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Purpose: Patients with MYC-amplified medulloblastoma (MB) have poor prognosis and frequently develop recurrence, thus new therapeutic approaches to prevent recurrence are needed. Experimental Design: We evaluated OLIG2 expression in a panel of mouse Myc-driven MB tumors, patient MB samples, and patient-derived xenograft (PDX) tumors and analyzed radiation sensitivity in OLIG2–high and OLIG2–low tumors in PDX lines. We assessed the effect of inhibition of OLIG2 by OLIG2-CRISPR or the small molecule inhibitor CT-179 combined with radiotherapy on tumor progression in PDX models. Results: We found that MYC-associated MB can be stratified into OLIG2–high and OLIG2–low tumors based on OLIG2 protein expression. In MYC-amplified MB PDX models, OLIG2–low tumors were sensitive to radiation and rarely relapsed, whereas OLIG2–high tumors were resistant to radiation and consistently developed recurrence. In OLIG2–high tumors, irradiation eliminated the bulk of tumor cells; however, a small number of tumor cells comprising OLIG2– tumor cells and rare OLIG2+ tumor cells remained in the cerebellar tumor bed when examined immediately post-irradiation. All animals harboring residual-resistant tumor cells developed relapse. The relapsed tumors mirrored the cellular composition of the primary tumors with enriched OLIG2 expression. Further studies demonstrated that OLIG2 was essential for recurrence, as OLIG2 disruption with CRISPR-mediated deletion or with the small molecule inhibitor CT-179 prevented recurrence from the residual radioresistant tumor cells. Conclusions: Our studies reveal that OLIG2 is a biomarker and an effective therapeutic target in a high-risk subset of MYC-amplified MB, and OLIG2 inhibitor combined with radiotherapy represents a novel effective approach for treating this devastating disease.

Fig. S1, S2, S3 and Table S1.

Medulloblastoma (MB) is the most common malignant pediatric brain tumor. MYC-driven MBs, commonly found in the group 3 MB, are aggressive and metastatic with the worst prognosis. Modeling MYC-driven MB is the foundation of therapeutic development. Here, we applied a synthetic mRNA-driven strategy to generate neuronal precursors from human-induced pluripotent stem cells (iPSCs). These neuronal precursors were transformed by the MYC oncogene combined with p53 loss of function to establish an MYC-driven MB model recapitulating the histologic and transcriptomic hallmarks of group 3 MB. We further show that the marine compound Frondoside A (FA) effectively inhibits this MYC-driven MB model without affecting isogenic neuronal precursors with undetectable MYC expression. Consistent results from a panel of MB models support that MYC levels are positively correlated with FA's antitumor potency. Next, we show that FA suppresses MYC expression and its downstream gene targets in MB cells, suggesting a potential mechanism underlying FA's inhibitory effects on MYC-driven cancers. In orthotopic xenografts of MYC-driven MB, intratumoral FA administration potently induces cytotoxicity in tumor xenografts, significantly extends the survival of tumor-bearing animals, and enhances the recruitment of microglia/macrophages and cytotoxic T lymphocytes to tumors. Moreover, we show that MYC levels also predict FA potency in glioblastoma and non–small cell lung cancer cells. Taken together, this study provides an efficient human iPSC-based strategy for personalizable cancer modeling, widely applicable to mechanistic studies (e.g., genetic predisposition to cancer) and drug discovery. Our preclinical results justify the clinical translation of FA in treating MYC-driven MB and other human cancers.

