Journal: Cell Death & Disease

Article Title: TM4SF1-AS1 inhibits apoptosis by promoting stress granule formation in cancer cells

doi: 10.1038/s41419-023-05953-3

Figure Lengend Snippet: A Workflow for comprehensive identification of transcriptionally active lncRNAs in the gastric mucosa of patients with GC. B Pie chart depicting gene loci harboring H3K4me3 peaks at transcription start sites (TSSs). These loci were categorized as protein-coding genes, lncRNA genes, or other genes. Peaks were categorized as patient-specific, healthy individual-specific, and common. C H3K4me3 peaks of representative genes in each category. D Summarized qRT-PCR results for 15 selected lncRNAs from eight GC cell lines. E qRT-PCR analysis of TCONS_00006264 (TM4SF1-AS1) and TM4SF1 in GC cell lines and normal stomach tissue. The locations of these two genes are shown at the top. ( n = 3). F Expression of TM4SF1-AS1 in primary GCs ( n = 374) and normal stomach tissues ( n = 32) from The Cancer Genome Atlas (TCGA) dataset. * P < 0.05.

Article Snippet: pCMV6 encoding GFP-fused TM4SF1 was purchased from OriGene Technologies (Rockville, MD, USA). pIDTSMART-AMP encoding TM4SF1-AS1 (ENST496491.1) was purchased from Codex DNA Inc. (San Diego, CA, USA).

Techniques: Quantitative RT-PCR, Expressing

Journal: Cell Death & Disease

Article Title: TM4SF1-AS1 inhibits apoptosis by promoting stress granule formation in cancer cells

doi: 10.1038/s41419-023-05953-3

Figure Lengend Snippet: A qRT-PCR analysis of TM4SF1-AS1 in the indicated GC cell lines transfected with siRNAs targeting TM4SF1-AS1 (si-1 and 2) or a control siRNA (si-Ctrl). ( n = 3). B Results of cell viability assays with GC cell lines transfected with the indicated siRNAs. ( n = 8). C qRT-PCR analysis of TM4SF1-AS1 in HSC-45 cells with inducible shRNAs targeting TM4SF1-AS1 (sh-1 and 2) or a control shRNA (sh-Ctrl). Cells were incubated for 8 days with or without doxycycline (Dox). ( n = 3). D Colony formation assays using HSC-45 cells with inducible shRNAs. Cells were incubated for 8 days with or without Dox. Summarized results are shown on the right; error bars represent SDs. ( n = 3). E Tumor growth in mice injected with HSC-45 cells inducibly expressing the indicated shRNAs. Mice were treated with or without Dox. Growth curves (left), resected tumors (middle), and tumor weights (right) are shown. F qRT-PCR analysis of TM4SF1-AS1 in the resected tumors in E . ( n = 4). G Tumor growth in mice injected with SNU638 cells stably expressing GFP or TM4SF1-AS1. Growth curves are shown on the left, and resected tumors are shown on the right. ( n = 4). H qRT-PCR analysis of TM4SF1-AS1 in the resected tumors in G . ( n = 4). * P < 0.05, ** P < 0.01, *** P < 0.001, NS not significant.

Article Snippet: pCMV6 encoding GFP-fused TM4SF1 was purchased from OriGene Technologies (Rockville, MD, USA). pIDTSMART-AMP encoding TM4SF1-AS1 (ENST496491.1) was purchased from Codex DNA Inc. (San Diego, CA, USA).

Techniques: Quantitative RT-PCR, Transfection, Control, shRNA, Incubation, Injection, Expressing, Stable Transfection

Journal: Cell Death & Disease

Article Title: TM4SF1-AS1 inhibits apoptosis by promoting stress granule formation in cancer cells

