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JOURNAL ARTICLE
Arun Kumar Burramsetty, Ken Nishimura, Takumi Kishimoto, Muhammad Hamzah, Akihiro Kuno, Aya Fukuda, Koji Hisatake
Pluripotency is a crucial feature of pluripotent stem cells, which are regulated by the core pluripotency network consisting of key transcription factors and signaling molecules. However, relatively less is known about the molecular mechanisms that modify the core pluripotency network. Here we used the CAPTURE (CRISPR Affinity Purification in situ of Regulatory Elements) to unbiasedly isolate proteins assembled on the Nanog promoter in mouse embryonic stem cells (mESCs), and then tested their functional relevance to the maintenance of mESCs and reprogramming of somatic cells...
December 3, 2022: International Journal of Molecular Sciences
#22
JOURNAL ARTICLE
Maaike Y Kapteijn, Fleur H J Kaptein, Milou A M Stals, Eva E Klaase, Inés García-Ortiz, Ronald van Eijk, Dina Ruano, Sjoerd G van Duinen, Suzanne C Cannegieter, Martin J B Taphoorn, Linda Dirven, Johan A F Koekkoek, Frederikus A Klok, Henri H Versteeg, Jeroen T Buijs
BACKGROUND AND OBJECTIVES: Patients with glioblastoma have a high risk of developing venous thromboembolism (VTE). However, the role of underlying genetic risk factors remains largely unknown. Therefore, the aim of this study was to discover whether genetic aberrations in glioblastoma associate with VTE risk. METHODS: In this cohort study, all consecutive patients diagnosed with glioblastoma in two Dutch hospitals between February 2017 and August 2020 were included...
November 17, 2022: Thrombosis Research
#23
JOURNAL ARTICLE
A mass spectrometry-based approach for the identification of Kpnβ1 binding partners in cancer cells.
Michael O Okpara, Clemens Hermann, Pauline J van der Watt, Shaun Garnett, Jonathan M Blackburn, Virna D Leaner
Karyopherin beta 1 (Kpnβ1) is the principal nuclear importer of cargo proteins and plays a role in many cellular processes. Its expression is upregulated in cancer and essential for cancer cell viability, thus the identification of its binding partners might help in the discovery of anti-cancer therapeutic targets and cancer biomarkers. Herein, we applied immunoprecipitation coupled to mass spectrometry (IP-MS) to identify Kpnβ1 binding partners in normal and cancer cells. IP-MS identified 100 potential Kpnβ1 binding partners in non-cancer hTERT-RPE1, 179 in HeLa cervical cancer, 147 in WHCO5 oesophageal cancer and 176 in KYSE30 oesophageal cancer cells, including expected and novel interaction partners...
November 23, 2022: Scientific Reports
#24
JOURNAL ARTICLE
Wanyun Nie, Mobai Li, Boqiang Liu, Ying Zhang, Yuxi Wang, Junni Wang, Lini Jin, Anqi Ni, Liang Xiao, Xiao Z Shen, Jianghua Chen, Weiqiang Lin, Fei Han
Fibrosis is a relentlessly progressive and irreversible cause of organ damage, as in chronic kidney disease (CKD), but its underlying mechanisms remain elusive. We found that a circular RNA, circPTPN14, is highly expressed in human kidneys with biopsy-proved chronic interstitial fibrosis, mouse kidneys subjected to ischemia/reperfusion (IR) or unilateral ureteral obstruction (UUO), and TGFβ1-stimulated renal tubule epithelial cells (TECs). The intrarenal injection of circPTPN14 shRNA alleviated the progression of fibrosis in kidneys subjected to IR or UUO...
