towards results trim

content/03.results.md

@@ -2,9 +2,8 @@
 
 ### Crowd-sourced Somatic Analyses to Create an Open Pediatric Brain Tumor Atlas
 
-We previously performed whole genome sequencing (WGS), whole exome sequencing (WXS), and RNA sequencing (RNA-Seq) on matched tumor/normal tissues as well as selected cell lines [@doi:10.1093/neuonc/noz192] from 943 patients from the Pediatric Brain Tumor Atlas (PBTA), consisting of 911 patients from the [CBTN](https://CBTN.org) [@doi:10.1016/j.neo.2022.100846] and 32 patients from [PNOC](https://pnoc.us/) [@doi:10.1002/ijc.32258; @doi:10.1158/1078-0432.CCR-22-0803] (**Figure {@fig:Fig1}A**).
-**Figure {@fig:Fig1}B** summarizes biospecimen numbers by phase of therapy and histology. 
-We harnessed, and built upon, the benchmarking efforts of the [Gabriella Miller Kids First Data Resource Center](https://kidsfirstdrc.org/) to develop robust and reproducible data analysis workflows within the [CAVATICA platform](https://www.cavatica.org/) to perform comprehensive somatic analyses (**Figure {@fig:S1}**) and **STAR Methods**) of the PBTA. 
+We previously performed whole genome sequencing (WGS), whole exome sequencing (WXS), and RNA sequencing (RNA-Seq) on matched tumor/normal tissues and selected cell lines [@doi:10.1093/neuonc/noz192] from 943 patients from the Pediatric Brain Tumor Atlas (PBTA), consisting of 911 patients from the [CBTN](https://CBTN.org) [@doi:10.1016/j.neo.2022.100846] and 32 patients from [PNOC](https://pnoc.us/) [@doi:10.1002/ijc.32258; @doi:10.1158/1078-0432.CCR-22-0803] (**Figure {@fig:Fig1}A**) across various histologies phrases of therapy (**Figure {@fig:Fig1}B**).
+We harnessed, and built upon, the benchmarking efforts of the [Gabriella Miller Kids First Data Resource Center](https://kidsfirstdrc.org/) to develop robust and reproducible data analysis workflows within the [CAVATICA platform](https://www.cavatica.org/) to perform comprehensive somatic analyses (**Figure {@fig:S1}**) and **STAR Methods**) of the PBTA.
 
 A key innovative feature of OpenPBTA is the contribution framework used for analyses (e.g., analytical code) and manuscript writing.
 We created a public Github analysis repository ([https://github.com/AlexsLemonade/OpenPBTA-analysis](https://github.com/AlexsLemonade/OpenPBTA-analysis)) to hold all analysis code downstream of Kids First workflows and a GitHub manuscript repository ([https://github.com/AlexsLemonade/OpenPBTA-manuscript](https://github.com/AlexsLemonade/OpenPBTA-manuscript)) with Manubot [@doi:10.1371/journal.pcbi.1007128] integration to enable real-time manuscript creation.
@@ -193,7 +192,7 @@ This result suggests that the classifier actually detects an oncogenic, or alter
 However, "activated" tumors showed higher _TP53_ expression compared to those with _TP53_ "loss" mutations (Wilcoxon p = 0.006, **Figure {@fig:Fig4}C**).
 Tumor types with the highest median _TP53_ scores included DMGs, medulloblastomas, HGGs, DNETs, ependymomas, and craniopharyngiomas (**Figure {@fig:Fig4}D**), all known to harbor _TP53_ mutations.
 By contrast, gangliogliomas, LGGs, meningiomas, and schwannomas had the lowest median scores.
-	
+
 We hypothesized that tumors from patients with LFS (N = 8) would have higher _TP53_ scores.
 Indeed, we observed higher scores in 8/10 tumors from LFS patients (**Table S3**).
 Although two tumors from LFS patients had low _TP53_ scores (`BS_DEHJF4C7` at 0.09 and `BS_ZD5HN296` at 0.28), we confirmed from pathology reports that both patients were diagnosed with LFS and had a pathogenic germline variant in _TP53_.
@@ -284,6 +283,6 @@ This result may be explained by the higher expression of _CD274_ observed in WNT
 Finally, we asked whether any subtypes might have a high ratio CD8+ to CD4+ T cells, a metric which has been associated with better immunotherapy response and prognosis following PD-L1 inhibition in non-small cell lung cancer or adoptive T cell therapy in multiple stage III or IV cancers [@doi:10.1136/jitc-2021-004012; @doi:10.4236/jct.2013.48164].
 While adamantinomatous craniopharyngiomas and Group 3 and Group 4 medulloblastomas had the highest CD8+ to CD4+ T cell ratios (**Figure {@fig:S6}F**), very few tumors had ratios greater than 1, highlighting an urgent need to identify novel therapeutics for pediatric brain tumors with poor prognosis.
 To explore the potential influence of tumor purity, selected transcriptomic analyses were repeated using samples with tumor purities at or above the median tumor purity of their cancer group (see **STAR Methods**).
-The analyses using all stranded samples were broadly consistent (**Figure {@fig:S7}D-I**) with those using samples with high tumor purity. 
+The analyses using all stranded samples were broadly consistent (**Figure {@fig:S7}D-I**) with those using samples with high tumor purity.
 
 ![**Transcriptomic and immune landscape of pediatric brain tumors** A, First two dimensions from UMAP of transcriptome data. Points colored by broad histology. B, Heatmap of with significant GSVA scores for Hallmark gene sets with tumors ordered by cancer group. C, Box plots of quanTIseq estimates of immune cell proportions in select cancer groups with N > 15 tumors. Note: other HGGs and other LGGs have immune cell proportions similar to DMG and pilocytic astrocytoma, respectively, and are not shown. D, Forest plot depicting additive effects of _CD274_ expression, immune cell proportion, and extent of tumor resection on OS of medulloblastoma patients. HRs with 95% confidence intervals and p-values (multivariate Cox) are listed. Significant p-values are denoted with black diamonds. Reference groups are denoted by grey diamonds. Note: the Macrophage M1 HR was 0 (coefficient = -9.90e+4) with infinite upper and lower CIs, and thus was not included in the figure. E, Box plot of _CD274_ expression (log<sub>2</sub> FPKM) for medulloblastomas grouped by subtype. Bonferroni-corrected p-values from Wilcoxon tests are shown. Box plot represents 5% (lower whisker), 25% (lower box), 50% (median), 75% (upper box), and 95% (upper whisker) quantiles. Only stranded RNA-Seq data is plotted.](https://raw.githubusercontent.com/AlexsLemonade/OpenPBTA-analysis/37ec62fdc2fd9ff157f2f2c10b69e9bb36673363/figures/pngs/figure5.png?sanitize=true){#fig:Fig5 width="7in"}