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1.
Cell ; 187(1): 14-16, 2024 01 04.
Article in English | MEDLINE | ID: mdl-38181738

ABSTRACT

Small cell lung cancer (SCLC) is a recalcitrant malignancy. Conquering it will require deep insight into its biology. In this issue of Cell, Liu and colleagues describe proteomic and phosphoproteomic landscapes of resected SCLC tumors and illustrate the potential of this knowledge to identify new SCLC vulnerabilities.


Subject(s)
Lung Neoplasms , Small Cell Lung Carcinoma , Humans , Proteomics , Knowledge
2.
Cell ; 173(4): 864-878.e29, 2018 05 03.
Article in English | MEDLINE | ID: mdl-29681454

ABSTRACT

Diversity in the genetic lesions that cause cancer is extreme. In consequence, a pressing challenge is the development of drugs that target patient-specific disease mechanisms. To address this challenge, we employed a chemistry-first discovery paradigm for de novo identification of druggable targets linked to robust patient selection hypotheses. In particular, a 200,000 compound diversity-oriented chemical library was profiled across a heavily annotated test-bed of >100 cellular models representative of the diverse and characteristic somatic lesions for lung cancer. This approach led to the delineation of 171 chemical-genetic associations, shedding light on the targetability of mechanistic vulnerabilities corresponding to a range of oncogenotypes present in patient populations lacking effective therapy. Chemically addressable addictions to ciliogenesis in TTC21B mutants and GLUT8-dependent serine biosynthesis in KRAS/KEAP1 double mutants are prominent examples. These observations indicate a wealth of actionable opportunities within the complex molecular etiology of cancer.


Subject(s)
Carcinoma, Non-Small-Cell Lung/pathology , Cell Proliferation/drug effects , Lung Neoplasms/pathology , Small Molecule Libraries/pharmacology , Carcinoma, Non-Small-Cell Lung/metabolism , Cell Line, Tumor , Cytochrome P450 Family 4/deficiency , Cytochrome P450 Family 4/genetics , Drug Discovery , G1 Phase Cell Cycle Checkpoints/drug effects , Glucocorticoids/pharmacology , Glucose Transport Proteins, Facilitative/antagonists & inhibitors , Glucose Transport Proteins, Facilitative/genetics , Glucose Transport Proteins, Facilitative/metabolism , Humans , Kelch-Like ECH-Associated Protein 1/genetics , Kelch-Like ECH-Associated Protein 1/metabolism , Lung Neoplasms/metabolism , Microtubule-Associated Proteins/genetics , Microtubule-Associated Proteins/metabolism , Mutation , NF-E2-Related Factor 2/antagonists & inhibitors , NF-E2-Related Factor 2/genetics , NF-E2-Related Factor 2/metabolism , Proto-Oncogene Proteins p21(ras)/genetics , Proto-Oncogene Proteins p21(ras)/metabolism , RNA Interference , RNA, Small Interfering/metabolism , Receptor, Notch2/genetics , Receptor, Notch2/metabolism , Receptors, Glucocorticoid/antagonists & inhibitors , Receptors, Glucocorticoid/genetics , Receptors, Glucocorticoid/metabolism , Small Molecule Libraries/chemistry , Small Molecule Libraries/metabolism
3.
Cell ; 166(2): 275-276, 2016 07 14.
Article in English | MEDLINE | ID: mdl-27419866

ABSTRACT

What changes need to occur in a primary tumor to make it metastatic? Denny et al. address this question for small cell lung cancer (SCLC), finding that changes in genomic accessibility mediated by a single transcription factor, NFIB, comprise at least one mechanism influencing metastasis.


Subject(s)
Cell Line, Tumor , Chromatin , Humans , Lung Neoplasms , Neoplasm Metastasis , Small Cell Lung Carcinoma/genetics , Transcription Factors/genetics
4.
Cell ; 152(3): 387-9, 2013 Jan 31.
Article in English | MEDLINE | ID: mdl-23374335

ABSTRACT

Genome-wide association studies (GWASs) have unraveled a large number of cancer risk alleles. Understanding how these allelic variants predispose to disease is a major bottleneck confronting translational application. In this issue, Li and colleagues combine GWASs with The Cancer Genome Atlas (TCGA) to disambiguate the contributions of germline and somatic variants to tumorigenic gene expression programs. They find that close to half of the known risk alleles for estrogen receptor (ER)-positive breast cancer are expression quantitative trait loci (eQTLs) acting upon major determinants of gene expression in tumors.

