Proteomic studies of pediatric medulloblastoma tumors with 17p deletion

Unmasking the tumourigenic role of SIN1/MAPKAP1 in the mTOR complex 2

BACKGROUND

Although the PI3K/AKT/mTOR pathway is one of the most altered pathways in human tumours, therapies targeting this pathway have shown numerous adverse effects due to positive feedback paradoxically activating upstream signaling nodes. The somewhat limited clinical efficacy of these inhibitors calls for the development of novel and more effective approaches for targeting the PI3K pathway for therapeutic benefit in cancer.

MAIN BODY

Recent studies have shown the central role of mTOR complex 2 (mTORC2) as a pro-tumourigenic factor of the PI3K/AKT/mTOR pathway in a number of cancers. SIN1/MAPKAP1 is a major partner of mTORC2, acting as a scaffold and responsible for the substrate specificity of the mTOR catalytic subunit. Its overexpression promotes the proliferation, invasion and metastasis of certain cancers whereas its inhibition decreases tumour growth in vitro and in vivo. It is also involved in epithelial-mesenchymal transition, stress response and lipogenesis. Moreover, the numerous interactions of SIN1 inside or outside mTORC2 connect it with other signaling pathways, which are often disrupted in human tumours such as Hippo, WNT, Notch and MAPK.

CONCLUSION

Therefore, SIN1's fundamental characteristics and numerous connexions with oncogenic pathways make it a particularly interesting therapeutic target. This review is an opportunity to highlight the tumourigenic role of SIN1 across many solid cancers and demonstrates the importance of targeting SIN1 with a specific therapy.

Differences in RNA and microRNA Expression Between PTCH1- and SUFU-mutated Medulloblastoma

BACKGROUND/AIM

Germline mutations in PTCH1 or SUFU in the sonic hedgehog (SHH) pathway cause Gorlin's syndrome with increased risk of developing SHH-subgroup medulloblastoma. Gorlin's syndrome precludes the use of radiotherapy (a standard component of treatment) due to the development of multiple basal cell carcinomas. Also, current SHH inhibitors are ineffective against SUFU-mutated medulloblastoma, as they inhibit upstream genes. In this study, we aimed to detect differences in the expression of genes and microRNAs between SUFU- and PTCH1-mutated SHH medulloblastomas which may hint at new treatment directions.

PATIENTS AND METHODS

We sequenced RNA and microRNA from tumors of two patients with germline Gorlin's syndrome - one having PTCH1 mutation and one with SUFU mutation - followed by bioinformatics analysis to detect changes in genes and miRNAs expression in these two tumors. Expression changes were validated using qRT-PCR. Ingenuity pathway analysis was performed in search for targetable pathways.

RESULTS

Compared to the PTCH1 tumor, the SUFU tumor demonstrated lower expression of miR-301a-3p and miR-181c-5p, matrix metallopeptidase 11 (MMP11) and OTX2, higher expression of miR-7-5p and corresponding lower expression of its targeted gene, connexin 30 (GJB6). We propose mechanisms to explain the phenotypic differences between the two types of tumors, and understand why PTCH1 and SUFU tumors tend to relapse locally (rather than metastatically as in other medulloblastoma subgroups).

CONCLUSION

Our results help towards finding new treatable molecular targets for these types of medulloblastomas.

A systematic view of pediatric medulloblastoma proteomics-current state of the field and future directions

Quantitative mass spectrometry (MS)-based approaches have allowed further characterization of medulloblastoma (MB) classification and clinical/biological behavior. By investigating protein expression, as well as the role of post-translational modifications in shaping cellular activity, novel avenues of research will clarify the current subgrouping, providing elements for tumor treatment-new molecular targets and signaling cascades-and introducing serum, urinary, and CSF markers of tumor growth and recurrence. We systematically searched and reviewed original research articles treating MB proteomics on PubMed. Reviews, opinion papers, and abstracts were excluded from the final work. A total of 30 novel articles treating the proteomic characterization of MB were included in our review. Research conducted on tissue samples, cell lines, CSF, and urine, as well as exosome and medullospheres, was considered, to picture a broad view of the different directions MS-based proteomic analysis is moving toward. In this review, we collect, summarize, and interpret the current literature on this topic. Significant progress has been achieved in the last decade in MB characterization, paving the way for further exploration of large biobanks of MB and other tissues that will allow a more systematic understanding of MB functioning and clinical progression.

