Quantitative Proteomics with siRNA Screening Identifies Novel Mechanisms of Trastuzumab Resistance in HER2 Amplified Breast Cancers

HER2 is a receptor tyrosine kinase that is overexpressed in 20% to 30% of human breast cancers and which affects patient prognosis and survival. Treatment of HER2-positive breast cancer with the monoclonal antibody trastuzumab (Herceptin) has improved patient survival, but the development of trastuzumab resistance is a major medical problem. Many of the known mechanisms of trastuzumab resistance cause changes in protein phosphorylation patterns, and therefore quantitative proteomics was used to examine phosphotyrosine signaling networks in trastuzumab-resistant cells. The model system used in this study was two pairs of trastuzumab-sensitive and -resistant breast cancer cell lines. Using stable isotope labeling, phosphotyrosine immunoprecipitations, and online TiO₂ chromatography utilizing a dual trap configuration, ∼1700 proteins were quantified. Comparing quantified proteins between the two cell line pairs showed only a small number of common protein ratio changes, demonstrating heterogeneity in phosphotyrosine signaling networks across different trastuzumab-resistant cancers. Proteins showing significant increases in resistant versus sensitive cells were subjected to a focused siRNA screen to evaluate their functional relevance to trastuzumab resistance. The screen revealed proteins related to the Src kinase pathway, such as CDCP1/Trask, embryonal Fyn substrate, and Paxillin. We also identify several novel proteins that increased trastuzumab sensitivity in resistant cells when targeted by siRNAs, including FAM83A and MAPK1. These proteins may present targets for the development of clinical diagnostics or therapeutic strategies to guide the treatment of HER2+ breast cancer patients who develop trastuzumab resistance.HER2 is a member of the epidermal growth factor receptor (EGFR)/ErbB family of receptor tyrosine kinases. Under normal physiologic conditions, HER2 tyrosine kinase signaling is tightly regulated spatially and temporally by the requirement for it to heterodimerize with a ligand bound family member, such as EGFR, HER3/ErbB3, or HER4/ErbB4 (1). However, in 20% to 30% of human breast cancer cases, HER2 gene amplification is present, resulting in a high level of HER2 protein overexpression and unregulated, constitutive HER2 tyrosine kinase signaling (2, 3). HER2 gene amplified breast cancer, also termed HER2-positive breast cancer, carries a poor prognosis, but the development of the HER2 targeted monoclonal antibody trastuzumab (Herceptin) has significantly improved patient survival (2). Despite the clinical effectiveness of trastuzumab, the development of drug resistance significantly increases the risk of patient death. This poses a major medical problem, as most metastatic HER2-positive breast cancer patients develop trastuzumab resistance over the course of their cancer treatment (4). The treatment approach for HER2+ breast cancer patients after trastuzumab resistance develops is mostly a trial-and-error process that subjects the patient to increased toxicity. Therefore, there is a substantial medical need for strategies to overcome trastuzumab resistance.Multiple trastuzumab-resistance mechanisms have been identified, and they alter signaling networks and protein phosphorylation patterns in either a direct or an indirect manner. These mechanisms can be grouped into three categories. The first category is the activation of a parallel signaling network by other tyrosine kinases. These kinases include the receptor tyrosine kinases, EGFR, IGF1R, Her3, Met, EphA2, and Axl, as well as the erythropoietin-receptor-mediated activation of the cytoplasmic tyrosine kinases Jak2 and Src (5–11). The second category is the activation of downstream signaling proteins. Multiple studies have demonstrated activation of the phosphatidylinositol-3-kinase (PI3K)/AKT pathway in trastuzumab resistance, which occurs either via deletion of the PTEN lipid phosphatase or mutation of the PI3K genes (12, 13). Activation of Src family kinases or overexpression of cyclin E, which increases the cyclin E–cyclin-dependent kinase 2 signaling pathway, has also been reported (14). The third category includes mechanisms that maintain HER2 signaling even in the presence of trastuzumab. The production of a truncated isoform of HER2, p95HER2, which lacks the trastuzumab binding site, causes constitutive HER2 signaling (15, 16). Overexpression of the MUC4 sialomucin complex inhibits trastuzumab binding to HER2 and thereby maintains HER2 signaling (17, 18).Given that multiple trastuzumab-resistance mechanisms alter signaling networks and protein phosphorylation patterns, we reasoned that mapping phosphotyrosine signaling networks using quantitative proteomics would be a highly useful strategy for analyzing known mechanisms and identifying novel mechanisms of trastuzumab resistance. Quantitative proteomics and phosphotyrosine enrichment approaches have been extensively used to study the EGFR signal networks (19–23). We and others have used these approaches to map the HER2 signaling network (22, 24, 25). Multiple other tyrosine kinase signaling networks were analyzed using quantitative proteomics, including Ephrin receptor, EphB2 (26–28), platelet-derived growth factor receptor (PDGFR) (21), insulin receptor (29, 30), and the receptor for hepatocyte growth factor, c-MET (31).The goal of this study is to identify, quantify, and functionally screen proteins that might be involved in trastuzumab resistance. We used two pairs of HER2 gene amplified trastuzumab-sensitive (parental, SkBr3 and BT474) and -resistant (SkBr3^R and BT474^R) human breast cancer cell lines as models for trastuzumab resistance. These cell lines and their trastuzumab-resistant derivatives have been extensively characterized and highly cited in the breast cancer literature (32, 33). Using stable isotope labeling of amino acids in cell culture (SILAC),¹ phosphotyrosine immunoprecipitations, and online TiO₂ chromatography with dual trap configuration, we quantified the changes in phosphotyrosine containing proteins and interactors between trastuzumab-sensitive and -resistant cells. Several of the known trastuzumab-resistance mechanisms were identified, which serves as a positive control and validation of our approach, and large protein ratio changes were measured in proteins that had not been previously connected with trastuzumab resistance. We then performed a focused siRNA screen targeting the proteins with significantly increased protein ratios. This screen functionally tested the role of the identified proteins and identifies which proteins might have the largest effect on reversing trastuzumab resistance.     

