Abstract
The purpose of this paper was to characterize proteins secreted from the human nonpigmented ciliary epithelial (HNPE) cells, which have differentiated a rat retinal ganglion cell line, RGC-5. Undifferentiated RGC-5 cells have been shown to express several marker proteins characteristic of retinal ganglion cells. However, RGC-5 cells do not respond to N-methyl-D aspartate (NMDA), or glutamate. HNPE cells have been shown to secrete numbers of neuropeptides or neuroproteins also found in the aqueous humor, many of which have the ability to influence the activity of neuronal cells. This paper details the profile of HNPE cell-secreted proteins by proteomic approaches. The experimental results revealed the identification of 132 unique proteins from the HNPE cell-conditioned SF-medium. The biological functions of a portion of these identified proteins are involved in cell differentiation. We hypothesized that a differentiation system of HNPE cell-conditioned SF-medium with RGC-5 cells can induce a differentiated phenotype in RGC-5 cells, with functional characteristics that more closely resemble primary cultures of rat retinal ganglion cells. These proteins may replace harsh chemicals, which are currently used to induce cell differentiation.
1. Introduction
Primary open angle glaucoma (POAG), a leading cause of irreversible blindness worldwide, is an optic neuropathy characterized by the gradual and progressive loss of retinal ganglion cells (RGCs), optic nerve degeneration, and excavation of the optic disks [1–4]. The hypothesis has been that larger RGCs were selectively lost in the early stage of glaucoma [5]. Although the mechanisms of optic nerve damage in glaucoma have not been completely determined, it appears that the optic nerve head is a major site of damage [6].
RGCs can generate action potentials that travel along the optic fibers [7]. In general, RGCs are a mixture of more than 20 cell subtypes. They have energy-dependent axonal transport functions—orthograde and retrograde transports [8]. These terminal projection areas are in the lateral geniculate body. RGCs can be subdivided by their morphology and physiology, but they are usually discussed without classifications.
The in vitro study of the physiology and pathophysiology of RGCs has been limited to primary cultures. Previous studies have characterized a transformed rat retinal ganglion cell-line (RGC-5), which expresses many neuronal cell markers, including Thy-1, a cell surface glycoprotein found predominantly in the retinal ganglion cells [6, 9, 10], and Brn-3C, a POU domain transcription factor expressed exclusively in the retinal ganglion cells [11]. RGC-5 cells also express receptors of N-methyl-D aspartate (NMDA), GABA-B, and neurotrophin [6]. However, unlike primary RGCs, these cells were not sensitive to glutamate excitotoxicity in their undifferentiated state. RGC-5 cells pretreated with succinyl concanavalin-A (sCon A) were sensitive to 500 μM glutamate [12]. Lacking glutamate sensitivity causes the difficulties of using the RGC-5 cells in experiments involving glutamate.
Ocular ciliary epithelium cells have been shown to be involved in the synthesis and secretion of various proteins found in aqueous humor [13]. Several proteins, including neuropeptides and their processing enzymes, synthesized and secreted by a human nonpigmented ciliary epithelial (HNPE) cell-line, have been evaluated [14], and it is suggested that these secreted proteins can act in an autocrine or paracrine manner to affect ciliary epithelial functions and other target ocular cells, such as the trabecular meshwork [13]. Because of the neuroendocrine properties of the ciliary epithelium cells, the ability to confer differentiated neuroendocrine phenotypes and the physical locations of these ciliary epithelium cells and RGCs [15], we hypothesized that factors secreted by these HNPE cells may induce the RGC-5 cells to differentiate, and possibly induce glutamate and NMDA sensitivities.
Proteomic analysis, including identification and characterization, is a powerful tool for determination of biological roles and functions of individual proteins. In the present report, we have utilized a system involving HNPE and RGC-5 cells, and this system may result in the morphological and functional differentiation of RGC-5 cells. Although the origin of RGC-5 has been still in question, the expression of neuronal markers was validated [16]. Proteomic approaches have been applied to establish a map of expressed proteins for the characteristics of HNPE cells.
2. Materials and Methods
2.1. Cell Culture
The human non-pigmented ciliary epithelium cells (HNPE) were SV-40 transformed and were a gift from Dr. Miguel Coca-Prados (Yale University). HNPE were maintained at 37°C and 5% CO2 in Dulbecco's modified Eagle's medium (DMEM, Gibco, Grand Island, NY, USA) supplemented with 10% fetal bovine serum (FBS, Hyclone Laboratories, Logan, UT), 1% penicillin/streptomycin (Gibco, Grand Island, NY, USA) and 44 mM NaHCO3. After three days, the cells were washed with phosphate buffered saline (PBS) and the medium was replaced by serum-free (SF) DMEM for 12 h.
The HNPE cell conditioned SF-medium was filtered by 0.22 μm filter and diluted 25 times with autoclaved Milli-Q grade water (Millipore Co., Inc.). For each 5 kD cutoff centrifugal tube (Amicon Ultra-15, Millipore Co., Inc.), a 15 mL diluted sample was loaded. Following centrifugation at 5000 ×g for 20 min, the sample in the filter unit was collected. The protein concentration of the HNPE cell conditioned SF-medium was measured by the Bio-Rad Bradford total protein assay kit (Bio-Rad Laboratories, Inc.).
RGC-5 cells, a secondary cell culture, were transformed rat retinal ganglion cells developed and obtained from Dr. Agarwal (University of North Texas Health Science Center). RGC-5 cells were maintained in low glucose DMEM in T-150 culture flasks supplemented with 44 mM NaHCO3, 10% FBS, and 1% penicillin/streptomycin (Gibco). Differentiated RGC-5 cells were obtained by using 50% HNPE cell conditioned SF-medium and 50% fresh DMEM (containing 10% FBS). HNPE conditioned medium, which consisted of low glucose DMEM, was incubated with human non-pigmented ciliary epithelial cells (HNPE).
2.2. Immunocytochemistry
RGCs were grown on glass coverslips for 1-2 days prior to experimentation. Coverslips were rinsed with PBS three times and then were fixed in 4% paraformaldehyde for 30 min. These cells were washed with PBS before being permeabilized in 0.1% Triton X-100 for 15 min, washed with PBS, and blocked with 5% bovine serum albumin for 60 min. After rinsing with PBS, the cells were incubated with a mixture of Thy-1 (monoclonal antibodies, Chemicon, Temecula, CA, 1 : 200) and Brn-3C (polyclonal antibodies, Convance Inc, Princeton, NJ, 1 : 1000) for 1.5 h at room temperature and subsequently incubated with a combination of secondary antibodies. After PBS rinses, these cells were incubated for 10 min in the dark with 300 nM DAPI to stain nuclear regions. Cover-slides were mounted on glass slides in antifade medium (FluorSave; Calbiochem, La Jolla, CA) and allowed to dry for 20 min in the dark. Cells were visualized and images were taken using a Zeiss LSM-410 Confocal Scanning Laser Microscope System. Controls were performed by omitting primary antibodies.
2.3. 1D SDS-PAGE
HNPE cell-secreted proteins were separated under denaturing conditions in a 4–12% polyacrylamide gel. The HNPE cell conditioned SF-medium was resuspended in the sample buffer (Invitrogen NuPAGE SDS sample buffer), heated at 80°C for 10 min and then stored on ice. Each well was loaded with 5 μg of sample solution. The SDS-PAGE gel was run in a Bio-Rad protean II xi cell (Richmond CA, USA) at 200 V for 1 h. After completion of electrophoresis, the protein bands in the gel were visualized by silver staining and image acquired using an image scanner (Amersham Biosciences, Uppsala, Sweden), which is operated by the software LabScan 5.00 (Amersham Biosciences).
2.4. Silver Staining
The gels were fixed in an aqueous solution having 40% ethanol and 10% acetic acid overnight, and then incubated in a buffer solution containing 30% ethanol, 6.8% w/v sodium acetate, and 0.312% w/v sodium thiosulfate for 30 min. After rinsing three times for 5 min each, the gels were stained in a 0.25% w/v silver nitrate solution containing 0.02% formaldehyde for 30 min. The development was performed for 10 min in a solution consisting of 2.5% sodium carbonate and 0.01% formaldehyde. An acetic acid solution (5% v/v) was used to stop the development, and the stained gels were then rinsed three times for 5 min each.
2.5. Protein Identification by Nano-HPLC-ESI-MS/MS
The protein bands were excised manually and digested using sequence grade trypsin (V511A, Promega, USA). The protein samples were reduced, alkylated, and then digested with trypsin using standard protocols [17, 18].
Reverse phase nano-high performance liquid chromatography electrospray ionization tandem mass spectrometry (RP-nano-HPLC-ESI-MS/MS) was used to identify the selected protein bands separated on the SDS-PAGE. The peptides obtained from the tryptic in-gel digestion were analyzed using a nano-HPLC system (LC Packings, Netherlands) coupled to an ion trap mass spectrometer (LCQ Deca XP Plus, ThermoFinnigan, San Jose, CA, USA) equipped with an electrospray ionization source. A linear acetonitrile gradient from 100% buffer A (5% acetonitrile/0.1% formic acid) to 60% buffer B (80% acetonitrile/0.1% formic acid) was used at a flow rate of approximately 200 nL/min for 70 min. The separation was performed on a C18 microcapillary column (Zorbax 300SB-C18, 3.5 μm, 75 μm I.D. ×150 mm, Agilent, Germany). Peptides eluted from the microcapillary column were electrosprayed into the nano-HPLC-ESI-MS/MS with the application of a distal 1.3 kV with heated capillary at the temperature of 200°C. Each cycle of one full scan mass spectrum (m/z 450–2000) was followed by three data-dependent tandem mass spectra with the collision energy was set at 35%.
2.6. Database Search
For protein identification, Mascot software (Version 2.2.1, Matrix Science, London, UK) was used to search the human protein sequence database (Swiss-Prot, Release 52.0 of 22-Feb-08). For proteolytic cleavages, only tryptic cleavage was allowed, and the number of maximal internal (missed) cleavage sites was set to 2. Variable modifications of cysteine with carboxyamidomethylation, methionine with oxidation, and asparagine/glutamine with deamidation were allowed. The mass tolerances of the precursor peptide ion and fragment ion were set to 1 Da. Positive protein identifications were defined if the Mowse scores of greater than 50 were considered significant (P < 0.05). Proteins were initially annotated by similar searches using UniProtKB/Swiss-Prot databases (Last modified September 22, 2009) [19–21].
3. Results and Discussion
Cell secretome (cell-conditional medium) studies can make major contributions in understand biomarker discovery and cell pathophysiological mechanisms. It is composed of proteins that are found in the extracellular growth medium. The cell secretome consists of proteins that are secreted, shed from the cell surface and intracellular proteins released into the supernatant due to cell lysis, apoptosis, and necrosis [22, 23]. The secretome which consists of proteins or peptides secreted from cells into the extracellular medium represents the major class of molecules involved in the intercellular communication in multicellular organisms. It constitutes an important class of proteins that control and regulate a multitude of biological and physiological processes and indicates a clinically relevant source for biomarker and therapeutic target discoveries [24].
Thus, secreted proteins constitute an important category of active molecules that play crucial roles in a number of physiological and pathological processes and may reflect a broad variety of pathological conditions and thus represent a rich source of biomarkers. Proteomic characterization of proteins for identification of specific biomarkers provides a powerful tool to gain deep insights into disease mechanisms in which proteins play major roles. In this study, we have used gel electrophoresis associated with mass spectrometry for identification of the proteome and secretome of HNPE cell conditioned SF-medium samples.
