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1.
Proc Natl Acad Sci U S A ; 109(33): 13237-42, 2012 Aug 14.
Artículo en Inglés | MEDLINE | ID: mdl-22733765

RESUMEN

The EGFR (ERBB) family provides a model system for receptor signaling, oncogenesis, and the development of targeted therapeutics. Heterodimers of the ligand-binding-deficient ERBB2 (HER2) receptor and the kinase impaired ERBB3 (HER3) create a potent mitogenic signal, but the phosphorylation of ERBB2 in this context presents a challenge to established models of phosphorylation in trans. Higher order complexes of ERBB receptors have been observed biophysically and offer a theoretical route for ERBB2 phosphorylation, but it is not clear whether such complexes provide functionality beyond the constituent dimers. We now show that a previously selected inhibitory RNA aptamer that targets the extracellular domain (ECD) of ERBB3 acts by sterically disrupting these higher order interactions. Ligand binding, heterodimerization, phosphorylation of ERBB3, and AKT signaling are only minimally affected, whereas ERBB2 phosphorylation and MAPK signaling are selectively inhibited. The mapping of the binding site and creation of aptamer-resistant point mutants are consistent with a model of side-by-side oriented heterodimers to facilitate proxy phosphorylation, even at very low endogenous levels of receptors (below 10,000 receptors per cell). Additional modes of signaling with relevance to pathological ERBB expression states emerge at high receptor levels. Hence, higher order complexes of nonoverexpressed ERBB receptors are an integral and qualitatively distinct part of normal ERBB2/ERBB3 signaling. This mechanism of activation has implications for models of allosteric control, specificity of interactions, possible mechanisms of cross-talk, and approaches to therapeutic intervention that at present often generate experimental and clinical outcomes that do not reconcile with purely canonical, dimer-based models.


Asunto(s)
Multimerización de Proteína , Receptor ErbB-2/metabolismo , Receptor ErbB-3/metabolismo , Transducción de Señal , Aptámeros de Nucleótidos/metabolismo , Línea Celular Tumoral , Activación Enzimática , Humanos , Ligandos , Proteínas Quinasas Activadas por Mitógenos/antagonistas & inhibidores , Proteínas Quinasas Activadas por Mitógenos/metabolismo , Fosforilación , Unión Proteica , Estructura Terciaria de Proteína , Receptor ErbB-2/química , Receptor ErbB-3/química , Homología Estructural de Proteína
2.
Prostate ; 73(3): 306-15, 2013 Feb 15.
Artículo en Inglés | MEDLINE | ID: mdl-22911164

RESUMEN

BACKGROUND: Anterior gradient 2 (AGR2) is associated with metastatic progression in prostate cancer cells as well as other normal and malignant tissues. We investigated AGR2 expression in patients with metastatic prostate cancer. METHODS: Blood was collected from 44 patients with metastatic prostate cancer separated as: castration sensitive prostate cancer (CSPC, n = 5); castration resistant prostate cancer (CRPC, n = 36); and neuroendocrine-predominate CRPC defined by PSA ≤ 1 ng/ml in the presence of wide-spread metastatic disease (NE-CRPC, n = 3). AGR2 mRNA levels were measured with RT-PCR in circulating tumor cell (CTC)-enriched peripheral blood. Plasma AGR2 levels were determined via ELISA assay. AGR2 expression was modulated in prostate cancer cell lines using plasmid and viral vectors. RESULTS: AGR2 mRNA levels are elevated in CTCs and strongly correlated with CTC enumeration. Plasma AGR2 levels are elevated in all sub-groups. AGR2 levels vary independently to PSA and change in some patients in response to androgen-directed and other therapies. Plasma AGR2 levels are highest in the NE-CRPC sub-group. A correlation between AGR2, chromagranin A (CGA), and neuron-specific enolase (NSE) expression is demonstrated in prostate cancer cell lines. CONCLUSIONS: We conclude that AGR2 expression is elevated at the mRNA and protein level in patients with metastatic prostate cancer. In particular, we find that AGR2 expression is associated features consistent with neuroendocrine, or anaplastic, prostate cancer, exemplified by an aggressive clinical phenotype without elevation in circulating PSA levels. Further studies are warranted to explore the mechanistic and prognostic implications of AGR2 expression in this patient population.


