Enhanced Prediction of Src Homology 2 (SH2) Domain Binding Potentials Using a Fluorescence Polarization-derived c-Met,c-Kit,ErbB, and Androgen Receptor Interactome

Many human diseases are associated with aberrant regulation of phosphoprotein signaling networks. Src homology 2 (SH2) domains represent the major class of protein domains in metazoans that interact with proteins phosphorylated on the amino acid residue tyrosine. Although current SH2 domain prediction algorithms perform well at predicting the sequences of phosphorylated peptides that are likely to result in the highest possible interaction affinity in the context of random peptide library screens, these algorithms do poorly at predicting the interaction potential of SH2 domains with physiologically derived protein sequences. We employed a high throughput interaction assay system to empirically determine the affinity between 93 human SH2 domains and phosphopeptides abstracted from several receptor tyrosine kinases and signaling proteins. The resulting interaction experiments revealed over 1000 novel peptide-protein interactions and provided a glimpse into the common and specific interaction potentials of c-Met, c-Kit, GAB1, and the human androgen receptor. We used these data to build a permutation-based logistic regression classifier that performed considerably better than existing algorithms for predicting the interaction potential of several SH2 domains.Src homology 2 protein domains (SH2)¹ are modular self-folding entities of about 100 amino acids that bind to tyrosine-phosphorylated peptide sequences contained within target proteins. The SH2 domain (1–3) was originally described nearly 20 years ago as an N-terminal region of the FES protein kinase that was not required for kinase activity but was important for its regulation. More recent studies have demonstrated that SH2 domains exist in many signaling molecules, including PLCγ1, Ras GAP, c-Src, and PI3KR. SH2 domains have been shown to enable the interaction of these signaling proteins with growth factor receptors such as FGFR1, EGFR, c-Met, and PDGFR in a phosphospecific manner (4–9). Subsequently, random peptide library screening approaches were used to define sequence motifs that resulted in the highest affinity interactions within particular SH2 domain classes (10, 11). For example, peptide sequences containing the pYEEI, pYXN, and pYMXM motifs were described to result in the highest affinity interactions with the SH2 domains from c-Src, Grb2, and the PI3KR SH2 domains, respectively. Data from such experiments have been used to generate predictions regarding the likelihood that any particular peptide sequence will interact with any particular SH2 domain (12–14).Unfortunately, the predictive performance of these algorithms has not been thoroughly empirically tested or optimized for biologically derived peptide sequences. We and others reported the first comprehensive cloning, expression, and functional analysis of human genome-encoded SH2 domains using a protein microarray-based interaction analysis approach (15–17). Similarly, peptide arrays have been used to query the interaction potential of SH2 domains with biologically derived peptide sequences in a semi-quantitative manner (18). These studies demonstrated that most biologically derived peptide sequences contained within RTKs and signaling proteins do not represent best fit sequence motifs and interact at a much lower affinity than with the optimal sequence motifs identified previously from random peptide libraries. Studies with biologically derived peptides indicated that context nonpermissive amino acids often contribute as much predictive information regarding interaction selectivity as positively contributing amino acids (19). Taken together, these results suggest that the collection of large quantitative protein interaction datasets between SH2 domains and biologically derived peptide sequences might be informative for building better algorithms that predict bona fide SH2 domain interaction sites within human protein sequences.Although protein microarrays enabled the first systems-level glimpse at SH2 domain selectivity (15, 17), they had several limitations that resulted in reduced ability to identify low affinity interactions in comparison with solution phase methods (20). We therefore designed a high throughput fluorescence polarization approach that allowed for lower affinity interactions to be defined between SH2 domains and phosphopeptides of the ErbB family of receptor tyrosine kinases (RTKs) than was possible with protein microarrays (20).RTKs are vital mediators of signal transduction in multicellular organisms. RTKs typically function as transmembrane receptors that contain a tyrosine kinase and other motifs that enable interaction with other intracellular proteins. Human cells often express many different RTK proteins from the set of 57 RTK genes encoded by the human genome (21). These RTKs may be activated in different combinations to transduce common and specific downstream signals (22). For a recent review of the complexity of RTK signaling networks, see Ref. 23. Following activation, RTKs are phosphorylated on several intracellular tyrosine residues that serve as recruitment sites for SH2 domains (15–18, 20). Activation of RTK signaling networks may cause changes in cellular motility, proliferation, survival, and cytoskeletal arrangement. Definition of their signaling capacity represents an important and unsolved problem in cell biology. Although most studies to date have focused on the role of singular RTKs in cancer progression, co-activation of RTKs derived from several unique RTK genes has recently emerged as an important driver of cancer progression (24–27). Co-activation of modules of RTKs may provide robustness against therapies designed to inhibit a single RTK (25).Herein, we profiled the interaction potential of two RTKs and two signaling proteins and compared them with the recruitment potential of the ErbB family that we have previously profiled (28). The ErbB family, c-Met, and c-Kit RTKs have been shown to drive the progression of many cancer types, including breast, head and neck, lung (29), gastrointestinal, and stomach cancers (30). Downstream adaptor proteins often augment the signaling potential of RTKs by acting as scaffolds for recruitment of many additional proteins (31–33). Therefore, we also included peptides in our study derived from the Gab1 adaptor protein, which is critical for mediating signaling networks downstream of c-Met and potentially other RTKs (34).Finally, alternative oncogenic signaling networks may have points of cross-talk with tyrosine kinase signaling networks. Steroid hormone receptors such as the androgen receptor (AR) have been shown to associate with RTKs such as EGFR (35), to be substrates of tyrosine kinases (36, 37), and to drive the progression of prostate cancer (36). We therefore queried the interaction potential of phosphopeptides derived from AR with a set of 93 of the 120 SH2 domains encoded in the human genome. We subsequently used this interaction dataset to develop a permutation-based logistic regression classifier (PEBL) for predicting the interaction potential of SH2 domains and biologically derived phosphotyrosine-containing peptides.     

