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1.
Nat Cancer ; 4(7): 984-1000, 2023 07.
Article in English | MEDLINE | ID: mdl-37365326

ABSTRACT

Molecular routes to metastatic dissemination are critical determinants of aggressive cancers. Through in vivo CRISPR-Cas9 genome editing, we generated somatic mosaic genetically engineered models that faithfully recapitulate metastatic renal tumors. Disruption of 9p21 locus is an evolutionary driver to systemic disease through the rapid acquisition of complex karyotypes in cancer cells. Cross-species analysis revealed that recurrent patterns of copy number variations, including 21q loss and dysregulation of the interferon pathway, are major drivers of metastatic potential. In vitro and in vivo genomic engineering, leveraging loss-of-function studies, along with a model of partial trisomy of chromosome 21q, demonstrated a dosage-dependent effect of the interferon receptor genes cluster as an adaptive mechanism to deleterious chromosomal instability in metastatic progression. This work provides critical knowledge on drivers of renal cell carcinoma progression and defines the primary role of interferon signaling in constraining the propagation of aneuploid clones in cancer evolution.


Subject(s)
Carcinoma, Renal Cell , Kidney Neoplasms , Humans , Carcinoma, Renal Cell/genetics , DNA Copy Number Variations/genetics , Chromosomal Instability/genetics , Aneuploidy , Kidney Neoplasms/genetics
2.
Proc Natl Acad Sci U S A ; 120(21): e2209639120, 2023 05 23.
Article in English | MEDLINE | ID: mdl-37186844

ABSTRACT

Renal medullary carcinoma (RMC) is an aggressive kidney cancer that almost exclusively develops in individuals with sickle cell trait (SCT) and is always characterized by loss of the tumor suppressor SMARCB1. Because renal ischemia induced by red blood cell sickling exacerbates chronic renal medullary hypoxia in vivo, we investigated whether the loss of SMARCB1 confers a survival advantage under the setting of SCT. Hypoxic stress, which naturally occurs within the renal medulla, is elevated under the setting of SCT. Our findings showed that hypoxia-induced SMARCB1 degradation protected renal cells from hypoxic stress. SMARCB1 wild-type renal tumors exhibited lower levels of SMARCB1 and more aggressive growth in mice harboring the SCT mutation in human hemoglobin A (HbA) than in control mice harboring wild-type human HbA. Consistent with established clinical observations, SMARCB1-null renal tumors were refractory to hypoxia-inducing therapeutic inhibition of angiogenesis. Further, reconstitution of SMARCB1 restored renal tumor sensitivity to hypoxic stress in vitro and in vivo. Together, our results demonstrate a physiological role for SMARCB1 degradation in response to hypoxic stress, connect the renal medullary hypoxia induced by SCT with an increased risk of SMARCB1-negative RMC, and shed light into the mechanisms mediating the resistance of SMARCB1-null renal tumors against angiogenesis inhibition therapies.


Subject(s)
Carcinoma, Renal Cell , Kidney Neoplasms , Sickle Cell Trait , Animals , Humans , Mice , Carcinoma, Renal Cell/pathology , Hypoxia/genetics , Hypoxia/metabolism , Kidney/metabolism , Kidney Neoplasms/pathology , Sickle Cell Trait/genetics , Sickle Cell Trait/metabolism , SMARCB1 Protein/genetics , SMARCB1 Protein/metabolism
4.
Nature ; 606(7915): 797-803, 2022 06.
Article in English | MEDLINE | ID: mdl-35705814

ABSTRACT

Treatment with therapy targeting BRAF and MEK (BRAF/MEK) has revolutionized care in melanoma and other cancers; however, therapeutic resistance is common and innovative treatment strategies are needed1,2. Here we studied a group of patients with melanoma who were treated with neoadjuvant BRAF/MEK-targeted therapy ( NCT02231775 , n = 51) and observed significantly higher rates of major pathological response (MPR; ≤10% viable tumour at resection) and improved recurrence-free survival (RFS) in female versus male patients (MPR, 66% versus 14%, P = 0.001; RFS, 64% versus 32% at 2 years, P = 0.021). The findings were validated in several additional cohorts2-4 of patients with unresectable metastatic melanoma who were treated with BRAF- and/or MEK-targeted therapy (n = 664 patients in total), demonstrating improved progression-free survival and overall survival in female versus male patients in several of these studies. Studies in preclinical models demonstrated significantly impaired anti-tumour activity in male versus female mice after BRAF/MEK-targeted therapy (P = 0.006), with significantly higher expression of the androgen receptor in tumours of male and female BRAF/MEK-treated mice versus the control (P = 0.0006 and P = 0.0025). Pharmacological inhibition of androgen receptor signalling improved responses to BRAF/MEK-targeted therapy in male and female mice (P = 0.018 and P = 0.003), whereas induction of androgen receptor signalling (through testosterone administration) was associated with a significantly impaired response to BRAF/MEK-targeted therapy in male and female patients (P = 0.021 and P < 0.0001). Together, these results have important implications for therapy.