3.1. RGC-5 Cell Differentiation
The differentiation system consisted of RGC-5 cells on coverslips inside 6-well plates, which were exposed to the conditioned medium from HNPE cells. RGC-5 cells proliferated rapidly with a doubling time of less than a day. Decreasing the percentage of serum in the medium may slow down proliferation. The control RGC-5 cells were heterogeneous in shape. Morphological changes of RGC-5 cells were induced by HNPE cell conditioned SF-medium (Figure 1) and caused the shrinkage of the cell body with elongated neurite outgrowth (Figure 1(b)), which allows comparison with undifferentiated RGC-5 cells (Figure 1(a)). The overall morphology of RGC-5 cells after the treatment was similar to those seen in primary cultures of rat retinal ganglion cells [25]. Moreover, the morphology of RGC-5 cells differentiated by our method was similar to the ones induced by a broad-spectrum protein kinase inhibitor staurosporine [26]. Nevertheless, Frassetto and coworkers did not conclude this to be the possible differentiation mechanism. This secretome map is a preliminary study to unveil the mechanism since the differentiation is probably the consequence of the action of several proteins and/or enzymes. It was also noted that the differentiation treatment led to decreased culture density compared with the control cells. This finding is consistent with the study from Wood et al. [27]. For subsequent studies, the conditioned medium from confluent flasks containing HNPE cells was used and found to be equally effective in promoting differentiation of RGC-5 cells.
Figure 1.
Morphological changes in RGC-5 cells after treatment with HNPE conditioned SF-medium (40x) (a) before, and (b) after. The RGC-5 cells treated with HNPE conditioned SF-medium induced morphological changes, including longer axons and more neurite outgrowth (Figure 1(b)), compared to RGC-5 cells without treatment (Figure 1(a)).
Thy-1 expression in undifferentiated RGC-5 cells was used as a marker to identify retinal ganglion cells [28]. After treatment with HNPE cell conditioned SF-medium, RGC-5 cells have an enhanced Thy-1 expression, compared to the undifferentiated cells (Figure 2). In the retina, the class IV POU domain transcription factor, Brn-3b, was expressed almost exclusively in subpopulations of ganglion cells and used to identify RGCs [29]. Brn-3b was regarded as a marker for differentiation of RGCs, since Brn-3 factors were not necessary for the initial specification of sensory neurons, but were essential for their normal differentiation and survival [30]. Specifically, Brn-3b was localized in the nuclear in RGC-5 cells; however, upon treatment with HNPE cell conditioned SF-medium, RGC-5 cells express Brn-3b in a more punctate cytosolic manner (Figure 2).
Figure 2.
Immunocytochemical analysis of Thy-1 and Brn-3b expression in RGC-5 cells differentiated by treatment with HNPE cell conditioned SF-medium. Staining with antibodies to the cell surface glycoprotein, Thy-1, have been commonly used as a marker to identify retinal ganglion cells. After cultivation with HNPE conditioned medium, RGC-5 cells have an enhanced Thy-1 expression, compared to the undifferentiated cells. RGC-5 cells without cultivation with HNPE conditioned medium express Brn-3b in a different pattern compared with treated RGC-5 cells. Specifically, Brn-3b has a nuclear localization in RGC-5 cells without cultivation with HNPE conditioned medium; however, upon treatment, RGC-5 cells express Brn-3b in a more punctate cytosolic manner.
3.2. Proteome Analysis
The SDS-PAGE followed by silver staining resolved the protein bands from HNPE cell conditioned SF-medium. Figure 3 shows the silver-stained 1D SDS-PAGE of secreted proteins from HNPE cells. Five micrograms of secreted protein was loaded on a gel for visualization, and more than 30 protein bands were detected in the HNPE conditioned SF-medium using the image analysis software. To identify the proteins, the position of the 1D SDS-PAGE lane was excised from the gel, washed to remove the stain, and subjected to tryptic digestion. The resulting peptides were characterized by nano-HPLC-MS/MS for protein identification. When a protein was identified by three or more unique peptides possessing MASCOT scores, no visual assessment of spectra was conducted and the protein was considered present in the sample.
Figure 3.
1D SDS-PAGE image of HNPE conditioned SF-medium (5 μg/well, silver stained, left-hand side: molecular weight marker, kDa). The gel bands on the middle lane with serial numbers were analyzed by nano-HPLC-ESI-MS/MS. In the 30 bands, 132 proteins were identified. The gel bands on the right-hand side were the cell lysised proteins.
In this study, all MS/MS spectra were manually confirmed (even if the above criteria were passed) by the visual assessment for their overall quality. In addition, the criteria for manual validation reported by Jaffe et al., which requires a readily observable series of at least four y-ions, was used [31]. Thus, the criteria should be enough for the validation of the identified proteins. By using this strategy, 132 unique proteins with at least three unique peptide sequences matched were identified, and a summary of the protein identifications achieved is listed in Table 1.
Table 1.
Proteins identified in HNPE conditioned SF-medium by proteomic analyses.
| Serial No. | SwissProt No. | Protein name | MW | Score | Subcellular location | Sequence coverage | Molecular function | Biological process |
|---|---|---|---|---|---|---|---|---|
| 1-1 | P02751 | Fibronectin precursor | 262442 | 1728 | Secreted | 25% | Collagen/heparin binding | cell adhesion/migration |
| 1-2 | Q08378 | Golgin subfamily A member 3 | 167252 | 37 | Cytoplasm | 4% | Transporter activity | Intra-Golgi vesicle-mediated transport |
| P02751 | Fibronectin precursor | 262442 | 810 | Secreted | 11% | Collagen/heparin binding | Cell adhesion/migration | |
| P02452 | Collagen α-1(I) chain precursor | 138799 | 163 | Secreted | 3% | Protein binding | Skeletal/epidermis development | |
| P11047 | Laminin γ-1 chain precursor | 177492 | 74 | Secreted | 2% | Extracellular matrix structural constituent | Cell adhesion/migration | |
| P07996 | Thrombospondin-1 precursor | 129330 | 50 | Secreted | 1% | Signal transducer activity | Multicellular organismal development | |
| O95239 | Chromosome-associated kinesin KIF4A | 139794 | 46 | Nucleus | 2% | Protein binding | Anterograde axon cargo transport | |
| Q5VTR2 | Ubiquitin-protein ligase BRE1A | 113592 | 39 | Nucleus | 1% | Transcription coactivator activity, ubiquitin-protein ligase activity and binding, zinc ion binding | Regulation of gene-specific transcription, protein polyubiquitination, negative regulation of cell migration | |
| 1-3 | Q8TF76 | Serine/threonine-protein kinase Haspin | 88405 | 36 | Nucleus | 6% | ATP binding/protein kinase activity | Protein amino acid phosphorylation |
| P07996 | Thrombospondin-1 precursor | 129330 | 427 | Secreted | 11% | Signal transducer activity | Multicellular organismal development | |
| P02452 | Collagen α-1(I) chain precursor | 138799 | 231 | Secreted | 8% | Protein binding | Epidermis/ skeletal development | |
| P01024 | Complement C3 precursor | 187046 | 145 | Secreted | 2% | Receptor binding | Complement activation | |
| P02751 | Fibronectin precursor | 262442 | 86 | Secreted | 3% | Collagen/heparin binding | Cell adhesion/migration | |
| Q14980 | Nuclear mitotic apparatus protein 1 | 238130 | 50 | Nucleus | 4% | Protein binding/structural molecule activity | Mitotic anaphase | |
| P35442 | Thrombospondin-2 precursor | 129872 | 48 | Secreted | 1% | Heparin binding | ||
| P07814 | Bifunctional aminoacyl-tRNA synthetase | 162923 | 39 | Cytoplasm | 1% | Protein binding | Protein complex assembly | |
| P81274 | G-protein signaling modulator 2 | 75798 | 56 | Cytoplasm | 5% | Identical protein binding | G-protein coupled receptor protein signaling pathway | |
| O14686 | Myeloid/lymphoid or mixed-lineage leukemia protein 2 | 563831 | 48 | Nucleus | 1% | Protein/DNA binding | Regulation of transcription, DNA-dependent | |
| Q9UQ26 | Regulating synaptic membrane exocytosis protein 2 | 160303 | 43 | Cell membrane | 2% | Zinc ion binding, Rab GTPase binding | Intracellular protein transport | |
| Q9UM54 | Myosin-6 | 148620 | 35 | Golgi apparatus | 4% | ADP/calmodulin binding | DNA damage response, intracellular protein transport | |
| O15020 | Spectrin β chain, brain 2 | 271127 | 38 | Cytoplasm, cytoskeleton | 2% | Actin binding | Vesicle-mediated transport | |
| 1-4 | O00339 | Matrilin-2 precursor | 106768 | 109 | Secreted | 3% | Calcium ion binding | |
| 1-5 | Q08380 | Galectin-3-binding protein precursor | 65289 | 404 | Secreted | 23% | Protein binding/scavenger receptor activity | Cellular defense response/signal transduction |
| O94985 | Calsyntenin-1 precursor | 109724 | 55 | Endoplasmic reticulum membrane, nucleus, Golgi membrane | 1% | Calcium ion binding, protein binding | Homophilic cell adhesion | |
| P13569 | Cystic fibrosis transmembrane conductance regulator | 168066 | 37 | Membrane | 1% | ATP-binding and phosphorylation-dependent chloride channel activity | Respiratory gaseous exchange, transport | |
| P12814 | α-actinin-1 | 102993 | 168 | Cytoplasm | 7% | Integrin binding | Regulation of apoptosis | |
| 1-6 | O43707 | α-actinin-4 | 104788 | 544 | Nucleus | 11% | Integrin binding | Regulation of apoptosis |
| P12814 | α-actinin-1 | 102993 | 521 | Cytoplasm | 14% | Integrin binding | Regulation of apoptosis | |
| Q08380 | Galectin-3-binding protein precursor | 65289 | 467 | Secreted | 18% | Protein binding/scavenger receptor activity | Cellular defense response/signal transduction | |
| P35609 | α-actinin-2 | 103788 | 165 | Cytoplasm | 6% | Integrin binding | Regulation of apoptosis | |
| P34932 | Heat shock 70 kDa protein 4 | 94240 | 82 | Cytoplasm | 4% | ATP binding | Response to unfolded protein | |
| P35711 | Transcription factor SOX-5 | 83973 | 40 | Nucleus | 8% | Transcription factor activity | Transcription from RNA polymerase II promoter | |
| 1-7 | Q08380 | Galectin-3-binding protein precursor | 65289 | 277 | Secreted | 15% | Protein binding/scavenger receptor activity | cellular defense response/signal transduction |
| O43707 | α-actinin-4 | 104788 | 163 | Nucleus | 10% | Integrin binding | Regulation of apoptosis | |
| P08238 | Heat shock protein HSP 90-β | 83081 | 159 | Cytoplasm | 5% | Nitric-oxide synthase regulator activity | Response to unfolded protein | |
| P29400 | Collagen α-5(IV) chain precursor | 160943 | 47 | Secreted | 4% | Binding, extracellular matrix structural constituent | ||
| Q13740 | CD166 antigen precursor | 65091 | 40 | Membrane | 4% | Receptor binding | Cell adhesion/signal transduction | |
| P07900 | Heat shock protein HSP 90- α | 84476 | 225 | Cytoplasm | 5% | ATP binding/nitric-oxide synthase regulator activity | Response to unfolded protein/signal transduction | |
