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1.
Adv Genet (Hoboken) ; 2(1): e10036, 2021 Mar.
Article in English | MEDLINE | ID: mdl-36618440

ABSTRACT

ERBB3 is a pseudokinase domain-containing member of the ERBB family of receptor tyrosine kinases (RTKs). Following ligand binding, ERBB receptors homo- or hetero-dimerize, leading to a head-to-tail arrangement of the intracellular kinase domains, where the "receiver" kinase domain of one ERBB is activated by the "activator" domain of the other ERBB in the dimer. In ERBB3, a conserved valine at codon 943 (V943) in the kinase C-terminal domain has been shown to be important for its function as an "activator" kinase in vitro. Here we report a knock-in mouse model where we have modified the endogenous Erbb3 allele to allow for tissue-specific conditional expression of Erbb3 V943R (Erbb3 CKI-V943R ). Additionally, we generated an Erbb3 D850N (Erbb3 CKI-D850N ) conditional knock-in mouse model where the conserved aspartate in the DFG motif of the pseudokinase domain was mutated to abolish any potential residual kinase activity. While Erbb3 D850N/D850N animals developed normally, homozygous Erbb3 V943R/V943R expression during development resulted in embryonic lethality. Further, tissue specific expression of Erbb3 V943R/V943R in the mammary gland epithelium following its activation using MMTV-Cre resulted in delayed elongation of the ductal network during puberty. Single-cell RNA-seq analysis of Erbb3 V943R/V943R mammary glands showed a reduction in a specific subset of fibrinogen-producing luminal epithelial cells.

2.
Nat Commun ; 11(1): 4225, 2020 08 24.
Article in English | MEDLINE | ID: mdl-32839463

ABSTRACT

Gallbladder cancer (GBC) is an aggressive gastrointestinal malignancy with no approved targeted therapy. Here, we analyze exomes (n = 160), transcriptomes (n = 115), and low pass whole genomes (n = 146) from 167 gallbladder cancers (GBCs) from patients in Korea, India and Chile. In addition, we also sequence samples from 39 GBC high-risk patients and detect evidence of early cancer-related genomic lesions. Among the several significantly mutated genes not previously linked to GBC are ETS domain genes ELF3 and EHF, CTNNB1, APC, NSD1, KAT8, STK11 and NFE2L2. A majority of ELF3 alterations are frame-shift mutations that result in several cancer-specific neoantigens that activate T-cells indicating that they are cancer vaccine candidates. In addition, we identify recurrent alterations in KEAP1/NFE2L2 and WNT pathway in GBC. Taken together, these define multiple targetable therapeutic interventions opportunities for GBC treatment and management.


Subject(s)
DNA-Binding Proteins/genetics , Frameshift Mutation , Gallbladder Neoplasms/genetics , Genetic Predisposition to Disease/genetics , Proto-Oncogene Proteins c-ets/genetics , Transcription Factors/genetics , Cancer Vaccines/genetics , Cancer Vaccines/immunology , Chile , DNA-Binding Proteins/immunology , DNA-Binding Proteins/metabolism , Gallbladder Neoplasms/diagnosis , Gallbladder Neoplasms/metabolism , Gene Expression Profiling/methods , Gene Expression Regulation, Neoplastic , Genomics/methods , Humans , India , Kelch-Like ECH-Associated Protein 1/genetics , Kelch-Like ECH-Associated Protein 1/metabolism , NF-E2-Related Factor 2/genetics , NF-E2-Related Factor 2/metabolism , Proto-Oncogene Proteins c-ets/immunology , Proto-Oncogene Proteins c-ets/metabolism , Republic of Korea , Transcription Factors/immunology , Transcription Factors/metabolism , Wnt Signaling Pathway/genetics , beta Catenin/genetics , beta Catenin/metabolism
3.
Commun Biol ; 2: 304, 2019.
Article in English | MEDLINE | ID: mdl-31428692

ABSTRACT

Obtaining full-length antibody heavy- and light-chain variable regions from individual B cells at scale remains a challenging problem. Here we use high-throughput single-cell B-cell receptor sequencing (scBCR-seq) to obtain accurately paired full-length variable regions in a massively parallel fashion. We sequenced more than 250,000 B cells from rat, mouse and human repertoires to characterize their lineages and expansion. In addition, we immunized rats with chicken ovalbumin and profiled antigen-reactive B cells from lymph nodes of immunized animals. The scBCR-seq data recovered 81% (n = 56/69) of B-cell lineages identified from hybridomas generated from the same set of B cells subjected to scBCR-seq. Importantly, scBCR-seq identified an additional 710 candidate lineages not recovered as hybridomas. We synthesized, expressed and tested 93 clones from the identified lineages and found that 99% (n = 92/93) of the clones were antigen-reactive. Our results establish scBCR-seq as a powerful tool for antibody discovery.