Subject(s)
Androgen Receptor Antagonists , Melanoma , Mitogen-Activated Protein Kinase Kinases , Molecular Targeted Therapy , Proto-Oncogene Proteins B-raf , Receptors, Androgen , Animals , Antineoplastic Combined Chemotherapy Protocols/adverse effects , Female , Humans , Male , Melanoma/drug therapy , Melanoma/pathology , Mice , Mitogen-Activated Protein Kinase Kinases/antagonists & inhibitors , Protein Kinase Inhibitors/therapeutic use , Proto-Oncogene Proteins B-raf/antagonists & inhibitors , Receptors, Androgen/metabolism , Skin Neoplasms/drug therapy , Skin Neoplasms/pathology , Survival Analysis
5.
Cancers (Basel) ; 13(15)2021 Jul 28.
Article in English | MEDLINE | ID: mdl-34359705

ABSTRACT

Colorectal cancer (CRC) is a heterogeneous disease showing significant variability in clinical aggressiveness. Primary and acquired resistance limits the efficacy of available treatments, and identification of effective drug combinations is needed to further improve patients' outcomes. We previously found that the NEDD8-activating enzyme inhibitor pevonedistat induced tumor stabilization in preclinical models of poorly differentiated, clinically aggressive CRC resistant to available therapies. To identify drugs that can be effectively combined with pevonedistat, we performed a "drop-out" loss-of-function synthetic lethality screening with an shRNA library covering 200 drug-target genes in four different CRC cell lines. Multiple screening hits were found to be involved in the EGFR signaling pathway, suggesting that, rather than inhibition of a specific gene, interference with the EGFR pathway at any level could be effectively leveraged for combination therapies based on pevonedistat. Exploiting both BRAF-mutant and RAS/RAF wild-type CRC models, we validated the therapeutic relevance of our findings by showing that combined blockade of NEDD8 and EGFR pathways led to increased growth arrest and apoptosis both in vitro and in vivo. Pathway modulation analysis showed that compensatory feedback loops induced by single treatments were blunted by the combinations. These results unveil possible therapeutic opportunities in specific CRC clinical settings.

6.
Blood Adv ; 5(16): 3134-3146, 2021 08 24.
Article in English | MEDLINE | ID: mdl-34424317

ABSTRACT

Although ibrutinib improves the overall survival of patients with chronic lymphocytic leukemia (CLL), some patients still develop resistance, most commonly through point mutations affecting cysteine residue 481 (C481) in Bruton's tyrosine kinase (BTKC481S and BTKC481R). To enhance our understanding of the biological impact of these mutations, we established cell lines that overexpress wild-type or mutant BTK in in vitro and in vivo models that mimic ibrutinib-sensitive and -resistant CLL. MEC-1 cell lines stably overexpressing wild-type or mutant BTK were generated. All cell lines coexpressed GFP, were CD19+ and CD23+, and overexpressed BTK. Overexpression of wild-type or mutant BTK resulted in increased signaling, as evidenced by the induction of p-BTK, p-PLCγ2, and p-extracellular signal-related kinase (ERK) levels, the latter further augmented upon IgM stimulation. In all cell lines, cell cycle profiles and levels of BTK expression were similar, but the RNA sequencing and reverse-phase protein array results revealed that the molecular transcript and protein profiles were distinct. To mimic aggressive CLL, we created xenograft mouse models by transplanting the generated cell lines into Rag2-/-γc-/- mice. Spleens, livers, bone marrow, and peripheral blood were collected. All mice developed CLL-like disease with systemic involvement (engraftment efficiency, 100%). We observed splenomegaly, accumulation of leukemic cells in the spleen and liver, and macroscopically evident necrosis. CD19+ cells accumulated in the spleen, bone marrow, and peripheral blood. The overall survival duration was slightly lower in mice expressing mutant BTK. Our cell lines and murine models mimicking ibrutinib-resistant CLL will serve as powerful tools to test reversible BTK inhibitors and novel, non-BTK-targeted therapeutics.


