ABSTRACT
PURPOSE: Several targeted agents demonstrated efficacy in early clinical trials for gastrointestinal (GI) cancers, but in many cases, phase-III trials and/or approval by the European Medicines Agency (EMA) are lacking. The primary focus of this study was to assess the regulatory processes associated with use and reimbursement of off-label treatment in precision oncology and to evaluate the benefit of targeted therapy in a real-world population in Germany. METHODS: Our cohort comprises 137 patients with GI cancers and is biased towards cancer entities with a high frequency of known targetable alterations, such as cholangiocarcinoma. Genetic testing was used to identify molecular targets, and therapy response was evaluated based on CT scans. RESULTS: A molecular target for precision oncology was identified in 53 patients and 43 requests for cost coverage were submitted to health insurance companies. 60% of the requests received approval after initial application and another 7% after appeal. Half of the rejected requests were denied despite ESCAT IA level evidence. The median time between initiation of molecular testing and start of therapy was 75 days. 35 patients received matched targeted therapies (n = 28) or, in the case of MSI, immunotherapy (IO) (n = 7). We observed a trend in favor of molecular therapy when compared to the immediate prior treatment. CONCLUSION: Relevant treatment options were identified by molecular testing in a significant subset of patients. When targeted therapies that lack EMA approval are considered, treatment initiation may be delayed by the duration of the molecular analysis and the regulatory processes.
Subject(s)
Antineoplastic Agents , Gastrointestinal Neoplasms , Antineoplastic Agents/therapeutic use , Cohort Studies , Gastrointestinal Neoplasms/diagnosis , Gastrointestinal Neoplasms/genetics , Gastrointestinal Neoplasms/therapy , Humans , Molecular Targeted Therapy , Pathology, Molecular , Precision MedicineABSTRACT
BACKGROUND AND AIMS: Intrahepatic cholangiocarcinoma (ICC) is the second most common primary liver cancer and a highly lethal malignancy. Chemotherapeutic options are limited, but a considerable subset of patients harbors genetic lesions for which targeted agents exist. Fibroblast growth factor receptor 2 (FGFR2) fusions belong to the most frequent and therapeutically relevant alterations in ICC, and the first FGFR inhibitor was recently approved for the treatment of patients with progressed, fusion-positive ICC. Response rates of up to 35% indicate that FGFR-targeted therapies are beneficial in many but not all patients. Thus far, no established biomarkers exist that predict resistance or response to FGFR-targeted therapies in patients with ICC. APPROACH AND RESULTS: In this study, we use an autochthonous murine model of ICC to demonstrate that FGFR2 fusions are potent drivers of malignant transformation. Furthermore, we provide preclinical evidence that the co-mutational spectrum acts not only as an accelerator of tumor development, but also modifies the response to targeted FGFR inhibitors. Using pharmacologic approaches and RNA-interference technology, we delineate that Kirsten rat sarcoma oncogene (KRAS)-activated mitogen-activated protein kinase signaling causes primary resistance to FGFR inhibitors in FGFR2 fusion-positive ICC. The translational relevance is supported by the observation that a subset of human FGFR2 fusion patients exhibits transcriptome profiles reminiscent of KRAS mutant ICC. Moreover, we demonstrate that combination therapy has the potential to overcome primary resistance and to sensitize tumors to FGFR inhibition. CONCLUSIONS: Our work highlights the importance of the co-mutational spectrum as a significant modifier of response in tumors that harbor potent oncogenic drivers. A better understanding of the genetic underpinnings of resistance will be pivotal to improve biomarker-guided patient selection and to design clinically relevant combination strategies.
