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Differential expression profiling of onco and tumor-suppressor genes from major-signaling pathways in Wilms' tumor. Pediatr Surg Int 2022; 38:1601-1617. [PMID: 36107237 DOI: 10.1007/s00383-022-05202-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 08/22/2022] [Indexed: 10/14/2022]
Abstract
PURPOSE Wilms' tumor is the most-frequent malignant-kidney tumor in children under 3-4 years of age and is caused by genetic alterations of oncogenes (OG) and tumor-suppressor genes (TG). Wilms' tumor has been linked to many OG-&-TG. However, only WT1 has a proven role in the development of this embryonic-tumor. METHODS The study investigates the level of mRNA expression of 16 OGs and 20 TGs involved in key-signaling pathways, including chromatin modification; RAS; APC; Cell Cycle/Apoptosis; Transcriptional Regulation; PI3K; NOTCH-&-HH; PI3K & RAS of 24-fresh Wilms'-tumor cases by capture-and-reporter probe Code-Sets chemistry, as CNVs in these pathway genes have been reported. RESULTS Upon extensively investigating, MEN1, MLL2, MLL3, PBRM1, PRDM1, SMARCB1, SETD2, WT1, PTPN11, KRAS, HRAS, NF1, APC, RB1, FUBP1, BCOR, U2AF1, PIK3CA, PTEN, EBXW7, SMO, ALK, CBL, EP300-and-GATA1 were found to be significantly up-regulated in 58.34, 62.5, 79.17, 91.67, 58, 66.66,54, 58.34, 66.67, 75, 62.5, 62.5, 58, 79.17, 79.17, 75, 70.84, 50, 50, 75, 66.66, 62.50, 61.66, 58.34-and-62.50% of cases respectively, whereas BRAF, NF2, CDH1, BCL2, FGFR3, ERBB2, MET, RET, EGFR-and-GATA2 were significantly down regulated in 58, 87.50, 79.16, 54.16, 79.17, 91.66, 66.66, 58.33, 91.66-and-62.50% of cases, respectively. Interestingly, the WT1 gene was five-fold down regulated in 41.66% of cases only. CONCLUSION Hence, extensive profiling of OGs and TGs association of major-signaling pathways in Wilms' tumor cases may aid in disease diagnosis. PBRM1 (up-regulated in 91.67% of cases), ERBB2 and EGFR (down-regulated in 91.66 and 91.66% of cases, respectively) could be marker genes. However, validation of all relevant results in a larger number of samples is required.
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Liu C, Barger CJ, Karpf AR. FOXM1: A Multifunctional Oncoprotein and Emerging Therapeutic Target in Ovarian Cancer. Cancers (Basel) 2021; 13:3065. [PMID: 34205406 PMCID: PMC8235333 DOI: 10.3390/cancers13123065] [Citation(s) in RCA: 36] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2021] [Revised: 06/11/2021] [Accepted: 06/16/2021] [Indexed: 02/08/2023] Open
Abstract
Forkhead box M1 (FOXM1) is a member of the conserved forkhead box (FOX) transcription factor family. Over the last two decades, FOXM1 has emerged as a multifunctional oncoprotein and a robust biomarker of poor prognosis in many human malignancies. In this review article, we address the current knowledge regarding the mechanisms of regulation and oncogenic functions of FOXM1, particularly in the context of ovarian cancer. FOXM1 and its associated oncogenic transcriptional signature are enriched in >85% of ovarian cancer cases and FOXM1 expression and activity can be enhanced by a plethora of genomic, transcriptional, post-transcriptional, and post-translational mechanisms. As a master transcriptional regulator, FOXM1 promotes critical oncogenic phenotypes in ovarian cancer, including: (1) cell proliferation, (2) invasion and metastasis, (3) chemotherapy resistance, (4) cancer stem cell (CSC) properties, (5) genomic instability, and (6) altered cellular metabolism. We additionally discuss the evidence for FOXM1 as a cancer biomarker, describe the rationale for FOXM1 as a cancer therapeutic target, and provide an overview of therapeutic strategies used to target FOXM1 for cancer treatment.
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Affiliation(s)
| | | | - Adam R. Karpf
- Eppley Institute and Fred & Pamela Buffett Cancer Center, University of Nebraska Medical Center, Omaha, NE 68918-6805, USA; (C.L.); (C.J.B.)