Purpose:Patients with MYC-amplified medulloblastoma (MB) have poor prognosis and frequently develop recurrence, thus new therapeutic approaches to prevent recurrence are needed.Experimental Design:We evaluated OLIG2 expression in a panel of mouse Myc-driven MB tumors, patient MB samples, and patient-derived xenograft (PDX) tumors and analyzed radiation sensitivity in OLIG2–high and OLIG2–low tumors in PDX lines. We assessed the effect of inhibition of OLIG2 by OLIG2-CRISPR or the small molecule inhibitor CT-179 combined with radiotherapy on tumor progression in PDX models.Results:We found that MYC-associated MB can be stratified into OLIG2–high and OLIG2–low tumors based on OLIG2 protein expression. In MYC-amplified MB PDX models, OLIG2–low tumors were sensitive to radiation and rarely relapsed, whereas OLIG2–high tumors were resistant to radiation and consistently developed recurrence. In OLIG2–high tumors, irradiation eliminated the bulk of tumor cells; however, a small number of tumor cells comprising OLIG2– tumor cells and rare OLIG2+ tumor cells remained in the cerebellar tumor bed when examined immediately post-irradiation. All animals harboring residual-resistant tumor cells developed relapse. The relapsed tumors mirrored the cellular composition of the primary tumors with enriched OLIG2 expression. Further studies demonstrated that OLIG2 was essential for recurrence, as OLIG2 disruption with CRISPR-mediated deletion or with the small molecule inhibitor CT-179 prevented recurrence from the residual radioresistant tumor cells.Conclusions:Our studies reveal that OLIG2 is a biomarker and an effective therapeutic target in a high-risk subset of MYC-amplified MB, and OLIG2 inhibitor combined with radiotherapy represents a novel effective approach for treating this devastating disease.

Supplementary Table from OLIG2 Is a Determinant for the Relapse of MYC-Amplified Medulloblastoma

Supplementary Data from OLIG2 Is a Determinant for the Relapse of MYC-Amplified Medulloblastoma

A subset of group 3 medulloblastoma frequently harbors amplification or overexpression of MYC lacking additional focal aberrations, yet it remains unclear whether MYC overexpression alone can induce tumorigenesis and which cells give rise to these tumors. Here, we showed that astrocyte progenitors in the early postnatal cerebellum were susceptible to transformation by MYC. The resulting tumors specifically resembled human group 3 medulloblastoma based on histology and gene-expression profiling. Gene-expression analysis of MYC-driven medulloblastoma cells revealed altered glucose metabolic pathways with marked overexpression of lactate dehydrogenase A (LDHA). LDHA abundance correlated positively with MYC expression and was associated with poor prognosis in human group 3 medulloblastoma. Inhibition of LDHA significantly reduced growth of both mouse and human MYC-driven tumors but had little effect on normal cerebellar cells or SHH-associated medulloblastoma. By generating a new mouse model, we demonstrated for the first time that astrocyte progenitors can be transformed by MYC and serve as the cells of origin for group 3 medulloblastoma. Moreover, we identified LDHA as a novel, specific therapeutic target for this devastating disease.Significance:Insights from a new model identified LDHA as a novel target for group 3 medulloblastoma, paving the way for the development of effective therapies against this disease.

RNA-Seq analysis

Figure S1 shows MYC driven tumors generated from early postnatal cerebellar cells. Figure S2 shows IHC staining of tdt+ or tdt- MYC-driven tumors. Figure S3 shows gene expression of mouse MYC-driven tumors compared to that of human medulloblastomas. Figure S4 shows properties of Sox2+/Aldh1L1high, Sox2+/Aldh1L1low and Sox2+/Aldh1L1neg cells. Figure S5 shows properties of Sox2+/CD133+, Sox2+/CD133- or Sox2-/CD133+ cells. Figure S6 shows gene expression of SOX family members in tumors or normal cerebellar cells. Figure S7 shows that LDHA is a potential target for treating human MYC-amplified medulloblastoma.