Subject(s)
Bile Duct Neoplasms/genetics , Bile Ducts, Intrahepatic , Cell Transformation, Neoplastic/genetics , Cholangiocarcinoma/genetics , Gene Fusion/genetics , Liver Neoplasms, Experimental/genetics , Proto-Oncogene Proteins p21(ras)/genetics , Receptor, Fibroblast Growth Factor, Type 2/genetics , Adenosylhomocysteinase/genetics , Animals , Antigens, Neoplasm/genetics , Antimetabolites, Antineoplastic/pharmacology , Bile Duct Neoplasms/pathology , Cell Proliferation/drug effects , Cell Transformation, Neoplastic/drug effects , Cholangiocarcinoma/pathology , Co-Repressor Proteins/genetics , Cyclic AMP Response Element-Binding Protein A/genetics , Deoxycytidine/analogs & derivatives , Deoxycytidine/pharmacology , Fetal Proteins/genetics , Mice , Microtubule-Associated Proteins/genetics , Mutation , Phenylurea Compounds/pharmacology , Protein Kinase Inhibitors/pharmacology , Pyrimidines/pharmacology , Receptor, Fibroblast Growth Factor, Type 2/antagonists & inhibitors , Vesicular Transport Proteins/genetics , GemcitabineABSTRACT
BACKGROUND & AIMS: A coordinated stress and regenerative response is important after hepatocyte damage. Here, we investigate the phenotypes that result from genetic abrogation of individual components of the checkpoint kinase 2/transformation-related protein 53 (p53)/cyclin-dependent kinase inhibitor 1A (p21) pathway in a murine model of metabolic liver injury. METHODS: Nitisinone was reduced or withdrawn in Fah-/- mice lacking Chk2, p53, or p21, and survival, tumor development, liver injury, and regeneration were analyzed. Partial hepatectomies were performed and mice were challenged with the Fas antibody Jo2. RESULTS: In a model of metabolic liver injury, loss of p53, but not Chk2, impairs the oxidative stress response and aggravates liver damage, indicative of a direct p53-dependent protective effect on hepatocytes. Cell-cycle control during chronic liver injury critically depends on the presence of both p53 and its downstream effector p21. In p53-deficient hepatocytes, unchecked proliferation occurs despite a strong induction of p21, showing a complex interdependency between p21 and p53. The increased regenerative potential in the absence of p53 cannot fully compensate the surplus injury and is not sufficient to promote survival. Despite the distinct phenotypes associated with the loss of individual components of the DNA damage response, gene expression patterns are dominated by the severity of liver injury, but reflect distinct effects of p53 on proliferation and the anti-oxidative stress response. CONCLUSIONS: Characteristic phenotypes result from the genetic abrogation of individual components of the DNA damage-response cascade in a liver injury model. The extent to which loss of gene function can be compensated, or affects injury and proliferation, is related to the level at which the cascade is interrupted. Accession numbers of repository for expression microarray data: GSE156983, GSE156263, GSE156852, and GSE156252.
Subject(s)
Acute Lung Injury/complications , Carcinogenesis/pathology , Checkpoint Kinase 2/physiology , Cyclin-Dependent Kinase Inhibitor p21/physiology , Liver Neoplasms/pathology , Liver Regeneration , Tumor Suppressor Protein p53/physiology , Animals , Liver Neoplasms/etiology , Liver Neoplasms/metabolism , Mice , Mice, Inbred C57BL , Mice, KnockoutABSTRACT
Beyond the nearly uniform presence of KRAS mutations, pancreatic cancer is increasingly recognized as a heterogeneous disease. Preclinical in vivo model systems exist, but with the advent of precision oncology, murine models with enhanced genetic flexibility are needed to functionally annotate genetic alterations found in the human malignancy. Here, we describe the generation of focal gene disruptions and large chromosomal deletions via inducible and pancreas-specific expression of Cas9 in adult mice. Experimental mice are derived on demand directly from genetically engineered embryonic stem cells, without the need for further intercrossing. To provide initial validation of our approach, we show that disruption of the E3 ubiquitin ligase Rnf43 accelerates KrasG12D-dependent tumourigenesis. Moreover, we demonstrate that this system can be used to rapidly interrogate the impact of complex cancer-associated alleles through the generation of a previously unstudied 1.2 megabase deletion surrounding the CDKN2A and CDKN2B tumour suppressors. Thus, our approach is capable of reproducibly generating biallelic and precise loss of large chromosomal fragments that, in conjunction with mutant Kras, leads to development of pancreatic ductal adenocarcinoma with full penetrance.
