cell line pairs  (ATCC)

Journal: Nature Communications

Article Title: The dysadherin/MMP9 axis modifies the extracellular matrix to accelerate colorectal cancer progression

doi: 10.1038/s41467-024-54920-9

Figure Lengend Snippet: a GSEA was performed using the mRNA-sequencing profiles of dysadherin KO and WT SW480 cells, which was performed in previous study . b Three candidate genes related to three gene signatures were identified. Heatmap indicated FC and p-value (unpaired two-tailed Student’s t tests) from mRNA-sequencing data. c Downstream analysis indicating the potential link between dysadherin/FAK pathway and MMP9, leading to ECM remodeling, malignancy, and metastasis. d Kaplan-Meier analysis of CRC patients by dividing into three groups according to dysadherin and MMP9 expression. Statistical significance was determined by log-rank tests. e Immunoblotting for dysadherin, E-cadherin, and MMP9 expression and gel zymography in human CRC and normal colon cell lines. f Immunoblotting for dysadherin and MMP9 and gel zymography in dysadherin KO or OE CRC cells. g Venn diagram showing overlapping transcription factors that are positively correlated with MMP9 expression. h Immunoblotting for p-FAK, total FAK, p-c-JUN, total c-JUN, and MMP9 in EV and dysadherin OE HCT116 cells treated with or without 1 µM PND-1186 or 20 µM T-5224. i Promoter activity of MMP9 was tested via luciferase reporter assay. MMP9 promoter region-containing vector was transfected into EV and dysadherin OE HCT116 cells, and cells were treated with or without PND-1186 or T-5224. Total transcription was normalized to β-galactosidase transcription and is presented as fold change with respect to nontreated HCT116 cells. j Binding affinity of c-JUN on MMP9 promoter with or without PND-1186 or T-5224 in SW480 cells was tested via ChIP assay. i, j n = 3 biological replicates, representative of three independent experiments with similar results. Immunoblot assays were independently repeated three times with similar results. The data are presented as the means ± SEMs. *, **, and *** indicate p < 0.05, p < 0.01 and p < 0.001, respectively. Statistical significance was determined by one-way ANOVA with Dunnett’s multiple comparison test for comparisons among three groups. Source data are provided as a Source Data file. FC fold change, P paired normal, T tumor, WT wild-type, KO knockout, EV empty vector, OE overexpression, Ct threshold of cycle, dCt delta Ct, difference of Ct value between target and housekeeping gene.

Article Snippet: To establish the MMP9 OE cell line, WT and dysadherin KO SW480 cells were transfected with an MMP9 expression vector (pCMV-MMP9, Sino Biological lnc.

Techniques: Sequencing, Two Tailed Test, Expressing, Western Blot, Zymography, Activity Assay, Luciferase, Reporter Assay, Plasmid Preparation, Transfection, Binding Assay, Comparison, Knock-Out, Over Expression

Journal: Nature Communications

Article Title: The dysadherin/MMP9 axis modifies the extracellular matrix to accelerate colorectal cancer progression

doi: 10.1038/s41467-024-54920-9

Figure Lengend Snippet: a Representative in vivo bioluminescence images of mice injected with luciferase-labeled wild-type or dysadherin KO SW480 cells with/without MMP9 OE, accompanied by a corresponding graph showing the quantitative analysis of the region of interest. Middle: Representative hematoxylin and eosin-stained livers with metastasis ( n = 5/group). b In situ zymography analysis and IF analysis of dysadherin, α-SMA, and collagen I expression in mouse liver tissue from metastatic tumors. c Heatmap comparing the relative expression of ECM deposition factors in metastatic tumors in the mouse liver ( n = 5/group). d Heatmap comparing the relative expression of macrophage polarization and T-cell related markers in metastatic tumors in the mouse liver ( n = 5/group). e Levels of IL-4 and IFN-γ in metastatic tumors, from ELISA data ( n = 3/group). f Quantitative analysis of CD8 IF data from mouse livers with metastatic tumors ( n = 5/group). g Heatmap comparing the relative expression of angiogenesis-related factors in metastatic tumors in the mouse liver ( n = 5/group). h Quantitative analysis of CD31 IF data from mouse livers with metastatic tumors ( n = 5/group). i Schematic summary of the study findings indicating the potential role of dysadherin in cancer cells in promoting ECM remodeling and CAF activation, which contributes to the formation of a malignant TME. BioRender software was used to create the figure under an academic license. The data are presented as means ± SEMs. *, **, and *** indicate p < 0.05, p < 0.01 and p < 0.001, respectively. Statistical significance was determined by one-way ANOVA with Dunnett’s multiple comparison test for comparisons among four groups. Source data are provided as a Source Data file.

