Aberrant DNA methylation distorts developmental trajectories in atypical teratoid/rhabdoid tumors

Atypical teratoid/rhabdoid tumors (AT/RTs) are pediatric brain tumors known for their aggressiveness and aberrant but still unresolved epigenetic regulation. To better understand their malignancy, we investigated how AT/RT-specific DNA hypermethylation was associated with gene expression and altered transcription factor binding and how it is linked to upstream regulation. Medulloblastomas, choroid plexus tumors, pluripotent stem cells, and fetal brain were used as references. A part of the genomic regions, which were hypermethylated in AT/RTs similarly as in pluripotent stem cells and demethylated in the fetal brain, were targeted by neural transcriptional regulators. AT/RT-unique DNA hypermethylation was associated with polycomb repressive complex 2 and linked to suppressed genes with a role in neural development and tumorigenesis. Activity of the several NEUROG/NEUROD pioneer factors, which are unable to bind to methylated DNA, was compromised via the suppressed expression or DNA hypermethylation of their target sites, which was also experimentally validated for NEUROD1 in medulloblastomas and AT/RT samples. These results highlight and characterize the role of DNA hypermethylation in AT/RT malignancy and halted neural cell differentiation.

Abstract 5644: Spatially resolved transcriptomics points to distinct malignant cell populations within primary and castration resistant prostate cancer

Background: Prostate cancer (PCa) is the second most common cancer in men. Despite its high prevalence, many patients carry an indolent form of the disease and are thus suspect to overtreatment. Conversely, some cases treated with androgen deprivation therapy can develop into castration resistant prostate cancer (CRPC), for which there is no curative treatment. Understanding why some tumors are more aggressive than others could lead to more accurate patient risk stratification. Here we characterize cancer and normal cell subpopulations within prostate tissue in their spatial context using a multimodal integrative approach.

Methods: We performed spatially resolved transcriptomics (ST) on a set of primary tumor PCa, CRPC and benign prostatic hyperplasia (BPH) patient samples. In addition to ST, we produced RNA-seq, DNA-seq and assay for transposase accessible chromatin using sequencing (ATAC-seq) data, allowing for multiomic integration within and across sample categories. We performed extensive analysis of ST data, employing unsupervised clustering, spot expression signal deconvolution, differential gene expression analysis and copy number variation (CNV) inference.

Main Results: The systematic analysis of spot expression profiles revealed a high degree of variation in nearby tissue regions, as we found up to three unique luminal cell populations inside a one millimeter radius in PCa. Similarly in locally recurrent CRPC, we identified cumulative CNVs in proximal luminal cell populations, with the inferred CNV profiles validated through DNA-seq. A set of marker genes was calculated for each unique cell population, with multiple PCa associated genes found to be differentially expressed. Although we observed significant variation in the luminal cell populations, the stromal gene expression was markedly similar across all samples.

Conclusions: We discovered shared, similar and unique cell populations both within and across different PCa and CRPC sections. We observed various luminal cell populations with distinct gene expression profiles in samples from both progression stages. The close spatial proximity of these cell clusters suggests that ST can be used to discover and examine finely detailed populations in their original spatial environment.

Citation Format: Antti Kiviaho, Heini M. Kallio, Sini K. Eerola, Elisa M. Vuorinen, Tomi Häkkinen, Sinja Taavitsainen, Ebrahim Afyounian, Teemu Tolonen, Juha Kesseli, Alfonso Urbanucci, Kirsi J. Rautajoki, Teuvo L. Tammela, Tapio Visakorpi, Matti Nykter. Spatially resolved transcriptomics points to distinct malignant cell populations within primary and castration resistant prostate cancer. [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 5644.