doi: 10.1038/s41419-023-05953-3

Figure Lengend Snippet: A qRT-PCR analysis of TM4SF1-AS1 in the indicated cellular fractions from HSC-45 cells. U6 snRNA and ACTB served as endogenous controls. ( n = 3). B Association between TM4SF1-AS1 and Pur-α in the indicated subcellular fractions from HSC-45 cells. Pur-α was detected by western blotting in proteins pulled-down with BrU-labeled TM4SF1-AS1, antisense of TM4SF1-AS1 or beads. C Association between Pur-α and YB-1. Immunoprecipitated YB-1 or Pur-α from HSC-45 cell extracts were probed for co-precipitating proteins. D YB-1 was immunoprecipitated from HSC-45 cells with or without RNase A treatment, after which Pur-α was detected by western blotting. E YB-1 or Pur-α in the indicated subcellular fractions from HSC-45 cells were immunoprecipitated with or without RNase A treatment and then probed for co-precipitating proteins. F Results of RIP assays. Pur-α (upper) or YB-1 (lower) was immunoprecipitated from HSC-45 cells, after which co-precipitated TM4SF1-AS1 was detected with qRT-PCR. IgG served as a negative control. ( n = 3). G qRT-PCR analysis of Pur-α (upper) and YB-1 (lower) in HSC-45 cells transfected with the indicated siRNAs. ( n = 3). H Results of cell viability assays with HSC-45 cells transfected with the indicated siRNAs. ( n = 3). * P < 0.05, ** P < 0.01, *** P < 0.001.

Article Snippet: pCMV6 encoding GFP-fused TM4SF1 was purchased from OriGene Technologies (Rockville, MD, USA). pIDTSMART-AMP encoding TM4SF1-AS1 (ENST496491.1) was purchased from Codex DNA Inc. (San Diego, CA, USA).

Techniques: Quantitative RT-PCR, Western Blot, Labeling, Immunoprecipitation, Negative Control, Transfection

Journal: Cell Death & Disease

Article Title: TM4SF1-AS1 inhibits apoptosis by promoting stress granule formation in cancer cells

doi: 10.1038/s41419-023-05953-3

Figure Lengend Snippet: A Heatmap showing expression of genes suppressed by TM4SF1-AS1 knockdown in HSC-45 cells. B GO analysis using the genes in A . C qRT-PCR analysis of representative IRDS genes in HSC-45 cells transfected with the indicated siRNAs. ( n = 3). D GSEA analysis using the microarray data. Gene sets with an FDR < 0.01 are shown on the left. Enrichment plots of indicated gene sets are shown on the right. E Western blot analysis of total and phosphorylated STAT1 in HSC-45 cells transfected with the indicated siRNAs. (F, G) qRT-PCR analysis of interferon genes in HSC-45 cells transfected with the indicated siRNAs ( F ) or in SNU638 cells stably transfected with the indicated genes ( G ). ( n = 3). H Western blot analysis of total and phosphorylated STAT1 in SNU638, SNU638-GFP, and SNU638-TM4SF1-AS1 cells. I qRT-PCR analysis of IRDS genes in SNU638-GFP and SNU638-TM4SF1-AS1 cells. ( n = 3). J Western blot analysis of STAT1 and Pur-α in SNU638-TM4SF1-AS1 cells transfected with the indicated siRNAs targeting Pur-α. K qRT-PCR analysis of IRDS genes in SNU638-TM4SF1-AS1 cells transfected with the indicated siRNAs. ( n = 3). * P < 0.05, ** P < 0.01, *** P < 0.001.

Article Snippet: pCMV6 encoding GFP-fused TM4SF1 was purchased from OriGene Technologies (Rockville, MD, USA). pIDTSMART-AMP encoding TM4SF1-AS1 (ENST496491.1) was purchased from Codex DNA Inc. (San Diego, CA, USA).

Techniques: Expressing, Knockdown, Quantitative RT-PCR, Transfection, Microarray, Western Blot, Stable Transfection

Journal: Cell Death & Disease

Article Title: TM4SF1-AS1 inhibits apoptosis by promoting stress granule formation in cancer cells

doi: 10.1038/s41419-023-05953-3

Figure Lengend Snippet: A Workflow of ChIRP coupled with mass spectrometry (ChIRP-MS) or RNA-seq (ChIRP-RNA-seq) to identify molecules associated with TM4SF1-AS1. B qRT-PCR confirming enrichment of TM4SF1-AS1 in ChIRP products derived from SNU638-TM4SF1-AS1 cells. ( n = 3). C Protein-protein interaction (PPI) network among the proteins identified by ChIRP-MS. Functional categories of the proteins are indicated by node colors. D RIP-qPCR assays validating the ChIRP-MS results. The indicated proteins in HSC-45 cells were immunoprecipitated, and co-precipitated TM4SF1-AS1 was detected by qRT-PCR. IgG served as a negative control. ( n = 3). E Immunofluorescence images showing staining of the SG marker G3PB2 in SNU638, SNU638-GFP, and SNU638-TM4SF1-AS1 cells treated with or without sodium arsenite (SA). Summarized results are shown on the right ( n = 5). Scale bars = 10 μm. F Immunofluorescence indicating G3BP2 (green), TIA1 (white), and inducible MS2-tagged TM4SF1-AS1 (red) in SNU638 cells. Cells were transfected with a MS2 coat protein (MCP)-RFP plasmid and incubated for 8 days with or without Dox. Magnified views of the respective markers are shown on the right. Scale bars = 10 μm. * P < 0.05, ** P < 0.01, *** P < 0.001.

