RESUMEN
Focal amplifications (FA) can mediate targeted therapy resistance in cancer. Understanding the structure and dynamics of FAs is critical for designing treatments that overcome plasticity-mediated resistance. We developed a melanoma model of dual MAPK inhibitor (MAPKi) resistance that bears BRAFV600 amplifications through either extrachromosomal DNA (ecDNA)/double minutes (DM) or intrachromosomal homogenously staining regions (HSR). Cells harboring BRAFV600E FAs displayed mode switching between DMs and HSRs, from both de novo genetic changes and selection of preexisting subpopulations. Plasticity is not exclusive to ecDNAs, as cells harboring HSRs exhibit drug addiction-driven structural loss of BRAF amplicons upon dose reduction. FA mechanisms can couple with kinase domain duplications and alternative splicing to enhance resistance. Drug-responsive amplicon plasticity is observed in the clinic and can involve other MAPK pathway genes, such as RAF1 and NRAS. BRAF FA-mediated dual MAPKi-resistant cells are more sensitive to proferroptotic drugs, extending the spectrum of ferroptosis sensitivity in MAPKi resistance beyond cases of dedifferentiation. SIGNIFICANCE: Understanding the structure and dynamics of oncogene amplifications is critical for overcoming tumor relapse. BRAF amplifications are highly plastic under MAPKi dosage challenges in melanoma, through involvement of de novo genomic alterations, even in the HSR mode. Moreover, BRAF FA-driven, dual MAPKi-resistant cells extend the spectrum of resistance-linked ferroptosis sensitivity. This article is highlighted in the In This Issue feature, p. 873.
Asunto(s)
Melanoma , Proteínas Proto-Oncogénicas B-raf , Línea Celular Tumoral , Resistencia a Antineoplásicos , Humanos , Melanoma/tratamiento farmacológico , Melanoma/genética , Melanoma/patología , Mutación , Recurrencia Local de Neoplasia/tratamiento farmacológico , Oncogenes , Inhibidores de Proteínas Quinasas/farmacología , Inhibidores de Proteínas Quinasas/uso terapéutico , Proteínas Proto-Oncogénicas B-raf/genética , Proteínas Proto-Oncogénicas B-raf/metabolismoRESUMEN
The importance of innate immunity in cancer is increasingly being recognized with recent reports suggesting tumor cell-intrinsic intracellular functions for innate immunity proteins. However, such functions are often poorly understood, and it is unclear whether these are affected by patient-specific mutations. Here, we show that C4b-binding protein alpha chain (C4BPA), typically thought to reside in the extracellular space, is expressed intracellularly in cancer cells, where it interacts with the NF-κB family member RelA and regulates apoptosis. Interestingly, intracellular C4BPA expression is regulated in a stress- and mutation-dependent manner and C4BPA mutations are associated with improved cancer survival outcome. Using cell lines harboring patient-specific C4BPA mutations, we show that increasing intracellular C4BPA levels correlate with sensitivity to oxaliplatin-induced apoptosis in vitro and in vivo. Mechanistically, sensitive C4BPA mutants display increased IκBα expression and increased inhibitory IκBα-RelA complex stability. These data suggest a non-canonical intracellular role for C4BPA in regulating NF-κB-dependent apoptosis.
RESUMEN
Small cell carcinoma of the bladder (SCCB) is a rare and lethal phenotype of bladder cancer. The pathogenesis and molecular features are unknown. Here, we established a genetically engineered SCCB model and a cohort of patient SCCB and urothelial carcinoma samples to characterize molecular similarities and differences between bladder cancer phenotypes. We demonstrate that SCCB shares a urothelial origin with other bladder cancer phenotypes by showing that urothelial cells driven by a set of defined oncogenic factors give rise to a mixture of tumor phenotypes, including small cell carcinoma, urothelial carcinoma, and squamous cell carcinoma. Tumor-derived single-cell clones also give rise to both SCCB and urothelial carcinoma in xenografts. Despite this shared urothelial origin, clinical SCCB samples have a distinct transcriptional profile and a unique transcriptional regulatory network. Using the transcriptional profile from our cohort, we identified cell surface proteins (CSPs) associated with the SCCB phenotype. We found that the majority of SCCB samples have PD-L1 expression in both tumor cells and tumor-infiltrating lymphocytes, suggesting that immune checkpoint inhibitors could be a treatment option for SCCB. We further demonstrate that our genetically engineered tumor model is a representative tool for investigating CSPs in SCCB by showing that it shares a similar a CSP profile with clinical samples and expresses SCCB-up-regulated CSPs at both the mRNA and protein levels. Our findings reveal distinct molecular features of SCCB and provide a transcriptional dataset and a preclinical model for further investigating SCCB biology.