EPCO-34. INTEGRATIVE DNA METHYLATION ANALYSIS OF PEDIATRIC BRAIN TUMORS REVEALS TUMOR TYPE-SPECIFIC DEVELOPMENTAL TRAJECTORIES AND EPIGENETIC SIGNATURES OF MALIGNANCY

Understanding oncogenic epigenetic mechanisms in brain tumors is crucial for improved diagnosis and treatment. Recently DNA methylation has proven to be powerful for brain tumor characterization and diagnostic classification. To evaluate tumor type specific features, we compared atypical teratoid/rhabdoid tumors (AT/RTs), medulloblastomas (MBs), and choroid plexus tumors with each other by integrating DNA methylation (507 samples), gene expression (120 samples), and transcription factor (TF) -binding data. Different tumor entities were used to find unique changes affecting each of the entities and further to identify functions driven by these changes. Our results provide insight on how the aberrant DNA methylation induces oncogenesis of AT/RTs. These tumors are known for their aggressiveness and exceptionally low mutation rates. Our results suggest that in AT/RT, elevated DNA methylation masks the binding sites of TFs such as NEUROD1, ASCL1 and MYCN driving neural development. DNA methylation in AT/RTs is also associated with reduced gene expression for specific neural regulators such as NEUROG1 and NEUROD2. For MBs, DNA methylation patterns predict a more advanced differentiation state. In MB, we found masked TF binding sites for TFs such as REST and ZEB1 that normally inhibit neural differentiation. We then wanted to further characterize DNA methylation and compared these tumors to pluripotent stem cells (PSCs) and normal fetal brain samples. As a result, we were able to find two different regulatory programs in AT/RTs: One in which DNA methylation is similar to PSCs and which harbors mostly neural TF binding sites. Second program has AT/RT-specific DNA methylation, and these sites are uniquely associated with polycomb repressive complex 2 members. However, this second program also covers neural TF binding sites and is likely to have relevance in oncogenic regulation.

Abstract LB-173: DNA methylation analysis reveals epigenetic regulation of neural differentiation in AT/RTs

DNA methylation has proven to be powerful for brain tumor characterization and diagnostic classification. To obtain information about the oncogenic role of DNA methylation, we analyzed medulloblastoma, choroid plexus, and atypical teratoid/rhabdoid tumors (AT/RTs) with public data from 450K-methylation arrays (N=584) and gene-expression arrays (N=110). In addition, two AT/RTs, five choroid plexus tumors and three medulloblastomas were analyzed by using reduced representation bisulfite sequencing, exome sequencing, and RNA-sequencing of matched samples. Only few somatic alterations in addition to SMARCB1 deletion were present in our AT/RTs. DNA methylation analysis generated 2325-5739 and 17175-25187 differentially methylated regions (DMRs) between tumor types in 450K array and RRBS sequencing data, respectively. AT/RTs harbored generally higher DNA methylation levels than the other tumor types. Next, DNA methylation differences were integrated with gene expression data. Surprisingly, only eight genes showed cancer-specific association between differential DNA methylation and an opposite expression change at promoter or linked enhancer in both public and in-house data. There were 44 cancer-specific genes with expression-methylation association when DNA methylation analysis was extended to genomic neighborhoods. To gain information about changes in epigenetic regulation between tumor types, we studied which previously experimentally validated transcription factor (TF) binding sites are enriched in cancer specific DMRs. Several TFs known to promote neural development, such as NEUROG2 and NEUROD1, were enriched in regions hypermethylated in AT/RT, whereas TFs, such as SMAD2, involved in the inhibition of neural development were associated with regions hypermethylated in medulloblastoma. This suggests that DNA methylation is regulating especially the target sites for neural regulators in AT/RT tumors, thus inhibiting neural development. Expression differences did not explain the predicted decreased activity of most of these neural TFs. Low number of genes with cancer-specific expression and methylation change is at least partly explained by the different gene expression patterns in medulloblastomas and choroid plexus tumors, thus providing different references for comparison. Also differences in the measurement techniques contribute to this. Taken together, these results suggest that DNA methylation has a role as an epigenetic regulator for the oncogenesis of AT/RTs.

