Journal: PLOS One

Article Title: Proteomic profiling of small extracellular vesicles from bovine nucleus pulposus cells

doi: 10.1371/journal.pone.0324179

Figure Lengend Snippet: A) STRING network of 141 more abundant NP small EV proteins; B) Cluster 1: Complement component C1q complex (red), complement and coagulation cascades (blue), complement activation classical pathway (green); C) Cluster 2: Proteasome (red); D) Cluster 3: Axon (blue), axon guidance receptor activity (red), Ephrin signaling (green); E) Cluster 4: Ras signaling (red), axon guidance (green) and MAPK signaling pathway (blue); F) Cluster 5: Hemostasis (green), regulation of MAPK cascade (blue), complement and coagulation cascades (red); G) Cluster 6: ECM (pink), integrin binding (light green), collagen binding (sky blue), ECM receptor interaction (red), PI3K/AKT signaling pathway (blue), ECM organization (yellow), signaling by RTKs (dark green). STRING: Search tool for the retrieval of interacting genes/proteins; NP: Nucleus pulposus.

Article Snippet: Environmental Information Processing , Regulation of actin cytoskeleton Focal adhesion Rap1 signaling pathway ECM-receptor interaction PI3K-Akt signaling pathway Chemokine signaling pathway Apelin signaling pathway Sphingolipid signaling pathway Ras signaling pathway cAMP signaling pathway MAPK signaling pathway , bta04810 bta04510 bta04015 bta04512 bta04151 bta04062 bta04371 bta04071 bta04014 bta04024 bta04010 , ACTN1, C9, COL6A1, COL6A3, FLNA, FN1, GNAI1, GNAI2, GNAI3, GNAQ, GNB1, GSN, HSPA8, HSPB1, HSPG2, ITGA3, ITGAV, ITGB1, LAMC1, MSN, MYH9, PFN1, RAB5B, RAB5C, RAC1, RHOA, RRAS, RRAS2, RAP1B, TLN1, YWHAQ, YWHAE, YWHAG, YWHAZ.

Techniques: Coagulation, Activation Assay, Activity Assay, Binding Assay

Journal: PLOS One

Article Title: Proteomic profiling of small extracellular vesicles from bovine nucleus pulposus cells

doi: 10.1371/journal.pone.0324179

Figure Lengend Snippet: A) STRING network of 484 NP small EV proteins; B) Cluster 1: Extracellular vesicle biogenesis (red), multivesicular body sorting pathway (blue), ESCRT I complex (pink), ESCRT (green), Flotillin complex (yellow); C) Cluster 2: Detection of oxidative stress (black), pentose phosphate pathway (red), glycolysis/gluconeogenesis (blue), biosynthesis of amino acids (green), carbon metabolism (pink), pyruvate metabolism (dark green), TCA cycle (yellow), glutathione metabolism (sky blue), HIF1 signaling pathway (purple), amino sugar and nucleotide sugar metabolism (ochre yellow), activation of BAD and translocation to mitochondria (brown), regulation of localization of FOXO transcription factors (grey); D) Cluster 3: Regulation of Schwann cell migration (blue), G-protein coupled receptor signaling pathway (green), axon guidance (red); E) Cluster 4: Rac protein signal transduction (red), RAS protein signal transduction (blue), small GTPase mediated signal transduction (green), RAP1 signaling pathway (yellow), EPHB-mediated forward signaling (pink), VEGFA/VEGFR2 pathway (dark green), signaling by Rho GTPases (sky blue); F); Cluster 5: MAP2K and MAPK activation (red), RAS signaling pathway (green), MAPK signaling pathway (pink), PI3K/AKT signaling pathway (yellow); G) Cluster 6 version 1: Cell adhesion mediated by integrin (red), mesodermal cell differentiation (blue), angiogenesis (green), regulation of small GTPase mediated signal transduction (yellow), negative regulation of apoptotic process (pink); H) Cluster 6 version 2: ECM receptor interaction (red), focal adhesion (green), PI3K/AKT signaling pathway (blue), axon guidance (yellow), TGFβ signaling pathway (pink); I) Cluster 7: Positive regulation of lamellipodium assembly (blue), actin cytoskeleton organization (red), EPHB mediated forward signaling (green); J) Cluster 8: ECM assembly (pink), cartilage development (green), angiogenesis (blue), blood vessel development (red), cell adhesion (yellow), PI3K/AKT signaling pathway (dark green). ECM: Extracellular matrix; ESCRT I: Endosomal sorting complex required for transport I; STRING: Search tool for the retrieval of interacting genes/proteins; NP: Nucleus pulposus.