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3
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Singh N, Mishra A, Sahu DK, Jain M, Shyam H, Tripathi RK, Shankar P, Kumar A, Alam N, Jaiswal R, Kumar S. Comprehensive Characterization of Stage IIIA Non-Small Cell Lung Carcinoma. Cancer Manag Res 2020; 12:11973-11988. [PMID: 33244273 PMCID: PMC7685366 DOI: 10.2147/cmar.s279974] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2020] [Accepted: 10/16/2020] [Indexed: 12/21/2022] Open
Abstract
Introduction Heterogeneity of non-small cell lung carcinoma (NSCLC) among patients is currently not well studied. Pathologic markers and staging systems have not been a precise predictor of the prognosis of an individual patient. Hence, we hypothesize to develop a transcript-based signature to categorize stage IIIA-NSCLC in lung adenocarcinoma (LUAD) and lung squamous cell carcinoma (LUSC), plus identify markers that could indicate the prognosis of the disease. Methods Human Transcriptome Array 2.0 (HTA) and NanoString nCounter® platform were used for high-throughput gene-expression profiling. Initially, we profiled stage IIIA-NSCLC through HTA and validated through NanoString. Additionally, two metastatic markers SPP1 and CDH2 were validated in 47 NSCLC stage IIIA samples through real-time PCR. Results We observed distinct gene clusters in LUAD and LUSC with down-regulation of six genes and up-regulation of 57 genes through HTA. Ninety-six transcripts were randomly selected after analyzing HTA data and validated on the NanoString platform. We found 40 differentially expressed transcripts that categorized NSCLC into LUAD and LUSC. SPP1 is significantly overexpressed (4.311±1.27 fold in LUAD and 13.41±3.82 fold in LUSC compared to control), and the CDH2 transcript was significantly overexpressed (11.53 ± 4.027-fold compared to control) only in LUSC. Discussion These markers enable us to categorize stage IIIA NSCLC into LUAD and LUSC plus these markers may be helpful to understand the pathophysiology of NSCLC. However, more data required to make these findings useful in general clinical practice.
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Affiliation(s)
- Neetu Singh
- Department of Centre for Advanced Research, King George's Medical University, Lucknow, 226003, India
| | - Archana Mishra
- Department of Surgery, King George's Medical University, Lucknow 226003, India
| | - Dinesh Kumar Sahu
- Department of Centre for Advanced Research, King George's Medical University, Lucknow, 226003, India
| | - Mayank Jain
- Department of Centre for Advanced Research, King George's Medical University, Lucknow, 226003, India
| | - Hari Shyam
- Department of Centre for Advanced Research, King George's Medical University, Lucknow, 226003, India
| | - Ratnesh Kumar Tripathi
- Department of Centre for Advanced Research, King George's Medical University, Lucknow, 226003, India
| | - Pratap Shankar
- Department of Centre for Advanced Research, King George's Medical University, Lucknow, 226003, India
| | - Anil Kumar
- Department of Centre for Advanced Research, King George's Medical University, Lucknow, 226003, India
| | - Nawazish Alam
- Department of Centre for Advanced Research, King George's Medical University, Lucknow, 226003, India
| | - Riddhi Jaiswal
- Department of Pathology, King George's Medical University, Lucknow 226003, India
| | - Shailendra Kumar
- Department of Surgery, King George's Medical University, Lucknow 226003, India
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Singh N, Sahu DK, Tripathi RK, Mishra A, Shyam H, Shankar P, Jain M, Alam N, Kumar A, Mishra A, Chowdhry R, Singh A, Gupta S, Mehrotra D, Agarwal P, Goel MM, Chaturvedi A, Agarwal SP, Bajpai M, Gupta DK, Bhatt MLB, Kant R. Differentially expressed full-length, fusion and novel isoforms transcripts-based signature of well-differentiated keratinized oral squamous cell carcinoma. Oncotarget 2020; 11:3227-3243. [PMID: 32922662 PMCID: PMC7456611 DOI: 10.18632/oncotarget.27693] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2020] [Accepted: 07/14/2020] [Indexed: 12/20/2022] Open
Abstract
Highly keratinized oral squamous cell carcinoma (OSCC) exhibits an improved response to treatment and prognosis compared with weakly keratinized OSCC. Therefore, we aimed to develop gene transcript signature and to identify novel full-length isoforms, fusion transcript and non-coding RNA to differentiate well-differentiated (WD) with Moderately Differentiated (MD)/Poorly Differentiated (PD)/WD-lymphadenopathy OSCC through, HTA, Isoform sequencing, and NanoString. Additionally, specific copy number gain and loss were also identify in WD keratinized OSCC through Oncoscan array and validated through Real-time PCR in histopathologically characterized FFPE-WD keratinized OSCC. Three-hundred-thirty-eight (338) differentially expressed full-length (FL) transcript isoforms (317 upregulated and 21 down-regulated in OSCC) were identified through Isoform Sequencing using the PacBio platform. Thirty-four (34) highly upregulated differentially expressed transcripts from IsoSeq data were also correlated with HTA2.0 and validated in 42 OSCC samples. We were able to identify 18 differentially expressed transcripts, 12 fusion transcripts, and two long noncoding RNAs. These transcripts were involved in increased cell proliferation, dysregulated metabolic reprogramming, oxidative stress, and immune system markers with enhanced immune rearrangements, suggesting a cancerous nature. However, an increase in proteasomal activity and hemidesmosome proteins suggested an improved prognosis and tumor cell stability in keratinized OSCC and helped to characterize WD with MD/PD/WD with lymphadenopathy OSCC. Additionally, novel isoforms of IL37, NAA10, UCHL3, SPAG7, and RAB24 were identified while in silico functionally validated SPAG7 represented the premalignant phenotype of keratinized (K4) OSCC. Most importantly we found copy number gain and overexpression of EGFR suggest that TKIs may also be used as therapeutics in WD-OSCCs.
