Abstract 6047: Identification of a 13 gene signature to predict survival in localized osteosarcoma

Osteosarcoma (OS) is the most prevalent bone tumor in pediatric patients. Regimens of neoadjuvant chemotherapy have improved survival of OS patients greatly, however the 5-year survival rate for localized OS is 75% with a 30-50% recurrence rate. We sought to identify genes which could predict chemo-response and survival in localized OS. The TARGET OS RNA-seq dataset was utilized to identify genes and pathways associated with localized patient relapse and survival. We identified 478 differentially expressed genes with a 1.5 FC and FDR < 0.05 common to overall survival and relapse We further performed string analysis to generate a protein-protein interaction network followed by hub analysis with Cytohubba using betweenness centrality and radiality measures. Combining the top 10 hub genes from these two methods resulted in a total of 13 genes: MYOM2, VEGFA, VCAM1, EGFR, MUC1, IHH, GLI1, GPC3, IGF2, GRIA1, GNG12, GNGT1 and C3. These 13 genes were used to stratify localized patients in the TARGET dataset into high-risk and low-risk tertiles. The low-risk group had 100% overall survival while the high-risk group had 44% 5-year survival (p=2e-4). We also found a significant correlation between the 13 genes and time to death in localized patients (p=0.04). Additionally, there was a significant difference in expression of the 13 genes between alive and deceased patients (p=2e-5) and patients who relapsed (p=1.5e-4). Overall, these data suggest that these 13 genes could predict relapse and overall survival in OS patients with localized disease in the TARGET cohort. We performed Weighted Gene Correlation Network Analysis (WGCNA) on the 478 overlapping genes and identified five modules, with our 13 genes split across these modules. All modules were also significantly correlated with vital status suggesting that the genes in our signature represent distinct sub-groups with possibly separate mechanisms. Over-representation analysis was performed for each module and while each module did have distinct pathways, there were 65 pathways which overlapped between 3 of the modules. Of particular interest was Hedgehog signaling, with 2 of our 13 genes, IHH and GLI1, key to Hedgehog signaling, and a Hedgehog pathway inhibitor, Gant-58, scored high in reversing the 478 gene signature as determined using Connectivity Map (Broad Institute). We tested Gant-58 against two PDX OS models. Gant-58 did not inhibit a non-relapsed, chemo sensitive localized PDX-derived cell line, but showed potent activity towards a recurrent localized PDX with elevated IHH and GLI1 expression (p<0.0001). In summary, we identified 13 genes that predict overall survival and relapse in localized OS patients. The 13 genes represent distinct modules of co-expressing genes that significantly correlate with survival. Furthermore, preliminary data indicate Hedgehog pathway has a key role in survival and recurrence of localized OS patients.

Citation Format: Tajhal D. Patel, Kshiti Dholakia, Tanmay R. Gandhi, Rupa S. Kanchi, Sandra L. Grimm, Chenlian Fu, Jason T. Yustein, Cristian Coarfa. Identification of a 13 gene signature to predict survival in localized osteosarcoma [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 6047.

Genomic, Pathway Network, and Immunologic Features Distinguishing Squamous Carcinomas

This integrated, multiplatform PanCancer Atlas study co-mapped and identified distinguishing molecular features of squamous cell carcinomas (SCCs) from five sites associated with smoking and/or human papillomavirus (HPV). SCCs harbor 3q, 5p, and other recurrent chromosomal copy-number alterations (CNAs), DNA mutations, and/or aberrant methylation of genes and microRNAs, which are correlated with the expression of multi-gene programs linked to squamous cell stemness, epithelial-to-mesenchymal differentiation, growth, genomic integrity, oxidative damage, death, and inflammation. Low-CNA SCCs tended to be HPV(+) and display hypermethylation with repression of TET1 demethylase and FANCF, previously linked to predisposition to SCC, or harbor mutations affecting CASP8, RAS-MAPK pathways, chromatin modifiers, and immunoregulatory molecules. We uncovered hypomethylation of the alternative promoter that drives expression of the ΔNp63 oncogene and embedded miR944. Co-expression of immune checkpoint, T-regulatory, and Myeloid suppressor cells signatures may explain reduced efficacy of immune therapy. These findings support possibilities for molecular classification and therapeutic approaches.

