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https://www.readbyqxmd.com/read/28932590/primary-pulmonary-malignant-fibrous-histiocytoma-case-report-and-literature-review
#1
Xiongfei Li, Renwang Liu, Tao Shi, Shangwen Dong, Fan Ren, Fan Yang, Dian Ren, Haiyang Fan, Sen Wei, Gang Chen, Jun Chen, Song Xu
Malignant fibrous histiocytoma (MFH) is an aggressive soft tissue sarcoma known to occur in various organs. Primary MFH arising in the lung is quite rare. Herein we report a case of a 61-year-old male with primary pulmonary MFH and explore the underlying molecular mechanisms by next-generation sequencing (NGS). Five gene mutations in TSC2, ARID1B, CDK8, KDM5C and CASP8 were detected, and the mTOR inhibitor might be an effective treatment for this patient. In addition, we reviewed the scientific literature of approximately 23 primary pulmonary MFH case reports since 1990 and summarized the clinical features and prognosis of this rare pulmonary malignant tumor...
August 2017: Journal of Thoracic Disease
https://www.readbyqxmd.com/read/28725537/the-emerging-role-of-histone-demethylases-in-renal-cell-carcinoma
#2
REVIEW
Xiaoqiang Guo, Qiaoxia Zhang
Renal cell carcinoma (RCC), the most common kidney cancer, is responsible for more than 100,000 deaths per year worldwide. The molecular mechanism of RCC is poorly understood. Many studies have indicated that epigenetic changes such as DNA methylation, noncoding RNAs, and histone modifications are central to the pathogenesis of cancer. Histone demethylases (KDMs) play a central role in histone modifications. There is emerging evidence that KDMs such as KDM3A, KDM5C, KDM6A, and KDM6B play important roles in RCC...
2017: Journal of Kidney Cancer and VHL
https://www.readbyqxmd.com/read/28630052/infection-exposure-promotes-etv6-runx1-precursor-b-cell-leukemia-via-impaired-h3k4-demethylases
#3
Guillermo Rodríguez-Hernández, Julia Hauer, Alberto Martín-Lorenzo, Daniel Schäfer, Christoph Bartenhagen, Idoia García-Ramírez, Franziska Auer, Inés González-Herrero, Lucia Ruiz-Roca, Michael Gombert, Vera Okpanyi, Ute Fischer, Cai Chen, Martin Dugas, Sanil Bhatia, René Martin Linka, Marta Garcia-Suquia, María Victoria Rascón-Trincado, Angel Garcia-Sanchez, Oscar Blanco, Maria Begoña García-Cenador, Francisco Javier García-Criado, César Cobaleda, Diego Alonso-López, Javier De Las Rivas, Markus Müschen, Carolina Vicente-Dueñas, Isidro Sánchez-García, Arndt Borkhardt
ETV6-RUNX1 is associated with the most common subtype of childhood leukemia. As few ETV6-RUNX1 carriers develop precursor B-cell acute lymphocytic leukemia (pB-ALL), the underlying genetic basis for development of full-blown leukemia remains to be identified, but the appearance of leukemia cases in time-space clusters keeps infection as a potential causal factor. Here, we present in vivo genetic evidence mechanistically connecting preleukemic ETV6-RUNX1 expression in hematopoetic stem cells/precursor cells (HSC/PC) and postnatal infections for human-like pB-ALL...
August 15, 2017: Cancer Research
https://www.readbyqxmd.com/read/28408295/genomic-alterations-as-predictors-of-survival-among-patients-within-a-combined-cohort-with-clear-cell-renal-cell-carcinoma-undergoing-cytoreductive-nephrectomy
#4
Daniel M Tennenbaum, Brandon J Manley, Emily Zabor, Maria F Becerra, Maria I Carlo, Jozefina Casuscelli, Almedina Redzematovic, Nabeela Khan, Maria E Arcila, Martin H Voss, Darren R Feldman, Robert J Motzer, Nicole E Benfante, Jonathan A Coleman, Paul Russo, James J Hsieh, Abraham Ari Hakimi
PURPOSE: To establish prognostic genomic biomarkers for patients with metastatic clear cell renal cell carcinoma (ccRCC). MATERIALS AND METHODS: We identified 60 patients who presented with metastatic ccRCC at our institution between 2001 and 2015 and had genomic sequencing on their primary tumor. We pooled these patients with 107 other patients with the same inclusion criteria from three well-known public databases. Five commonly mutated genes were chosen for analysis: VHL, PBRM1, BAP1, SETD2, and KDM5C...