| P12814 | α-actinin-1 | 102993 | 194 | Cytoplasm | 6% | Integrin binding | Regulation of apoptosis | |
| P35609 | α-actinin-2 | 103788 | 74 | Cytoplasm | 3% | Integrin binding | Regulation of apoptosis | |
| O00469 | Procollagen-lysine,2-oxoglutarate 5-dioxygenase 2 precursor | 84632 | 48 | Rough endoplasmic reticulum membrane | 4% | Protein binding | Protein modification process/response to hypoxia | |
| P34932 | Heat shock 70 kDa protein 4 | 94240 | 44 | Cytoplasm | 3% | ATP binding | Response to unfolded protein | |
| Q13045 | Protein flightless-1 homolog | 144659 | 43 | Nucleus | 3% | Actin binding | Muscle contraction | |
| 1-8 | P02768 | Serum albumin precursor | 69321 | 87 | Secreted | 3% | Protein binding/pyridoxal phosphate binding | Negative regulation of apoptosis /transport |
| Q8TEU7 | Rap guanine nucleotide exchange factor 6 | 179294 | 44 | Cytoplasm | 3% | GTP-dependent protein binding | Ras protein signal transduction | |
| 1-9 | O95248 | SET-binding factor 1 | 208125 | 41 | Nucleus | 1% | Protein tyrosine/serine/threonine phosphatase activity | Protein amino acid dephosphorylation |
| Q9UPQ9 | Trinucleotide repeat-containing 6B protein | 182703 | 36 | Cytoplasmic mRNA processing body | 2% | RNA binding, nucleotide binding | Gene silencing by RNA, regulation of translation | |
| P29401 | Transketolase | 67835 | 134 | Cytosol | 7% | Protein binding | Transketolase activity | |
| P02768 | Serum albumin precursor | 69321 | 82 | Secreted | 5% | Protein binding/pyridoxal phosphate binding | Negative regulation of apoptosis/transport | |
| O60333 | Kinesin-like protein KIF1B | 204305 | 58 | Cytoplasmic vesicle | 1% | ATPase activity/microtubule motor activity | Neuromuscular synaptic transmission/nerve-nerve synaptic transmission | |
| O75095 | Multiple epidermal growth factor-like domains 6 precursor | 128524 | 46 | 6% | Calcium ion binding | |||
| 1-10 | P06744 | Glucose-6-phosphate isomerase | 62976 | 334 | Cytoplasm | 8% | Humoral immune response/carbohydrate metabolic process | |
| P27797 | Calreticulin precursor | 48112 | 67 | Endoplasmic reticulum lumen, Cytoplasm, Secreted | 5% | DNA/protein binding | Regulation of apoptosis/transcription, DNA-dependent, protein export from nucleus | |
| P09493 | Tropomyosin 1 α chain | 32689 | 44 | Cytoplasm | 8% | Structural constituent of muscle | Cell motility, regulation of heart/muscle contraction | |
| 1-11 | Q06495 | Sodium-dependent phosphate transport protein 2A | 68893 | 49 | Membrane | 1% | Sodium-dependent phosphate transmembrane transporter activity | Body fluid secretion, phosphate transport |
| P37268 | Squalene synthetase | 48084 | 40 | Endoplasmic reticulum membrane | 5% | Farnesyl-diphosphate farnesyltransferase activity | Steroid biosynthetic process | |
| Q12799 | T-complex protein 10A homolog | 45440 | 39 | Cytosol | 7% | |||
| O75095 | Multiple epidermal growth factor-like domains 6 precursor | 128524 | 46 | 1% | Calcium ion binding | |||
| Q9UM47 | Neurogenic locus notch homolog protein 3 precursor | 243496 | 37 | Cell membrane | 5% | Protein binding | ||
| P39191 | Alu subfamily SB2 sequence contamination warning entry | 65263 | 59 | 5% | ||||
| Q12841 | Follistatin-related protein 1 precursor | 34963 | 52 | Secreted | 2% | Heparin binding | BMP signaling pathway | |
| Q14980 | Nuclear mitotic apparatus protein 1 | 238130 | 41 | Nucleus | 2% | Protein binding/structural molecule activity | Mitotic anaphase/nuclear organization and biogenesis | |
| 1-12 | P14136 | Glial fibrillary acidic protein, astrocyte | 49850 | 80 | Cytoplasm | 7% | Structural constituent of cytoskeleton | |
| P78527 | DNA-dependent protein kinase catalytic subunit | 468788 | 39 | Nucleus | 1% | DNA-dependent protein kinase activity | Peptidyl-serine phosphorylation | |
| Q9UPQ9 | Trinucleotide repeat-containing 6B protein | 182703 | 49 | 4% | ||||
| P06744 | Glucose-6-phosphate isomerase | 62976 | 401 | Cytoplasm | 16% | Humoral immune response/carbohydrate metabolic process | ||
| P14618 | Pyruvate kinase isozymes M1/M2 | 57769 | 145 | Cytosol | 7% | Pyruvate kinase activity | Glycolysis | |
| P00390 | Glutathione reductase, mitochondrial precursor | 56221 | 69 | Mitochondrion | 2% | Glutathione-disulfide reductase activity/electron carrier activity | ||
| P09622 | Dihydrolipoyl dehydrogenase, mitochondrial precursor | 54116 | 47 | Mitochondrion matrix | 4% | Dihydrolipoyl dehydrogenase activity | ||
| P30154 | Serine/threonine-protein phosphatase 2A 65 kDa regulatory subunit A β isoform | 66159 | 42 | 3% | Protein heterodimerization activity | |||
| O95271 | Tankyrase-1 | 141922 | 37 | Cytoplasm | 2% | NAD+ ADP-ribosyltransferase activity | Peptidyl-serine/threonine phosphorylation | |
| 1-13 | P06733 | α-enolase | 47008 | 697 | Cytoplasm | 27% | Transcription factor activity, phosphopyruvate hydratase activity | Negative regulation of cell growth |
| Q15113 | Procollagen C-endopeptidase enhancer 1 precursor | 47942 | 114 | Secreted | 10% | Multicellular organismal development | ||
| P13929 | β-enolase | 46826 | 242 | Cytoplasm | 10% | Phosphopyruvate hydratase activity | ||
| P09104 | γ-enolase | 47108 | 135 | Cytoplasm | 4% | Phosphopyruvate hydratase activity | ||
| Q7Z3E2 | Protein C10orf118 | 103623 | 42 | 2% | ||||
| P11117 | Lysosomal acid phosphatase precursor | 48285 | 42 | Lysosome | 2% | Acid phosphatase activity | ||
| P02686 | Myelin basic protein | 33097 | 40 | Myelin membrane | 7% | Axon ensheathment, immune response, central nervous system development | ||
| P50395 | Rab GDP dissociation inhibitor β | 50631 | 40 | Cytoplasm | 2% | Rab GDP-dissociation inhibitor activity | Signal transduction | |
| Q13371 | Phosducin-like protein | 34260 | 40 | Cytoplasm | 8% | Regulator of G-protein signaling activity | Signal transduction | |
| P35573 | Glycogen debranching enzyme | 174523 | 39 | Cytosol | 1% | Amylo-α-1,6-glucosidase activity | ||
| Q6ZU80 | Protein C14orf145 | 73526 | 38 | 4% | ||||
| P49746 | Thrombospondin-3 precursor | 104135 | 36 | Secreted | 1% | Calcium ion binding | Cell-matrix adhesion | |
| Q7L1I2 | Synaptic vesicle glycoprotein 2B | 77393 | 35 | Cytoplasmic vesicle | 3% | |||
| 1-14 | P09486 | SPARC precursor | 34610 | 36 | Secreted | 14% | Calcium/calcium ion binding | Ossification, transmembrane receptor protein tyrosine kinase signaling pathway |
| 1-15 | P04075 | Fructose-bisphosphate aldolase A | 39264 | 341 | Cytoskeleton | 37% | Fructose-bisphosphate aldolase activity | Fructose metabolic process, glycolysis |
| P09972 | Fructose-bisphosphate aldolase C | 39300 | 134 | Cytoskeleton | 13% | Fructose-bisphosphate aldolase activity | Fructose metabolic process | |
| P00505 | Aspartate aminotransferase, mitochondrial precursor | 47445 | 45 | Mitochondrion matrix | 3% | Aspartate transaminase activity | Fatty acid transport, response to ethanol | |
| 1-16 | P40925 | Malate dehydrogenase, cytoplasmic | 36272 | 40 | Cytoplasm | 11% | L-malate dehydrogenase activity, malic enzyme activity | |
| O00623 | Peroxisome assembly protein 12 | 40771 | 37 | Peroxisome membrane | 5% | Zinc ion/protein C-terminus binding | Protein import into peroxisome matrix | |
| Q9NVP4 | Protein C20orf12 | 62868 | 33 | Intracellular | 2% | zinc ion binding | ||
| P07195 | L-lactate dehydrogenase B chain | 36484 | 52 | Cytoplasm | 5% | L-lactate dehydrogenase activity | ||
| P10909 | Clusterin precursor | 52461 | 42 | Secreted | 5% | Protein binding | Complement activation, lipid metabolic process | |
| 1-17 | P11117 | Lysosomal acid phosphatase precursor | 48285 | 44 | Lysosome | 2% | Acid phosphatase activity | |
| P09493 | Tropomyosin 1 α chain | 32689 | 59 | Cytoplasm | 3% | Structural constituent of muscle | Cell motility, regulation of heart/muscle contraction | |
| 1-18 | P18669 | Phosphoglycerate mutase 1 | 28655 | 151 | Cytosol | 16% | Bisphosphoglycerate 2-phosphatase activity | Glycolysis |
| P63104 | 14-3-3 protein zeta/delta | 27728 | 110 | Cytoplasm | 12% | Transcription factor binding | Antiapoptosis, signal transduction | |
| O60242 | Brain-specific angiogenesis inhibitor 3 precursor | 171379 | 38 | Cell membrane | 1% | |||
| O00459 | Phosphatidylinositol 3-kinase regulatory subunit β | 81574 | 34 | Cytosol | 2% | Protein binding | Negative regulation of antiapoptosis | |
| P46940 | Ras GTPase-activating-like protein IQGAP1 | 189134 | 34 | Cell membrane | 2% | GTPase activator/inhibitor activity, calmodulin binding | Signal transduction | |
| 1-19 | P60174 | Triosephosphate isomerase | 26522 | 156 | Cytosol | 18% | Triose-phosphate isomerase activity | |
| P26232 | α-2 catenin | 105085 | 34 | Cytoplasm | 1% | Structural constituent of cytoskeleton | Cell adhesion | |
| 1-20 | P60174 | Triosephosphate isomerase | 26522 | 373 | Cytosol | 37% | Triose-phosphate isomerase activity | |
| Q06495 | Sodium-dependent phosphate transport protein 2A | 68893 | 49 | Membrane | 1% | Sodium-dependent phosphate transmembrane transporter activity, protein binding | Body fluid secretion, phosphate metabolic process and transport | |
| Q14980 | Nuclear mitotic apparatus protein 1 | 238115 | 44 | Nucleus | 4% | Protein binding, structural molecule activity | Mitotic anaphase, nuclear organization and biogenesis | |
| P78527 | DNA-dependent protein kinase catalytic subunit | 468788 | 36 | Nucleus | 1% | DNA-dependent protein kinase activity/protein binding | Peptidyl-serine phosphorylation | |
| 1-21 | Q06830 | Peroxiredoxin-1 | 22096 | 231 | Cytoplasm, melanosome | 19% | Peroxidase activity/protein binding | Cell proliferation, hydrogen peroxide catabolic process, skeletal development |
| P30086 | Phosphatidylethanolamine-binding protein 1 | 20913 | 122 | Cytoplasm | 10% | Phosphatidylethanolamine binding/protein binding | ||
| P16035 | Metalloproteinase inhibitor 2 precursor | 24383 | 104 | Secreted | 13% | Metalloendopeptidase inhibitor activity/protein binding | ||
| P04179 | Superoxide dismutase | 24707 | 66 | Mitochondrion matrix | 6% | Superoxide dismutase activity | Age-dependent response to reactive oxygen species, regulation of transcription from RNA polymerase II promoter, response to superoxide, superoxide metabolic process | |
| P53618 | Coatomer subunit β | 107071 | 51 | Cytoplasm | 2% | Protein binding | COPI coating of Golgi vesicle, intra-Golgi vesicle-mediated transport, retrograde vesicle-mediated transport, Golgi to ER | |
| O43395 | U4/U6 small nuclear ribonucleoprotein Prp3 | 77481 | 45 | Nucleus speckle | 3% | Protein binding/RNA splicing factor activity, transesterification mechanism | Nuclear mRNA splicing, via spliceosome | |
| O15240 | Neurosecretory protein VGF precursor | 67247 | 44 | Secreted | 7% | Response to cAMP | ||
| Q06495 | Sodium-dependent phosphate transport protein 2A | 68893 | 42 | Membrane | 1% | Protein binding/sodium-dependent phosphate transmembrane transporter activity | Body fluid secretion, phosphate metabolic process, phosphate transport | |