5.
Cell ; 154(6): 1269-84, 2013 Sep 12.
Article in English | MEDLINE | ID: mdl-24034250

ABSTRACT

Cell surface growth factor receptors couple environmental cues to the regulation of cytoplasmic homeostatic processes, including autophagy, and aberrant activation of such receptors is a common feature of human malignancies. Here, we defined the molecular basis by which the epidermal growth factor receptor (EGFR) tyrosine kinase regulates autophagy. Active EGFR binds the autophagy protein Beclin 1, leading to its multisite tyrosine phosphorylation, enhanced binding to inhibitors, and decreased Beclin 1-associated VPS34 kinase activity. EGFR tyrosine kinase inhibitor (TKI) therapy disrupts Beclin 1 tyrosine phosphorylation and binding to its inhibitors and restores autophagy in non-small-cell lung carcinoma (NSCLC) cells with a TKI-sensitive EGFR mutation. In NSCLC tumor xenografts, the expression of a tyrosine phosphomimetic Beclin 1 mutant leads to reduced autophagy, enhanced tumor growth, tumor dedifferentiation, and resistance to TKI therapy. Thus, oncogenic receptor tyrosine kinases directly regulate the core autophagy machinery, which may contribute to tumor progression and chemoresistance.


Subject(s)
Apoptosis Regulatory Proteins/metabolism , Autophagy , Drug Resistance, Neoplasm , ErbB Receptors/metabolism , Membrane Proteins/metabolism , Animals , Apoptosis Regulatory Proteins/genetics , Beclin-1 , Carcinoma, Non-Small-Cell Lung/drug therapy , Cell Line, Tumor , ErbB Receptors/genetics , Heterografts , Humans , Lung Neoplasms/drug therapy , Membrane Proteins/genetics , Mice , Mice, Inbred NOD , Mice, SCID , Neoplasm Transplantation , Phosphorylation
6.
Cell ; 155(3): 552-66, 2013 Oct 24.
Article in English | MEDLINE | ID: mdl-24243015

ABSTRACT

Context-specific molecular vulnerabilities that arise during tumor evolution represent an attractive intervention target class. However, the frequency and diversity of somatic lesions detected among lung tumors can confound efforts to identify these targets. To confront this challenge, we have applied parallel screening of chemical and genetic perturbations within a panel of molecularly annotated NSCLC lines to identify intervention opportunities tightly linked to molecular response indicators predictive of target sensitivity. Anchoring this analysis on a matched tumor/normal cell model from a lung adenocarcinoma patient identified three distinct target/response-indicator pairings that are represented with significant frequencies (6%-16%) in the patient population. These include NLRP3 mutation/inflammasome activation-dependent FLIP addiction, co-occurring KRAS and LKB1 mutation-driven COPI addiction, and selective sensitivity to a synthetic indolotriazine that is specified by a seven-gene expression signature. Target efficacies were validated in vivo, and mechanism-of-action studies informed generalizable principles underpinning cancer cell biology.


Subject(s)
Carcinoma, Non-Small-Cell Lung/metabolism , Drug Screening Assays, Antitumor , Indoles/pharmacology , Lung Neoplasms/metabolism , Triazines/pharmacology , Animals , CASP8 and FADD-Like Apoptosis Regulating Protein/metabolism , Carcinoma, Non-Small-Cell Lung/pathology , Carrier Proteins , Cell Line, Tumor , Coatomer Protein/metabolism , Female , Genes, ras , Heterografts , Humans , Lung Neoplasms/pathology , Lysosomes/metabolism , Mice , Molecular Targeted Therapy , NLR Family, Pyrin Domain-Containing 3 Protein , Neoplasm Transplantation , Oxidative Phosphorylation
7.
Nature ; 590(7846): 504-508, 2021 02.
Article in English | MEDLINE | ID: mdl-33536620

ABSTRACT

Amplification of chromosomal region 8p11-12 is a common genetic alteration that has been implicated in the aetiology of lung squamous cell carcinoma (LUSC)1-3. The FGFR1 gene is the main candidate driver of tumorigenesis within this region4. However, clinical trials evaluating FGFR1 inhibition as a targeted therapy have been unsuccessful5. Here we identify the histone H3 lysine 36 (H3K36) methyltransferase NSD3, the gene for which is located in the 8p11-12 amplicon, as a key regulator of LUSC tumorigenesis. In contrast to other 8p11-12 candidate LUSC drivers, increased expression of NSD3 correlated strongly with its gene amplification. Ablation of NSD3, but not of FGFR1, attenuated tumour growth and extended survival in a mouse model of LUSC. We identify an LUSC-associated variant NSD3(T1232A) that shows increased catalytic activity for dimethylation of H3K36 (H3K36me2) in vitro and in vivo. Structural dynamic analyses revealed that the T1232A substitution elicited localized mobility changes throughout the catalytic domain of NSD3 to relieve auto-inhibition and to increase accessibility of the H3 substrate. Expression of NSD3(T1232A) in vivo accelerated tumorigenesis and decreased overall survival in mouse models of LUSC. Pathological generation of H3K36me2 by NSD3(T1232A) reprograms the chromatin landscape to promote oncogenic gene expression signatures. Furthermore, NSD3, in a manner dependent on its catalytic activity, promoted transformation in human tracheobronchial cells and growth of xenografted human LUSC cell lines with amplification of 8p11-12. Depletion of NSD3 in patient-derived xenografts from primary LUSCs containing NSD3 amplification or the NSD3(T1232A)-encoding variant attenuated neoplastic growth in mice. Finally, NSD3-regulated LUSC-derived xenografts were hypersensitive to bromodomain inhibition. Thus, our work identifies NSD3 as a principal 8p11-12 amplicon-associated oncogenic driver in LUSC, and suggests that NSD3-dependency renders LUSC therapeutically vulnerable to bromodomain inhibition.


