Temporal Proteomic Profiling During Differentiation of Normal and Dystrophin-Deficient Human Muscle Cells

2021 ◽  
pp. 1-18
Author(s):  
Mansi V. Goswami ◽  
Shefa M. Tawalbeh ◽  
Emily H. Canessa ◽  
Yetrib Hathout
Keyword(s):  
Protein Expression ◽  
Muscle Development ◽  
Expression Profiles ◽  
Temporal Changes ◽  
Myoblast Differentiation ◽  
Proteomic Profiling ◽  
Proteome Profiling ◽  
Proteome Discoverer ◽  
Attractive Therapeutic Target ◽  
Major Alteration

Background: Myogenesis is a dynamic process involving temporal changes in the expression of many genes. Lack of dystrophin protein such as in Duchenne muscular dystrophy might alter the natural course of gene expression dynamics during myogenesis. Objective: To gain insight into the dynamic temporal changes in protein expression during differentiation of normal and dystrophin deficient myoblasts to myotubes. Method: A super SILAC spike-in strategy in combination and LC-MS/MS was used for temporal proteome profiling of normal and dystrophin deficient myoblasts during differentiation. The acquired data was analyzed using Proteome Discoverer 2.2. and data clustering using R to define significant temporal changes in protein expression. Results: sFour major temporal protein clusters that showed sequential dynamic expression profiles during myogenesis of normal myoblasts were identified. Clusters 1 and 2, consisting mainly of proteins involved mRNA splicing and processing expression, were elevated at days 0 and 0.5 of differentiation then gradually decreased by day 7 of differentiation, then remained lower thereafter. Cluster 3 consisted of proteins involved contractile muscle and actomyosin organization. They increased in their expression reaching maximum at day 7 of differentiation then stabilized thereafter. Cluster 4 consisting of proteins involved in skeletal muscle development glucogenesis and extracellular remodeling had a lower expression during myoblast stage then gradually increased in their expression to reach a maximum at days 11–15 of differentiation. Lack of dystrophin expression in DMD muscle myoblast caused major alteration in temporal expression of proteins involved in cell adhesion, cytoskeleton, and organelle organization as well as the ubiquitination machinery. Conclusion: Time series proteome profiling using super SILAC strategy is a powerful method to assess temporal changes in protein expression during myogenesis and to define the downstream consequences of lack of dystrophin on these temporal protein expressions. Key alterations were identified in dystrophin deficient myoblast differentiation compared to normal myoblasts. These alterations could be an attractive therapeutic target.

Cytokine Profiling of Acute Meylogenous Leukemia and Myelodysplasia.

Blood ◽  
2006 ◽  
Vol 108 (11) ◽  
pp. 2355-2355
Author(s):  
Steven M. Kornblau ◽  
David McCue ◽  
Kang L. Lu ◽  
Wenjing Chen ◽  
Kevin R. Coombes
Keyword(s):  
Protein Expression ◽  
Expression Profiles ◽  
Pearson Correlation ◽  
Expression Patterns ◽  
Myelogenous Leukemia ◽  
High Expression ◽  
Leukemic Cells ◽  
Proteomic Profiling ◽  
Serum Samples ◽  
Average Linkage

