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  • 1
    In: OncoImmunology, Informa UK Limited, Vol. 5, No. 12 ( 2016-12), p. e1221556-
    Type of Medium: Online Resource
    ISSN: 2162-402X
    Language: English
    Publisher: Informa UK Limited
    Publication Date: 2016
    detail.hit.zdb_id: 2645309-5
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  • 2
    In: Diagnosis, Walter de Gruyter GmbH, Vol. 9, No. 1 ( 2022-02-01), p. 115-122
    Abstract: The Next Generation Sequencing (NGS) based mutational study of hereditary cancer genes is crucial to design tailored prevention strategies in subjects with different hereditary cancer risk. The ease of amplicon-based NGS library construction protocols contrasts with the greater uniformity of enrichment provided by capture-based protocols and so with greater chances for detecting larger genomic rearrangements and copy-number variations. Capture-based protocols, however, are characterized by a higher level of complexity of sample handling, extremely susceptible to human bias. Robotics platforms may definitely help dealing with these limits, reducing hands-on time, limiting random errors and guaranteeing process standardization. Methods We implemented the automation of the CE-IVD SOPHiA Hereditary Cancer Solution™ (HCS) libraries preparation workflow by SOPHiA GENETICS on the Hamilton’s STARlet platform. We present the comparison of results between this automated approach, used for more than 1,000 DNA patients’ samples, and the performances of the manual protocol evaluated by SOPHiA GENETICS onto 240 samples summarized in their HCS evaluation study. Results We demonstrate that this automated workflow achieved the same expected goals of manual setup in terms of coverages and reads uniformity, with extremely lower standard deviations among samples considering the sequencing reads mapped onto the regions of interest. Conclusions This automated solution offers same reliable and affordable NGS data, but with the essential advantages of a flexible, automated and integrated framework, minimizing possible human errors and depicting a laboratory’s walk-away scenario.
    Type of Medium: Online Resource
    ISSN: 2194-8011 , 2194-802X
    Language: English
    Publisher: Walter de Gruyter GmbH
    Publication Date: 2022
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  • 3
    In: Journal of Clinical Pathology, BMJ, Vol. 74, No. 10 ( 2021-10), p. 668-672
    Abstract: BRCA tumour testing is a crucial tool for personalised therapy of patients with ovarian cancer. Since different next-generation sequencing (NGS) platforms and BRCA panels are available, the NGS Italian Network proposed to assess the robustness of different technologies. Methods Six centres, using four different technologies, provided raw data of 284 cases, including 75 cases with pathogenic/likely pathogenic variants, for a revision blindly performed by an external bioinformatic platform. Results The third-party revision assessed that all the 284 raw data reached good quality parameters. The variant calling analysis confirmed all the 75 pathogenic/likely pathogenic variants, including challenging variants, achieving a concordance rate of 100% regardless of the panel, instrument and bioinformatic pipeline adopted. No additional variants were identified in the reanalysis of a subset of 41 cases. Conclusions BRCA tumour testing performed with different technologies in different centres, may achieve the realibility and reproducibility required for clinical diagnostic procedures.