Neoantigen discovery in pediatric brain tumors is hampered by their low mutational burden and scant tissue availability. Here we develop a proteogenomic approach combining tumor DNA/RNA sequencing and mass spectrometry proteomics to identify tumor-restricted (neoantigen) peptides arising from multiple genomic aberrations to generate a highly target-specific, autologous, personalized T cell immunotherapy. Our data indicate that aberrant splice junctions are the primary source of neoantigens in medulloblastoma, a common pediatric brain tumor. Proteogenomically identified tumor-specific peptides are immunogenic and generate MHC II-based T cell responses. Moreover, polyclonal and polyfunctional T cells specific for tumor-specific peptides effectively eliminate tumor cells in vitro. Targeting tumor-specific antigens obviates the issue of central immune tolerance while potentially providing a safety margin favoring combination with other immune-activating therapies. These findings demonstrate the proteogenomic discovery of immunogenic tumor-specific peptides and lay the groundwork for personalized targeted T cell therapies for children with brain tumors., Targeting tumor-associated antigens in paediatric medulloblastomas (MB) is challenging due to their low mutational burden. Here, the authors develop a sensitive proteogenomic approach to identify tumour specific neoantigens, which may enable personalised T cell immunotherapy in paediatric MB.

Background: The causes of the rising incidence of early-onset colorectal cancer (EOCRC), defined as CRC in patients aged 60). Methods: The international cohort included 13,262 patients diagnosed with stages I-III colon or rectal cancer who had ctDNA testing using a personalized and tumor-informed multiplex PCR assay (Signatera™ 16-plex bespoke mPCR NGS assay), from which whole-exome sequencing (WES) on the surgically resected tumor was performed. Tumor mutational burden (TMB) and microsatellite instability (MSI) status were derived from WES analysis. The prevalence of gene-wide mutations, pathogenic gene variants, and mutations in known oncogenic pathways was compared between EOCRC and LOCRC groups, stratified by TMB and MSI status. Fisher’s exact test was used to test significance between the groups and p-values were adjusted using the FDR method for multiple test correction. Results: A total of 3,093 patients with EOCRC (70.8% colon, 27.4% rectal, 1.9% unknown) and 10,169 patients with LOCRC (79.9% colon, 18.3% rectal, 1.7% unknown) were included, where 9.0%/37.3%/53.7% were AJCC stages I, II, and III, respectively. Early-onset patients compared to late-onset patients had fewer cases of stage II CRC (30.7% vs. 39.3%, p Conclusion: Patients with LOCRC were more likely to have pathogenic gene variants and mutations in established pathways of CRC carcinogenesis. Tumors in EOCRC cases harbored unique genomic alterations that varied between the TMB-low/MSS, TMB-H/MSI-H, and TMB-H/MSS subpopulations. Citation Format: Eric M. Lander, Samuel Rivero-Hinojosa, Vasily N. Aushev, Jesús Izaguirre-Carbonell, Adham Jurdi, Minetta C. Liu, Cathy Eng. Genomic alterations associated with early-onset and late-onset colorectal 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 6696.

Cancer testis antigens are ideal for tumor immunotherapy due to their testis-restricted expression. We previously showed that an immunotherapeutic vaccine targeting the germ cell-specific transcription factor BORIS (CTCFL) was highly effective in treating aggressive breast cancer in the 4T1 mouse model. Here, we further tested the therapeutic efficacy of BORIS in a rat 13762 breast cancer model. We generated a recombinant VEE-VRP (Venezuelan Equine Encephalitis-derived replicon particle) vector-expressing modified rat BORIS lacking a DNA-binding domain (VRP-mBORIS). Rats were inoculated with the 13762 cells, immunized with VRP-mBORIS 48 h later, and then, subsequently, boosted at 10-day intervals. The Kaplan–Meier method was used for survival analysis. Cured rats were re-challenged with the same 13762 cells. We demonstrated that BORIS was expressed in a small population of the 13762 cells, called cancer stem cells. Treatment of rats with VRP-BORIS suppressed tumor growth leading to its complete disappearance in up to 50% of the rats and significantly improved their survival. This improvement was associated with the induction of BORIS-specific cellular immune responses measured by T-helper cell proliferation and INFγ secretion. The re-challenging of cured rats with the same 13762 cells indicated that the immune response prevented tumor growth. Thus, a therapeutic vaccine against rat BORIS showed high efficacy in treating the rat 13762 carcinoma. These data suggest that targeting BORIS can lead to the elimination of mammary tumors and cure animals even though BORIS expression is detected only in cancer stem cells.