Proteomic Signatures of Acquired Letrozole Resistance in Breast Cancer: Suppressed Estrogen Signaling and Increased Cell Motility and Invasiveness

Aromatase inhibitors, such as letrozole, have become the first-line treatment for postmenopausal women with estrogen-dependent breast cancer. However, acquired resistance remains a major clinical obstacle. Previous studies demonstrated constitutive activation of the MAPK signaling, overexpression of HER2, and down-regulation of aromatase and ERα in letrozole-resistant breast cancer cells. Given the complex signaling network involved in letrozole-refractory breast cancer and the lack of effective treatment for hormone resistance, further investigation of aromatase inhibitor resistance by a novel systems biology approach may reveal previously unconsidered molecular changes that could be utilized as therapeutic targets. This study was undertaken to characterize for the first time global proteomic alterations occurring in a letrozole-resistant cell line. A quantitative proteomic analysis of the whole cell lysates of LTLT-Ca (resistant) versus AC-1 cells (sensitive) was performed to identify significant protein expression changes. A total of 1743 proteins were identified and quantified, of which 411 were significantly up-regulated and 452 significantly down-regulated (p < 0.05, fold change > 1.20). Bioinformatics analysis revealed that acquired letrozole resistance is associated with a hormone-independent, more aggressive phenotype. LTLT-Ca cells exhibited 84% and 138% increase in migration and invasion compared with the control cells. The ROCK inhibitor partially abrogated the enhanced migration and invasion of the letrozole-resistant cells. Flow cytometric analyses also demonstrated an increase in vimentin and twist expression in letrozole-resistance cells, suggesting an onset of epithelial to mesenchymal transition (EMT). Moreover, targeted gene expression arrays confirmed a 28-fold and sixfold up-regulation of EGFR and HER2, respectively, whereas ERα and pS2 were dramatically reduced by 28-fold and 1100-fold, respectively. Taken together, our study revealed global proteomic signatures of a letrozole-resistant cell line associated with hormone independence, enhanced cell motility, EMT and the potential values of several altered proteins as novel prognostic markers or therapeutic targets for letrozole resistant breast cancer.Aromatase inhibitors (AIs)¹ have increasingly been used to treat ER positive breast cancer in postmenopausal women as adjuvant or neoadjuvant therapy (1, 2). AIs block estrogen production by inhibiting the aromatization reaction that converts androgens to estrogens, resulting in the remission of estrogen dependent breast tumors. However, acquired resistance occurs in the majority of patients after several years of AI treatment, and this may ultimately lead to eventual relapse of the disease (3, 4). Therefore it is necessary to better understand the resistance mechanisms to abrogate or delay the onset of AI resistance. Numerous studies have used in vitro and in vivo models to dissect the adaptive signaling events in the development of AI resistance in breast cancer (5, 6). The in vitro long term estrogen deprivation (LTED) model has been proposed to represent AI resistance in breast cancer that also showed cross-resistance to other hormonal treatment (7). However, the LTEDaro lines did not cluster with the AI-resistant lines (8). Alternatively, in vivo models using cells derived from mouse xenografts have been widely used to study the mechanism of AI resistance and potential therapeutic strategies (3, 9–11). Notably, ER expression levels were up-regulated in the LTED model (7) but down-regulated in the letrozole resistant breast cancer cells (12, 13).In in vitro experiments, it has been found that although MCF-7 and T47D (both ER+ breast cancer cell lines) express detectable levels of aromatase, the enzymatic activity is rather low for experimental studies of the action of aromatase inhibitors and subsequent resistance to AIs. It is recognized that the aromatase activity in MCF-7aro cells is significantly higher than that in typical breast cancer and surrounding adipose stromal cells. However, the aromatase activity in breast tumors can be elevated in situ by cytokines, cAMP, and cancer-promoting agents which stimulate protein kinase C activity (14–17). Thus these MCF-7 and AC1 cell lines are appropriate models for studying the balance between the androgenic and estrogenic effect in breast cancer as they express significant levels of AR and ER. Clinically, it has been observed that ∼66% of breast carcinomas contain aromatase (the rate-limiting enzyme responsible for estrogen biosynthesis), and the estrogen synthesized in situ has a role in stimulating the tumor (18, 19). In breast, ovarian, uterine, and prostate cancer, activation of PI.3/II leads to the overexpression of aromatase within the tissues themselves, and this has been associated with an increase in tumor growth (20, 21).In the mouse xenograft model established in Brodie''s laboratory, MCF-7 cells were stably transfected with the human aromatase gene and grown in ovariectomized female nude mice treated with letrozole for over 56 weeks (12, 22). Subsequent studies of these long-term letrozole treated (LTLT-Ca) cells isolated from these tumors confirmed the up-regulation of Her2/MAPK signaling cascade and the p160 coactivator, amplified in breast cancer 1 (AIB1), as an adaptive survival pathway (5, 12, 13, 23). Inhibition of MAPK led to reduced cell proliferation and restoration of ER expression, implicating the occurrence of crosstalk between ER and growth factor receptor signaling. Moreover, inhibition of Her2 restored the sensitivity of LTLT-Ca cells to letrozole (10, 23). In the genome-wide analysis of several hormone resistant cell lines, elevated DNA replication, recombination, repair function, cell cycle control, and the pyrimidine metabolism pathway were also found as an enhanced survival mechanism in the resistant cells (6, 7). Given the complex signaling network involved in AI refractory breast cancer and the lack of effective treatment for hormone resistance, further investigation of AI resistance by a global proteomics-based systems biology approach may reveal previously unconsidered molecular changes that could be used as therapeutic targets. Therefore, the objective of this study is to characterize global proteomic alterations occurring in the letrozole resistant cell line, originating from the Brodie laboratory (12).Here we have performed a quantitative proteomic analysis of the whole cell lysis samples of LTLT-Ca against the letrozole sensitive control cell line, AC-1, using a gel-free approach. To achieve relative quantitation of proteins we used a tandem mass tag labeling technique where each sample is triply labeled for analytical precision. Fractionation and nanoflow reverse phase HPLC were employed in combination with a high-resolution tandem mass spectrometer for peptide separation and identification. Identified protein markers were then analyzed by bioinformatics tools to gain insight into global adaptive signaling modulations as a result of acquired resistance to letrozole.     