August 2017: Urologic Oncology
https://www.readbyqxmd.com/read/28212566/genetic-characterization-of-polish-ccrcc-patients-somatic-mutation-analysis-of-pbrm1-bap1-and-kdmc5-genomic-snp-array-analysis-in-tumor-biopsy-and-preliminary-results-of-chromosome-aberrations-analysis-in-plasma-cell-free-dna
#5
Katarzyna Kluzek, Malgorzata I Srebniak, Weronika Majer, Agnieszka Ida, Tomasz Milecki, Kinga Huminska, Robert M van der Helm, Adrian Silesian, Tomasz M Wrzesinski, Jacek Wojciechowicz, Berna H Beverloo, Zbigniew Kwias, Hans A R Bluyssen, Joanna Wesoly
BACKGROUND: Mutation analysis and cytogenetic testing in clear cell renal cell carcinoma (ccRCC) is not yet implemented in a routine diagnostics of ccRCC. MATERIAL AND METHODS: We characterized the chromosomal alterations in 83 ccRCC tumors from Polish patients using whole genome SNP genotyping assay. Moreover, the utility of next generation sequencing of cell free DNA (cfDNA) in patients plasma as a potential tool for non-invasive cytogenetic analysis was tested...
April 25, 2017: Oncotarget
https://www.readbyqxmd.com/read/27923837/the-nci-60-methylome-and-its-integration-into-cellminer
#6
William C Reinhold, Sudhir Varma, Margot Sunshine, Vinodh Rajapakse, Augustin Luna, Kurt W Kohn, Holly Stevenson, Yonghong Wang, Holger Heyn, Vanesa Nogales, Sebastian Moran, David J Goldstein, James H Doroshow, Paul S Meltzer, Manel Esteller, Yves Pommier
A unique resource for systems pharmacology and genomic studies is the NCI-60 cancer cell line panel, which provides data for the largest publicly available library of compounds with cytotoxic activity (∼21,000 compounds), including 108 FDA-approved and 70 clinical trial drugs as well as genomic data, including whole-exome sequencing, gene and miRNA transcripts, DNA copy number, and protein levels. Here, we provide the first readily usable genome-wide DNA methylation database for the NCI-60, including 485,577 probes from the Infinium HumanMethylation450k BeadChip array, which yielded DNA methylation signatures for 17,559 genes integrated into our open access CellMiner version 2...
February 1, 2017: Cancer Research
https://www.readbyqxmd.com/read/27896428/xci-escaping-gene-kdm5c-contributes-to-ovarian-development-via-downregulating-mir-320a
#7
Yi-Xi Sun, Yi-Xin Zhang, Dan Zhang, Chen-Ming Xu, Song-Chang Chen, Jun-Yu Zhang, Ye-Chun Ruan, Feng Chen, Run-Ju Zhang, Ye-Qing Qian, Yi-Feng Liu, Lu-Yang Jin, Tian-Tian Yu, Hai-Yan Xu, Yu-Qin Luo, Xin-Mei Liu, Fei Sun, Jian-Zhong Sheng, He-Feng Huang
Mechanisms underlying female gonadal dysgenesis remain unclarified and relatively unstudied. Whether X-chromosome inactivation (XCI)-escaping genes and microRNAs (miRNAs) contribute to this condition is currently unknown. We compared 45,X Turner Syndrome women with 46,XX normal women, and investigated differentially expressed miRNAs in Turner Syndrome through plasma miRNA sequencing. We found that miR-320a was consistently upregulated not only in 45,X plasma and peripheral blood mononuclear cells (PBMCs), but also in 45,X fetal gonadal tissues...
February 2017: Human Genetics
https://www.readbyqxmd.com/read/27879032/altered-expression-of-brg1-and-histone-demethylases-and-aberrant-h3k4-methylation-in-less-developmentally-competent-embryos-at-the-time-of-embryonic-genome-activation
#8
Werner G Glanzner, Audrey Wachter, Ana Rita S Coutinho, Marcelo S Albornoz, Raj Duggavathi, Paulo B D GonÇAlves, Vilceu Bordignon
Epigenetics is a fundamental regulator underlying many biological functions, such as development and cell differentiation. Epigenetic modifications affect key chromatin regulation, including transcription and DNA repair, which are critical for normal embryo development. In this study, we profiled the expression of epigenetic modifiers and patterns of epigenetic changes in porcine embryos around the period of embryonic genome activation (EGA). We observed that Brahma-related gene 1 (BRG1) and Lysine demethylase 1A (KDM1A), which can alter the methylation status of lysine 4 in histone 3 (H3K4), localize to the nucleus at Day 3-4 of development...