Article Snippet: pCMV6 encoding GFP-fused TM4SF1 was purchased from OriGene Technologies (Rockville, MD, USA). pIDTSMART-AMP encoding TM4SF1-AS1 (ENST496491.1) was purchased from Codex DNA Inc. (San Diego, CA, USA).

Techniques: Mass Spectrometry, RNA Sequencing Assay, Quantitative RT-PCR, Derivative Assay, Functional Assay, Immunoprecipitation, Negative Control, Immunofluorescence, Staining, Marker, Transfection, Plasmid Preparation, Incubation

Journal: Cell Death & Disease

Article Title: TM4SF1-AS1 inhibits apoptosis by promoting stress granule formation in cancer cells

doi: 10.1038/s41419-023-05953-3

Figure Lengend Snippet: A Immunofluorescence indicating RACK1 (green), G3BP1 (white), and inducible MS2-tagged TM4SF1-AS1 (red) in SNU638 cells. The cells were transfected with a MS2 coat protein (MCP)-RFP plasmid and incubated for 8 days with or without Dox. Magnified views of the respective markers are shown on the right. Scale bars = 10 μm. B Immunofluorescence images of G3PB2 in HSC-45 cells incubated for 8 days with or without Dox and expressing the indicated inducible shRNAs. Representative images are shown on the left. Summarized results are on the right. ( n = 5). C , D Apoptosis ( C ) and cell cycle ( D ) assays in HSC-45 cells incubated with or without Dox for 8 days and expressing the indicated inducible shRNAs. Representative results are shown on the left. Summarized results are shown on the right. ( n = 3). E , F Western blot analysis of PARP, caspase-3 ( E ) and p38 ( F ) in HSC-45 cells incubated with or without Dox for 8 days and expressing the indicated inducible shRNAs. Cleaved PARP and cleaved caspase-3 are indicated by arrows ( E ). Phosphorylated p38 is indicated by an arrow ( F ). ** P < 0.01, *** P < 0.001.

Article Snippet: pCMV6 encoding GFP-fused TM4SF1 was purchased from OriGene Technologies (Rockville, MD, USA). pIDTSMART-AMP encoding TM4SF1-AS1 (ENST496491.1) was purchased from Codex DNA Inc. (San Diego, CA, USA).

Techniques: Immunofluorescence, Transfection, Plasmid Preparation, Incubation, Expressing, Western Blot

Journal: Cell Death & Disease

Article Title: TM4SF1-AS1 inhibits apoptosis by promoting stress granule formation in cancer cells

doi: 10.1038/s41419-023-05953-3

Figure Lengend Snippet: A , B Immunofluorescence images showing Pur-α (A) or YB-1 (B), TIA1 and inducible MS2-tagged TM4SF1-AS1 in SNU638 cells incubated for 8 days with or without Dox. Scale bars = 10 μm. C Immunofluorescent staining of G3PB2 in SNU638-TM4SF1-AS1 cells transfected with the indicated siRNAs. Representative results are shown on the left. Summarized results are shown on the right. ( n = 5). Scale bars = 10 μm. D Localization of GFP-tagged Pur-α or YB-1, G3BP1 and TIA1 immunofluorescence in SNU638 cells. Cells were transfected with vectors encoding GFP (upper), GFP-tagged Pur-α (middle) or GFP-tagged YB1 (bottom). Magnified views of the respective markers are shown on the right. Scale bars = 10 μm. E Cell cycle analysis of HSC-45 cells expressing the indicated siRNAs. ( n = 3). F , G Western blot analysis of PARP and caspase-3 ( F ) and total and phosphorylated p38 ( G ) in HSC-45 cells transfected with the indicated siRNAs. Cleaved PARP, cleaved caspase-3 and phosphorylated p38 are indicated by arrows. ** P < 0.01, *** P < 0.001.

Article Snippet: pCMV6 encoding GFP-fused TM4SF1 was purchased from OriGene Technologies (Rockville, MD, USA). pIDTSMART-AMP encoding TM4SF1-AS1 (ENST496491.1) was purchased from Codex DNA Inc. (San Diego, CA, USA).