Blocking autophagy enhanced cytotoxicity induced by recombinant human arginase in triple-negative breast cancer cells

Depletion of arginine by recombinant human arginase (rhArg) has proven to be an effective cancer therapeutic approach for a variety of malignant tumors. Triple-negative breast cancers (TNBCs) lack of specific therapeutic targets, resulting in poor prognosis and limited therapeutic efficacy. To explore new therapeutic approaches for TNBC we studied the cytotoxicity of rhArg in five TNBC cells. We found that rhArg could inhibit cell growth in these five TNBC cells. Intriguingly, accumulation of autophagosomes and autophagic flux was observed in rhArg-treated MDA-MB-231 cells. Inhibition of autophagy by chloroquine (CQ), 3-methyladenine (3-MA) and siRNA targeting Beclin1 significantly enhanced rhArg-induced cytotoxic effect, indicating the cytoprotective role of autophagy in rhArg-induced cell death. In addition, N-acetyl-l-cysteine (NAC), a common antioxidant, blocked autophagy induced by rhArg, suggesting that reactive oxygen species (ROS) had an essential role in the cytotoxicity of rhArg. This study provides new insights into the molecular mechanism of autophagy involved in rhArg-induced cytotoxicity in TNBC cells. Meanwhile, our results revealed that rhArg, either alone or in combination with autophagic inhibitors, might be a potential novel therapy for the treatment of TNBC.Breast cancer, the most common cause of cancer death in women, is a kind of complex and heterogeneous neoplasm.¹ Approximately 15% of breast carcinomas are triple-negative breast cancers (TNBCs), which have high rates of recurrences and mortality.² TNBCs are defined by the lack of expression of estrogen receptor, progesterone receptor and human epidermal growth factor receptor type 2 (HER2). These tumors are characterized by clinically aggressive behaviors, high recurrence rate and poor prognosis. Owing to lack of targeted therapies (such as hormone therapy or anti-HER2 therapy), currently chemotherapy is the primary treatment for TNBC.³ Therefore, investigating new therapeutic approaches is urgently needed for improving the clinical outcome of TNBC therapy.Recently, deprivation of l-arginine has been a potential therapeutic method for cancers.⁴ By culturing cells in the arginine-free media, a variety of human cancer cells have been found to be auxotrophic for arginine, depletion of which resulted in cell death. Importantly, recombinant human arginase (rhArg) has shown potent anticancer effect in acute myeloid leukemia and acute lymphoblastic T-cell leukemia and solid tumors in vitro and in vivo^{5, 6, 7, 8, 9} and is currently under clinical investigation for the treatment of melanoma¹⁰ and hepatocellular carcinoma (HCC).¹¹ These carcinomas are auxotrophic for arginine, mainly because of the absence of arginine endogenous synthetical pathway. However, there are no reports about the efficiency in the therapy of breast cancer by rhArg through depletion of arginine.An increasing number of studies have shown that autophagy is stimulated in response to external stressors (such as starvation and oxidative stress) and internal needs (for example, removal of aggregate-prone proteins).¹² Autophagy is an evolutionarily conserved catabolic process responsible for the routine degradation of bulk superfluous or dysfunctional proteins and organelles.¹³ Autophagy serves as a protective role in response to a majority of anticancer drugs and in the pathogenesis process.^{14, 15} Not surprisingly, the relationship between autophagy and apoptosis, both genetically regulated and evolutionarily conserved, is complex, and appears to be related to cellular contexts.¹⁶ Meanwhile, mounting evidence accumulated has revealed that autophagy stimulation and reactive oxygen species (ROS) are closely linked in response to cancer therapeutics.^{17, 18} Notably, the essential contribution of mitochondrially generated ROS in the modulation of autophagy during starvation has been highlighted.In this study, we investigated whether rhArg might be a potential therapy for TNBC. We reported for the first time that rhArg-induced cell growth inhibition and caspase 3-independent apoptosis in MDA-MB-231 cells. Also, we found that rhArg could induce autophagy in MDA-MB-231 cells in a dose- and time-dependent manner. Interestingly, blocking autophagy potentiated cytotoxicity induced by rhArg, indicating that autophagy had a cytoprotective role in the treatment of rhArg. Meanwhile, ROS was involved in the autophagy and cell growth inhibition induced by rhArg. With our findings mentioned above, rhArg has shown potential to be a promising therapy for TNBC. Furthermore, the combination with autophagy-targeting drugs displayed multipronged treatment for breast cancer therapy.     