Subject(s)
Antibodies/metabolism , Antigens/metabolism , High-Throughput Nucleotide Sequencing/methods , Receptors, Antigen, B-Cell/genetics , Single-Cell Analysis , Animals , Germ Cells/metabolism , Humans , Immunoglobulin Heavy Chains/genetics , Immunoglobulin Light Chains/genetics , Mice , Rats , Reproducibility of Results
4.
Cancer Cell ; 34(5): 792-806.e5, 2018 11 12.
Article in English | MEDLINE | ID: mdl-30449325

ABSTRACT

Deregulated HER2 is a target of many approved cancer drugs. We analyzed 111,176 patient tumors and identified recurrent mutations in HER2 transmembrane domain (TMD) and juxtamembrane domain (JMD) that include G660D, R678Q, E693K, and Q709L. Using a saturation mutagenesis screen and testing of patient-derived mutations we found several activating TMD and JMD mutations. Structural modeling and analysis showed that the TMD/JMD mutations function by improving the active dimer interface or stabilizing an activating conformation. Further, we found that HER2 G660D employed asymmetric kinase dimerization for activation and signaling. Importantly, anti-HER2 antibodies and small-molecule kinase inhibitors blocked the activity of TMD/JMD mutants. Consistent with this, a G660D germline mutant lung cancer patient showed remarkable clinical response to HER2 blockade.


Subject(s)
Lung Neoplasms/genetics , Protein Domains/genetics , Receptor, ErbB-2/genetics , Receptor, ErbB-2/metabolism , Adult , Animals , Antineoplastic Agents/pharmacology , Cell Line, Tumor , Female , Humans , Lung Neoplasms/drug therapy , Male , Mice , Mice, Inbred BALB C , Middle Aged , Molecular Dynamics Simulation , Mutation/genetics , Protein Conformation , Protein Kinase Inhibitors/pharmacology , Receptor, ErbB-2/antagonists & inhibitors , Signal Transduction
5.
Cancer Discov ; 8(9): 1142-1155, 2018 09.
Article in English | MEDLINE | ID: mdl-29884728

ABSTRACT

By leveraging tumorgraft (patient-derived xenograft) RNA-sequencing data, we developed an empirical approach, DisHet, to dissect the tumor microenvironment (eTME). We found that 65% of previously defined immune signature genes are not abundantly expressed in renal cell carcinoma (RCC) and identified 610 novel immune/stromal transcripts. Using eTME, genomics, pathology, and medical record data involving >1,000 patients, we established an inflamed pan-RCC subtype (IS) enriched for regulatory T cells, natural killer cells, TH1 cells, neutrophils, macrophages, B cells, and CD8+ T cells. IS is enriched for aggressive RCCs, including BAP1-deficient clear-cell and type 2 papillary tumors. The IS subtype correlated with systemic manifestations of inflammation such as thrombocytosis and anemia, which are enigmatic predictors of poor prognosis. Furthermore, IS was a strong predictor of poor survival. Our analyses suggest that tumor cells drive the stromal immune response. These data provide a missing link between tumor cells, the TME, and systemic factors.Significance: We undertook a novel empirical approach to dissect the renal cell carcinoma TME by leveraging tumorgrafts. The dissection and downstream analyses uncovered missing links between tumor cells, the TME, systemic manifestations of inflammation, and poor prognosis. Cancer Discov; 8(9); 1142-55. ©2018 AACR.This article is highlighted in the In This Issue feature, p. 1047.


Subject(s)
Carcinoma, Renal Cell/pathology , Gene Expression Profiling/methods , Gene Regulatory Networks , Inflammation/genetics , Kidney Neoplasms/pathology , Animals , Carcinoma, Renal Cell/complications , Carcinoma, Renal Cell/genetics , Cluster Analysis , Gene Expression Regulation, Neoplastic , High-Throughput Nucleotide Sequencing/methods , Humans , Inflammation/pathology , Kidney Neoplasms/genetics , Kidney Neoplasms/immunology , Mice , Neoplasm Transplantation , Prognosis , Sequence Analysis, RNA/methods , Survival Analysis , Tumor Microenvironment , Unsupervised Machine Learning , Exome Sequencing/methods
6.
Clin Cancer Res ; 24(16): 4044-4055, 2018 08 15.
Article in English | MEDLINE | ID: mdl-29760222

ABSTRACT

Purpose: MAPK pathway inhibitors targeting BRAF and MEK have shown clinical efficacy in patients with RAF- and/or RAS-mutated tumors. However, acquired resistance to these agents has been an impediment to improved long-term survival in the clinic. In such cases, targeting ERK downstream of BRAF/MEK has been proposed as a potential strategy for overcoming acquired resistance. Preclinical studies suggest that ERK inhibitors are effective at inhibiting BRAF/RAS-mutated tumor growth and overcome BRAF or/and MEK inhibitor resistance. However, as observed with other MAPK pathway inhibitors, treatment with ERK inhibitors is likely to cause resistance in the clinic. Here, we aimed to model the mechanism of resistance to ERK inhibitors.Experimental Design: We tested five structurally different ATP-competitive ERK inhibitors representing three different scaffolds on BRAF/RAS-mutant cancer cell lines of different tissue types to generate resistant lines. We have used in vitro modeling, structural biology, and genomic analysis to understand the development of resistance to ERK inhibitors and the mechanisms leading to it.Results: We have identified mutations in ERK1/2, amplification and overexpression of ERK2, and overexpression of EGFR/ERBB2 as mechanisms of acquired resistance. Structural analysis of ERK showed that specific compounds that induced on-target ERK mutations were impaired in their ability to bind mutant ERK. We show that in addition to MEK inhibitors, ERBB receptor and PI3K/mTOR pathway inhibitors are effective in overcoming ERK-inhibitor resistance.Conclusions: These findings suggest that combination therapy with MEK or ERBB receptor or PI3K/mTOR and ERK inhibitors may be an effective strategy for managing the emergence of resistance in the clinic. Clin Cancer Res; 24(16); 4044-55. ©2018 AACR.