Article Snippet: To establish the MMP9 OE cell line, WT and dysadherin KO SW480 cells were transfected with an MMP9 expression vector (pCMV-MMP9, Sino Biological lnc.

Techniques: In Vivo, Injection, Luciferase, Labeling, Staining, In Situ, Zymography, Expressing, Enzyme-linked Immunosorbent Assay, Activation Assay, Software, Comparison

Journal: GigaScience

Article Title: VC@Scale: Scalable and high-performance variant calling on cluster environments

doi: 10.1093/gigascience/giab057

Figure Lengend Snippet: VC@Scale, SparkGA2, and ADAM comparisons of scalability for pre-processing stages using different number of nodes for ERR194147 (2×) dataset.

Article Snippet: In addition, we used Illumina HiSeq 2000 paired-end NA12878 cell line data sequencing sample ERR194147 [ ] with sequencing coverage of 30×.

Techniques:

Journal: GigaScience

Article Title: VC@Scale: Scalable and high-performance variant calling on cluster environments

doi: 10.1093/gigascience/giab057

Figure Lengend Snippet: Single-node CPU-only and GPU accelerated DeepVariant for ERR194147 (30×) dataset.

Article Snippet: In addition, we used Illumina HiSeq 2000 paired-end NA12878 cell line data sequencing sample ERR194147 [ ] with sequencing coverage of 30×.

Techniques:

Journal: GigaScience

Article Title: VC@Scale: Scalable and high-performance variant calling on cluster environments

doi: 10.1093/gigascience/giab057

Figure Lengend Snippet: GPUs accelerated VC@Scale-DeepVariant scalability for ERR194147 (30×) dataset.

Article Snippet: In addition, we used Illumina HiSeq 2000 paired-end NA12878 cell line data sequencing sample ERR194147 [ ] with sequencing coverage of 30×.

Techniques:

Journal: Cancer letters

Article Title: Human papillomavirus insertions identify the PIM family of serine/threonine kinases as targetable driver genes in head and neck squamous cell carcinoma

doi: 10.1016/j.canlet.2020.01.012

Figure Lengend Snippet: (A) HPV integrant-mediated genomic amplification of the PIM1 locus in UPCI:SCC090 HNSCC cells. (Top) Histograms show (y-axis) depth of WGS coverage by (blue) well-aligned sequence reads, and (middle) counts of (red) HPV insertional and (gray) host-host breakpoint reads in UPCI:SCC090 cells, mapped to the (bottom) reference human genome (hg19) at (x-axis) the PIM1 locus on Chr. 6 (bottom, gene schematics, chromosomal coordinates in Mb). Reproduced from Akagi et al. with permission [4]. See also Supp. Fig. S1. (B) RNA-seq expression levels (y-axis; FPKM) of PIM1, PIM2 and PIM3 transcripts expressed in HNSCC cell lines (i.e. UD-SCC-2, UM-SCC-47, UPCI:SCC090, CAL 27, D562). (C) Western blot analysis of PIM1 (L, long and S, short isoforms), PIM2, and PIM3 expressed in panel of HNSCC cell lines, with beta-tubulin as loading control. Arrows, expected protein mass.

Article Snippet: Human HNSCC cancer cell lines and primary HNSCC tumor /normal pairs Human HNSCC cell lines FaDu (HPV-negative), SCC-4 (HPV-negative), SCC-9 (HPV-negative), SCC-15 (HPV-negative), CAL 27 (HPV-negative), Detroit 562 (hereafter called D562, HPV-negative), and SCC-25 (HPV-negative) were purchased from American Type Culture Collection (ATCC) [ 12 – 15 ]; UM-SCC-47 (HPV-positive) and UM-SCC-104 (HPV-positive) [ 15 ], kindly provided by Dr. Thomas Carey, University of Michigan; UPCI:SCC090 (HPV-positive) [ 16 ], Dr. Susanne M. Gollin, University of Pittsburgh; UD-SCC-2 (HPV-positive) [ 17 ], Dr. Henning Bier, University of Dusseldorf; and HMS001 (HPV-positive) [ 4 ], Dr. James Rocco, Ohio State University.