    Type of Medium: Online Resource
    ISSN: 0021-9746 , 1472-4146
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    Language: English
    Publisher: BMJ
    Publication Date: 2021
    detail.hit.zdb_id: 2028928-5
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  • 4
    In: Proceedings of the National Academy of Sciences, Proceedings of the National Academy of Sciences, Vol. 109, No. 47 ( 2012-11-20), p. 19280-19285
    Abstract: Human mena (hMENA), a member of the actin cytoskeleton regulators Ena/VASP, is overexpressed in high-risk preneoplastic lesions and in primary breast tumors and has been identified as playing a role in invasiveness and poor prognosis in breast cancers that express HER2. Here we identify a unique isoform, hMENAΔv6, derived from the hMENA alternative splicing program. In an isogenic model of human breast cancer progression, we show that hMENA 11a is expressed in premalignant cells, whereas hMENAΔv6 expression is restricted to invasive cancer cells. “Reversion” of the malignant phenotype leads to concurrent down-regulation of all hMENA isoforms. In breast cancer cell lines, isoform-specific hMENA overexpression or knockdown revealed that in the absence of hMENA 11a , overexpression of hMENAΔv6 increased cell invasion, whereas overexpression of hMENA 11a reduced the migratory and invasive ability of these cells. hMENA 11a splicing was shown to be dependent on the epithelial regulator of splicing 1 (ESRP1), and forced expression of ESRP1 in invasive mesenchymal breast cancer cells caused a phenotypic switch reminiscent of a mesenchymal-to-epithelial transition (MET) characterized by changes in the cytoskeletal architecture, reexpression of hMENA 11a , and a reduction in cell invasion. hMENA-positive primary breast tumors, which are hMENA 11a -negative, are more frequently E-cadherin low in comparison with tumors expressing hMENA 11a . These data suggest that polarized and growth-arrested cellular architecture correlates with absence of alternative hMENA isoform expression, and that the hMENA splicing program is relevant to malignant progression in invasive disease.
    Type of Medium: Online Resource
    ISSN: 0027-8424 , 1091-6490
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    Language: English
    Publisher: Proceedings of the National Academy of Sciences
    Publication Date: 2012
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    detail.hit.zdb_id: 1461794-8
    SSG: 11
    SSG: 12
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  • 5
    In: Cancer Research, American Association for Cancer Research (AACR), Vol. 74, No. 19_Supplement ( 2014-10-01), p. 1035-1035
    Abstract: Background Epithelial to mesenchymal transition (EMT) is an early event in pancreatic cancer and has been involved in cancer invasiveness. An intense stromal reaction, peculiar to the pancreatic tumor microenvironment, includes cancer-associated fibroblasts(CAFs), abundant cells in the tumor stroma, recently linked to the induction of EMT. On the other hand, the EMT process requires a dynamic remodeling of the actin cytoskeleton, and the splicing program of hMENA, a regulator of actin, has been associated with the EMT process. We have described two alternatively expressed isoforms, hMENA11a and hMENAΔv6, with opposite functions in invasiveness in breast cancer (1). hMENA expression was detected in human pancreatic ductal adenocarcinoma samples (PDAC) (2), but no data are available on the alternative isoform expression in this neoplasia. The aim of this study is to investigate the role of hMENA splicing in TGF-β -mediated EMT in pancreatic cancer, the mechanisms involved in hMENA induction in PDAC and the role of CAFs in this process. Methods hMENA isoform expression was evaluated in PDAC tissues by immunohistochemistry using isoform-specific antibodies. Human PDAC cell lines, untreated or TGF-β treated, were characterized for the expression of hMENA isoforms and markers of EMT by qRT-PCR and WB analysis. The effects of both hMENAΔv6 knockdown or overexpression were also evaluated. Pancreatic cancer associated-fibroblasts were isolated from primary PDAC tissues. To study the role of fibroblast-cancer cell interactions on hMENA expression, a noncontact coculture system was used. Results IHC analysis of PDAC tissues revealed that epithelial hMENA11a is rarely expressed in primary pancreatic tumors that express a high level of hMENA and hMENAΔv6 isoforms. In a panel of pancreatic cancer cell lines, hMENA11a expression correlates with an epithelial phenotype, wherea hMENAΔv6 expression is associated with a mesechymal phenotype. TGF-β treatment specifically upregulated the invasive hMENAΔv6 isoform expression. Knockdown of endogenous hMENA/hMENAΔv6 isoform reduced cell invasiveness, reverted cells to an epithelial -“like” phenotype with an increased E-cadherin expression and impaired the TGF-β-mediated vimentin