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Affiliation(s)
- Neetu Singh
- Department of Molecular Biology, Center for Advance Research, King George's Medical University, Lucknow, India.,These authors contributed equally to this work
| | - Dinesh Kumar Sahu
- Department of Molecular Biology, Center for Advance Research, King George's Medical University, Lucknow, India.,These authors contributed equally to this work
| | - Ratnesh Kumar Tripathi
- Department of Molecular Biology, Center for Advance Research, King George's Medical University, Lucknow, India.,These authors contributed equally to this work
| | - Archana Mishra
- Department of Molecular Biology, Center for Advance Research, King George's Medical University, Lucknow, India.,Department of Surgery, King George's Medical University, Lucknow, India
| | - Hari Shyam
- Department of Molecular Biology, Center for Advance Research, King George's Medical University, Lucknow, India
| | - Pratap Shankar
- Department of Molecular Biology, Center for Advance Research, King George's Medical University, Lucknow, India
| | - Mayank Jain
- Department of Molecular Biology, Center for Advance Research, King George's Medical University, Lucknow, India
| | - Nawazish Alam
- Department of Molecular Biology, Center for Advance Research, King George's Medical University, Lucknow, India
| | - Anil Kumar
- Department of Molecular Biology, Center for Advance Research, King George's Medical University, Lucknow, India
| | - Abhishek Mishra
- Department of Molecular Biology, Center for Advance Research, King George's Medical University, Lucknow, India
| | - Rebecca Chowdhry
- Department of Periodontology, All India Institute of Medical Sciences, Rishikesh, India
| | - Anjana Singh
- Department of Biochemistry, All India Institute of Medical Sciences, Rishikesh, India
| | - Sameer Gupta
- Department of Surgical Oncology, King George's Medical University, Lucknow, India
| | - Divya Mehrotra
- Department of Oral and Maxillofacial Surgery, King George's Medical University, Lucknow, India
| | - Preeti Agarwal
- Department of Pathology, King George's Medical University, Lucknow, India
| | - Madhu Mati Goel
- Department of Pathology, King George's Medical University, Lucknow, India
| | - Arun Chaturvedi
- Department of Surgical Oncology, King George's Medical University, Lucknow, India
| | | | - Manish Bajpai
- Department of Physiology, King George's Medical University, Lucknow, India
| | - Devendra Kumar Gupta
- Department of Pediatric Surgery, Super Speciality Pediatric Hospital and Post Graduate Teaching Institute, Noida, India
| | | | - Ravi Kant
- Department of Surgical Oncology, All India Institute of Medical Sciences, Rishikesh, India
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Abstract
BACKGROUND The prognostic role of copy number variation is upcoming in Wilms tumor, and its identification will help in tailored therapy for improved cure. STUDY DESIGN This was a retrospective, nested case-control, pilot study. MATERIALS AND METHODS Formalin-fixed paraffin-embedded blocks of nephrectomy specimens were retrieved for the study and control groups (children with relapse and survivors for ≥2 y). Multiplex ligand probe amplification (MRC-Holland probe-mix P 380 A1) was performed, with 3 reference samples of normal kidney DNA run for every 7 cases. RESULTS At least 1 variation was detected in 41 (97.8%) specimens. Loss of heterozygosity 1p was not observed. Loss of 16q, 1q gain, and MYCN gain were observed in 5 (11.9%), 29 (69%), and 39 (92.9%) specimens, respectively. The occurrence of copy number variations was similar in both groups: 1q gain: 15 versus 14 (P=1.0), 16q loss: 4 versus 1 (P=0.34), MYCN gain: 19 versus 20 (P=1.0). The gain of 1q, 16p loss, and MYCN gain did not differ across stage or age. CONCLUSIONS The gain of 1q, MYCN gain, and 16p loss were identified. A higher occurrence of 1q gain and MYCN gain and a lack of difference in the distribution of variations among survivors and those with a relapse suggest a different molecular profile of Wilms tumor in Indian children.