Article Snippet: Environmental Information Processing , Regulation of actin cytoskeleton Focal adhesion Rap1 signaling pathway ECM-receptor interaction PI3K-Akt signaling pathway Chemokine signaling pathway Apelin signaling pathway Sphingolipid signaling pathway Ras signaling pathway cAMP signaling pathway MAPK signaling pathway , bta04810 bta04510 bta04015 bta04512 bta04151 bta04062 bta04371 bta04071 bta04014 bta04024 bta04010 , ACTN1, C9, COL6A1, COL6A3, FLNA, FN1, GNAI1, GNAI2, GNAI3, GNAQ, GNB1, GSN, HSPA8, HSPB1, HSPG2, ITGA3, ITGAV, ITGB1, LAMC1, MSN, MYH9, PFN1, RAB5B, RAB5C, RAC1, RHOA, RRAS, RRAS2, RAP1B, TLN1, YWHAQ, YWHAE, YWHAG, YWHAZ.

Techniques: Activation Assay, Translocation Assay, Migration, Transduction, Cell Differentiation

Journal: PLOS One

Article Title: Proteomic profiling of small extracellular vesicles from bovine nucleus pulposus cells

doi: 10.1371/journal.pone.0324179

Figure Lengend Snippet: NP small EV protein cargo and membrane constituents are involved in key metabolic pathways, including glycolysis, gluconeogenesis, Krebs cycle and PPP. They are crucial for energy production and to maintain the cellular redox balance. NP small EVs with the aid of the 20S proteasome, ensure protein quality control and reduced inflammation in a recipient cell. NP small EVs modulate signaling through EPH receptors, impacting cellular communication and tissue organization. Additionally, NP small EV interact with the complement system, influencing the classical, alternative, and lectin pathways involved in immune responses and inflammation. The PI3K/AKT/RAS signaling pathway is axis is impacted by the NP small EV proteome, which could promote ECM synthesis, cell growth and proliferation. Together, these processes underscore the essential role of the NP small EV proteome in sustaining NP cell function and NP niche homeostasis. ECM: Extracellular matrix; EPH: Ephrin receptor, ER: endoplasmic reticulum, ERK: extracellular signal-regulated kinase, MEK: mitogen-activated protein kinase, NP: nucleus pulposus, PDK1: phosphoinositide-dependent protein kinase 1, PPP: pentose phosphate pathway, PI3K/AKT: phosphoinositide 3-kinase/protein kinase B, RAF: rapidly accelerated fibrosarcoma, RHEB: RAS homolog enriched in brain, mTORC1: mammalian target of rapamycin complex 1, small EV: small extracellular vesicles, TSC1/2: tuberous sclerosis proteins 1 and 2. This illustration was created on Biorender. ( www.biorender.com/ ).