Asunto(s)
Carcinoma de Células Pequeñas/patología , Carcinoma de Células Transicionales/patología , Transformación Celular Neoplásica/genética , Neoplasias de la Vejiga Urinaria/patología , Vejiga Urinaria/patología , Urotelio/patología , Animales , Antineoplásicos Inmunológicos/farmacología , Antineoplásicos Inmunológicos/uso terapéutico , Antígeno B7-H1/antagonistas & inhibidores , Antígeno B7-H1/metabolismo , Carcinoma de Células Pequeñas/genética , Carcinoma de Células Pequeñas/terapia , Carcinoma de Células Transicionales/genética , Carcinoma de Células Transicionales/terapia , Transformación Celular Neoplásica/efectos de los fármacos , Células Cultivadas , Cistectomía , Conjuntos de Datos como Asunto , Células Epiteliales , Regulación Neoplásica de la Expresión Génica , Ingeniería Genética , Humanos , Linfocitos Infiltrantes de Tumor/metabolismo , Ratones , Cultivo Primario de Células , RNA-Seq , Vejiga Urinaria/citología , Vejiga Urinaria/cirugía , Neoplasias de la Vejiga Urinaria/genética , Neoplasias de la Vejiga Urinaria/terapia , Urotelio/citología , Ensayos Antitumor por Modelo de XenoinjertoRESUMEN
Aneuploidy, defined as abnormal chromosome number or somatic DNA copy number, is a characteristic of many aggressive tumors and is thought to drive tumorigenesis. Gene expression-aneuploidy association studies have previously been conducted to explore cellular mechanisms associated with aneuploidy. However, in an observational setting, gene expression is influenced by many factors that can act as confounders between gene expression and aneuploidy, leading to spurious correlations between the two variables. These factors include known confounders such as sample purity or batch effect, as well as gene co-regulation which induces correlations between the expression of causal genes and non-causal genes. We use a linear mixed-effects model (LMM) to account for confounding effects of tumor purity and gene co-regulation on gene expression-aneuploidy associations. When applied to patient tumor data across diverse tumor types, we observe that the LMM both accounts for the impact of purity on aneuploidy measurements and identifies a new association between histone gene expression and aneuploidy.
Asunto(s)
Aneuploidia , Regulación Neoplásica de la Expresión Génica , Histonas/genética , Proteínas de Neoplasias/genética , Neoplasias/diagnóstico , Neoplasias/genética , Carcinogénesis/genética , Carcinogénesis/metabolismo , Carcinogénesis/patología , Variaciones en el Número de Copia de ADN , Conjuntos de Datos como Asunto , Estudio de Asociación del Genoma Completo , Inestabilidad Genómica , Histonas/metabolismo , Humanos , Modelos Lineales , Proteínas de Neoplasias/metabolismo , Neoplasias/metabolismo , Neoplasias/patologíaRESUMEN
Small-cell neuroendocrine cancers (SCNCs) are an aggressive cancer subtype. Transdifferentiation toward an SCN phenotype has been reported as a resistance route in response to targeted therapies. Here, we identified a convergence to an SCN state that is widespread across epithelial cancers and is associated with poor prognosis. More broadly, non-SCN metastases have higher expression of SCN-associated transcription factors than non-SCN primary tumors. Drug sensitivity and gene dependency screens demonstrate that these convergent SCNCs have shared vulnerabilities. These common vulnerabilities are found across unannotated SCN-like epithelial cases, small-round-blue cell tumors, and unexpectedly in hematological malignancies. The SCN convergent phenotype and common sensitivity profiles with hematological cancers can guide treatment options beyond tissue-specific targeted therapies.