Abstract Protein expression and activation determines the pathophysiology of leukemic cells in Myelodysplasia (MDS) and Acute Myelogenous Leukemia (AML) and is dependent on endogenous changes (e.g mutation, methylation) and exogenous signals from stromal interactions, cytokines (CTKN) and chemokines. We have previously performed proteomics on primary AML sample (using reverse phase protein arrays) and wanted to assess how cytokines affect protein expression and phosphorylation. Prior studies of CTKN expression in AML and MDS have generally measured individual CTKNs, but not provided an overall assessment of CTKN expression. We measured the level of 26 CTKN (IL-1RA, 1B, 2, 4 5, 6, 7 , 8 , 9, 10,12, 13, 15, 17, Eotaxin, FGFB, G-CSF, GM-CSF, IFNγ, IP10, MCP1, MIP1α, MIP1β, PDGF, TNFα and VEGF) using multiplex cytometry (Bioplex™, Biorad) in serum samples from 176 AML (138 untreated (New), 38 relapsed (REL)) and 114 MDS patients (97 New, 10 post biological therapy, 7 REL) and 19 normal (NL) subjects. Individual CTKN expression was not correlated with clinical features (e.g. age, gender, cytogenetics, FAB, HB, WBC, platelet etc). The levels of IL -1β, 4, 5, 6, 7,10,12, 13, 17, IFNγ, FGFB and MIP1α were significantly lower and IL-8 and 15 higher in AML/MDS compared to NL. The expression profiles of AML and MDS were statistically indistinguishable whether analyzed individually or by unsupervised hierarchical clustering, except for IL-8 and 13 (higher in AML) and VEGF (higher in MDS). When CTKN were evaluated individually in new AML cases higher levels of IL4, 5 and 10 correlated significantly with remission attainment, and higher levels of IL8, Il1Ra, IP-10, Mip1β, VEGF and ILR, correlated significantly with shorter survival. No CTKN predicted remission attainment or survival in MDS. Unsupervised hierarchical bootstrap clustering using Pearson correlation and average linkage of CTKN expression relative to other CTKN expression, where high levels of one CTKN correlated with high expression of the other, revealed 6 highly reproducible expression patterns: IL-1β 4, 7, 10, 12, 13, G-CSF, IFNγ, MIP1α and PDGF IL 1ra, 6, 8 Eotaxin, IP-10, MIP1β and VEGF, IL2, 9, 15 and GMCSF, IL5 IL-7, FGF-Basic, TNFα and MCP1. Similar unsupervised clustering of the samples based on CTKN expression using average linkage also revealed 5 disease clusters and a NL sample cluster (containing all 19 NL samples). Average expression levels of each CTKN in these 5 clusters show diminished expression of most CTKN that had high expression in the NL samples, with each group showing increase in expression in a distinct subset of CTKN relative to NL. Remission attainment was strongly associated with cytokine signature (P=0.005). Additional CTKN are being studied (SCF, TGFβ, IL3). Comparison of CTKN expression patterns with proteomic profiling of expression and phosphorylation status is pending. In summary, this is the largest sample set studied for multiple CTKN expression in AML and MDS and the first assessment of many of these CTKN in these diseases. Most CTKNs showed different expression in AML and MDS compared to NL. Interestingly, CTKN expression in AML and MDS were similar. Many CTKN are predictive of outcome individually. CTKN signatures distinguish groups of patients and are predictive of outcome. Correlation with proteomic profiling may suggest CTKN to target in combination with other targeted therapies to maximally affect activated pathways.

Comparative proteomic profiling of Hodgkin lymphoma cell lines

2016 ◽  
Vol 12 (1) ◽  
pp. 219-232 ◽  
Author(s):  
D. Vergara ◽  
P. Simeone ◽  
S. De Matteis ◽  
S. Carloni ◽  
P. Lanuti ◽  
...  
Keyword(s):  
Protein Expression ◽  
B Cell ◽  
Hodgkin Lymphoma ◽  
Cell Lines ◽  
Expression Profiles ◽  
Lymphoma Cell ◽  
Classical Hodgkin Lymphoma ◽  
Proteomic Profiling ◽  
Hodgkin Lymphoma Cell ◽  
Protein Expression Profiles

Classical Hodgkin lymphoma models of T- and B-cell derivation show significant differences in their protein expression profiles.

scholarly journals Comprehensive Analysis of mRNA, lncRNA, circRNA, and miRNA Expression Profiles and Their ceRNA Networks in the Longissimus Dorsi Muscle of Cattle-Yak and Yak

2021 ◽  
Vol 12 ◽  
Author(s):  
Chun Huang ◽  
Fei Ge ◽  
Xiaoming Ma ◽  
Rongfeng Dai ◽  
Renqing Dingkao ◽  
...  
Keyword(s):  
Signaling Pathway ◽  
Molecular Basis ◽  
Muscle Development ◽  
Expression Profiles ◽  
Economic Benefits ◽  
Production Performance ◽  
Differentially Expressed ◽  
Myoblast Differentiation ◽  
Longissimus Dorsi ◽  
Non Coding Rnas