Asunto(s)
Adenocarcinoma/metabolismo , Biomarcadores de Tumor/metabolismo , Tumores Neuroendocrinos/patología , Fenotipo , Neoplasias de la Próstata/metabolismo , Neoplasias de la Próstata/secundario , Proteínas/metabolismo , Adenocarcinoma/secundario , Anciano , Estudios de Casos y Controles , Línea Celular Tumoral , Cromogranina A/metabolismo , Progresión de la Enfermedad , Humanos , Masculino , Persona de Mediana Edad , Mucoproteínas , Metástasis de la Neoplasia , Células Neoplásicas Circulantes/metabolismo , Células Neoplásicas Circulantes/patología , Proteínas Oncogénicas , Fosfopiruvato Hidratasa/metabolismo , Antígeno Prostático Específico/sangre , ARN Mensajero/metabolismo
3.
J Control Release ; 329: 614-623, 2021 01 10.
Artículo en Inglés | MEDLINE | ID: mdl-33011241

RESUMEN

Signaling between the CC chemokine receptor 2 (CCR2) with its ligand, monocyte chemoattractant protein-1 (MCP-1) promotes cancer progression by directly stimulating tumor cell proliferation and downregulating the expression of apoptotic proteins. Additionally, the MCP-1/CCR2 signaling axis drives the migration of circulating monocytes into the tumor microenvironment, where they mature into tumor-associated macrophages (TAMs) that promote disease progression through induction of angiogenesis, tissue remodeling, and suppression of the cytotoxic T lymphocyte (CTL) response. In order to simultaneously disrupt MCP-1/CCR2 signaling and target CCR2-expressing cancer cells for drug delivery, KLAK-MCP-1 micelles consisting of a CCR2-targeting peptide sequence (MCP-1 peptide) and the apoptotic KLAKLAK peptide were synthesized. In vitro, KLAK-MCP-1 micelles were observed to bind and induce cytotoxicity to cancer cells through interaction with CCR2. In vivo, KLAK-MCP-1 micelles inhibited tumor growth (34 ± 11%) in a subcutaneous B16F10 murine melanoma model despite minimal tumor accumulation upon intravenous injection. Tumors treated with KLAK-MCP1 demonstrated reduced intratumor CCR2 expression and altered infiltration of TAMs and CTLs as evidenced by immunohistochemical and flow cytometric analysis. These studies highlight the potential application of CCR2-targeted nanotherapeutic micelles in cancer treatment.


Asunto(s)
Neoplasias , Receptores CCR2 , Animales , Ratones , Micelas , Monocitos , Péptidos , Microambiente Tumoral
4.
Oncogene ; 38(16): 3003-3018, 2019 04.
Artículo en Inglés | MEDLINE | ID: mdl-30575818

RESUMEN

Anterior gradient 2 (AGR2) is a member of the protein disulfide isomerase (PDI) family, which plays a role in the regulation of protein homeostasis and the unfolded protein response pathway (UPR). AGR2 has also been characterized as a proto-oncogene and a potential cancer biomarker. Cellular localization of AGR2 is emerging as a key component for understanding the role of AGR2 as a proto-oncogene. Here, we provide evidence that extracellular AGR2 (eAGR2) promotes tumor metastasis in various in vivo models. To further characterize the role of the intracellular-resident versus extracellular protein, we performed a comprehensive protein-protein interaction screen. Based on these results, we identify AGR2 as an interacting partner of the mTORC2 pathway. Importantly, our data indicates that eAGR2 promotes increased phosphorylation of RICTOR (T1135), while intracellular AGR2 (iAGR2) antagonizes its levels and phosphorylation. Localization of AGR2 also has opposing effects on the Hippo pathway, spheroid formation, and response to chemotherapy in vitro. Collectively, our results identify disparate phenotypes predicated on AGR2 localization. Our findings also provide credence for screening of eAGR2 to guide therapeutic decisions.


Asunto(s)
Retículo Endoplásmico/genética , Diana Mecanicista del Complejo 2 de la Rapamicina/genética , Metástasis de la Neoplasia/genética , Metástasis de la Neoplasia/patología , Neoplasias/genética , Neoplasias/patología , Proteínas/genética , Animales , Línea Celular , Línea Celular Tumoral , Células HEK293 , Humanos , Células MCF-7 , Masculino , Ratones , Ratones Desnudos , Mucoproteínas , Proteínas Oncogénicas , Células PC-3 , Proteína Disulfuro Isomerasas/genética , Proto-Oncogenes Mas , Transducción de Señal/genética , Respuesta de Proteína Desplegada/genética
5.
J Vis Exp ; (139)2018 09 19.
Artículo en Inglés | MEDLINE | ID: mdl-30295648