Subject(s)
Leukemia, Lymphocytic, Chronic, B-Cell , Adenine/analogs & derivatives , Agammaglobulinaemia Tyrosine Kinase , Animals , Humans , Leukemia, Lymphocytic, Chronic, B-Cell/drug therapy , Leukemia, Lymphocytic, Chronic, B-Cell/genetics , Mice , Piperidines , Pyrazoles/pharmacology , Pyrimidines/pharmacology
7.
JCI Insight ; 6(17)2021 09 08.
Article in English | MEDLINE | ID: mdl-34309585

ABSTRACT

Lack of sustained response to therapeutic agents in patients with KRAS-mutant lung cancer poses a major challenge and arises partly due to intratumor heterogeneity that defines phenotypically distinct tumor subpopulations. To attain better therapeutic outcomes, it is important to understand the differential therapeutic sensitivities of tumor cell subsets. Epithelial-mesenchymal transition is a biological phenomenon that can alter the state of cells along a phenotypic spectrum and cause transcriptional rewiring to produce distinct tumor cell subpopulations. We utilized functional shRNA screens, in in vitro and in vivo models, to identify and validate an increased dependence of mesenchymal tumor cells on cyclin-dependent kinase 4 (CDK4) for survival, as well as a mechanism of resistance to MEK inhibitors. High zinc finger E-box binding homeobox 1 levels in mesenchymal tumor cells repressed p21, leading to perturbed CDK4 pathway activity. Increased dependence on CDK4 rendered mesenchymal cancer cells particularly vulnerable to selective CDK4 inhibitors. Coadministration of CDK4 and MEK inhibitors in heterogeneous tumors effectively targeted different tumor subpopulations, subverting the resistance to either single-agent treatment.


Subject(s)
Cyclin-Dependent Kinase 4/genetics , Drug Resistance, Neoplasm/genetics , Lung Neoplasms/genetics , Mutation , Organic Cation Transport Proteins/genetics , Proto-Oncogene Proteins p21(ras)/genetics , Animals , Cell Line, Tumor , Cyclin-Dependent Kinase 4/metabolism , DNA, Neoplasm/genetics , Humans , Lung Neoplasms/drug therapy , Lung Neoplasms/metabolism , Lung Neoplasms/pathology , Mice , Mice, Knockout , Neoplasms, Experimental , Organic Cation Transport Proteins/metabolism , Proto-Oncogene Proteins p21(ras)/metabolism
8.
Nat Commun ; 12(1): 4626, 2021 07 30.
Article in English | MEDLINE | ID: mdl-34330913

ABSTRACT

Pancreatic ductal adenocarcinoma (PDAC) is an aggressive cancer that has remained clinically challenging to manage. Here we employ an RNAi-based in vivo functional genomics platform to determine epigenetic vulnerabilities across a panel of patient-derived PDAC models. Through this, we identify protein arginine methyltransferase 1 (PRMT1) as a critical dependency required for PDAC maintenance. Genetic and pharmacological studies validate the role of PRMT1 in maintaining PDAC growth. Mechanistically, using proteomic and transcriptomic analyses, we demonstrate that global inhibition of asymmetric arginine methylation impairs RNA metabolism, which includes RNA splicing, alternative polyadenylation, and transcription termination. This triggers a robust downregulation of multiple pathways involved in the DNA damage response, thereby promoting genomic instability and inhibiting tumor growth. Taken together, our data support PRMT1 as a compelling target in PDAC and informs a mechanism-based translational strategy for future therapeutic development.Statement of significancePDAC is a highly lethal cancer with limited therapeutic options. This study identified and characterized PRMT1-dependent regulation of RNA metabolism and coordination of key cellular processes required for PDAC tumor growth, defining a mechanism-based translational hypothesis for PRMT1 inhibitors.


Subject(s)
Carcinoma, Pancreatic Ductal/genetics , DNA Damage , Pancreatic Neoplasms/genetics , Protein-Arginine N-Methyltransferases/genetics , RNA/genetics , Repressor Proteins/genetics , Animals , Biocatalysis/drug effects , Carcinoma, Pancreatic Ductal/metabolism , Carcinoma, Pancreatic Ductal/prevention & control , Cell Line, Tumor , Cell Proliferation/drug effects , Cell Proliferation/genetics , Enzyme Inhibitors/pharmacology , Female , Humans , Mice, Inbred NOD , Mice, Knockout , Mice, SCID , Pancreatic Neoplasms/metabolism , Pancreatic Neoplasms/prevention & control , Protein-Arginine N-Methyltransferases/metabolism , RNA/metabolism , RNA Interference , Repressor Proteins/metabolism , Tumor Burden/drug effects , Xenograft Model Antitumor Assays/methods
9.
Oncogene ; 40(26): 4425-4439, 2021 07.
Article in English | MEDLINE | ID: mdl-34108622