SWAP-70: A New Type of Oncogene

SWAP-70 is a protein that has been suggested to be involved in regulation of actin rearrangement. Having discovered that an artificially-derived mutant of SWAP-70 can transform mouse embryo fibroblasts, we searched for naturally-occurring mutations in the SWAP-70 gene, finding listings for several on the Web at www.sanger.ac.uk/genetics/CGP/cosmic/, including three mutations found in ovarian cancers. (The number of such mutations has now reached 13 out of 228 tumors). We created expression vectors for the mutant SWAP-70 proteins and introduced these into NIH3T3 cells. The cells expressing the mutant SWAP-70 constructs exhibited faster growth than the parental or wild-type SWAP-70-expressing cells. In most instances, cells that are able to grow in soft agar will form tumors in nude mice. While SWAP-70-transformed cells grew in soft agar, they failed to form tumors in nude mice. This result implies that transformation by the SWAP-70 mutants is unique. The cells bearing the mutant SWAP-70 genes were sensitive to nutrient starvation, supporting the idea that they are transformed cells. However, they failed to pile up and demonstrated contact inhibition, unlike most normal transformed cells. Upon expression of human SWAP-70 genes, MEK1 was activated. This activation appeared to contribute to the saturation density of the cells. As SWAP-70 has been shown to be the last protein to receive signals from cytokines, it is likely that there is a putative feedback signaling pathway, and that disorder of this signaling pathway can transform cells. Accordingly, this may explain why SWAP-70-transformed cells have different characteristics than most transformed cells.     

Androgens as therapy for androgen receptor-positive castration-resistant prostate cancer

Prostate cancer is the most frequently diagnosed non-cutaneous tumor of men in Western countries. While surgery is often successful for organ-confined prostate cancer, androgen ablation therapy is the primary treatment for metastatic prostate cancer. However, this therapy is associated with several undesired side-effects, including increased risk of cardiovascular diseases. Shortening the period of androgen ablation therapy may benefit prostate cancer patients. Intermittent Androgen Deprivation therapy improves quality of life, reduces toxicity and medical costs, and delays disease progression in some patients. Cell culture and xenograft studies using androgen receptor (AR)-positive castration-resistant human prostate cancers cells (LNCaP, ARCaP, and PC-3 cells over-expressing AR) suggest that androgens may suppress the growth of AR-rich prostate cancer cells. Androgens cause growth inhibition and G1 cell cycle arrest in these cells by regulating c-Myc, Skp2, and p27^Kip via AR. Higher dosages of testosterone cause greater growth inhibition of relapsed tumors. Manipulating androgen/AR signaling may therefore be a potential therapy for AR-positive advanced prostate cancer.     

Caffeic Acid Phenethyl Ester Causes p21Cip1 Induction, Akt Signaling Reduction, and Growth Inhibition in PC-3 Human Prostate Cancer Cells

Caffeic acid phenethyl ester (CAPE) treatment suppressed proliferation, colony formation, and cell cycle progression in PC-3 human prostate cancer cells. CAPE decreased protein expression of cyclin D1, cyclin E, SKP2, c-Myc, Akt1, Akt2, Akt3, total Akt, mTOR, Bcl-2, Rb, as well as phosphorylation of Rb, ERK1/2, Akt, mTOR, GSK3α, GSK3β, PDK1; but increased protein expression of KLF6 and p21^Cip1. Microarray analysis indicated that pathways involved in cellular movement, cell death, proliferation, and cell cycle were affected by CAPE. Co-treatment of CAPE with chemotherapeutic drugs vinblastine, paclitaxol, and estramustine indicated synergistic suppression effect. CAPE administration may serve as a potential adjuvant therapy for prostate cancer.     