| Q9Y587 | AP-4 complex subunit sigma-1 | 16994 | 41 | Golgi apparatus | 9% | Transporter activity | ||
| Q04760 | Lactoylglutathione lyase | 20575 | 40 | Cytoplasm | 4% | Lactoylglutathione lyase activity | Antiapoptosis, carbohydrate metabolic process | |
| P11117 | Lysosomal acid phosphatase precursor | 48285 | 40 | Lysosome | 2% | Acid phosphatase activity | ||
| Q9P0K1 | ADAM 22 precursor | 100368 | 39 | Membrane | 5% | Integrin binding | Central nervous system development, negative regulation of cell adhesion | |
| Q96Q42 | Alsin | 183550 | 38 | Cytosol | 1% | Protein homodimerization activity/protein serine/threonine kinase activator activity/Rab GTPase binding/Rac guanyl-nucleotide exchange factor activity | Cell death, endosome organization, neuron projection morphogenesis, positive regulation of Rac GTPase activity, positive regulation of Rac protein signal transduction, positive regulation of protein kinase activity, regulation of endosome size | |
| 1-22 | Q06830 | Peroxiredoxin-1 | 22096 | 110 | Cytoplasm, Melanosome | 21% | Peroxidase activity/protein binding | Cell proliferation, hydrogen peroxide catabolic process, skeletal development |
| Q8N1I0 | Dedicator of cytokinesis protein 4 | 225005 | 41 | Intracytoplasmic membrane | 1% | PDZ domain binding/Rac GTPase activator activity/Rac GTPase binding | ||
| P11117 | Lysosomal acid phosphatase precursor | 48285 | 39 | Lysosome | 2% | Acid phosphatase activity | ||
| 1-23 | O95274 | Ly6/PLAUR domain-containing protein 3 precursor | 35948 | 38 | Cell membrane | 8% | ||
| P00441 | Superoxide dismutase [Cu-Zn] | 15795 | 73 | Cytoplasm, cytosol, nucleus | 4% | Chaperone/phosphatase 2B/copper ion/zinc ionbinding, protein homodimerization activity, superoxide dismutase activity/antioxidant activity | Cell aging, oxidation reduction, regulation of organ growth, positive regulation of apoptosis | |
| O15516 | Circadian locomoter output cycles protein kaput | 95244 | 55 | Cytoplasm, nucleus | 1% | Transcription factor activity | Circadian rhythm, photoperiodism, positive regulation of transcription from RNA polymerase II promoter, signal transduction | |
| O00160 | Myosin If | 124725 | 39 | 2% | Actin binding/ATP binding/calmodulin binding | |||
| Q13075 | Baculoviral IAP repeat-containing protein 1 | 159479 | 39 | Intracellular | 1% | Nucleoside-triphosphatase activity, nucleotide binding, zinc ion binding | Antiapoptosis, nervous system development | |
| 1-24 | Q6ZUB1 | Protein C9orf79 | 157037 | 35 | Membrane | 1% | ||
| Q9BXM0 | Periaxin | 154906 | 35 | cytoplasm, nucleus | 1% | Protein binding | Axon ensheathment | |
| Q15084 | Protein disulfide-isomerase A6 precursor | 48091 | 38 | Endoplasmic reticulum lumen, melanosome | 2% | Protein binding/protein disulfide isomerase activity | Protein folding | |
| Q13136 | Liprin-α-1 | 135695 | 42 | Cytoplasm | 2% | Protein binding/signal transducer activity | Cell-matrix adhesion, signal transduction | |
| Q32MQ0 | Protein ZNF750 | 77312 | 44 | Intracellular | 5% | Zinc ion binding | ||
| Q15113 | Procollagen C-endopeptidase enhancer 1 precursor | 47942 | 48 | Secreted | 3% | Multicellular organismal development | ||
| P15531 | Nucleoside diphosphate kinase A | 17138 | 67 | Cytoplasm, nucleus | 17% | Deoxyribonuclease activity, DNA/GTP/magnesium ion binding, nucleoside diphosphate kinase activity | Negative regulation of cell proliferation, positive regulation of DNA binding, positive regulation of epithelial cell proliferation, regulation of apoptosis | |
| P00441 | Superoxide dismutase [Cu-Zn] | 15795 | 70 | Cytoplasm, cytosol, nucleus | 19% | Chaperone/phosphatase 2B/copper ion/zinc ionbinding, protein homodimerization activity, superoxide dismutase activity/antioxidant activity | Cell aging, oxidation reduction, regulation of organ growth, positive regulation of apoptosis | |
| P23528 | Cofilin-1 | 18360 | 139 | Nucleus matrix, cytoplasm | 17% | Protein binding | Actin cytoskeleton organization and biogenesis, antiapoptosis, Rho protein signal transduction | |
| 1-25 | Q96EZ8 | Microspherule protein 1 | 51771 | 35 | Nucleus | 2% | Protein binding | Protein modification process |
| O95271 | Tankyrase 1 | 141922 | 35 | Cytoplasm, Golgi apparatus membrane, nucleus | 1% | NAD+ ADP-ribosyltransferase activity | Peptidyl-serine phosphorylation, peptidyl-threonine phosphorylation, telomere maintenance via telomerase | |
| Q14980 | Nuclear mitotic apparatus protein 1 | 238115 | 35 | Nucleus | 1% | Protein binding, structural molecule activity | Mitotic anaphase, nuclear organization and biogenesis | |
| P17612 | cAMP-dependent protein kinase, α-catalytic subunit | 40433 | 37 | Cytoplasm, nucleus | 1% | ATP binding, cAMP-dependent protein kinase activity | Hormone-mediated signaling, protein amino acid phosphorylation, protein kinase cascade | |
| P11117 | Lysosomal acid phosphatase precursor | 48285 | 39 | Lysosome | 2% | acid phosphatase activity | ||
| P10071 | Zinc finger protein GLI3 | 169743 | 39 | Nucleus | 1% | Protein binding, transcription factor activity | Anatomical structure morphogenesis, multicellular organismal development, protein import into nucleus, translocation, signal transduction | |
| P78527 | DNA-dependent protein kinase catalytic subunit | 468788 | 40 | Nucleus | 1% | DNA-dependent protein kinase activity | Peptidyl-serine phosphorylation | |
| Q06495 | Sodium-dependent phosphate transport protein 2A | 68893 | 40 | Membrane | 1% | Protein binding, sodium-dependent phosphate transmembrane transporter activity | Body fluid secretion, phosphate metabolic process, phosphate transport | |
| P15531 | Nucleoside diphosphate kinase A | 17138 | 86 | Cytoplasm, nucleus | 17% | Deoxyribonuclease activity, DNA/GTP/magnesium ion binding, nucleoside diphosphate kinase activity | Negative regulation of cell proliferation, positive regulation of DNA binding, positive regulation of epithelial cell proliferation, regulation of apoptosis | |
| P62937 | Peptidyl-prolyl cis-trans isomerase A | 17870 | 422 | Cytoplasm | 37% | Unfolded protein binding, virion binding | Initiation of viral infection, protein folding, provirus integration, regulation of viral genome replication | |
| 1-26 | P62937 | Peptidyl-prolyl cis-trans isomerase A | 17870 | 171 | Cytoplasm | 32% | Unfolded protein binding, virion binding | Initiation of viral infection, protein folding, provirus integration, regulation of viral genome replication |
| O95352 | Autophagy-related protein 7 | 77909 | 34 | Cytoplasm | 2% | Protein homodimerization activity, ubiquitin activating enzyme activity | Membrane fusion, positive regulation of protein modification process, protein amino acid lipidation | |
| 1-27 | Q9UPT6 | C-jun-amino-terminal kinase-interacting protein 3 | 146962 | 54 | Cytoplasm | 2% | kinesin/protein kinase binding, MAP-kinase scaffold activity | Regulation of JNK cascade, vesicle-mediated transport |
| Q8IWJ2 | GRIP and coiled-coil domain-containing protein 2 | 184545 | 38 | Cytoplasm, Golgi apparatus membrane | 1% | Identical protein binding | ||
| Q9NX63 | Coiled-coil-helix-coiled-coil-helix domain-containing protein 3 | 26136 | 39 | Mitochondrion | 13% | Protein binding | ||
| P02452 | Collagen α-1(I) chain precursor | 138799 | 44 | Secreted | 3% | Protein binding | Epidermis development, skeletal development | |
| P59998 | Actin-related protein 2/3 complex subunit 4 | 19523 | 45 | Cytoplasm | 2% | Protein binding, structural constituent of cytoskeleton | Actin nucleation | |
| P01034 | Cystatin C precursor | 15789 | 56 | Secreted | 7% | Cysteine protease inhibitor activity, protein homodimerization activity | ||
| P23528 | Cofilin-1 | 18360 | 178 | Nucleus matrix, cytoplasm | 19% | Protein binding | Actin cytoskeleton organization and biogenesis, antiapoptosis, Rho protein signal transduction | |
| P07737 | Profilin-1 | 14914 | 478 | Cytoplasm | 45% | Actin binding, proline-rich region binding | Actin cytoskeleton organization | |
| 1-28 | P09382 | Galectin-1 | 14575 | 41 | Cytoplasm | 7% | Protein binding, signal transducer activity | Positive regulation of I-κB kinase, NF-κB cascade, regulation of apoptosis |
| P10599 | Thioredoxin | 11599 | 59 | Cytoplasm | 13% | Protein binding | Cell motility, cell proliferation, cell-cell signaling, signal transduction | |
| P04080 | Cystatin B | 11133 | 61 | Cytoplasm, nucleus | 12% | Endopeptidase inhibitor activity, protein binding | ||
| P07737 | Profilin-1 | 14914 | 320 | Cytoplasm | 42% | Actin binding, proline-rich region binding | Actin cytoskeleton organization | |
| 1-29 | Q9UPQ9 | Trinucleotide repeat-containing 6B protein | 182703 | 34 | Cytoplasmic mRNA processing body | 4% | RNA binding, nucleotide binding | Gene silencing by RNA, regulation of translation |
| P78527 | DNA-dependent protein kinase catalytic subunit | 468788 | 35 | Nucleus | 1% | DNA-dependent protein kinase activity, protein binding | Peptidyl-serine phosphorylation | |
| P81605 | Dermcidin precursor | 11277 | 45 | Secreted | 12% | Protein binding | ||
| P10599 | Thioredoxin | 11599 | 76 | Cytoplasm | 19% | Protein binding | Cell motility, cell proliferation, cell-cell signaling, signal transduction | |
| 1-30 | Q6NUM9 | All-trans-retinol 13,14-reductase precursor | 66777 | 39 | Endoplasmic reticulum membrane | 3% | All-trans-retinol 13,14-reductase activity | Oxidation reduction, retinol metabolic process |
| P14174 | Macrophage migration inhibitory factor | 12337 | 39 | Cytoplasm, secreted | 11% | Cytokine activity | Cell proliferation, cell surface receptor linked signal transduction, negative regulation of apoptosis, prostaglandin biosynthetic process, regulation of macrophage activation | |
| Q6KC79 | Nipped-B-like protein | 315854 | 36 | Nucleus | 1% | Protein C-terminus binding | Maintenance of mitotic sister chromatid cohesion | |
| P82279 | Crumbs homolog 1 precursor | 154081 | 36 | Secreted | 1% | Calcium ion binding | Cell-cell signaling, establishment and/or maintenance of cell polarity, response to stimulus | |
| Q9NX63 | Coiled-coil-helix-coiled-coil-helix domain-containing protein 3 | 26136 | 39 | Mitochondrion | 13% | Protein binding | ||
| Q8N0X7 | Spartin | 72788 | 41 | 2% | Cell death | |||
| P14174 | Macrophage migration inhibitory factor | 12337 | 60 | Cytoplasm, secreted | 5% | Cytokine activity | Cell proliferation, cell surface receptor linked signal transduction, negative regulation of apoptosis, prostaglandin biosynthetic process, regulation of macrophage activation | |
| P58546 | Myotrophin | 12756 | 71 | Cytoplasm | 7% | Protein binding | Cell growth, neuron differentiation | |
| 1-31 | Q8WUT4 | Uncharacterized protein C20orf75 precursor | 78794 | 37 | Membrane | 5% | Protein binding | |
| O94851 | Protein MICAL-2 | 126609 | 40 | Cytoplasm | 1% | Monooxygenase activity, zinc ion binding | Metabolic process | |
| Q9Y333 | U6 snRNA-associated Sm-like protein LSm2 | 10828 | 69 | Nucleus | 20% | Protein/U6 snRNA binding | Nuclear mRNA splicing | |
These serial numbers are designated as in Figure 3.
