Journal: Frontiers in Medicine

Article Title: Evidence of Antitumor and Antimetastatic Potential of Induced Pluripotent Stem Cell-Based Vaccines in Cancer Immunotherapy

doi: 10.3389/fmed.2021.729018

Figure Lengend Snippet: Treatment with valproic acid (VPA) induced an upregulation of the immune response in 4T1 cells in vitro : Transcriptome analysis was performed on 4T1 cells treated with or without 0.5 mM of valproic acid for 10 days. Microarray probes were synthetized, labeled (Affymetrix microarray station, Affymetrix, CA) and hybridized on a Mouse Clariom S microarray (Thermo Fisher Scientific). The CEL files of microarray data obtained from the Affymetrix platform were normalized using the RMA method in Affymetrix Expression Console software (Affymetrix, CA). (A) A representation of the immune gene network upregulated by in vitro VPA treatment of 4T1 cells. Octagons represent enriched immune modules; circles are genes, which are connected to their respective enriched modules by blue edges (NES, normalized enrichment score). (B) Immune gene sets that were significantly enriched in VPA-treated 4T1 cells compared to untreated 4T1 cells (NES, normalized enrichment score, p -value and FDR were obtained by a hypergeometric test performed using the MSigDB 6.1 Hallmark database). (C) Expression heatmap depicting the immune genes that were significantly overexpressed in VPA-treated 4T1 cells (SAM algorithm, unsupervised classification on Euclidean distances with Ward method). (D) Unsupervised principal component analysis performed on upregulated immune genes in VPA-treated 4T1 cells. (E ) Boxplot of three immune genes that were found to be significantly overexpressed as a result of VPA treatment (fold-change >2).

Article Snippet: The labeled microarray probes were hybridized on a Mouse Clariom S (mm10) microarray (Thermo Fisher Scientific), and the CEL files of microarray data obtained from the Affymetrix platform were normalized using the RMA method in Affymetrix Expression Console software (Affymetrix, CA).

Techniques: In Vitro, Microarray, Labeling, Expressing, Software

Journal: Frontiers in Medicine

Article Title: Evidence of Antitumor and Antimetastatic Potential of Induced Pluripotent Stem Cell-Based Vaccines in Cancer Immunotherapy

doi: 10.3389/fmed.2021.729018

Figure Lengend Snippet: Profiling of immune-associated genes in 4T1 tumors in mice primed with miPSCs. Transcriptome analysis was performed on tumors from untreated mice and from mice primed with 6 doses of miPSCs and VPA in order to find genes that were differentially expressed between the two conditions. Total RNA was extracted from 4T1 tumors in treated and control mice, following the instructions of the manufacturer (TRIzol, Life Technologies). Microarray probes was synthetized by one cycle of RNA amplification in which molecules were labeled in an Affymetrix microarray station (Affymetrix, CA). Labeled microarray probes were hybridized on a Mouse Clariom S (mm10) microarray (Thermo Fisher Scientific). (A) Differentially expressed genes (DEGs) between control and vaccinated mice xeno-transplanted with 4T1 cancer cells; expression heatmap was produced with an unsupervised classification algorithm (Euclidean distances, Ward method). (B) Barplot of functional enrichment in Gene Ontology Biological Processes of genes that were overexpressed in vaccinated mice. (C) Immune profiling carried out by gene-set enrichment analysis on the transcriptome of 4T1-transplanted mice (NES: normalized enriched score). (D) Genes associated with the immune network that were enriched in 4T1 tumors from miPSC+VPA-treated mice.

Article Snippet: The labeled microarray probes were hybridized on a Mouse Clariom S (mm10) microarray (Thermo Fisher Scientific), and the CEL files of microarray data obtained from the Affymetrix platform were normalized using the RMA method in Affymetrix Expression Console software (Affymetrix, CA).

Techniques: Control, Microarray, RNA Amplification, Labeling, Expressing, Produced, Functional Assay

Journal: International Journal of Molecular Sciences

Article Title: Olive Oil, Palm Oil, and Hybrid Palm Oil Distinctly Modulate Liver Transcriptome and Induce NAFLD in Mice Fed a High-Fat Diet

doi: 10.3390/ijms20010008

Figure Lengend Snippet: Liver gene expression analysis. ( A ) Heatmap of microarrays data of different dietary groups. Scatter plots in mice liver receiving either olive oil ( B ), palm oil ( C ), or hybrid palm oil ( D ). ( E ) Venn diagram showing the intersections of differentially expressed genes. O, olive oil group; P, palm oil group; HP, hybrid palm oil group.