up-regulation. Conversely, overexpression of hMENAΔv6 increased the expression of the mesenchymal marker vimentin. Freshly explanted CAFs expressed the “mesenchymal” hMENAΔv6, and not hMENA11a and produced paracrine factors involved in the induction of hMENA isoforms in tumor cells. Conclusions These data provide new and critical insights into the role of hMENA splicing in TGF-β mediated EMT and identify the hMENA splicing program as a promising pathway for the development of new diagnostics and therapeutics in PDAC. (1) Di Modugno F. et al PNAS 2012 (2) Pino S. et al Clin Cancer Res 2008 Citation Format: Roberta Melchionna, Pierluigi Iapicca, Francesca Di Modugno, Paola Trono, Novella Gualtieri, Maria Grazia Diodoro, Sheila Spada, Giuliana Falasca, Gian Luca Grazi, Mina J Bissell, Paola Nisticò. hMENA splicing program and TGF-β1-mediated EMT in pancreatic cancer. [abstract]. In: Proceedings of the 105th Annual Meeting of the American Association for Cancer Research; 2014 Apr 5-9; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2014;74(19 Suppl):Abstract nr 1035. doi:10.1158/1538-7445.AM2014-1035
    Type of Medium: Online Resource
    ISSN: 0008-5472 , 1538-7445
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    Language: English
    Publisher: American Association for Cancer Research (AACR)
    Publication Date: 2014
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  • 6
    In: Cancer Research, American Association for Cancer Research (AACR), Vol. 78, No. 13_Supplement ( 2018-07-01), p. 5224-5224
    Abstract: The splicing of the actin regulator hMENA generates different isoforms and we have demonstrated that the two alternatively expressed isoforms, hMENA11a and hMENAΔv6, have opposite functions in cell invasiveness. This general mechanism is of great clinical relevance in early NSCLC patients, where the pattern of hMENA isoform expression is a powerful prognostic factor. However the mechanism of action of the two isoforms have remained unclear. Herein, we evaluated whether hMENA and its isoforms influence β1 integrin expression and signaling considering the role of this integrin in cancer cell invasiveness and tumor progression. We performed hMENA silencing by siRNA and shRNA, to evaluate by QRT-PCR and biochemical approaches the expression of β1 integrin; by immunofluorescence the MRTF1 localization, by in vivo assay G-Actin/F-Actin ratio and by luciferase reporter assay the SRF activity. β1 integrin activation and signaling was evaluated by flow cytometry using an antibody specific for the β1 active conformation and by biochemical analysis of the phosphorylation of FAK, SRC and Paxillin. The secretoma of hMENA11a transfected cancer cell lines was analyzed by LC-MS/MS. Immunohistochemical analysis was performed using pan-hMENA, hMENA11a, and fibronectin antibodies in primary cancer tissues from node negative NSCLC patients. The Chi-Square or Fisher Exact tests were used to estimate associations among categorical variables and disease-free survival was calculated by the Kaplan-Meier product limit method. We show that the depletion of all hMENA isoforms inhibits the Serum Response Factor (SRF) activity, and the expression of its target gene β1 Integrin, by affecting G-Actin/F-Actin ratio, critical for the nuclear localization of the SRF co-factor myocardin related transcription factor 1 (MRTF1). Furthermore, we provide new insights into the mechanisms involved in the opposite functions of hMENA11a and hMENAΔv6 in cell invasiveness and we identify a new role of these isoforms in the β1 integrin-ECM signalling axis. Indeed, hMENAΔv6-drives cancer cell invasion by increasing β1 integrin activation and signalling, which is reduced by the anti-invasive hMENA11a isoform. Moreover, exogenous expression of hMENA11a in hMENAΔv6 positive cancer cells dramatically reduces secretion of extracellular matrix (ECM) components, including β1 integrin ligands and metalloproteinases. On the other hand overexpression of the pro-invasive hMENAΔv6 increases fibronectin production. In primary tumors high hMENA11a correlates with low stromal fibronectin and favorable clinical outcome of early node-negative non-small cell lung cancer patients. This newly discovered signature, which pays attention to the alternative splicing of hMENA and ECM components such as fibronectin in the stroma, might help fill in the gap in the still controversial clinical management of early node-negative NSCLC patients. Citation Format: Francesca Di Modugno, Sheila Spada, Belinda Palermo, Paolo Visca, Pierluigi Iapicca, Anna Di Carlo, Barbara Antoniani, Isabella Sperduti, Anna Di Benedetto, Irene Terrenato, Marcella Mottolese, Francesco Gandolfi, Francesco Facciolo, Emily Chen, Martin A. Schwartz, Angela Santoni, Mina J. Bissell, Paola Nisticò. hMENA isoforms impact NSCLC patient outcome through fibronectin/β1 integrin axis [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 5224.