Proteomics of pediatric ependymomas: a review

Ependymomas, affecting both children and adults, are neuroepithelial tumors occurring throughout all compartments of the central nervous system. Pediatric ependymomas arise almost exclusively intracranially and are associated with a poor 10-year overall survival of around 60%. During the last years, the application of multi-omics technologies on the study and understanding of neuro-cancer diseases has become a standard; in this regard, application of these approaches on ependymomas has gained noticeable momentum. The objective of this review article was to summarize all knowledge generated by the application of modern omics approaches with regard to pediatric ependymal tumors, aiming at elucidating molecular mechanisms of oncogenesis as well as identification of pathway strategies that will help in therapeutic intervention.

Xenograft models for pediatric cancer therapies

The prognosis for childhood cancer has improved considerably over the past 50 years. This improvement is attributed to well-designed clinical trials which have incorporated chemotherapy, surgery, and radiation. With an increased understanding of cancer biology and genetics, we have entered an era of precision medicine and immunotherapy that provides potential for improved cure rates. However, preclinical evaluation of these therapies is more nuanced, requiring more robust animal models. Evaluation of targeted treatments requires molecularly defined xenograft models that can capture the diversity within pediatric cancer. The development of novel immunotherapies ideally involves the use of animal models that can accurately recapitulate the human immune response. In this review, we provide an overview of xenograft models for childhood cancers, review successful examples of novel therapies translated from xenograft models to the clinic, and describe the modern tools of xenograft biobanks and humanized xenograft models for the study of immunotherapies.

Urinary protein biomarkers for pediatric medulloblastoma

OBJECTIVE

To identify candidate urinary protein biomarkers to distinguish medulloblastoma (MB) patients from healthy patients or benign brain disease control patients.

METHODS

The tandem mass tag (TMT)-labeled quantitative proteomics approach was used to identify differential proteins in the urinary proteome of 9 pre- and postsurgery MB patients and 9 healthy control patients, respectively. Ingenuity pathway analysis was used for functional annotation of differential proteins. The biomarker candidates were validated by the parallel reaction monitoring (PRM) method in 112 samples (29 pre- and postsurgery MB patients, 26 healthy control patients, and 28 benign brain disease control patients). Receiver operating characteristic (ROC) curves were developed to evaluate candidate biomarkers.

RESULTS

A total of 114 differential proteins were found. Bioinformatic analysis revealed that the urinary proteome could reflect changes in MB. Seventeen candidate biomarkers were validated by PRM. The combination of CADH1, FGFR4 and FIBB could be used to discriminate MB patients from healthy control patients with an area under the curve (AUC) of 0.973, and the combination of CADH1 and FIBB showed good discriminative power for differentiating MB from benign brain disease with an AUC of 0.884.

CONCLUSION

This report describes the first application of a TMT-PRM workflow to identify and validate MB-specific biomarkers in urine. These findings might contribute to the application of urinary proteomics for detecting and monitoring MB.

BIOLOGICAL SIGNIFICANCE

Medulloblastoma (MB) is among the most common pediatric brain malignancies. This tumor has a highly aggressive clinical course with a high tendency for relapses. Magnetic resonance imaging (MRI) is the major means of diagnosis and for radiographic surveillance after surgery. In MRI, sedation is often required in young children, which could expose them to a series of risks, including airway obstruction and even death. Aside from MRI, there is no reliable biomarker for clinical screening or monitoring of the disease. These facts introduce the clinical need of noninvasive biomarkers for early screening or monitoring of MB. This study is focused on the investigation of a marker panel based on urinary proteome, as a tool for the detection of MB in selected patients at risk. Upon evaluation of the marker model in an independent blinded set of 112 samples, the panel (CADH1, FGFR4 and FIBB) could be used to discriminate MB patients from healthy control patients with an area under the curve (AUC) of 0.973, and the combination of CADH1 and FIBB showed good discriminative power for differentiating MB from benign brain disease with an AUC of 0.884.

