Distinct molecular and clinical correlates of H3F3A mutation subgroups

Slides:

Advertisements

Similar presentations

Gene Set Enrichment Analysis Genome 559: Introduction to Statistical and Computational Genomics Elhanan Borenstein.

Advertisements

Volume 44, Issue 1, Pages (January 2016)

CD25 expression is associated with unfavorable clinical outcome.

Volume 71, Issue 2, Pages (February 2017)

A Long Noncoding RNA Signature That Predicts Pathological Complete Remission Rate Sensitively in Neoadjuvant Treatment of Breast Cancer Gen Wang, Xiaosong.

WT G>A G>C G>T (n = 93) (n = 21) (n = 10) (n = 51)

The immune metagene model has prognostic value in IBE but not in IBD breast cancer. The immune metagene model has prognostic value in IBE but not in IBD.

Frequency of JAK1 and JAK2 alterations and their association with overall survival in TCGA datasets. Frequency of JAK1 and JAK2 alterations and their association.

RNA-seq analysis of iWAT and eWAT.

Gene expression and genomic profiling reveal estrogen-independent ER transcriptional activity. Gene expression and genomic profiling reveal estrogen-independent.

Uncovering a Tumor Suppressor for Triple-Negative Breast Cancers

Volume 5, Issue 4, Pages e5 (October 2017)

Volume 23, Issue 11, Pages (June 2018)

Molecular Subtypes of Non-muscle Invasive Bladder Cancer

(A) Hierarchical clustering was performed to identify groups of patients with similar RNASeq expression of 20 genes associated with reduced survivability.

Volume 15, Issue 11, Pages (June 2016)

Volume 140, Issue 3, Pages e8 (March 2011)

Recurrence-Associated Long Non-coding RNA Signature for Determining the Risk of Recurrence in Patients with Colon Cancer Meng Zhou, Long Hu, Zicheng.

B7-H4 expression correlates with MHC-I expression and improved prognosis in patients with breast cancer. B7-H4 expression correlates with MHC-I expression.

Deletion of Lats1 is phenotypically distinct from Lats2 deletion in PyMT tumors. Deletion of Lats1 is phenotypically distinct from Lats2 deletion in PyMT.

G34 induces a transcriptional program linked to forebrain development and self-renewal. G34 induces a transcriptional program linked to forebrain development.

Volume 24, Issue 12, Pages e5 (September 2018)

Molecular prognostication of liver cancer: End of the beginning

Down-regulation of LATS1 promotes the formation of tumors enriched in basal-like features. Down-regulation of LATS1 promotes the formation of tumors enriched.

Genomic Profiling of Human Leishmania braziliensis Lesions Identifies Transcriptional Modules Associated with Cutaneous Immunopathology Fernanda O. Novais,

Differential binding of H3K36me3 in G34-mutant KNS42 cells drives pediatric GBM expression signatures. Differential binding of H3K36me3 in G34-mutant KNS42.

DNMT3A1 signatures are not recapitulated in AML.

Volume 26, Issue 12, Pages e5 (March 2019)

DNMT3A2 signatures are coherently modified in AML.

Figure 1. Identification of three tumour molecular subtypes in CIT and TCGA cohorts. We used CIT multi-omics data ( Figure 1. Identification of.

Extended analysis of differential expression datasets.

Survival based on V gene mutation status and CD38 expression among B-CLL patients who stratify to the Rai intermediate risk category. Survival based on.

Fig. 2 Inflammatory pathways with STAT1 as a key regulator are enriched in ICB responsive tumors in mouse models and patients. Inflammatory pathways with.

Integrated mRNA and microRNA expression and DNA methylation clusters.

PD-L1 expression correlates with T-cell markers and an IFN response signature in human melanomas. PD-L1 expression correlates with T-cell markers and an.

CXCL14-positive CAFs induce overexpression of LINC00092 in ovarian cancer. CXCL14-positive CAFs induce overexpression of LINC00092 in ovarian cancer. A,

JAK2V617F leads to increased 5-hmC and genome-wide loss of cytosine methylation in primary patient samples. JAK2V617F leads to increased 5-hmC and genome-wide.

Fig. 4 Bcl11b regulates expression of key Treg cell genes while suppressing inflammatory and innate genes. Bcl11b regulates expression of key Treg cell.

Immune signatures of patients with short-, medium-, and long-term survival. Immune signatures of patients with short-, medium-, and long-term survival.

The expression of VCX3A and other CT antigens in pediatric HGG

Overview of TIMER modules on the website.

EN1-associated chromatin complexes in breast cancer cells.

EN1 expression in breast cancer and clinical outcome.

Somatic mutational rates and survival analysis of IBD-CRC.

Survival risk prediction analysis and application of the metastasis gene signature. Survival risk prediction analysis and application of the metastasis.

Kaplan-Meier survival analysis of p53 mutation in the overall breast tumor series. Kaplan-Meier survival analysis of p53 mutation in the overall breast.

CREBBP loss-of-function results in gene expression repression signature. CREBBP loss-of-function results in gene expression repression signature. A–D,

Bortezomib induces an NRF2 signature and NRF2 protein in tumor cells from leukemic MCL. Gene sets regulated by bortezomib (Supplementary Tables S3 and.

