Comparative analysis of phosphoprotein-enriched myocyte proteomes reveals widespread alterations during differentiation

Caspase-3-resistant uncleavable form of acidic leucine-rich nuclear phosphoprotein 32B potentiates leukemic cell apoptosis

One member of the highly conserved acidic leucine‑rich nuclear phosphoprotein 32 kDa (ANP32) family of proteins, ANP32B, is critical for normal development, as demonstrated by a study in ANP32B‑deficient mice. Another study indicated that ANP32B was a direct substrate of caspase‑3, and was primarily cleaved at the sequence Ala‑Glu‑Val‑Asp, following Asp‑163. To investigate the significance of ANP32B cleavage in apoptosis, leukemic U937T cell lines were generated with inducible expression of ANP32B(wild type; WT), the uncleavable mutant ANP32B(D163A) and the N‑terminal fragment ANP32B(1‑163). Notably, overexpression of ANP32B(WT) and ANP32B(D163A) moderately increased and significantly enhanced etoposide‑induced apoptosis and caspase‑3 activation, whereas expression of ANP32B(1‑163) produced no effect. Two hypotheses have been generated, which may explain the distinct roles of the various ANP32B forms: i) ANP32B(WT) and ANP32B(D163A) localize in the nucleus while ANP32B(1‑163) mainly resides in the cytosol; or ii) ANP32B(WT) and ANP32B(D163A), but not ANP32B(1‑163), inhibit the expression of the anti‑apoptotic protein Bcl‑2. Based on these observations, caspase‑3‑resistant uncleavable ANP32B(D163A) is hypothesized to be pro‑apoptotic in leukemic cells.

Global analysis of muscle-specific kinase signaling by quantitative phosphoproteomics

The development of the neuromuscular synapse depends on signaling processes that involve protein phosphorylation as a crucial regulatory event. Muscle-specific kinase (MuSK) is the key signaling molecule at the neuromuscular synapse whose activity is required for the formation of a mature and functional synapse. However, the signaling cascade downstream of MuSK and the regulation of the different components are still poorly understood. In this study we used a quantitative phosphoproteomics approach to study the phosphorylation events and their temporal regulation downstream of MuSK. We identified a total of 10,183 phosphopeptides, of which 203 were significantly up- or down-regulated. Regulated phosphopeptides were classified into four different clusters according to their temporal profiles. Within these clusters we found an overrepresentation of specific protein classes associated with different cellular functions. In particular, we found an enrichment of regulated phosphoproteins involved in posttranscriptional mechanisms and in cytoskeletal organization. These findings provide novel insights into the complex signaling network downstream of MuSK and form the basis for future mechanistic studies.

A combination of affinity chromatography, 2D DIGE, and mass spectrometry to analyze the phosphoproteome of liver progenitor cells

Reversible protein phosphorylation is a ubiquitous posttranslational modification that regulates cellular signaling pathways in multiple biological processes. A comprehensive analysis of protein phosphorylation patterns can only be achieved by employing different complementary experimental strategies all aiming at selective enrichment of phosphorylated proteins/peptides. In this chapter, we describe a method that utilizes a phosphoprotein affinity chromatography (Qiagen) to isolate intact phosphoproteins. These are subsequently detected by difference in two-dimensional gel electrophoresis and identified by mass spectrometry techniques. Additional experiments using a specific stain for phosphoproteins demonstrated that phosphoprotein affinity column was an effective method for enriching phosphate-containing proteins. Further validating the method, this workflow was applied to probe changes in the activation patterns of intermediates involved in different signaling pathways, such as NDRG1 and stathmin, in liver progenitor cells (MLP-29) upon proteasome inhibition.

Acidic nuclear phosphoprotein 32kDa (ANP32)B-deficient mouse reveals a hierarchy of ANP32 importance in mammalian development