Subject(s)
Carcinogenesis/genetics , Carcinoma, Pancreatic Ductal/genetics , Gene Editing , Pancreatic Neoplasms/genetics , Animals , Carcinoma, Pancreatic Ductal/pathology , Cell Line, Tumor , Disease Models, Animal , Genome, Human/genetics , Humans , Mice , Mutation/genetics , Pancreas/pathology , Pancreatic Neoplasms/pathology , Precision Medicine , Sequence Deletion/genetics , Pancreatic NeoplasmsABSTRACT
Gallbladder cancer is associated with a dismal prognosis, and accurate in vivo models will be elemental to improve our understanding of this deadly disease and develop better treatment options. We have generated a transplantation-based murine model for gallbladder cancer that histologically mimics the human disease, including the development of distant metastasis. Murine gallbladder-derived organoids are genetically modified by either retroviral transduction or transfection with CRISPR/Cas9 encoding plasmids, thereby allowing the rapid generation of complex cancer genotypes. We characterize the model in the presence of two of the most frequent oncogenic drivers-Kras and ERBB2-and provide evidence that the tumor histology is highly dependent on the driver oncogene. Further, we demonstrate the utility of the model for the preclinical assessment of novel therapeutic approaches by showing that liposomal Irinotecan (Nal-IRI) is retained in tumor cells and significantly prolongs the survival of gallbladder cancer-bearing mice compared to conventional irinotecan.
ABSTRACT
Cholangiocarcinoma (CCA) is a genetically and histologically complex disease with a highly dismal prognosis. A deeper understanding of the underlying cellular and molecular mechanisms of human CCA will increase our current knowledge of the disease and expedite the eventual development of novel therapeutic strategies for this fatal cancer. This endeavor is effectively supported by genetic mouse models, which serve as sophisticated tools to systematically investigate CCA pathobiology and treatment response. These in vivo models feature many of the genetic alterations found in humans, recapitulate multiple hallmarks of cholangiocarcinogenesis (encompassing cell transformation, preneoplastic lesions, established tumors and metastatic disease) and provide an ideal experimental setting to study the interplay between tumor cells and the surrounding stroma. This review is intended to serve as a compendium of CCA mouse models, including traditional transgenic models but also genetically flexible approaches based on either the direct introduction of DNA into liver cells or transplantation of pre-malignant cells, and is meant as a resource for CCA researchers to aid in the selection of the most appropriate in vivo model system.
ABSTRACT
The rising incidence of cholangiocarcinoma (CCA) coupled with a low 5-year survival rate that remains below 10% delineates the urgent need for more effective treatment strategies. Although several recent studies provided detailed information on the genetic landscape of this fatal malignancy, versatile model systems to functionally dissect the immediate clinical relevance of the identified genetic alterations are still missing. To enhance our understanding of CCA pathophysiology and facilitate rapid functional annotation of putative CCA driver and tumor maintenance genes, we developed a tractable murine CCA model by combining the cyclization recombination (Cre)-lox system, RNA interference, and clustered regularly interspaced short palindromic repeats/CRISPR associated protein 9 (CRISPR/Cas9) technology with liver organoids, followed by subsequent transplantation into immunocompetent, syngeneic mice. Histologically, resulting tumors displayed cytokeratin 19-positive ductal structures surrounded by a desmoplastic stroma-hallmark features of human CCAs. Despite their initial biliary phenotype in vitro, organoids retained the plasticity to induce a broader differentiation spectrum of primary liver cancers following transplantation into recipient mice, depending on their genetic context. Thus, the organoid system combines the advantage of using nontransformed, premalignant cells to recapitulate liver tumorigenesis as a multistep process, with the advantage of a reproducible and expandable cell culture system that abrogates the need for recurrent isolations of primary cells. Conclusion: Genetically modified liver organoids are able to transform into histologically accurate CCAs. Depending on the oncogenic context, they are also able to give rise to liver cancers that show features of hepatocellular carcinomas. The model can be used to functionally explore candidate cancer genes of primary liver cancers in immunocompetent animals and evaluate novel treatment regimens.
ABSTRACT
OBJECTIVES: The clinical relevance of spontaneous portosystemic shunts detected by ultrasound is insufficiently investigated. The aim of this retrospective study was to assess the frequency and clinical relevance of spontaneous portosystemic shunts in patients with liver cirrhosis. METHODS: We evaluated portosystemic shunts, liver cirrhosis and spleen size by ultrasound in 982 patients with liver cirrhosis and correlated these with laboratory results, clinical data and the incidence of clinical endpoint deaths, liver transplantation and the development of HCC during the follow-up period (mean 1.26 ± 1.53 years [range 0-7.2 years]). RESULTS: Portosystemic shunts were detected in 34% of the patients. These patients had a higher rate of alcohol-related cirrhosis (37% vs. 30%, p = .003), a higher MELD score (p < .001) and Child-Pugh grade (p < .001), as well as more frequent hepatic encephalopathy (p < .001) and oesophageal varices (p < .003). The most frequent portosystemic shunt in this cohort was an umbilical vein shunt (69%) followed by splenorenal (16%), mesenteric (7%) and combined/other shunts (8%). Patients with umbilical vein shunts had a higher rate of alcohol-related cirrhosis (p = .041) and suffered more frequently from Child B/C stages (p = .03), hepatorenal syndrome (p = .03), massive ascites (p = .001) and spontaneous bacterial peritonitis (p = .011). CONCLUSIONS: Patients with portosystemic shunts that are detected by ultrasound should be monitored carefully as these patients are associated with advanced liver disease and multiple clinical risk factors.