Interchromosomal template-switching as a novel molecular mechanism for imprinting perturbations associated with Temple syndrome

Background

Intrachromosomal triplications (TRP) can contribute to disease etiology via gene dosage effects, gene disruption, position effects, or fusion gene formation. Recently, post-zygotic de novo triplications adjacent to copy-number neutral genomic intervals with runs of homozygosity (ROH) have been shown to result in uniparental isodisomy (UPD). The genomic structure of these complex genomic rearrangements (CGRs) shows a consistent pattern of an inverted triplication flanked by duplications (DUP-TRP/INV-DUP) formed by an iterative DNA replisome template-switching mechanism during replicative repair of a single-ended, double-stranded DNA (seDNA), the ROH results from an interhomolog or nonsister chromatid template switch. It has been postulated that these CGRs may lead to genetic abnormalities in carriers due to dosage-sensitive genes mapping within the copy-number variant regions, homozygosity for alleles at a locus causing an autosomal recessive (AR) disease trait within the ROH region, or imprinting-associated diseases.

Methods

Here, we report a family wherein the affected subject carries a de novo 2.2-Mb TRP followed by 42.2 Mb of ROH and manifests clinical features overlapping with those observed in association with chromosome 14 maternal UPD (UPD(14)mat). UPD(14)mat can cause clinical phenotypic features enabling a diagnosis of Temple syndrome. This CGR was then molecularly characterized by high-density custom aCGH, genome-wide single-nucleotide polymorphism (SNP) and methylation arrays, exome sequencing (ES), and the Oxford Nanopore long-read sequencing technology.

Results

We confirmed the postulated DUP-TRP/INV-DUP structure by multiple orthogonal genomic technologies in the proband. The methylation status of known differentially methylated regions (DMRs) on chromosome 14 revealed that the subject shows the typical methylation pattern of UPD(14)mat. Consistent with these molecular findings, the clinical features overlap with those observed in Temple syndrome, including speech delay.

Conclusions

These data provide experimental evidence that, in humans, triplication can lead to segmental UPD and imprinting disease. Importantly, genotype/phenotype analyses further reveal how a post-zygotically generated complex structural variant, resulting from a replication-based mutational mechanism, contributes to expanding the clinical phenotype of known genetic syndromes. Mechanistically, such events can distort transmission genetics resulting in homozygosity at a locus for which only one parent is a carrier as well as cause imprinting diseases.

Electronic supplementary material

The online version of this article (10.1186/s13073-019-0633-y) contains supplementary material, which is available to authorized users.

A Pan-Cancer Analysis Reveals High-Frequency Genetic Alterations in Mediators of Signaling by the TGF-β Superfamily

We present an integromic analysis of gene alterations that modulate transforming growth factor β (TGF-β)-Smad-mediated signaling in 9,125 tumor samples across 33 cancer types in The Cancer Genome Atlas (TCGA). Focusing on genes that encode mediators and regulators of TGF-β signaling, we found at least one genomic alteration (mutation, homozygous deletion, or amplification) in 39% of samples, with highest frequencies in gastrointestinal cancers. We identified mutation hotspots in genes that encode TGF-β ligands (BMP5), receptors (TGFBR2, AVCR2A, and BMPR2), and Smads (SMAD2 and SMAD4). Alterations in the TGF-β superfamily correlated positively with expression of metastasis-associated genes and with decreased survival. Correlation analyses showed the contributions of mutation, amplification, deletion, DNA methylation, and miRNA expression to transcriptional activity of TGF-β signaling in each cancer type. This study provides a broad molecular perspective relevant for future functional and therapeutic studies of the diverse cancer pathways mediated by the TGF-β superfamily.