Background The germline genetic events underpinning medulloblastoma (MB) initiation, and therefore the ability to determine who is at risk, are still unknown for the majority of cases. Microsatellites are short repeated sequences that make up ~3% of the genome. Repeat lengths vary among individuals and are often nonrandomly associated with disease, including several cancers such as breast, glioma, lung, and ovarian. Due to their effects on gene function, they have been called the “tuning knobs of the genome.” Methods We have developed a novel approach for identifying a microsatellite-based signature to differentiate MB patients from controls using germline DNA. Results Analyzing germline whole exome sequencing data from a training set of 120 MB subjects and 425 controls, we identified 139 individual microsatellite loci whose genotypes differ significantly between the groups. Using a genetic algorithm, we identified a subset of 43 microsatellites that distinguish MB subjects from controls with a sensitivity and specificity of 92% and 88%, respectively. This microsatellite signature was validated in an independent dataset consisting of 102 subjects and 428 controls, with comparable sensitivity and specificity of 95% and 90%, respectively. Analysis of the allele genotypes of those 139 informative loci demonstrates that their association with MB is a consequence of individual microsatellites' genotypes rather than their hypermutability. Finally, an analysis of the genes harboring these microsatellite loci reveals cellular functions important for tumorigenesis. Conclusion This study demonstrates that MB-specific germline microsatellite variations mark those at risk for MB development and suggests mechanisms of predisposition.

T cell immunotherapies are promising new tools to combat high-risk subgroups of medulloblastoma without increasing the late effects burden. The ideal target antigen of an effective antitumor T-cell response is abundantly expressed by tumor cells but not by normal tissues, in order to limit off-target effects. Tumors translate a host of highly novel transcripts that are the result of aberrations in tumor DNA and the unmasking of alternative or novel exons. We developed a novel proteogenomic approach to identify tumor-restricted peptides and used them to select and expand T cells capable of mounting a tumor-specific cytotoxic immune response. Using RNA-seq and WGS data, we created personalized custom searchable databases containing predicted novel proteins from somatic mutations, novel junctions and fusion transcripts from 56 medulloblastoma tumors. By searching these databases with raw mass spectrometry data from paired medulloblastoma tumors, we identified tens of neoantigen peptides arising from the translation of tumor-specific transcripts; novel isoforms being the predominant source. We tested these peptides for their ability to select and expand autologous polyclonal populations of T cells and tested the immunogenicity of each individual peptide. Flow cytometry revealed populations of CD4+ and CD8+ cells with an activation profile marked by IFN-γ and TNF-α. Immunosuppressive marker profiles were also characterized. Using cytotoxicity assays, we demonstrated that tumor specific T cells can eliminate neoantigen bearing tumor cells. Thus, proteogenomics can identify immunogenic tumor specific peptides that can be used to create a personalized, targeted T cell therapy for children with high risk medulloblastoma.

We report a comprehensive proteogenomics analysis, including whole-genome sequencing, RNA sequencing, and proteomics and phosphoproteomics profiling, of 218 tumors across 7 histological types of childhood brain cancer: low-grade glioma (n = 93), ependymoma (32), high-grade glioma (25), medulloblastoma (22), ganglioglioma (18), craniopharyngioma (16), and atypical teratoid rhabdoid tumor (12). Proteomics data identify common biological themes that span histological boundaries, suggesting that treatments used for one histological type may be applied effectively to other tumors sharing similar proteomics features. Immune landscape characterization reveals diverse tumor microenvironments across and within diagnoses. Proteomics data further reveal functional effects of somatic mutations and copy number variations (CNVs) not evident in transcriptomics data. Kinase-substrate association and co-expression network analysis identify important biological mechanisms of tumorigenesis. This is the first large-scale proteogenomics analysis across traditional histological boundaries to uncover foundational pediatric brain tumor biology and inform rational treatment selection.