ABSTRACT

Molecular alterations in the PI3K/AKT pathway occur frequently in hormone receptor-positive breast tumors. Patients with ER-positive, HER2-negative metastatic breast cancer are often treated with CDK4/6 inhibitors such as palbociclib in combination with endocrine therapy. Although this is an effective regimen, most patients ultimately progress. The purpose of this study was identifying synthetic lethality partners that can enhance palbociclib's antitumor efficacy in the presence of PIK3CA/AKT1 mutations. We utilized a barcoded shRNA library to determine critical targets for survival in isogenic MCF7 cells with PIK3CA/AKT1 mutations. We demonstrated that the efficacy of palbociclib is reduced in the presence of PIK3CA/AKT1 mutations. We also identified that the downregulation of discoidin domain receptor 1 (DDR1) is synthetically lethal with palbociclib. DDR1 knockdown and DDR1 pharmacological inhibitor decreased cell growth and inhibited cell cycle progression in all cell lines, while enhanced the sensitivity of PIK3CA/AKT1 mutant cells to palbociclib. Combined treatment of palbociclib and 7rh further induced cell cycle arrest in PIK3CA/AKT1 mutant cell lines. In vivo, 7rh significantly enhanced palbociclib's antitumor efficacy. Our data indicates that DDR1 inhibition can augment cell cycle suppressive effect of palbociclib and could be effective strategy for targeted therapy of ER-positive, HER2-negative breast cancers with PI3K pathway activation.


Subject(s)
Breast Neoplasms/genetics , Class I Phosphatidylinositol 3-Kinases/genetics , Cyclin-Dependent Kinases/antagonists & inhibitors , Discoidin Domain Receptor 1/antagonists & inhibitors , Proto-Oncogene Proteins c-akt/genetics , Receptor, ErbB-2/genetics , Receptors, Estrogen/genetics , Animals , Antineoplastic Combined Chemotherapy Protocols/pharmacology , Breast Neoplasms/drug therapy , Cell Cycle Checkpoints/drug effects , Cell Cycle Checkpoints/genetics , Cell Line, Tumor , Cell Proliferation/drug effects , Cell Proliferation/genetics , Female , Humans , MCF-7 Cells , Mutation/genetics , Protein Kinase Inhibitors/pharmacology , Signal Transduction/drug effects , Signal Transduction/genetics
10.
Gastroenterology ; 161(1): 196-210, 2021 07.
Article in English | MEDLINE | ID: mdl-33745946

ABSTRACT

BACKGROUND & AIMS: Understanding the mechanisms by which tumors adapt to therapy is critical for developing effective combination therapeutic approaches to improve clinical outcomes for patients with cancer. METHODS: To identify promising and clinically actionable targets for managing colorectal cancer (CRC), we conducted a patient-centered functional genomics platform that includes approximately 200 genes and paired this with a high-throughput drug screen that includes 262 compounds in four patient-derived xenografts (PDXs) from patients with CRC. RESULTS: Both screening methods identified exportin 1 (XPO1) inhibitors as drivers of DNA damage-induced lethality in CRC. Molecular characterization of the cellular response to XPO1 inhibition uncovered an adaptive mechanism that limited the duration of response in TP53-mutated, but not in TP53-wild-type CRC models. Comprehensive proteomic and transcriptomic characterization revealed that the ATM/ATR-CHK1/2 axes were selectively engaged in TP53-mutant CRC cells upon XPO1 inhibitor treatment and that this response was required for adapting to therapy and escaping cell death. Administration of KPT-8602, an XPO1 inhibitor, followed by AZD-6738, an ATR inhibitor, resulted in dramatic antitumor effects and prolonged survival in TP53-mutant models of CRC. CONCLUSIONS: Our findings anticipate tremendous therapeutic benefit and support the further evaluation of XPO1 inhibitors, especially in combination with DNA damage checkpoint inhibitors, to elicit an enduring clinical response in patients with CRC harboring TP53 mutations.


Subject(s)
Antineoplastic Combined Chemotherapy Protocols/administration & dosage , Ataxia Telangiectasia Mutated Proteins/antagonists & inhibitors , Biomarkers, Tumor/genetics , Colorectal Neoplasms/drug therapy , Karyopherins/antagonists & inhibitors , Mutation , Protein Kinase Inhibitors/administration & dosage , Receptors, Cytoplasmic and Nuclear/antagonists & inhibitors , Tumor Suppressor Protein p53/genetics , Animals , Ataxia Telangiectasia Mutated Proteins/metabolism , Colorectal Neoplasms/genetics , Colorectal Neoplasms/metabolism , Colorectal Neoplasms/pathology , Databases, Genetic , HCT116 Cells , HT29 Cells , Humans , Indoles/administration & dosage , Karyopherins/metabolism , Mice , Morpholines/administration & dosage , Piperazines/administration & dosage , Pyridines/administration & dosage , Pyrimidines/administration & dosage , Receptors, Cytoplasmic and Nuclear/metabolism , Sulfonamides/administration & dosage , Xenograft Model Antitumor Assays , Exportin 1 Protein
11.
Cancer Res ; 80(21): 4840-4853, 2020 11 01.
Article in English | MEDLINE | ID: mdl-32928921