November 23, 2016: Molecular Reproduction and Development
https://www.readbyqxmd.com/read/27869828/tumor-suppressor-genes-that-escape-from-x-inactivation-contribute-to-cancer-sex-bias
#9
Andrew Dunford, David M Weinstock, Virginia Savova, Steven E Schumacher, John P Cleary, Akinori Yoda, Timothy J Sullivan, Julian M Hess, Alexander A Gimelbrant, Rameen Beroukhim, Michael S Lawrence, Gad Getz, Andrew A Lane
There is a striking and unexplained male predominance across many cancer types. A subset of X-chromosome genes can escape X-inactivation, which would protect females from complete functional loss by a single mutation. To identify putative 'escape from X-inactivation tumor-suppressor' (EXITS) genes, we examined somatic alterations from >4,100 cancers across 21 tumor types for sex bias. Six of 783 non-pseudoautosomal region (PAR) X-chromosome genes (ATRX, CNKSR2, DDX3X, KDM5C, KDM6A, and MAGEC3) harbored loss-of-function mutations more frequently in males (based on a false discovery rate < 0...
January 2017: Nature Genetics
https://www.readbyqxmd.com/read/27799067/identification-of-a-rai1-associated-disease-network-through-integration-of-exome-sequencing-transcriptomics-and-3d-genomics
#10
Maria Nicla Loviglio, Christine R Beck, Janson J White, Marion Leleu, Tamar Harel, Nicolas Guex, Anne Niknejad, Weimin Bi, Edward S Chen, Isaac Crespo, Jiong Yan, Wu-Lin Charng, Shen Gu, Ping Fang, Zeynep Coban-Akdemir, Chad A Shaw, Shalini N Jhangiani, Donna M Muzny, Richard A Gibbs, Jacques Rougemont, Ioannis Xenarios, James R Lupski, Alexandre Reymond
BACKGROUND: Smith-Magenis syndrome (SMS) is a developmental disability/multiple congenital anomaly disorder resulting from haploinsufficiency of RAI1. It is characterized by distinctive facial features, brachydactyly, sleep disturbances, and stereotypic behaviors. METHODS: We investigated a cohort of 15 individuals with a clinical suspicion of SMS who showed neither deletion in the SMS critical region nor damaging variants in RAI1 using whole exome sequencing. A combination of network analysis (co-expression and biomedical text mining), transcriptomics, and circularized chromatin conformation capture (4C-seq) was applied to verify whether modified genes are part of the same disease network as known SMS-causing genes...
November 1, 2016: Genome Medicine
https://www.readbyqxmd.com/read/27751729/genomic-biomarkers-of-a-randomized-trial-comparing-first-line-everolimus-and-sunitinib-in-patients-with-metastatic-renal-cell-carcinoma
#11
James J Hsieh, David Chen, Patricia I Wang, Mahtab Marker, Almedina Redzematovic, Ying-Bei Chen, S Duygu Selcuklu, Nils Weinhold, Nancy Bouvier, Kety H Huberman, Umesh Bhanot, Michael S Chevinsky, Parul Patel, Patrizia Pinciroli, Helen H Won, Daoqi You, Agnes Viale, William Lee, A Ari Hakimi, Michael F Berger, Nicholas D Socci, Emily H Cheng, Jennifer Knox, Martin H Voss, Maurizio Voi, Robert J Motzer
BACKGROUND: Metastatic renal cell carcinoma (RCC) patients are commonly treated with vascular endothelial growth factor (VEGF) inhibitors or mammalian target of rapamycin inhibitors. Correlations between somatic mutations and first-line targeted therapy outcomes have not been reported on a randomized trial. OBJECTIVE: To evaluate the relationship between tumor mutations and treatment outcomes in RECORD-3, a randomized trial comparing first-line everolimus (mTOR inhibitor) followed by sunitinib (VEGF inhibitor) at progression with the opposite sequence in 471 metastatic RCC patients...