Swiss-Prot/TrEMBL accession number was given from http://us.expasy.org/.
In this study, 47 proteins (35.6%) were known to be present in cytoplasm. Twenty-two proteins (16.7%) were known to be secreted into the extracellular space. Twenty-five proteins (18.9%) were known to be nuclear proteins. Eleven proteins (8.3%) were known to be membrane proteins. Ten proteins (7.6%) were known to be cytosol proteins. A few mitochondrial, endoplasmic reticulum, intracellular, cytoskeleton, and golgi apparatus proteins were also identified. A considerable portion of the identified proteins (6%, 8 proteins) has not been reported for their synthesized locations. Some proteins were described as found in different subcellular locations, which explains the total sum being substantially larger than 100%.
Some identified proteins in the distribution of cellular location were not secreted proteins, but they were still present in the secreted medium. To clarify the puzzle, a cell viability test was applied. The survival rate of HNPE cells was determined by the dimethylthiazol-diphenyltetrazolium bromide (MTT) assay, which was about 97%. Thus, those identified proteins were not corresponding to released proteins from dead cells. Also, according the protein profiles in Figure 3, the protein patterns obtained from secreted medium and cell lysate were very different. As a result, these proteins identified in this study can be considered as secreted proteins, which may have been synthesized inside the cells and transferred out.
Based on the functional categories in the Swiss-Prot and TrEMBL protein database, the identified proteins were classified into several groups. The Swiss-Prot identifiers could be employed for linkages of proteins to defined vocabulary of terms describing the cellular components, biological processes, and molecular functions of known gene ontology (GO). Gene Ontology Consortium provides annotations of each protein and its structure, which allowed us to organize selected proteins into biologically relevant groups. These groupings can be utilized as the basis for identifying biological information showing correlated protein changes [20, 32]. Such protein functions were listed in Table 2.
Table 2.
The functions of 132 proteins identified in this study were presented into functional categories based on their annotations in the GO database.
| SwissProt No. | Protein name | Protein function |
|---|---|---|
| O00160 | Myosin If | Myosins are actin-based motor molecules with ATPase activity. Unconventional myosins serve in intracellular movements |
| O00339 | Matrilin-2 precursor | Involved in matrix assembly |
| O00459 | Phosphatidylinositol 3-kinase regulatory subunit β | Binds to activated (phosphorylated) protein-tyrosine kinases, through its SH2 domain, and acts as an adapter, mediating the association of the p110 catalytic unit to the plasma membrane. |
| O00469 | Procollagen-lysine,2-oxoglutarate 5-dioxygenase 2 precursor | Forms hydroxylysine residues in -Xaa-Lys-Gly- sequences in collagens. These hydroxylysines serve as sites of attachment for carbohydrate units and are essential for the stability of the intermolecular collagen cross-links |
| O00623 | Peroxisome assembly protein 12 | Required for protein import into peroxisomes |
| O14686 | Myeloid/lymphoid or mixed-lineage leukemia protein 2 | Histone methyltransferase. Methylates “Lys-4” of histone H3. H3 “Lys-4” methylation represents a specific tag for epigenetic transcriptional activation. Plays a central role in β-globin locus transcription regulation by being recruited by NFE2. Acts as a coactivator for estrogen receptor by being recruited by ESR1, thereby activating transcription |
| O15020 | Spectrin β chain, brain 2 | Probably plays an important role in neuronal membrane skeleton |
| O15240 | Neurosecretory protein VGF precursor | May be involved in the regulation of cell-cell interactions or in synaptogenesis during the maturation of the nervous system |
| O15516 | Circadian locomotors output cycles protein kaput | ARNTL/2-CLOCK heterodimers activate E-box element (3′-CACGTG-5′) transcription of a number of proteins of the circadian clock. Activates transcription of PER1 and PER2. This transcription is inhibited in a feedback loop by PER and CRY proteins. Has intrinsic histone acetyltransferase activity and this enzymatic function contributes to chromatin-remodeling events implicated in circadian control of gene expression |
| O43395 | U4/U6 small nuclear ribonucleoprotein Prp3 | Participates in pre-mRNA splicing. May play a role in the assembly of the U4/U5/U6 tri-snRNP complex |
| O43707 | α-actinin-4 | F-actin cross-linking protein which is thought to anchor actin to a variety of intracellular structures. This is a bundling protein |
| O60242 | Brain-specific angiogenesis inhibitor 3 precursor | Might be involved in angiogenesis inhibition and suppression of glioblastoma |
| O60333 | Kinesin-like protein KIF1B | Motor for anterograde transport of mitochondria. Has a microtubule plus end-directed motility |
| O75095 | Multiple epidermal growth factor-like domains 6 precursor | |
| O94851 | Protein MICAL-2 | |
| O94985 | Calsyntenin-1 precursor | Induces KLC1 association with vesicles and functions as a cargo in axonal anterograde transport. Complex formation with APBA2 and APP, stabilizes APP metabolism and enhances APBA2-mediated suppression of β-APP40 secretion, due to the retardation of intracellular APP maturation. In complex with APBA2 and C99, a C-terminal APP fragment, abolishes C99 interaction with PSEN1 and thus APP C99 cleavage by γ-secretase, most probably through stabilization of the direct interaction between APBA2 and APP. The intracellular fragment AlcICD suppresses APBB1-dependent transactivation stimulated by APP C-terminal intracellular fragment (AICD), most probably by competing with AICD for APBB1-binding. May modulate calcium-mediated postsynaptic signals |
| O95239 | Chromosome-associated kinesin KIF4A | Motor protein that translocates PRC1 to the plus ends of interdigitating spindle microtubules during the metaphase to anaphase transition, an essential step for the formation of an organized central spindle midzone and midbody and for successful cytokinesis. May play a role in mitotic chromosomal positioning and bipolar spindle stabilization |
| O95248 | SET-binding factor 1 | Probable pseudophosphatase. Lacks several amino acids in the catalytic pocket which renders it catalytically inactive as a phosphatase. The pocket is, however, sufficiently preserved to bind phosphorylated substrates, and may be protect them from phosphatases. Inhibits myoblast differentiation in vitro and induces oncogenic transformation in fibroblasts |
| O95271 | Tankyrase 1 | Regulate vesicle trafficking and modulate the subcellular distribution of SLC2A4/GLUT4-vesicles. Has PARP activity and can modify TERF1, and thereby contribute to the regulation of telomere length |
| O95274 | Ly6/PLAUR domain-containing protein 3 precursor | Supports cell migration. May be involved in urothelial cell-matrix interactions. May be involved in tumor progression |
| O95352 | Autophagy-related protein 7 | E1 enzyme essential for multisubstrates such as GABARAPL1 and ATG12 |
| P00390 | Glutathione reductase, mitochondrial precursor | Maintains high levels of reduced glutathione in the cytosol |
| P00441 | Superoxide dismutase (Cu-Zn) | Destroys radicals which are normally produced within the cells and which are toxic to biological systems |
| P00505 | Aspartate aminotransferase, mitochondrial precursor | Facilitates cellular uptake of long-chain free fatty acids |
| P01024 | Complement C3 precursor | C3 plays a central role in the activation of the complement system. Its processing by C3 convertase is the central reaction in both classical and alternative complement pathways. After activation C3b can bind covalently, via its reactive thioester, to cell surface carbohydrates or immune aggregates. Derived from proteolytic degradation of complement C3, C3a anaphylatoxin is a mediator of local inflammatory process. It induces the contraction of smooth muscle, increases vascular permeability, and causes histamine release from mast cells and basophilic leukocytes |
| P01034 | Cystatin C precursor | As an inhibitor of cysteine proteinases, this protein is thought to serve an important physiological role as a local regulator of this enzyme activity |
| P02452 | Collagen α-1(I) chain precursor | Type I collagen is a member of group I collagen (fibrillar forming collagen) |
| P02686 | Myelin basic protein | The classic group of MBP isoforms (isoform 4-isoform 14) are with PLP the most abundant protein components of the myelin membrane in the CNS. They have a role in both its formation and stabilization. The smaller isoforms might have an important role in remyelination of denuded axons in multiple sclerosis. The nonclassic group of MBP isoforms (isoform 1-isoform 3/Golli-MBPs) may preferentially have a role in the early developing brain long before myelination, maybe as components of transcriptional complexes, and may also be involved in signaling pathways in T-cells and neural cells. Differential splicing events combined with optional posttranslational modifications give a wide spectrum of isomers, with each of them potentially having a specialized function. Induces T-cell proliferation |
| P02751 | Fibronectin precursor | Fibronectins bind cell surfaces and various compounds including collagen, fibrin, heparin, DNA, and actin. Fibronectins are involved in cell adhesion, cell motility, opsonization, wound healing, and maintenance of cell shape. Interaction with TNR mediates inhibition of cell adhesion and neurite outgrowth |
| P02768 | Serum albumin precursor | Serum albumin, the main protein of plasma, has a good binding capacity for water, Ca(2+), Na(+), K(+), fatty acids, hormones, bilirubin, and drugs. Its main function is the regulation of the colloidal osmotic pressure of blood |
| P04075 | Fructose-bisphosphate aldolase A | |
| P04080 | Cystatin B | Intracellular thiol proteinase inhibitor |
| P04179 | Superoxide dismutase | Destroys radicals which are normally produced within the cells and which are toxic to biological systems |
| P06733 | α-enolase | Multifunctional enzyme that, as well as its role in glycolysis, plays a part in various processes such as growth control, hypoxia tolerance, and allergic responses. May also function in the intravascular and pericellular fibrinolytic system due to its ability to serve as a receptor and activator of plasminogen on the cell surface of several cell-types such as leukocytes and neurons. May be a tumor suppressor |
| P06744 | Glucose-6-phosphate isomerase | Neuroleukin is a neurotrophic factor for spinal and sensory neurons |
| P07195 | L-lactate dehydrogenase B chain | |
| P07737 | Profilin-1 | Binds to actin and affects the structure of the cytoskeleton. At high concentrations, profilin prevents the polymerization of actin, whereas it enhances it at low concentrations. By binding to PIP2, it inhibits the formation of IP3 and DG |
| P07814 | Bifunctional aminoacyl-tRNA synthetase | Catalyzes the attachment of the cognate amino acid to the corresponding tRNA in a two-step reaction: the amino acid is first activated by ATP to form a covalent intermediate with AMP and is then transferred to the acceptor end of the cognate tRNA |
| P07900 | Heat shock protein HSP 90-α | Molecular chaperone. Has ATPase activity |
| P07996 | Thrombospondin-1 precursor | Adhesive glycoprotein that mediates cell-to-cell and cell-to-matrix interactions. Can bind to fibrinogen, fibronectin, laminin, type V collagen, and integrins α-V/ β-1, α-V/ β-3 and α-IIb/ β-3 |