Subject(s)
Hepatic Encephalopathy/complications , Hypertension, Portal/diagnostic imaging , Liver Cirrhosis/physiopathology , Spleen/diagnostic imaging , Ultrasonography , Adolescent , Adult , Aged , Aged, 80 and over , Ascites/complications , Child , Esophageal and Gastric Varices/complications , Female , Humans , Hypertension, Portal/etiology , Linear Models , Liver Cirrhosis/complications , Male , Middle Aged , Portal Vein/diagnostic imaging , Retrospective Studies , Tertiary Care Centers , Young AdultABSTRACT
Mutations in members of the SWI/SNF chromatin remodeling family are common events in cancer, but the mechanisms whereby disruption of SWI/SNF components alters tumorigenesis remain poorly understood. To model the effect of loss of function mutations in the SWI/SNF subunit Arid1a in pancreatic ductal adenocarcinoma (PDAC) initiation, we directed shRNA triggered, inducible and reversible suppression of Arid1a to the mouse pancreas in the setting of oncogenic KrasG12D. Arid1a cooperates with Kras in the adult pancreas as postnatal silencing of Arid1a following sustained KrasG12D expression induces rapid and irreversible reprogramming of acinar cells into mucinous PDAC precursor lesions. In contrast, Arid1a silencing during embryogenesis, concurrent with KrasG12D activation, leads to retention of acinar cell fate. Together, our results demonstrate Arid1a as a critical modulator of Kras-dependent changes in acinar cell identity, and underscore an unanticipated influence of timing and genetic context on the effects of SWI/SNF complex alterations in epithelial tumorigenesis.
Subject(s)
Acinar Cells/physiology , Carcinogenesis , Cell Differentiation , Cell Transformation, Neoplastic , DNA-Binding Proteins/metabolism , Morphogenesis , Nuclear Proteins/metabolism , Proto-Oncogene Proteins p21(ras)/metabolism , Animals , Carcinoma, Pancreatic Ductal/physiopathology , Gene Expression Regulation , Mice , Transcription FactorsABSTRACT
BACKGROUND: Proprotein convertase subtilisin/kexin type 9 (PCSK9)-inhibitors have shown great po-tential in efficient lipid lowering to achieve low-density lipoprotein-cholesterol (LDL-C) treatment goals. The aim of the study was too describe the clinical use of PCSK9-inhibitors and to investigate therapy adherence and safety outside of clinical trials. METHODS: Thirty-eight patients were treated with PSCK9-inhibitors. Patients were eligible for this therapy based on their individual cardiovascular risk and when all other available lipid-lowering regi-men had failed. Every patient answered a questionnaire concerning medical history and relevant side effects and therapy adherence. RESULTS: Conventional therapy reduced patient LDL-C levels by about 38%. However, in 26 of the 38 patients, LDL-C treatment goals were not fulfilled because patients did not tolerate further dose es-calation due to side effects. Using a PCSK9 inhibitor, LDL-C levels were reduced by another 54% and 42% of patients reaching treatment goals. The results show that most patients still require concomitant therapy to reach LDL-C target levels. Three patients required dose reduction or change of the PCSK9 inhibitor. 16% did not inject the PCSK9 inhibitor regularly. CONCLUSIONS: Only a minority of patients reached the recommended LDL-C goals. PCSK9-inhibitors were generally well tolerated. Despite low rates of reported side effects, therapy adherence was incom-plete, with 6 patients not injecting PCSK9-inhibitors on a regular basis. In-depth information about the medication and close supervision is advisable. PCSK9 inhibitors have shown great potential in aggressive lipid lowering therapy, but basic therapy is still required in most cases. Close supervision is recommended to improve therapy adherence. (Cardiol J 2018; 25, 1: 32-41).
