Nat Methods ; 5(4): 347-53, 2008 Apr.
Article in English | MEDLINE | ID: mdl-18311145

ABSTRACT

We developed an algorithm, Lever, that systematically maps metazoan DNA regulatory motifs or motif combinations to sets of genes. Lever assesses whether the motifs are enriched in cis-regulatory modules (CRMs), predicted by our PhylCRM algorithm, in the noncoding sequences surrounding the genes. Lever analysis allows unbiased inference of functional annotations to regulatory motifs and candidate CRMs. We used human myogenic differentiation as a model system to statistically assess greater than 25,000 pairings of gene sets and motifs or motif combinations. We assigned functional annotations to candidate regulatory motifs predicted previously and identified gene sets that are likely to be co-regulated via shared regulatory motifs. Lever allows moving beyond the identification of putative regulatory motifs in mammalian genomes, toward understanding their biological roles. This approach is general and can be applied readily to any cell type, gene expression pattern or organism of interest.


Subject(s)
Computational Biology/methods , DNA/genetics , Regulatory Elements, Transcriptional/genetics , Regulatory Sequences, Nucleic Acid/genetics , Algorithms , Animals , Genome , Humans , Molecular Sequence Data , Species Specificity
19.
J Nerv Ment Dis ; 195(5): 369-77, 2007 May.
Article in English | MEDLINE | ID: mdl-17502801

ABSTRACT

Controversy exists about the role of mental disorders in the consistently documented association between smoking and suicidal behavior. This controversy is addressed here with data from the nationally representative National Comorbidity Survey-Replication (NCS-R). Assessments were made of 12-month smoking, suicidal behaviors (ideation, plans, attempts), and DSM-IV disorders (anxiety, mood, impulse-control, and substance use disorders). Statistically significant odds ratios (2.9-3.1) were found between 12-month smoking and 12-month suicidal behaviors. However, the associations of smoking with the outcomes became insignificant with controls for DSM-IV mental disorders. Although clear adjudication among contending hypotheses about causal mechanisms cannot be made from the cross-sectional NCS-R data, the results make it clear that future research on smoking and suicidal behaviors should focus more centrally than previous research on mental disorders either as common causes, markers, or mediators.


Subject(s)
Mental Disorders/epidemiology , Smoking/epidemiology , Suicide/psychology , Suicide/statistics & numerical data , Adolescent , Adult , Age Distribution , Comorbidity , Cross-Sectional Studies , Diagnostic and Statistical Manual of Mental Disorders , Female , Health Surveys , Humans , Logistic Models , Male , Mental Disorders/diagnosis , Mental Disorders/psychology , Middle Aged , Models, Statistical , Odds Ratio , Prevalence , Psychiatric Status Rating Scales , Smoking/psychology , United States/epidemiology
20.
Biol Psychiatry ; 60(12): 1364-71, 2006 Dec 15.
Article in English | MEDLINE | ID: mdl-16952333

ABSTRACT

BACKGROUND: Little is known about the population prevalence of sleep problems or whether the associations of sleep problems with role impairment are due to comorbid mental disorders. METHODS: The associations of four 12-month sleep problems (difficulty initiating or maintaining sleep, early morning awakening, nonrestorative sleep) with role impairment were analyzed in the National Comorbidity Survey Replication controlling 12-month DSM-IV anxiety, mood, impulse-control, and substance disorders. The WHO Composite International Diagnostic Interview was used to assess sleep problems and DSM-IV disorders. The WHO Disability Schedule-II (WHO-DAS) was used to assess role impairment. RESULTS: Prevalence estimates of the separate sleep problems were in the range 16.4-25.0%, with 36.3% reporting at least one of the four. Mean 12-month duration was 24.4 weeks. All four problems were significantly comorbid with all the 12-month DMS-IV disorders assessed in the survey (median OR: 3.4; 25(th)-75(th) percentile: 2.8-3.9) and significantly related to role impairment. Relationships with role impairment generally remained significant after controlling comorbid mental disorders. Nonrestorative sleep was more strongly and consistently related to role impairment than were the other sleep problems. CONCLUSIONS: The four sleep problems considered here are of public health significance because of their high prevalence and significant associations with role impairment.


Subject(s)
Mental Disorders/complications , Mental Disorders/epidemiology , Sleep Wake Disorders/complications , Sleep Wake Disorders/epidemiology , Activities of Daily Living , Adult , Affect/physiology , Aged , Anxiety/psychology , Comorbidity , Epidemiologic Studies , Female , Health Surveys , Humans , Impulsive Behavior/psychology , Interview, Psychological , Male , Mental Disorders/psychology , Middle Aged , Multivariate Analysis , Psychiatric Status Rating Scales , Regression Analysis , Sleep Initiation and Maintenance Disorders/complications , Sleep Initiation and Maintenance Disorders/epidemiology , Sleep Initiation and Maintenance Disorders/psychology , Sleep Wake Disorders/psychology , Socioeconomic Factors , Substance-Related Disorders/complications , Substance-Related Disorders/psychology , Surveys and Questionnaires , United States/epidemiology
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