RESUMEN

Cancer patients with an aberrant regulation of the protein phosphorylation networks are often treated with the tyrosine kinase inhibitors. Response rates approaching 85% are common. Unfortunately, patients often become refractory to the treatment by altering their signal transduction pathways. An implementation of the expression profiling with microarrays can identify the overall mRNA-level changes, and proteomics can identify the overall changes in protein levels or can identify the proteins involved, but the activity of the signal transduction pathways can only be established by interrogating post-translational modifications of the proteins. As a result, the ability to identify whether a drug treatment is successful or whether resistance arose, or the ability to characterize any alterations in the signaling pathways, is an important clinical challenge. Here, we provide a detailed explanation of antibody arrays as a tool which can identify system-wide alterations in various post-translational modifications (e.g., phosphorylation). One of the advantages of using antibody arrays includes their accessibility (an array does not require either an expert in proteomics or costly equipment) and speed. The availability of arrays targeting a combination of post-translational modifications is the primary limitation. In addition, unbiased approaches (phosphoproteomics) may be more suitable for the novel discovery, whereas antibody arrays are ideal for the most widely characterized targets.


Asunto(s)
Anticuerpos , Resistencia a Antineoplásicos , Proteínas Tirosina Quinasas/antagonistas & inhibidores , Transducción de Señal , Humanos , Neoplasias/tratamiento farmacológico , Fosforilación , Análisis por Matrices de Proteínas/métodos , Procesamiento Proteico-Postraduccional , Proteómica
6.
Oncotarget ; 9(44): 27363-27379, 2018 Jun 08.
Artículo en Inglés | MEDLINE | ID: mdl-29937991

RESUMEN

The cancer-associated protein Anterior Gradient 2 (AGR2) has been described, predominantly in adenocarcinomas. Increased levels of extracellular AGR2 (eAGR2) have been correlated with poor prognosis in cancer patients, making it a potential biomarker. Additionally, neutralizing AGR2 antibodies showed preclinical effectiveness in murine cancer models suggesting eAGR2 may be a therapeutic target. We set out to identify a peptide by mRNA display that would serve as a theranostic tool targeting AGR2. This method enables the selection of peptides from a complex (>1011) library and incorporates a protease incubation step that filters the selection for serum stable peptides. We performed six successive rounds of enrichment using a 10-amino acid mRNA display library and identified several AGR2 binding peptides. One of these peptides (H10), demonstrated high affinity binding to AGR2 with a binding constant (KD) of 6.4 nM. We developed an AGR2 ELISA with the H10 peptide as the capture reagent. Our H10-based ELISA detected eAGR2 from cancer cell spent media with a detection limit of (20-50 ng/ml). Furthermore, we investigated the therapeutic utility of H10 and discovered that it inhibited cell viability at IC50 (9-12 µmoles/L) in cancer cell lines. We also determined that 10 µg/ml of H10 was sufficient to inhibit cancer cell migration in breast and prostate cancer cell lines. A control peptide did not show any appreciable activity in these cells. The H10 peptide showed promise as both a novel diagnostic and a potential therapeutic peptide.

7.
Cancer Biomark ; 22(2): 333-344, 2018.
Artículo en Inglés | MEDLINE | ID: mdl-29689709

RESUMEN

BACKGROUND AND OBJECTIVE: To monitor therapies targeted to epidermal growth factor receptors (EGFR) in non-small cell lung cancer (NSCLC), we investigated Peroxiredoxin 6 (PRDX6) as a biomarker of response to anti-EGFR agents. METHODS: We studied cells that are sensitive (H3255, HCC827) or resistant (H1975, H460) to gefitinib. PRDX6 was examined with either gefitinib or vehicle treatment using enzyme-linked immunosorbent assays. We created xenograft models from one sensitive (HCC827) and one resistant cell line (H1975) and monitored serum PRDX6 levels during treatment. RESULTS: PRDX6 levels in cell media from sensitive cell lines increased significantly after gefitinib treatment vs. vehicle, whereas there was no significant difference for resistant lines. PRDX6 accumulation over time correlated positively with gefitinib sensitivity. Serum PRDX6 levels in gefitinib-sensitive xenograft models increased markedly during the first 24 hours of treatment and then decreased dramatically during the following 48 hours. Differences in serum PRDX6 levels between vehicle and gefitinib-treated animals could not be explained by differences in tumor burden. CONCLUSIONS: Our results show that changes in serum PRDX6 during the course of gefitinib treatment of xenograft models provide insight into tumor response and such an approach offers several advantages over imaging-based strategies for monitoring response to anti-EGFR agents.