The highly conserved ANP32 proteins are proposed to function in a broad array of physiological activities through molecular mechanisms as diverse as phosphatase inhibition, chromatin regulation, caspase activation, and intracellular transport. On the basis of previous analyses of mice bearing targeted mutations of Anp32a or Anp32e, there has been speculation that all ANP32 proteins play redundant roles and are dispensable for normal development. However, more recent work has suggested that ANP32B may in fact have functions that are not shared by other ANP32 family members. Here we report that ANP32B expression is associated with a poor prognosis in human breast cancer, consistent with the increased levels of Anp32b mRNA present in proliferating wild-type (WT) murine embryonic fibroblasts and stimulated WT B and T lymphocytes. Moreover, we show that, contrary to previous assumptions, Anp32b is very important for murine embryogenesis. In a mixed genetic background, ANP32B-deficient mice displayed a partially penetrant perinatal lethality that became fully penetrant in a pure C57BL/6 background. Surviving ANP32B-deficient mice showed reduced viability due to variable defects in various organ systems. Study of compound mutants lacking ANP32A, ANP32B, and/or ANP32E revealed previously hidden roles for ANP32A in mouse development that became apparent only in the complete absence of ANP32B. Our data demonstrate a hierarchy of importance for the mammalian Anp32 genes, with Anp32b being the most critical for normal development.

Generation and characterization of the Anp32e-deficient mouse

Background

Accumulated literature suggests that the acidic nuclear phosphoprotein 32 kilodalton (Anp32) proteins control multiple cellular activities through different molecular mechanisms. Like other Anp32 family members, Anp32e (a.k.a. Cpd1, PhapIII) has been conserved throughout vertebrate evolution, suggesting that it has an important function in organismal survival.

Principal Findings

Here, we demonstrate that the Anp32e gene can be deleted in mice without any apparent effect on their wellbeing. No defects in thymocyte apoptosis in response to various stresses, fibroblast growth, gross behaviour, physical ability, or pathogenesis were defined. Furthermore, combined deletion of Anp32a and Anp32e also resulted in a viable and apparently healthy mouse.

Significance

These results provide evidence that significant functional redundancy exists among Anp32 family members.

Relationship between proteome changes of Longissimus muscle and intramuscular fat content in finishing pigs fed conjugated linoleic acid

The present experiment was conducted to determine proteome changes in Longissimus muscle of finishing pigs fed conjugated linoleic acid (CLA), in association with alteration of intramuscular fat content. Previously, seventy-two Duroc × Landrace × Large White gilts (approximately 60 kg) had been fed maize–soyabean meal-based diets with 0, 12·5 and 25 g CLA/kg diet. The CLA contained 369·1 mg/g cis-9, trans-11 CLA, 374·6 mg/g trans-10, cis-12 CLA and 53·7 mg/g other isomers. Six pigs per treatment were slaughtered when they reached a body weight of approximately 100 kg. Data published from a previous experiment demonstrated that supplementation with 12·5 or 25 g CLA/kg diet increased intramuscular fat content (P < 0·05). The present study investigated the proteome changes in Longissimus muscle of control and pigs supplemented with 25 g CLA/kg diet. CLA significantly influenced the abundance of proteins related to energy metabolism, fatty acid oxidation and synthesis, amino acid metabolism, defence, transport and other miscellaneous processes (P < 0·05). The increase in intramuscular fat content was positively correlated with the increased abundance of carbonic anhydrase 3 and aspartate aminotransferase (P < 0·05). We suggest that the proteome changes in Longissimus muscle contributed to greater intramuscular lipid content in CLA-supplemented pigs.

Glycogenome expression dynamics during mouse C2C12 myoblast differentiation suggests a sequential reorganization of membrane glycoconjugates

Background

Several global transcriptomic and proteomic approaches have been applied in order to obtain new molecular insights on skeletal myogenesis, but none has generated any specific data on glycogenome expression, and thus on the role of glycan structures in this process, despite the involvement of glycoconjugates in various biological events including differentiation and development. In the present study, a quantitative real-time RT-PCR technology was used to profile the dynamic expression of 375 glycogenes during the differentiation of C2C12 myoblasts into myotubes.

Results

Of the 276 genes expressed, 95 exhibited altered mRNA expression when C2C12 cells differentiated and 37 displayed more than 4-fold up- or down-regulations. Principal Component Analysis and Hierarchical Component Analysis of the expression dynamics identified three groups of coordinately and sequentially regulated genes. The first group included 12 down-regulated genes, the second group four genes with an expression peak at 24 h of differentiation, and the last 21 up-regulated genes. These genes mainly encode cell adhesion molecules and key enzymes involved in the biosynthesis of glycosaminoglycans and glycolipids (neolactoseries, lactoseries and ganglioseries), providing a clearer indication of how the plasma membrane and extracellular matrix may be modified prior to cell fusion. In particular, an increase in the quantity of ganglioside G_M3 at the cell surface of myoblasts is suggestive of its potential role during the initial steps of myogenic differentiation.