Cattle-yak, as the hybrid offspring of cattle (Bos taurus) and yak (Bos grunniens), demonstrates obvious heterosis in production performance. Male hybrid sterility has been focused on for a long time; however, the mRNAs and non-coding RNAs related to muscle development as well as their regulatory networks remain unclear. The phenotypic data showed that the production performance (i.e., body weight, withers height, body length, and chest girth) of cattle-yak was significantly better than that of the yak, and the economic benefits of the cattle-yak were higher under the same feeding conditions. Then, we detected the expression profiles of the longissimus dorsi muscle of cattle-yak and yak to systematically reveal the molecular basis using the high-throughput sequencing technology. Here, 7,126 mRNAs, 791 lncRNAs, and 1,057 circRNAs were identified to be differentially expressed between cattle-yaks and yaks in the longissimus dorsi muscle. These mRNAs, lncRNA targeted genes, and circRNA host genes were significantly enriched in myoblast differentiation and some signaling pathways related to muscle development (such as HIF-1 signaling pathway and PI3K-Akt signaling pathway). We constructed a competing endogenous RNA (ceRNA) network and found that some non-coding RNAs differentially expressed may be involved in the regulation of muscle traits. Taken together, this study may be used as a reference tool to provide the molecular basis for studying muscle development.

scholarly journals Temporal Profiling of the Cortical Synaptic Mitochondrial Proteome Identifies Ageing Associated Regulators of Stability

Cells ◽  
2021 ◽  
Vol 10 (12) ◽  
pp. 3403
Author(s):  
Laura C. Graham ◽  
Rachel A. Kline ◽  
Douglas J. Lamont ◽  
Thomas H. Gillingwater ◽  
Neil A. Mabbott ◽  
...  
Keyword(s):  
Protein Expression ◽  
Expression Profiles ◽  
Mitochondrial Protein ◽  
Wild Type Mouse ◽  
Proteomic Profiling ◽  
Temporal Regulation ◽  
Mitochondrial Proteome ◽  
Age Dependent ◽  
Protein Expression Profiles

Synapses are particularly susceptible to the effects of advancing age, and mitochondria have long been implicated as organelles contributing to this compartmental vulnerability. Despite this, the mitochondrial molecular cascades promoting age-dependent synaptic demise remain to be elucidated. Here, we sought to examine how the synaptic mitochondrial proteome (including strongly mitochondrial associated proteins) was dynamically and temporally regulated throughout ageing to determine whether alterations in the expression of individual candidates can influence synaptic stability/morphology. Proteomic profiling of wild-type mouse cortical synaptic and non-synaptic mitochondria across the lifespan revealed significant age-dependent heterogeneity between mitochondrial subpopulations, with aged organelles exhibiting unique protein expression profiles. Recapitulation of aged synaptic mitochondrial protein expression at the Drosophila neuromuscular junction has the propensity to perturb the synaptic architecture, demonstrating that temporal regulation of the mitochondrial proteome may directly modulate the stability of the synapse in vivo.

scholarly journals Temporal proteomic profiling of postnatal human cortical development

2017 ◽  
Author(s):  
Michael S. Breen ◽  
Sureyya Ozcan ◽  
Jordan M. Ramsey ◽  
Zichen Wang ◽  
Avi Ma’ayan ◽  
...  
Keyword(s):  
Protein Expression ◽  
Developmental Trajectories ◽  
Expression Profiles ◽  
Cortical Development ◽  
Postnatal Life ◽  
Regulation Of Transcription ◽  
Transcriptome Data ◽  
Proteomic Profiling ◽  
Data Resource ◽  
Age Related

AbstractHealthy cortical development depends on precise regulation of transcription and translation. However, the dynamics of how proteins are expressed, function and interact across postnatal human cortical development remain poorly understood. We surveyed the proteomic landscape of 69 dorsolateral prefrontal cortex samples across seven stages of postnatal life and integrated these data with paired transcriptome data. We detected 911 proteins by liquid chromatography-mass spectrometry, and 83 were significantly associated with postnatal age (FDR p < 0.05). Network analysis identified three modules of co-regulated proteins correlated with age, including two modules with increasing expression involved in gliogenesis and NADH-metabolism and one neurogenesis-related module with decreasing expression throughout development. Integration with paired transcriptome data revealed that these age-related protein modules overlapped with RNA modules and displayed collinear developmental trajectories. Importantly, RNA expression profiles that are dynamically regulated throughout cortical development display tighter correlations with their respective translated protein expression compared to those RNA profiles that are not. Moreover, the correspondence between RNA and protein expression significantly decreases as a function of cortical aging, especially for genes involved in myelination and cytoskeleton organization. Finally, we used this data resource to elucidate the functional impact of genetic risk loci for intellectual disability, converging on gliogenesis, myelination and ATP-metabolism modules in the proteome and transcriptome. We share all data in an interactive, searchable companion website. Collectively, our findings reveal dynamic aspects of protein regulation and provide new insights into brain development, maturation and disease.