Asunto(s)
Antineoplásicos/farmacología , Carcinoma de Pulmón de Células no Pequeñas/sangre , Receptores ErbB/antagonistas & inhibidores , Neoplasias Pulmonares/sangre , Inhibidores de Proteínas Quinasas/farmacología , Animales , Antineoplásicos/uso terapéutico , Biomarcadores , Carcinoma de Pulmón de Células no Pequeñas/tratamiento farmacológico , Línea Celular Tumoral , Modelos Animales de Enfermedad , Ensayo de Inmunoadsorción Enzimática , Femenino , Gefitinib , Humanos , Neoplasias Pulmonares/tratamiento farmacológico , Ratones , Peroxiredoxina VI/sangre , Peroxiredoxina VI/genética , Peroxiredoxina VI/metabolismo , Inhibidores de Proteínas Quinasas/uso terapéutico , Quinazolinas/farmacología , Quinazolinas/uso terapéutico , Resultado del Tratamiento , Ensayos Antitumor por Modelo de Xenoinjerto
8.
Methods Mol Biol ; 1550: 171-184, 2017.
Artículo en Inglés | MEDLINE | ID: mdl-28188530

RESUMEN

The ability to enumerate all of the proteins in a cell is quickly becoming a reality. Quantitative proteomics adds an extra dimension to proteome-wide discovery experiments by enabling differential measurements of protein concentrations, characterization of protein turnover, increased stringency of co-immunoprecipitation reactions, as well as many other intriguing applications. One of the most widely used techniques that enable relative protein quantitation is stable isotope labeling by amino acids in cell culture (SILAC) (Ong et al., Mol Cell Proteomics 1(5):376-386, 2002). Over the past decade, SILAC has become the preferred approach for proteome-wide quantitation by mass spectrometry. This approach relies on the metabolic incorporation of isotopically enriched amino acids into the proteome of cells-the proteome of "light" (1H, 12C, 14N) cells can then be compared to "heavy" (2H, 13C, 15N) cells as the isotopically labeled proteins and peptides are easily distinguished in a mass spectrometer. Since cellular uptake and response to isotopically different amino acid(s) is naïve, it is without impact on cell physiology. We provide a detailed step-by-step procedure for performing SILAC-based experiment for proteome-wide quantitation in this chapter.


Asunto(s)
Aminoácidos/química , Técnicas de Cultivo de Célula , Marcaje Isotópico , Proteoma , Proteómica/métodos , Línea Celular , Humanos , Reproducibilidad de los Resultados , Flujo de Trabajo
9.
Endocr Relat Cancer ; 24(4): 157-170, 2017 04.
Artículo en Inglés | MEDLINE | ID: mdl-28264911

RESUMEN

Androgen receptor (AR) regulation pathways are essential for supporting the growth and survival of prostate cancer cells. Recently, sub-populations of prostate cancer cells have been identified with stem cell features and are associated with the emergence of treatment-resistant prostate cancer. Here, we explored the function of AR in prostate cancer-associated fibroblasts (CAFs) relative to growth and stem cell-associated characteristics. CAFs were isolated from the murine cPten-/-L prostate cancer model and cultured with human prostate cancer epithelial (hPCa) cells. A murine-specific AR antisense oligonucleotide (ASO) was used to suppress the expression of AR in the CAF cells. CAFs express low, but significant levels of AR relative to fibroblasts derived from non-malignant tissue. CAFs promoted growth and colony formation of hPCa cells, which was attenuated by the suppression of AR expression. Surprisingly, AR-depleted CAFs promoted increased stem cell marker expression in hPCa cells. Interferon gamma (IFN-γ) and macrophage colony-stimulating factor (M-CSF) were increased in AR-depleted CAF cells and exhibited similar effects on stem cell marker expression as seen in the CAF co-culture systems. Clinically, elevated IFN-γ expression was found to correlate with histologic grade in primary prostate cancer samples. In summary, AR and androgen-dependent signaling are active in CAFs and exert significant effects on prostate cancer cells. IFN-γ and M-CSF are AR-regulated factors secreted by CAF cells, which promote the expression of stem cell markers in prostate cancer epithelial cells. Understanding how CAFs and other constituents of stromal tissue react to anti-cancer therapies may provide insight into the development and progression of prostate cancer.


Asunto(s)
Fibroblastos Asociados al Cáncer/metabolismo , Neoplasias de la Próstata/metabolismo , Receptores Androgénicos/metabolismo , Animales , Línea Celular Tumoral , Técnicas de Cocultivo , Citocinas/metabolismo , Humanos , Masculino , Ratones Noqueados , Fosfohidrolasa PTEN/genética , Antígeno Prostático Específico/metabolismo , Neoplasias de la Próstata/patología
10.
ACS Biomater Sci Eng ; 3(12): 3273-3282, 2017 Dec 11.
Artículo en Inglés | MEDLINE | ID: mdl-29302619