November 17, 2022: Cellular and Molecular Life Sciences: CMLS
#25
JOURNAL ARTICLE
Aiste Dobrovolskaite, Holly Moots, Mukund P Tantak, Kunal Shah, Jenna Thomas, Sharifa Dinara, Chelsea Massaro, Paul M Hershberger, Patrick R Maloney, Satyamaheshwar Peddibhotla, Eliot Sugarman, Sally Litherland, Juan Pablo Arnoletti, Rajiv Kumar Jha, David Levens, Otto Phanstiel
Polyamine biosynthesis is regulated by ornithine decarboxylase (ODC), which is transcriptionally activated by c-Myc. A large library was screened to find molecules that potentiate the ODC inhibitor, difluoromethylornithine (DFMO). Anthranilic acid derivatives were identified as DFMO adjunct agents. Further studies identified the far upstream binding protein 1 (FUBP1) as the target of lead compound 9 . FUBP1 is a single-stranded DNA/RNA binding protein and a master controller of specific genes including c-Myc and p21...
November 16, 2022: Journal of Medicinal Chemistry
#26
JOURNAL ARTICLE
Weichen Wang, Zhichao Lu, Maoyu Wang, Zongheng Liu, Bing Wu, Chengkai Yang, He Huan, Peipei Gong
BACKGROUND: Copper ions are essential for cellular physiology. Cuproptosis is a novel method of copper-dependent cell death, and the cuproptosis-based signature for glioma remains less studied. METHODS: Several glioma datasets with clinicopathological information were collected from TCGA, GEO and CGGA. Robust Multichip Average (RMA) algorithm was used for background correction and normalization, cuproptosis-related genes (CRGs) were then collected. The TCGA-glioma cohort was clustered using ConsensusClusterPlus...
2022: Frontiers in Immunology
#27
JOURNAL ARTICLE
Dinesh Kumar Sahu, Neetu Singh, Mumani Das, Jiledar Rawat, Devendra Kumar Gupta
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...
November 2022: Pediatric Surgery International
#28
JOURNAL ARTICLE
Jie Yu, Wen Peng, Yingbo Xue, Yun Li, Lei Yang, Yang Geng
BACKGROUND AND AIM: Lung cancer is a common malignancy. Non-small cell lung cancer (NSCLC) is divided into lung squamous cancer (LUSC), large cell carcinoma, and adenocarcinoma. More than 85% of lung cancer cases are NSCLC patients. Further exploration of the pathogenesis of lung cancer is of great significance. In this study, functions of far upstream element-binding protein 1 (FUBP1) on the proliferation and tumor immunity of LUSC cells were evaluated. MATERIALS AND METHODS: The Cancer Genome Atlas (TCGA) database, Western blot analysis, and immunohistochemistry (IHC) analysis were used to examine the overexpression levels of FUBP1 in LUSC and paracancerous tissues, LUSC cell line, and human normal lung cell line...
2022: Allergologia et Immunopathologia
#29
JOURNAL ARTICLE
Marco Dicanio, Matteo Giaccherini, Alyssa Clay-Gilmour, Angelica Macauda, Juan Sainz, Mitchell J Machiela, Malwina Rybicka-Ramos, Aaron D Norman, Agata Tyczyńska, Stephen J Chanock, Torben Barington, Shaji K Kumar, Parveen Bhatti, Wendy Cozen, Elizabeth E Brown, Anna Suska, Eva K Haastrup, Robert Z Orlowski, Marek Dudziński, Ramon Garcia-Sanz, Marcin Kruszewski, Joaquin Martinez-Lopez, Katia Beider, Elżbieta Iskierka-Jazdzewska, Matteo Pelosini, Sonja I Berndt, Małgorzata Raźny, Krzysztof Jamroziak, S Vincent Rajkumar, Artur Jurczyszyn, Annette Juul Vangsted, Pilar Garrido Collado, Ulla Vogel, Jonathan N Hofmann, Mario Petrini, Aleksandra Butrym, Susan L Slager, Elad Ziv, Edyta Subocz, Graham G Giles, Niels Frost Andersen, Grzegorz Mazur, Marzena Watek, Fabienne Lesueur, Michelle A T Hildebrandt, Daria Zawirska, Lene Hyldahl Ebbesen, Herlander Marques, Federica Gemignani, Charles Dumontet, Judit Várkonyi, Gabriele Buda, Arnon Nagler, Agnieszka Druzd-Sitek, Xifeng Wu, Katalin Kadar, Nicola J Camp, Norbert Grzasko, Rosalie G Waller, Celine Vachon, Federico Canzian, Daniele Campa
Pleiotropy, which consists of a single gene or allelic variant affecting multiple unrelated traits, is common across cancers, with evidence for genome-wide significant loci shared across cancer and non-cancer traits. This feature is particularly relevant in multiple myeloma (MM) because several susceptibility loci that have been identified to date are pleiotropic. Therefore, the aim of this study was to identify novel pleiotropic variants involved in MM risk using 28,684 independent single nucleotide polymorphisms (SNPs) from GWAS Catalog that reached a significant association (P<5x10-8 ) with their respective trait...