Salvage Re-irradiation Options in Adult Medulloblastoma: A Case Report and Review of the Literature

BACKGROUND/AIM

Medulloblastoma is a rare tumor of adult age, while it occurs more frequently in children. Given the rarity, there is a lack of evidence for the treatment of recurrent disease. Few data are available about salvage re-irradiation collecting very heterogeneous series.

CASE REPORT

A 51-year-old male presented with headache, nausea, double vision, and gait disorders. A contrast-enhanced brain-MRI showed the presence of multifocal medulloblastoma. After surgery, adjuvant craniospinal radiotherapy was performed, chemotherapy was stopped due to toxicity. After 27 months, a new MRI and a Methionine-PET revealed a late pontocerebellar relapse; multidisciplinary board decided for a SBRT treatment. The second course of RT was well tolerated and 14 months later, the patient is alive in good general conditions, with no evidence of disease.

CONCLUSION

Our experience supports the use of salvage stereotactic radiotherapy as a safe and effective treatment option.

Identification of Two Protein-Signaling States Delineating Transcriptionally Heterogeneous Human Medulloblastoma

The brain cancer medulloblastoma consists of different transcriptional subgroups. To characterize medulloblastoma at the phosphoprotein-signaling level, we performed high-throughput peptide phosphorylation profiling on a large cohort of SHH (Sonic Hedgehog), group 3, and group 4 medulloblastomas. We identified two major protein-signaling profiles. One profile was associated with rapid death post-recurrence and resembled MYC-like signaling for which MYC lesions are sufficient but not necessary. The second profile showed enrichment for DNA damage, as well as apoptotic and neuronal signaling. Integrative analysis demonstrated that heterogeneous transcriptional input converges on these protein-signaling profiles: all SHH and a subset of group 3 patients exhibited the MYC-like protein-signaling profile; the majority of the other group 3 subset and group 4 patients displayed the DNA damage/apoptotic/neuronal signaling profile. Functional analysis of enriched pathways highlighted cell-cycle progression and protein synthesis as therapeutic targets for MYC-like medulloblastoma.

Differential quantitative proteomics study of experimental Mannheimia haemolytica mastitis in sheep

Objective was the differential quantitative proteomics study of ovine mastitis induced by Mannheimia haemolytica; clinical, microbiological, cytological and histopathological methods were employed for confirmation and monitoring. Proteins were separated by two-dimensional gel electrophoresis (2-DE) for all samples and differentially abundant proteins were identified by mass spectrometry; comparisons were performed with pre- (blood, milk) and post- (milk of contralateral gland) inoculation findings. Animals developed mastitis, confirmed by isolation of challenge strain and increase of neutrophils in milk and by histopathological evidence. In blood plasma, 33 differentially abundant proteins (compared to findings before challenge) were identified: 6 with decrease, 13 with new appearance and 14 with varying abundance. In a post-challenge milk whey protein reference map, 65 proteins were identified; actin cytoplasmic-1, beta-lactoglobulin-1/B, cathelicidin-1 predominated. Further, 89 differentially abundant proteins (compared to findings before challenge) were identified: 18 with decrease, 53 with new appearance, 3 with increase and 15 with varying abundance; 15 proteins showed status changes in blood plasma and milk whey. Differential abundance from inoculated and contralateral glands revealed 74 proteins only from the inoculated gland. Most differentially abundant proteins in milk whey were involved in cell organisation and biogenesis (n = 17) or in inflammatory and defence response (n = 13). SIGNIFICANCE: The proteomes of blood and milk from ewes with experimental mastitis caused by Mannheimia haemolytica and the differential proteomics in sequential samples after challenge are presented for the first time. This is the first detailed proteomics study in M. haemolytica-associated mastitis in ewes. An experimental model fully simulating natural mastitis has been used. Use of experimentally induced mastitis minimised potential variations and allowed consistency of results. The study included evaluation of changes in blood plasma and milk whey. Protein patterns have been studied, indicating with great accuracy changes that had occurred as part of the disease process and development, during the acute phase of infection. Relevant protein-protein interactions were studied. The entirety of proteomics findings has suggested that affected ewes had mounted a defence response that had been regulated by many proteins (e.g., cathelicidins, haptoglobin, serum amyloid A) and through various pathways (e.g., acute phase response, binding and transporting significant ions and molecules); these were interdependent at various points. Potential biomarkers have been indicated for use in diagnostic assays of mastitis.