RESUMEN

Monocyte chemoattractant protein-1 (MCP-1) stimulates the migration of monocytes to inflammatory sites, leading to the progression of many diseases. Recently, we described a monocyte-targeting peptide amphiphile micelle (MCP-1 PAM) incorporated with the chemokine receptor CCR2 binding motif of MCP-1, which has a high affinity for monocytes in atherosclerotic plaques. We further report here the biomimetic components of MCP-1 PAMs and the influence of the nanoparticle upon binding to monocytes. We report that MCP-1 PAMs have enhanced secondary structure compared to the MCP-1 peptide. As a result, MCP-1 PAMs displayed improved binding and chemoattractant properties to monocytes, which upregulated the inflammatory signaling pathways responsible for monocyte migration. Interestingly, when MCP-1 PAMs were incubated in the presence of prostate cancer cells in vitro, the particle displayed anticancer efficacy by reducing CCR2 expression. Given that monocytes play an important role in tumor cell migration and invasion, our results demonstrate that PAMs can improve the native biofunctional properties of the peptide and may be used as an effective inhibitor to prevent chemokine-receptor interactions that promote disease progression.

11.
Mol Cancer Ther ; 16(8): 1645-1657, 2017 08.
Artículo en Inglés | MEDLINE | ID: mdl-28566434

RESUMEN

Mutations or deletions in exons 18-21 in the EGFR) are present in approximately 15% of tumors in patients with non-small cell lung cancer (NSCLC). They lead to activation of the EGFR kinase domain and sensitivity to molecularly targeted therapeutics aimed at this domain (gefitinib or erlotinib). These drugs have demonstrated objective clinical response in many of these patients; however, invariably, all patients acquire resistance. To examine the molecular origins of resistance, we derived a set of gefitinib-resistant cells by exposing lung adenocarcinoma cell line, HCC827, with an activating mutation in the EGFR tyrosine kinase domain, to increasing gefitinib concentrations. Gefitinib-resistant cells acquired an increased expression and activation of JUN, a known oncogene involved in cancer progression. Ectopic overexpression of JUN in HCC827 cells increased gefitinib IC50 from 49 nmol/L to 8 µmol/L (P < 0.001). Downregulation of JUN expression through shRNA resensitized HCC827 cells to gefitinib (IC50 from 49 nmol/L to 2 nmol/L; P < 0.01). Inhibitors targeting JUN were 3-fold more effective in the gefitinib-resistant cells than in the parental cell line (P < 0.01). Analysis of gene expression in patient tumors with EGFR-activating mutations and poor response to erlotinib revealed a similar pattern as the top 260 differentially expressed genes in the gefitinib-resistant cells (Spearman correlation coefficient of 0.78, P < 0.01). These findings suggest that increased JUN expression and activity may contribute to gefitinib resistance in NSCLC and that JUN pathway therapeutics merit investigation as an alternate treatment strategy. Mol Cancer Ther; 16(8); 1645-57. ©2017 AACR.


Asunto(s)
Carcinoma de Pulmón de Células no Pequeñas/tratamiento farmacológico , Regulación hacia Abajo , Resistencia a Antineoplásicos , Receptores ErbB/metabolismo , Neoplasias Pulmonares/tratamiento farmacológico , Proteínas Proto-Oncogénicas c-jun/metabolismo , Quinazolinas/uso terapéutico , Transducción de Señal , Carcinoma de Pulmón de Células no Pequeñas/genética , Línea Celular Tumoral , Cromatina/metabolismo , Regulación hacia Abajo/efectos de los fármacos , Resistencia a Antineoplásicos/efectos de los fármacos , Gefitinib , Humanos , Neoplasias Pulmonares/genética , Mutación/genética , Fenotipo , Fosforilación/efectos de los fármacos , Unión Proteica/efectos de los fármacos , Proteómica , Quinazolinas/farmacología , Transducción de Señal/efectos de los fármacos , Regulación hacia Arriba/efectos de los fármacos
12.
Cancer Inform ; 14: 163-75, 2015.
Artículo en Inglés | MEDLINE | ID: mdl-26715830

RESUMEN

Circulating biomarkers are of significant interest for cancer detection and treatment personalization. However, the biophysical processes that determine how proteins are shed from cancer cells or their microenvironment, diffuse through tissue, enter blood vasculature, and persist in circulation remain poorly understood. Since approaches primarily focused on experimental evaluation are incapable of measuring the shedding and persistence for every possible marker candidate, we propose an interdisciplinary computational/experimental approach that includes computational modeling of tumor tissue heterogeneity. The model implements protein production, transport, and shedding based on tumor vascularization, cell proliferation, hypoxia, and necrosis, thus quantitatively relating the tumor and circulating proteomes. The results highlight the dynamics of shedding as a function of protein diffusivity and production. Linking the simulated tumor parameters to clinical tumor and vascularization measurements could potentially enable this approach to reveal the tumor-specific conditions based on the protein detected in circulation and thus help to more accurately manage cancer diagnosis and treatment.