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Singh N, Tripathi AK, Sahu DK, Mishra A, Linan M, Argente B, Varkey J, Parida N, Chowdhry R, Shyam H, Alam N, Dixit S, Shankar P, Mishra A, Agarwal A, Yoo C, Bhatt MLB, Kant R. Differential genomics and transcriptomics between tyrosine kinase inhibitor-sensitive and -resistant BCR-ABL-dependent chronic myeloid leukemia. Oncotarget 2018; 9:30385-30418. [PMID: 30100996 PMCID: PMC6084383 DOI: 10.18632/oncotarget.25752] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2018] [Accepted: 05/28/2018] [Indexed: 01/11/2023] Open
Abstract
Previously, it has been stated that the BCR-ABL fusion-protein is sufficient to induce Chronic Myeloid Leukemia (CML), but additional genomic-changes are required for disease progression. Hence, we profiled control and tyrosine kinase inhibitors (TKI) alone or in combination with other drug-treated CML-samples in different phases, categorized as drug-sensitive and drug-resistant on the basis of BCR-ABL transcripts, the marker of major molecular-response. Molecular-profiling was done using the molecular-inversion probe-based-array, Human Transcriptomics-Array2.0, and Axiom-Biobank genotyping-arrays. At the transcript-level, clusters of control, TKI-resistant and TKI-sensitive cases were correlated with BCR-ABL transcript-levels. Both at the gene- and exon-levels, up-regulation of MPO, TPX2, and TYMS and down-regulation of STAT6, FOS, TGFBR2, and ITK lead up-regulation of the cell-cycle, DNA-replication, DNA-repair pathways and down-regulation of the immune-system, chemokine- and interleukin-signaling, TCR, TGF beta and MAPK signaling pathways. A comparison between TKI-sensitive and TKI-resistant cases revealed up-regulation of LAPTM4B, HLTF, PIEZO2, CFH, CD109, ANGPT1 in CML-resistant cases, leading to up-regulation of autophagy-, protein-ubiquitination-, stem-cell-, complement-, TGFβ- and homeostasis-pathways with specific involvement of the Tie2 and Basigin signaling-pathway. Dysregulated pathways were accompanied with low CNVs in CP-new and CP-UT-TKI-sensitive-cases with undetectable BCR-ABL-copies. High CNVs (previously reported gain of 9q34) were observed in BCR-ABL-independent and -dependent TKI, non-sensitive-CP-UT/AP-UT/B-UT and B-new samples. Further, genotyping CML-CP-UT cases with BCR-ABL 0-to-77.02%-copies, the identified, rsID239798 and rsID9475077, were associated with FAM83B, a candidate for therapeutic resistance. The presence of BCR-ABL, additional genetic-events, dysregulated-signaling-pathways and rsIDs associated with FAM83B in TKI-resistant-cases can be used to develop a signature-profile that may help in monitoring therapy.
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Affiliation(s)
- Neetu Singh
- Molecular Biology Unit, Center for Advance Research, King George's Medical University, Lucknow, India
| | - Anil Kumar Tripathi
- Department of Clinical Hematology, King George's Medical University, Lucknow, India
| | - Dinesh Kumar Sahu
- Molecular Biology Unit, Center for Advance Research, King George's Medical University, Lucknow, India
| | - Archana Mishra
- Department of Cardio Thoracic and Vascular Surgery, King George's Medical University, Lucknow, India
| | | | | | | | - Niranjan Parida
- Molecular Biology Unit, Center for Advance Research, King George's Medical University, Lucknow, India
| | - Rebecca Chowdhry
- Department of Periodontics, King George's Medical University, Lucknow, India
| | - Hari Shyam
- Molecular Biology Unit, Center for Advance Research, King George's Medical University, Lucknow, India
| | - Nawazish Alam
- Molecular Biology Unit, Center for Advance Research, King George's Medical University, Lucknow, India
| | - Shivani Dixit
- Molecular Biology Unit, Center for Advance Research, King George's Medical University, Lucknow, India
| | - Pratap Shankar
- Molecular Biology Unit, Center for Advance Research, King George's Medical University, Lucknow, India
| | - Abhishek Mishra
- Molecular Biology Unit, Center for Advance Research, King George's Medical University, Lucknow, India
| | - Avinash Agarwal
- Department of Medicine, King George's Medical University, Lucknow, India
| | - Chris Yoo
- Systems Imagination, Scottsdale, Arizona, USA
| | | | - Ravi Kant
- All India Institute of Medical Sciences, Rishikesh, India
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Alexandrescu S, Akhavanfard S, Harris MH, Vargas SO. Clinical, Pathologic, and Genetic Features of Wilms Tumors With WTX Gene Mutation. Pediatr Dev Pathol 2017; 20:105-111. [PMID: 28326956 DOI: 10.1177/1093526616683881] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Clinical and pathologic features of patients with WTX-mutated Wilms tumor (WT) have not been studied in detail. We characterize the clinical and pathologic findings in WT with WTX abnormalities and provide comparison with WT without WTX mutation. Clinical, gross, and microscopic features in 35 patients with WT were examined. Karyotype was examined in a subset of cases. All cases had been previously analyzed for WTX, WT1, and CTNNB1 aberrations via array comparative genomic hybridization; OncoMap 4 high throughput genotyping was performed on 18 cases. Eleven tumors had WTX abnormality. No significant differences were identified between patients with mutated versus nonmutated WTX with respect to gender (45% versus 33% male), age (mean 3.9 versus 4.1 years), tumor size (mean 12.7 cm versus 12.8 cm), anaplasia (9% versus 12%), rhabdomyoblastic differentiation (18% versus 8%), cartilage differentiation (9% versus 4%), mucinous epithelial differentiation (9% versus 4%), nephrogenic rests (28% versus 21%), or relapse rate (11% versus 25%). Mutations in KRAS, MYC, and PIK3R1 were restricted to WTX-mutated WT, mutations in AKT, CKDN2A, EFGR, HRAS, MET, and RET were restricted to WT without WTX mutation, and mutations in BRAF, CTTNB1, NRAS, PDGFRA, and STK11 were seen in both groups. Our study revealed no clinical or pathologic distinctions between WT with and without WTX abnormality. This similarity lends support to the concept of a common tumorigenic pathway between WT with aberrant WTX and those without.