Subject(s)
Mitogen-Activated Protein Kinase 1/genetics , Mitogen-Activated Protein Kinase 3/genetics , Neoplasms/drug therapy , Protein Kinase Inhibitors/pharmacology , Adenosine Triphosphate/chemistry , Cell Line, Tumor , Drug Resistance, Neoplasm/genetics , ErbB Receptors/antagonists & inhibitors , ErbB Receptors/genetics , Gene Expression Regulation, Neoplastic/drug effects , HCT116 Cells , Humans , Mitogen-Activated Protein Kinase 1/antagonists & inhibitors , Mitogen-Activated Protein Kinase 3/antagonists & inhibitors , Mutation , Neoplasms/genetics , Neoplasms/pathology , Phosphatidylinositol 3-Kinases/genetics , Phosphoinositide-3 Kinase Inhibitors , Receptor, ErbB-2/antagonists & inhibitors , Receptor, ErbB-2/genetics , Signal Transduction/drug effects , TOR Serine-Threonine Kinases/antagonists & inhibitors , TOR Serine-Threonine Kinases/genetics
7.
OMICS ; 21(5): 295-303, 2017 05.
Article in English | MEDLINE | ID: mdl-28481730

ABSTRACT

Robust diagnostics for many human genetic disorders are much needed in the pursuit of global personalized medicine. Next-generation sequencing now offers new promise for biomarker and diagnostic discovery, in developed as well as resource-limited countries. In this broader global health context, X-linked intellectual disability (XLID) is an inherited genetic disorder that is associated with a range of phenotypes impacting societies in both developed and developing countries. Although intellectual disability arises due to diverse causes, a substantial proportion is caused by genomic alterations. Studies have identified causal XLID genomic alterations in more than 100 protein-coding genes located on the X-chromosome. However, the causes for a substantial number of intellectual disability and associated phenotypes still remain unknown. Identification of causative genes and novel mutations will help in early diagnosis as well as genetic counseling of families. Advent of next-generation sequencing methods has accelerated the discovery of new genes involved in mental health disorders. In this study, we analyzed the exomes of three families from India with nonsyndromic XLID comprising seven affected individuals. The affected individuals had varying degrees of intellectual disability, microcephaly, and delayed motor and language milestones. We identified potential causal variants in three XLID genes, including PAK3 (V294M), CASK (complex structural variant), and MECP2 (P354T). Our findings reported in this study extend the spectrum of mutations and phenotypes associated with XLID, and calls for further studies of intellectual disability and mental health disorders with use of next-generation sequencing technologies.


Subject(s)
Genes, X-Linked , Genetic Diseases, X-Linked/genetics , Guanylate Kinases/genetics , Intellectual Disability/genetics , Methyl-CpG-Binding Protein 2/genetics , Microcephaly/genetics , p21-Activated Kinases/genetics , Adult , Child , Child, Preschool , DNA/blood , Exome/genetics , Female , Genetic Association Studies , Genetic Diseases, X-Linked/diagnosis , High-Throughput Nucleotide Sequencing , Humans , India , Intellectual Disability/diagnosis , Male , Microcephaly/diagnosis , Mutation , Pedigree , Phenotype , Exome Sequencing
8.
Nat Genet ; 48(4): 407-16, 2016 Apr.
Article in English | MEDLINE | ID: mdl-26928227

ABSTRACT

We analyzed transcriptomes (n = 211), whole exomes (n = 99) and targeted exomes (n = 103) from 216 malignant pleural mesothelioma (MPM) tumors. Using RNA-seq data, we identified four distinct molecular subtypes: sarcomatoid, epithelioid, biphasic-epithelioid (biphasic-E) and biphasic-sarcomatoid (biphasic-S). Through exome analysis, we found BAP1, NF2, TP53, SETD2, DDX3X, ULK2, RYR2, CFAP45, SETDB1 and DDX51 to be significantly mutated (q-score ≥ 0.8) in MPMs. We identified recurrent mutations in several genes, including SF3B1 (∼2%; 4/216) and TRAF7 (∼2%; 5/216). SF3B1-mutant samples showed a splicing profile distinct from that of wild-type tumors. TRAF7 alterations occurred primarily in the WD40 domain and were, except in one case, mutually exclusive with NF2 alterations. We found recurrent gene fusions and splice alterations to be frequent mechanisms for inactivation of NF2, BAP1 and SETD2. Through integrated analyses, we identified alterations in Hippo, mTOR, histone methylation, RNA helicase and p53 signaling pathways in MPMs.


