Journal: bioRxiv

Article Title: The long noncoding RNA Meg3 regulates myoblast plasticity and muscle regeneration through epithelial-mesenchymal transition

doi: 10.1101/2020.06.15.152884

Figure Lengend Snippet: A) Violin plots depict limb muscle single cell RNAseq data for Dlk1 - Dio3 megacluster-encoded lncRNAs Meg3 , Rian , and Mirg . All lncRNAs showed enrichment in satellite (sat.) and mesenchymal (mes.) cell types, with Meg3 as the most abundant. CPM = counts per million reads mapped. B) qPCR temporal Meg3 expression profiling was performed on regenerating mouse Tibialis anterior (TA) muscle tissue harvested before (uninjured), and on the indicated days after cardiotoxin injection (+CTX). Meg3 lncRNA transcripts were upregulated following CTX-induced injury, which corresponds with satellite and mesenchymal cell expansion (n=3 mice per time point). C) qPCR temporal expression profiling of Meg3 in C2C2 myoblast differentiation. Meg3 transcripts were most enriched during proliferation (prolif.), and progressively downregulated during course of differentiation (n=4). D) RNA immunoprecipitation (RNA-IP) was performed on subconfluent C2C12 myoblast lysates to examine for Meg3 -PRC2 interaction. Immunoprecipitated RNA was quantified by qPCR, using supernatant as an internal normalization control. Compared to normal IgG controls, Meg3 was enriched in anti-Ezh2 immunoprecipitates (n=3 sets of 60 plates).

Article Snippet: For overexpression, human MEG3 cDNA was PCR amplified from the pCI-Meg3 (Addgene Plasmid #44727) using NEB Q5 high-fidelity polymerase, and cloned into pShuttleCMV vector (Agilent AdEasy Adenoviral Vector System).

Techniques: Expressing, Injection, RNA Immunoprecipitation, Immunoprecipitation, Control

Journal: bioRxiv

Article Title: The long noncoding RNA Meg3 regulates myoblast plasticity and muscle regeneration through epithelial-mesenchymal transition

doi: 10.1101/2020.06.15.152884

Figure Lengend Snippet: A) qPCR quantification of Meg3 transcript levels in heterogeneous cell populations derived from G418 selection (C2C12 het.), and subsequently derived clonal populations (C2C12 clones) indicate that stable shRNA integration resulted in Meg3 knockdown (n=3). B) Immunofluorescence quantification of MYH4 indicates markedly reduced expression in sh Meg3 C2C12 clones. Quantification of nuclei within α-actinin cell-boundaries show reduced fusion index in sh Meg3 clones (n=3). qPCR expression profiling indicated unchanged Myf5 transcript levels, but significant reduction in other myogenic differentiation markers (n=3). C) Western blot quantification of MF20 signal (normalized to β-tubulin) showed marked reduction specific to sh Meg3 clones (n=4). D) qPCR quantification confirmed overexpression of human MEG3 in sh LacZ and sh Meg3 myoblasts, and restoration of endogenous Meg3 transcript levels relative to β-galactosidease controls (n=3). E) Human MEG3 restored both MYH4 expression and fusion index in sh Meg3 but not sh LacZ myoblasts (n=6 MYH4, n=3 fusion index). F) qPCR expression profiling of heterogeneous rescue clones revealed an increase in Mef2C, Ckm , MyoD and Myog levels in sh Meg3 + MEG3 myotubes. MYH4 = myosin heavy chain 4 (Proteintech antibody), MF20 = myosin heavy chain 4 (DHSB antibody), Myf5 = myogenic factor 5 , MyoD = myogenic differentiation 1, Mef2C = myogenic enhancing factor- 2 C , Myog = Myogenin , Ckm = Muscle Creatine Kinase , Acta1 = skeletal muscle actin.

Article Snippet: For overexpression, human MEG3 cDNA was PCR amplified from the pCI-Meg3 (Addgene Plasmid #44727) using NEB Q5 high-fidelity polymerase, and cloned into pShuttleCMV vector (Agilent AdEasy Adenoviral Vector System).

Techniques: Derivative Assay, Selection, Clone Assay, shRNA, Knockdown, Immunofluorescence, Expressing, Western Blot, Over Expression

Journal: bioRxiv

Article Title: The long noncoding RNA Meg3 regulates myoblast plasticity and muscle regeneration through epithelial-mesenchymal transition

doi: 10.1101/2020.06.15.152884

Figure Lengend Snippet: A) Quantification of BrdU+ nuclei (green arrowheads) indicated that sh Meg3 myoblasts divided at a reduced frequency (n=3). B) Cleaved caspase 3 assay revealed higher apoptosis in sh Meg3 myoblasts and myotubes relative to control (n=3). Cell Titer Blue viability assay indicated reduced viability in sh Meg3 myoblasts and myotubes relative to control (n=3). C) sh Meg3 myoblasts seeded at increasing densities was not sufficient to restore MYH4 expression or fusion index (n=3).