PKCλ/ι signaling promotes triple-negative breast cancer growth and metastasis

Triple-negative breast cancer (TNBC) is a distinct breast cancer subtype defined by the absence of estrogen receptor (ER), progesterone receptor (PR) and epidermal growth factor receptor 2 (HER2/neu), and the patients with TNBC are often diagnosed with higher rates of recurrence and metastasis. Because of the absence of ER, PR and HER2/neu expressions, TNBC patients are insensitive to HER2-directed and endocrine therapies available for breast cancer treatment. Here, we report that expression of atypical protein kinase C isoform, PKCλ/ι, significantly increased and activated in all invasive breast cancer (invasive ductal carcinoma or IDC) subtypes including the TNBC subtype. Because of the lack of targeted therapies for TNBC, we choose to study PKCλ/ι signaling as a potential therapeutic target for TNBC. Our observations indicated that PKCλ/ι signaling is highly active during breast cancer invasive progression, and metastatic breast cancers, the advanced stages of breast cancer disease that developed more frequently in TNBC patients, are also characterized with high levels of PKCλ/ι expression and activation. Functional analysis in experimental mouse models revealed that depletion of PKCλ/ι significantly reduces TNBC growth as well as lung metastatic colonization. Furthermore, we have identified a PKCλ/ι-regulated gene signature consisting of 110 genes, which are significantly associated with indolent to invasive progression of human breast cancer and poor prognosis. Mechanistically, cytokines such as TGFβ and IL1β could activate PKCλ/ι signaling in TNBC cells and depletion of PKCλ/ι impairs NF-κB p65 (RelA) nuclear localization. We observed that cytokine-PKCλ/ι-RelA signaling axis, at least in part, involved in modulating gene expression to regulate invasion of TNBC cells. Overall, our results indicate that induction and activation of PKCλ/ι promote TNBC growth, invasion and metastasis. Thus, targeting PKCλ/ι signaling could be a therapeutic option for breast cancer, including the TNBC subtype.Breast cancer is a clinically heterogeneous disease and both intra and inter-tumor heterogeneities provide great challenges for developing successful therapies. Expressions (or absence thereof) of estrogen receptor (ER), progesterone receptor (PR) and epidermal growth factor receptor 2 (HER2)/neu are widely used to clinically classify breast tumors into multiple therapeutic groups.¹ The ER/PR-positive and the HER2-positive breast cancer patients could be benefited from endocrine and HER2-targeted therapies.¹ However, triple-negative breast cancers (TNBCs), which represent ∼12–17% of all breast cancer,² lack ER, PR and HER2/neu expressions² and are not responsive to therapies targeting these receptors. Therefore, the only systemic therapy available for TNBC is chemotherapy.³ Furthermore, TNBC is associated with aggressive pathologic features like higher histology grade and mitotic index⁴ and often found to be associated with higher rate of metastasis and recurrence leading to limited clinical outcome.^{5, 6, 7, 8} Recurrence of TNBC tends to recur within a few years after successful initial treatment^{6, 9} and often develops metastasis to the bone, brain and lungs with poor prognosis.^{2, 6} Thus, identification of signaling pathways that regulate malignant progression of breast cancer subtypes, especially TNBCs, would be therapeutically important.In recent years, PKC signaling has been implicated in modulating invasion and metastasis of multiple tumors.^{10, 11} The PKC family consists of multiple serine/threonine kinases and the relative contribution of individual PKC isoforms during cancer progression varies due to pleiotropism.¹² PKC isoforms regulate diverse cellular functions such as cell-cycle regulation, cellular survival, cell–cell communications and apoptosis.¹³ In particular, atypical PKC isoforms, PKCζ and atypical protein kinase C lamda/iota (PKCλ/ι), are known to be important for chemotaxis, cell polarity, migration and wound healing processes.^{14, 15} Aberrations in all these processes are manifested in tumor progression and metastasis.¹⁴ Consistent with these notions, recent studies indicated that atypical PKCs are associated with various human cancers.^{10, 11} Importantly, the PKCλ/ι gene is located at the 3q26.2 genomic region, which is most frequently amplified in human cancer^{16, 17}, and overexpression of PKCλ/ι has been implicated in cancer development in multiple tissues including the lung,^{18, 19} pancreas,²⁰ stomach,²¹ colon,²² esophagus,²³ liver,²⁴ bile duct,²⁵ ovary,¹⁷ prostate²⁶ and brain.²⁷ Recently, few studies have been reported higher expression of PKCλ/ι in ER/PR- and HER-positive breast cancer and also in lymph node metastases.^{28, 29} Kojima et. al.²⁸ showed that PKCλ/ι expression is highly induced in the ER/PR- and HER2-positive IDCs compared with ductal carcinoma in situ (DCIS) and normal breast. PKCλ/ι forms apical-junctional complexes (AJCs) with other polarity proteins such as partitioning defective 3 homolog (PAR3) and partitioning defective 6 homolog (PAR6),^{30, 31, 32, 33} and invasiveness of breast tumor cells was shown to be associated with loss of PKCλ/ι localization from their apical domains.²⁸ In addition, predominant nuclear localization of PKCλ/ι in both normal and atypical ductal hyperplasia (ADH) lesions prompted the concept that PKCλ/ι might be in an inactive state in these lesions.²⁸ However, expression and activation of PKCλ/ι in TNBCs and the functional importance of PKCλ/ι signaling in relation to invasive breast cancer progression and metastasis are very poorly understood.^{10, 11}Here, we studied PKCλ/ι signaling during invasive progression of TNBC. We utilized expression evaluations in triple-negative IDCs as well as metastatic breast cancers of human patients, in vitro and in vivo functional assays, and global gene expression analysis of human patient samples. We concluded that PKCλ/ι signaling is an important regulator for invasion and metastatic progression of human breast cancers including triple-negative subtypes.     