| P08238 | Heat shock protein HSP 90- β | Molecular chaperone. Has ATPase activity. |
| P09104 | γ-enolase | Has neurotrophic and neuroprotective properties on a broad spectrum of central nervous system (CNS) neurons. Binds, in a calcium-dependent manner, to cultured neocortical neurons and promotes cell survival |
| P09382 | Galectin-1 | Cell apoptosis and cell differentiation |
| P09486 | SPARC precursor | Appears to regulate cell growth through interactions with the extracellular matrix and cytokines. Binds calcium and copper, several types of collagen, albumin, thrombospondin, PDGF and cell membranes. There are two calcium binding sites; an acidic domain that binds 5 to 8 Ca(2+) with a low affinity and an EF-hand loop that binds a Ca(2+) ion with a high affinity |
| P09493 | Tropomyosin 1 α chain | Binds to actin filaments in muscle and nonmuscle cells. Plays a central role, in association with the troponin complex, in the calcium dependent regulation of vertebrate striated muscle contraction. Smooth muscle contraction is regulated by interaction with caldesmon. In non-muscle cells is implicated in stabilizing cytoskeleton actin filaments |
| P09622 | Dihydrolipoyl dehydrogenase, mitochondrial precursor | Lipoamide dehydrogenase is a component of the glycine cleavage system as well as of the α-ketoacid dehydrogenase complexes |
| P09972 | Fructose-bisphosphate aldolase C | |
| P10071 | Zinc finger protein GLI3 | A role in limb and brain development |
| P10599 | Thioredoxin | Participates in various redox reactions through the reversible oxidation of its active center dithiol to a disulfide and catalyzes dithiol-disulfide exchange reactions |
| P10909 | Clusterin precursor | Not yet clear. It is known to be expressed in a variety of tissues, and it seems to be able to bind to cells, membranes, and hydrophobic proteins. It has been associated with programmed cell death (apoptosis) |
| P11047 | Laminin γ-1 chain precursor | Binding to cells via a high-affinity receptor, laminin is thought to mediate the attachment, migration, and organization of cells into tissues during embryonic development by interacting with other extracellular matrix components |
| P11117 | Lysosomal acid phosphatase precursor | |
| P12814 | α-actinin-1 | F-actin cross-linking protein which is thought to anchor actin to a variety of intracellular structures. This is a bundling protein |
| P13569 | Cystic fibrosis transmembrane conductance regulator | Involved in the transport of chloride ions. May regulate bicarbonate secretion and salvage in epithelial cells by regulating the SLC4A7 transporter |
| P13929 | β-enolase | Appears to have a function in striated muscle development and regeneration |
| P14136 | Glial fibrillary acidic protein, astrocyte | GFAP, a class-III intermediate filament, is a cell-specific marker that, during the development of the central nervous system, distinguishes astrocytes from other glial cells |
| P14174 | Macrophage migration inhibitory factor | Mediator in regulating the function of macrophage in host defense |
| P14618 | Pyruvate kinase isozymes M1/M2 | Glycolytic enzyme that catalyzes the transfer of a phosphoryl group from phosphoenolpyruvate (PEP) to ADP, generating ATP |
| P15531 | Nucleoside diphosphate kinase A | Synthesis of nucleoside triphosphates other than ATP |
| P16035 | Metalloproteinase inhibitor 2 precursor | Complexes with metalloproteinases (such as collagenases) and irreversibly inactivates them. Known to act on MMP-1, MMP-2, MMP-3, MMP-7, MMP-8, MMP-9, MMP-10, MMP-13, MMP-14, MMP-15, MMP-16, and MMP-19 |
| P17612 | cAMP-dependent protein kinase, α-catalytic subunit | Phosphorylates a large number of substrates in the cytoplasm and the nucleus |
| P18669 | Phosphoglycerate mutase 1 | Interconversion of 3- and 2-phosphoglycerate with 2,3-bisphosphoglycerate as the primer of the reaction. Can also catalyze the reaction of synthase and phosphatase, but with a reduced activity |
| P23528 | Cofilin-1 | Controls reversibly actin polymerization and depolymerization |
| P26232 | α-2 catenin | |
| P27797 | Calreticulin precursor | Molecular calcium binding chaperone promoting folding, oligomeric assembly and quality control in the ER via the calreticulin/calnexin cycle. This lectin interacts transiently with almost all of the monoglucosylated glycoproteins that are synthesized in the ER. Interacts with the DNA-binding domain of NR3C1 and mediates its nuclear export |
| P29400 | Collagen α-5(IV) chain precursor | Type IV collagen is the major structural component of glomerular basement membranes (GBM), forming a “chicken-wire” meshwork together with laminins, proteoglycans and entactin/nidogen |
| P29401 | Transketolase | |
| P30086 | Phosphatidylethanolamine-binding protein 1 | Binds ATP, opioids, and phosphatidylethanolamine. Has lower affinity for phosphatidylinositol and phosphatidylcholine. Serine protease inhibitor which inhibits thrombin, neuropsin, and chymotrypsin but not trypsin, tissue type plasminogen activator, and elastase/HCNP may be involved in the function of the presynaptic cholinergic neurons of the central nervous system. HCNP increases the production of choline acetyltransferase but not acetylcholinesterase. Seems to be mediated by a specific receptor |
| P30154 | Serine/threonine-protein phosphatase 2A 65 kDa regulatory subunit A β isoform | The PR65 subunit of protein phosphatase 2A serves as a scaffolding molecule to coordinate the assembly of the catalytic subunit and a variable regulatory B subunit |
| P34932 | Heat shock 70 kDa protein 4 | |
| P35442 | Thrombospondin-2 precursor | Adhesive glycoprotein that mediates cell-to-cell and cell-to-matrix interactions. Can bind to fibrinogen, fibronectin, laminin, and type V collagen |
| P35573 | Glycogen debranching enzyme | Multifunctional enzyme acting as 1,4-α-D-glucan:1,4-α-D-glucan 4-α-D-glycosyltransferase and amylo-1,6-glucosidase in glycogen degradation |
| P35609 | α-actinin-2 | F-actin cross-linking protein which is thought to anchor actin to a variety of intracellular structures. This is a bundling protein |
| P35711 | Transcription factor SOX-5 | Binds specifically to the DNA sequence 5′-AACAAT-3′. Activates transcription of COL2A1 and AGC1 in vitro |
| P37268 | Squalene synthetase | |
| P39191 | Alu subfamily SB2 sequence contamination warning entry | |
| P40925 | Malate dehydrogenase, cytoplasmic | |
| P46940 | Ras GTPase-activating-like protein IQGAP1 | Binds to activated CDC42 but does not stimulate its GTPase activity. It associates with calmodulin. Could serve as an assembly scaffold for the organization of a multimolecular complex that would interface incoming signals to the reorganization of the actin cytoskeleton at the plasma membrane. May promote neurite outgrowth |
| P49746 | Thrombospondin-3 precursor | Adhesive glycoprotein that mediates cell-to-cell and cell-to-matrix interactions. Can bind to fibrinogen, fibronectin, laminin, and type V collagen |
| P50395 | Rab GDP dissociation inhibitor β | Regulates the GDP/GTP exchange reaction of most Rab proteins by inhibiting the dissociation of GDP from them, and the subsequent binding of GTP to them |
| P53618 | Coatomer subunit β | The coatomer is a cytosolic protein complex that binds to dilysine motifs and reversibly associates with Golgi nonclathrin-coated vesicles, which further mediate biosynthetic protein transport from the ER, via the Golgi up to the trans Golgi network. Coatomer complex is required for budding from Golgi membranes, and is essential for the retrograde Golgi-to-ER transport of dilysine-tagged proteins. In mammals, the coatomer can only be recruited by membranes associated to ADP-ribosylation factors (ARFs), which are small GTP-binding proteins; the complex also influences the Golgi structural integrity, as well as the processing, activity, and endocytic recycling of LDL receptors |
| P58546 | Myotrophin | Cerebellar morphogenesis |
| P59998 | Actin-related protein 2/3 complex subunit 4 | Actin-binding component of the Arp2/3 complex which is involved in regulation of actin polymerization and together with an activating nucleation-promoting factor (NPF) mediates the formation of branched actin networks |
| P60174 | Triosephosphate isomerase | |
| P62937 | Peptidyl-prolyl cis-trans isomerase A | PPIases accelerate the folding of proteins |
| P63104 | 14-3-3 protein zeta/delta | Adapter protein implicated in the regulation of a large spectrum of both general and specialized signaling pathway. Binds to a large number of partners, usually by recognition of a phosphoserine or phosphothreonine motif. Binding generally results in the modulation of the activity of the binding partner |
| P78527 | DNA-dependent protein kinase catalytic subunit | Serine/threonine-protein kinase that acts as a molecular sensor for DNA damage. Involved in DNA nonhomologous end joining (NHEJ) required for double-strand break (DSB) repair and V(D)J recombination. Must be bound to DNA to express its catalytic properties. Promotes processing of hairpin DNA structures in V(D)J recombination by activation of the hairpin endonuclease artemis (DCLRE1C). The assembly of the DNA-PK complex at DNA ends is also required for the NHEJ ligation step. Required to protect and align broken ends of DNA. May also act as a scaffold protein to aid the localization of DNA repair proteins to the site of damage. Found at the ends of chromosomes, suggesting a further role in the maintenance of telomeric stability and the prevention of chromosomal end fusion. Also involved in modulation of transcription. Recognizes the substrate consensus sequence (ST)-Q. Phosphorylates “Ser-139” of histone variant H2AX/H2AFX, thereby regulating DNA damage response mechanism. Phosphorylates DCLRE1C, c-Abl/ABL1, histone H1, HSPCA, c-jun/JUN, p53/TP53, PARP1, POU2F1, DHX9, SRF, XRCC1, XRCC1, XRCC4, XRCC5, XRCC6, WRN, c-myc/MYC, and RFA2. Can phosphorylate C1D not only in the presence of linear DNA but also in the presence of supercoiled DNA. Ability to phosphorylate TP53/p53 in the presence of supercoiled DNA is dependent on C1D |
| P81274 | G-protein signaling modulator 2 | Plays an important role in spindle pole orientation. Interacts and contributes to the functional activity of G(i) α proteins. Acts to stabilize the apical complex during neuroblast divisions |
| P81605 | Dermcidin precursor | DCD-1 displays antimicrobial activity thereby limiting skin infection by potential pathogens in the first few hours after bacterial colonization. Highly effective against E. coli, E. faecalis, S. aureus and C. albicans. Optimal pH and salt concentration resemble the conditions in sweat. Survival-promoting peptide promotes survival of neurons and displays phosphatase activity. It may bind IgG |
| P82279 | Crumbs homolog 1 precursor | Photoreceptor morphogenesis in the retina/May maintain cell polarization and adhesion |
| Q04760 | Lactoylglutathione lyase | Catalyzes the conversion of hemimercaptal, formed from methylglyoxal and glutathione, to S-lactoylglutathione |
| Q06495 | Sodium-dependent phosphate transport protein 2A | May be involved in actively transporting phosphate into cells via Na(+) cotransport in the renal brush border membrane. Probably mediates 70–80% of the apical influx |
| Q06830 | Peroxiredoxin-1 | Involved in redox regulation of the cell. Reduces peroxides with reducing equivalents provided through the thioredoxin system but not from glutaredoxin. May play an important role in eliminating peroxides generated during metabolism. Might participate in the signaling cascades of growth factors and tumor necrosis factor-α by regulating the intracellular concentrations of H2O2 |