Citation Format: Kirsi Johanna Granberg, Joonas Tuominen, Kristiina Nordfors, Meeri Pekkarinen, Ville Kytölä, Sergei Häyrynen, Ebrahim Afyounian, Olli Lohi, Pauli Helen, Juha Kesseli, Joonas Haapasalo, Hannu Haapasalo, Matti Nykter. DNA methylation analysis reveals epigenetic regulation of neural differentiation in AT/RTs [abstract]. In: Proceedings of the Annual Meeting of the American Association for Cancer Research 2020; 2020 Apr 27-28 and Jun 22-24. Philadelphia (PA): AACR; Cancer Res 2020;80(16 Suppl):Abstract nr LB-173.

Abstract LB-096: Chromatin alterations in human prostate cancer

Whole human genome is packed into chromatin, which is dynamically remodeled. Chromatin structure has been extensively studied with cell lines, but information about chromatin structure in tissue context is lacking. We present genome-wide chromatin accessibility analysis of clinical tissue samples using transposase-accessible chromatin sequencing (ATAC-seq). Our sample cohort consist 11 benign prostatic hyperplasia (BPH), 16 primary prostate cancer (PC), and 11 castration resistant prostate cancer (CRPC) samples. We identified 23,307 to 136,104 regions of accessible chromatin per sample using MACS2 peak calling. Utilizing a peak unification method resulted in a unified set of 178,333 high confidence peaks across sample set. To find out which loci are differentially accessible during disease progression, we further compared normalized ATAC-seq signal between sample groups across the genome. We identified 4747 and 9445 differentially accessible regions (DARs) for BPH to PC and PC to CRPC comparison, respectively. Out of these, in 2961 and 6652 chromatin was opening and in 1786 and 2793 chromatin was closing in respective comparison. Using DARs, we observe clear separation of the sample groups. Earlier, we have characterized this cohort using DNA, RNA and DNA methylation sequencing as well as SWATH proteomics. Using these data and the same analysis approach as with DARs, we identified 2061 and 2723 differentially methylated regions (DMRs) in BPH to PC and PC to CRPC comparisons, respectively. We compared locations of DARs and DMRs and found out that these occur in different loci overlapping only in 27 and 35 loci in respective comparisons. When integrated with gene expression data, the chromatin accessibility correlated (|coefficient| &gt0.5) with the expression of at least one gene located in the same topologically associating domain (TAD) in altogether 2713 DARs. Next, we examined which transcription factors (TFs) are binding to DARs and thus putatively regulating gene-expression. Using HOMER database, we found several TFs with binding motif enrichment in our DARs. In BPH to PC comparison, opening DARs contain binding sites e.g. for AR and FOXA1 and, in PC to CRPC comparison, opening DARs contain binding sites e.g. for HOXB13, as expected. Interestingly, in PC to CRPC comparison closing DARs contain binding sites for AR and FOXA1 indicating that these TFs have smaller role or alternative regulatory programs when disease progresses. We utilized publicly available CHIP-seq datasets to study this more closely in DARs where ATAC-seq signal correlates with gene-expression within a TAD. Here, while the total number of AR binding sites doubles, the number of AR binding sites in closing DARs is ten times higher in CRPC to PC comparison than in PC to BPH comparison. These results suggest that chromatin accessibility is an important regulator of prostate cancer progression and changes occur in specific loci to where several relevant prostate cancer TFs can bind.

Citation Format: Joonas I. Tuominen, Ebrahim Afyounian, Francesco Tabaro, Tomi Häkkinen, Anastasia Shcherban, Matti Annala, Kati Kivinummi, Teuvo Tammela, Juha Kesseli, Leena Latonen, Kirsi Granberg, Tapio Visakorpi, Matti Nykter. Chromatin alterations in human prostate cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr LB-096.

Abstract 4393: Integrative proteomic analysis of prostate cancer reveals distinct regulation of RNA binding proteins during disease progression

To understand the etiology of the disease, and to find novel and more specific drug targets, the driver mutations and expressional changes in prostate cancer have been examined through extensive genomic and transcriptomic characterization. Although significant insight has been gained through these efforts, it is clear that not all molecular alterations influencing the tumor outcome can be captured through these approaches, and that a comprehensive understanding of the molecular events in cancer require thorough investigation of the proteome.