Segregation of partly melted molecules: isolation of CpG islands by polyacrylamide gel electrophoresis

The technique of segregation of partly melted molecules (SPM) is a convenient and efficient method to isolate DNA fragments associated with CpG islands. The approach is conceptually simple and uses denaturant gradient gel electrophoresis to separate DNA molecules digested with restriction endonucleases. The SPM methodology has successfully been applied to the identification of genes from anonymous, unsequenced DNA fragments and CpG islands methylated in human cancer. In this article the theoretical background and practical application of the SPM method is reviewed.     

Effects of methyl mercury, mercuric sulfide and cinnabar on active avoidance responses, Na+/K+-ATPase activities and tissue mercury contents in rats

This study compared the neurobehavioral toxicities of three mercurial compounds: methyl mercury (MeHg) which is soluble and organic. and mercuric sulfide (HgS) and cinnabar (naturally occurring HgS), which are insoluble and inorganic. Cinnabar, a Chinese mineral medicine, is still used as a sedative in some Asian countries, but there is relatively little toxicological information about it. These mercurial compounds were administered intraperitoneally (MeHg, 2 mg/ kg) or orally (HgS and cinnabar, 1.0 g/kg) to male rats once every day for 13 consecutive days with assays conducted during or after discontinuous administration for 1 h, 2, 8 and 33 weeks. Neurotoxicity was assessed based on the active avoid-ance response and locomotor activity. The results obtained showed that MeHg and cinnabar prominently and irreversibly caused a decrease in body weight, prolongation of latency for escape from electric shock, a decrease in the percentage for the conditioned avoidance response (CAR) to electric shock, impairment of spontaneous locomotion and inhibition of Na+/K+-ATPase activity of the cerebral cortex. In contrast. HgS reversibly inhibited spontaneous locomotion and Na+/K+-ATPase activity. It was noted that HgS significantly decreased the latency of escape from electric shock during the ad-ministration period, which lasted for 33 weeks after discontinuous administration. In fact that pretreatment with arecoline (a cholinergic receptor agonist) but not fipexide (a dopaminergic receptor agonist) could significantly shorten the prolonged latency for escape caused by MeHg and cinnabar, suggested that the deficit in the active avoidance response was perhaps, at least in part, mediated by the dysfunction of the cholinergic rather than the dopaminergic system. Determination of the Hg levels of the whole blood and cerebral cortex revealed that the tissue mercury content was highly correlated with the degree of neurobehavioral toxicity of these Hg compounds. These findings suggest that insoluble HgS and cinnabar can be absorbed from the G-I tract and distributed to the brain. The possibility that contamination due to other minerals in the cinnabar is responsible for the greater neurotoxic effects compared to HgS is under investigation.     

Identification of thioridazine,an antipsychotic drug,as an antiglioblastoma and anticancer stem cell agent using public gene expression data