| Q08378 | Golgin subfamily A member 3 | Golgi autoantigen; probably involved in maintaining Golgi structure |
| Q08380 | Galectin-3-binding protein precursor | Promotes integrin-mediated cell adhesion. May stimulate host defense against viruses and tumor cells |
| Q12799 | T-complex protein 10A homolog | |
| Q12841 | Follistatin-related protein 1 precursor | May modulate the action of some growth factors on cell proliferation and differentiation. Binds heparin |
| Q13045 | Protein flightless-1 homolog | May play a role as coactivator in transcriptional activation by hormone-activated nuclear receptors (NR) and acts in cooperation with NCOA2 and CARM1. Involved in estrogen hormone signaling. Involved in early embryonic development (By similarity). May play a role in regulation of cytoskeletal rearrangements involved in cytokinesis and cell migration |
| Q13075 | Baculoviral IAP repeat-containing protein 1 | Prevents motor-neuron apoptosis induced by a variety of signals |
| Q13136 | Liprin-α-1 | Regulate the disassembly of focal adhesions/may localize receptor-like tyrosine phosphatases type 2A at specific sites on the plasma membrane, possibly regulating their interaction with the extracellular environment and their association with substrates |
| Q13371 | Phosducin-like protein | |
| Q13740 | CD166 antigen precursor | Cell adhesion molecule that binds to CD6. Involved in neurite extension by neurons via heterophilic and homophilic interactions. May play a role in the binding of T- and B-cells to activated leukocytes, as well as in interactions between cells of the nervous system |
| Q14980 | Nuclear mitotic apparatus protein 1 | May be a structural component of the nucleus |
| Q15084 | Protein disulfide-isomerase A6 precursor | Catalyzes the rearrangement of -S-S- bonds in proteins |
| Q15113 | Procollagen C-endopeptidase enhancer 1 precursor | Binds to the C-terminal propeptide of type I procollagen and enhances procollagen C-proteinase activity |
| Q32MQ0 | Protein ZNF750 | |
| Q5VTR2 | Ubiquitin-protein ligase BRE1A | E3 ubiquitin-protein ligase that mediates monoubiquitination of “Lys-120” of histone H2B. H2B “Lys-120” ubiquitination gives a specific tag for epigenetic transcriptional activation and is also prerequisite for histone H3 “Lys-4” and “Lys-79” methylation. Forms a ubiquitin ligase complex in cooperation with the E2 enzyme UBE2E1/UBCH6. It thereby plays a central role in histone code and gene regulation. Required for transcriptional activation of Hox genes. Recruited to the MDM2 promoter, probably by being recruited by p53/TP53, and thereby acts as a transcriptional coactivator |
| Q6KC79 | Nipped-B-like protein | Probably plays a structural role in chromatin. Involved in sister chromatid cohesion, possibly by interacting with the cohesin complex |
| Q6NUM9 | All-trans-retinol 13,14-reductase precursor | Play a role in the metabolism of vitamin A |
| Q6ZU80 | Protein C14orf145 | |
| Q6ZUB1 | Protein C9orf79 | |
| Q7L1I2 | Synaptic vesicle glycoprotein 2B | Probably plays a role in the control of regulated secretion in neural and endocrine cells |
| Q7Z3E2 | Protein C10orf118 | |
| Q8IWJ2 | GRIP and coiled-coil domain-containing protein 2 | Function probably involved in maintaining Golgi structure |
| Q8N0X7 | Spartin | May be implicated in endosomal trafficking, or microtubule dynamics, or both. |
| Q8N1I0 | Dedicator of cytokinesis protein 4 | Involved in regulation of adherens junction between cells. Functions as a guanine nucleotide exchange factor (GEF), which activates Rap1 small GTPase by exchanging bound GDP for free GTP |
| Q8TEU7 | Rap guanine nucleotide exchange factor 6 | Guanine nucleotide exchange factor (GEF) for Rap1A, Rap2A, and M-Ras GTPases. Does not interact with cAMP |
| Q8TF76 | Serine/threonine-protein kinase Haspin | Required for normal alignment of chromosomes at metaphase. Phosphorylates histone H3 “Thr-3” during mitosis |
| Q8WUT4 | Uncharacterized protein C20orf75 precursor | May play an important role in hippocampus-dependent long-lasting memory |
| Q96EZ8 | Microspherule protein 1 | Modulates the transcription repressor activity of DAXX by recruiting it to the nucleolus. May be an inhibitor of TERT telomerase activity |
| Q96Q42 | Alsin | May act as a GTPase regulator. Controls survival and growth of spinal motoneurons |
| Q9BXM0 | Periaxin | Is required for maintenance of peripheral nerve myelin sheath/may have a role in axon-glial interactions |
| Q9NVP4 | Protein C20orf12 | |
| Q9NX63 | Coiled-coil-helix-coiled-coil-helix domain-containing protein 3 | |
| Q9P0K1 | ADAM 22 precursor | Probable ligand for integrin in the brain. This is a noncatalytic metalloprotease-like protein. Involved in regulation of cell adhesion and spreading and in inhibition of cell proliferation |
| Q9UM47 | Neurogenic locus notch homolog protein 3 precursor | Functions as a receptor for membrane-bound ligands Jagged1, Jagged2, and Delta1 to regulate cell-fate determination. Upon ligand activation through the released notch intracellular domain (NICD) it forms a transcriptional activator complex with RBP-Jκ and activates genes of the enhancer of split locus. Affects the implementation of differentiation, proliferation, and apoptotic programs |
| Q9UM54 | Myosin-6 | Myosins are actin-based motor molecules with ATPase activity. Unconventional myosins serve in intracellular movements. Myosin 6 is a reverse-direction motor protein that moves towards the minus-end of actin filaments. Has slow rate of actin-activated ADP release due to weak ATP binding. Functions in a variety of intracellular processes such as vesicular membrane trafficking and cell migration. Required for the structural integrity of the Golgi apparatus via the p53-dependent prosurvival pathway. Appears to be involved in a very early step of clathrin-mediated endocytosis in polarized epithelial cells. May act as a regulator of F-actin dynamics. May play a role in transporting DAB2 from the plasma membrane to specific cellular targets. Required for structural integrity of inner ear hair cells |
| Q9UPQ9 | Trinucleotide repeat-containing 6B protein | Plays a role in RNA-mediated gene silencing by both micro-RNAs (miRNAs) and short interfering RNAs (siRNAs). Required for miRNA-dependent translational repression and siRNA-dependent endonucleolytic cleavage of complementary mRNAs by argonaute family proteins |
| Q9UPT6 | C-jun-amino-terminal kinase-interacting protein 3 | Mediates JNK signaling by aggregating specific components of the MAPK cascade to form a functional JNK signaling module. May function as a regulator of vesicle transport, through interactions with the JNK-signaling components and motor proteins |
| Q9UQ26 | Regulating synaptic membrane exocytosis protein 2 | Rab effector involved in exocytosis. May act as scaffold protein. |
| Q9Y333 | U6 snRNA-associated Sm-like protein LSm2 | Binds specifically to the 3′-terminal U-tract of U6 snRNA. May be involved in pre-mRNA splicing |
| Q9Y587 | AP-4 complex subunit sigma-1 | Subunit of novel type of clathrin- or nonclathrin-associated protein coat involved in targeting proteins from the trans-Golgi network (TGN) to the endosomal-lysosomal system |
*sort by SwissProt No.
In this study, some of the proteins secreted by HNPE cells, which were confirmed by the Western blotting method, may be candidate factors responsible for promoting differentiation of RGC-5 cells including thrombospondin-1, 2, 3 precursor (1-2, 1-3, 1-13), galectin-3-binding protein (1-5~1-7), neurogenic locus notch homolog protein 3 (Notch-3, 1-11), follistatin-related protein 1 precursor (1-11), sPARC precursor (1-14), peroxiredoxin-1 (1-21, 1-22), cofilin 1 (1-24, 1-27), profilin 1 (1-27, 1-28), galectin-1 (1-28), and myotrophin (1-30). Cell differentiation is directed by a variety of intra- and extracellular events including signals generated by extracellular matrix (ECM) components, which mediate adhesive cell-to-cell interactions and trigger a cascade of post-receptor intracellular signaling pathways. The roles for ECM proteins in cell growth and differentiation can be indicated by their abilities to modulate a variety of growth factors [33].
Thrombospondin (TSP, MW~420 kDa), which belongs to a multigene family of modular modular glycoproteins, is composed of three identical subunits within a disulfide linkage. TSP is synthesized by several matrix-forming cells and is incorporated into their extracellular matrix. In several cell types, this protein supports cell growth and proliferation. As a component of ECM, TSP is involved in the regulation of mediate platelet aggregation, inflammation, and angiogenesis as well as adhesion, migration, growth, and differentiation of a number of normal and transformed cells [34, 35]. The expression of the TSP has been also investigated during the process of differentiation of embryonal carcinoma cells, granulose cells and HL-60 cells in vitro [36–39]. Although the TSP is prevalent in differentiated cells, the induced TSP syntheses during the differentiation may function differently during neurogenesis.
In the eye, TSP-1 is localized in the epiretinal membrane and between the retinal pigment epithelial layer and Bruch's membrane, which is a cell-attachment factor with cell-specific affinity. TSP-1 production by retinal pigment epithelial cells is affected by the state of proliferation and cell density. With its anti-angiogenic activity, TSP-1 may play several biologic roles on Bruch's membrane [35]. In another report, the authors evaluated the bone marrow stromal cells (BMSCs) secretion of TSP-1, which is a putative mechanistic agent acting on RGCs for survival and growth [40]. The BMSC-derived TSP-1 is identified as a specific mediator of reparative processes in neurons, which functions included enhanced RGC neurite formation, cell survival, and expression of synaptophysin. It suggested that the TSP-1 signaling pathway might be an important role in neural-like differentiation in BMSCs and outgrowth in RGCs [40]. These observations suggest that the synthesis of TSP contributes to the differentiation options/alternatives of RGC-5 cells toward a neural fate, reminiscent of their neural crest origin.
TSP-2 and SPARC (secreted protein, acidic and rich in cysteine) are classified as matricellular proteins. TSP-2 appears to play a role in reducing proliferation, while SPARC may have a positive role in progenitor cell expansion. TSP-2 and SPARC have been shown to positively influence osteoblast differentiation, with the ability to limit adipogenesis [41, 42].
TSP-3 is structurally similar to cartilage oligomeric matrix protein (COMP/TSP-5), and was a recently described member with the calcium binding Type 3 repeats. Like Type 1 and 2 repeats, TSP-3 is absence of the complement and contains four epidermal growth factor receptors with a distinct N terminus that has no significant homology to other TSPs. TSP-3 is also an oligomeric heparin binding protein present in both the cell layer and medium [43].
Galectin-3-binding protein (G3BP), also known as Mac-2 binding protein, is a secreted glycoprotein with a molecular mass of ~90 kDa present in the extracellular matrix of cells. Gelectins and their binding proteins have primarily been described in cell-cell and cell-matrix interactions and play roles in autoimmunity, inflammation and tumor progression or metastasis [44]. G3BP promotes integrin-mediated cell adhesion and functions in cancer progression of human tumor cells. It also binds to multiple proteins in the extracellular matrix including collagen, fibronectin, and nidogen, and to molecules mediating cell-cell and cell-matrix adhesions that are critical during tumor cell invasion and migration [45–48].