13.
Methods Mol Biol ; 795: 233-53, 2012.
Artículo en Inglés | MEDLINE | ID: mdl-21960227

RESUMEN

Clinical tools to accurately describe, evaluate, and predict an individual's response to cancer therapy are a field-wide priority; in many advanced cancers, only 10-20% of individuals will have a clinical benefit from therapy, yet we treat the entire population. Furthermore, many therapies are initially effective, but lose effectiveness over time. Here we describe methods to derive in vitro models of resistance to EGFR tyrosine kinase inhibitors. We additionally describe approaches to characterize possible mechanisms of resistance by genomic and transcriptomic approaches.


Asunto(s)
Antineoplásicos/farmacología , Carcinoma de Pulmón de Células no Pequeñas/genética , Receptores ErbB/genética , Neoplasias Pulmonares/genética , Análisis de Secuencia por Matrices de Oligonucleótidos , Inhibidores de Proteínas Quinasas/farmacología , Antineoplásicos/uso terapéutico , Carcinoma de Pulmón de Células no Pequeñas/tratamiento farmacológico , Línea Celular Tumoral , Resistencia a Antineoplásicos/efectos de los fármacos , Resistencia a Antineoplásicos/genética , Transición Epitelial-Mesenquimal/genética , Receptores ErbB/antagonistas & inhibidores , Gefitinib , Perfilación de la Expresión Génica , Marcadores Genéticos/genética , Humanos , Neoplasias Pulmonares/tratamiento farmacológico , Inhibidores de Proteínas Quinasas/uso terapéutico , Quinazolinas/farmacología , Análisis de Secuencia de ADN
14.
Mol Cancer Ther ; 11(5): 1071-81, 2012 May.
Artículo en Inglés | MEDLINE | ID: mdl-22411897

RESUMEN

Clinical oncology is hampered by lack of tools to accurately assess a patient's response to pathway-targeted therapies. Serum and tumor cell surface proteins whose abundance, or change in abundance in response to therapy, differentiates patients responding to a therapy from patients not responding to a therapy could be usefully incorporated into tools for monitoring response. Here, we posit and then verify that proteomic discovery in in vitro tissue culture models can identify proteins with concordant in vivo behavior and further, can be a valuable approach for identifying tumor-derived serum proteins. In this study, we use stable isotope labeling of amino acids in culture (SILAC) with proteomic technologies to quantitatively analyze the gefitinib-related protein changes in a model system for sensitivity to EGF receptor (EGFR)-targeted tyrosine kinase inhibitors. We identified 3,707 intracellular proteins, 1,276 cell surface proteins, and 879 shed proteins. More than 75% of the proteins identified had quantitative information, and a subset consisting of 400 proteins showed a statistically significant change in abundance following gefitinib treatment. We validated the change in expression profile in vitro and screened our panel of response markers in an in vivo isogenic resistant model and showed that these were markers of gefitinib response and not simply markers of phospho-EGFR downregulation. In doing so, we also were able to identify which proteins might be useful as markers for monitoring response and which proteins might be useful as markers for a priori prediction of response.


Asunto(s)
Antineoplásicos/farmacología , Receptores ErbB/antagonistas & inhibidores , Inhibidores de Proteínas Quinasas/farmacología , Proteoma , Animales , Línea Celular Tumoral , Resistencia a Antineoplásicos , Receptores ErbB/metabolismo , Femenino , Gefitinib , Humanos , Ratones , Ratones Endogámicos BALB C , Ratones Desnudos , Proteómica , Quinazolinas/farmacología , Reproducibilidad de los Resultados , Transducción de Señal/efectos de los fármacos , Ensayos Antitumor por Modelo de Xenoinjerto
15.
Methods Mol Biol ; 728: 87-107, 2011.
Artículo en Inglés | MEDLINE | ID: mdl-21468942

RESUMEN

Proteomic-based biomarker discovery approaches broadly attempt to identify proteins whose basal abundance, or change in abundance in response to a perturbation (e.g., a therapeutic intervention) is able to discriminate between populations of patients. Up until recently, the majority of approaches for discovering circulating biomarkers have focused on directly profiling serum or plasma to identify such proteins. However, the complexity and dynamic range of protein abundance in serum and plasma create a significant challenge for proteomics methods. To overcome these barriers, diverse approaches to simplify or to fractionate serum and plasma have been developed. For some diseases, such as those related to specific organs, there may be useful marker proteins that originate in the organ. Here, we describe an approach for marker discovery that focuses on the profiling of either primary tissue or cell culture models thereof.