Proteomic analysis of cerebrospinal fluid from children with central nervous system tumors identifies candidate proteins relating to tumor metastatic spread

Central nervous system (CNS) tumors are the most common solid tumors in childhood. Since the sensitivity of combined cerebrospinal fluid (CSF) cytology and radiological neuroimaging in detecting meningeal metastases remains relatively low, we sought to characterize the CSF proteome of patients with CSF tumors to identify biomarkers predictive of metastatic spread. CSF samples from 27 children with brain tumors and 13 controls (extra-CNS non-Hodgkin lymphoma) were processed using core-shell hydrogel nanoparticles, and analyzed with reverse-phase liquid chromatography/electrospray tandem mass spectrometry (LC-MS/MS). Candidate proteins were identified with Fisher's exact test and/or a univariate logistic regression model. Reverse phase protein array (RPPA), Western blot (WB), and ELISA were used in the training set and in an independent set of CFS samples (60 cases, 14 controls) to validate our discovery findings. Among the 558 non-redundant proteins identified by LC-MS/MS, 147 were missing from the CSF database at http://www.biosino.org. Fourteen of the 26 final top-candidate proteins were chosen for validation with WB, RPPA and ELISA methods. Six proteins (type 1 collagen, insulin-like growth factor binding protein 4, procollagen C-endopeptidase enhancer 1, glial cell-line derived neurotrophic factor receptor α2, inter-alpha-trypsin inhibitor heavy chain 4, neural proliferation and differentiation control protein-1) revealed the ability to discriminate metastatic cases from controls. Combining a unique dataset of CSFs from pediatric CNS tumors with a novel enabling nanotechnology led us to identify CSF proteins potentially related to metastatic status.

Pediatric brain tumors: Update of proteome-based studies

Pediatric brain tumors (PBTs) are the most common solid malignancies in childhood and continue to pose a serious burden to modern societies. Existing treatments impose debilitating effects on the developing child, highlighting the need for molecularly targeted treatments with reduced toxicity, as well as the necessity of markers that reliably assess efficacy of, and tumor response to targeted-therapies of PBTs. On this regard advances in technologies of protein identification and quantification, the large-scale, high-throughput investigation of the proteome, as well the newly-emerging field of "proteogenomics" aim to further our knowledge towards understanding the molecular pathophysiology of PBTs. This mini review article presents all updates on knowledge produced and published during the last years on PBT research derived from "omics" technologies, mainly involving protein research and proteomics.

Molecular Proteomic Characterization of a Pediatric Medulloblastoma Xenograft

BACKGROUND/AIM

Medulloblastoma (MBL), an archetypal primitive neuroectodermal tumor of the cerebellum, is the most common pediatric central nervous system malignancy representing approximately 20% of all childhood brain tumors. Herein, we report on a new xenotransplantable tumor cell line, derived from a 6-year-old female patient with cerebellar medulloblastoma, and the completele proteome molecular characterization of subsequent tumors from MBL xenotrasplanted mice.

MATERIALS AND METHODS

Tumors were grown in nude mice as subcutaneous xenografts (MBLX) composed of small round cells with hyperchromatic nuclei and scant cytoplasm. Tumor specimen were extracted from animals upon their sacrifice and their molecular proteomic content was analyzed by 2-DE coupled to MALDI-TOF MS analysis.

RESULTS

Altogether 350 single-gene products were identified through the current approach, reported as the MBLX database.

CONCLUSION

This new xenotransplantable tumor model, offers the scientific community valuable insight on the validity of xenografts altogether, while providing the means for a novel experimental model towards the study of human MBL.