Techniques: Immunofluorescence, Incubation, Staining, Transfection, Cell Cycle Assay, Expressing, Western Blot

Journal: Cell Death & Disease

Article Title: TM4SF1-AS1 inhibits apoptosis by promoting stress granule formation in cancer cells

doi: 10.1038/s41419-023-05953-3

Figure Lengend Snippet: In the early steps of gastric tumorigenesis, TM4SF1-AS1 is transcriptionally activated. TM4SF1-AS1 sequesters RACK1 within SGs, which leads to suppression of stress-responsive MAPK signaling and inhibition of apoptosis (created with BioRender.com).

Article Snippet: pCMV6 encoding GFP-fused TM4SF1 was purchased from OriGene Technologies (Rockville, MD, USA). pIDTSMART-AMP encoding TM4SF1-AS1 (ENST496491.1) was purchased from Codex DNA Inc. (San Diego, CA, USA).

Techniques: Inhibition

Journal: Journal of Nanobiotechnology

Article Title: Inverse-designed plasmonic biosensors with LSPR-SPP-wood anomaly coupling enhanced for biomolecular analysis

doi: 10.1186/s12951-025-03930-w

Figure Lengend Snippet: High-throughput affinity sensing platform for ADC drug development. ( a ) The association process of incubating PD-1 on the chip to detect Sintilimab. ( b ) The long-time dissociation process of PD-1 with Sintilimab. ( c ) Dynamic real-time and fitting curves of the association and dissociation phases of the interaction between PD-1 and Sintilimab. ( d ) Schematic diagram of the high-throughput antibody affinity detection protocol, with each group, repeated three times in the three samples tested, and the concentration of A-H in each column decreasing incrementally. ( e ) Schematic diagram of the main events in the antibody drug fishing and affinity detection process. ( f-h ) Dynamic real-time and fitting curves of the association and dissociation phases for Polatuzumab with CD79B, Adalimumab with TNF-α, and Sacituzumab govitecan with TROP2, detected using the unoptimized sensor. ( i-k ) Dynamic real-time and fitting curves of the association and dissociation phases for Polatuzumab with CD79B, Adalimumab with TNF-α, and Sacituzumab govitecan with TROP2, detected using the optimized IDMM-SPR sensor

Article Snippet: Bovine serum albumin (BSA), Phosphate-buffered saline (PBST), 11-mercaptoundecanoic acid (MUA), 1-ethyl3-(dimethylaminopropyl) carbodiimide (EDC), N-hydroxysuccinimide (NHS), Dimethyl Sulfoxide (DMSO), Fish gelatin,, ethanolamine, and phosphate-buffered saline (PBS) buffer, Polyethylene glycol 2000 (PEG) were purchased from Sigma-Aldrich; Protein A, IgG, CRP, and CRP ab, hTGFBR1 were purchased from monoclonal anti-CRP capture and detection antibodies were purchased from Beijing Sino Biological, Inc. (Beijing, China); Sintilimab, Adalimumab, Polatuzumab, Sacituzumab, PD-1, TNF-α, CD79B, TROP2, Quercetin were purchased from MedChemExpress.

Techniques: High Throughput Screening Assay, Concentration Assay

Journal: PLoS ONE

Article Title: Hepatitis C Virus Core-Derived Peptides Inhibit Genotype 1b Viral Genome Replication via Interaction with DDX3X

doi: 10.1371/journal.pone.0012826

Figure Lengend Snippet: Plasmids used in this study.

Article Snippet: The DDX3X and mCherry fusions to DDX3X were detected by a rabbit anti-DDX3X antibody (ProSci Incorporated; 1∶1,000).

Techniques: Expressing, Plasmid Preparation, Derivative Assay, Luciferase

Journal: PLoS ONE

Article Title: Hepatitis C Virus Core-Derived Peptides Inhibit Genotype 1b Viral Genome Replication via Interaction with DDX3X

doi: 10.1371/journal.pone.0012826

Figure Lengend Snippet: ( A ). Schematic of the different GST fusions to the N-terminal fragments of the HCV core protein. Also shown is a schematic of DDX3X, with the DEADc and HELICc domains of the DEAD-box helicase labeled. ( B ). Schematic diagram of the regions of HCV core protein interacting with the DDX3X helicase domain (DDX3Xh) in pull-down assays. ( C ). Analysis of the interaction between DDX3Xh, GST or various GST fusions to HCV core proteins. Glutathione beads were used to pull down bound proteins prior to SDS gel electrophoresis. Lanes 1–4, GST fusions to the denoted HCV peptides incubated with DDX3Xh. Lane 5, DDX3Xh marker. Molecular weight markers are shown to the left, in kDa.