September 8, 2022: International Journal of Cancer. Journal International du Cancer
#30
JOURNAL ARTICLE
Baiqing Tang, Hyung-Ok Lee, Sapna Gupta, Liqun Wang, Alison M Kurimchak, James S Duncan, Warren D Kruger
Methylthioadenosine phosphorylase (MTAP) is a key enzyme in the methionine salvage pathway that converts the polyamine synthesis byproduct 5'-deoxy-5'-methylthioadenosine (MTA) into methionine. Inactivation of MTAP, often by homozygous deletion, is found in both solid and hematologic malignancies and is one of the most frequently observed genetic alterations in human cancer. Previous work established that MTAP-deleted cells accumulate MTA and contain decreased amounts of proteins with arginine residues symmetrically dimethylated (sDMA)...
August 10, 2022: Journal of Biological Chemistry
#31
JOURNAL ARTICLE
Jinyoung Byun, Younghun Han, Yafang Li, Jun Xia, Erping Long, Jiyeon Choi, Xiangjun Xiao, Meng Zhu, Wen Zhou, Ryan Sun, Yohan Bossé, Zhuoyi Song, Ann Schwartz, Christine Lusk, Thorunn Rafnar, Kari Stefansson, Tongwu Zhang, Wei Zhao, Rowland W Pettit, Yanhong Liu, Xihao Li, Hufeng Zhou, Kyle M Walsh, Ivan Gorlov, Olga Gorlova, Dakai Zhu, Susan M Rosenberg, Susan Pinney, Joan E Bailey-Wilson, Diptasri Mandal, Mariza de Andrade, Colette Gaba, James C Willey, Ming You, Marshall Anderson, John K Wiencke, Demetrius Albanes, Stephan Lam, Adonina Tardon, Chu Chen, Gary Goodman, Stig Bojeson, Hermann Brenner, Maria Teresa Landi, Stephen J Chanock, Mattias Johansson, Thomas Muley, Angela Risch, H-Erich Wichmann, Heike Bickeböller, David C Christiani, Gad Rennert, Susanne Arnold, John K Field, Sanjay Shete, Loic Le Marchand, Olle Melander, Hans Brunnstrom, Geoffrey Liu, Angeline S Andrew, Lambertus A Kiemeney, Hongbing Shen, Shanbeh Zienolddiny, Kjell Grankvist, Mikael Johansson, Neil Caporaso, Angela Cox, Yun-Chul Hong, Jian-Min Yuan, Philip Lazarus, Matthew B Schabath, Melinda C Aldrich, Alpa Patel, Qing Lan, Nathaniel Rothman, Fiona Taylor, Linda Kachuri, John S Witte, Lori C Sakoda, Margaret Spitz, Paul Brennan, Xihong Lin, James McKay, Rayjean J Hung, Christopher I Amos
To identify new susceptibility loci to lung cancer among diverse populations, we performed cross-ancestry genome-wide association studies in European, East Asian and African populations and discovered five loci that have not been previously reported. We replicated 26 signals and identified 10 new lead associations from previously reported loci. Rare-variant associations tended to be specific to populations, but even common-variant associations influencing smoking behavior, such as those with CHRNA5 and CYP2A6, showed population specificity...
