Additional file 2: of Antisense suppression of the nonsense mediated decay factor Upf3b as a potential treatment for diseases caused by nonsense mutations

This file contains four supplementary tables (Tables S1–S4). (XLSX 95 kb

Additional file 1: of Antisense suppression of the nonsense mediated decay factor Upf3b as a potential treatment for diseases caused by nonsense mutations

This file contains seven supplementary figures (Figures S1–S7). (PDF 679 kb

Protein Adsorption Alters Hydrophobic Surfaces Used for Suspension Culture of Pluripotent Stem Cells

This Letter examines the physical and chemical changes that occur at the interface of methyl-terminated alkanethiol self-assembled monolayers (SAMs) after exposure to cell culture media used to derive embryoid bodies (EBs) from pluripotent stem cells. Attenuated total reflectance Fourier transform infrared (ATR-FTIR) spectroscopy analysis of the SAMs indicates that protein components within the EB cell culture medium preferentially adsorb at the hydrophobic interface. In addition, we examined the adsorption process using surface plasmon resonance and atomic force microscopy. These studies identify the formation of a porous, mat-like adsorbed protein film with an approximate thickness of 2.5 nm. Captive bubble contact angle analysis reveals a shift toward superhydrophilic wetting behavior at the cell culture interface due to adsorption of these proteins. These results show how EBs are able to remain in suspension when derived on hydrophobic materials, which carries implications for the rational design of suspension culture interfaces for lineage specific stem-cell differentiation

Protein Adsorption Alters Hydrophobic Surfaces Used for Suspension Culture of Pluripotent Stem Cells

This Letter examines the physical and chemical changes that occur at the interface of methyl-terminated alkanethiol self-assembled monolayers (SAMs) after exposure to cell culture media used to derive embryoid bodies (EBs) from pluripotent stem cells. Attenuated total reflectance Fourier transform infrared (ATR-FTIR) spectroscopy analysis of the SAMs indicates that protein components within the EB cell culture medium preferentially adsorb at the hydrophobic interface. In addition, we examined the adsorption process using surface plasmon resonance and atomic force microscopy. These studies identify the formation of a porous, mat-like adsorbed protein film with an approximate thickness of 2.5 nm. Captive bubble contact angle analysis reveals a shift toward superhydrophilic wetting behavior at the cell culture interface due to adsorption of these proteins. These results show how EBs are able to remain in suspension when derived on hydrophobic materials, which carries implications for the rational design of suspension culture interfaces for lineage specific stem-cell differentiation

Partial Hepatectomy Induced Long Noncoding RNA Inhibits Hepatocyte Proliferation during Liver Regeneration

<div><p>Liver regeneration after partial hepatectomy (PHx) is a complex and well-orchestrated biological process in which synchronized cell proliferation is induced in response to the loss of liver mass. To define long noncoding RNAs (lncRNAs) that participate in the regulation of liver regeneration, we performed microarray analysis and identified more than 400 lncRNAs exhibiting significantly altered expression. Of these, one lncRNA, <i>LncPHx2</i> (Long noncoding RNA induced by PHx 2), was highly upregulated during liver regeneration. Depletion of <i>LncPHx2</i> during liver regeneration using antisense oligonucleotides led to a transient increase in hepatocyte proliferation and more rapid liver regeneration. Gene expression analysis showed that <i>LncPHx2</i> depletion resulted in upregulation of mRNAs encoding proteins known to promote cell proliferation, including MCM components, DNA polymerases, histone proteins, and transcription factors. <i>LncPHx2</i> interacts with the mRNAs of MCM components, making it a candidate to regulate the expression of MCMs and other genes post-transcriptionally. Collectively, our data demonstrate that LncPHx2 is a key lncRNA that participates in a negative feedback loop modulating hepatocyte proliferation through RNA-RNA interactions.</p></div

Additional file 2: Table S1. of The human lncRNA LINC-PINT inhibits tumor cell invasion through a highly conserved sequence element

shows the genes affected upon LINC-PINT overexpression. (XLSX 81 kb

Suppressing transthyretin production in mice, monkeys and humans using 2nd-Generation antisense oligonucleotides