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Affiliation(s)
- Sanda Alexandrescu
- 1 Department of Pathology, Boston Children's Hospital, Boston, Massachusetts, USA.,2 Department of Pathology, Harvard Medical School, Boston, Massachusetts, USA
| | - Sara Akhavanfard
- 3 Department of Pathology, Massachusetts General Hospital, Boston, Massachusetts, USA
| | - Marian H Harris
- 1 Department of Pathology, Boston Children's Hospital, Boston, Massachusetts, USA.,2 Department of Pathology, Harvard Medical School, Boston, Massachusetts, USA
| | - Sara O Vargas
- 1 Department of Pathology, Boston Children's Hospital, Boston, Massachusetts, USA.,2 Department of Pathology, Harvard Medical School, Boston, Massachusetts, USA
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Ludwig N, Werner TV, Backes C, Trampert P, Gessler M, Keller A, Lenhof HP, Graf N, Meese E. Combining miRNA and mRNA Expression Profiles in Wilms Tumor Subtypes. Int J Mol Sci 2016; 17:475. [PMID: 27043538 PMCID: PMC4848931 DOI: 10.3390/ijms17040475] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2016] [Revised: 03/18/2016] [Accepted: 03/22/2016] [Indexed: 12/22/2022] Open
Abstract
Wilms tumor (WT) is the most common childhood renal cancer. Recent findings of mutations in microRNA (miRNA) processing proteins suggest a pivotal role of miRNAs in WT genesis. We performed miRNA expression profiling of 36 WTs of different subtypes and four normal kidney tissues using microarrays. Additionally, we determined the gene expression profile of 28 of these tumors to identify potentially correlated target genes and affected pathways. We identified 85 miRNAs and 2107 messenger RNAs (mRNA) differentially expressed in blastemal WT, and 266 miRNAs and 1267 mRNAs differentially expressed in regressive subtype. The hierarchical clustering of the samples, using either the miRNA or mRNA profile, showed the clear separation of WT from normal kidney samples, but the miRNA pattern yielded better separation of WT subtypes. A correlation analysis of the deregulated miRNA and mRNAs identified 13,026 miRNA/mRNA pairs with inversely correlated expression, of which 2844 are potential interactions of miRNA and their predicted mRNA targets. We found significant upregulation of miRNAs-183, -301a/b and -335 for the blastemal subtype, and miRNAs-181b, -223 and -630 for the regressive subtype. We found marked deregulation of miRNAs regulating epithelial to mesenchymal transition, especially in the blastemal subtype, and miRNAs influencing chemosensitivity, especially in regressive subtypes. Further research is needed to assess the influence of preoperative chemotherapy and tumor infiltrating lymphocytes on the miRNA and mRNA patterns in WT.
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Affiliation(s)
- Nicole Ludwig
- Department of Human Genetics, Saarland University, 66421 Homburg/Saar, Germany.
| | - Tamara V Werner
- Department of Human Genetics, Saarland University, 66421 Homburg/Saar, Germany.
| | - Christina Backes
- Chair for Clinical Bioinformatics, Building E2.1, 66123 Saarbruecken, Germany.
| | - Patrick Trampert
- Center for Bioinformatics, Saarland University, Building E.1.1, 66041 Saarbruecken, Germany.
| | - Manfred Gessler
- Developmental Biochemistry, Biocenter, and Comprehensive Cancer Center Mainfranken, University of Wuerzburg, 97074 Wuerzburg, Germany.
| | - Andreas Keller
- Chair for Clinical Bioinformatics, Building E2.1, 66123 Saarbruecken, Germany.
| | - Hans-Peter Lenhof
- Center for Bioinformatics, Saarland University, Building E.1.1, 66041 Saarbruecken, Germany.
| | - Norbert Graf
- Department of Pediatric Oncology and Hematology, Medical School, Saarland University, 66421 Homburg, Germany.
| | - Eckart Meese
- Department of Human Genetics, Saarland University, 66421 Homburg/Saar, Germany.