The genetic events leading to medulloblastoma initiation, and therefore the ability to determine who is at risk and why, are still unknown. Microsatellites are short tandem repeated sequences that comprise ~3% of the genome. The number of repeats varies between individuals and are often non-randomly associated with disease, including several cancers such as breast, glioma, lung and ovarian. We have developed a novel approach for identifying and validating a microsatellite signature set for medulloblastoma tumors using germline DNA. Analyzing germline DNA sequence from a training set of 120 medulloblastoma subjects and 425 healthy controls, we have identified a set of 139 microsatellite loci whose genotype are significantly different between medulloblastoma subjects and controls. Using an iterative classification algorithm, we found a subset of 43 microsatellites able to distinguish medulloblastoma subjects from controls with a sensitivity and specificity of 0.88 and 0.92, respectively. This signature set was validated in an independent dataset with greater sensitivity and specificity. Analysis of the minor alleles of those 139 informative loci demonstrates that these loci are more mutable in medulloblastoma patients than controls. Finally, a downstream analysis of the genes harboring these microsatellite loci revealed significantly enriched pathways (Autophagy and mTOR signaling) and genes associated with cell cycle and DNA replication, recombination, and repair. Interestedly, we identified two exonic microsatellites in the transcription factors RAI1 and BCL6B associated with medulloblastoma. This study demonstrates that medulloblastoma-specific microsatellite variations in the germline DNA can distinguish individuals with medulloblastoma as well as provide insight into mechanisms of predisposition.

Despite sharing the same sequence specificity in vitro and in vivo, CCCTC-binding factor (CTCF) and its paralog brother of the regulator of imprinted sites (BORIS) are simultaneously expressed in germ cells. Recently, ChIP-seq analysis revealed two classes of CTCF/BORIS-bound regions: single CTCF target sites (1xCTSes) that are bound by CTCF alone (CTCF-only) or double CTCF target sites (2xCTSes) simultaneously bound by CTCF and BORIS (CTCFBORIS) or BORIS alone (BORIS-only) in germ cells and in BORIS-positive somatic cancer cells. BORIS-bound regions (CTCFBORIS and BORIS-only sites) are, on average, enriched for RNA polymerase II (RNAPII) binding and histone retention in mature spermatozoa relative to CTCF-only sites, but little else is known about them. We show that subsets of CTCFBORIS and BORIS-only sites are occupied by several testis-specific transcriptional regulators (TSTRs) and associated with highly expressed germ cell-specific genes and histone retention in mature spermatozoa. We also demonstrate a physical interaction between BORIS and one of the analyzed TSTRs, TATA-binding protein (TBP)-associated factor 7-like (TAF7L). Our data suggest that CTCF and BORIS cooperate with additional TSTRs to regulate gene expression in developing male gametes and histone retention in mature spermatozoa, potentially priming certain regions of the genome for rapid activation following fertilization.

The genomic characterization of medulloblastoma at the level of the chromosome, epigenome and transcriptome has radically redefined diagnostic classifications and reoriented disease definitions toward a biological underpinning. However, it still remains a challenge to leverage this wealth of data toward a true understanding of disease biology and subsequently to capitalize on the promise of biologically based therapies. One reason for this difficulty is the loose correlation between the genetic and the functional aspects of the cancer cell resulting from multilayered regulatory mechanisms governing protein production, the predominant functional moiety of the cell. To better actualize the promise of genomics, it is necessary to add an understanding of the proteomic dimension to cancer cell biology. We have undertaken a super-SILAC based quantitative proteomics survey of 42 tissue samples spanning the 4 genomic subgroups of medulloblastoma and control cerebellum. We have identified and quantitated thousands of proteins across these groups and find that we are able to recapitulate the genomic subgroups based upon subgroup restricted and differentially abundant proteins while also identifying one additional subgroup. Adding array gene expression data to this analysis, we calculate a relatively poor correlation between mRNA and protein abundance with the best concordance found among stable proteins. EPIC 850k methylation array data performed on the same samples extend this analysis to the epigenome yielding chromosomal copy number variations and correlations to gene promoter methylation. From the quantitative proteomic data, we are able to discern networks of functional pathways with differential activation between the medulloblastoma subgroups and normal control cerebellum yielding potential avenues for clinical intervention. This work demonstrates that quantitative proteomics can further elucidate the biology inherent in a genomically based classification regime.