March 2017: European Urology
https://www.readbyqxmd.com/read/27696497/cofactors-loaded-quaternary-structure-of-lysine-specific-demethylase-5c-kdm5c-protein-computational-model
#12
Yunhui Peng, Emil Alexov
The KDM5C gene (also known as JARID1C and SMCX) is located on the X chromosome and encodes a ubiquitously expressed 1560-aa protein, which plays an important role in lysine methylation (specifically reverses tri- and di-methylation of Lys4 of histone H3). Currently, 13 missense mutations in KDM5C have been linked to X-linked mental retardation. However, the molecular mechanism of disease is currently unknown due to the experimental difficulties in expressing such large protein and the lack of experimental 3D structure...
December 2016: Proteins
https://www.readbyqxmd.com/read/27626165/mutational-burdens-and-evolutionary-ages-of-thyroid-follicular-adenoma-are-comparable-to-those-of-follicular-carcinoma
#13
Seung-Hyun Jung, Min Sung Kim, Chan Kwon Jung, Hyun-Chun Park, So Youn Kim, Jieying Liu, Ja-Seong Bae, Sung Hak Lee, Tae-Min Kim, Sug Hyung Lee, Yeun-Jun Chung
Follicular thyroid adenoma (FTA) precedes follicular thyroid carcinoma (FTC) by definition with a favorable prognosis compared to FTC. However, the genetic mechanism of FTA to FTC progression remains unknown. For this, it is required to disclose FTA and FTC genomes in mutational and evolutionary perspectives. We performed whole-exome sequencing and copy number profiling of 14 FTAs and 13 FTCs, which exhibited previously-known gene mutations (NRAS, HRAS, BRAF, TSHR and EIF1AX) and copy number alterations (CNAs) (22q loss and 1q gain) in follicular tumors...
October 25, 2016: Oncotarget
https://www.readbyqxmd.com/read/27556922/an-integrative-genomics-approach-for-identifying-novel-functional-consequences-of-pbrm1-truncated-mutations-in-clear-cell-renal-cell-carcinoma-ccrcc
#14
Yuanyuan Wang, Xingyi Guo, Michael J Bray, Zhiyong Ding, Zhongming Zhao
BACKGROUND: Clear cell renal cell carcinoma (ccRCC) is the most common type of kidney cancer. Recent large-scale next-generation sequencing analyses reveal that PBRM1 is the second most frequently mutated gene harboring many truncated mutations and has a suspected tumor suppressor role in ccRCC. However, the biological consequences of PBRM1 somatic mutations (e.g., truncated mutations) that drive tumor progression in ccRCC remain unclear. METHODS: In this study, we proposed an integrative genomics approach to explore the functional consequences of PBRM1 truncated mutations in ccRCC by incorporating somatic mutations, mRNA expression, DNA methylation, and microRNA (miRNA) expression profiles from The Cancer Genome Atlas (TCGA)...
August 22, 2016: BMC Genomics
https://www.readbyqxmd.com/read/27421841/patient-mutations-of-the-intellectual-disability-gene-kdm5c-downregulate-netrin-g2-and-suppress-neurite-growth-in-neuro2a-cells
#15
Gengze Wei, Xinxian Deng, Saurabh Agarwal, Shigeki Iwase, Christine Disteche, Jun Xu
The X-linked lysine (K)-specific demethylase 5C (KDM5C) gene plays an important role in brain development and behavior. It encodes a histone demethylase that is involved in gene regulation in neuronal differentiation and morphogenesis. When mutated, it causes neuropsychiatric symptoms, such as intellectual disability, delayed language development, epilepsy, and impulsivity. To better understand how the patient mutations affect neuronal development, we expressed KDM5C mutants in Neuro2a cells, a mouse neuroblastoma cell line...
September 2016: Journal of Molecular Neuroscience: MN
https://www.readbyqxmd.com/read/27282397/histopathologic-review-of-pineal-parenchymal-tumors-identifies-novel-morphologic-subtypes-and-prognostic-factors-for-outcome
#16
David R Raleigh, David A Solomon, Shane A Lloyd, Ann Lazar, Michael A Garcia, Penny K Sneed, Jennifer L Clarke, Michael W McDermott, Mitchel S Berger, Tarik Tihan, Daphne A Haas-Kogan
BACKGROUND: Pineal parenchymal tumors (PPTs) are rare neoplasms of the central nervous system, and data concerning clinical outcomes are limited. The purpose of this study was to define the clinical behavior of PPT according to current histopathologic criteria and identify prognostic factors to guide therapeutic decisions. METHODS: Seventy-five patients treated for PPT at a single institution between 1992 and 2015 were retrospectively identified. Forty-five resection specimens were available and re-reviewed...