August 1, 2022: Nature Genetics
#32
JOURNAL ARTICLE
Parisa Prathaphan, Onrapak Reamtong, Utapin Ngaokrajang, Tavan Janvilisri, Napachanok Mongkoldhumrongkul Swainson, Pichamon Kiatwuthinon
BACKGROUND/AIM: Nasopharyngeal carcinoma (NPC) originates in the hidden nasopharynx, causing NPC patients to be diagnosed at a late stage and develop drug resistance. Therefore, the identification of drug-resistance biomarkers is indispensable to improve NPC detection and treatment. Hence, this study aimed to identify novel cisplatinresistance biomarkers using comparative proteomic profiles of cisplatin-resistant (CDDP/NPC) cell lines. MATERIALS AND METHODS: Two cisplatin-resistant NPC cell lines (CDDP/5-8F and CDDP/6-10B) were established by a continuous cisplatin treatment...
July 2022: Anticancer Research
#33
Georgia Kaidonis, Melike Pekmezci, Jessica Van Ziffle, Kurtis I Auguste, Jonathan C Horton
BACKGROUND: In the past decade, next-generation sequencing has spurred significant progress in the understanding of cytogenetic alterations that occur in meningiomas. Eighty percent of adult meningiomas harbor pathogenic somatic variants involving NF2 , TRAF7 , SMARCB1 , KLF4 , PI3K , or POLR2A. Somatic variants in TRAF7 associated with meningiomas usually localize to the gene's WD40 domains but are mutually exclusive to germline mutations, which cause a distinctive autosomal dominant syndrome...
June 6, 2022: J Neurosurg Case Lessons
#34
JOURNAL ARTICLE
Aparna Pallavajjala, Lisa Haley, Victoria Stinnett, Emily Adams, Roshni Pallavajjala, Jialing Huang, Laura Morsberger, Melanie Hardy, Patty Long, Christopher D Gocke, James R Eshleman, Fausto J Rodriguez, Ying S Zou
Molecular classification of brain neoplasms is important for diagnosis, prognosis, and treatment outcome of histologically similar tumors. Oligodendroglioma is a glioma subtype characterized by 1p/19q co-deletion and IDH1/IDH2 mutations, which predict a good prognosis, responsiveness to therapy, and an improved overall survival compared to other adult gliomas. In a routine clinical setting, 1p/19q co-deletion is detected by interphase-FISH and SNP microarray, and somatic mutations are detected by targeted next-generation sequencing (NGS)...
August 2022: Human Pathology
#35
JOURNAL ARTICLE
Priyanka Patel, Courtney N Buchanan, Matthew D Zdradzinski, Pabitra K Sahoo, Amar N Kar, Seung Joon Lee, Lauren S Vaughn, Anatoly Urisman, Juan Oses-Prieto, Michela Dell'Orco, Devon E Cassidy, Irene Dalla Costa, Sharmina Miller, Elizabeth Thames, Terika P Smith, Alma L Burlingame, Nora Perrone-Bizzozero, Jeffery L Twiss
Axonally synthesized proteins support nerve regeneration through retrograde signaling and local growth mechanisms. RNA binding proteins (RBP) are needed for this and other aspects of post-transcriptional regulation of neuronal mRNAs, but only a limited number of axonal RBPs are known. We used targeted proteomics to profile RBPs in peripheral nerve axons. We detected 76 proteins with reported RNA binding activity in axoplasm, and levels of several change with axon injury and regeneration. RBPs with altered levels include KHSRP that decreases neurite outgrowth in developing CNS neurons...