Despite sharing the same sequence specificity in vitro and in vivo, CCCTC-binding factor (CTCF) and its paralog brother of the regulator of imprinted sites (BORIS) are simultaneously expressed in germ cells. Recently, ChIP-seq analysis revealed two classes of CTCF/BORIS-bound regions: single CTCF target sites (1xCTSes) that are bound by CTCF alone (CTCF-only) or double CTCF target sites (2xCTSes) simultaneously bound by CTCF and BORIS (CTCF&BORIS) or BORIS alone (BORIS-only) in germ cells and in BORIS-positive somatic cancer cells. BORIS-bound regions (CTCF&BORIS and BORIS-only sites) are, on average, enriched for RNA polymerase II (RNAPII) binding and histone retention in mature spermatozoa relative to CTCF-only sites, but little else is known about them. We show that subsets of CTCF&BORIS and BORIS-only sites are occupied by several testis-specific transcriptional regulators (TSTRs) and associated with highly expressed germ cell-specific genes and histone retention in mature spermatozoa. We also demonstrate a physical interaction between BORIS and one of the analyzed TSTRs, TATA-binding protein (TBP)-associated factor 7-like (TAF7L). Our data suggest that CTCF and BORIS cooperate with additional TSTRs to regulate gene expression in developing male gametes and histone retention in mature spermatozoa, potentially priming certain regions of the genome for rapid activation following fertilization.

Medulloblastoma (MB) is the most common malignant brain tumor in children. Among the four molecular subgroups of MB (WNT, SHH, Group 3 and Group 4), patients with Group 3 MB exhibit the worst prognosis. Group 3 MB is associated with amplification and overexpression of the MYC oncogene. However, whether MYC overexpression alone is sufficient to induce Group 3 MB tumorigenesis in specific cell type(s) in the cerebellum remains unclear. The study of the etiology of Group 3 MB and the development of effective, targeted therapies for this disease has also been impeded by lack of appropriate disease models that faithfully recapitulate Group 3 MB. Here, we generated a novel mouse model for Group 3 MB and demonstrated that overexpression of MYC alone is sufficient to transform astrocyte progenitors and granule neuron progenitors in the early postnatal cerebellum. The resulting tumors resemble human Group 3 MB in terms of histology and gene expression profiles, making this animal model a valuable tool for the development and testing of new therapies. To identify potential therapeutic targets, we analyzed dysregulated gene expression and revealed that the genes involved in the glucose metabolism pathways were significantly upregulated in murine and human Group 3 MB compared to normal cerebellar cells or SHH Group MB. Among these genes, expression of lactate dehydrogenase A (LDHA), which catalyzes the conversion of pyruvate to lactate during energy metabolism, is associated with poor prognosis in Group 3 MB. Inhibition of LDHA by either RNA interference or pharmacological agents significantly reduced growth of both mouse and human Group 3 tumor cells, without affecting SHH Group MB, suggesting that LDHA is a potential specific target for treating Group 3 MB.