Chemokine (C-C Motif) Ligand 2 Engages CCR2+ Stromal Cells of Monocytic Origin to Promote Breast Cancer Metastasis to Lung and Bone

Metastatic spread of cancer to distant vital organs, including lung and bone, is the overwhelming cause of breast cancer mortality and morbidity. Effective treatment of systemic metastasis relies on the identification and functional characterization of metastasis mediators to multiple organs. Overexpression of the chemokine (C-C motif) ligand 2 (CCL2) is frequently associated with advanced tumor stage and metastatic relapse in breast cancer. However, the functional mechanism of CCL2 in promoting organ-specific metastasis of breast cancer has not been rigorously investigated. Here, we used organ-specific metastatic sublines of the MDA-MB-231 human breast cancer cell line to demonstrate that overexpression of CCL2 promotes breast cancer metastasis to both lung and bone. Conversely, blocking CCL2 function with a neutralizing antibody reduced lung and bone metastases. The enhancement of lung and bone metastases by CCL2 was associated with increased macrophage infiltration and osteoclast differentiation, respectively. By performing functional assays with primary cells isolated from the wild type, CCL2 and CCR2 knock-out mice, we showed that tumor cell-derived CCL2 depends on its receptor CCR2 (chemokine, CC motif, receptor 2) expressed on stromal cells to exert its function in promoting macrophage recruitment and osteoclast differentiation. Overall, these data demonstrated that CCL2-expressing breast tumor cells engage CCR2⁺ stromal cells of monocytic origin, including macrophages and preosteoclasts, to facilitate colonization in lung and bone. Therefore, CCL2 and CCR2 are promising therapeutic targets for simultaneously inhibiting lung and bone metastasis of breast cancer.Breast cancer is the most common malignancy in women in the United States, with an estimated 182,000 new cases and 40,000 deaths in 2008 (1). Late stage breast cancer patients develop metastases in bone, lung, liver, brain, and other organs, which are responsible for most breast cancer-related mortality and morbidity (2). Severe complications from bone metastasis include debilitating bone fractures, nerve compression and bone pain, and hypercalcemia (3–5), whereas lung metastasis is accompanied by cough, bloody sputum, rib cage pain, and, eventually, failure of the respiratory functions (6). Colonization of different secondary organs by breast cancer is believed to be a complex, multigenic process that depends on productive interactions between tumor cells and stromal microenvironments through concerted actions of organ-specific metastasis genes (7, 8). Functional genomic analysis of preclinical models of breast cancer to bone, lung, and brain have identified distinct sets of organ-specific metastasis genes (9–11), providing novel mechanistic insights into key rate-limiting steps of metastasis to different organs. However, as advanced breast cancer patients often suffer from metastases at several secondary organs, identifying genes that are capable of instigating metastasis to multiple sites may provide the ideal targets for therapeutic intervention of systemic metastasis.Chemokines are small (8–14 kDa) proteins classified into four conserved groups (CXC, CC, C, and CX3C) based on the position of the first two cysteines that are adjacent to the amino terminus (12). They are chemotactic cytokines that stimulate directed migration of leukocytes in response to inflammatory signals. Chemokines are also involved in the maintenance of hematopoietic homeostasis, regulation of cell proliferation, tissue morphogenesis, and angiogenesis (13). Chemokines bind to the seven-transmembrane domain receptors to elicit downstream molecular events that coordinate cell movement. Even though chemokines are unlikely to be a contributing factor for tumor initiation, they can have pleiotropic effects on tumor progression (13, 14). Among more than 50 human chemokines, CCL2 is of particular importance. CCL2, also called monocyte chemoattractant protein-1 (MCP-1), is a potent chemoattractant for monocytes, memory T lymphocytes, and natural killer cells (15). It is involved in a number of inflammatory conditions associated with monocyte recruitment, including delayed hypersensitivity reactions, bacterial infection, arthritis, and renal disease (15). The importance of CCL2 in cancer was manifested by its overexpression in a variety of tumor types, including glioma, ovarian, esophagus, lung, breast, and prostate cancers (15–17). In prostate cancer, CCL2 expression levels was associated with advanced pathological stage (16). Importantly, CCL2-neutralizing antibodies inhibit bone resorption in vitro and bone metastasis in vivo (18–20). In lung cancer, serum CCL2 levels were elevated in lung cancer patients with bone metastasis compared with localized diseases. Neutralizing antibodies against CCL2 also inhibited the tumor conditioned media-induced osteoclast formation in vitro and bone metastasis in vivo (17). Taken together, these findings suggested a role of CCL2 in bone metastasis.A potential role of CCL2 in breast cancer progression and metastasis has been indicated by the analysis of CCL2 expression of tumor and serum samples from breast cancer patients. Serum CCL2 levels were significantly higher in postmenopausal breast cancer patients than in age-matched controls (21). Over 50% of breast cancer tumor samples had intense staining of CCL2 in tumor cells (22). Prognostic analysis further revealed that high expression of CCL2 was correlated with advanced tumor stage, lymph node metastasis (23), and early relapse (24). CCL2 up-regulation in breast tumors was also associated with the infiltration of tissue-associated macrophages (TAMs)³ and with increased microvessel density (22, 24). TAMs have been known to contribute to primary tumor progression and metastasis of breast cancer (25), which is supported by epidemiological evidence showing that TAM infiltration portended a poor clinical outcome (26, 27). However, whether the function of CCL2 in modulating activity of macrophages and possibly other cell types is important for breast tumor organotropic metastasis has not been rigorously investigated. CCL2 may engage organ-specific cell types derived from the same bone marrow myelomonocytic progenitors. These progenitors differentiate into osteoclast precursors in bone or into blood monocytes that eventually become mature macrophages in different tissues, like alveolar macrophages in lung (28). These stromal cell types of myelomonocytic origin may contribute to different functions in different organ-specific metastases. Another unresolved question regarding the function of CCL2 in tumor-stroma interaction is the functional involvement of CCL2 receptors. CCL2 can bind to both CCR2 and CCR4 (29, 30). Loss of function studies in mice showed CCL2 and CCR2 knock-out mice displayed similar impairments in monocyte migration (31, 32), suggesting that CCR2 is the major functional receptor for CCL2. Understanding whether CCR2 deficiency in stromal cells leads to compromised monocyte engagement by CCL2-expressing tumor cells may have important implications in designing targeting therapeutics against the CCL2/CCR2 axis.In this study, we used the recently developed organ-specific metastatic sublines of the human breast cancer cell MDA-MB-231 (9, 10, 33) and showed that overexpression of CCL2 promotes both lung and bone metastases. This function was associated with increased TAM infiltration in lung metastasis and increased osteoclast differentiation in bone metastasis, respectively. Furthermore, by using macrophages and bone marrow cells isolated from wild type, CCL2-deficient, and CCR2-deficient mice, we showed that CCR2 expression in stromal cells is essential for tumor-derived CCL2 to recruit macrophages and promote osteoclastogenesis. Targeting tumor-derived CCL2 by a neutralizing antibody significantly reduced metastasis formation in both bone and lung.     