Article Snippet: Gene expression analysis was performed using Affymetrix Clariom S Mouse Assay microarrays.

Techniques: Expressing

Journal: The EMBO Journal

Article Title: DELE1 maintains muscle proteostasis to promote growth and survival in mitochondrial myopathy

doi: 10.1038/s44318-024-00242-x

Figure Lengend Snippet: ( A ) Venn diagram depicting intersection of 51 DELE1-dependent DEGs common to all three MM/CM models (the DELE1 mt-ISR heart signature), identified in microarray data. Data from the C10 G58R; Dele1 KO dataset also appears in Appendix Fig. , Figs. and . ( B ) Heat map depicting fold change for DELE1-dependent DEGs identified in all three models (left). Those annotated as regulating transcription in Lambert et al, are separated from other genes. * Shmt2 is in both the “AA transport/biosynthesis” and the “1C metabolism” categories. Reported FDR was calculated in TAC v4.0.3 software across all genes in dataset, using the default settings, which uses a one-way ANOVA corrected with the Benjamini-Hochberg procedure for multiple procedures. ( C ) DELE1-dependent DEGs common to two of three myopathy/cardiomyopathy models (color coded as in ( A )). ( D ) Venn diagram shows overlap between DELE1 mt-ISR heart signature and previously identified ATF4 targets in mouse cells, using ATF4 ChIP-Seq from (Han et al, ). ( E ) Heat map showing significant DELE1-dependent changes in mitochondrial protein abundance in C10 G58R hearts. N = 4 mice per condition. Statistics for proteomics data (which also appear in Dataset ) were performed as described in the Methods with correction for multiple comparisons across all protein groups in the dataset. ( F ) Heat map showing significant DELE1-dependent changes in mitochondrial protein abundance in Tfam mKO hearts. N = 4 mice per condition, except for C10 S59L group2 which was N = 3 mice. Statistics for proteomics data (which also appear in Dataset ) were performed as described in the Methods with correction for multiple comparisons across all protein groups in the dataset. ( G ) Scatterplots compares RNA log 2 FC for C10 G58 vs. control (in the presence of Dele1 ) and mitochondrial protein log 2 FC for C10 G58R vs. control animals in the presence of Dele1 (left) or the absence of Dele1 (right). .

Article Snippet: RNA expression was measured using the Clariom S Mouse microarray (Affymetrix) by the NHGRI Microarray Core.

Techniques: Microarray, Software, ChIP-sequencing, Control

Journal: The EMBO Journal

Article Title: DELE1 maintains muscle proteostasis to promote growth and survival in mitochondrial myopathy