Techniques: Amplification, Sequencing, RNA Sequencing, Expressing, Western Blot, Control

Journal: Cancer letters

Article Title: Human papillomavirus insertions identify the PIM family of serine/threonine kinases as targetable driver genes in head and neck squamous cell carcinoma

doi: 10.1016/j.canlet.2020.01.012

Figure Lengend Snippet: (A) Western blot analysis of PIM1 expression and (B) cell proliferation curves (y-axis, Log10 average cell count) of parental UPCI:SCC090 cell line, 2 negative controls (empty vector mock-edited by CRISPR, clones C1, C2), and 5 PIM1 knockout clones (gene edited by CRISPR, clones C9, C2, C5, C4, C11) cultured over time (x-axis, days). Key: colors, symbols: cell clones. Slopes of linear regression lines indicative of growth rates are: parental, 0.157; empty C1,0.156; empty C2, 0.157; PIM1 C9, 0.135; PIM1 C2, 0.148; PIM1 C5, 0.104; PIM1 C4, 0.121; and PIM1 C11, 0.066. Error bars, range of cell counts in duplicate wells. (C) Western blot analysis of downstream proteins and phosphorylation targets of PIM1, in a selected PIM1 knockout clone derived from UPCI:SCC090 cells by CRISPR gene editing, compared with parental UPCI:SCC090 control cells. (D) Schematic of possible mechanism of resistance in response to PIM inhibition in HNSCC cells such as CAL 27 cells, through feedback loops involving increased expression of PIM protein through STAT activation. Downstream targets of PIM kinases are displayed showing activating (green) and inactivating (orange) phosphorylation, and biological responses associated with these signaling interactions. GF, growth factor ligand, e.g. EGF, epidermal growth factor; RTK, receptor tyrosine kinase, e.g. EGFR, epidermal growth factor receptor; STAT, signal transducer and activator of transcription. See also Supp. Figs. S6 and S11.

Article Snippet: Human HNSCC cancer cell lines and primary HNSCC tumor /normal pairs Human HNSCC cell lines FaDu (HPV-negative), SCC-4 (HPV-negative), SCC-9 (HPV-negative), SCC-15 (HPV-negative), CAL 27 (HPV-negative), Detroit 562 (hereafter called D562, HPV-negative), and SCC-25 (HPV-negative) were purchased from American Type Culture Collection (ATCC) [ 12 – 15 ]; UM-SCC-47 (HPV-positive) and UM-SCC-104 (HPV-positive) [ 15 ], kindly provided by Dr. Thomas Carey, University of Michigan; UPCI:SCC090 (HPV-positive) [ 16 ], Dr. Susanne M. Gollin, University of Pittsburgh; UD-SCC-2 (HPV-positive) [ 17 ], Dr. Henning Bier, University of Dusseldorf; and HMS001 (HPV-positive) [ 4 ], Dr. James Rocco, Ohio State University.

Techniques: Western Blot, Expressing, Cell Counting, Plasmid Preparation, CRISPR, Clone Assay, Knock-Out, Cell Culture, Phospho-proteomics, Derivative Assay, Control, Inhibition, Activation Assay

Journal: Cancer letters

Article Title: Human papillomavirus insertions identify the PIM family of serine/threonine kinases as targetable driver genes in head and neck squamous cell carcinoma

doi: 10.1016/j.canlet.2020.01.012

Figure Lengend Snippet: The histogram shows the distribution of median gene expression levels in 151 primary human HNSCC tumors for each of 18,640 genes [3]. After normalization and batch correction of RNA-seq data, genes expressed in at least in one sample (log2(TPM + 1) > 0) were compared. Gencode v18 genes were used as a reference set of annotated genes for comparison of expression. X-axis, median of transcript levels for each gene across all HNSCC samples (transformed as log2 TPM+1), ranging from 0.014 to 13.7; y-axis, number of genes. Blue vertical lines, log2 transformed median expression levels of PIM1 = 6.51 (top 6.5th percentile), PIM2 =4.94 (21.4th percentile), PIM3 =8.43 (1.3rd percentile) and EGFR = 6.29 (7.7th percentile).

Article Snippet: Human HNSCC cancer cell lines and primary HNSCC tumor /normal pairs Human HNSCC cell lines FaDu (HPV-negative), SCC-4 (HPV-negative), SCC-9 (HPV-negative), SCC-15 (HPV-negative), CAL 27 (HPV-negative), Detroit 562 (hereafter called D562, HPV-negative), and SCC-25 (HPV-negative) were purchased from American Type Culture Collection (ATCC) [ 12 – 15 ]; UM-SCC-47 (HPV-positive) and UM-SCC-104 (HPV-positive) [ 15 ], kindly provided by Dr. Thomas Carey, University of Michigan; UPCI:SCC090 (HPV-positive) [ 16 ], Dr. Susanne M. Gollin, University of Pittsburgh; UD-SCC-2 (HPV-positive) [ 17 ], Dr. Henning Bier, University of Dusseldorf; and HMS001 (HPV-positive) [ 4 ], Dr. James Rocco, Ohio State University.

Techniques: Gene Expression, RNA Sequencing, Comparison, Expressing, Transformation Assay