Asunto(s)
Biomarcadores/sangre , Modelos Biológicos , Proteómica/métodos , Fraccionamiento Celular , Línea Celular Tumoral , Fraccionamiento Químico , Humanos , Marcaje Isotópico , Espectrometría de Masas , Estadística como Asunto
16.
PLoS One ; 6(7): e23090, 2011.
Artículo en Inglés | MEDLINE | ID: mdl-21829587

RESUMEN

Tumor-derived, circulating proteins are potentially useful as biomarkers for detection of cancer, for monitoring of disease progression, regression and recurrence, and for assessment of therapeutic response. Here we interrogated how a protein's stability, cellular localization, and abundance affect its observability in blood by mass-spectrometry-based proteomics techniques. We performed proteomic profiling on tumors and plasma from two different xenograft mouse models. A statistical analysis of this data revealed protein properties indicative of the detection level in plasma. Though 20% of the proteins identified in plasma were tumor-derived, only 5% of the proteins observed in the tumor tissue were found in plasma. Both intracellular and extracellular tumor proteins were observed in plasma; however, after normalizing for tumor abundance, extracellular proteins were seven times more likely to be detected. Although proteins that were more abundant in the tumor were also more likely to be observed in plasma, the relationship was nonlinear: Doubling the spectral count increased detection rate by only 50%. Many secreted proteins, even those with relatively low spectral count, were observed in plasma, but few low abundance intracellular proteins were observed. Proteins predicted to be stable by dipeptide composition were significantly more likely to be identified in plasma than less stable proteins. The number of tryptic peptides in a protein was not significantly related to the chance of a protein being observed in plasma. Quantitative comparison of large versus small tumors revealed that the abundance of proteins in plasma as measured by spectral count was associated with the tumor size, but the relationship was not one-to-one; a 3-fold decrease in tumor size resulted in a 16-fold decrease in protein abundance in plasma. This study provides quantitative support for a tumor-derived marker prioritization strategy that favors secreted and stable proteins over all but the most abundant intracellular proteins.


Asunto(s)
Proteínas Sanguíneas/metabolismo , Carcinoma de Células Escamosas/metabolismo , Proteínas de Neoplasias/metabolismo , Estabilidad Proteica , Proteoma/análisis , Proteómica , Neoplasias Cutáneas/metabolismo , Animales , Antineoplásicos/uso terapéutico , Biomarcadores de Tumor/metabolismo , Proteínas Sanguíneas/química , Carcinoma de Células Escamosas/tratamiento farmacológico , Resistencia a Antineoplásicos , Femenino , Humanos , Espectrometría de Masas , Ratones , Ratones Endogámicos BALB C , Proteínas de Neoplasias/química , Neoplasias Cutáneas/tratamiento farmacológico , Células Tumorales Cultivadas
17.
J Proteome Res ; 7(9): 4031-9, 2008 Sep.
Artículo en Inglés | MEDLINE | ID: mdl-18707148

RESUMEN

Mass spectrometry-based proteomics experiments have become an important tool for studying biological systems. Identifying the proteins in complex mixtures by assigning peptide fragmentation spectra to peptide sequences is an important step in the proteomics process. The 1-2 ppm mass-accuracy of hybrid instruments, like the LTQ-FT, has been cited as a key factor in their ability to identify a larger number of peptides with greater confidence than competing instruments. However, in replicate experiments of an 18-protein mixture, we note parent masses deviate 171 ppm, on average, for ion-trap data directed identifications and 8 ppm, on average, for preview Fourier transform (FT) data directed identifications. These deviations are neither caused by poor calibration nor by excessive ion-loading and are most likely due to errors in parent mass estimation. To improve these deviations, we introduce msPrefix, a program to re-estimate a peptide's parent mass from an associated high-accuracy full-scan survey spectrum. In 18-protein mixture experiments, msPrefix parent mass estimates deviate only 1 ppm, on average, from the identified peptides. In a cell lysate experiment searched with a tolerance of 50 ppm, 2295 peptides were confidently identified using native data and 4560 using msPrefixed data. Likewise, in a plasma experiment searched with a tolerance of 50 ppm, 326 peptides were identified using native data and 1216 using msPrefixed data. msPrefix is also able to determine which MS/MS spectra were possibly derived from multiple precursor ions. In complex mixture experiments, we demonstrate that more than 50% of triggered MS/MS may have had multiple precursor ions and note that spectra with multiple candidate ions are less likely to result in an identification using TANDEM. These results demonstrate integration of msPrefix into traditional shotgun proteomics workflows significantly improves identification results.