Subject(s)
Lung Neoplasms/genetics , Mesothelioma/genetics , Oncogene Proteins, Fusion/genetics , Pleural Neoplasms/genetics , Alternative Splicing , Cell Line, Tumor , DNA Mutational Analysis , Exome , Humans , Kaplan-Meier Estimate , Lung Neoplasms/metabolism , Lung Neoplasms/mortality , Mesothelioma/metabolism , Mesothelioma/mortality , Mesothelioma, Malignant , Mutation , Oncogene Proteins, Fusion/metabolism , Phosphoproteins/genetics , Phosphoproteins/metabolism , Pleural Neoplasms/metabolism , Pleural Neoplasms/mortality , Polymorphism, Single Nucleotide , Proportional Hazards Models , Protein Isoforms/genetics , Protein Isoforms/metabolism , RNA Splicing Factors , Ribonucleoprotein, U2 Small Nuclear/genetics , Ribonucleoprotein, U2 Small Nuclear/metabolism
9.
Nat Genet ; 47(1): 13-21, 2015 Jan.
Article in English | MEDLINE | ID: mdl-25401301

ABSTRACT

To further understand the molecular distinctions between kidney cancer subtypes, we analyzed exome, transcriptome and copy number alteration data from 167 primary human tumors that included renal oncocytomas and non-clear cell renal cell carcinomas (nccRCCs), consisting of papillary (pRCC), chromophobe (chRCC) and translocation (tRCC) subtypes. We identified ten significantly mutated genes in pRCC, including MET, NF2, SLC5A3, PNKD and CPQ. MET mutations occurred in 15% (10/65) of pRCC samples and included previously unreported recurrent activating mutations. In chRCC, we found TP53, PTEN, FAAH2, PDHB, PDXDC1 and ZNF765 to be significantly mutated. Gene expression analysis identified a five-gene set that enabled the molecular classification of chRCC, renal oncocytoma and pRCC. Using RNA sequencing, we identified previously unreported gene fusions, including ACTG1-MITF fusion. Ectopic expression of the ACTG1-MITF fusion led to cellular transformation and induced the expression of downstream target genes. Finally, we observed upregulation of the anti-apoptotic factor BIRC7 in MiTF-high RCC tumors, suggesting a potential therapeutic role for BIRC7 inhibitors.


Subject(s)
Carcinoma, Renal Cell/classification , Gene Expression Profiling , Gene Expression Regulation, Neoplastic , Kidney Neoplasms/genetics , Mutation , Adenoma, Oxyphilic/classification , Adenoma, Oxyphilic/genetics , Adenoma, Oxyphilic/pathology , Amino Acid Sequence , Base Sequence , Biomarkers, Tumor/genetics , Carcinoma, Renal Cell/genetics , Carcinoma, Renal Cell/pathology , DNA, Neoplasm , Gene Dosage , Genomic Instability , Humans , Kidney Neoplasms/classification , Kidney Neoplasms/pathology , Molecular Sequence Data , Neoplasm Proteins/genetics , Neoplasm Proteins/physiology , Oncogene Proteins, Fusion/genetics , Oncogene Proteins, Fusion/physiology , Polymorphism, Single Nucleotide , Protein Conformation , Proto-Oncogene Proteins c-met/chemistry , Proto-Oncogene Proteins c-met/genetics , Translocation, Genetic
10.
Sci Signal ; 7(337): ra73, 2014 Aug 05.
Article in English | MEDLINE | ID: mdl-25097033

ABSTRACT

The RAF family of kinases mediates RAS signaling, and RAF inhibitors can be effective for treating tumors with BRAF(V600E) mutant protein. However, RAF inhibitors paradoxically accelerate metastasis in RAS-mutant tumors and become ineffective in BRAF(V600E) tumors because of reactivation of downstream mitogen-activated protein kinase (MAPK) signaling. We found that the RAF isoform ARAF has an obligatory role in promoting MAPK activity and cell migration in a cell type-dependent manner. Knocking down ARAF prevented the activation of MAPK kinase 1 (MEK1) and extracellular signal-regulated kinase 1 and 2 (ERK1/2) and decreased the number of protrusions from tumor cell spheroids in three-dimensional culture that were induced by BRAF(V600E)-specific or BRAF/CRAF inhibitors (GDC-0879 and sorafenib, respectively). RAF inhibitors induced the homodimerization of ARAF and the heterodimerization of BRAF with CRAF and the scaffolding protein KSR1. In a purified protein solution, recombinant proteins of the three RAF isoforms competed for binding to MEK1. In cells in culture, overexpressing mutants of ARAF that could not homodimerize impaired the interaction between ARAF and endogenous MEK1 and thus prevented the subsequent activation of MEK1 and ERK1/2. Our findings reveal a new role for ARAF in directly activating the MAPK cascade and promoting tumor cell invasion and suggest a new therapeutic target for RAS- and RAF-mediated cancers.


Subject(s)
Cell Movement/physiology , MAP Kinase Signaling System/physiology , Models, Molecular , Proto-Oncogene Proteins A-raf/metabolism , Analysis of Variance , Binding, Competitive , Blotting, Western , Dimerization , Electrophoresis, Polyacrylamide Gel , Enzyme Activation/genetics , Gene Knockdown Techniques , HEK293 Cells , Humans , Indenes/pharmacology , MAP Kinase Kinase 1/metabolism , MAP Kinase Signaling System/genetics , Neoplasm Invasiveness , Niacinamide/analogs & derivatives , Niacinamide/pharmacology , Phenylurea Compounds/pharmacology , Proto-Oncogene Proteins A-raf/chemistry , Proto-Oncogene Proteins A-raf/genetics , Proto-Oncogene Proteins B-raf/antagonists & inhibitors , Proto-Oncogene Proteins c-raf/antagonists & inhibitors , Pyrazoles/pharmacology , RNA, Small Interfering/genetics , Sorafenib , Time-Lapse Imaging , Tumor Cells, Cultured
11.
MAbs ; 6(1): 95-107, 2014.
Article in English | MEDLINE | ID: mdl-24121517