Subject(s)
Carcinoma, Squamous Cell/metabolism , Carcinoma, Squamous Cell/pathology , Histone-Lysine N-Methyltransferase/metabolism , Histones/chemistry , Histones/metabolism , Lung Neoplasms/metabolism , Lung Neoplasms/pathology , Nuclear Proteins/metabolism , Animals , Biocatalysis , Carcinogenesis/genetics , Carcinoma, Squamous Cell/genetics , Female , Histone-Lysine N-Methyltransferase/deficiency , Histone-Lysine N-Methyltransferase/genetics , Humans , Lung Neoplasms/genetics , Male , Methylation , Mice , Models, Molecular , Mutation , Nuclear Proteins/deficiency , Nuclear Proteins/genetics , Receptor, Fibroblast Growth Factor, Type 1/deficiency , Receptor, Fibroblast Growth Factor, Type 1/genetics , Receptor, Fibroblast Growth Factor, Type 1/metabolism , Xenograft Model Antitumor Assays
8.
Mol Cell ; 76(5): 838-851.e5, 2019 12 05.
Article in English | MEDLINE | ID: mdl-31564558

ABSTRACT

Intermediary metabolism in cancer cells is regulated by diverse cell-autonomous processes, including signal transduction and gene expression patterns, arising from specific oncogenotypes and cell lineages. Although it is well established that metabolic reprogramming is a hallmark of cancer, we lack a full view of the diversity of metabolic programs in cancer cells and an unbiased assessment of the associations between metabolic pathway preferences and other cell-autonomous processes. Here, we quantified metabolic features, mostly from the 13C enrichment of molecules from central carbon metabolism, in over 80 non-small cell lung cancer (NSCLC) cell lines cultured under identical conditions. Because these cell lines were extensively annotated for oncogenotype, gene expression, protein expression, and therapeutic sensitivity, the resulting database enables the user to uncover new relationships between metabolism and these orthogonal processes.


Subject(s)
Carcinoma, Non-Small-Cell Lung/metabolism , Carcinoma, Non-Small-Cell Lung/pathology , Cell Line, Tumor/metabolism , Metabolome/physiology , Biomarkers, Tumor/metabolism , Gas Chromatography-Mass Spectrometry/methods , Gene Expression Regulation, Neoplastic/physiology , Glucose/metabolism , Glutamine/metabolism , Humans , Metabolic Networks and Pathways/genetics , Metabolomics/methods , Neoplasms/metabolism
9.
Nature ; 578(7796): 621-626, 2020 02.
Article in English | MEDLINE | ID: mdl-32051585

ABSTRACT

The mechanics of the cellular microenvironment continuously modulates cell functions such as growth, survival, apoptosis, differentiation and morphogenesis via cytoskeletal remodelling and actomyosin contractility1-3. Although all of these processes consume energy4,5, it is unknown whether and how cells adapt their metabolic activity to variable mechanical cues. Here we report that the transfer of human bronchial epithelial cells from stiff to soft substrates causes a downregulation of glycolysis via proteasomal degradation of the rate-limiting metabolic enzyme phosphofructokinase (PFK). PFK degradation is triggered by the disassembly of stress fibres, which releases the PFK-targeting E3 ubiquitin ligase tripartite motif (TRIM)-containing protein 21 (TRIM21). Transformed non-small-cell lung cancer cells, which maintain high glycolytic rates regardless of changing environmental mechanics, retain PFK expression by downregulating TRIM21, and by sequestering residual TRIM21 on a stress-fibre subset that is insensitive to substrate stiffness. Our data reveal a mechanism by which glycolysis responds to architectural features of the actomyosin cytoskeleton, thus coupling cell metabolism to the mechanical properties of the surrounding tissue. These processes enable normal cells to tune energy production in variable microenvironments, whereas the resistance of the cytoskeleton in response to mechanical cues enables the persistence of high glycolytic rates in cancer cells despite constant alterations of the tumour tissue.