Article Snippet: For overexpression, human MEG3 cDNA was PCR amplified from the pCI-Meg3 (Addgene Plasmid #44727) using NEB Q5 high-fidelity polymerase, and cloned into pShuttleCMV vector (Agilent AdEasy Adenoviral Vector System).

Techniques: Caspase-3 Assay, Control, Viability Assay, Expressing

Journal: bioRxiv

Article Title: The long noncoding RNA Meg3 regulates myoblast plasticity and muscle regeneration through epithelial-mesenchymal transition

doi: 10.1101/2020.06.15.152884

Figure Lengend Snippet: C2C12 myoblasts and myotubes were pulsed with MitoTracker CMXRos for 40 minutes, and co-stained with α-actinin. Quantification of Mitotracker (restricted to α-actinin+ cells) indicated reduced mitochondrial signal in sh Meg3 myoblasts, but not myotubes (n=3). Both treatment groups displayed increased MitoTracker signal with differentiation.

Article Snippet: For overexpression, human MEG3 cDNA was PCR amplified from the pCI-Meg3 (Addgene Plasmid #44727) using NEB Q5 high-fidelity polymerase, and cloned into pShuttleCMV vector (Agilent AdEasy Adenoviral Vector System).

Techniques: Staining

Journal: bioRxiv

Article Title: The long noncoding RNA Meg3 regulates myoblast plasticity and muscle regeneration through epithelial-mesenchymal transition

doi: 10.1101/2020.06.15.152884

Figure Lengend Snippet: RNAseq data indicated that transcripts of master regulators of myogenic fusion, notably Myomaker and Myomixer , were not significantly downregulated in sh Meg3 myotubes.

Article Snippet: For overexpression, human MEG3 cDNA was PCR amplified from the pCI-Meg3 (Addgene Plasmid #44727) using NEB Q5 high-fidelity polymerase, and cloned into pShuttleCMV vector (Agilent AdEasy Adenoviral Vector System).

Techniques:

Journal: bioRxiv

Article Title: The long noncoding RNA Meg3 regulates myoblast plasticity and muscle regeneration through epithelial-mesenchymal transition

doi: 10.1101/2020.06.15.152884

Figure Lengend Snippet: A) Cadherin switching was assessed by qPCR (left) and Western blot (right) quantification of E-cadherin (Cdh1) and N-cadherin (Cdh2) in day 3 myotubes. Cdh1 transcripts were significantly downregulated in sh Meg3 myotubes relative to sh LacZ controls (n=3), but Cdh1 protein signal from myotubes lysates was extremely faint (n=4). Cdh2 transcripts were upregulated (n=3), as was Cdh2 protein (n=4). B) qPCR expression profiling indicated significant downregulation of epithelial Plakophilin and PatJ transcripts in sh Meg3 myotubes, with simultaneous upregulation of mesenchymal Fibronectin and Snai2 (n=3). C) Western blot of Vimentin normalized to β-tubulin indicated no change in mesenchymal Vimentin (n=4). D) Scratch-wound assays revealed no detectable change in wound-healing efficiency, as measured by % scratch area (n=3). Brightfield (BF) microscopy of wound-healing morphology differed between sh LacZ control and sh Meg3 clones, with a higher proportion of myoblasts invading the scratch territory with fewer than 2 cell contacts (black arrowheads, n=3).

Article Snippet: For overexpression, human MEG3 cDNA was PCR amplified from the pCI-Meg3 (Addgene Plasmid #44727) using NEB Q5 high-fidelity polymerase, and cloned into pShuttleCMV vector (Agilent AdEasy Adenoviral Vector System).

Techniques: Western Blot, Expressing, Microscopy, Control, Clone Assay

Journal: bioRxiv

Article Title: The long noncoding RNA Meg3 regulates myoblast plasticity and muscle regeneration through epithelial-mesenchymal transition

doi: 10.1101/2020.06.15.152884

Figure Lengend Snippet: A) Following incubation with 10μM LY2157299 (LY), myoblasts were induced to differentiate and examined for MYH4 expression and fusion index. LY-treated sh Meg3 myotubes adopted an elongated morphology, and displayed increased MYH4, decreased myotubes with 1-nuclei, and increased myotubes with 2- and ≥3 nuclei relative to untreated sh Meg3 controls (n=3). B) Western blot for MF20 indicated that LY-treatment restored myosin heavy chain 4 expression to sh Meg3 myotubes (n=3). C) qPCR expression profiling of LY-treated myotubes indicate significant upregulation of all myogenic markers surveyed ( Myf5 , MyoD , Mef2C , Myog , Ckm , Acta1 ) relative to untreated sh LacZ myotubes.