MYC–HOXB7–HER2 predicts clinical outcome in breast cancer patients treated with tamoxifen. MYC–HOXB7–HER2 predicts clinical outcome in breast cancer patients.

High-risk neuroblastoma molecular subtypes classification and inference of master regulators. High-risk neuroblastoma molecular subtypes classification.

Gene expression signature that predicts early molecular response failure in chronic-phase CML patients on frontline imatinib by Chung H. Kok, David T.

Expression of 20 genes significantly associated with reduced survivability in GBM is shown across 33 TCGA diseases. Expression of 20 genes significantly.

Frequently mutated genes in colorectal cancer.

Molecular definitions of lung adenocarcinoma subtypes.

KRAS-mutant lung adenocarcinoma subsets exhibit distinct patterns of immune system engagement. KRAS-mutant lung adenocarcinoma subsets exhibit distinct.

G34 H3K36me3 upregulates MYCN which is selectively targetable by kinases that destabilize the protein. G34 H3K36me3 upregulates MYCN which is selectively.

Distinct subtypes of CAFs are detected in human PDAC

EZH2-driven lung cancer as a molecularly distinct entity.

Expression of TGFβ ligands in GBM

STK11/LKB1 mutations are a genomic determinant of poor clinical outcome with PD-1 axis blockade in PD-L1–positive nonsquamous NSCLC, regardless of KRAS.

CASP8 mutations are associated with fewer CNAs and RAS family mutations. CASP8 mutations are associated with fewer CNAs and RAS family mutations. A, number.

Highly metastatic PDAC cells have a unique gene signature, which is not preserved in metastases but predicts poor patient outcome. Highly metastatic PDAC.

Transcriptome traits and clinical characteristics of TME phenotypes in the ACRG cohort. Transcriptome traits and clinical characteristics of TME phenotypes.

TME characteristics of TCGA-STAD subtype and cancer somatic genome.

STK11/LKB1 genetic alterations are associated with shorter progression-free and overall survival with PD-1 blockade among KRAS-mutant LUAC in the SU2C.

DYNLRB1, AIMP1, and NPIPA1 expression correlate with survival in neuroblastoma. DYNLRB1, AIMP1, and NPIPA1 expression correlate with survival in neuroblastoma.

Isolation of large soft agar clones from HBEC3p53,KRAS and HBEC3p53,KRAS,MYC identifies tumorigenic and nontumorigenic clones and genome-wide mRNA expression.

Construction of TME signatures and functional annotation.

Characteristic gene expression patterns distinguish LCH cells from other immune cells present in LCH lesions. Characteristic gene expression patterns distinguish.

Genome-wide DNA hypomethylation associated with DNMT3A mutation in murine and human FLT3ITD AML. Human: A–C, volcano plot (A) representation of mean methylation.

Presentation transcript:

Distinct molecular and clinical correlates of H3F3A mutation subgroups. Distinct molecular and clinical correlates of H3F3A mutation subgroups. A, heatmap representing differential gene expression signatures between G34 versus K27, and G34 versus wild-type, pediatric GBM specimens identified by Paugh and colleagues (3). Top 100 differentially expressed genes are shown for each comparison. B, gene set enrichment analysis (GSEA) for differential gene expression signatures identified by Schwartzentruberand colleagues (2) versus those from Paugh and colleagues (3). Top, G34 versus K27: enrichment score (ES) = 0.833, P [family-wise error rate (FWER)] = 0.0, q [false discovery rate (FDR)] = 0.0. Bottom, G34 versus wild-type: ES = 0.94, FWER P = 0.0, FDR q = 0.0. C, heatmap representing differential gene expression signatures between G34 versus K27, and G34 versus wild-type, pediatric GBM specimens from (2). Top 100 differentially expressed genes are shown for each comparison. D, GSEA for differential gene expression signatures identified in (3) versus those in (2). Top, G34 versus K27: ES = 0.88, FWER P = 0.03, FDR q = 0.04. Bottom, G34 versus wild-type: ES = 0.90, FWER P = 0.0, FDR q = 0.0. E, hierarchical clustering of the integrated gene expression datasets, highlighting specific clusters of G34- and K27-mutant tumors, distinct from a more heterogeneous group of wild-type cases. G34V tumors are represented by asterisks. F, K-means consensus clustering finds the most stable number of subgroups to be 3, marked by H3F3A mutation status. G, K27- and G34-mutant pediatric GBM in our integrated dataset have distinct age incidence profiles, with K27 tumors peaking at 7 years in contrast to G34 at age 14. The 2 G34V tumors were diagnosed at age 14 and 20. H, Kaplan–Meier plot for overall survival of pediatric patients with GBM stratified by H3F3A status. K27-mutant tumors have significantly shorter survival than G34 (P = 0.0164, log-rank test). A single G34V case for which data were available had an overall survival of 1.4 years. wt, wild-type. Lynn Bjerke et al. Cancer Discovery 2013;3:512-519 ©2013 by American Association for Cancer Research