<p>Transthyretin amyloidosis (ATTR amyloidosis) is a rare disease that results from the deposition of misfolded transthyretin (TTR) protein from the plasma into tissues as amyloid fibrils, leading to polyneuropathy and cardiomyopathy. IONIS-TTR_Rx (ISIS 420915) is a 2nd-Generation 2′-<i>O</i>-(2-methoxyethyl) modified “2′-MOE” antisense oligonucleotide (ASO) that targets the TTR RNA transcript and reduces the levels of the TTR transcript through an RNaseH1 mechanism of action, leading to reductions in both mutant and wild-type TTR protein. The activity of IONIS-TTR_Rx to decrease TTR protein levels was studied in transgenic mice bearing the Ile84Ser human TTR mutant, in cynomolgus monkeys and in healthy human volunteers. Robust (>80%) reductions of plasma TTR protein were obtained in all three species treated with IONIS-TTR_Rx, which in mice and monkeys was associated with substantial reductions in hepatic TTR RNA levels. These effects were dose-dependent and lasted for weeks post-dosing. In a Phase 1 healthy volunteer study, treatment with IONIS-TTR_Rx for four weeks was well tolerated without any remarkable safety issues. TTR protein reductions up to 96% in plasma were observed. These nonclinical and clinical results support the ongoing Phase 3 development of IONIS-TTR_Rx in patients with ATTR amyloidosis.</p

Additional file 3: Table S2. of The human lncRNA LINC-PINT inhibits tumor cell invasion through a highly conserved sequence element

shows the biofunctions associated to genes affected upon LINC-PINT overexpression. (XLSX 109 kb

Gene expression profiling of mouse liver regeneration after PHx.

<p>(A) Differentially expressed mRNAs and putative lncRNAs were clustered based on their expression pattern during liver regeneration after PHx. Normalized average probe intensity was plotted over the time course of liver regeneration. Cluster 1 contains 401 mRNA and 30 lncRNA transcripts. Cluster 2 contains 471 mRNA and 91 lncRNA transcripts. Cluster 3 contains 610 mRNA and 110 lncRNA transcripts. Cluster 4 contains 385 mRNA and 46 lncRNA transcripts. Cluster 5 contains 146 mRNA and 17 lncRNA transcripts. Cluster 6 contains 410 mRNA and 73 lncRNA transcripts. Cluster 7 contains 254 mRNA and 37 lncRNA transcripts. Cluster 8 contains 330 mRNA and 17 lncRNA transcripts. Cluster 9 contains 646 mRNA and 44 lncRNA transcripts. Sham: liver RNAs of mice subjected to sham surgery. PHx: liver RNAs of mice subjected to PHx surgery. n = 5 for each time point. (B) Pathway analysis of the eight gene clusters using David KEGG pathway tools. Cluster 5 has no enriched pathway (not shown). * Pathway with FDR<0.05. (C) qPCR analysis of the levels of lncRNA transcripts. The mRNA level of the housekeeping gene <i>Gapdh</i> and total RNA amount determined by Ribogreen staining (Life Technology) were used as controls. The RNA levels in livers of mice subjected to sham surgery were set as 1. n = 5. Statistical analysis was performed using the Student's t test. * p<0.05; **p < 0.01; ***p < 0.001. (D) LncRNA expression in nine mouse tissues collected from Encode RNA-seq database. FPKM of lncRNA expression in each tissue was plotted against the mean value of each row. Red indicates higher expression. Blue indicates lower expression.</p

Additional file 1: Figure S1. of The human lncRNA LINC-PINT inhibits tumor cell invasion through a highly conserved sequence element

LINC-PINT is downregulated in colon and lung adenocarcinoma. Figure S2. LINC-PINT is localized in cell nucleus and LINC-PINT overexpression in HCT116 decreases tumor formation in vivo. Figure S3. A highly conserved short region of LINC-PINT is required for its function. Figure S4. LINC-PINT inhibits a pro-invasion gene signature. Figure S5. LINC-PINT inhibits the expression of EGR1 transcriptional target genes. Figure S6. PRC2 mediates the LINC-PINT-dependent silencing of pro-invasion genes. List of oligonucleotides (PDF 4621 kb