Abstract 3303: A comprehensive TCGA Pan-Cancer molecular study of gynecologic and breast cancers

The Pan-Gynecologic (Pan-Gyn) molecular study analyzed data from 2,579 tumors representing five TCGA tumor-type projects: high-grade serous ovarian cystadenocarcinoma (OV), invasive breast carcinoma (BRCA), uterine corpus endometrial carcinoma (UCEC), cervical squamous cell carcinoma and endocervical adenocarcinoma (CESC), and uterine carcinosarcoma (UCS). Principal aims were to identify shared and unique molecular features, clinically meaningful subtypes, and potential future therapeutic targets. We analyzed data of multiple types, including somatic copy number alterations (SCNAs), mutations, DNA methylation, mRNA expression (from mRNA-seq), microRNA (miRNA) expression (from miRNA-seq), long non-coding RNA (lncRNA) expression (from miRNA-seq), and protein expression (from reverse-phase protein arrays; RPPA).

We found multiple genomic and epigenomic features that were shared across the Pan-Gyn tumor types and distinguished them from other cancer types. Sixty-one somatic copy number alterations (SCNAs) and 46 significantly mutated genes (SMGs) were found in the Pan-Gyn cohort; 11 of the SCNAs and 11 of the SMGs had not been reported in previous TCGA single-disease papers on the same tumor types. Ten predominant mutation signatures were found that correlated with COSMIC signatures, whereas 10% of the samples had no SMGs. Most of the Pan-Gyn tumor types shared similar miRNA profiles. The exception, ovarian cancer, was extremely different from the rest, and, unexpectedly, the miRNA profiles of basal-like breast cancers closely resembled those of cervical cancers. Protein expression analysis (RPPA) revealed some OV and UCEC samples with the “reactive” signature previously identified in BRCA and shown to be prognostically relevant. It also revealed a subtype with low ER and AR expression levels (important markers for hormone therapy) that spanned all 5 tumor types. Novel lncRNA analysis showed several functionally significant ER-regulated lncRNAs and gene/lncRNA interaction networks. Pathway analysis identified subsets of tumor samples that had high levels of leukocyte infiltration, with potential implications for immunotherapy. Using 16 key molecular features across the Pan-Gyn cancers, we identified five novel cross-tumor and prognostic subtypes with possible clinical implications. Finally, we developed a decision tree that can classify patients into the five subtypes based on just 6 of the 16 molecular features. Those 6 features are potentially assessable in clinical laboratories.

Citation Format: Ashton Berger, Anil Korkut, Rupa S. Kanchi, TCGA Pan-Gynecologic Group and Research Network, Gordon B. Mills, Douglas A. Levine, Rehan Akbani. A comprehensive TCGA Pan-Cancer molecular study of gynecologic and breast cancers [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 3303.

A Comprehensive Pan-Cancer Molecular Study of Gynecologic and Breast Cancers

We analyzed molecular data on 2,579 tumors from The Cancer Genome Atlas (TCGA) of four gynecological types plus breast. Our aims were to identify shared and unique molecular features, clinically significant subtypes, and potential therapeutic targets. We found 61 somatic copy-number alterations (SCNAs) and 46 significantly mutated genes (SMGs). Eleven SCNAs and 11 SMGs had not been identified in previous TCGA studies of the individual tumor types. We found functionally significant estrogen receptor-regulated long non-coding RNAs (lncRNAs) and gene/lncRNA interaction networks. Pathway analysis identified subtypes with high leukocyte infiltration, raising potential implications for immunotherapy. Using 16 key molecular features, we identified five prognostic subtypes and developed a decision tree that classified patients into the subtypes based on just six features that are assessable in clinical laboratories.

Comparative Molecular Analysis of Gastrointestinal Adenocarcinomas

We analyzed 921 adenocarcinomas of the esophagus, stomach, colon, and rectum to examine shared and distinguishing molecular characteristics of gastrointestinal tract adenocarcinomas (GIACs). Hypermutated tumors were distinct regardless of cancer type and comprised those enriched for insertions/deletions, representing microsatellite instability cases with epigenetic silencing of MLH1 in the context of CpG island methylator phenotype, plus tumors with elevated single-nucleotide variants associated with mutations in POLE. Tumors with chromosomal instability were diverse, with gastroesophageal adenocarcinomas harboring fragmented genomes associated with genomic doubling and distinct mutational signatures. We identified a group of tumors in the colon and rectum lacking hypermutation and aneuploidy termed genome stable and enriched in DNA hypermethylation and mutations in KRAS, SOX9, and PCBP1.