scholarly journals Circular RNA profiling of buffalo myoblasts reveals an abundant circPICALM that promotes myoblast differentiation

2020 ◽  
Author(s):  
Mingming Song ◽  
Mengjie Chen ◽  
Kongwei Huang ◽  
Dandan Zhong ◽  
Yaling Chen ◽  
...  
Keyword(s):  
Skeletal Muscle ◽  
Muscle Regeneration ◽  
Muscle Development ◽  
Expression Profiles ◽  
Muscle Growth ◽  
Circular Rna ◽  
Skeletal Muscle Regeneration ◽  
Myoblast Differentiation ◽  
Circular Rnas

Abstract Background Muscle development is a precisely orchestrated and complex process, and circular RNAs (circRNAs) has been demonstrated to play important roles in skeletal muscle growth and development. However, the regulatory functions of circRNA during buffalo muscle developmental processes have not been understood.Results In this study, Ribo-Zero RNA-Seq was performed to investigate the circRNAs expression profiles of proliferated and differentiated buffalo myoblasts. A stringent set of 3,142 circRNAs was finally characterized. Comparing the expression profiles of circRNAs revealed that 110 circRNAs were expressed differentially during myoblast differentiation. We focused on the role of a candidate circRNA, which was named circPICALM based on its host gene PICALM, and was highly (but differentially) expressed in proliferated and differentiated myoblasts. Flow cytometry, EdU incorporation, and Western blotting assays demonstrate that circPICALM promoted myoblasts proliferation and inhibited cells apoptosis. Moreover, overexpression of circPICALM promoted the differentiation of primary buffalo myoblasts. Moreover, circPICALM in vivo stimulated skeletal muscle regeneration in cardiotoxin-induced muscle injury. The RNA pulldown results showed that circPICALM could capture TUBA1B protein, revealing that circPICALM might exert its biological function by binding TUBA1B protein. Conclusions These results demonstrate that the novel non-coding regulator circPICALM induces myoblast differentiation and skeletal muscle regeneration.

scholarly journals Male-Biased gga-miR-2954 Regulates Myoblast Proliferation and Differentiation of Chicken Embryos by Targeting YY1

Genes ◽  
2021 ◽  
Vol 12 (9) ◽  
pp. 1325
Author(s):  
Xiuxue Dong ◽  
Yu Cheng ◽  
Lingyun Qiao ◽  
Xin Wang ◽  
Cuiping Zeng ◽  
...  
Keyword(s):  
Skeletal Muscle ◽  
Muscle Development ◽  
Expression Profiles ◽  
Myoblast Differentiation ◽  
Mammalian Skeletal Muscle ◽  
Loss Of Function ◽  
Skeletal Muscle Development ◽  
Chicken Muscle ◽  
Proliferation And Differentiation ◽  
Myoblast Proliferation

Previous studies have shown that gga-miR-2954 was highly expressed in the gonads and other tissues of male chickens, including muscle tissue. Yin Yang1 (YY1), which has functions in mammalian skeletal muscle development, was predicted to be a target gene of gga-miR-2954. The purpose of this study was to investigate whether gga-miR-2954 plays a role in skeletal muscle development by targeting YY1, and evaluate its function in the sexual dimorphism development of chicken muscle. Here, all the temporal and spatial expression profiles in chicken embryonic muscles showed that gga-miR-2954 is highly expressed in males and mainly localized in cytoplasm. Gga-miR-2954 exhibited upregulated expression of in vitro myoblast differentiation stages. Next, through the overexpression and loss-of-function experiments performed in chicken primary myoblasts, we found that gga-miR-2954 inhibited myoblast proliferation but promoted differentiation. During myogenesis, gga-miR-2954 could suppress the expression of YY1, which promoted myoblast proliferation and inhibited the process of myoblast cell differentiation into multinucleated myotubes. Overall, these findings reveal a novel role of gga-miR-2954 in skeletal muscle development through its function of the myoblast proliferation and differentiation by suppressing the expression of YY1. Moreover, gga-miR-2954 may contribute to the sex difference in chicken muscle development.