    Type of Medium: Online Resource
    ISSN: 0008-5472 , 1538-7445
    RVK:
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    Language: English
    Publisher: American Association for Cancer Research (AACR)
    Publication Date: 2018
    detail.hit.zdb_id: 2036785-5
    detail.hit.zdb_id: 1432-1
    detail.hit.zdb_id: 410466-3
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  • 7
    In: Cancer Research, American Association for Cancer Research (AACR), Vol. 75, No. 13_Supplement ( 2015-07-01), p. A60-A60
    Abstract: Background: The pancreatic ductal adenocarcinoma tumor microenvironment plays an important role in promoting the epithelial to mesenchymal transition (EMT), an early event in pancreatic cancer, involved in cancer invasiveness and in tumor progression. Among the stromal components the cancer-associated fibroblasts (CAFs) are responsible for the peculiar pancreatic tumor microenvironment and are known to be linked to the induction of EMT. The EMT process requires a dynamic remodeling of the actin cytoskeleton and we have suggested that the splicing program of hMENA, an actin regulator, play a role in EMT. Two alternatively expressed isoforms, hMENA11a and hMENAΔv6, with opposite functions in invasiveness have been described in breast cancer (Di Modugno et al PNAS 2012). hMENA expression has not been detected in normal pancreatic ducts, whereas expressed in the human pancreatic ductal adenocarcinoma (PDAC) samples, but no data are available on hMENA alternative isoform expression in this neoplasia. The aim of this study is to investigate whether TGFβ1-mediated EMT in pancreatic cancer cells is affected by hMENA overexpression and splicing and how CAFs affect this process in cancer cell lines and in human tissues. Methods: hMENA isoform expression was evaluated in PDAC tissues by immunohistochemistry using isoform specific antibodies. hMENA isoforms and EMT markers expression were characterized in human PDAC cell lines, TGFβ1-treated or untreated, by qRT-PCR and WB analysis. The effects of either hMENA isoform specific knockdown or overexpression in the TGFβ1-induced EMT were also evaluated. Pancreatic CAFs were isolated from human tissues of resected PDAC patients. The effect of the conditioned medium of cultured CAFs was evaluated on hMENA expression. In parallel, the role of CAF-cancer cell interaction on the expression of the different hMENA isoforms was analysed using a co-culture system. Results: Freshly explanted CAFs expressed the “mesenchymal” hMENAΔv6, and not hMENA11a and secreted paracrine factors involved in the induction of hMENA isoforms in tumor cells. In a panel of pancreatic cancer cell lines, hMENA11a expression correlated with an epithelial phenotype, while hMENAΔv6 expression was correlated with a mesenchymal phenotype. Interestingly, the expression of the invasive hMENAΔv6 isoform is specifically up-regulated by TGFβ1 treatment. hMENA isoform expression levels influenced molecular changes induced by TGFβ1. Thus, the hMENA11a specific silencing led to E-cadherin down-regulation that is more evident in TGFβ1 treated cells. On the contrary, hMENA11a overexpression led to a reduction of vimentin expression and to E-cadherin up-regulation. Knockdown of the endogenous hMENA/hMENAΔv6 isoform expression prevented the activation of TGFβ1 signaling and up-regulation of mesenchymal markers. In addition, hMENA/hMENAΔv6 isoform depletion impaired the TGFβ1-induced invasiveness, migration and production of MMPs. IHC analysis of PDAC tissues revealed that the epithelial hMENA11a is rarely expressed in primary pancreatic tumour, while high levels of hMENA and hMENAΔv6 isoforms were found in 75% of primary tumours analysed. Conclusions: This data suggests that the lack of the epithelial hMENA11a isoform is an early event in pancreatic cancer, provides new insights into the role of hMENA splicing in TGFβ1-mediated EMT and highlights hMENA splicing program as an attractive pathway for the development of new therapies in PDAC. Citation Format: Roberta Melchionna, Pierluigi Iapicca, Francesca Di Modugno, Paola Trono, Novella Gualtieri, Maria Grazia Diodoro, Marcella Mottolese, Gian Luca Grazi, Matteo Fassan, Aldo Scarpa, Mina J. Bissell, Paola Nisticò. The hMENA Splicing Program: An important regulator of TGFβ1-driven EMT and invasiveness in pancreatic cancer. [abstract]. In: Proceedings of the AACR Special Conference on Pancreatic Cancer: Innovations in Research and Treatment; May 18-21, 2014; New Orleans, LA. Philadelphia (PA): AACR; Cancer Res 2015;75(13 Suppl):Abstract nr A60.
