Journal: Glia

Article Title: Generation of a microglial developmental index in mice and in humans reveals a sex difference in maturation and immune reactivity

doi: 10.1002/glia.23176

Figure Lengend Snippet: (a) Hippocampal microglia isolated from male and female mice at different developmental time points were subjected to RNA extraction and Next Generation sequencing. (b) A total of 4645 genes were found to be down-regulated over development whereas 3038 genes were up-regulated from E18 to P60 in mouse microglia. (c) Developmental indices were created by taking the ratio of the average scaled expression levels of genes that were up-regulated during development in microglia, divided by the average expression levels of all down-regulated genes. (d) Line graph plots microglia index (MDI) across development against log2 age in weeks post conception (Non-linear fit, MDI R2 = 0.8525). (e) In order to validate the robustness of the index, gene group size was progressively increased 2-fold from 2 to 256 up- and down-regulated genes. (f) MDI was calculated from transcriptome data of mouse male and female microglia obtained from different developmental time points (E18, P4, P4 and P60, n = 4–10 per group, two-way ANOVA, post-hoc * p < 0.05). (g) Log fold-changes in gene expression between males and females at P60 were compared to those of P60vsE18 (developmental gene expression changes) to obtain positive correlation (Linear regression, Pearson’s r = 0.3311, *** p < 0.0001).

Article Snippet: NextGen RNA sequencing and whole transcriptome analysis All RNA samples were coded numerically prior to shipping to University of Pennsylvania and sequencing was performed blind to sample identity.

Techniques: Isolation, RNA Extraction, Next-Generation Sequencing, Expressing, Gene Expression

Journal: Glia

Article Title: Generation of a microglial developmental index in mice and in humans reveals a sex difference in maturation and immune reactivity

doi: 10.1002/glia.23176

Figure Lengend Snippet: (a) C57BL/6 male and female P60 mice were sacrificed 2 hours after saline or LPS (330 ug/kg, i.p.) injections following which microglia were isolated from the hippocampus and subject to RNA sequencing. (b) Out of the total number of genes changed in males and females following LPS treatment, about 21% (10% up and 11% down) were changed significantly in males (vs. male SAL), and 16% (5% up and 11% down) were changed significantly in females (vs. female SAL). (c) Microglial developmental index was calculated for P60 samples as described above (two-way ANOVA, post-hoc * p < 0.05, n = 6–8 per group). (d) Gene expression changes between P14 and E18 were compared with those in P60 vs. P4 (black line, linear regression, Pearson’s r = 0.48, *** p < 0.0001), P60 females vs. males (purple line, linear regression, Pearson’s r = 0.33, *** p < 0.0001), P60 male LPS vs. SAL (blue line, linear regression, Pearson’s r = 0.31, *** p < 0.0001) and P60 female LPS vs. SAL (red line, linear regression, Pearson’s r = 0.0.1, not significant).

Article Snippet: NextGen RNA sequencing and whole transcriptome analysis All RNA samples were coded numerically prior to shipping to University of Pennsylvania and sequencing was performed blind to sample identity.

Techniques: Saline, Isolation, RNA Sequencing, Gene Expression

Journal: Glia

Article Title: Generation of a microglial developmental index in mice and in humans reveals a sex difference in maturation and immune reactivity

doi: 10.1002/glia.23176

Figure Lengend Snippet: Microglial enriched genes that are positively correlated with MDI in pure developing microglia are also positively correlated with MDI in heterogeneous tissue from multiple gene expression studies where microglia contribute only a fraction of total mRNA.

Article Snippet: NextGen RNA sequencing and whole transcriptome analysis All RNA samples were coded numerically prior to shipping to University of Pennsylvania and sequencing was performed blind to sample identity.

Techniques: Gene Expression

Journal: Clinical cancer research : an official journal of the American Association for Cancer Research

Article Title: Molecular characterization of KRAS wild type tumors in patients with pancreatic adenocarcinoma

doi: 10.1158/1078-0432.CCR-21-3581

Figure Lengend Snippet: Molecular alterations seen in KRAS-WT tumors. 1A: Mutation rates detected by NGS. 1B: Alteration rates detected by immunohistochemistry, copy number amplification rates detected by NGS and fusion rates detected by RNA sequencing. Bars are color coded according to the oncogenic pathways of each biomarker. 1C: BRAF mutations seen in the cohort categorized into class 1, 2 and 3 based on mechanism of action.

Article Snippet: Treatment and survival information were available from a total of 5324 pancreatic cancer patients tested as either KRAS WT (N=705) or KRAS MT (N=4619) using NextGen sequencing platforms (NextSeq or Novaseq).