Printor, a Novel TorsinA-interacting Protein Implicated in Dystonia Pathogenesis

Early onset generalized dystonia (DYT1) is an autosomal dominant neurological disorder caused by deletion of a single glutamate residue (torsinA ΔE) in the C-terminal region of the AAA⁺ (ATPases associated with a variety of cellular activities) protein torsinA. The pathogenic mechanism by which torsinA ΔE mutation leads to dystonia remains unknown. Here we report the identification and characterization of a 628-amino acid novel protein, printor, that interacts with torsinA. Printor co-distributes with torsinA in multiple brain regions and co-localizes with torsinA in the endoplasmic reticulum. Interestingly, printor selectively binds to the ATP-free form but not to the ATP-bound form of torsinA, supporting a role for printor as a cofactor rather than a substrate of torsinA. The interaction of printor with torsinA is completely abolished by the dystonia-associated torsinA ΔE mutation. Our findings suggest that printor is a new component of the DYT1 pathogenic pathway and provide a potential molecular target for therapeutic intervention in dystonia.Early onset generalized torsion dystonia (DYT1) is the most common and severe form of hereditary dystonia, a movement disorder characterized by involuntary movements and sustained muscle spasms (1). This autosomal dominant disease has childhood onset and its dystonic symptoms are thought to result from neuronal dysfunction rather than neurodegeneration (2, 3). Most DYT1 cases are caused by deletion of a single glutamate residue at positions 302 or 303 (torsinA ΔE) of the 332-amino acid protein torsinA (4). In addition, a different torsinA mutation that deletes amino acids Phe³²³–Tyr³²⁸ (torsinA Δ323–328) was identified in a single family with dystonia (5), although the pathogenic significance of this torsinA mutation is unclear because these patients contain a concomitant mutation in another dystonia-related protein, ϵ-sarcoglycan (6). Recently, genetic association studies have implicated polymorphisms in the torsinA gene as a genetic risk factor in the development of adult-onset idiopathic dystonia (7, 8).TorsinA contains an N-terminal endoplasmic reticulum (ER)³ signal sequence and a 20-amino acid hydrophobic region followed by a conserved AAA⁺ (ATPases associated with a variety of cellular activities) domain (9, 10). Because members of the AAA⁺ family are known to facilitate conformational changes in target proteins (11, 12), it has been proposed that torsinA may function as a molecular chaperone (13, 14). TorsinA is widely expressed in brain and multiple other tissues (15) and is primarily associated with the ER and nuclear envelope (NE) compartments in cells (16–20). TorsinA is believed to mainly reside in the lumen of the ER and NE (17–19) and has been shown to bind lamina-associated polypeptide 1 (LAP1) (21), lumenal domain-like LAP1 (LULL1) (21), and nesprins (22). In addition, recent evidence indicates that a significant pool of torsinA exhibits a topology in which the AAA⁺ domain faces the cytoplasm (20). In support of this topology, torsinA is found in the cytoplasm, neuronal processes, and synaptic terminals (2, 3, 15, 23–26) and has been shown to bind cytosolic proteins snapin (27) and kinesin light chain 1 (20). TorsinA has been proposed to play a role in several cellular processes, including dopaminergic neurotransmission (28–31), NE organization and dynamics (17, 22, 32), and protein trafficking (27, 33). However, the precise biological function of torsinA and its regulation remain unknown.To gain insights into torsinA function, we performed yeast two-hybrid screens to search for torsinA-interacting proteins in the brain. We report here the isolation and characterization of a novel protein named printor (protein interactor of torsinA) that interacts selectively with wild-type (WT) torsinA but not the dystonia-associated torsinA ΔE mutant. Our data suggest that printor may serve as a cofactor of torsinA and provide a new molecular target for understanding and treating dystonia.     