Conclusion

For the first time, these results provide a broad description of the expression dynamics of glycogenes during C2C12 differentiation. Among the 37 highly deregulated glycogenes, 29 had never been associated with myogenesis. Their biological functions suggest new roles for glycans in skeletal myogenesis.

Differentiation-dependent PTPIP51 expression in human skeletal muscle cell culture

Protein tyrosine phosphatase-interacting protein 51 (PTPIP51) expression was analyzed in proliferating and differentiating human myogenic cells cultured in vitro. Satellite cell cultures derived from four different individuals were used in this study. To analyze the expression of PTPIP51, myoblasts were cultured under conditions promoting either proliferation or differentiation. In addition, further differentiation of already-differentiated myobtubes was inhibited by resubmitting the cells to conditions promoting proliferation. PTPIP51 protein and mRNA were investigated in samples taken at defined time intervals by immunostaining, immunoblotting, in situ hybridization, and PCR. Image analyses of fluorescence immunostainings were used to quantify PTPIP51 in cultured myoblasts and myotubes. Myoblasts grown in the presence of epidermal and fibroblast growth factors (EGF and FGF), both promoting proliferation, expressed PTPIP51 on a basic level. Differentiation to multinuclear myotubes displayed a linear increase in PTPIP51 expression. The rise in PTPIP51 protein was paralleled by an augmented expression of muscle-specific proteins, namely, sarcoplasmic reticulum Ca(2+) ATPase and myosin heavy-chain protein, both linked to a progressive state of myotubal differentiation. This differentiation-induced increase in PTPIP51 was partly reversible by resubmission of differentiated myotubes to conditions boosting proliferation. The results clearly point toward a strong association between PTPIP51 expression and differentiation in human muscle cells.

Identification of phosphoproteins in kidney tissues from patients with autosomal dominant polycystic kidney disease

Protein phosphorylation is a very important PTM. Phosphorylation/dephosphorylation of a protein can alter its behavior in almost every conceivable way. Previous studies indicate that abnormal phosphorylation is involved in the pathogenesis of autosomal dominant polycystic kidney disease (ADPKD). However, large-scale proteomic analysis of altered phosphoproteins in ADPKD has not been reported. In this study, total proteins from ADPKD cystic kidney tissues (n = 5) and normal kidney tissues (n = 5) were extracted and phosphoproteins were enriched by phosphate metal affinity chromatography, then separated by 2-DE and identified by LC-MS/MS. Between the two groups, 48 protein spots showing more than a twofold difference were detected. Among them, 28 spots were up-regulated and 20 down-regulated in ADPKD kidney tissues. Of these, 38 different proteins were identified including cell signaling proteins, cytoskeleton proteins, mitochondria metabolic enzymes, antioxidant proteins, molecular chaperones, transcription factors and regulators. Two differential phosphoproteins, annexin II and tropomyosin, were further confirmed by immunoprecipitation and Western blot analysis. The results show that there are many kinds of abnormal phosphoproteins in ADPKD cystic kidney tissues. More studies on the functions of the differential phosphoproteins may provide us new clues for ADPKD pathogenesis and treatment.

Isolation of phosphoproteins

Phosphorylation is one of the most abundant post-translational modifications on protein and one that frequently has functional biological consequences. For this reason, screening protein samples for phosphorylations has become an important tool in biochemical research. Affinity purification by immunological or chemical reagents can be used to isolate phosphoproteins from other cellular materials.

Reconstructing the regulatory kinase pathways of myogenesis from phosphopeptide data

Multiple kinase activities are required for skeletal muscle differentiation. However, the mechanisms by which these kinase pathways converge to coordinate the myogenic process are unknown. Using multiple phosphoprotein and phosphopeptide enrichment techniques we obtained phosphopeptides from growing and differentiating C2C12 muscle cells and determined specific peptide sequences using LC-MS/MS. To place these phosphopeptides into a rational context, a bioinformatics approach was used. Phosphorylation sites were matched to known site-specific and to site non-specific kinase-substrate interactions, and then other substrates and upstream regulators of the implicated kinases were incorporated into a model network of protein-protein interactions. The model network implicated several kinases of known relevance to myogenesis including AKT, GSK3, CDK5, p38, DYRK, and MAPKAPK2 kinases. This combination of proteomics and bioinformatics technologies should offer great utility as the volume of protein-protein and kinase-substrate information continues to increase.