Subject(s)
Cellular Microenvironment , Cytoskeleton/metabolism , Epithelial Cells/cytology , Epithelial Cells/metabolism , Glucose/metabolism , Glycolysis , Hardness , Actins/metabolism , Actomyosin/metabolism , Animals , Bronchi/cytology , Cattle , Cell Differentiation , Cell Line , Humans , Neoplasms/metabolism , Neoplasms/pathology , Phosphofructokinases/chemistry , Phosphofructokinases/metabolism , Proteasome Endopeptidase Complex/metabolism , Ribonucleoproteins/metabolism , Stress Fibers/metabolism , Ubiquitin-Protein Ligases/metabolism
10.
Genes Dev ; 32(13-14): 865-867, 2018 07 01.
Article in English | MEDLINE | ID: mdl-29967289

ABSTRACT

Tumor heterogeneity of a primary histologic cancer type has major implications for cancer research and therapeutics. An important and understudied aspect of this heterogeneity is the role of transcription factors that serve as "lineage oncogenes" in a tumor type. A demonstration that different subgroups have distinct dependencies on lineage-specific transcription factors is highlighted in a relatively homogenous cancer type: the pulmonary neuroendocrine cancer small cell lung carcinoma (SCLC). Identification of these factors is providing new insights into the origin of the heterogeneity and subtype-specific vulnerabilities in SCLC and provides a template for studying heterogeneity in other cancer types.


Subject(s)
Carcinoma, Neuroendocrine/physiopathology , Lung Neoplasms/physiopathology , Small Cell Lung Carcinoma/physiopathology , Transcription Factors/genetics , Transcription Factors/metabolism , Cell Lineage , Genetic Heterogeneity , Humans , Mutation
11.
Exp Cell Res ; 439(1): 114057, 2024 Jun 01.
Article in English | MEDLINE | ID: mdl-38679315

ABSTRACT

Certain oncogenes, including mutant RAS and BRAF, induce a type of senescence known as oncogene-induced senescence (OIS) in normal cells in a cell-type-specific manner. OIS serves as a barrier to transformation by activated oncogenes. Our previous studies showed that mutant KRASV12 did not efficiently induce OIS in an hTERT/Cdk4-immortalized normal human bronchial epithelial cell line (HBEC3), but it did enhance both anchorage-dependent and anchorage-independent growth. In this study, we investigated whether mutant BRAF, a well-known inducer of OIS, could trigger OIS in HBEC3 cells. We also assessed the impact of mutant BRAF on the growth of HBEC3 cells, as no previous studies have examined this using a normal bronchial epithelial cell line model. We established an HBEC3 cell line, designated as HBEC3-BIN, that expresses mutant BRAFV600E in a doxycycline-regulated manner. Unlike our previous finding that KRASV12 upregulated both pERK and pAKT, mutant BRAFV600E upregulated pERK but not pAKT in HBEC3-BIN cells. Similar to KRASV12, BRAFV600E did not efficiently induce OIS. Interestingly, while BRAFV600E inhibited colony formation in anchorage-dependent conditions, it dramatically enhanced colony formation in anchorage-independent conditions in HBEC3-BIN. In HBEC3 cells without BRAFV600E or KRASV12 expression, p21 was only detected in the cytoplasm, and its localization was not altered by the expression of BRAFV600E or KRASV12. Next-generation sequencing analysis revealed an enrichment of gene sets known to be involved in carcinogenesis, including IL3/JAK/STAT3, IL2, STAT5, and the EMT pathway. Our results indicate that, unlike KRASV12, which promoted both, BRAFV600E enhances anchorage-independent growth but inhibits anchorage-dependent growth of HBEC3. This contrast may result from differences in activation signaling in the downstream pathways. Furthermore, HBEC3 cells appear to be inherently resistant to OIS, which may be partly due to the fact that p21 remains localized in the cytoplasm upon expression of BRAFV600E or KRASV12.


Subject(s)
Proto-Oncogene Proteins B-raf , Proto-Oncogene Proteins p21(ras) , Humans , Proto-Oncogene Proteins B-raf/genetics , Proto-Oncogene Proteins B-raf/metabolism , Proto-Oncogene Proteins p21(ras)/genetics , Proto-Oncogene Proteins p21(ras)/metabolism , Cellular Senescence/genetics , Mutation , Cell Proliferation/genetics , Cell Line , Epithelial Cells/metabolism , Bronchi/metabolism , Bronchi/cytology , Oncogenes/genetics , Signal Transduction
12.
Nature ; 569(7756): E4, 2019 May.
Article in English | MEDLINE | ID: mdl-31043737

ABSTRACT

Further analysis has revealed that the signal reported in Extended Data Fig. 1c of this Letter is attributed to phosphorylethanolamine, not carbamoyl phosphate. A newly developed derivatization method revealed that the level of carbamoyl phosphate in these NSCLC extracts is below the detection threshold of approximately 10 nanomoles. These findings do not alter the overall conclusions of the Letter; see associated Amendment for full details. The Letter has not been corrected online.