Article Snippet: For overexpression, human MEG3 cDNA was PCR amplified from the pCI-Meg3 (Addgene Plasmid #44727) using NEB Q5 high-fidelity polymerase, and cloned into pShuttleCMV vector (Agilent AdEasy Adenoviral Vector System).

Techniques: Incubation, Expressing, Western Blot

Journal: bioRxiv

Article Title: The long noncoding RNA Meg3 regulates myoblast plasticity and muscle regeneration through epithelial-mesenchymal transition

doi: 10.1101/2020.06.15.152884

Figure Lengend Snippet: A) qPCR indicated that LY2157299 (LY) treatment resulted in reduced E-cadherin ( Cdh1 ) transcripts regardless of sh RNA treatment, with simultaneous upregulation of N-cadherin ( Cdh2 ) transcripts (n=3). Western blot revealed modest Cdh1 band detection, and quantification of β-tubulin-normalized signal revealed that LY-treatment restored Cdh1 levels to sh Meg3 myotubes, while Cdh1 in sh LacZ myotubes remained unchanged. While LY treatment did not change Cdh2 expression in sh LacZ myotubes, LY-treatment enhanced Cdh2 signal in sh Meg3 myotubes. B) qPCR profiling indicated upregulation of epithelial transcripts Plakophilin and PatJ regardless of sh RNA background (n=3). Fibronectin transcript levels returned to normal levels in LY-treated sh Meg3 myotubes. LY treatment intensified upregulation of Snai2 transcripts in sh Meg3 cells, but did not affect Twist2 or Mmp9 levels relative to sh Meg3 myotubes. sh LacZ + LY myotubes displayed reduced Mmp9 , with simultaneous upregulation of Twist2 when compared to untreated sh LacZ cells (n=3). C) Western blot quantification of Vimentin suggests that LY treatment reduced Vimentin expression in sh LacZ controls, but did not change Vimentin expression in sh Meg3 myotubes (n=3). D) Myoblasts pre-treated with 5ng/mL BMP4 (BMP) were subjected to differentiation, and examined for changes in MYH4 expression and fusion index. BMP4 treated sh Meg3 myotubes had improved MYH4 expression (n=3), reduced mononucleated myotubes, and improved 2-cell fusion, but not ≥3 nuclei fusion.

Article Snippet: For overexpression, human MEG3 cDNA was PCR amplified from the pCI-Meg3 (Addgene Plasmid #44727) using NEB Q5 high-fidelity polymerase, and cloned into pShuttleCMV vector (Agilent AdEasy Adenoviral Vector System).

Techniques: Western Blot, Expressing

Journal: bioRxiv

Article Title: The long noncoding RNA Meg3 regulates myoblast plasticity and muscle regeneration through epithelial-mesenchymal transition

doi: 10.1101/2020.06.15.152884

Figure Lengend Snippet: A) Following incubation with 40μM ROCK1/2 inhibitor (Y-27632), myoblasts were induced to differentiate and examined for MYH4 expression and fusion index. Y-27632-treated sh Meg3 myotubes adopted an elongated morphology, and fusion quantification indicated decreased myotubes with 1-nuclei, and increased myotubes with 2- and ≥3 nuclei relative to sh Meg3 control (n=3). While MYH4 expression was enhanced in sh LacZ + Y-27631 myotubes, MYH4 levels remained unchanged with Y-27632 treatment in sh Meg3 cells (n=3). B) Following incubation with 5μM p38 inhibitor (SB203580), myoblasts were induced to differentiate and examined for MYH4 expression and fusion index. SB203580-treated sh Meg3 myotubes adopted an elongated spindle-like morphology, and fusion quantification indicated decreased myotubes with 1-nuclei, and increased myotubes with 2- and ≥3 nuclei relative to sh Meg3 control (n=3). MYH4 expression was unaffected by SB203580 treatment (n=3).

Article Snippet: For overexpression, human MEG3 cDNA was PCR amplified from the pCI-Meg3 (Addgene Plasmid #44727) using NEB Q5 high-fidelity polymerase, and cloned into pShuttleCMV vector (Agilent AdEasy Adenoviral Vector System).