January 2017: Neuro-oncology
https://www.readbyqxmd.com/read/27188282/epigenetically-maintained-sw13-and-sw13-subtypes-have-different-oncogenic-potential-and-convert-with-hdac1-inhibition
#17
McKale R Davis, Juliane J Daggett, Agnes S Pascual, Jessica M Lam, Kathryn J Leyva, Kimbal E Cooper, Elizabeth E Hull
BACKGROUND: The BRM and BRG1 tumor suppressor genes are mutually exclusive ATPase subunits of the SWI/SNF chromatin remodeling complex. The human adrenal carcinoma SW13 cell line can switch between a subtype which expresses these subunits, SW13+, and one that expresses neither subunit, SW13-. Loss of BRM expression occurs post-transcriptionally and can be restored via histone deacetylase (HDAC) inhibition. However, most previously used HDAC inhibitors are toxic and broad-spectrum, providing little insight into the mechanism of the switch between subtypes...
2016: BMC Cancer
https://www.readbyqxmd.com/read/27173781/unclassified-renal-cell-carcinoma-with-tubulopapillary-architecture-clear-cell-phenotype-and-chromosome-8-monosomy-a-new-kid-on-the-block
#18
Thanh T H Lan, Jennifer Keller-Ramey, Carrie Fitzpatrick, Sabah Kadri, Jerome B Taxy, Jeremy P Segal, Larissa V Furtado, Tatjana Antic
Accurate subtyping of renal cell carcinomas (RCCs) has become clinically important for therapy and prognostication. RCC subtypes are defined by distinct morphologic and immunohistochemical profiles, and in some instances recurrent cytogenetic and molecular properties. However, some tumors exhibit overlapping morphologic and immunophenotypic features, frequent enough to pose diagnostic dilemmas. This report concerns six histologically unusual RCCs that showed tubulopapillary architecture, clear cell phenotype, and non-diagnostic immunohistochemical profiles...
July 2016: Virchows Archiv: An International Journal of Pathology
https://www.readbyqxmd.com/read/27100321/a-combinative-analysis-of-gene-expression-profiles-and-microrna-expression-profiles-identifies-critical-genes-and-micrornas-in-oral-lichen-planus
#19
Qing Liu, Xinwen Wang, Yuan Liu, Minghui Wei, Lihua Chen
OBJECTIVE: Oral lichen planus (OLP) is a chronic inflammatory disease but aetiology and pathogenesis has not fully elucidated. To gain insight into the mechanism of OLP, bioinformatic analysis was performed in this study. DESIGN: GSE38616 and GSE38615 were downloaded from GEO, including 7 cases of OLP and 7 healthy controls. Differentially expressed genes (DEGs) and miRNAs (DEMs) between OLP and control were screened with package Limma of R. Potential regulatory miRNAs were screened via gene set enrichment analysis...
August 2016: Archives of Oral Biology
https://www.readbyqxmd.com/read/27058665/suppression-of-enhancer-overactivation-by-a-rack7-histone-demethylase-complex
#20
Hongjie Shen, Wenqi Xu, Rui Guo, Bowen Rong, Lei Gu, Zhentian Wang, Chenxi He, Lijuan Zheng, Xin Hu, Zhen Hu, Zhi-Ming Shao, Pengyuan Yang, Feizhen Wu, Yujiang Geno Shi, Yang Shi, Fei Lan
Regulation of enhancer activity is important for controlling gene expression programs. Here, we report that a biochemical complex containing a potential chromatin reader, RACK7, and the histone lysine 4 tri-methyl (H3K4me3)-specific demethylase KDM5C occupies many active enhancers, including almost all super-enhancers. Loss of RACK7 or KDM5C results in overactivation of enhancers, characterized by the deposition of H3K4me3 and H3K27Ac, together with increased transcription of eRNAs and nearby genes. Furthermore, loss of RACK7 or KDM5C leads to de-repression of S100A oncogenes and various cancer-related phenotypes...
April 7, 2016: Cell
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