The Cancer Genome Atlas Comprehensive Molecular Characterization of Renal Cell Carcinoma

Renal cell carcinoma (RCC) is not a single disease, but several histologically defined cancers with different genetic drivers, clinical courses, and therapeutic responses. The current study evaluated 843 RCC from the three major histologic subtypes, including 488 clear cell RCC, 274 papillary RCC, and 81 chromophobe RCC. Comprehensive genomic and phenotypic analysis of the RCC subtypes reveals distinctive features of each subtype that provide the foundation for the development of subtype-specific therapeutic and management strategies for patients affected with these cancers. Somatic alteration of BAP1, PBRM1, and PTEN and altered metabolic pathways correlated with subtype-specific decreased survival, while CDKN2A alteration, increased DNA hypermethylation, and increases in the immune-related Th2 gene expression signature correlated with decreased survival within all major histologic subtypes. CIMP-RCC demonstrated an increased immune signature, and a uniform and distinct metabolic expression pattern identified a subset of metabolically divergent (MD) ChRCC that associated with extremely poor survival.

Comprehensive Molecular Characterization of Muscle-Invasive Bladder Cancer

We report a comprehensive analysis of 412 muscle-invasive bladder cancers characterized by multiple TCGA analytical platforms. Fifty-eight genes were significantly mutated, and the overall mutational load was associated with APOBEC-signature mutagenesis. Clustering by mutation signature identified a high-mutation subset with 75% 5-year survival. mRNA expression clustering refined prior clustering analyses and identified a poor-survival "neuronal" subtype in which the majority of tumors lacked small cell or neuroendocrine histology. Clustering by mRNA, long non-coding RNA (lncRNA), and miRNA expression converged to identify subsets with differential epithelial-mesenchymal transition status, carcinoma in situ scores, histologic features, and survival. Our analyses identified 5 expression subtypes that may stratify response to different treatments.

Comprehensive molecular characterization and analysis of muscle-invasive urothelial carcinomas

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Background: We reported the integrated molecular analysis of 131 tumors in 2014 (Nature 507:315, 2014) and now report on the entire cohort of 412 tumors from the TCGA project in chemotherapy-naïve, muscle-invasive urothelial bladder cancer. Methods: Following strict clinical and pathologic quality control, tumors were analyzed for DNA copy number variants, somatic mutations (WES), DNA methylation, mRNA, non-coding RNA (lncRNA and miRNA) and (phospho-) protein expression, gene fusions, viral integration, pathway perturbation, clinical correlates, outcomes, and histopathology. Results: There was a high overall somatic mutation rate (8.2/Mb), as previously reported. There were 58 significantly mutated genes (SMGs) (MutSig_2CV), increased from 32 in the original report. We identified 5 mutation signatures including APOBEC-a and b, ERCC2, C > T_CpG, and a single ultra-mutated sample with a functional POLE mutation. APOBEC mutagenesis explained 70% of the mutation burden and was associated with survival (p = 0.0013). High mutation burden and neoantigen load were also associated with improved outcome (p = 0.00014 and 0.00078). The previously identified four mRNA subtypes were predicted on the larger set and also identified a novel poor-survival ‘neuronal’ subtype that nevertheless lacked small cell or neuroendocrine histology. Clustering converged for mRNA, lncRNA and miRNA expression, and for inferred activity of gene sets associated with regulator expression. We identified subsets with differential epithelial-mesenchymal transition scores, carcinoma-in-situ scores, and survival, with implications for distinct therapeutic potential. Conclusions: This integrated analysis of 412 TCGA patient samples validates and extends observations from the first 131 patients and significantly increases our power to detect additional low-frequency aberrations. The results provide unique insights into mechanisms of bladder cancer development, and identify novel subsets of MIBC that may benefit from differential treatment approaches.