13.
PLoS Pathog ; 17(11): e1009743, 2021 11.
Article in English | MEDLINE | ID: mdl-34797899

ABSTRACT

Phosphatidylserine (PS) receptors enhance infection of many enveloped viruses through virion-associated PS binding that is termed apoptotic mimicry. Here we show that this broadly shared uptake mechanism is utilized by SARS-CoV-2 in cells that express low surface levels of ACE2. Expression of members of the TIM (TIM-1 and TIM-4) and TAM (AXL) families of PS receptors enhance SARS-CoV-2 binding to cells, facilitate internalization of fluorescently-labeled virions and increase ACE2-dependent infection of SARS-CoV-2; however, PS receptors alone did not mediate infection. We were unable to detect direct interactions of the PS receptor AXL with purified SARS-CoV-2 spike, contrary to a previous report. Instead, our studies indicate that the PS receptors interact with PS on the surface of SARS-CoV-2 virions. In support of this, we demonstrate that: 1) significant quantities of PS are located on the outer leaflet of SARS-CoV-2 virions, 2) PS liposomes, but not phosphatidylcholine liposomes, reduced entry of VSV/Spike pseudovirions and 3) an established mutant of TIM-1 which does not bind to PS is unable to facilitate entry of SARS-CoV-2. As AXL is an abundant PS receptor on a number of airway lines, we evaluated small molecule inhibitors of AXL signaling such as bemcentinib for their ability to inhibit SARS-CoV-2 infection. Bemcentinib robustly inhibited virus infection of Vero E6 cells as well as multiple human lung cell lines that expressed AXL. This inhibition correlated well with inhibitors that block endosomal acidification and cathepsin activity, consistent with AXL-mediated uptake of SARS-CoV-2 into the endosomal compartment. We extended our observations to the related betacoronavirus mouse hepatitis virus (MHV), showing that inhibition or ablation of AXL reduces MHV infection of murine cells. In total, our findings provide evidence that PS receptors facilitate infection of the pandemic coronavirus SARS-CoV-2 and suggest that inhibition of the PS receptor AXL has therapeutic potential against SARS-CoV-2.


Subject(s)
COVID-19/etiology , Receptors, Cell Surface/physiology , SARS-CoV-2 , Angiotensin-Converting Enzyme 2/physiology , Animals , Female , HEK293 Cells , Humans , Mice , Mice, Inbred C57BL , Proto-Oncogene Proteins/physiology , Receptor Protein-Tyrosine Kinases/physiology , Receptors, Cell Surface/antagonists & inhibitors , Virus Internalization , Axl Receptor Tyrosine Kinase , COVID-19 Drug Treatment
14.
Cell Commun Signal ; 21(1): 331, 2023 11 20.
Article in English | MEDLINE | ID: mdl-37985999

ABSTRACT

INTRODUCTION: Inflammation plays a significant role in various cancers, including lung cancer, where the inflammatory cytokine IL-1ß is often elevated in the tumor microenvironment. Patients with lung adenocarcinoma show higher levels of serum IL-1ß compared to healthy individual. Moreover, IL-1ß blockade reduces the incidence and mortality of lung cancer. Our prior studies revealed that alveolar type-II cells, the precursors for lung adenocarcinoma, display an induction in the expression of the enzyme tryptophan 2,3-dioxygenase (TDO2) during normal lung development. This induction of TDO2 coincides with an increase in IL-1ß levels and is likely caused by IL-1ß. Given that cancer cells can co-opt developmentally regulated pathways, we hypothesized that IL-1ß may exert its pro-tumoral function by stimulating TDO2 and indoleamine 2, 3-dioxygenase-1 (IDO1), parallel enzymes involved in the conversion of tryptophan (Trp) into the immune-suppressive oncometabolite kynurenine (Kyn). Our goal was to determine whether IL-1ß is a common upstream regulator of immune checkpoint regulators. METHODS: To determine whether IL-1ß regulates IDO1, TDO2, PD-L1, and PD-L2, we measured mRNA and protein levels in lung adenocarcinoma cells lines (A549, H1792, H1838, H2347, H2228, HCC364 and HCC827) grown in 2D or 3D and in immortalized normal lung epithelial cells (HBEC3-KT and HSAEC1-KT). To determine the importance of the NFκB pathway in mediating IL-1ß -regulated cellular effects, we used siRNA to knockdown RelA/p65 in IL-1ß treated cells. The levels of Trp and Kyn in the IL-1ß-treated cells and media were measured by mass spectrometry. RESULTS: Upon IL-1ß stimulation, lung adenocarcinoma cells exhibited significant increases in IDO1 mRNA and protein levels, a response that depended on the NFκB pathway. Interestingly, this induction was more pronounced in 3D spheroid cultures compared to monolayer cultures and was not observed in normal immortalized lung epithelial cells. Furthermore, the conversion of Trp to Kyn increased in cells exposed to IL-1ß, aligning with the heightened IDO1 expression. Remarkably, IL-1ß also upregulated the expression of programmed death ligand-1 (PD-L1) and PD-L2 in multiple cell lines, indicating that IL-1ß triggers parallel immune-suppressive mechanisms in lung adenocarcinoma cells. CONCLUSIONS: Our studies demonstrate that lung adenocarcinoma cells, but not normal immortalized lung epithelial cells, respond to IL-1ß signaling by inducing the expression of parallel immune checkpoint proteins that have the potential to promote immune evasion. Video Abstract.