Article Snippet: Environmental Information Processing , Regulation of actin cytoskeleton Focal adhesion Rap1 signaling pathway ECM-receptor interaction PI3K-Akt signaling pathway Chemokine signaling pathway Apelin signaling pathway Sphingolipid signaling pathway Ras signaling pathway cAMP signaling pathway MAPK signaling pathway , bta04810 bta04510 bta04015 bta04512 bta04151 bta04062 bta04371 bta04071 bta04014 bta04024 bta04010 , ACTN1, C9, COL6A1, COL6A3, FLNA, FN1, GNAI1, GNAI2, GNAI3, GNAQ, GNB1, GSN, HSPA8, HSPB1, HSPG2, ITGA3, ITGAV, ITGB1, LAMC1, MSN, MYH9, PFN1, RAB5B, RAB5C, RAC1, RHOA, RRAS, RRAS2, RAP1B, TLN1, YWHAQ, YWHAE, YWHAG, YWHAZ.

Techniques: Membrane, Control, Cell Function Assay

Journal: Biomedicines

Article Title: GDF6 Alleviates Pathological Cardiac Hypertrophy via AMPKα Signaling Pathway

doi: 10.3390/biomedicines13122935

Figure Lengend Snippet: GDF6 activates AMPKα through cyclic AMP/exchange protein directly activated by cAMP 1 (cAMP/Epac1) pathway. ( A ) The levels of cAMP and protein kinase A (PKA) activity in PE-stimulated NRVMs with or without GDF6 knockdown. ( B ) The levels of cAMP and PKA activity in PE-stimulated NRVMs with or without rhGDF6 treatment. ( C ) Quantification of cell area in rhGDF6-treated NRVMs with or without adenylyl cyclase (AC) inhibition. ( D ) Rap1-GTP and total Rap1 protein levels in PE-stimulated NRVMs treated with si Gdf6 or rhGDF6. ( E ) AMPKα protein levels in PE-stimulated NRVMs with or without Epac1 silence in the presence or absence of rhGDF6. ( F ) Quantification of cell area. ( G ) Epac1 mRNA levels in NRVMs with or without Epac1 silence. ( H ) Quantification of cell area. ( I ) Epac1 mRNA levels in murine hearts with or without Epac1 silence. ( J ) HW/TL in TAC mice with or without Epac1 silence in the presence or absence of AAV9- Gdf6 . ( K ) Quantification of CSA. ( L ) IVSd and IVSs. ( M ) FS, LVEDd, and LVEDs. n = 6 per group. * p < 0.05 versus matched AAV9- Ctrl -injected TAC mice receiving si Ctrl injection, # p < 0.05 versus matched AAV9- Gdf6 -injected TAC mice receiving si Ctrl injection. In ( A – D , G – I ), * p < 0.05 versus the matched groups. In ( E , F ), * p < 0.05 versus matched si Ctrl -transfected NRVMs with DMSO treatment under PE incubation, # p < 0.05 versus matched si Ctrl -transfected NRVMs with rhGDF6 treatment under PE incubation. One-way ANOVA followed by Tukey post hoc test was applied. In ( A , B , D , G – I ), Student’s two-tailed t -test was performed.

Article Snippet: Active Rap1 Detection Kit (#8818) was purchased from Cell Signaling Technology (Danvers, MA, USA).

Techniques: Activity Assay, Knockdown, Inhibition, Injection, Transfection, Incubation, Two Tailed Test

Journal: World Journal of Gastrointestinal Oncology

Article Title: Downregulation of uncoupling protein 1 by hypermethylation in gastric cancer activates Rap1 signaling

doi: 10.4251/wjgo.v17.i9.108760

Figure Lengend Snippet: Uncoupling protein 1 regulates the Rap-1 signaling pathway in gastric cancer cells. A: Volcano plot for differential gene expression; B: The Kyoto Encyclopedia of Genes and Genomes enrichment of the upregulated genes in the low- Uncoupling protein 1 (UCP1)-expression group; C: Western blot for active and total Rap1 in gastric cancer cells with UCP1 knockdown (left) or overexpression (right). UCP1: Uncoupling protein 1; Ctrl: Control; OE: Overexpression.

Article Snippet: Active Rap1 (GTP-bound) was detected using an active Rap1 detection kit (Cell Signaling Technology, United States).

Techniques: Gene Expression, Expressing, Western Blot, Knockdown, Over Expression, Control