June 10, 2022: Nucleic Acids Research
#36
JOURNAL ARTICLE
Shanwei Wang, Yanli Wang, Sheng Li, Shen Nian, Wenjing Xu, Fenli Liang
Human distal upstream element (Fuse) binding protein 1 (FUBP1) is a transcriptional regulator of c-Myc and represents an important prognostic marker in many cancers. Therefore, the present study aimed to investigate whether FUBP1 could combine with c-Myc to participate in the progression of colon cancer. Detection of FUBP1 expression was done through reverse transcription-quantitative PCR (RT-qPCR), and the combination of FUBP1 and c-Myc was detected by immunoprecipitation assay. Cell counting kit (CCK)-8, colony formation, transwell and wound healing were applied for assessing the ability of cells to proliferate, migrate, and invade; glycolysis and lactic acid detection kits were used to detect glucose uptake and lactic acid content, while western blotting was adopted to detect the protein expression of glycolysis-related genes...
May 2022: Bioengineered
#37
JOURNAL ARTICLE
Fucheng Zhang, Yingge Zhang, Yaojun Wang
BACKGROUND: The research aimed to observe the effect of gene silencing on the proliferation, migration, cell cycle, apoptosis, and other biological functions of human gastric cancer cells with RNA interference inhibiting the expression of the far upstream element-binding protein 1 (FUBP1) in the gastric cancer cell line SGC7901. METHODS: The shRNA lentivirus vector of the target gene FUBP1 was constructed to transfect the gastric cancer cell line SGC7901. The qRT-PCR and western blot assays were used to detect the expression levels of FUBP1 mRNA and protein in the gastric cancer cells...
November 2021: Turkish Journal of Gastroenterology: the Official Journal of Turkish Society of Gastroenterology
#38
JOURNAL ARTICLE
Hai Wen, Yang Fu, Yapeng Zhu, Siyue Tao, Xifu Shang, Zhongqi Li, Tao You, Wenzhi Zhang
Chordomas are low-grade malignancies accounting for 1-4% of primary bone malignancies. Moreover, local recurrences increase the rate of metastasis. Our previous study identified the far upstream element (FUSE)-binding protein 1 (FUBP1) as a biomarker and potential therapeutic target for chordoma. In this study, lncRNA KRT8P41 was identified as a lncRNA positively correlated with FUBP1. In chordoma patients, higher lncRNA KRT8P41 expression was correlated with a poorer prognosis. LncRNA KRT8P41 silencing significantly inhibited chordoma cell proliferation and invasion...
December 2021: Journal of Bone Oncology
#39
JOURNAL ARTICLE
Jessica L Fleming, Stephanie L Pugh, Barbara J Fisher, Glenn J Lesser, David R Macdonald, Erica H Bell, Joseph P McElroy, Aline P Becker, Cynthia D Timmers, Kenneth D Aldape, C Leland Rogers, Thomas J Doyle, Maria Werner-Wasik, Jean-Paul Bahary, Hsiang-Hsuan Michael Yu, David P D'Souza, Nadia N Laack, Penny K Sneed, Young Kwok, Minhee Won, Minesh P Mehta, Arnab Chakravarti
PURPOSE: This study sought to determine the prognostic significance of the WHO-defined glioma molecular subgroups along with additional alterations, including MGMT promoter methylation and mutations in ATRX , CIC , FUBP1 , TERT , and TP53 , in NRG/RTOG 0424 using long-term follow-up data. METHODS: Mutations were determined using an Ion Torrent sequencing panel. 1p/19q co-deletion and MGMT promoter methylation were determined by Affymetrix OncoScan and Illumina 450K arrays...
2021: JCO Precision Oncology
#40
JOURNAL ARTICLE
Jun Lu, Yanwei Zhang, Yuqing Lou, Bo Yan, Benkun Zou, Minjuan Hu, Yanan Wang, Ya Chen, Zhengyu Yang, Huimin Wang, Wei Zhang, Baohui Han
Atezolizumab, an immune checkpoint inhibitor, has been approved for use in clinical practice in non-small cell lung cancer (NSCLC) patients, but potential biomarkers for response stratification still need further screening. In the present study, a total of 399 patients with high-quality ctDNA profiling results were included. The mutation status of ubiquitin-like conjugation (UBL) biological process genes (including ABL1 , APC , LRP6 , FUBP1 , KEAP1 , and TOP2A ) and clinical information were further integrated...
2021: Frontiers in Genetics
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