Subject(s)
Antibodies, Monoclonal/therapeutic use , Hypercholesterolemia/drug therapy , PCSK9 Inhibitors , Treatment Adherence and Compliance , Antibodies, Monoclonal, Humanized , Anticholesteremic Agents/therapeutic use , Apoptosis , Cohort Studies , Female , Humans , Hypercholesterolemia/blood , Male , Middle Aged , Retrospective Studies , Risk Factors , Surveys and Questionnaires , Treatment OutcomeABSTRACT
The outstanding clinical success of immune checkpoint blockade has revived the interest in underlying mechanisms of the immune system that are capable of eliminating tumors even in advanced stages. In this scenario, CD4 and CD8 T cell responses are part of the cancer immune cycle and both populations significantly influence the clinical outcome. In general, the immune system has evolved several mechanisms to protect the host against cancer. Each of them has to be undermined or evaded during cancer development to enable tumor outgrowth. In this review, we give an overview of T lymphocyte-driven control of tumor growth and discuss the involved tumor-suppressive mechanisms of the immune system, such as senescence surveillance, cancer immunosurveillance, and cancer immunoediting with respect to recent clinical developments of immunotherapies. The main focus is on the currently existing knowledge about the CD4 and CD8 T lymphocyte interplay that mediates the control of tumor growth.
Subject(s)
CD4-Positive T-Lymphocytes/physiology , CD8-Positive T-Lymphocytes/physiology , Cell Communication/immunology , Cell Proliferation , Neoplasms/immunology , Neoplasms/pathology , Animals , Humans , Immunotherapy/methods , Tumor Escape/immunologyABSTRACT
CD4 and CD8 T cells play a pivotal role in controlling tumor growth. However, the interplay of both cell types and their role in tumor suppression still remain elusive. In this study, we investigated the regulation of CD4 and CD8 T cell responses to different classes of tumor-specific antigens in liver cancer mouse models. Tumors were induced in p19Arf-deficient mice by hydrodynamic injection of transposon plasmids encoding NrasG12V and pre-defined tumor antigens. This allowed for assessing the regulation of tumor-specific CD4 and CD8 T cell responses. We showed that MHC class I tumor immunogenicity was essential to trigger tumor-directed CD4 T cells. Tumor-specific CD8 T cell responses arose independently of CD4 T cells, but they required Th1-polarized CD4 T cells for efficient tumor suppression. Our results further indicate that the immune system is incapable of eliciting sufficient numbers of T cells directed against antigens derived from immunoedited tumors, which consequently leads to a lack of T-cell-mediated tumor suppression in untreated hosts.
Subject(s)
CD4-Positive T-Lymphocytes/immunology , CD8-Positive T-Lymphocytes/immunology , Neoplasms/immunology , Animals , Antigens, Neoplasm/immunology , Carcinogenesis/immunology , Carcinogenesis/pathology , Cytotoxicity, Immunologic , Genes, MHC Class I , Genes, ras , Immunologic Surveillance , Mice, Inbred C57BL , Neoplasms/pathology , Survival Analysis , T-Lymphocytes, Cytotoxic/immunology , Th1 Cells/immunologyABSTRACT
BACKGROUND & AIMS: Even after potentially curative R0 resection, patients with pancreatic ductal adenocarcinoma (PDAC) have a poor prognosis owing to high rates of local recurrence and metastasis to distant organs. However, we have no suitable transgenic animal models for surgical interventions. METHODS: To induce formation of pancreatic tumor foci, we electroporated oncogenic plasmids into pancreata of LSL-KrasG12D × p53fl/fl mice; mutant Kras was expressed in p53fl/fl mice using a sleeping beauty transposon. We co-delivered a transposon encoding a constitutively active form of Akt2 (myrAkt2). Carcinogenesis and histopathologic features of tumors were examined. Metastasis was monitored by bioluminescence imaging. Tumors were resected and mice were given gemcitabine, and tumor recurrence patterns and survival were determined. Immune cells were collected from resection sites and analyzed by flow cytometry and in depletion experiments. RESULTS: After electroporation of oncogenic plasmids, mice developed a single pancreatic tumor nodule with histopathologic features of human PDAC. Pancreatic tumors that expressed myrAkt2 infiltrated the surrounding pancreatic tissue and neurons and became widely metastatic, reflecting the aggressive clinical features of PDAC in patients. Despite early tumor resection, mice died from locally recurring and distant tumors, but adjuvant administration of gemcitabine after tumor resection prolonged survival. In mice given adjuvant gemcitabine or vehicle, gemcitabine significantly inhibited local recurrence of tumors, but not metastasis to distant organs, similar to observations in clinical trials. Gemcitabine inhibited accumulation of CD11b+Gr1intF4/80int myeloid-derived suppressor cells at the resection margin and increased the number of natural killer (NK) cells at this location. NK cells but not T cells were required for gemcitabine-mediated antitumor responses. CONCLUSIONS: Gemcitabine administration after resection of pancreatic tumors in mice activates NK cell-mediated antitumor responses and inhibits local recurrence of tumors, consistent with observations from patients with PDAC. Transgenic mice with resectable pancreatic tumors might be promising tools to study adjuvant therapy strategies for patients.