Techniques: Incubation, Expressing, Control

Journal: bioRxiv

Article Title: The long noncoding RNA Meg3 regulates myoblast plasticity and muscle regeneration through epithelial-mesenchymal transition

doi: 10.1101/2020.06.15.152884

Figure Lengend Snippet: A) qPCR expression profiling indicated reduced Meg3 expression in TA muscles co-injected with sh Meg3 adenovirus (n=3). B) Whole mount morphology of regenerating muscles co-injected with adeno-sh LacZ (top) or adeno-sh Meg3 . C) Hematoxylin and eosin (H&E) staining of muscle sections. D) Cross-sectional area (CSA) of laminin-ensheathed regenerating myofibers was measured for days 3, 7, and 14 post-CTX injury. sh Meg3 muscle displayed reduced CSA for all time points surveyed. E) Immunofluorescence quantification indicated sh Meg3 TA sections harbor increased Ki67 signal (left bar graph). Co-staining for Pax7 indicated no change in satellite-cell specific Ki67 signal (left graph) and no change in satellite cell abundance (white, red arrowheads). Marker quantification revealed an increase in proliferating cells lacking Pax7 co-stain (green arrowheads). F ) Immunofluorescence quantification indicated an increase in PDGFR signal, as well as increased abundance of PDGFRα+ cells (red arrowheads).

Article Snippet: For overexpression, human MEG3 cDNA was PCR amplified from the pCI-Meg3 (Addgene Plasmid #44727) using NEB Q5 high-fidelity polymerase, and cloned into pShuttleCMV vector (Agilent AdEasy Adenoviral Vector System).

Techniques: Expressing, Muscles, Injection, Staining, Immunofluorescence, Marker

Journal: bioRxiv

Article Title: The long noncoding RNA Meg3 regulates myoblast plasticity and muscle regeneration through epithelial-mesenchymal transition

doi: 10.1101/2020.06.15.152884

Figure Lengend Snippet: A) Expression profiling by qPCR indicated no change in E-cadherin , while day 7 sh Meg3 muscle was enriched for N-cadherin transcripts (n=3). Immunofluorescence revealed that, while numerous satellite cells were not N-cad+ (red arrowheads), N-cad signal was largely restricted to Pax7+ satellite cells in regenerating muscle (white arrowheads). Cell quantification (% mononuc. cells) revealed that sh Meg3 muscle harbored increased abundance of N-cadherin+ satellite cells, whereas levels of N-cadherin per cell was unchanged (n=3). B) qPCR expression profiling indicated no change in epithelial markers Plakophilin and PatJ , but mesenchymal markers Fibronectin and Snai2 were significantly upregulated in sh Meg3 muscle (n=3). C) Immunofluorescence revealed the presence of satellite cells lacking Snai2 (red arrowheads), Snai2+ satellite cells (white arrowheads), Snai2+ non-satellite cells (green arrowheads), and Snai2+ nuclei in regenerating myofibers (green asterisks). Quantification of Snai2+ cells indicated no change in the occurance of Snai2+ nuclei (bar graph, % Snai2+ nuclei). Generalized analysis (DAPI) indicated significant upregulation of cytoplasmic Snai2 signal per cell, but no change nuclear intensity; Snai2 signal in satellite cells (Pax7+) was increased for both cytoplasmic and nuclear compartments (n=3). D) Immunofluorescence revealed the presence of satellite cells lacking Vimentin (red arrowheads), Vimentin+ satellite cells (white arrowheads), and Vimentin+ non-satellite cells (green arrowheads). Cell quantification (% mononuc. cells) revealed increased abundance of Vimentin+ mononucleated cells that were not Pax7+, and that Pax7+/Vimentin+ cells were reduced in sh Meg3 muscle. Vimentin signal per cell was downregulated in mononucleated cells (bottom right bar graph), which may reflect sh Meg3 -specifici differences in Vimentin+ cell morphology (green channel) (n=3).

Article Snippet: For overexpression, human MEG3 cDNA was PCR amplified from the pCI-Meg3 (Addgene Plasmid #44727) using NEB Q5 high-fidelity polymerase, and cloned into pShuttleCMV vector (Agilent AdEasy Adenoviral Vector System).