Article Snippet: The DDX3X and mCherry fusions to DDX3X were detected by a rabbit anti-DDX3X antibody (ProSci Incorporated; 1∶1,000).

Techniques: Labeling, SDS-Gel, Electrophoresis, Incubation, Marker, Molecular Weight

Journal: PLoS ONE

Article Title: Hepatitis C Virus Core-Derived Peptides Inhibit Genotype 1b Viral Genome Replication via Interaction with DDX3X

doi: 10.1371/journal.pone.0012826

Figure Lengend Snippet: ( A ). In vitro binding analysis of endogenous DDX3X and the various truncated forms of HCV core proteins. Western blot of GST or GST fusions to the denoted HCV core peptides incubated in HuH-7 cell lysate, pelleted using glutathione beads, and resolved by SDS gel electrophoresis. Lane 1, HuH-7 cell lysate input. Lanes 2–4, GST pull-down experiments. ( B ). Co-immunoprecipitation of GFP fusions to HCV core peptides and DDX3X from co-transfected HuH-7 cells. Immunoprecipitates were analysed by sequential immunoblotting with anti-DDX3X and anti-GFP antibodies. Lane 1, DDX3X marker from HuH-7 cell lysate. Lanes 2–4, co-immunoprecipitations of GFP fusions to the denoted HCV peptides using anti-GFP antibodies.

Article Snippet: The DDX3X and mCherry fusions to DDX3X were detected by a rabbit anti-DDX3X antibody (ProSci Incorporated; 1∶1,000).

Techniques: In Vitro, Binding Assay, Western Blot, Incubation, SDS-Gel, Electrophoresis, Immunoprecipitation, Transfection, Marker

Journal: PLoS ONE

Article Title: Hepatitis C Virus Core-Derived Peptides Inhibit Genotype 1b Viral Genome Replication via Interaction with DDX3X

doi: 10.1371/journal.pone.0012826

Figure Lengend Snippet: ( A ). Schematic of the pDiLuc plasmid, and the effects of expression of GFP fusions to HCV core peptides on cap- and HCV IRES-dependent luciferase expression in 5B cells. RLuc, Renilla luciferase; FLuc, Firefly luciferase. ( B ). Northern blot analysis of the dicistronic luciferase mRNA from cells transfected with plasmids encoding GFP or GFP fusions to HCV core peptides (HCVc16-35 and HCVc16-36) and dicistronic luciferase vectors. ( C ). Western blot analysis of the expression of GFP fusions to HCV core peptides of the samples used in panels A and B. ( D ). Partial rescue of activities of cap- and HCV IRES-dependent luciferases repressed by the HCVc16-36. Co-expression of mCherry in controls is compared to co-expression of DDX3X-mCherry.

Article Snippet: The DDX3X and mCherry fusions to DDX3X were detected by a rabbit anti-DDX3X antibody (ProSci Incorporated; 1∶1,000).

Techniques: Plasmid Preparation, Expressing, Luciferase, Northern Blot, Transfection, Western Blot

Journal: PLoS ONE

Article Title: Hepatitis C Virus Core-Derived Peptides Inhibit Genotype 1b Viral Genome Replication via Interaction with DDX3X

doi: 10.1371/journal.pone.0012826

Figure Lengend Snippet: ( A ). Northern blot of HCV replicon RNA levels in cells expressing GFP fusions to HCV core peptides (HCVc16-35, HCVc16-36) in the absence (mCherry) or presence of exogenously expressed DDX3X fused to mCherry (DDX3X-mCherry). ( B ). Quantification of the HCV replicon RNA levels in panel A. Experiments were done in duplicate and columns represent the percentage of HCV replicon RNA normalized to β-actin mRNA levels. ( C ). Western blot analysis of the expression of DDX3X and GFP fusions to HCV core peptides in the samples used in panel A.

Article Snippet: The DDX3X and mCherry fusions to DDX3X were detected by a rabbit anti-DDX3X antibody (ProSci Incorporated; 1∶1,000).

Techniques: Northern Blot, Expressing, Western Blot