doi: 10.1038/s44318-024-00242-x

Figure Lengend Snippet: ( A ) Dele1 KO and WT littermates were challenged with cold stress for 9 h and interscapular BAT was analyzed by immunoblotting for OPA1 cleavage by OMA1. OMA1 cleavage generated OPA1 isoforms are in indicated in red as c* and e*. ( B ) Volcano plot of global gene expression changes in cold stressed Dele1 KO vs. WT littermates measured by microarray; significant genes (FDR < 0.05 and |Log 2 FC| > 1) are in black. Statistics were performed as described in Methods for all microarray-based transcriptomics. N = 7 mice per group. ( C ) Heat map shows overlap among DELE1-dependent DEGS in four mitochondrial-rich tissues: heart, gastrocnemius (gastroc) skeletal muscle, and liver from C10 G58R mice, in addition to BAT from mice subjected to cold stress. BAT microarray data from same dataset that also appears in Appendix Fig. . C10 G58R heart microarray data are from the same dataset that also appears in Appendix Fig. , Fig. , and Fig. . Statistics on all microarray data (which also appear in Dataset ) were performed as described in Methods for all microarray-based transcriptomics. FDR values were corrected for multiple comparisons across all transcripts in dataset. N = 4 for all groups except for C10 G58R; Dele1+ liver, which was N = 3. ( D ) Venn diagram shows intersection of C10 G58R DELE1-dependent DEGs from three muscles (gastrocnemius, tibalis anterior, and heart), measured by RNA-Seq at P28 (data also available in Dataset – ). ( E ) Venn diagram shows intersection of skeletal and and heart muscle DELE1-dependent DEGs as in ( D ) with ATF4 target genes, from previously published ATF4 ChIP-Seq dataset (Han et al, ). ( F ) Scatterplot shows correlation between genes that increase in tibalis anterior of P28 C10 G58R mice vs. CTRL and those that decrease in abundance in tibalis anterior from 6-month-old ATF4 skeletal muscle knockout mice vs. CTRL, from a previously published dataset (Miller et al, ). ( G , H ) Individual data is shown for select DELE1-dependent genes detected from skeletal muscle and/or heart from P28 C10 G58R mice, by RNA-Seq (data for all detected genes in Dataset – ). Fgf21 was below detection limit (not detected, “nd”) in all but the C10 G58R; Dele1+ condition. Significance was first tested with a two-way ANCOVA including genotype and sex as variables. For post hoc testing) after ANCOVA (shown in Figure), the general linear hypotheses was used in conjunction with the multiple comparisons of means (“mcp”) function to test for all possible two-way comparisons via “Tukey” method. For ( G ), p -values were 1.98E−08 and 6.98E−07 (for bottom row) and 7.12E−10 and 6.62E−08 (for top row). For ( H , top graph, gastrocnemius) p -values for C10 WT; Dele1+ vs. C10 G58R; Dele1+ (for genes left to right) were 0, 0, 2.58E−09, 1.89E−15, 0, 0, 0, 0, and 1.11E−16, and for C10 G58R; Dele1+ vs. C10 G58R; Dele1 KO (for genes left to right) were 0, 0, 1.19E−12, 2.50E−13, 0, 0, 0, 0, and 0. For ( H , middle graph, tibialis anterior) p -values for C10 WT; Dele1+ vs. C10 G58R; Dele1+ (for genes left to right) were 4.37E−07, 0, 4.63E−06, 7.99E−09, 4.97E−11, 0, 0, 2.33E−15, 3.42E−13 and for C10 G58R; Dele1+ vs. C10 G58R; Dele1 KO (for genes left to right) were 8.51E−08, 0, 2.24E−05, 1.37E−08, 1.24E−12, 0, 2.22E−16, 7.77E−16, and 0. For ( H , top graph, heart) p -values for C10 WT; Dele1+ vs. C10 G58R; Dele1+ (for genes left to right) were 1.57E−10, 0, 1.42E−11, 1.63E−12, 0, 2.71E−09, 0, 0, and 0, and for C10 G58R; Dele1+ vs. C10 G58R; Dele1 KO (for genes left to right) were 6.21E−10, 1.22E−12, 1.55E−15, 3.22E−15, 1.16E−13, 0.0001011, 0, 0, 0. In all graphs, **** indicates p ≤ 0.0001, respectively, and “ns” not significant. Error bars represent SD. N ≥ 4 mice per group (genotype). ( I ) individual data is shown for select genes significantly elevated in skeletal muscles of only C10 G58R; Dele1 KO and no other genotypes relative to control. Significance was first tested with a two-way ANCOVA including genotype and sex as variables. For post hoc testing) after ANCOVA (shown in Figure), the general linear hypotheses was used in conjunction with the multiple comparisons of means (“mcp”) function to test for all possible two-way comparisons via “Tukey” method. For gastrocnemius (top graph), p -values for C10 WT; Dele1+ vs. C10 G58R; Dele1+ (for genes left to right) were 0.7386, 0.3720, 0.8302, 0.8152, 0.9998, and 0.9999, and for C10 G58R; Dele1+ vs. C10 G58R; Dele1 KO (for genes left to right) were 0.0007080, 0.001020, 7.28E−05, 2.80E−05, 0.003794, 0.005845. For tibialis anterior (bottom graph), p -values for C10 WT; Dele1+ vs. C10 G58R; Dele1+ (for genes left to right) were 0.9919, 0.3088, 0.9999, 0.9984, 0.2705, 0.9920, and for C10 G58R; Dele1+ vs. C10 G58R; Dele1 KO (for genes left to right) were 3.52E−05, 0.002405, 1.66E−05, 0.001349, 1.16E−07, 1.30E−08. In all graphs, **, ***, **** indicates p ≤ 0.01, 0.001, 0.0001, respectively, and “ns” not significant. Error bars represent SD. N ≥ 4 mice per group (genotype). ( J ) Heat map of 13 mouse genes that are DELE1-dependent in C10 G58R gastrocnemius and tibialis anterior model (as in D ) and have human orthologs that are upregulated by >2-fold (on average) in three previously published datasets from mitochondrial myopathy patients (Hathazi et al, ; Pirinen et al, ; Kalko et al, ). P -values were corrected for multiple comparisons across all transcripts in dataset. .