scholarly journals Long noncoding RNASYISLregulates myogenesis by interacting with polycomb repressive complex 2

2018 ◽  
Vol 115 (42) ◽  
pp. E9802-E9811 ◽  
Author(s):  
Jian Jun Jin ◽  
Wei Lv ◽  
Pan Xia ◽  
Zai Yan Xu ◽  
An Dai Zheng ◽  
...  
Keyword(s):  
Muscle Development ◽  
Target Genes ◽  
Myogenic Differentiation ◽  
Expression Profiles ◽  
Myoblast Differentiation ◽  
C2c12 Myoblast ◽  
Polycomb Repressive Complex ◽  
Fiber Density ◽  
Muscle Creatine Kinase ◽  
Polycomb Repressive Complex 2

Although many long noncoding RNAs (lncRNAs) have been identified in muscle, their physiological function and regulatory mechanisms remain largely unexplored. In this study, we systematically characterized the expression profiles of lncRNAs during C2C12 myoblast differentiation and identified an intronic lncRNA,SYISL(SYNPO2intron sense-overlapping lncRNA), that is highly expressed in muscle. Functionally,SYISLpromotes myoblast proliferation and fusion but inhibits myogenic differentiation.SYISLknockout in mice results in significantly increased muscle fiber density and muscle mass. Mechanistically,SYISLrecruits the enhancer of zeste homolog 2 (EZH2) protein, the core component of polycomb repressive complex 2 (PRC2), to the promoters of the cell-cycle inhibitor genep21and muscle-specific genes such as myogenin (MyoG), muscle creatine kinase (MCK), and myosin heavy chain 4 (Myh4), leading to H3K27 trimethylation and epigenetic silencing of target genes. Taken together, our results reveal thatSYISLis a repressor of muscle development and plays a vital role in PRC2-mediated myogenesis.

scholarly journals Honeysuckle Aqueous Extracts Induced let-7a Suppress EV71 Replication and Pathogenesis In Vitro and In Vivo and Is Predicted to Inhibit SARS-CoV-2

Viruses ◽  
2021 ◽  
Vol 13 (2) ◽  
pp. 308
Author(s):  
Ying-Ray Lee ◽  
Chia-Ming Chang ◽  
Yuan-Chieh Yeh ◽  
Chi-Ying F. Huang ◽  
Feng-Mao Lin ◽  
...  
Keyword(s):  
Protein Expression ◽  
Western Blotting ◽  
Expression Profiles ◽  
Plaque Assay ◽  
Virus Titer ◽  
Enterovirus 71 ◽  
Luciferase Reporter ◽  
Pathogen Invasion

Honeysuckle (Lonicera japonica Thunb) is a traditional Chinese medicine (TCM) with an antipathogenic activity. MicroRNAs (miRNAs) are small non-coding RNA molecules that are ubiquitously expressed in cells. Endogenous miRNA may function as an innate response to block pathogen invasion. The miRNA expression profiles of both mice and humans after the ingestion of honeysuckle were obtained. Fifteen overexpressed miRNAs overlapped and were predicted to be capable of targeting three viruses: dengue virus (DENV), enterovirus 71 (EV71) and SARS-CoV-2. Among them, let-7a was examined to be capable of targeting the EV71 RNA genome by reporter assay and Western blotting. Moreover, honeysuckle-induced let-7a suppression of EV71 RNA and protein expression as well as viral replication were investigated both in vitro and in vivo. We demonstrated that let-7a targeted EV71 at the predicted sequences using luciferase reporter plasmids as well as two infectious replicons (pMP4-y-5 and pTOPO-4643). The suppression of EV71 replication and viral load was demonstrated in two cell lines by luciferase activity, RT-PCR, real-time PCR, Western blotting and plaque assay. Furthermore, EV71-infected suckling mice fed honeysuckle extract or inoculated with let-7a showed decreased clinical scores and a prolonged survival time accompanied with decreased viral RNA, protein expression and virus titer. The ingestion of honeysuckle attenuates EV71 replication and related pathogenesis partially through the upregulation of let-7a expression both in vitro and in vivo. Our previous report and the current findings imply that both honeysuckle and upregulated let-7a can execute a suppressive function against the replication of DENV and EV71. Taken together, this evidence indicates that honeysuckle can induce the expression of let-7a and that this miRNA as well as 11 other miRNAs have great potential to prevent and suppress EV71 replication.

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