Glioblastoma (GBM) is a common and malignant tumor with a poor prognosis. Glioblastoma stem cells (GSCs) have been reported to be involved in tumorigenesis, tumor maintenance and therapeutic resistance. Thus, to discover novel candidate therapeutic drugs for anti-GBM and anti-GSCs is an urgent need. We hypothesized that if treatment with a drug could reverse, at least in part, the gene expression signature of GBM and GSCs, this drug may have the potential to inhibit pathways essential in the formation of GBM and thereby treat GBM. Here, we collected 356 GBM gene signatures from public databases and queried the Connectivity Map. We systematically evaluated the in vitro antitumor effects of 79 drugs in GBM cell lines. Of the drugs screened, thioridazine was selected for further characterization because it has potent anti-GBM and anti-GSCs properties. When investigating the mechanisms underlying the cytocidal effects of thioridazine, we found that thioridazine induces autophagy in GBM cell lines, and upregulates AMPK activity. Moreover, LC3-II was upregulated in U87MG sphere cells treated with thioridazine. In addition, thioridazine suppressed GBM tumorigenesis and induced autophagy in vivo. We not only repurposed the antipsychotic drug thioridazine as a potent anti-GBM and anti-GSCs agent, but also provided a new strategy to search for drugs with anticancer and anticancer stem cell properties.Glioblastomas (GBM), the most common and most aggressive primary brain tumors in adults, are classified as grade IV astrocytomas by the World Health Organization and account for 54% of all gliomas.¹ Surgery is typically followed by radiation therapy and chemotherapy with temozolomide (TMZ), which has been in clinical use since 2005.^{2, 3} Despite this multimodal approach, the median survival time of GBM patients is ~14.6 months.³ Therefore, a large number of new drugs are in development for GBM treatment.Instead of focusing on a single drug target, using a batch of genes to query the Connectivity Map (Cmap, http://www.broad.mit.edu/cmap/) may not only allow multiple targets to be considered simultaneously, but it may also identify potential new drugs. Cmap is a database that provides ~7000 microarray expression profiles (conducted on Affymetrix HG-U133A arrays) from four different cancer cell lines treated with 1309 molecular drugs. Of the 1309 drugs included in Cmap, most are currently used in clinical treatment or are well-developed drugs; thus, we can rapidly identify potential drugs and proceed to clinical trial.Thioridazine is an antipsychotic drug and is widely used to treat schizophrenia and psychosis. Recently, it has been shown that patients with schizophrenia have a lower risk of getting cancer (1.93%) than patients without schizophrenia (2.97%).⁴ In addition, inverse cancer comorbidity has been reported in people with certain CNS disorders, and pharmacological treatments is one of possible explanations.⁵Using in silico drug screening via Cmap followed by empirical validations, we discovered that thioridazine can reduce the viability of GBM cells and GBM stem cells, induce autophagy and affect the expressions of related proteins in GBM cells. Thus, thioridazine has potential to treat GBM.     

Presence of diabetes-inhibiting, glutamic acid decarboxylase-specific, IL-10-dependent, regulatory T cells in naive nonobese diabetic mice

Immunization of NOD mice with autoantigens such as glutamic acid decarboxylase (GAD) 221-235 peptide (p221) can induce Ag-specific CD4(+) T regulatory (Tr) cells. However, it is unclear whether these Tr cells acquire their regulatory capacity due to immunization or whether they are constitutively harbored in unimmunized naive mice. To address this question, we used an I-Ag7 tetramer to isolate p221-specific T cells from naive NOD mice (N221(+) cells) after peptide-specific in vitro expansion. The N221(+) T cells produced IFN-gamma and IL-10, but very little IL-4, in response to p221 stimulation. These T cells could function as regulatory cells and inhibit in vitro proliferation of diabetogenic BDC2.5 cells. This suppressive activity was cell contact-independent and was abrogated by Abs to IL-10 or IL-10R. Interestingly, IL-2 produced by other T cells present in the cell culture induced unactivated N221(+) T cells to exhibit regulatory activities involving production of IL-10. In vivo, N221(+) cells inhibited diabetes development when cotransferred with NOD splenocytes into NOD/scid recipients. Together, these results demonstrate that p221-specific IL-10-dependent Tr cells, including Tr type 1 cells, are present in naive NOD mice. The use of spontaneously arising populations of GAD peptide-specific Tr cells may represent a promising immunotherapeutic approach for preventing type 1 diabetes.     

Polarized development of memory cell-like IFN-gamma-producing cells in the absence of TCR zeta-chain

TCR/CD3 complex-mediated signals play critical roles in regulating CD4(+) Th cell differentiation. In this report, we have examined the in vivo role of a key TCR/CD3 complex molecule zeta-chain in regulating the differentiation of Th cells. We have studied T cells from zeta-chain-deficient mice (zetaKO mice), zeta-chain-bearing mice (zeta(+) mice), and from zetaKO mice expressing a FcRgamma chain transgene (FcRgammaTG, zetaKO mice). Our results demonstrated that, compared with those of control mice, CD4(+) T cells and not CD8(+) T cells from zetaKO mice were polarized into IFN-gamma-producing cells. Some of these IFN-gamma-producing cells could also secrete IL-10. Interestingly, zetaKO mouse T cells produced IFN-gamma even after they were cultured in a Th2 condition. Our studies to determine the molecular mechanisms underlying the polarized IFN-gamma production revealed that the expression level of STAT4 and T-bet were up-regulated in freshly isolated T cells from zetaKO mice. Further studies showed that noncultured zetaKO mice CD4(+) T cells and thymocytes bore a unique memory cell-like CD44(high), CD62L(low/neg) phenotype. Altogether, these results suggest that, in the absence of the zeta-chain, CD4(+) T cells develop as polarized IFN-gamma-producing cells that bear a memory cell-like phenotype. The zeta-chain-bearing T cells may produce a large amount of IFN-gamma only after they are cultured in a condition favoring Th1 cell differentiation. This study may provide important implications for the down-regulation of zeta-chain in T cells of patients bearing a variety of tumors, chronic inflammatory and infectious diseases.