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Deng C, Dai R, Li X, Liu F. Genetic variation frequencies in Wilms' tumor: A meta-analysis and systematic review. Cancer Sci 2016; 107:690-9. [PMID: 26892980 PMCID: PMC4970837 DOI: 10.1111/cas.12910] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2015] [Revised: 02/11/2016] [Accepted: 02/12/2016] [Indexed: 12/11/2022] Open
Abstract
Over the last few decades, numerous biomarkers in Wilms' tumor have been confirmed and shown variations in prevalence. Most of these studies were based on small sample sizes. We carried out a meta-analysis of the research published from 1992 to 2015 to obtain more precise and comprehensive outcomes for genetic tests. In the present study, 70 out of 5175 published reports were eligible for the meta-analysis, which was carried out using Stata 12.0 software. Pooled prevalence for gene mutations WT1, WTX, CTNNB1, TP53, MYCN, DROSHA, and DGCR8 was 0.141 (0.104, 0.178), 0.147 (0.110, 0.184), 0.140 (0.100, 0.190), 0.410 (0.214, 0.605), 0.071 (0.041, 0.100), 0.082 (0.048, 0.116), and 0.036 (0.026, 0.046), respectively. Pooled prevalence of loss of heterozygosity at 1p, 11p, 11q, 16q, and 22q was 0.109 (0.084, 0.133), 0.334 (0.295, 0.373), 0.199 (0.146, 0.252), 0.151 (0.129, 0.172), and 0.148 (0.108, 0.189), respectively. Pooled prevalence of 1q and chromosome 12 gain was 0.218 (0.161, 0.275) and 0.273 (0.195, 0.350), respectively. The limited prevalence of currently known genetic alterations in Wilms' tumors indicates that significant drivers of initiation and progression remain to be discovered. Subgroup analyses indicated that ethnicity may be one of the sources of heterogeneity. However, in meta-regression analyses, no study-level characteristics of indicators were found to be significant. In addition, the findings of our sensitivity analysis and possible publication bias remind us to interpret results with caution.
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Affiliation(s)
- Changkai Deng
- Department of Urology Surgery, Children's Hospital of Chongqing Medical University, Ministry of Education Key Laboratory of Child Development and Disorder, Key Laboratory of Pediatrics in Chongqing (CSTC2009CA5002), Chongqing International Science and Technology Cooperation Center for Child Development and Disorders, Chongqing, China.,Chengdu Women and Children's Central Hospital, Chengdu, China
| | - Rong Dai
- Chengdu Center for Disease Control and Prevention, Chengdu, China
| | - Xuliang Li
- Department of Urology Surgery, Children's Hospital of Chongqing Medical University, Ministry of Education Key Laboratory of Child Development and Disorder, Key Laboratory of Pediatrics in Chongqing (CSTC2009CA5002), Chongqing International Science and Technology Cooperation Center for Child Development and Disorders, Chongqing, China
| | - Feng Liu
- Department of Urology Surgery, Children's Hospital of Chongqing Medical University, Ministry of Education Key Laboratory of Child Development and Disorder, Key Laboratory of Pediatrics in Chongqing (CSTC2009CA5002), Chongqing International Science and Technology Cooperation Center for Child Development and Disorders, Chongqing, China
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10
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Singh N, Sahu DK, Mishra A, Agarwal P, Goel MM, Chandra A, Singh SK, Srivastava C, Ojha BK, Gupta DK, Kant R. Multiomics approach showing genome-wide copy number alterations and differential gene expression in different types of North-Indian pediatric brain tumors. Gene 2015; 576:734-42. [PMID: 26456192 DOI: 10.1016/j.gene.2015.09.078] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2015] [Revised: 09/28/2015] [Accepted: 09/29/2015] [Indexed: 12/07/2022]
Abstract
PURPOSE Based on copy number alterations and transcriptional profiles, the posterior fossa tumors (medulloblastoma (MB), ependymoma and pilocytic astrocytoma) have been classified into various subgroups. The study design was aimed to identify and catalog genome-wide copy number alterations and differential gene expression in different types of North-Indian pediatric posterior fossa tumors and matched control tissue through Molecular Inversion Probe (MIP) Based and Human Transcriptome Array. EXPERIMENTAL DESIGN MIP based OncoScan Array and Human Transcriptome Array 2.0 were used to molecularly-categorize histopathologically and immunohistochemically proven tumor samples on the basis of copy number variations and altered gene expression patterns and/or alternative splicing events. RESULTS Based on molecular, histopathological/immunohistochemical and age-dependent factors MB was subgrouped into group-3 MB, Wnt and SHH; ependymoma into balanced, numerical and structural/anaplastic; and pilocytic astrocytoma was stratified age-dependently. Compared with the vermis tissue of MB, the vermis tissue of ependymoma showed higher levels of gain and losses compared with their counter tumor parts implicating metastasis within the confined region. Group-3 MB and anaplastic ependymoma represented highest differentially expressed genes both at gene and exon levels in the CN altered regions compared with other subgroups of MB and ependymoma respectively. CONCLUSION This multiomics approach based molecular characterization of posterior fossa tumors together with clinical and histopathological factors may help us in the area of personalized medicine.