Asunto(s)
Proteínas Sanguíneas/química , Péptidos/análisis , Espectrometría de Masas en Tándem/métodos , Algoritmos , Bases de Datos de Proteínas , Humanos , Espectrometría de Masas en Tándem/instrumentación
19.
J Biol Chem ; 281(37): 27306-16, 2006 Sep 15.
Artículo en Inglés | MEDLINE | ID: mdl-16825199

RESUMEN

Degradation of activated ERBB receptors is an important mechanism for signal attenuation. However, compared with epidermal growth factor (EGF) receptor, the ERBB2/ERBB3 signaling pair is considered to be attenuation-deficient. The ERBB2/ERBB3 ligands of the neuregulin family rely on an EGF-like domain for signaling and are generated from larger membrane-bound precursors. In contrast to EGF, which is processed to yield a 6-kDa peptide ligand, mature neuregulins retain a variety of segments N-terminal to the EGF-like domain. Here we evaluate the role of the N-terminal domain of neuregulin 1 in signaling and turnover of ERBB2/ERBB3. Our data suggest that whereas the EGF-like domain of neuregulin 1 is required and sufficient for the formation of active receptor heterodimers, the presence of the N-terminal Ig-like domain is required for efficient signal attenuation. This manifests itself for both ERBB2 and ERBB3 but is more pronounced and coupled directly to degradation for ERBB3. When stimulated with only the EGF-like domain, ERBB3 shows degradation rates comparable with constitutive turnover, but stimulation with full-length neuregulin 1 resulted in receptor degradation at rates that are comparable with activated EGF receptor. Most of the enhancement in down-regulation was maintained after replacing the Ig-like domain with a thioredoxin protein of comparable size but different amino acid composition, suggesting that the physical presence but not specific properties of the Ig-like domain are needed. This sequence-independent effect of the N-terminal domain correlates with an enhanced ability of full-size neuregulin 1 to disrupt higher order oligomers of the ERBB3 extracellular domains in vitro.


Asunto(s)
Regulación Neoplásica de la Expresión Génica , Neurregulina-1/química , Neurregulina-1/fisiología , Línea Celular Tumoral , Dimerización , Humanos , Ligandos , Modelos Moleculares , Neurregulinas/química , Fosforilación , Isoformas de Proteínas , Estructura Terciaria de Proteína , Transducción de Señal , Tirosina/química
20.
Biochemistry ; 44(48): 15842-57, 2005 Dec 06.
Artículo en Inglés | MEDLINE | ID: mdl-16313187

RESUMEN

The extracellular, ligand binding regions of ErbB receptors consist of four domains that can assume at least two alternative conformations, extended and locked. The locked conformation, observed in several crystal structures, is held together by a noncovalent intramolecular tether and is incompatible with current models for receptor dimerization and ligand activation. Based on structures of ligand-receptor complexes in the extended conformation, the high affinity ligand binding pocket between domains I and III is disrupted in the locked conformation. Therefore the biological role of the locked conformation is not clear. To address the impact of the locked conformation on ligand binding, we compared extracellular domains of wild-type ErbB3, mutant domains in a constitutively locked or extended conformation and partial extracellular domain constructs. We found that the constitutively locked receptor domains and truncated constructs carrying only domains I-II or III-IV strongly bind ligand, albeit with reduced affinity compared to wild-type receptor. This suggests that the locked conformation cannot be discounted for ligand binding. The significant binding by both partial interfaces in domains I and III also suggests that "partial bivalency" may be the reason for the low nanomolar and high picomolar binding observed for ErbB3 in the respective "low" and high affinity states. In contrast to EGFR (ErbB1), ErbB3 retains high ligand binding affinity at an endosome-comparable pH in both the extended and locked conformations. Ligand affinity for the locked conformation even improves at low pH. For ErbB3, the contribution of domain I to ligand binding is strong and increases at low pH while its contribution is thought to be minimal for EGFR, regardless of pH. This shift in domain contribution and pH dependency provides a mechanistic explanation for some of the divergent properties of EGFR and ErbB3.


Asunto(s)
Endosomas/metabolismo , Neurregulina-1/metabolismo , Conformación Proteica , Estructura Terciaria de Proteína , Receptor ErbB-3/química , Receptor ErbB-3/metabolismo , Sustitución de Aminoácidos , Animales , Disulfuros/química , Drosophila , Concentración de Iones de Hidrógeno , Ligandos , Modelos Moleculares , Mutación , Receptor ErbB-3/genética , Resonancia por Plasmón de Superficie
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