The Rho-specific Guanine Nucleotide Exchange Factor Dbs Regulates Breast Cancer Cell Migration

Dbs is a Rho-specific guanine nucleotide exchange factor (RhoGEF) that regulates neurotrophin-3-induced cell migration in Schwann cells. Here we report that Dbs regulates cell motility in tumor-derived, human breast epithelial cells through activation of Cdc42 and Rac1. Cdc42 and Rac1 are activated in T47D cells that stably express onco- or proto-Dbs, and activation is dependent upon growth of the cells on collagen I. Transient suppression of expression of Cdc42 or Rac1 by small interfering RNAs attenuates Dbs-enhanced motility. Both onco- and proto-Dbs-enhanced motility correlates with an increase in tyrosine phosphorylation of focal adhesion kinase on Tyr-397 and p130^Cas on Tyr-410 and an increase in the abundance of the Crk·p130^Cas complex. Suppression of expression of Cdc42 or its effector, Ack1, reduces tyrosine phosphorylation of focal adhesion kinase and p130^Cas and disrupts the Crk·p130^Cas complex. We further determined that suppression of expression of Cdc42, Ack1, p130^Cas, or Crk reduces Rac1 activation and cell motility in Dbs-expressing cells to a level comparable with that in vector cells. Therefore, a cascade of activation of Cdc42 and Rac1 by Dbs through the Cdc42 effector Ack1 and the Crk·p130^Cas complex is established. Suppression of the expression of endogenous Dbs reduces cell motility in both T47D cells and MDA-MB-231 cells, which correlates with the down-regulation of Cdc42 activity. This suggests that Dbs activates Cdc42 in these two human breast cancer cell lines and that the normal function of Dbs may be required to support cell movement.Rho GTPases are a subfamily of the Ras superfamily of small signaling molecules that are widely expressed in mammalian cells (1). RhoA, Cdc42, and Rac1 are the most extensively studied members of the Rho GTPase family, and each plays a prominent and discrete role in cell migration (2, 3). Cdc42 promotes the formation of filopodia and is required to establish cell polarity (3–5); Rac1 promotes the formation of lamellipodia at the leading edge of motile cells (6), and RhoA promotes the formation of stress fibers which generate the traction forces needed to retract the cell tail and move the cell body beyond the leading edge (7, 8). Consistent with this important role in cell motility, RhoA, Cdc42, and Rac1 are often overexpressed in human tumors including breast, lung, and colon (9), and overexpression of constitutively active RhoA, Cdc42, or Rac1 increases cell migration and invasion (2, 10, 11).The spatiotemporal regulation of Rho GTPase activity is tightly controlled by three classes of proteins. Rho-specific guanine nucleotide exchange factors (RhoGEFs)2 activate Rho proteins by facilitating the exchange of GDP for GTP; Rho GTPase-activating proteins (RhoGAPs) stimulate the intrinsic rate of hydrolysis of Rho proteins, thus converting them into their inactive state; Rho-specific guanine nucleotide dissociation inhibitors (RhoGDIs) compete with RhoGEFs for binding to GDP-bound Rho proteins and sequester Rho in the inactive state (12).Dbs was identified in the screen for proteins whose overexpression cause malignant growth in murine fibroblasts (13, 14). The full-length Dbs protein (proto-Dbs) is a RhoGEF family member which contains multiple recognizable domains (Fig. 1A) including a Sec14-like domain, spectrin-like repeats, a RhoGEF domain (includes a DH and PH domain), and an SH3 domain (13). The original oncogenic version of Dbs that was identified (amino acid residues 525–1097; designated onco-Dbs) contains the RhoGEF domain alone. When expressed in murine fibroblasts, the transforming and catalytic activity of Dbs is subject to autoinhibition that is mediated by the NH₂-terminal Sec14 domain (15). Although the endogenous function of Dbs is not known, recent studies suggest that Dbs and the Rac-specific exchange factor Tiam1 regulate neurotrophin-stimulated cell migration in Schwann cells through activation of Cdc42 and Rac1, respectively (16, 17).Open in a separate windowFIGURE 1.Onco-Dbs and proto-Dbs induce cell migration in tumor-derived breast epithelial cells. A, domain structure of the onco-Dbs and proto-Dbs proteins (Sec14 = Sec14-like domain; Spec = Spectrin-like repeats; DH = Dbl homology domain; PH = pleckstrin homology domain; SH3 = Src homology 3 domain). B, stable expression of HA-epitope-tagged onco-Dbs (M_r = 65) and proto-Dbs (M_r = 129 kDa) was confirmed by Western blot using an anti-HA antibody. Three independent sets of cell lines were generated. C, T47D cells stably expressing vector (Vec), onco-Dbs, or proto-Dbs were compared in a transwell motility assay on filters pre-coated with collagen I. The motility of cells stably expressing onco-Dbs or proto-Dbs is expressed relative to that of cells stably expressing vector. Data are represented as the mean ± S.D. of three independent experiments performed in triplicate. D, T47D cells stably expressing vector, onco-Dbs, or proto-Dbs were cultured to monolayer on dishes coated with poly-l-lysine or collagen I, as indicated. Cells were serum-starved overnight, and then the surface of the plate was scraped. Migration of cells at the wound edge was monitored and photographed at 18 h. Representative images are shown. E, growth curves of T47D cells stably expressing vector, onco-Dbs, or proto-Dbs. Cells were cultured in triplicate on poly-l-lysine (filled symbols) or on dishes pre-coated with collagen I (open symbols) and counted on the indicated days. Data shown are representative of three independent experiments.Conversion of Rho proteins to their active GTP-bound state allows them to interact with effector signaling molecules. Ack1 is a nonreceptor-tyrosine kinase that binds to active Cdc42 but not Rac1 or RhoA (18, 19). Activated Ack1 is overexpressed in primary tumors and cancer cell lines and has been implicated in cancer metastasis (20). Recent studies have identified a signaling complex that regulates the motility of human breast epithelial cells that contains Cdc42, Ack1, p130^Cas, and Crk (21). Ack1 and p130^Cas interact through their respective SH3 domains, and Ack1 phosphorylates p130^Cas in a collagen I-dependent manner. p130^Cas was first identified as a hyperphosphorylated adapter protein in cells transformed by v-Src and v-Crk (22, 23). Further studies showed that p130^Cas is associated with both cellular Src and Crk in a tyrosine phosphorylation-dependent manner (24, 25). Focal adhesion kinase (FAK) binds to the NH₂ terminus of p130^Cas and phosphorylates the COOH terminus in a region that is involved in p130^Cas binding to Src (26). The binding of Crk to p130^Cas recruits binding partners to the SH3 domain of Crk, including C3G and DOCK180, which activate Rap1 and Rac1, respectively (27–31). Thus, formation of the Crk·p130^Cas complex is considered to be a molecular switch that can induce cell migration by activating Rac1 (32).Here we show that both proto-Dbs and onco-Dbs increase cell migration in human breast adenocarcinoma cells in a collagen I-dependent manner. Increased motility is dependent upon the activation of Rac1 and Cdc42 and is mediated by the assembly of Crk·p130^Cas complexes. Suppression of endogenous Dbs expression in human tumor-derived breast epithelial cells limits cell motility, suggesting that Dbs may be a critical regulator of cell behavior in breast cancer.     