Notch-3 was the third discovered human homologue of the Drosophila melanogaster type I membrane protein notch. In Drosophila, the interaction of notch with its cell-bound ligands (delta and serrate) establishes an intercellular signaling pathway that plays a key role in neural development. Members of the Notch gene family were thought to be involved as receptors for membrane-bound ligands Jagged1, Jagged2, and Delta1 in the regulation of cell fate in a variety of neurogenesis of embryos, particularly in the developing central nervous system (CNS) from the homogenous cell population of the neural tube [49, 50]. The Notch-3 activation induces the increase of the progenitor cell number in the CNS and affected CNS development. The Notch-3 mutation may lead to cerebral autosomal dominant arteriopathy with subcortical infarcts and leukoencephalopathy (CADASIL). CADASIL leads to stroke and dementia and is the main feature of recurrent subcortical ischemic events and vascular dementia. Such mutations affect highly-conserved cysteine residues in epidermal growth factor- (EGF-) like repeat domain in the extracellular part of the receptor [51, 52].
Follistatin-related protein (FSRP) is a recently discovered glycoprotein that is highly homologous in both primary sequence and exon/intron domain structure to the activin-binding protein, follistatin (FS). FS is a secreted monomeric glycoprotein and a member of a large group of proteins containing a highly conserved module of cysteine-rich sequence termed the follistatin domain. It was first isolated from ovarian follicular fluid on the basis of its ability to suppress FSH secretion by pituitary cells in vitro [53]. This follistatin gene family includes follistatin, follistatin-related gene (FLRG) protein, follistatin-related protein (FSRP), agrin, secreted protein acidic, and it is rich in cysteine (SPARC), and Mac25 [54]. A follistatin-like sequence containing 10 conserved cysteine residues may modulate the action of some growth factors on cell proliferation and differentiation. It was also thought to be an autoantigen associated with rheumatoid arthritis [55].
SPARC, also known as osteonectin, 43 K protein, or BM-40, is a 32.7 kDa calcium- and copper-binding glycoprotein, which is a product of natural synthesis from osteoblasts, endothelial cells, and megakaryocytes. It functions as a counteradhesive protein, as a modulator of growth factor activity, and as a cell-cycle inhibitor [56]. SPARC belongs to matrix-associated factors that mediate cell-matrix interactions. Other members of this group include TSP-1 and -2, osteopontin (OPN), tenascins, and the SPARC-related proteins. Expressed during many stages of development in a variety of organisms, the expression of this matricellular protein, SPARC, is restricted in adult vertebrates primarily to tissues that undergo consistent turnover or to sites of injuries and diseases [56]. Vertebrate SPARC binds to a number of different ECM components including albumin, thrombospondin 1, PDGF, vitronectin, entactin/nidogen, fibrillar collagens (types I, II, III, and V), and collagen type IV, the prevalent collagen in basement membranes [57]. The ability of SPARC to bind to several resident ECM proteins affects the expression of matrix metalloproteinases and adjusts effects of growth factors; as a counteradhesive factor of cell shape change, this supports SPARC to regulate cell interactions during their development [57]. SPARC appears to regulate cell growth through interactions with the extracellular matrix and cytokines. It is also a matricellular protein that modulates cell adhesion and proliferation and is thought to function in tissue remodeling and angiogenesis [58, 59].
Peroxiredoxin (PRDX) is a recently identified family of antioxidative proteins that includes six isoforms in mammals. They share a common reactive Cys residue in the N-terminal region and are capable of serving as a peroxidase, involving thioredoxin and/or glutathione as the electron donor. PRDX 1–4 have an additional reactive Cys residue in the conserved C-terminal region and show >70% amino acid sequence homology. In this capacity, they may be involved in the protection of cells from oxidative stress. Peroxiredoxin1 (PRDX1) is ubiquitously expressed and functions as an antioxidant enzyme, which reduces hydrogen peroxide and alkyl hydroperoxide and is involved in cellular proliferation, differentiation, apoptosis, and innate immunity [60]. PRDX1 may participate in the signal cascades of growth factors and tumor necrosis factor-α by regulating the intracellular concentrations of hydrogen peroxide [61–63]. A previous study also applied a proteomic approach to study PRDX1, -2, and -3 expressions in Alzheimer's diseases and Down's syndrome, and found a significant increase in PRDX1 expression associated with the neurodegenerative diseases [64].
The human cofilin protein has a molecular weight of approximately 21 kDa. It is a member of the actin depolymerization factor (ADF)/cofilin family. Cofilin is an essential cellular protein that can bind the barbed end of actin and is required for cell viability [65]. In cells, cofilin acts in harmony with other regulatory proteins to mediate the response of the actin cytoskeleton to extracellular signals. In vertebrates, cofilin is regulated by pH, phosphorylation and phosphoinositides. It is involved in the translocation of the actin-cofilin complex from cytoplasm to nucleus. Cofilin plays an essential role in actin filament dynamics by enhancing depolymerization and severance of actin filaments [66]. These activities of cofilin can be abolished by phosphorylation at Ser-3; therefore, phosphorylation/dephosphorylation of cofilin at Ser-3 is regarded as one of the important mechanisms for regulating cofilin activities and actin filament dynamics [67]. Sinha et al. reported that the suppression of cofilin might lead to cancer regression [68].
Profilin-1 (PFN1) is a widely and highly expressed 14- to 17-kDa cytoplasmic and nuclear ligand protein of the microfilament system. It is a ubiquitous actin monomer-binding protein involved in actin polymerization in response to extracellular signaling pathways. PFN1 plays a central role in the regulation of de novo actin assembly by preventing spontaneous actin polymerisation through the binding of actin monomers and addition of monomeric actin to the barbed actin-filament ends [69]. The importance of profilins for normal cell proliferation, differentiation, cellular survival, motility, adhesion, migration, and cytoskeleton remodelling has been verified [69–72]. PFN1 may be a tumor suppressor because its expression was reduced in several types of invasive cancers and it was able to suppress tumorigenicity when overexpressed [73]. In addition, the immunohistochemistry analysis also showed low levels of PFN1 in several human breast cancers. Other than being a tumor suppressor, PFN1 was reported as a necessary element for differentiation of human epithelial cells [74].
Galectins are a family of structurally related carbohydrate-binding proteins and widely distributed in nematodes, insects, and porifer, as well as vertebrates and fungi [75]. They are defined by their affinity for poly-N-acetyllactosamine-enriched glycoconjugates and sequence similarities in the carbohydrate recognition domain. The galectins are a family of β-galactoside-binding proteins implicated in modulating cell-cell and cell-matrix interactions, which would be required for protein secretion through the classical secretory pathways found in the extracellular space [76].
Galectin-1 is expressed during human embryogenesis, and many adult cell types express and secrete galectin-1 into the extracellular matrix [76]. Galectin-1 contributes to different events associated with cancer biology, including tumour transformation, proliferation, differentiation, cell cycle regulation, growth arrest, apoptosis, cell adhesion, migration, inflammation, and inhibition of full cell activation [77]. A previous study has shown that galectin-1 induced sustained exposure of phosphatidylserine on the cell surface in a carbohydrate-dependent fashion, but phosphatidylserine exposure is not associated with cell death by apoptosis and does not affect cell viability. There is evidence that galectin-1 contributes to tumour evasion of immune responses [78].
A positive correlation has recently been shown between galectin-3 expression and the degree of malignant transformation in certain types of cell lines, and the amount of galectin-3 expression is expected to possibly serve as an index of degree for neoplastic transformation, tumor cell survival, angiogenesis, tumor metastasis, and tumor malignancy [79, 80]. Recent studies have revealed that intracellular galectin-3 exhibits the activity to suppress drug-induced apoptosis and anoikis that contribute to cell survival. Resistance to apoptosis is essential for cancer cell survival and plays a role in tumor progression [81].
Moreover, both galectin-1 and galectin-3 expressions are necessary for the initiation of the transformed phenotype of tumors. Inhibition of galectin-1 expression can suppress the transformed phenotype of human glioma cells [82]. In addition, following the inhibition of galectin-3 expression, breast carcinoma cells and thyroid papillary carcinoma cells lose their transformed characteristic phenotypes in cell culture [83, 84].
Myotrophin, a 12 kDa protein consists of 117 amino acids, has a potential role in cerebellar morphogenesis and may be involved in differentiation of cerebellar neurons, particularly of granule cells, and associated with cardiac hypertrophy. It appears to be a primary modulator for myocardial cell growth and differentiation [85]. Myotrophin accelerates myocyte growth by stimulating protein synthesis and may be correlated with cardiac hypertrophy in the pathogenesis, where it is involved in the conversion of NF-κ B p50-p65 heterodimers to p50-p50 and p65-p65 homodimers as well as in the normal development of cardiac myocytes [86]. A previous study also indicated that myotrophin may be involved in the upregulation of myofibrillar protein and the activation of cardiac gene transcription during the growth and hypertrophy of myocardium; thus, the induction of early response of gene expression may be linked to this response [87].
The 132 proteins identified in this study may be involved in some biologic processes that are associated with cell differentiation, proliferation, and adhesion. We have tested some proteins incorporated into the medium; however, none of those proteins can solely induce cell differentiation. The results form a database with a diversity and relative abundance of various proteins found in the HNPE cell-secreted proteins. The database provides not only information on the nature of protein contents in HNPE cells but also potential proteins to be examined in further investigations.
4. Conclusions
In this study, we established the first secretome database for HNPE cells. The experimental results obtained by SDS-PAGE and nano-high performance liquid chromatography electrospray ionization tandem mass spectrometry (nano-HPLC-ESI-MS/MS) system revealed the identification of 132 unique proteins from HNPE cell secretome. Among these 132 proteins identified with higher confidence levels, some proteins have been reported involving in cell differentiation, such as thrombospondin-1, 2, 3 precursor, galectin-3-binding protein, neurogenic locus notch homolog protein 3, follistatin-related protein 1 precursor, sPARC precursor, peroxiredoxin-1, cofilin 1, profilin 1, galectin-1, and myotrophin. However, none of those proteins can induce cell differentiation solely. This list serves as a starting point for buildingup a comprehensive database of the proteome of this cell-line. The database can include diverse repertoires of proteins expressed by HNPE cells. All of this data will enhance our understanding of the molecular mechanisms involved in maintaining the differentiated states of HNPE cells and directing their differentiation and, in turn, will bring us closer to fulfill the vast clinical potentials of the cells.
In conclusion, we have demonstrated that RGC-5 cells upon coculturing with HNPE cell conditioned SF-medium developed a differentiated morphology and continued to express the necessary RGC markers. The differentiated RGC-5 cells would therefore be useful to study apoptotic pathways of retinal ganglion cell death. The findings from this study may have significant impacts on HNPE cell biology and cell engineering.
Supplementary Material
In Figure S1, MS/MS Fragmentation of SSFYVNGLTLGGQK found in PROF1_HUMAN, (P07737) Profilin-1 (M/Z 736.36, 2+).
In Figure S2, the cellular locations of 132 proteins synthetized were classified in this study. Assignments were made on the basis of information provided on the Swiss-Prot database at the ExPASy Molecular Biology Server. Some proteins were described to be from a different subcellular location, which explains the total sum being substantially larger than 100%.
Acknowledgments
This paper was supported by research Grants Q097004 from the Kaohsiung Medical University Research Foundation, NSC96-2321-B-037-006, NSC-099-2811-E-224-002, and NSC97-2320-B-037-012-MY3 from the National Science Council, Taiwan.
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Associated Data
This section collects any data citations, data availability statements, or supplementary materials included in this article.
Supplementary Materials
In Figure S1, MS/MS Fragmentation of SSFYVNGLTLGGQK found in PROF1_HUMAN, (P07737) Profilin-1 (M/Z 736.36, 2+).
In Figure S2, the cellular locations of 132 proteins synthetized were classified in this study. Assignments were made on the basis of information provided on the Swiss-Prot database at the ExPASy Molecular Biology Server. Some proteins were described to be from a different subcellular location, which explains the total sum being substantially larger than 100%.