Subject(s)
Antimetabolites, Antineoplastic/pharmacology , Deoxycytidine/analogs & derivatives , Killer Cells, Natural/drug effects , Pancreatic Neoplasms/drug therapy , Animals , Combined Modality Therapy , Deoxycytidine/pharmacology , Disease Models, Animal , Mice , Neoplasm Invasiveness , Neoplasm Recurrence, Local/prevention & control , Pancreatic Neoplasms/immunology , Pancreatic Neoplasms/pathology , Pancreatic Neoplasms/surgery , Proto-Oncogene Proteins c-akt/metabolism , GemcitabineABSTRACT
There is evidence that viral oncolysis is synergistic with immune checkpoint inhibition in cancer therapy but the underlying mechanisms are unclear. Here, we investigated whether local viral infection of malignant tumors is capable of overcoming systemic resistance to PD-1-immunotherapy by modulating the spectrum of tumor-directed CD8 T-cells. To focus on neoantigen-specific CD8 T-cell responses, we performed transcriptomic sequencing of PD-1-resistant CMT64 lung adenocarcinoma cells followed by algorithm-based neoepitope prediction. Investigations on neoepitope-specific T-cell responses in tumor-bearing mice demonstrated that PD-1 immunotherapy was insufficient whereas viral oncolysis elicited cytotoxic T-cell responses to a conserved panel of neoepitopes. After combined treatment, we observed that PD-1-blockade did not affect the magnitude of oncolysis-mediated antitumoral immune responses but a broader spectrum of T-cell responses including additional neoepitopes was observed. Oncolysis of the primary tumor significantly abrogated systemic resistance to PD-1-immunotherapy leading to improved elimination of disseminated lung tumors. Our observations were confirmed in a transgenic murine model of liver cancer where viral oncolysis strongly induced PD-L1 expression in primary liver tumors and lung metastasis. Furthermore, we demonstrated that combined treatment completely inhibited dissemination in a CD8 T-cell-dependent manner. Therefore, our results strongly recommend further evaluation of virotherapy and concomitant PD-1 immunotherapy in clinical studies.
Subject(s)
Neoplasms/etiology , Neoplasms/metabolism , T-Lymphocyte Subsets/immunology , T-Lymphocyte Subsets/metabolism , Tumor Virus Infections , Animals , Antigens, Neoplasm/genetics , Antigens, Neoplasm/immunology , Antigens, Neoplasm/metabolism , Antineoplastic Agents , B7-H1 Antigen/genetics , B7-H1 Antigen/metabolism , Disease Models, Animal , Epitopes, T-Lymphocyte/genetics , Epitopes, T-Lymphocyte/immunology , Gene Expression , Immunotherapy , Isografts , Ligands , Mice , Mice, Transgenic , Mutation , Neoplasms/pathology , Neoplasms/therapy , Oncolytic Virotherapy , Oncolytic Viruses/immunology , Programmed Cell Death 1 Receptor/antagonists & inhibitors , Toll-Like Receptors/metabolismABSTRACT
Genome-wide analysis at the level of single cells has recently emerged as a powerful tool to dissect genome heterogeneity in cancer, neurobiology, and development. To be truly transformative, single-cell approaches must affordably accommodate large numbers of single cells. This is feasible in the case of copy number variation (CNV), because CNV determination requires only sparse sequence coverage. We have used a combination of bioinformatic and molecular approaches to optimize single-cell DNA amplification and library preparation for highly multiplexed sequencing, yielding a method that can produce genome-wide CNV profiles of up to a hundred individual cells on a single lane of an Illumina HiSeq instrument. We apply the method to human cancer cell lines and biopsied cancer tissue, thereby illustrating its efficiency, reproducibility, and power to reveal underlying genetic heterogeneity and clonal phylogeny. The capacity of the method to facilitate the rapid profiling of hundreds to thousands of single-cell genomes represents a key step in making single-cell profiling an easily accessible tool for studying cell lineage.