Techniques: Expressing, Immunofluorescence

Journal: Cell Reports

Article Title: Cancer-Specific Loss of p53 Leads to a Modulation of Myeloid and T Cell Responses

doi: 10.1016/j.celrep.2019.12.028

Figure Lengend Snippet:

Article Snippet: Retroviral introduction of ovalbumin sequence for membrane bound ovalbumin (mOVA) was cloned out of the pCl-neo-mOVA plasmid (Addgene No 25099) ( ) and into the MSCV-based MIGR1 (Addgene 27490) vector ( ).

Techniques: Control, Functional Assay, Purification, Recombinant, Enzyme-linked Immunosorbent Assay, Plasmid Preparation, Software

Journal: Oncology Research Featuring Preclinical and Clinical Cancer Therapeutics

Article Title: Induction of Apoptosis by Berberine in Hepatocellular Carcinoma HepG2 Cells via Downregulation of NF-κB

doi: 10.3727/096504016x14742891049073

Figure Lengend Snippet: Figure 4. HepG2 cells were transfected with p65, and the protein levels of p65 were determined. (A) Western blotting assay. (B) Immuno fluorescence staining.

Article Snippet: The NF-kB p65 expression vector pCMV4-p65 (plasmid #21966; Addgene) and empty vector (pCMV4-3HA; plasmid #24165; Addgene) were a gift from Dr. Warner Greene.

Techniques: Transfection, Western Blot, Fluorescence, Staining

Journal: Oncology Research Featuring Preclinical and Clinical Cancer Therapeutics

Article Title: Induction of Apoptosis by Berberine in Hepatocellular Carcinoma HepG2 Cells via Downregulation of NF-κB

doi: 10.3727/096504016x14742891049073

Figure Lengend Snippet: Figure 3. Effects of berberine on expression of NF-kB p65 proteins and mRNA levels in HepG2 cells. (A) NF-kB p65 mRNA expres- sion levels. (B) NF-kB p65 was examined by immunofluorescence staining. *p < 0.05 versus control; ***p < 0.001 versus control.

Article Snippet: The NF-kB p65 expression vector pCMV4-p65 (plasmid #21966; Addgene) and empty vector (pCMV4-3HA; plasmid #24165; Addgene) were a gift from Dr. Warner Greene.

Techniques: Expressing, Immunofluorescence, Staining, Control

Journal: Scientific reports

Article Title: Generation of transgenic marmosets expressing genetically encoded calcium indicators.

doi: 10.1038/srep34931

Figure Lengend Snippet: Figure 1. Generation of GCaMP-expressing transgenic marmosets derived by infection of wild-type zygotes with lentiviral vectors. (A) Schematic diagram of the lentiviral vectors used. Only the relevant portions of the plasmid are shown. (B) Verification of transgene expression in IVF embryos 4 days after lentiviral injection. Left, bright field image. Middle, green fluorescence image shows clear expression of GCaMP. Right, merged image. The arrow shows a naïve embryo. Scale bar = 100 μm. (C–G) Photographs of the infant transgenic marmosets. Shown are: (C) TG-Y (CMV-GCaMP5g); (D) TG-E (CMV-mKO-GCaMP6s). The inset shows an epifluorescence image of the left front paw of TG-E (left, arrow) placed against that of a wild-type animal. Note mosaic expression of the inert orange tag mKO in the fur of the digits; (E) TG-S (hSyn-mKO- GCaMP6s); (F) TG-L (hSyn-mKO-GCaMP6s); and (G) TG-J (CMV-GCaMP6s). (H) PCR products of the transgene in animals born alive (TG-Y, E, S, L, D1, D2, J, and D3) and aborted fetuses (M01-03) showing the presence of the GCaMP transgene in different tissues. M: DNA marker; Naïve cell/CMV-mKO-GCaMP6s: genomic DNAs extracted from wild type marmoset fibroblasts infected with CMV-mKO-GCaMP6s lentiviruses for positive control; Naïve: genomic DNAs extracted from wild type marmoset fibroblasts for negative control.

Article Snippet: For the CMV-GCaMP5g and CMV-GCaMP6s construct, the open reading frame of CMV-GCaMP5g (pCMV-GCaMP5g was a gift from Douglas Kim and Loren Logger, plasmid 31788, Addgene, Cambridge, MA, USA)4 or CMV-GCaMP6s (pGP-CMV-GCaMP6s was a gift from Douglas Kim, plasmid 40753, Addgene)5 used to replace the PGK-EGFP sequence in the parental pRRLsin.cPPT.PGK-EGFP.WPRE lentiviral vector plasmid (plasmid 12252, Addgene).

Techniques: Expressing, Transgenic Assay, Derivative Assay, Infection, Plasmid Preparation, Injection, Fluorescence, Marker, Positive Control, Negative Control