To understand the functional consequences of genetic and transcriptional aberrations in prostate cancer, we aimed to reveal the proteomic changes during disease formation and progression. We performed high throughput mass spectrometry on clinical tissue samples of benign prostatic hyperplasia (BPH), untreated primary prostate cancer (PC) and castration resistant prostate cancer (CRPC). We performed an integrative analysis of the proteomic data with gene copy number, DNA methylation, and RNA expression data from the same samples. Furthermore, proteomic events correlating with the androgen receptor (AR) status of the tumors were analysed.

We uncovered previously unrecognized molecular and pathway events and several novel AR-associated events in the prostate cancer proteomes to study further. We found significant changes in expression of RNA-binding proteins during disease formation and progression. Examining the relationship of RNA binding proteins at the RNA and protein expression level reveal that while many RNA binding proteins exhibit correlation between the expression levels, some seem regulated at the posttranslational level. Two RNA binding proteins, TDP-43 and FUS, which regulated at the protein, but not at RNA level during prostate cancer progression, show opposite behavior during disease progression and correlation with AR status of the tumors. In cultured prostate cancer cell models, we show that these proteins have specific, but divergent interactions with AR at the RNA and protein levels, and that they contribute differentially to AR activity-mediated responses. Thus, these proteins may significantly contribute to prostate cancer molecular evolution and may pinpoint possible targetable pathways in future prostate cancer therapy.

Citation Format: Mauro Scaravilli, Annika Kohvakka, Pekka Ruusuvuori, Ebrahim Afyounian, Matti Nykter, Tapio Visakorpi, Leena Latonen. Integrative proteomic analysis of prostate cancer reveals distinct regulation of RNA binding proteins during disease progression [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr 4393.

Abstract A020: Integrative analysis of the proteome in primary and advanced prostate cancer

To fully understand the output of alterations in cancer genomes and transcriptomes, we need to know how these aberrations are translated into the functional protein units in cells. We assessed proteomic changes during disease formation and progression in prostate cancer by performing high-throughput mass spectrometry on clinical tissue samples of benign prostatic hyperplasia (BPH), untreated primary prostate cancer (PC), and castration-resistant prostate cancer (CRPC). With SWATH-MS quantitation-based proteomics we found that each of these sample groups show a distinct protein profile. By integrative analysis of this mass spectrometry dataset with genetic, epigenetic, and transcriptional data from the same samples, we show that, especially in CRPC, gene copy number, DNA methylation, and RNA expression levels do not reliably predict proteomic changes. From our analysis, we have identified sets of novel expression changes occurring primarily at the protein level, in addition to identification of several miRNA-target correlations present at protein but not at mRNA level. We find novel expression changes in previously unrecognized pathways in prostate cancer that are likely to affect disease development and progression. For example, we identify two metabolic shifts in the citric acid cycle (TCA cycle), one occurring during primary cancer development and the second during castration resistance, having implications on drug targeting against cancer metabolism. Our proteogenomic analysis of prostate cancer uncovers robustness against genomic and transcriptomic aberrations during disease progression, reveals new disease mechanisms, and significantly extends understanding of prostate cancer biology.

Citation Format: Leena Latonen, Ebrahim Afyounian, Antti Jylhä, Janika Nättinen, Ulla Aapola, Matti Annala, Kati Kivinummi, Teuvo Tammela, Roger W. Beuerman, Hannu Uusitalo, Matti Nykter, Tapio Visakorpi. Integrative analysis of the proteome in primary and advanced prostate cancer [abstract]. In: Proceedings of the AACR Special Conference: Prostate Cancer: Advances in Basic, Translational, and Clinical Research; 2017 Dec 2-5; Orlando, Florida. Philadelphia (PA): AACR; Cancer Res 2018;78(16 Suppl):Abstract nr A020.