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Affiliation(s)
- Neetu Singh
- Advanced Molecular Science Research Centre (Centre for Advanced Research), King George's Medical University, Lucknow 226 003, India.
| | - Dinesh Kumar Sahu
- Imperial Life Sciences, 463 Phase City 2nd, Sector 37, Gurgaon, Haryana 122001, India
| | - Archana Mishra
- Department of Biochemistry, King George's Medical University, Lucknow 226 003, India
| | - Preeti Agarwal
- Department of Pathology, King George's Medical University, Lucknow 226 003, India
| | - Madhu Mati Goel
- Department of Pathology, King George's Medical University, Lucknow 226 003, India
| | - Anil Chandra
- Department of Neurosurgery, King George's Medical University, Lucknow 226 003, Uttar Pradesh, India
| | - Sunil Kumar Singh
- Department of Neurosurgery, King George's Medical University, Lucknow 226 003, Uttar Pradesh, India
| | - Chhitij Srivastava
- Department of Neurosurgery, King George's Medical University, Lucknow 226 003, Uttar Pradesh, India
| | - Bal Krishna Ojha
- Department of Neurosurgery, King George's Medical University, Lucknow 226 003, Uttar Pradesh, India
| | - Devendra Kumar Gupta
- Department of Pediatric Surgery, All India Institute of Medical Sciences, New Delhi 110029, India
| | - Ravi Kant
- Department of Surgical Oncology, King George's Medical University, Lucknow, Uttar Pradesh 226 003, India
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11
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Cabral de Almeida Cardoso L, Rodriguez-Laguna L, del Carmen Crespo M, Vallespín E, Palomares-Bralo M, Martin-Arenas R, Rueda-Arenas I, Silvestre de Faria PA, García-Miguel P, Lapunzina P, Regla Vargas F, Seuanez HN, Martínez-Glez V. Array CGH Analysis of Paired Blood and Tumor Samples from Patients with Sporadic Wilms Tumor. PLoS One 2015; 10:e0136812. [PMID: 26317783 PMCID: PMC4552764 DOI: 10.1371/journal.pone.0136812] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2015] [Accepted: 08/07/2015] [Indexed: 11/24/2022] Open
Abstract
Wilms tumor (WT), the most common cancer of the kidney in infants and children, has a complex etiology that is still poorly understood. Identification of genomic copy number variants (CNV) in tumor genomes provides a better understanding of cancer development which may be useful for diagnosis and therapeutic targets. In paired blood and tumor DNA samples from 14 patients with sporadic WT, analyzed by aCGH, 22% of chromosome abnormalities were novel. All constitutional alterations identified in blood were segmental (in 28.6% of patients) and were also present in the paired tumor samples. Two segmental gains (2p21 and 20q13.3) and one loss (19q13.31) present in blood had not been previously described in WT. We also describe, for the first time, a small, constitutive partial gain of 3p22.1 comprising 2 exons of CTNNB1, a gene associated to WT. Among somatic alterations, novel structural chromosomal abnormalities were found, like gain of 19p13.3 and 20p12.3, and losses of 2p16.1-p15, 4q32.5-q35.1, 4q35.2-q28.1 and 19p13.3. Candidate genes included in these regions might be constitutively (SIX3, SALL4) or somatically (NEK1, PIAS4, BMP2) operational in the development and progression of WT. To our knowledge this is the first report of CNV in paired blood and tumor samples in sporadic WT.