Pediatric Ependymoma: A Proteomics Perspective

BACKGROUND/AIM

Proteomics based on high-resolution mass spectrometry (MS) is the tool of choice for the analysis of protein presence, modifications and interactions, with increasing emphasis on the examination of tumor tissues. Application of MS-based proteomics offers a detailed picture of tumor tissue characteristics, facilitating the appreciation of different tumor entities, whilst providing reliable and fast results for therapeutic marker targeting and prognostic factor assessment. Through use of the high analytical resolution of nano-high-pressure liquid chromatography (nanoHPLC) and the high resolution of an Orbitrap Elite mass spectrometer, the present study aimed to provide knowledge on the proteome of the generally unknown entity of pediatric ependymal tumors.

MATERIALS AND METHODS

Ten resected specimens of childhood ependymoma were analyzed through a one-dimensional (1D) nanoLC-MS/MS approach. Method optimization steps were undertaken for both the sample preparation/protein extraction procedure and LC parameters, aiming to achieve the highest possible identification rates.

RESULTS

Following method optimization, each nanoLC-MS/MS run resulted in identification of more than 5,000 proteins and more than 25,000 peptides for every analyzed sample, thus detailing the greater part of the ependymoma proteome. Identified proteins were found to spread throughout all known tumor categories regarding their molecular function and subcellular localization.

CONCLUSION

Through the proposed nanoLC-MS/MS method herein we report, for the firs time, the ependymoma proteome database. A large number of similarities regarding proteome content are revealed compared to other two pediatric brain tumor entities; astrocytomas and medulloblastomas. Furthermore, through our approach, the majority of currently proposed markers for ependymoma (e.g. nucleolin, nestin, Ki67 and laminin subunit A2) as well as all major key players of the phosphoinositide 3-kinase pathway (seemingly implicated in ependymoma), were definitely detected.

The ubiquitin-proteasome system and chromosome 17 in cerebellar granule cells and medulloblastoma subgroups

Chromosome 17 abnormalities are often observed in medulloblastomas (MBs), particularly those classified in the consensus Groups 3 and 4. Herein we review MB signature genes associated with chromosome 17 and the relationship of these signature genes to the ubiquitin-proteasome system. While clinical investigators have not focused on the ubiquitin-proteasome system in relation to MB, a substantial amount of data on the topic has been hidden in the form of supplemental datasets of gene expression. A supplemental dataset associated with the Thompson classification of MBs shows that a subgroup of MB with 17p deletions is characterized by reduced expression of genes for several core particle subunits of the beta ring of the proteasome (β1, β4, β5, β7). One of these genes (PSMB6, the gene for the β1 subunit) is located on chromosome 17, near the telomeric end of 17p. By comparison, in the WNT group of MBs only one core proteasome subunit, β6, associated with loss of a gene (PSMB1) on chromosome 6, was down-regulated in this dataset. The MB subgroups with the worst prognosis have a significant association with chromosome 17 abnormalities and irregularities of APC/C cyclosome genes. We conclude that the expression of proteasome subunit genes and genes for ubiquitin ligases can contribute to prognostic classification of MBs. The therapeutic value of targeting proteasome subunits and ubiquitin ligases in the various subgroups of MB remains to be determined separately for each classification of MB.

A Proteogenomic Approach to Understanding MYC Function in Metastatic Medulloblastoma Tumors

Brain tumors are the leading cause of cancer-related deaths in children, and medulloblastoma is the most prevalent malignant childhood/pediatric brain tumor. Providing effective treatment for these cancers, with minimal damage to the still-developing brain, remains one of the greatest challenges faced by clinicians. Understanding the diverse events driving tumor formation, maintenance, progression, and recurrence is necessary for identifying novel targeted therapeutics and improving survival of patients with this disease. Genomic copy number alteration data, together with clinical studies, identifies c-MYC amplification as an important risk factor associated with the most aggressive forms of medulloblastoma with marked metastatic potential. Yet despite this, very little is known regarding the impact of such genomic abnormalities upon the functional biology of the tumor cell. We discuss here how recent advances in quantitative proteomic techniques are now providing new insights into the functional biology of these aggressive tumors, as illustrated by the use of proteomics to bridge the gap between the genotype and phenotype in the case of c-MYC-amplified/associated medulloblastoma. These integrated proteogenomic approaches now provide a new platform for understanding cancer biology by providing a functional context to frame genomic abnormalities.