Subject(s)
Adenocarcinoma of Lung , Lung Neoplasms , Humans , Adenocarcinoma of Lung/metabolism , B7-H1 Antigen/metabolism , Kynurenine/metabolism , Lung Neoplasms/pathology , RNA, Messenger , Tryptophan , Tumor Microenvironment
15.
Exp Cell Res ; 414(1): 113053, 2022 05 01.
Article in English | MEDLINE | ID: mdl-35149086

ABSTRACT

Mutant KRAS, the most frequently occurring (∼30%) driver oncogene in lung adenocarcinoma, induces normal epithelial cells to undergo senescence. This phenomenon, called "oncogene-induced senescence (OIS)", prevents mutant KRAS-induced malignant transformation. We have previously reported that mutant KRASV12 induces OIS in a subset of normal human bronchial epithelial cell line immortalized with hTERT and Cdk4. Understanding the mechanism and efficacy of this important cancer prevention mechanism is a key knowledge gap. Therefore, this study investigates mutant KRASV12-induced OIS in upregulated telomerase combined with the p16/RB pathway inactivation in normal bronchial epithelial cells. The normal (non-transformed and non-tumorigenic) human bronchial epithelial cell line HBEC3 (also called "HBEC3KT"), immortalized with hTERT ("T") and Cdk4 ("K"), was used in this study. HBEC3 that expressed mutant KRASV12 in a doxycycline-regulated manner was established (designated as HBEC3-RIN2). Controlled induction of mutant KRASV12 expression induced partial epithelial-to-mesenchymal transition in HBEC3-RIN2 cells, which was associated with upregulated expression of ZEB1 and SNAIL. Mutant KRASV12 caused the majority of HBEC3-RIN2 to undergo morphological changes; suggestive of senescence, which was associated with enhanced autophagic flux. Upon mutant KRASV12 expression, only a small HBEC3-RIN2 cell subset underwent senescence, as assessed by a senescence-associated ß-galactosidase staining (SA-ßG) method. Furthermore, mutant KRASV12 enhanced cell growth, evaluated by colorimetric proliferation assay, and liquid and soft agar colony formation assays, partially through increased phosphorylated AKT and ERK expression but did not affect cell division, or cell cycle status. Intriguingly, mutant KRASV12 reduced p53 protein expression but increased p21 protein expression by prolonging its half-life. These results indicate that an hTERT/Cdk4 -immortalized normal bronchial epithelial cell line is partially resistant to mutant KRASV12-induced senescence. This suggests that OIS does not efficiently suppress KRASV12-induced transformation in the context of the simultaneous occurrence of telomerase upregulation and inactivation of the p16/Rb pathway.


Subject(s)
Telomerase , Bronchi/metabolism , Carrier Proteins/metabolism , Cell Line , Cell Transformation, Neoplastic/metabolism , Cellular Senescence/genetics , Cyclin-Dependent Kinase 4/genetics , Cyclin-Dependent Kinase 4/metabolism , Epithelial Cells/metabolism , Guanine Nucleotide Exchange Factors/metabolism , Humans , Proto-Oncogene Proteins p21(ras)/genetics , Telomerase/genetics , Telomerase/metabolism
16.
Nature ; 546(7656): 168-172, 2017 06 01.
Article in English | MEDLINE | ID: mdl-28538732

ABSTRACT

Metabolic reprogramming by oncogenic signals promotes cancer initiation and progression. The oncogene KRAS and tumour suppressor STK11, which encodes the kinase LKB1, regulate metabolism and are frequently mutated in non-small-cell lung cancer (NSCLC). Concurrent occurrence of oncogenic KRAS and loss of LKB1 (KL) in cells specifies aggressive oncological behaviour. Here we show that human KL cells and tumours share metabolomic signatures of perturbed nitrogen handling. KL cells express the urea cycle enzyme carbamoyl phosphate synthetase-1 (CPS1), which produces carbamoyl phosphate in the mitochondria from ammonia and bicarbonate, initiating nitrogen disposal. Transcription of CPS1 is suppressed by LKB1 through AMPK, and CPS1 expression correlates inversely with LKB1 in human NSCLC. Silencing CPS1 in KL cells induces cell death and reduces tumour growth. Notably, cell death results from pyrimidine depletion rather than ammonia toxicity, as CPS1 enables an unconventional pathway of nitrogen flow from ammonia into pyrimidines. CPS1 loss reduces the pyrimidine to purine ratio, compromises S-phase progression and induces DNA-polymerase stalling and DNA damage. Exogenous pyrimidines reverse DNA damage and rescue growth. The data indicate that the KL oncological genotype imposes a metabolic vulnerability related to a dependence on a cross-compartmental pathway of pyrimidine metabolism in an aggressive subset of NSCLC.