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Affiliation(s)
| | - Lara Rodriguez-Laguna
- Section of Functional and Structural Genomics, Institute of Medical and Molecular Genetics (INGEMM)-IdiPAZ, Hospital Universitario La Paz, Madrid, Spain
| | - María del Carmen Crespo
- Section of Functional and Structural Genomics, Institute of Medical and Molecular Genetics (INGEMM)-IdiPAZ, Hospital Universitario La Paz, Madrid, Spain
| | - Elena Vallespín
- Section of Functional and Structural Genomics, Institute of Medical and Molecular Genetics (INGEMM)-IdiPAZ, Hospital Universitario La Paz, Madrid, Spain
- CIBERER, Centro de Investigación Biomédica en Red de Enfermedades Raras, Madrid, Spain
| | - María Palomares-Bralo
- Section of Functional and Structural Genomics, Institute of Medical and Molecular Genetics (INGEMM)-IdiPAZ, Hospital Universitario La Paz, Madrid, Spain
- CIBERER, Centro de Investigación Biomédica en Red de Enfermedades Raras, Madrid, Spain
| | - Rubén Martin-Arenas
- Section of Functional and Structural Genomics, Institute of Medical and Molecular Genetics (INGEMM)-IdiPAZ, Hospital Universitario La Paz, Madrid, Spain
| | - Inmaculada Rueda-Arenas
- Section of Functional and Structural Genomics, Institute of Medical and Molecular Genetics (INGEMM)-IdiPAZ, Hospital Universitario La Paz, Madrid, Spain
| | | | | | | | - Pablo Lapunzina
- CIBERER, Centro de Investigación Biomédica en Red de Enfermedades Raras, Madrid, Spain
- Section of Clinical Genetics, Institute of Medical and Molecular Genetics (INGEMM)-IdiPAZ, Hospital Universitario La Paz, Madrid, Spain
| | - Fernando Regla Vargas
- Genetics Department, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
- Birth Defects Epidemiology Laboratory, Fundação Oswaldo Cruz, Rio de Janeiro, Brazil
| | - Hector N. Seuanez
- Genetics Division, Instituto Nacional de Câncer, Rio de Janeiro, Brazil
- Genetics Department, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Víctor Martínez-Glez
- Section of Functional and Structural Genomics, Institute of Medical and Molecular Genetics (INGEMM)-IdiPAZ, Hospital Universitario La Paz, Madrid, Spain
- CIBERER, Centro de Investigación Biomédica en Red de Enfermedades Raras, Madrid, Spain
- * E-mail:
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12
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Lovvorn HN, Pierce J, Libes J, Li B, Wei Q, Correa H, Gouffon J, Clark PE, Axt JR, Hansen E, Newton M, O'Neill JA. Genetic and chromosomal alterations in Kenyan Wilms Tumor. Genes Chromosomes Cancer 2015; 54:702-15. [PMID: 26274016 PMCID: PMC4567398 DOI: 10.1002/gcc.22281] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2015] [Revised: 06/08/2015] [Accepted: 06/08/2015] [Indexed: 12/31/2022] Open
Abstract
Wilms tumor (WT) is the most common childhood kidney cancer worldwide and poses a cancer health disparity to black children of sub-Saharan African ancestry. Although overall survival from WT at 5 years exceeds 90% in developed countries, this pediatric cancer is alarmingly lethal in sub-Saharan Africa and specifically in Kenya (36% survival at 2 years). Although multiple barriers to adequate WT therapy contribute to this dismal outcome, we hypothesized that a uniquely aggressive and treatment-resistant biology compromises survival further. To explore the biologic composition of Kenyan WT (KWT), we completed a next generation sequencing analysis targeting 10 WT-associated genes and evaluated whole-genome copy number variation. The study cohort was comprised of 44 KWT patients and their specimens. Fourteen children are confirmed dead at 2 years and 11 remain lost to follow-up despite multiple tracing attempts. TP53 was mutated most commonly in 11 KWT specimens (25%), CTNNB1 in 10 (23%), MYCN in 8 (18%), AMER1 in 5 (11%), WT1 and TOP2A in 4 (9%), and IGF2 in 3 (7%). Loss of heterozygosity (LOH) at 17p, which covers TP53, was detected in 18% of specimens examined. Copy number gain at 1q, a poor prognostic indicator of WT biology in developed countries, was detected in 32% of KWT analyzed, and 89% of these children are deceased. Similarly, LOH at 11q was detected in 32% of KWT, and 80% of these patients are deceased. From this genomic analysis, KWT biology appears uniquely aggressive and treatment-resistant.
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Affiliation(s)
- Harold N Lovvorn
- Department of Pediatric Surgery, Vanderbilt University School of Medicine, Nashville, TN
| | - Janene Pierce
- Department of Pediatric Surgery, Vanderbilt University School of Medicine, Nashville, TN
| | - Jaime Libes
- Department of Pediatrics, University of Illinois College of Medicine, Peoria, IL.,Division of Hematology/Oncology, University of Illinois College of Medicine, Peoria, IL
| | - Bingshan Li
- Department of Molecular Physiology and Biophysics, Vanderbilt University School of Medicine, Nashville, TN
| | - Qiang Wei
- Department of Molecular Physiology and Biophysics, Vanderbilt University School of Medicine, Nashville, TN
| | - Hernan Correa
- Division of Pediatric Pathology, Vanderbilt University School of Medicine, Nashville, TN
| | | | - Peter E Clark
- Department of Urologic Surgery, Vanderbilt University School of Medicine, Nashville, TN
| | - Jason R Axt
- Department of Pediatric Surgery, Vanderbilt University School of Medicine, Nashville, TN
| | - Erik Hansen
- Department of Pediatric Surgery, Vanderbilt University School of Medicine, Nashville, TN
| | - Mark Newton
- Division of Pediatric Anesthesia, Vanderbilt University School of Medicine, Nashville, TN
| | - James A O'Neill
- Department of Pediatric Surgery, Vanderbilt University School of Medicine, Nashville, TN
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