The effect of experimental osteoporosis on bone regeneration: part 2, proteomics results

OBJECTIVES

To identify and describe protein expression in a Wistar rat calvarial critical size defect (CSD) model following treatment with guided bone regeneration in healthy and osteoporotic conditions.

MATERIAL AND METHODS

Thirty-six 10-month-old female Wistar rats were used. Half of them were ovariectomized (OVX) and fed with a low-calcium diet to induce an osteoporotic-like status. In each animal of both groups, two 5-mm calvarial CSDs were treated with deproteinized bovine bone mineral graft particles and a bilayer collagen membrane. Six OVX and six control rats were randomly euthanized at 7, 14, and 30 days. One defect/animal was randomly chosen for proteomic analysis. Differently expressed proteins between the two groups were identified with matrix-assisted laser desorption time-of-flight mass spectrometry and liquid chromatography-mass spectrometry/mass spectrometry.

RESULTS

At 7 days, 29 and 27 proteins were, respectively, identified in the healthy and OVX animals. At 14 days, 103 proteins were detected in the healthy controls and 20 proteins in the OVX rats, while at 30 days, 31 and 75 proteins were identified, respectively. Only limited proteins known to play a role in the later stages of bone formation and maturation were identified within the animals 'proteomes.

DISCUSSION

The osseous formation process was quite immature even at 30 days of healing. An overexpression of inflammatory and stress response pathways was detected in the OVX animals, as well as a tendency toward a delayed maturation of the osseous wound and a reduced/delayed differentiation of osteoblast cell precursors.

Milk of Greek sheep and goat breeds; characterization by means of proteomics

Over the past 30years there has been a growing interest to unravel the dynamic framework of the milk proteome, and now that available technology is mature enough to enable techniques of protein fractionation and identification, this process is on-going. Due to its rarity and unique biological traits, as well as its growing financial value, milk of dairy Greek animals is continuously attracting interest from both the scientific community and industry. In the present study we employed cutting-edge proteomics methodologies to investigate and characterize, in depth, the proteome of whey from all pure-breed Greek sheep and goats. A mean of >500 protein groups were identified in whey from each breed of each animal species, reporting for the first time the proteome dataset of this precious biological material. Given its high nutritional value, the protein properties exposed herein will govern future steps in optimizing characteristics and features of sheep and goat milk products.

SIGNIFICANCE

In the present study we employed cutting-edge proteomics methodologies to investigate and characterize, in depth, the proteome of milk from all pure-breed Greek sheep and goats. A mean of >500 protein groups were identified in milk whey from each breed of each animal species, reporting for the first time the proteome dataset of this precious biological material. Given its high nutritional value, the protein properties exposed herein will govern future steps in optimizing characteristics and features of sheep and goat milk products.

Top-down proteomic characterization of DAOY medulloblastoma tumor cell line

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DAOY cells have been analyzed by top-down LC-high resolution-MS proteomic platform.

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New protein identifications in medulloblastoma cells are reported.

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PTMs, isoforms and naturally occurring peptide fragments were identified.

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Most of the identified proteins were connected in a biological interacting network.

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The data contribute to the further molecular characterization of medulloblastoma.

The proteome of the DAOY medulloblastoma cell line has been investigated by an LC–MS top-down platform. This approach, unlike bottom-up ones, allows identifying proteins and peptides in their intact/native forms, disclosing post-translational modifications, proteoforms and naturally occurring peptides. Indeed, 25 out of the 53 proteins identified, were not previously characterized in DAOY cells. Most of them were functionally interconnected, being mainly involved in binding, catalytic and structural activities, and metabolic processes. The top-down approach, applied in this preliminary study, disclosed the presence of several naturally occurring peptide fragments that characterize DAOY cells.