Subject(s)
Carbamoyl-Phosphate Synthase (Ammonia)/metabolism , DNA/biosynthesis , Lung Neoplasms/genetics , Lung Neoplasms/metabolism , Protein Serine-Threonine Kinases/genetics , Proto-Oncogene Proteins p21(ras)/genetics , Pyrimidines/metabolism , AMP-Activated Protein Kinase Kinases , AMP-Activated Protein Kinases/metabolism , Ammonia/metabolism , Animals , Bicarbonates/metabolism , Carbamoyl-Phosphate Synthase (Ammonia)/deficiency , Carbamoyl-Phosphate Synthase (Ammonia)/genetics , Carbamyl Phosphate/metabolism , Carcinoma, Non-Small-Cell Lung/enzymology , Carcinoma, Non-Small-Cell Lung/genetics , Carcinoma, Non-Small-Cell Lung/metabolism , Carcinoma, Non-Small-Cell Lung/pathology , Cell Death , Cell Proliferation , DNA Damage/drug effects , DNA Replication , DNA-Directed DNA Polymerase/metabolism , Female , Gene Silencing , Humans , Lung Neoplasms/enzymology , Lung Neoplasms/pathology , Male , Metabolomics , Mice , Mitochondria/metabolism , Nitrogen/metabolism , Protein Serine-Threonine Kinases/metabolism , Purines/metabolism , Pyrimidines/pharmacology , S Phase , Transcription, Genetic , Xenograft Model Antitumor Assays
17.
Bioinformatics ; 37(23): 4540-4547, 2021 12 07.
Article in English | MEDLINE | ID: mdl-34081116

ABSTRACT

MOTIVATION: Many high-throughput screening studies have been carried out in cancer cell lines to identify therapeutic agents and targets. Existing consistency assessment studies only examined two datasets at a time, with conclusions based on a subset of carefully selected features rather than considering global consistency of all the data. However, poor concordance can still be observed for a large part of the data even when selected features are highly consistent. RESULTS: In this study, we assembled nine compound screening datasets and three functional genomics datasets. We derived direct measures of consistency as well as indirect measures of consistency based on association between functional data and copy number-adjusted gene expression data. These results have been integrated into a web application-the Functional Data Consistency Explorer (FDCE), to allow users to make queries and generate interactive visualizations so that functional data consistency can be assessed for individual features of interest. AVAILABILITY AND IMPLEMENTATION: The FDCE web tool and we have developed and the functional data consistency measures we have generated are available at https://lccl.shinyapps.io/FDCE/. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.


Subject(s)
Early Detection of Cancer , Neoplasms , Humans , Genomics , Software , Cell Line
18.
Bioorg Med Chem ; 58: 116673, 2022 03 15.
Article in English | MEDLINE | ID: mdl-35189561

ABSTRACT

To identify potential new reagents and biomarkers for early lung cancer detection we combined the use of a novel preclinical isogenic model of human lung epithelial cells comparing non-malignant cells with those transformed to full malignancy using defined oncogenic changes and our on-bead two color (red and green stained cells) (OBTC) peptoid combinatorial screening methodology. The preclinical model used normal parent lung epithelial cells (HBEC3-KT, labeled with green dye) and isogenic fully malignant transformed derivatives (labeled with a red dye) via the sequential introduction of key genetic alterations of p53 knockdown, oncogenic KRAS and overexpression of cMYC (HBEC3p53, KRAS, cMYC). Using the unbiased OBTC screening approach, we tested 100,000 different peptoids and identified only one (named JM3A) that bound to the surface of the HBEC3p53, KRAS, cMYC cells (red cells) but not HBEC3-KT cells (green cells). Using the JM3A peptoid and proteomics, we identified the protein bound as vimentin using multiple validation approaches. These all confirmed the cell surface expression of vimentin (CSV) on transformed (HBEC3p53, KRAS, cMYC) but not on untransformed (HBEC3-KT) cells. JM3A coupled with fluorophores was able to detect and stain cell surface vimentin on very early stage lung cancers but not normal lung epithelial cells in a fashion comparable to that using anti-vimentin antibodies. We conclude: using a combined isogenic preclinical model of lung cancer and two color screening of a large peptoid library, we have identified differential expression of cell surface vimentin (CSV) after malignant transformation of lung epithelial cells, and developed a new peptoid reagent (JM3A) for detection of CSV which works well in staining of early stage NSCLCs. This new, highly specific, easy to prepare, CSV detecting JM3A peptoid provides an important new reagent for identifying cancer cells in early stage tumors as well as a resource for detection and isolating of CSV expressing circulating tumor cells.