ABSTRACT

Src homology 2 domain-containing phosphatase (SHP2) is a phosphatase that mediates signaling downstream of multiple receptor tyrosine kinases (RTK) and is required for full activation of the MAPK pathway. SHP2 inhibition has demonstrated tumor growth inhibition in RTK-activated cancers in preclinical studies. The long-term effectiveness of tyrosine kinase inhibitors such as the EGFR inhibitor (EGFRi), osimertinib, in non-small cell lung cancer (NSCLC) is limited by acquired resistance. Multiple clinically identified mechanisms underlie resistance to osimertinib, including mutations in EGFR that preclude drug binding as well as EGFR-independent activation of the MAPK pathway through alternate RTK (RTK-bypass). It has also been noted that frequently a tumor from a single patient harbors more than one resistance mechanism, and the plasticity between multiple resistance mechanisms could restrict the effectiveness of therapies targeting a single node of the oncogenic signaling network. Here, we report the discovery of IACS-13909, a specific and potent allosteric inhibitor of SHP2, that suppresses signaling through the MAPK pathway. IACS-13909 potently impeded proliferation of tumors harboring a broad spectrum of activated RTKs as the oncogenic driver. In EGFR-mutant osimertinib-resistant NSCLC models with EGFR-dependent and EGFR-independent resistance mechanisms, IACS-13909, administered as a single agent or in combination with osimertinib, potently suppressed tumor cell proliferation in vitro and caused tumor regression in vivo. Together, our findings provide preclinical evidence for using a SHP2 inhibitor as a therapeutic strategy in acquired EGFRi-resistant NSCLC. SIGNIFICANCE: These findings highlight the discovery of IACS-13909 as a potent, selective inhibitor of SHP2 with drug-like properties, and targeting SHP2 may serve as a therapeutic strategy to overcome tumor resistance to osimertinib.


Subject(s)
Antineoplastic Agents/pharmacology , Drug Resistance, Neoplasm/drug effects , Neoplasms, Experimental/pathology , Protein Tyrosine Phosphatase, Non-Receptor Type 11/antagonists & inhibitors , Acrylamides/pharmacology , Aniline Compounds/pharmacology , Animals , Carcinoma, Non-Small-Cell Lung/genetics , Carcinoma, Non-Small-Cell Lung/pathology , Cell Line, Tumor , Cell Proliferation/drug effects , ErbB Receptors/genetics , Humans , Lung Neoplasms/genetics , Lung Neoplasms/pathology , Mice , Mutation , Neoplasms, Experimental/genetics , Xenograft Model Antitumor Assays
12.
Nat Commun ; 10(1): 5125, 2019 11 12.
Article in English | MEDLINE | ID: mdl-31719531

ABSTRACT

Non-small cell lung cancer (NSCLC) is the leading cause of cancer-related death worldwide, due in part to the propensity of lung cancer to metastasize. Aberrant epithelial-to-mesenchymal transition (EMT) is a proposed model for the initiation of metastasis. During EMT cell-cell adhesion is reduced allowing cells to dissociate and invade. Of the EMT-associated transcription factors, ZEB1 uniquely promotes NSCLC disease progression. Here we apply two independent screens, BioID and an Epigenome shRNA dropout screen, to define ZEB1 interactors that are critical to metastatic NSCLC. We identify the NuRD complex as a ZEB1 co-repressor and the Rab22 GTPase-activating protein TBC1D2b as a ZEB1/NuRD complex target. We find that TBC1D2b suppresses E-cadherin internalization, thus hindering cancer cell invasion and metastasis.


Subject(s)
Cadherins/metabolism , Endocytosis , GTPase-Activating Proteins/metabolism , Lung Neoplasms/metabolism , Lung Neoplasms/pathology , Mi-2 Nucleosome Remodeling and Deacetylase Complex/metabolism , Zinc Finger E-box-Binding Homeobox 1/metabolism , Animals , Carcinoma, Non-Small-Cell Lung/metabolism , Carcinoma, Non-Small-Cell Lung/pathology , Cell Line, Tumor , Co-Repressor Proteins/metabolism , Humans , Mice , Models, Biological , Neoplasm Metastasis , Protein Binding , rab GTP-Binding Proteins/metabolism
13.
Cancers (Basel) ; 11(4)2019 Apr 02.
Article in English | MEDLINE | ID: mdl-30986992