Article Snippet: RNA expression was measured using the Clariom S Mouse microarray (Affymetrix) by the NHGRI Microarray Core.

Techniques: Western Blot, Generated, Expressing, Microarray, Muscles, RNA Sequencing Assay, ChIP-sequencing, Knock-Out, Control

Journal: The EMBO Journal

Article Title: DELE1 maintains muscle proteostasis to promote growth and survival in mitochondrial myopathy

doi: 10.1038/s44318-024-00242-x

Figure Lengend Snippet: Reagents and tools table

Article Snippet: RNA expression was measured using the Clariom S Mouse microarray (Affymetrix) by the NHGRI Microarray Core.

Techniques: Recombinant, Control, Sequencing, Electron Microscopy, Saline, Staining, Microarray, Software, Laser-Scanning Microscopy, High Performance Liquid Chromatography, Mass Spectrometry

Journal: The Journal of Clinical Investigation

Article Title: OMA1 mediates local and global stress responses against protein misfolding in CHCHD10 mitochondrial myopathy

doi: 10.1172/JCI157504

Figure Lengend Snippet: ( A ) Microarray data on hearts from 14-week-old C10 G58R versus C10 WT mice and 20-week-old C10 S59L versus C10 WT mice, all on the OMA1 +/– background. Each column represents a mouse, and q values represent genome-wide significance. * q < 0.05. ( B ) Microarray data for 33-week-old C10 G58R mouse hearts on the OMA1 +/– background treated with either a nontargeting control ASO or an OMA1 ASO. Each column represents a mouse, and q values represent genome-wide significance. * q < 0.01. ( C ) GSEA of reactome pathways for the listed comparisons. Pathways shown are all the pathways with a q value of less than 0.025 in the C10 G58R OMA1 ASO versus control ASO comparison. ( D ) Effect of OMA1 ASO on the expression of G58R DEGs identified in the comparison from A . See also and .

Article Snippet: RNA was extracted from mouse hearts using either the Direct-zol RNA Miniprep Kit (Zymo, catalog R2051) or the RNeasy Fibrous Tissue Mini Kit (QIAGEN, catalog 74704, used for the ASO experiment), and RNA expression was measured using the Clariom_S_Mouse microarray (Affymetrix).

Techniques: Microarray, Genome Wide, Expressing

Journal: The Journal of Clinical Investigation

Article Title: Meningeal lymphatic CGRP signaling governs pain via cerebrospinal fluid efflux and neuroinflammation in migraine models

doi: 10.1172/JCI175616

Figure Lengend Snippet: ( A ) RiboTag Lyve1-Cre schematic depicting experimental protocol. ( B ) Mean Grimace Score for RiboTag mice, confirming initiation of chronic migraine model. n = 3 animals per group. Data not recorded from final injection day (Day 8). Graph shows mean ± SD. ( C ) Heatmap of differentially translated genes. Red, up with NTG; Blue, down with NTG. n = 3 animals per group from 1 cohort. ( D ) IPA analysis of differentially expressed genes from microarray. Top 10 pathways with more than 4 identified transcripts per pathway displayed. ( E ) Volcano plot of significant differentially genes in MLVs. Labeled genes were selected because PubMed searches resulted in over 7 papers with the topic trend of lymphatic biology. Red text, upregulated and investigated. Significance determined by 1-way ANOVA. Significant P values < 0.05 (above dashed line).

Article Snippet: Clariom S Pico microarray targeting mouse (902932, Thermo Fisher Scientific) was used in collaboration with the UNC Functional Genomics Core to measure expression changes.

Techniques: Injection, Microarray, Labeling