Subject(s)
Epithelial Cells/metabolism , Lung Neoplasms/metabolism , Peptoids/metabolism , Vimentin/genetics , Cell Line , Humans , Lung Neoplasms/pathology , Molecular Structure , Peptoids/chemistry , Vimentin/metabolism
19.
Nature ; 538(7623): 114-117, 2016 Oct 06.
Article in English | MEDLINE | ID: mdl-27680702

ABSTRACT

The common participation of oncogenic KRAS proteins in many of the most lethal human cancers, together with the ease of detecting somatic KRAS mutant alleles in patient samples, has spurred persistent and intensive efforts to develop drugs that inhibit KRAS activity. However, advances have been hindered by the pervasive inter- and intra-lineage diversity in the targetable mechanisms that underlie KRAS-driven cancers, limited pharmacological accessibility of many candidate synthetic-lethal interactions and the swift emergence of unanticipated resistance mechanisms to otherwise effective targeted therapies. Here we demonstrate the acute and specific cell-autonomous addiction of KRAS-mutant non-small-cell lung cancer cells to receptor-dependent nuclear export. A multi-genomic, data-driven approach, utilizing 106 human non-small-cell lung cancer cell lines, was used to interrogate 4,725 biological processes with 39,760 short interfering RNA pools for those selectively required for the survival of KRAS-mutant cells that harbour a broad spectrum of phenotypic variation. Nuclear transport machinery was the sole process-level discriminator of statistical significance. Chemical perturbation of the nuclear export receptor XPO1 (also known as CRM1), with a clinically available drug, revealed a robust synthetic-lethal interaction with native or engineered oncogenic KRAS both in vitro and in vivo. The primary mechanism underpinning XPO1 inhibitor sensitivity was intolerance to the accumulation of nuclear IκBα (also known as NFKBIA), with consequent inhibition of NFκB transcription factor activity. Intrinsic resistance associated with concurrent FSTL5 mutations was detected and determined to be a consequence of YAP1 activation via a previously unappreciated FSTL5-Hippo pathway regulatory axis. This occurs in approximately 17% of KRAS-mutant lung cancers, and can be overcome with the co-administration of a YAP1-TEAD inhibitor. These findings indicate that clinically available XPO1 inhibitors are a promising therapeutic strategy for a considerable cohort of patients with lung cancer when coupled to genomics-guided patient selection and observation.


Subject(s)
Active Transport, Cell Nucleus/drug effects , Cell Nucleus/metabolism , Karyopherins/antagonists & inhibitors , Karyopherins/metabolism , Lung Neoplasms/genetics , Lung Neoplasms/metabolism , Proto-Oncogene Proteins p21(ras)/genetics , Receptors, Cytoplasmic and Nuclear/antagonists & inhibitors , Receptors, Cytoplasmic and Nuclear/metabolism , Adaptor Proteins, Signal Transducing/antagonists & inhibitors , Adaptor Proteins, Signal Transducing/metabolism , Animals , Carcinoma, Non-Small-Cell Lung/drug therapy , Carcinoma, Non-Small-Cell Lung/genetics , Carcinoma, Non-Small-Cell Lung/metabolism , Carcinoma, Non-Small-Cell Lung/pathology , Cell Line, Tumor , Cell Nucleus/drug effects , Cell Proliferation/drug effects , Cell Survival/drug effects , Cell Survival/genetics , DNA-Binding Proteins/antagonists & inhibitors , DNA-Binding Proteins/metabolism , Female , Follistatin-Related Proteins/genetics , Genes, Lethal/genetics , Hippo Signaling Pathway , Humans , Lung Neoplasms/drug therapy , Lung Neoplasms/pathology , Mice , Mutation , NF-KappaB Inhibitor alpha/metabolism , NF-kappa B/antagonists & inhibitors , NF-kappa B/metabolism , Nuclear Proteins/antagonists & inhibitors , Nuclear Proteins/metabolism , Phosphoproteins/antagonists & inhibitors , Phosphoproteins/metabolism , Porphyrins/pharmacology , Protein Serine-Threonine Kinases/metabolism , RNA Interference , RNA, Small Interfering , Signal Transduction , TEA Domain Transcription Factors , Transcription Factors/antagonists & inhibitors , Transcription Factors/metabolism , Verteporfin , Xenograft Model Antitumor Assays , YAP-Signaling Proteins , Exportin 1 Protein
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