ABSTRACT

The implementation of cancer immunotherapeutics for solid tumors including lung cancers has improved clinical outcomes in a small percentage of patients. However, the majority of patients show little to no response or acquire resistance during treatment with checkpoint inhibitors delivered as a monotherapy. Therefore, identifying resistance mechanisms and novel combination therapy approaches is imperative to improve responses to immune checkpoint inhibitors. To address this, we performed an in vivo shRNA dropout screen that focused on genes encoding for FDA-approved drug targets (FDAome). We implanted epithelial and mesenchymal Kras/p53 (KP) mutant murine lung cancer cells expressing the FDAome shRNA library into syngeneic mice treated with an anti-PD-1 antibody. Sequencing for the barcoded shRNAs revealed Ntrk1 was significantly depleted from mesenchymal tumors challenged with PD-1 blockade, suggesting it provides a survival advantage to tumor cells when under immune system pressure. Our data confirmed Ntrk1 transcript levels are upregulated in tumors treated with PD-1 inhibitors. Additionally, analysis of tumor-infiltrating T cell populations revealed that Ntrk1 can promote CD8+ T cell exhaustion. Lastly, we found that Ntrk1 regulates Jak/Stat signaling to promote expression of PD-L1 on tumor cells. Together, these data suggest that Ntrk1 activates Jak/Stat signaling to regulate expression of immunosuppressive molecules including PD-L1, promoting exhaustion within the tumor microenvironment.

14.
Sci Transl Med ; 11(488)2019 04 17.
Article in English | MEDLINE | ID: mdl-30996079

ABSTRACT

Eradicating triple-negative breast cancer (TNBC) resistant to neoadjuvant chemotherapy (NACT) is a critical unmet clinical need. In this study, patient-derived xenograft (PDX) models of treatment-naïve TNBC and serial biopsies from TNBC patients undergoing NACT were used to elucidate mechanisms of chemoresistance in the neoadjuvant setting. Barcode-mediated clonal tracking and genomic sequencing of PDX tumors revealed that residual tumors remaining after treatment with standard frontline chemotherapies, doxorubicin (Adriamycin) combined with cyclophosphamide (AC), maintained the subclonal architecture of untreated tumors, yet their transcriptomes, proteomes, and histologic features were distinct from those of untreated tumors. Once treatment was halted, residual tumors gave rise to AC-sensitive tumors with similar transcriptomes, proteomes, and histological features to those of untreated tumors. Together, these results demonstrated that tumors can adopt a reversible drug-tolerant state that does not involve clonal selection as an AC resistance mechanism. Serial biopsies obtained from patients with TNBC undergoing NACT revealed similar histologic changes and maintenance of stable subclonal architecture, demonstrating that AC-treated PDXs capture molecular features characteristic of human TNBC chemoresistance. Last, pharmacologic inhibition of oxidative phosphorylation using an inhibitor currently in phase 1 clinical development delayed residual tumor regrowth. Thus, AC resistance in treatment-naïve TNBC can be mediated by nonselective mechanisms that confer a reversible chemotherapy-tolerant state with targetable vulnerabilities.


Subject(s)
Doxorubicin/therapeutic use , Triple Negative Breast Neoplasms/drug therapy , Animals , Cell Line, Tumor , Cyclophosphamide/therapeutic use , Drug Resistance, Neoplasm/genetics , Female , Humans , Mice, SCID , Neoadjuvant Therapy , Transcriptome/genetics , Xenograft Model Antitumor Assays
15.
Sci Transl Med ; 11(483)2019 03 13.
Article in English | MEDLINE | ID: mdl-30867319

ABSTRACT

Mitogen-activated protein kinase (MAPK) kinase (MEK) inhibitors have failed to show clinical benefit in Kirsten rat sarcoma (KRAS) mutant lung cancer due to various resistance mechanisms. To identify differential therapeutic sensitivities between epithelial and mesenchymal lung tumors, we performed in vivo small hairpin RNA screens, proteomic profiling, and analysis of patient tumor datasets, which revealed an inverse correlation between mitogen-activated protein kinase (MAPK) signaling dependency and a zinc finger E-box binding homeobox 1 (ZEB1)-regulated epithelial-to-mesenchymal transition. Mechanistic studies determined that MAPK signaling dependency in epithelial lung cancer cells is due to the scaffold protein interleukin-17 receptor D (IL17RD), which is directly repressed by ZEB1. Lung tumors in multiple Kras mutant murine models with increased ZEB1 displayed low IL17RD expression, accompanied by MAPK-independent tumor growth and therapeutic resistance to MEK inhibition. Suppression of ZEB1 function with miR-200 expression or the histone deacetylase inhibitor mocetinostat sensitized resistant cancer cells to MEK inhibition and markedly reduced in vivo tumor growth, showing a promising combinatorial treatment strategy for KRAS mutant cancers. In human lung tumor samples, high ZEB1 and low IL17RD expression correlated with low MAPK signaling, presenting potential markers that predict patient response to MEK inhibitors.