    Type of Medium: Online Resource
    ISSN: 0008-5472 , 1538-7445
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    Language: English
    Publisher: American Association for Cancer Research (AACR)
    Publication Date: 2015
    detail.hit.zdb_id: 2036785-5
    detail.hit.zdb_id: 1432-1
    detail.hit.zdb_id: 410466-3
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  • 8
    In: Genes, MDPI AG, Vol. 11, No. 12 ( 2020-12-18), p. 1519-
    Abstract: Congenital myasthenic syndromes (CMSs) are caused by mutations in genes that encode proteins involved in the organization, maintenance, function, or modification of the neuromuscular junction. Among these, the collagenic tail of endplate acetylcholinesterase protein (COLQ; MIM 603033) has a crucial role in anchoring the enzyme into the synaptic basal lamina. Here, we report on the first case of a patient with a homozygous deletion affecting the last exons of the COLQ gene in a CMS patient born to consanguineous parents of Pakistani origin. Electromyography (EMG), electroencephalography (EEG), clinical exome sequencing (CES), and single nucleotide polymorphism (SNP) array analyses were performed. The subject was born at term after an uneventful pregnancy and developed significant hypotonia and dystonia, clinical pseudoseizures, and recurring respiratory insufficiency with a need for mechanical ventilation. CES analysis of the patient revealed a homozygous deletion of the COLQ gene located on the 3p25.1 chromosome region. The SNP-array confirmed the presence of deletion that extended from exon 11 to the last exon 17 with a size of 19.5 Kb. Our results add new insights about the underlying pathogenetic mechanisms expanding the spectrum of causative COLQ mutations. It is relevant, considering the therapeutic implications, to apply suitable molecular approaches so that no type of mutation is missed: “each lost mutation means a baby treated improperly”.
    Type of Medium: Online Resource
    ISSN: 2073-4425
    Language: English
    Publisher: MDPI AG
    Publication Date: 2020
    detail.hit.zdb_id: 2527218-4
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  • 9
    In: Cancer Immunology Research, American Association for Cancer Research (AACR), Vol. 4, No. 11_Supplement ( 2016-11-01), p. A113-A113
    Abstract: Background: Pancreatic ductal adenocarcinoma (PDAC) is an aggressive disease with the worst survival rate among solid cancers. The pressing needs for extending life expectancy of patients are the identification of early prognostic markers and novel druggable pathways. PDAC arises generally from pancreatic intraepithelial neoplasia (PanIN) and a dynamic interactions between tumor, stromal cells and autocrine and paracrine signaling lead to epithelial to mesenchymal transition (EMT), an early process in the natural history of pancreatic cancer. Cytoskeletal reorganization, extracellular matrix (ECM) remodeling, and matrix metalloproteinases (MMPs) contribute to PDAC aggressiveness in cooperation with soluble growth factors or cytokines, with TGF-β1 as crucial player. hMENA is an actin regulatory protein whose splicing program, mediated by the epithelial splicing regulatory proteins (ESRPs), has been associated with the EMT process. Our previous studies indicated that alternative splicing of hMENA, generates hMENA11a and hMENAΔv6 isoforms with opposite roles in cell proliferation and invasion in breast and lung cancers. Alternative splicing is known to play a prominent role in tumor progression and tumorigenesis and the derived isoforms may represent powerful diagnostic and prognostic factors as we have recently shown for hMENA alternative splicing in early stage non-small cell lung cancer (NSCLC). The aim of this study is to