Subject(s)
DNA Copy Number Variations , DNA, Neoplasm/genetics , Multiplex Polymerase Chain Reaction/methods , Sequence Analysis, DNA/methods , Single-Cell Analysis/methods , Algorithms , Base Sequence , Cell Line, Tumor , Genome, Human , Humans , Molecular Sequence DataABSTRACT
The inability to visualize the true extent of cancers represents a significant challenge in many areas of oncology. The margins of most cancer types are not well demarcated because the cancer diffusely infiltrates the surrounding tissues. Furthermore, cancers may be multifocal and characterized by the presence of microscopic satellite lesions. Such microscopic foci represent a major reason for persistence of cancer, local recurrences, and metastatic spread, and are usually impossible to visualize with currently available imaging technologies. An imaging method to reveal the true extent of tumors is desired clinically and surgically. We show the precise visualization of tumor margins, microscopic tumor invasion, and multifocal locoregional tumor spread using a new generation of surface-enhanced resonance Raman scattering (SERRS) nanoparticles, which are termed SERRS nanostars. The SERRS nanostars feature a star-shaped gold core, a Raman reporter resonant in the near-infrared spectrum, and a primer-free silication method. In genetically engineered mouse models of pancreatic cancer, breast cancer, prostate cancer, and sarcoma, and in one human sarcoma xenograft model, SERRS nanostars enabled accurate detection of macroscopic malignant lesions, as well as microscopic disease, without the need for a targeting moiety. Moreover, the sensitivity (1.5 fM limit of detection) of SERRS nanostars allowed imaging of premalignant lesions of pancreatic and prostatic neoplasias. High sensitivity and broad applicability, in conjunction with their inert gold-silica composition, render SERRS nanostars a promising imaging agent for more precise cancer imaging and resection.
Subject(s)
Diagnostic Imaging/methods , Nanoparticles , Neoplasms/diagnosis , Spectrum Analysis, Raman/methods , Animals , Cell Line, Tumor , Disease Models, Animal , Female , Humans , Neoplasm Metastasis , Pinocytosis , Precancerous Conditions/pathology , Tissue DistributionABSTRACT
MEK inhibitors are clinically active in BRAF(V600E) melanomas but only marginally so in KRAS mutant tumors. Here, we found that MEK inhibitors suppress ERK signaling more potently in BRAF(V600E), than in KRAS mutant tumors. To understand this, we performed an RNAi screen in a KRAS mutant model and found that CRAF knockdown enhanced MEK inhibition. MEK activated by CRAF was less susceptible to MEK inhibitors than when activated by BRAF(V600E). MEK inhibitors induced RAF-MEK complexes in KRAS mutant models, and disrupting such complexes enhanced inhibition of CRAF-dependent ERK signaling. Newer MEK inhibitors target MEK catalytic activity and also impair its reactivation by CRAF, either by disrupting RAF-MEK complexes or by interacting with Ser 222 to prevent MEK phosphorylation by RAF.