Whole-exome sequencing identifies germline mutation in TP53 and ATRX in a child with genomically aberrant AT/RT and her mother with anaplastic astrocytoma

Brain tumors typically arise sporadically and do not affect several family members simultaneously. In the present study, we describe clinical and genetic data from two patients, a mother and her daughter, with familial brain tumors. Exome sequencing revealed a germline missense mutation in the TP53 and ATRX genes in both cases, and a somatic copy-neutral loss of heterozygosity (LOH) in TP53 in both atypical teratoid/rhabdoid tumor (AT/RT) and astrocytoma tumors. ATRX mutation was associated with the loss of ATRX protein expression. In the astrocytoma case, R132C missense mutation was found in the known hotspot site in isocitrate dehydrogenase 1 (IDH1) and LOH was detected in TP53 The mother carried few other somatic alterations, suggesting that the IDH1 mutation and LOH in TP53 were sufficient to drive tumor development. The genome in the AT/RT tumor was atypically aneuploid: Most chromosomes had experienced copy-neutral LOH or whole-chromosome gains. Only Chromosome 18 had normal diploid status. INI1/hSNF5/SMARCB1 was homozygously deleted in the AT/RT tumor. This report provides further information about tumor development in a predisposed genetic background and describes two special Li-Fraumeni cases with a familial brain tumor.

Integrative proteomics in prostate cancer uncovers robustness against genomic and transcriptomic aberrations during disease progression

To understand functional consequences of genetic and transcriptional aberrations in prostate cancer, the proteomic changes during disease formation and progression need to be revealed. Here we report high-throughput mass spectrometry on clinical tissue samples of benign prostatic hyperplasia (BPH), untreated primary prostate cancer (PC) and castration resistant prostate cancer (CRPC). Each sample group shows a distinct protein profile. By integrative analysis we show that, especially in CRPC, gene copy number, DNA methylation, and RNA expression levels do not reliably predict proteomic changes. Instead, we uncover previously unrecognized molecular and pathway events, for example, several miRNA target correlations present at protein but not at mRNA level. Notably, we identify two metabolic shifts in the citric acid cycle (TCA cycle) during prostate cancer development and progression. Our proteogenomic analysis uncovers robustness against genomic and transcriptomic aberrations during prostate cancer progression, and significantly extends understanding of prostate cancer disease mechanisms.

Understanding of molecular events in cancer requires proteome-level characterisation. Here, proteome profiling of patient samples representing primary and progressed prostate cancer enables the authors to identify pathway alterations that are not reflected at the genomic and transcriptomic levels.

Segmentum: a tool for copy number analysis of cancer genomes

BACKGROUND

Somatic alterations, including loss of heterozygosity, can affect the expression of oncogenes and tumor suppressor genes. Whole genome sequencing enables detailed characterization of such aberrations. However, due to the limitations of current high throughput sequencing technologies, this task remains challenging. Hence, accurate and reliable detection of such events is crucial for the identification of cancer-related alterations.

RESULTS

We introduce a new tool called Segmentum for determining somatic copy numbers using whole genome sequencing from paired tumor/normal samples. In our approach, read depth and B-allele fraction signals are smoothed, and double sliding windows are used to detect breakpoints, which makes our approach fast and straightforward. Because the breakpoint detection is performed simultaneously at different scales, it allows accurate detection as suggested by the evaluation results from simulated and real data. We applied Segmentum to paired tumor/normal whole genome sequencing samples from 38 patients with low-grade glioma from the TCGA dataset and were able to confirm the recurrence of copy-neutral loss of heterozygosity in chromosome 17p in low-grade astrocytoma characterized by IDH1/2 mutation and lack of 1p/19q co-deletion, which was previously reported using SNP array data.

CONCLUSIONS

Segmentum is an accurate, user-friendly tool for somatic copy number analysis of tumor samples. We demonstrate that this tool is suitable for the analysis of large cohorts, such as the TCGA dataset.