Group 3 medulloblastoma (MB) has been characterized with MYC amplification or overexpression. However, the function of MYC in tumor initiation and progression has not been well studied. A few years ago, two groups demonstrated that Group 3 MB can be generated from cerebellar stem cells with overexpression of MYC and mutant p53. However, this tumor may not faithfully recapitulate human tumors because mutation or deletion of p53 is rarely detected in human Group 3 MB at diagnosis. In our recent studies, we found that MYC alone is sufficient to transform granule neuron progenitors (Math1+) and Bergmann glia (Sox2+) in the neonatal cerebellum. Comprehensive gene expression analysis shows that these tumors faithfully resemble Group 3 MB. Moreover, the tumors generated from Math1+ and Sox2+ cells represent two distinct subtypes of Group 3 MB. Thus, these models are valuable tools to study tumor biology and test novel therapies. We identified that lactate dehydrogenase A (LDH-A), which contributes to the conversion of pyruvate to lactate during energy metabolism, is overexpressed in both mouse and human tumors and highly correlated with MYC expression levels. These observations indicate that targeting LDH-A may represent a new therapeutic avenue to treat this disease. We will use our new murine models and human xenografts to determine whether inhibition of LDH-A prevents tumor growth. If successful, this approach could be translated for the development of new anti-cancer therapies for Group 3 MB, with preferential killing of cancer cells without significant toxicity to normal cells.

The genomic characterization of medulloblastoma at the level of the chromosome, epigenome and transcriptome has radically redefined diagnostic classifications and reoriented disease definitions toward a biological underpinning. However, it still remains a challenge to leverage this wealth of data toward a true understanding of disease biology and subsequently to capitalize on the promise of biologically based therapies. One reason for this difficulty is the loose correlation between the genetic and the functional aspects of the cancer cell resulting from multilayered regulatory mechanisms governing protein production, the predominant functional moiety of the cell. To better actualize the promise of genomics, it is necessary to add an understanding of the proteomic dimension to cancer cell biology. We have undertaken a super-SILAC based quantitative proteomics survey of 42 tissue samples spanning the 4 genomic subgroups of medulloblastoma and control cerebellum. We have identified and quantitated thousands of proteins across these groups and find that we are able to recapitulate the genomic subgroups based upon subgroup restricted and differentially abundant proteins while also identifying one additional subgroup. Employing a custom built RNA-seq based searchable proteome database, we are also able to use peptide sequence data to discover medulloblastoma specific protein isoforms. Adding array gene expression data to this analysis, we calculate a relatively poor correlation between mRNA and protein abundance with the best concordance found among stable proteins. From the quantitative proteomic data, we are able to discern networks of functional pathways with differential activation between the medulloblastoma subgroups and normal control cerebellum yielding potential avenues for clinical intervention. This work demonstrates that quantitative proteomics can further elucidate the biology inherent in a genomically based classification regime.

Background CTCF and BORIS (CTCFL), two paralogous mammalian proteins sharing nearly identical DNA binding domains, are thought to function in a mutually exclusive manner in DNA binding and transcriptional regulation. Results Here we show that these two proteins co-occupy a specific subset of regulatory elements consisting of clustered CTCF binding motifs (termed 2xCTSes). BORIS occupancy at 2xCTSes is largely invariant in BORIS-positive cancer cells, with the genomic pattern recapitulating the germline-specific BORIS binding to chromatin. In contrast to the single-motif CTCF target sites (1xCTSes), the 2xCTS elements are preferentially found at active promoters and enhancers, both in cancer and germ cells. 2xCTSes are also enriched in genomic regions that escape histone to protamine replacement in human and mouse sperm. Depletion of the BORIS gene leads to altered transcription of a large number of genes and the differentiation of K562 cells, while the ectopic expression of this CTCF paralog leads to specific changes in transcription in MCF7 cells. Conclusions We discover two functionally and structurally different classes of CTCF binding regions, 2xCTSes and 1xCTSes, revealed by their predisposition to bind BORIS. We propose that 2xCTSes play key roles in the transcriptional program of cancer and germ cells. Electronic supplementary material The online version of this article (doi:10.1186/s13059-015-0736-8) contains supplementary material, which is available to authorized users.