ABSTRACT

Multi-transmembrane proteins are especially difficult targets for antibody generation largely due to the challenge of producing a protein that maintains its native conformation in the absence of a stabilizing membrane. Here, we describe an immunization strategy that successfully resulted in the identification of monoclonal antibodies that bind specifically to extracellular epitopes of a 12 transmembrane protein, multi-drug resistant protein 4 (MRP4). These monoclonal antibodies were developed following hydrodynamic tail vein immunization with a cytomegalovirus (CMV) promoter-based plasmid expressing MRP4 cDNA and were characterized by flow cytometry. As expected, the use of the immune modulators fetal liver tyrosine kinase 3 ligand (Flt3L) and granulocyte-macrophage colony-stimulating factor positively enhanced the immune response against MRP4. Imaging studies using CMV-based plasmids expressing luciferase showed that the in vivo half-life of the target antigen was less than 48 h using CMV-based plasmids, thus necessitating frequent boosting with DNA to achieve an adequate immune response. We also describe a comparison of plasmids, which contained MRP4 cDNA with either the CMV or CAG promoters, used for immunizations. The observed luciferase activity in this comparison demonstrated that the CAG promoter-containing plasmid pCAGGS induced prolonged constitutive expression of MRP4 and an increased anti-MRP4 specific immune response even when the plasmid was injected less frequently. The method described here is one that can be broadly applicable as a general immunization strategy to develop antibodies against multi-transmembrane proteins, as well as target antigens that are difficult to express or purify in native and functionally active conformation.


Subject(s)
Antibodies/immunology , Immunization , Multidrug Resistance-Associated Proteins/immunology , Plasmids , Vaccines, DNA , Animals , Cell Line , DNA, Complementary/immunology , DNA, Complementary/pharmacology , Humans , Mice, Inbred BALB C , Mice, Knockout , Multidrug Resistance-Associated Proteins/biosynthesis , Multidrug Resistance-Associated Proteins/genetics , Plasmids/immunology , Plasmids/pharmacology , Protein Structure, Secondary , Vaccines, DNA/immunology , Vaccines, DNA/pharmacology
12.
Cancer Cell ; 23(5): 603-17, 2013 May 13.
Article in English | MEDLINE | ID: mdl-23680147

ABSTRACT

The human epidermal growth factor receptor (HER) family of tyrosine kinases is deregulated in multiple cancers either through amplification, overexpression, or mutation. ERBB3/HER3, the only member with an impaired kinase domain, although amplified or overexpressed in some cancers, has not been reported to carry oncogenic mutations. Here, we report the identification of ERBB3 somatic mutations in ~11% of colon and gastric cancers. We found that the ERBB3 mutants transformed colonic and breast epithelial cells in a ligand-independent manner. However, the mutant ERBB3 oncogenic activity was dependent on kinase-active ERBB2. Furthermore, we found that anti-ERBB antibodies and small molecule inhibitors effectively blocked mutant ERBB3-mediated oncogenic signaling and disease progression in vivo.


Subject(s)
Colonic Neoplasms/genetics , Mutation , Receptor, ErbB-3/genetics , Stomach Neoplasms/genetics , Binding Sites , Cell Proliferation , Cell Survival/genetics , Cell Transformation, Neoplastic/genetics , Gene Knockdown Techniques , Humans , Models, Molecular , Protein Structure, Tertiary , Receptor, ErbB-3/metabolism , Receptor, ErbB-3/physiology
13.
Nat Genet ; 44(10): 1111-6, 2012 Oct.
Article in English | MEDLINE | ID: mdl-22941189

ABSTRACT

Small-cell lung cancer (SCLC) is an exceptionally aggressive disease with poor prognosis. Here, we obtained exome, transcriptome and copy-number alteration data from approximately 53 samples consisting of 36 primary human SCLC and normal tissue pairs and 17 matched SCLC and lymphoblastoid cell lines. We also obtained data for 4 primary tumors and 23 SCLC cell lines. We identified 22 significantly mutated genes in SCLC, including genes encoding kinases, G protein-coupled receptors and chromatin-modifying proteins. We found that several members of the SOX family of genes were mutated in SCLC. We also found SOX2 amplification in ∼27% of the samples. Suppression of SOX2 using shRNAs blocked proliferation of SOX2-amplified SCLC lines. RNA sequencing identified multiple fusion transcripts and a recurrent RLF-MYCL1 fusion. Silencing of MYCL1 in SCLC cell lines that had the RLF-MYCL1 fusion decreased cell proliferation. These data provide an in-depth view of the spectrum of genomic alterations in SCLC and identify several potential targets for therapeutic intervention.