Subject(s)
Mitogen-Activated Protein Kinase Kinases/antagonists & inhibitors , Mutation/genetics , Neoplasms/genetics , Protein Kinase Inhibitors/therapeutic use , Proto-Oncogene Proteins p21(ras)/genetics , Receptors, Interleukin-17/metabolism , Zinc Finger E-box-Binding Homeobox 1/metabolism , Animals , Benzamides/pharmacology , Benzamides/therapeutic use , Cell Line, Tumor , Cell Proliferation , Disease Models, Animal , Drug Resistance, Neoplasm , Epithelial Cells/pathology , Humans , Lung Neoplasms/drug therapy , Lung Neoplasms/pathology , MAP Kinase Signaling System , Mesoderm/pathology , Mice , MicroRNAs/genetics , MicroRNAs/metabolism , Mitogen-Activated Protein Kinase Kinases/metabolism , Neoplasms/drug therapy , Phosphorylation/drug effects , Protein Kinase Inhibitors/pharmacology , Proto-Oncogene Proteins p21(ras)/metabolism , Pyrimidines/pharmacology , Pyrimidines/therapeutic use
16.
Cell Rep ; 26(6): 1518-1532.e9, 2019 02 05.
Article in English | MEDLINE | ID: mdl-30726735

ABSTRACT

Adaptive drug-resistance mechanisms allow human tumors to evade treatment through selection and expansion of treatment-resistant clones. Here, studying clonal evolution of tumor cells derived from human pancreatic tumors, we demonstrate that in vitro cultures and in vivo tumors are maintained by a common set of tumorigenic cells that can be used to establish clonal replica tumors (CRTs), large cohorts of animals bearing human tumors with identical clonal composition. Using CRTs to conduct quantitative assessments of adaptive responses to therapeutics, we uncovered a multitude of functionally heterogeneous subpopulations of cells with differential degrees of drug sensitivity. High-throughput isolation and deep characterization of unique clonal lineages showed genetic and transcriptomic diversity underlying functionally diverse subpopulations. Molecular annotation of gemcitabine-naive clonal lineages with distinct responses to treatment in the context of CRTs generated signatures that can predict the response to chemotherapy, representing a potential biomarker to stratify patients with pancreatic cancer.


Subject(s)
Drug Resistance, Neoplasm , Genetic Heterogeneity , Pancreatic Neoplasms/genetics , Transcriptome , Aged , Animals , Antimetabolites, Antineoplastic/pharmacology , Cells, Cultured , Clonal Evolution , Deoxycytidine/analogs & derivatives , Deoxycytidine/pharmacology , Humans , Male , Mice , Middle Aged , Neoplastic Stem Cells/drug effects , Neoplastic Stem Cells/metabolism , Pancreatic Neoplasms/pathology , Gemcitabine
17.
Cell Rep ; 26(2): 469-482.e5, 2019 01 08.
Article in English | MEDLINE | ID: mdl-30625329

ABSTRACT

The plasticity of a preexisting regulatory circuit compromises the effectiveness of targeted therapies, and leveraging genetic vulnerabilities in cancer cells may overcome such adaptations. Hereditary leiomyomatosis renal cell carcinoma (HLRCC) is characterized by oxidative phosphorylation (OXPHOS) deficiency caused by fumarate hydratase (FH) nullizyogosity. To identify metabolic genes that are synthetically lethal with OXPHOS deficiency, we conducted a genetic loss-of-function screen and found that phosphogluconate dehydrogenase (PGD) inhibition robustly blocks the proliferation of FH mutant cancer cells both in vitro and in vivo. Mechanistically, PGD inhibition blocks glycolysis, suppresses reductive carboxylation of glutamine, and increases the NADP+/NADPH ratio to disrupt redox homeostasis. Furthermore, in the OXPHOS-proficient context, blocking OXPHOS using the small-molecule inhibitor IACS-010759 enhances sensitivity to PGD inhibition in vitro and in vivo. Together, our study reveals a dependency on PGD in OXPHOS-deficient tumors that might inform therapeutic intervention in specific patient populations.