Relative quantification in proteomics: new approaches for biochemistry

Recent developments in mass spectrometry and protein arrays provide opportunities to derive systematically proteomic information from small samples of cellular material. Relative quantification among samples can be achieved with either gel-based or gel-free approaches. Furthermore, the adaptation of specific techniques facilitates absolute quantification. Here, relative quantification in two-dimensional gel electrophoresis is contrasted with that in non-gel-based approaches such as isobaric tagging of peptides, pre-labelling of living cells with isotopomeric forms of essential amino acids and protein array platforms. In addition, novel flow-cytometry-based approaches are considered. These technologies can all be used to determine accurately the levels of proteins or biomarkers in a wide range of samples.

Identification of novel pathway regulation during myogenic differentiation

Stem cell differentiation is governed by extracellular signals that activate intracellular networks (or pathways) to drive phenotypic specification. Using a novel gene clustering strategy we determined pathway relationships from a genome-wide transcriptional dataset of skeletal myoblast differentiation. Established myogenic pathways, including cell contractility and cell-cycle arrest, were predicted with extreme statistical significance (p approximately 0). In addition, gene sets associated with angiogenesis, neuronal activity, and mRNA splicing were regulated, exposing developmental and therapeutic implications. Acquisition of transcriptional data spanning the entire differentiation time course provided context for a dynamic landscape of functional pathway regulation. This novel perspective on myogenic cell differentiation revealed previously unrecognized patterns of regulation. We predict that similar analyses will facilitate ongoing efforts to define molecular mechanisms in other stem cell and developmental paradigms. Finally, by combining an iterative process of analysis with supplementation of novel pathways, this application may evolve into a powerful discovery tool.

Identification of candidate regulators of embryonic stem cell differentiation by comparative phosphoprotein affinity profiling

Embryonic stem cells are a unique cell population capable both of self-renewal and of differentiation into all tissues in the adult organism. Despite the central importance of these cells, little information is available regarding the intracellular signaling pathways that govern self-renewal or early steps in the differentiation program. Embryonic stem cell growth and differentiation correlates with kinase activities, but with the exception of the JAK/STAT3 pathway, the relevant substrates are unknown. To identify candidate phosphoproteins with potential relevance to embryonic stem cell differentiation, a systems biology approach was used. Proteins were purified using phosphoprotein affinity columns, then separated by two-dimensional gel electrophoresis, and detected by silver stain before being identified by tandem mass spectrometry. By comparing preparations from undifferentiated and differentiating mouse embryonic stem cells, a set of proteins was identified that exhibited altered post-translational modifications that correlated with differentiation state. Evidence for altered post-translational modification included altered gel mobility, altered recovery after affinity purification, and direct mass spectra evidence. Affymetrix microarray analysis indicated that gene expression levels of these same proteins had minimal variability over the same differentiation period. Bioinformatic annotations indicated that this set of proteins is enriched with chromatin remodeling, catabolic, and chaperone functions. This set of candidate phosphoprotein regulators of stem cell differentiation includes products of genes previously noted to be enriched in embryonic stem cells at the mRNA expression level as well as proteins not associated previously with stem cell differentiation status.

An effective skeletal muscle prefractionation method to remove abundant structural proteins for optimized two-dimensional gel electrophoresis

Proteomic analysis of biological samples in disease models or therapeutic intervention studies requires the ability to detect and identify biologically relevant proteins present in relatively low concentrations. The detection and analysis of these low-level proteins is hindered by the presence of a few proteins that are expressed in relatively high concentrations. In the case of muscle tissue, highly abundant structural proteins, such as actin, myosin, and tropomyosin, compromise the detection and analysis of more biologically relevant proteins. We have developed a practical protocol which exploits high-pH extraction to reduce or remove abundant structural proteins from skeletal muscle crude membrane preparations in a manner suitable for two dimensional gel electrophoresis. An initial whole-cell muscle lysate is generated by homogenization of powdered tissue in Tris-base. This lysate is subsequently partitioned into a supernatant and pellet containing the majority of structural proteins. Treatment of the pellet with high-pH conditions effectively releases structural proteins from membrane compartments which are then removed through ultracentrifugation. Mass spectrometric identification shows that the majority of protein spots reduced or removed by high-pH treatment were contractile proteins or contractile-related proteins. Removal of these proteins enabled successful detection and identification of minor proteins. Structural protein removal also results in significant improvement of gel quality and the ability to load higher amounts of total protein for the detection of lower abundant protein classes.