Subject(s)
Gene Amplification , Lung Neoplasms/genetics , SOXB1 Transcription Factors/genetics , Small Cell Lung Carcinoma/genetics , Base Sequence , Cell Line, Tumor , DNA Copy Number Variations , DNA Mutational Analysis , Exome , Gene Expression , Genome-Wide Association Study , High-Throughput Nucleotide Sequencing , Humans , Lung Neoplasms/metabolism , Molecular Sequence Data , Mutation , Oncogene Proteins, Fusion/genetics , Protein Kinases/genetics , SOXB1 Transcription Factors/metabolism , Small Cell Lung Carcinoma/metabolism
14.
Nature ; 488(7413): 660-4, 2012 Aug 30.
Article in English | MEDLINE | ID: mdl-22895193

ABSTRACT

Identifying and understanding changes in cancer genomes is essential for the development of targeted therapeutics. Here we analyse systematically more than 70 pairs of primary human colon tumours by applying next-generation sequencing to characterize their exomes, transcriptomes and copy-number alterations. We have identified 36,303 protein-altering somatic changes that include several new recurrent mutations in the Wnt pathway gene TCF7L2, chromatin-remodelling genes such as TET2 and TET3 and receptor tyrosine kinases including ERBB3. Our analysis for significantly mutated cancer genes identified 23 candidates, including the cell cycle checkpoint kinase ATM. Copy-number and RNA-seq data analysis identified amplifications and corresponding overexpression of IGF2 in a subset of colon tumours. Furthermore, using RNA-seq data we identified multiple fusion transcripts including recurrent gene fusions involving R-spondin family members RSPO2 and RSPO3 that together occur in 10% of colon tumours. The RSPO fusions were mutually exclusive with APC mutations, indicating that they probably have a role in the activation of Wnt signalling and tumorigenesis. Consistent with this we show that the RSPO fusion proteins were capable of potentiating Wnt signalling. The R-spondin gene fusions and several other gene mutations identified in this study provide new potential opportunities for therapeutic intervention in colon cancer.


Subject(s)
Colonic Neoplasms/genetics , Gene Fusion/genetics , Genes, Neoplasm/genetics , Intercellular Signaling Peptides and Proteins/genetics , Thrombospondins/genetics , Ataxia Telangiectasia Mutated Proteins , Base Sequence , Cell Cycle Proteins/genetics , Colonic Neoplasms/metabolism , Colonic Neoplasms/pathology , DNA Copy Number Variations/genetics , DNA-Binding Proteins/genetics , Dioxygenases/genetics , Exome/genetics , Gene Expression Profiling , Gene Expression Regulation, Neoplastic/genetics , Genes, APC , Humans , Insulin-Like Growth Factor II/genetics , Molecular Sequence Data , Mutation/genetics , Polymorphism, Single Nucleotide/genetics , Protein Serine-Threonine Kinases/genetics , Proto-Oncogene Proteins/genetics , Receptor, ErbB-3/genetics , Sequence Analysis, RNA , Signal Transduction/genetics , Transcription Factor 7-Like 2 Protein/genetics , Tumor Suppressor Proteins/genetics , Wnt Proteins/metabolism
15.
Nature ; 466(7308): 869-73, 2010 Aug 12.
Article in English | MEDLINE | ID: mdl-20668451

ABSTRACT

The systematic characterization of somatic mutations in cancer genomes is essential for understanding the disease and for developing targeted therapeutics. Here we report the identification of 2,576 somatic mutations across approximately 1,800 megabases of DNA representing 1,507 coding genes from 441 tumours comprising breast, lung, ovarian and prostate cancer types and subtypes. We found that mutation rates and the sets of mutated genes varied substantially across tumour types and subtypes. Statistical analysis identified 77 significantly mutated genes including protein kinases, G-protein-coupled receptors such as GRM8, BAI3, AGTRL1 (also called APLNR) and LPHN3, and other druggable targets. Integrated analysis of somatic mutations and copy number alterations identified another 35 significantly altered genes including GNAS, indicating an expanded role for galpha subunits in multiple cancer types. Furthermore, our experimental analyses demonstrate the functional roles of mutant GNAO1 (a Galpha subunit) and mutant MAP2K4 (a member of the JNK signalling pathway) in oncogenesis. Our study provides an overview of the mutational spectra across major human cancers and identifies several potential therapeutic targets.


Subject(s)
Genes, Neoplasm/genetics , Mutation/genetics , Neoplasms/genetics , Neoplasms/metabolism , Signal Transduction/genetics , Breast Neoplasms/classification , Breast Neoplasms/genetics , DNA Copy Number Variations/genetics , DNA Mutational Analysis , Female , GTP-Binding Protein alpha Subunits/genetics , Humans , Lung Neoplasms/classification , Lung Neoplasms/genetics , MAP Kinase Kinase 4/genetics , Male , Neoplasms/enzymology , Neoplasms/pathology , Ovarian Neoplasms/classification , Ovarian Neoplasms/genetics , Prostatic Neoplasms/classification , Prostatic Neoplasms/genetics , Protein Kinases/genetics , Receptors, G-Protein-Coupled/genetics
16.
Nature ; 464(7287): 431-5, 2010 Mar 18.
Article in English | MEDLINE | ID: mdl-20130576