Asunto(s)
Carcinoma de Células Pequeñas/diagnóstico , Carcinoma de Células Pequeñas/etiología , Neoplasias Hematológicas/diagnóstico , Neoplasias Hematológicas/etiología , Tumores Neuroendocrinos/diagnóstico , Tumores Neuroendocrinos/etiología , Fenotipo , Carcinoma de Células Pequeñas/tratamiento farmacológico , Biología Computacional/métodos , Variaciones en el Número de Copia de ADN , Susceptibilidad a Enfermedades , Resistencia a Antineoplásicos/genética , Perfilación de la Expresión Génica , Regulación Neoplásica de la Expresión Génica , Neoplasias Hematológicas/tratamiento farmacológico , Humanos , Mutación , Tumores Neuroendocrinos/tratamiento farmacológico , TranscriptomaRESUMEN
Complement-mediated cytotoxicity may act as a selective pressure for tumor overexpression of complement regulators. We hypothesize that the same selective pressure could lead to complement alterations at the genetic level. We find that, when analyzed as a pathway, mutations in complement genes occur at a relatively high frequency and are associated with changes in overall survival across a number of cancer types. Analysis of pathways expressed in patients with complement mutations that are associated with poor overall survival reveals crosstalk between complement and hypoxia in colorectal cancer. The importance of this crosstalk is highlighted by two key findings: hypoxic signaling is increased in tumors harboring complement mutations, and hypoxic tumor cells are resistant to complement-mediated cytotoxicity due, in part, to hypoxia-induced expression of complement regulator CD55. The range of strategies employed by tumors to dysregulate the complement system testifies to the importance of this pathway in tumor progression.
Asunto(s)
Neoplasias Colorrectales/genética , Neoplasias Colorrectales/inmunología , Inmunidad Innata/genética , Mutación/genética , Transducción de Señal , Hipoxia Tumoral/genética , Adulto , Animales , Antígenos de Neoplasias/metabolismo , Neoplasias Colorrectales/patología , Proteínas del Sistema Complemento/genética , Citotoxicidad Inmunológica/genética , Células HCT116 , Humanos , Masculino , Ratones , Análisis de SupervivenciaRESUMEN
The use of potent therapies inhibiting critical oncogenic pathways active in epithelial cancers has led to multiple resistance mechanisms, including the development of highly aggressive, small cell neuroendocrine carcinoma (SCNC). SCNC patients have a dismal prognosis due in part to a limited understanding of the molecular mechanisms driving this malignancy and the lack of effective treatments. Here, we demonstrate that a common set of defined oncogenic drivers reproducibly reprograms normal human prostate and lung epithelial cells to small cell prostate cancer (SCPC) and small cell lung cancer (SCLC), respectively. We identify shared active transcription factor binding regions in the reprogrammed prostate and lung SCNCs by integrative analyses of epigenetic and transcriptional landscapes. These results suggest that neuroendocrine cancers arising from distinct epithelial tissues may share common vulnerabilities that could be exploited for the development of drugs targeting SCNCs.
Asunto(s)
Carcinogénesis/genética , Carcinoma Neuroendocrino/patología , Reprogramación Celular/genética , Neoplasias Pulmonares/patología , Pulmón/patología , Próstata/patología , Neoplasias de la Próstata/patología , Carcinoma Pulmonar de Células Pequeñas/patología , Carcinoma Neuroendocrino/genética , Línea Celular Tumoral , Linaje de la Célula , Técnicas de Reprogramación Celular , Sistemas de Liberación de Medicamentos , Células Epiteliales/patología , Epitelio/patología , Humanos , Masculino , Neoplasias de la Próstata/genética , Proteína de Retinoblastoma/genética , Carcinoma Pulmonar de Células Pequeñas/genética , Proteína p53 Supresora de Tumor/genéticaRESUMEN
Cancer progression to an aggressive phenotype often co-opts aspects of stem cell biology. Here, we developed gene signatures for normal human stem cell populations to understand the relationship between epithelial cancers and stem cell transcriptional programs. Using a pan-cancer approach, we reveal that aggressive epithelial cancers are enriched for a transcriptional signature shared by epithelial adult stem cells. The adult stem cell signature selected for epithelial cancers with worse overall survival and alterations of oncogenic drivers. Lethal small cell neuroendocrine lung, prostate, and bladder cancers transcriptionally converged onto the adult stem cell signature and not other stem cell signatures tested. We found that DNA methyltransferase expression correlated with adult stem cell signature status and was enriched in small cell neuroendocrine cancers. DNA methylation analysis uncovered a shared epigenomic profile between small cell neuroendocrine cancers. These pan-cancer findings establish a molecular link between human adult stem cells and aggressive epithelial cancers.