Multipattern Consensus Regions in Multiple Aligned Protein Sequences and Their Segmentation

Decomposing a biological sequence into its functional regions is an important prerequisite to understand the molecule. Using the multiple alignments of the sequences, we evaluate a segmentation based on the type of statistical variation pattern from each of the aligned sites. To describe such a more general pattern, we introduce multipattern consensus regions as segmented regions based on conserved as well as interdependent patterns. Thus the proposed consensus region considers patterns that are statistically significant and extends a local neighborhood. To show its relevance in protein sequence analysis, a cancer suppressor gene called p53 is examined. The results show significant associations between the detected regions and tendency of mutations, location on the 3D structure, and cancer hereditable factors that can be inferred from human twin studies.[1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27]     

Analysis of Free Energy Signals Arising from Nucleotide Hybridization Between rRNA and mRNA Sequences during Translation in Eubacteria

A decoding algorithm is tested that mechanistically models the progressive alignments that arise as the mRNA moves past the rRNA tail during translation elongation. Each of these alignments provides an opportunity for hybridization between the single-stranded, -terminal nucleotides of the 16S rRNA and the spatially accessible window of mRNA sequence, from which a free energy value can be calculated. Using this algorithm we show that a periodic, energetic pattern of frequency 1/3 is revealed. This periodic signal exists in the majority of coding regions of eubacterial genes, but not in the non-coding regions encoding the 16S and 23S rRNAs. Signal analysis reveals that the population of coding regions of each bacterial species has a mean phase that is correlated in a statistically significant way with species () content. These results suggest that the periodic signal could function as a synchronization signal for the maintenance of reading frame and that codon usage provides a mechanism for manipulation of signal phase.[1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29,30,31,32]     

Proinsulin and the Genetics of Diabetes Mellitus

Insulin plays a central role in the regulation of vertebrate metabolism. The hormone, the post-translational product of a single-chain precursor, is a globular protein containing two chains, A (21 residues) and B (30 residues). Recent advances in human genetics have identified dominant mutations in the insulin gene causing permanent neonatal-onset DM² (1–4). The mutations are predicted to block folding of the precursor in the ER of pancreatic β-cells. Although expression of the wild-type allele would in other circumstances be sufficient to maintain homeostasis, studies of a corresponding mouse model (5–7) suggest that the misfolded variant perturbs wild-type biosynthesis (8, 9). Impaired β-cell secretion is associated with ER stress, distorted organelle architecture, and cell death (10). These findings have renewed interest in insulin biosynthesis (11–13) and the structural basis of disulfide pairing (14–19). Protein evolution is constrained not only by structure and function but also by susceptibility to toxic misfolding.Insulin plays a central role in the regulation of vertebrate metabolism. The hormone, the post-translational product of a single-chain precursor, is a globular protein containing two chains, A (21 residues) and B (30 residues). Recent advances in human genetics have identified dominant mutations in the insulin gene causing permanent neonatal-onset DM² (1–4). The mutations are predicted to block folding of the precursor in the ER of pancreatic β-cells. Although expression of the wild-type allele would in other circumstances be sufficient to maintain homeostasis, studies of a corresponding mouse model (5–7) suggest that the misfolded variant perturbs wild-type biosynthesis (8, 9). Impaired β-cell secretion is associated with ER stress, distorted organelle architecture, and cell death (10). These findings have renewed interest in insulin biosynthesis (11–13) and the structural basis of disulfide pairing (14–19). Protein evolution is constrained not only by structure and function but also by susceptibility to toxic misfolding.