Subject(s)
Drug Resistance, Neoplasm/genetics , MAP Kinase Kinase 1/antagonists & inhibitors , Melanoma/enzymology , Protein Kinase Inhibitors/pharmacology , Proto-Oncogene Proteins/genetics , TNF Receptor-Associated Factor 3/genetics , ras Proteins/genetics , Animals , Benzamides/pharmacology , Cell Line , Coumarins/pharmacology , Diphenylamine/analogs & derivatives , Diphenylamine/pharmacology , Extracellular Signal-Regulated MAP Kinases/antagonists & inhibitors , Extracellular Signal-Regulated MAP Kinases/metabolism , HEK293 Cells , Humans , Indoles/pharmacology , MAP Kinase Kinase 1/chemistry , MAP Kinase Kinase 1/genetics , MAP Kinase Signaling System/drug effects , Melanoma/drug therapy , Melanoma/genetics , Mice , Mice, Nude , Phosphorylation/drug effects , Proto-Oncogene Proteins B-raf/antagonists & inhibitors , Proto-Oncogene Proteins B-raf/genetics , Proto-Oncogene Proteins p21(ras) , Pyridones/pharmacology , Pyrimidinones/pharmacology , RNA Interference , RNA, Small Interfering , Sulfonamides/pharmacology , Surface Plasmon Resonance , TNF Receptor-Associated Factor 3/metabolism , Vemurafenib , raf Kinases/metabolismABSTRACT
Tetracycline or doxycycline (dox)-regulated control of genetic elements allows inducible, reversible and tissue specific regulation of gene expression in mice. This approach provides a means to investigate protein function in specific cell lineages and at defined periods of development and disease. Efficient and stable regulation of cDNAs or non-coding elements (e.g. shRNAs) downstream of the tetracycline-regulated element (TRE) requires the robust expression of a tet-transactivator protein, commonly the reverse tet-transactivator, rtTA. Most rtTA strains rely on tissue specific promoters that often do not provide sufficient rtTA levels for optimal inducible expression. Here we describe the generation of two mouse strains that enable Cre-dependent, robust expression of rtTA3, providing tissue-restricted and consistent induction of TRE-controlled transgenes. We show that these transgenic strains can be effectively combined with established mouse models of disease, including both Cre/LoxP-based approaches and non Cre-dependent disease models. The integration of these new tools with established mouse models promises the development of more flexible genetic systems to uncover the mechanisms of development and disease pathogenesis.
Subject(s)
Gene Expression Regulation/genetics , Models, Genetic , Repressor Proteins , Response Elements , Transgenes , Animals , Mice , Mice, Transgenic , Repressor Proteins/genetics , Repressor Proteins/metabolismABSTRACT
Missense mutations in the p53 tumor suppressor inactivate its antiproliferative properties but can also promote metastasis through a gain-of-function activity. We show that sustained expression of mutant p53 is required to maintain the prometastatic phenotype of a murine model of pancreatic cancer, a highly metastatic disease that frequently displays p53 mutations. Transcriptional profiling and functional screening identified the platelet-derived growth factor receptor b (PDGFRb) as both necessary and sufficient to mediate these effects. Mutant p53 induced PDGFRb through a cell-autonomous mechanism involving inhibition of a p73/NF-Y complex that represses PDGFRb expression in p53-deficient, noninvasive cells. Blocking PDGFRb signaling by RNA interference or by small molecule inhibitors prevented pancreatic cancer cell invasion in vitro and metastasis formation in vivo. Finally, high PDGFRb expression correlates with poor disease-free survival in pancreatic, colon, and ovarian cancer patients, implicating PDGFRb as a prognostic marker and possible target for attenuating metastasis in p53 mutant tumors.
Subject(s)
Carcinoma, Pancreatic Ductal/metabolism , Neoplasm Metastasis , Pancreatic Neoplasms/metabolism , Receptor, Platelet-Derived Growth Factor beta/metabolism , Tumor Suppressor Protein p53/metabolism , Animals , Carcinoma, Pancreatic Ductal/pathology , Disease Models, Animal , Gene Expression Profiling , Humans , Mice , Pancreatic Neoplasms/genetics , Pancreatic Neoplasms/pathology , Tumor Suppressor Protein p53/geneticsABSTRACT
Genetically engineered mouse models (GEMMs) have greatly expanded our knowledge of pancreatic ductal adenocarcinoma (PDAC) and serve as a critical tool to identify and evaluate new treatment strategies. However, the cost and time required to generate conventional pancreatic cancer GEMMs limits their use for investigating novel genetic interactions in tumor development and maintenance. To address this problem, we developed flexible embryonic stem cell (ESC)-based GEMMs that facilitate the rapid generation of genetically defined multiallelic chimeric mice without further strain intercrossing. The ESCs harbor a latent Kras mutant (a nearly ubiquitous feature of pancreatic cancer), a homing cassette, and other genetic elements needed for rapid insertion and conditional expression of tetracycline-controlled transgenes, including fluorescence-coupled shRNAs capable of efficiently silencing gene function by RNAi. This system produces a disease that recapitulates the progression of pancreatic cancer in human patients and enables the study and visualization of the impact of gene perturbation at any stage of pancreas cancer progression. We describe the use of this approach to dissect temporal roles for the tumor suppressor Pten and the oncogene c-Myc in pancreatic cancer development and maintenance.