Techniques: Mutagenesis, Immunohistochemistry, Amplification, RNA Sequencing, Biomarker Discovery

Journal: Clinical cancer research : an official journal of the American Association for Cancer Research

Article Title: Molecular characterization of KRAS wild type tumors in patients with pancreatic adenocarcinoma

doi: 10.1158/1078-0432.CCR-21-3581

Figure Lengend Snippet: Volcano plot comparing molecular alterations of KRAS MT vs. WT tumors. NGS: Next-Gen Sequencing detected mutations. Only molecular alterations significantly different (adjusted p<0.05) are labeled. Full results can be found in Supplemental table 4.

Article Snippet: Treatment and survival information were available from a total of 5324 pancreatic cancer patients tested as either KRAS WT (N=705) or KRAS MT (N=4619) using NextGen sequencing platforms (NextSeq or Novaseq).

Techniques: Sequencing, Labeling

Journal: Clinical cancer research : an official journal of the American Association for Cancer Research

Article Title: Molecular characterization of KRAS wild type tumors in patients with pancreatic adenocarcinoma

doi: 10.1158/1078-0432.CCR-21-3581

Figure Lengend Snippet: An oncoprint displaying the molecular alteration patten of the 233 PDAC tumors. Each row represents a biomarker of either fusion, mutation or copy number amplification, as well as genomic signatures such as TMB or MSI/MMR. Red, blue and green represents TMB-H, MSI-high/MMR-deficient or mutations detected using DNA-sequencing; green represents copy number amplification detected by DNA sequencing, while navy blue represents fusions detected by RNA Sequencing. Grey represents no alteration detected while blanks represent unavailable data (indeterminate results due to low coverage or noisy signals). Bars on the right represents the prevalence of molecular alterations of each row.

Article Snippet: Treatment and survival information were available from a total of 5324 pancreatic cancer patients tested as either KRAS WT (N=705) or KRAS MT (N=4619) using NextGen sequencing platforms (NextSeq or Novaseq).

Techniques: Biomarker Discovery, Mutagenesis, Amplification, DNA Sequencing, RNA Sequencing

Journal: Clinical cancer research : an official journal of the American Association for Cancer Research

Article Title: Molecular characterization of KRAS wild type tumors in patients with pancreatic adenocarcinoma

doi: 10.1158/1078-0432.CCR-21-3581

Figure Lengend Snippet: Comparison of Tumor Microenvironment (TME) characteristics in KRAS MT vs. WT tumors. 5A: Lymphocyte cell fractions estimated by RNA sequencing using Quantiseq.5B: Stromal cell populations estimated by RNA sequencing using MCP counter.**: significantly different after correcting for multiple comparison; * trending differences.

Article Snippet: Treatment and survival information were available from a total of 5324 pancreatic cancer patients tested as either KRAS WT (N=705) or KRAS MT (N=4619) using NextGen sequencing platforms (NextSeq or Novaseq).

Techniques: Comparison, RNA Sequencing

Journal: International Journal of Cancer

Article Title: Comprehensive characterization of MCL‐1 in patients with colorectal cancer: Expression, molecular profiles, and outcomes

doi: 10.1002/ijc.35304

Figure Lengend Snippet: Correlation of MCL‐1 high (Q4) and MCL‐1 low (Q1) expression with immune‐oncology‐related markers, programmed death ligand 1 (PD‐L1) expression, TMB status (high), and dMMR/MSI‐H status in (A) all CRC and (B) pMMR/MSS cohorts. ** q < 0.05 by chi‐squared or Fisher exact test was considered statistically significant. dMMR, deficient mismatch repair; IHC, immunohistochemistry; MCL‐1, myeloid cell leukemia 1; MSI‐H, microsatellite instability‐high; TMB, tumor mutation burden. (C) Gene co‐alterations associated with MCL‐1 high (Q4) and MCL‐1 low (Q1) colorectal cancer (CRC) patients. Mutations in genes involved in signaling pathways important in cancer (including apoptosis, cell cycle, DNA damage response, etc.) were correlated with MCL‐1 expression, and q < 0.05 by chi‐squared or Fisher exact test was considered statistically significant. DDR, DNA damage repair; NGS, next‐generation sequencing. (D) Gene co‐amplifications or copy number amplifications (CNA) associated with MCL‐1 high (Q4) and MCL‐1 low (Q1) CRC patients. Copy number amplifications in genes involved in signaling pathways important in cancer (including apoptosis, cell cycle, DNA damage response, etc.) were correlated with MCL‐1 expression, and q < 0.05 by chi‐squared or Fisher exact test was considered statistically significant.

Article Snippet: CRC samples from Caris Life Sciences (Phoenix, AZ) were analyzed using NextGen DNA sequencing, whole transcriptome sequencing, whole exome sequencing, and immunohistochemistry (IHC); and stratified based on MCL‐1 expression as top quartile MCL‐1 high (Q4) and bottom quartile MCL‐1 low (Q1).

Techniques: Expressing, Immunohistochemistry, Mutagenesis, Protein-Protein interactions, Next-Generation Sequencing