Subject(s)
Oxidative Phosphorylation , Phosphogluconate Dehydrogenase/genetics , Synthetic Lethal Mutations , Animals , Cell Line, Tumor , Female , Fumarate Hydratase/genetics , Genomics/methods , Glycolysis , Humans , Loss of Function Mutation , Mice , Mice, Nude
18.
Nat Commun ; 9(1): 5079, 2018 11 29.
Article in English | MEDLINE | ID: mdl-30498242

ABSTRACT

Most triple negative breast cancers (TNBCs) are aggressively metastatic with a high degree of intra-tumoral heterogeneity (ITH), but how ITH contributes to metastasis is unclear. Here, clonal dynamics during metastasis were studied in vivo using two patient-derived xenograft (PDX) models established from the treatment-naive primary breast tumors of TNBC patients diagnosed with synchronous metastasis. Genomic sequencing and high-complexity barcode-mediated clonal tracking reveal robust alterations in clonal architecture between primary tumors and corresponding metastases. Polyclonal seeding and maintenance of heterogeneous populations of low-abundance subclones is observed in each metastasis. However, lung, liver, and brain metastases are enriched for an identical population of high-abundance subclones, demonstrating that primary tumor clones harbor properties enabling them to seed and thrive in multiple organ sites. Further, clones that dominate multi-organ metastases share a genomic lineage. Thus, intrinsic properties of rare primary tumor subclones enable the seeding and colonization of metastases in secondary organs in these models.


Subject(s)
Neoplasm Metastasis/genetics , Triple Negative Breast Neoplasms/complications , Triple Negative Breast Neoplasms/genetics , Animals , Brain Neoplasms/genetics , Brain Neoplasms/secondary , Disease Models, Animal , Female , Humans , Liver Neoplasms/genetics , Liver Neoplasms/secondary , Lung Neoplasms/genetics , Lung Neoplasms/secondary , Mice , Mice, SCID , Neoplasm Metastasis/pathology , Xenograft Model Antitumor Assays
19.
Nat Med ; 24(7): 1036-1046, 2018 07.
Article in English | MEDLINE | ID: mdl-29892070

ABSTRACT

Metabolic reprograming is an emerging hallmark of tumor biology and an actively pursued opportunity in discovery of oncology drugs. Extensive efforts have focused on therapeutic targeting of glycolysis, whereas drugging mitochondrial oxidative phosphorylation (OXPHOS) has remained largely unexplored, partly owing to an incomplete understanding of tumor contexts in which OXPHOS is essential. Here, we report the discovery of IACS-010759, a clinical-grade small-molecule inhibitor of complex I of the mitochondrial electron transport chain. Treatment with IACS-010759 robustly inhibited proliferation and induced apoptosis in models of brain cancer and acute myeloid leukemia (AML) reliant on OXPHOS, likely owing to a combination of energy depletion and reduced aspartate production that leads to impaired nucleotide biosynthesis. In models of brain cancer and AML, tumor growth was potently inhibited in vivo following IACS-010759 treatment at well-tolerated doses. IACS-010759 is currently being evaluated in phase 1 clinical trials in relapsed/refractory AML and solid tumors.


Subject(s)
Neoplasms/pathology , Oxidative Phosphorylation , Animals , Biomarkers, Tumor/metabolism , Cell Line, Tumor , Energy Metabolism , Glycolysis/drug effects , HEK293 Cells , Humans , Lactic Acid/metabolism , Leukemia, Myeloid, Acute/pathology , Mice , Mitochondria/metabolism , Nucleotides/biosynthesis , Tumor Burden , Xenograft Model Antitumor Assays
20.
NPJ Breast Cancer ; 4: 9, 2018.
Article in English | MEDLINE | ID: mdl-29736411

ABSTRACT

Tumor cells disseminate early in tumor development making metastasis-prevention strategies difficult. Identifying proteins that promote the outgrowth of disseminated tumor cells may provide opportunities for novel therapeutic strategies. Despite multiple studies demonstrating that the mesenchymal-to-epithelial transition (MET) is critical for metastatic colonization, key regulators that initiate this transition remain unknown. We serially passaged lung metastases from a primary triple negative breast cancer xenograft to the mammary fat pads of recipient mice to enrich for gene expression changes that drive metastasis. An unbiased transcriptomic signature of potential metastatic drivers was generated, and a high throughput gain-of-function screen was performed in vivo to validate candidates. Carcinoembryonic antigen-related cell adhesion molecule 5 (CEACAM5) was identified as a metastatic driver. CEACAM5 overproduction enriched for an epithelial gene expression pattern and facilitated tumor outgrowth at metastatic sites. Tissues from patients with metastatic breast cancer confirmed elevated levels of CEACAM5 in lung metastases relative to breast tumors, and an inverse correlation between CEACAM5 and the mesenchymal marker vimentin was demonstrated. Thus, CEACAM5 facilitates tumor outgrowth at metastatic sites by promoting MET, warranting its investigation as a therapeutic target and biomarker of aggressiveness in breast cancer.

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