investigate the role of TGF-β1 on the expression and function of hMENA isoforms in PDAC, and verify whether the expression pattern of hMENA isoforms may impact patient outcome. Methods: We analyzed the expression pattern of hMENA isoforms by immunohistochemistry, using anti-pan hMENA and specific anti-hMENA11a antibodies, in 285 PDACs, 15 PanINs, 10 pancreatitis, and normal pancreas, evaluating the patient outcome. The functional role of hMENA isoforms were analyzed by loss and gain of function experiments in untreated and TGF-β1-treated PDAC cell lines. Results: In a panel of pancreatic cancer cell lines, hMENA11a expression correlates with an epithelial phenotype, while hMENAΔv6 expression with a mesechymal phenotype, with low E-cadherin and high vimentin expression. hMENA11a knock-down in PDAC cell lines affected cell-cell adhesion but not cell invasion. TGF-β1 cooperated with β-catenin signalling to up-regulate hMENA and hMENAΔv6 expression but not hMENA11a. The hMENA/hMENAΔv6 up-regulation play a crucial role in cell invasiveness and in TGF-β1-induced EMT. After TGF-β1 treatment, hMENA/hMENAΔv6 were mobilized from focal adhesion to actin stress fibers, and the silencing of these isoforms significantly inhibited the TGF-β1-induced EMT in PANC-1. Functionally, in the absence of hMENA11a, the hMENA/hMENAΔv6 up-regulationis crucial for SMAD2-mediated TGF-β1 signalling, migration, invasion and MMPs activities. Pan hMENA immunostaining, absent in normal pancreas and low-grade PanINs, was weak in PanIN-3 and had higher levels in virtually all PDACs with 64% of cases showing strong staining. Conversely, the anti-invasive hMENA11a isoform only showed strong staining in 26% of PDAC. The absence of hMENA11a in a subset (34%) of pan-hMENA-positive tumors significantly correlated with poor outcome, in agreement with experimental results. Conclusions: hMENA isoforms are regulated differently by TGF-β1, and the pattern of expression of hMENA isoforms is crucial in TGF-β1-dependent EMT and cell invasion. The pattern of expression of hMENA isoforms correlates with PDAC patient outcome and it could be used in specific clinical settings for the choice of the most effective treatment of PDAC patients. Our data provide new insights into molecular pathways involved in PDAC biology and suggest that hMENA-related pathways are promising targets for the development of new prognostic and therapeutic tools in PDAC. Citation Format: Roberta Melchionna, Pierluigi Iapicca, Francesca Di Modugno, Paola Trono, Isabella Sperduti, Matteo Fassan, Ivana Cataldo, Borislav C. Rusev, Rita T. Lawlor, Maria Grazia Diodoro, Michele Milella, Gian Luca Grazi, Mina J. Bissell, Aldo Scarpa, Paola Nisticò. The pattern of hMENA isoforms is regulated by TGF-β1 in pancreatic cancer and may predict patient outcome [abstract]. In: Proceedings of the Second CRI-CIMT-EATI-AACR International Cancer Immunotherapy Conference: Translating Science into Survival; 2016 Sept 25-28; New York, NY. Philadelphia (PA): AACR; Cancer Immunol Res 2016;4(11 Suppl):Abstract nr A113.
    Type of Medium: Online Resource
    ISSN: 2326-6066 , 2326-6074
    Language: English
    Publisher: American Association for Cancer Research (AACR)
    Publication Date: 2016
    detail.hit.zdb_id: 2732517-9
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  • 10
    In: Oncogene, Springer Science and Business Media LLC, Vol. 37, No. 42 ( 2018-10), p. 5605-5617
    Type of Medium: Online Resource
    ISSN: 0950-9232 , 1476-5594
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    Language: English
    Publisher: Springer Science and Business Media LLC
    Publication Date: 2018
    detail.hit.zdb_id: 2008404-3
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