ABSTRACT

Activating mutations in KRAS and BRAF are found in more than 30% of all human tumours and 40% of melanoma, respectively, thus targeting this pathway could have broad therapeutic effects. Small molecule ATP-competitive RAF kinase inhibitors have potent antitumour effects on mutant BRAF(V600E) tumours but, in contrast to mitogen-activated protein kinase kinase (MEK) inhibitors, are not potent against RAS mutant tumour models, despite RAF functioning as a key effector downstream of RAS and upstream of MEK. Here we show that ATP-competitive RAF inhibitors have two opposing mechanisms of action depending on the cellular context. In BRAF(V600E) tumours, RAF inhibitors effectively block the mitogen-activated protein kinase (MAPK) signalling pathway and decrease tumour growth. Notably, in KRAS mutant and RAS/RAF wild-type tumours, RAF inhibitors activate the RAF-MEK-ERK pathway in a RAS-dependent manner, thus enhancing tumour growth in some xenograft models. Inhibitor binding activates wild-type RAF isoforms by inducing dimerization, membrane localization and interaction with RAS-GTP. These events occur independently of kinase inhibition and are, instead, linked to direct conformational effects of inhibitors on the RAF kinase domain. On the basis of these findings, we demonstrate that ATP-competitive kinase inhibitors can have opposing functions as inhibitors or activators of signalling pathways, depending on the cellular context. Furthermore, this work provides new insights into the therapeutic use of ATP-competitive RAF inhibitors.


Subject(s)
MAP Kinase Signaling System/drug effects , Neoplasms/pathology , Protein Kinase Inhibitors/pharmacology , raf Kinases/antagonists & inhibitors , raf Kinases/metabolism , Adenosine Triphosphate/metabolism , Animals , Benzamides/pharmacology , Cell Line , Cell Membrane/drug effects , Cell Membrane/metabolism , Cell Proliferation/drug effects , Diphenylamine/analogs & derivatives , Diphenylamine/pharmacology , Enzyme Activation/drug effects , Extracellular Signal-Regulated MAP Kinases/metabolism , Humans , Indenes/pharmacology , Indoles/pharmacology , Mice , Mitogen-Activated Protein Kinase Kinases/antagonists & inhibitors , Mitogen-Activated Protein Kinase Kinases/metabolism , Neoplasms/drug therapy , Neoplasms/enzymology , Neoplasms/metabolism , Protein Kinase Inhibitors/therapeutic use , Protein Multimerization , Protein Structure, Tertiary , Protein Transport/drug effects , Proto-Oncogene Proteins/genetics , Proto-Oncogene Proteins/metabolism , Proto-Oncogene Proteins B-raf/antagonists & inhibitors , Proto-Oncogene Proteins B-raf/chemistry , Proto-Oncogene Proteins B-raf/genetics , Proto-Oncogene Proteins B-raf/metabolism , Proto-Oncogene Proteins c-raf/deficiency , Proto-Oncogene Proteins c-raf/genetics , Proto-Oncogene Proteins c-raf/metabolism , Proto-Oncogene Proteins p21(ras) , Pyrazoles/pharmacology , Sulfonamides/pharmacology , Xenograft Model Antitumor Assays , raf Kinases/chemistry , raf Kinases/genetics , ras Proteins/genetics , ras Proteins/metabolism
17.
Cancer Cell ; 16(6): 463-74, 2009 Dec 08.
Article in English | MEDLINE | ID: mdl-19962665

ABSTRACT

Members of the mammalian phosphoinositide-3-OH kinase (PI3K) family of proteins are critical regulators of various cellular process including cell survival, growth, proliferation, and motility. Oncogenic activating mutations in the p110alpha catalytic subunit of the heterodimeric p110/p85 PI3K enzyme are frequent in human cancers. Here we show the presence of frequent mutations in p85alpha in colon cancer, a majority of which occurs in the inter-Src homology-2 (iSH2) domain. These mutations uncouple and retain p85alpha's p110-stabilizing activity, while abrogating its p110-inhibitory activity. The p85alpha mutants promote cell survival, AKT activation, anchorage-independent cell growth, and oncogenesis in a p110-dependent manner.


Subject(s)
Colonic Neoplasms/pathology , Mutation , Phosphatidylinositol 3-Kinases/metabolism , Animals , Cell Line , Cell Transformation, Neoplastic , Colonic Neoplasms/enzymology , Enzyme Activation , Humans , Mice , Phosphatidylinositol 3-Kinases/chemistry , Phosphatidylinositol 3-Kinases/genetics
18.
Proc Natl Acad Sci U S A ; 106(48): 20258-63, 2009 Dec 01.
Article in English | MEDLINE | ID: mdl-19915146

ABSTRACT

We previously proposed a model of Class IA PI3K regulation in which p85 inhibition of p110alpha requires (i) an inhibitory contact between the p85 nSH2 domain and the p110alpha helical domain, and (ii) a contact between the p85 nSH2 and iSH2 domains that orients the nSH2 so as to inhibit p110alpha. We proposed that oncogenic truncations of p85 fail to inhibit p110 due to a loss of the iSH2-nSH2 contact. However, we now find that within the context of a minimal regulatory fragment of p85 (the nSH2-iSH2 fragment, termed p85ni), the nSH2 domain rotates much more freely (tau(c) approximately 12.7 ns) than it could if it were interacting rigidly with the iSH2 domain. These data are not compatible with our previous model. We therefore tested an alternative model in which oncogenic p85 truncations destabilize an interface between the p110alpha C2 domain (residue N345) and the p85 iSH2 domain (residues D560 and N564). p85ni-D560K/N564K shows reduced inhibition of p110alpha, similar to the truncated p85ni-572(STOP). Conversely, wild-type p85ni poorly inhibits p110alphaN345K. Strikingly, the p110alphaN345K mutant is inhibited to the same extent by the wild-type or truncated p85ni, suggesting that mutation of p110alpha-N345 is not additive with the p85ni-572(STOP) mutation. Similarly, the D560K/N564K mutation is not additive with the p85ni-572(STOP) mutant for downstream signaling or cellular transformation. Thus, our data suggests that mutations at the C2-iSH2 domain contact and truncations of the iSH2 domain, which are found in human tumors, both act by disrupting the C2-iSH2 domain interface.