Asunto(s)
Células Madre Adultas/metabolismo , Células Epiteliales/metabolismo , Neoplasias Pulmonares/genética , Neoplasias de la Próstata/genética , Transcriptoma , Neoplasias de la Vejiga Urinaria/genética , Animales , Línea Celular , ADN (Citosina-5-)-Metiltransferasas/genética , ADN (Citosina-5-)-Metiltransferasas/metabolismo , Regulación Neoplásica de la Expresión Génica , Neoplasias Pulmonares/metabolismo , Masculino , Ratones , Ratones Endogámicos NOD , Neoplasias de la Próstata/metabolismo , Neoplasias de la Vejiga Urinaria/metabolismoRESUMEN
Lethal cancers have genomes that can reflect a jigsaw puzzle put together in a hurricane. The missing, misjoined, and extra pieces contribute to the driving forces behind the cancer phenotypes. But is this the only reason genomic instability is so prevalent in aggressive cancers? New findings support that the hurricane winds themselves, not just their aftermath, contribute to the cancer phenotype of metastasis.
Asunto(s)
Neoplasias , Aneuploidia , Inestabilidad Cromosómica , ADN , Inestabilidad Genómica , HumanosRESUMEN
Copy number alteration (CNA) profiling of human tumors has revealed recurrent patterns of DNA amplifications and deletions across diverse cancer types. These patterns are suggestive of conserved selection pressures during tumor evolution but cannot be fully explained by known oncogenes and tumor suppressor genes. Using a pan-cancer analysis of CNA data from patient tumors and experimental systems, here we show that principal component analysis-defined CNA signatures are predictive of glycolytic phenotypes, including 18F-fluorodeoxy-glucose (FDG) avidity of patient tumors, and increased proliferation. The primary CNA signature is enriched for p53 mutations and is associated with glycolysis through coordinate amplification of glycolytic genes and other cancer-linked metabolic enzymes. A pan-cancer and cross-species comparison of CNAs highlighted 26 consistently altered DNA regions, containing 11 enzymes in the glycolysis pathway in addition to known cancer-driving genes. Furthermore, exogenous expression of hexokinase and enolase enzymes in an experimental immortalization system altered the subsequent copy number status of the corresponding endogenous loci, supporting the hypothesis that these metabolic genes act as drivers within the conserved CNA amplification regions. Taken together, these results demonstrate that metabolic stress acts as a selective pressure underlying the recurrent CNAs observed in human tumors, and further cast genomic instability as an enabling event in tumorigenesis and metabolic evolution.
Asunto(s)
Variaciones en el Número de Copia de ADN , Perfilación de la Expresión Génica/métodos , Glucólisis , Neoplasias/genética , Línea Celular Tumoral , Evolución Molecular , Amplificación de Genes , Eliminación de Gen , Regulación Neoplásica de la Expresión Génica , Inestabilidad Genómica , Humanos , Redes y Vías Metabólicas , Análisis de Componente Principal , Selección GenéticaRESUMEN
Numerous studies by our lab and others demonstrate that epidermal growth factor receptor (EGFR) plays critical roles in primary breast cancer (BC) initiation, growth and dissemination. However, clinical trials targeting EGFR function in BC have lead to disappointing results. In the current study we sought to identify the mechanisms responsible for this disparity by investigating the function of EGFR across the continuum of the metastatic cascade. We previously established that overexpression of EGFR is sufficient for formation of in situ primary tumors by otherwise nontransformed murine mammary gland cells. Induction of epithelial-mesenchymal transition (EMT) is sufficient to drive the metastasis of these EGFR-transformed tumors. Examining growth factor receptor expression across this and other models revealed a potent downregulation of EGFR through metastatic progression. Consistent with diminution of EGFR following EMT and metastasis EGF stimulation changes from a proliferative to an apoptotic response in in situ versus metastatic tumor cells, respectively. Furthermore, overexpression of EGFR in metastatic MDA-MB-231 BC cells promoted their antitumorigenic response to EGF in three dimensional (3D) metastatic outgrowth assays. In line with the paradoxical function of EGFR through EMT and metastasis we demonstrate that the EGFR inhibitory molecule, Mitogen Induced Gene-6 (Mig6), is tumor suppressive in in situ tumor cells. However, Mig6 expression is absolutely required for prevention of apoptosis and ultimate metastasis of MDA-MB-231 cells. Further understanding of the paradoxical function of EGFR between primary and metastatic tumors will be essential for application of its targeted molecular therapies in BC.