Subject(s)
Phosphatidylinositol 3-Kinases/metabolism , Protein Structure, Tertiary/genetics , Signal Transduction/physiology , Analysis of Variance , Animals , Blotting, Western , Cell Line , HeLa Cells , Humans , Magnetic Resonance Spectroscopy , Mice , Models, Biological , Mutation/genetics , Phosphatidylinositol 3-Kinases/genetics , Signal Transduction/genetics
19.
PLoS One ; 4(5): e5717, 2009 May 27.
Article in English | MEDLINE | ID: mdl-19492075

ABSTRACT

BACKGROUND: Oncogenic RAS is a highly validated cancer target. Attempts at targeting RAS directly have so far not succeeded in the clinic. Understanding downstream RAS-effectors that mediate oncogenesis in a RAS mutant setting will help tailor treatments that use RAS-effector inhibitors either alone or in combination to target RAS-driven tumors. METHODOLOGY/PRINCIPAL FINDINGS: In this study, we have investigated the sufficiency of targeting RAS-effectors, RAF, MEK and PI3-Kinase either alone or in combination in RAS mutant lines, using an inducible shRNA in vivo mouse model system. We find that in colon cancer cells harboring a KRAS(G13D) mutant allele, knocking down KRAS alone or the RAFs in combination or the RAF effectors, MEK1 and MEK2, together is effective in delaying tumor growth in vivo. In melanoma cells harboring an NRAS(Q61L) or NRAS(Q61K) mutant allele, we find that targeting NRAS alone or both BRAF and CRAF in combination or both BRAF and PIK3CA together showed efficacy. CONCLUSION/SIGNIFICANCE: Our data indicates that targeting oncogenic NRAS-driven melanomas require decrease in both pERK and pAKT downstream of RAS-effectors for efficacy. This can be achieved by either targeting both BRAF and CRAF or BRAF and PIK3CA simultaneously in NRAS mutant tumor cells.


Subject(s)
Mutation/genetics , Neoplasms/enzymology , Neoplasms/pathology , Phosphatidylinositol 3-Kinases/metabolism , Proto-Oncogene Proteins B-raf/metabolism , Proto-Oncogene Proteins c-raf/metabolism , ras Proteins/metabolism , Animals , Cell Adhesion , Cell Cycle , Cell Line, Tumor , Cell Proliferation , Gene Knockdown Techniques , Humans , Mice , Mutant Proteins , Signal Transduction
20.
Dev Biol ; 296(2): 353-62, 2006 Aug 15.
Article in English | MEDLINE | ID: mdl-16842770

ABSTRACT

We previously demonstrated that male mice deficient in the soluble adenylyl cyclase (sAC) are sterile and produce spermatozoa with deficits in progressive motility and are unable to fertilize zona-intact eggs. Here, analyses of sAC(-/-) spermatozoa provide additional insights into the functions linked to cAMP signaling. Adenylyl cyclase activity and cAMP content are greatly diminished in crude preparations of sAC(-/-) spermatozoa and are undetectable after sperm purification. HCO(3)(-) is unable to rapidly accelerate the flagellar beat or facilitate evoked Ca(2+) entry into sAC(-/-) spermatozoa. Moreover, the delayed HCO(3)(-)-dependent increases in protein tyrosine phosphorylation and hyperactivated motility, which occur late in capacitation of wild-type spermatozoa, do not develop in sAC(-/-) spermatozoa. However, sAC(-/-) sperm fertilize zona-free oocytes, indicating that gamete fusion does not require sAC. Although ATP levels are significantly reduced in sAC(-/-) sperm, cAMP-AM ester increases flagellar beat frequency, progressive motility, and alters the pattern of tyrosine phosphorylated proteins. These results indicate that sAC and cAMP coordinate cellular energy balance in wild-type sperm and that the ATP generating machinery is not operating normally in sAC(-/-) spermatozoa. These findings demonstrate that sAC plays a critical role in cAMP signaling in spermatozoa and that defective cAMP production prevents engagement of multiple components of capacitation resulting in male infertility.


Subject(s)
Adenylyl Cyclases/physiology , Fertilization/physiology , Spermatozoa/physiology , Adenylyl Cyclases/deficiency , Adenylyl Cyclases/genetics , Animals , Cyclic AMP/metabolism , Female , Fertilization/genetics , Infertility, Male/enzymology , Infertility, Male/genetics , Male , Mice , Mice, Inbred C57BL , Mice, Knockout , Signal Transduction/genetics , Signal Transduction/physiology , Solubility , Sperm Capacitation/genetics , Spermatozoa/enzymology
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