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Ryan J Golden, Beibei Chen, Tuo Li, Juliane Braun, Hema Manjunath, Xiang Chen, Jiaxi Wu, Vanessa Schmid, Tsung-Cheng Chang, Florian Kopp, Andres Ramirez-Martinez, Vincent S Tagliabracci, Zhijian J Chen, Yang Xie, Joshua T Mendell
MicroRNAs (miRNAs) perform critical functions in normal physiology and disease by associating with Argonaute proteins and downregulating partially complementary messenger RNAs (mRNAs). Here we use clustered regularly interspaced short palindromic repeats (CRISPR) and CRISPR-associated protein 9 (Cas9) genome-wide loss-of-function screening coupled with a fluorescent reporter of miRNA activity in human cells to identify new regulators of the miRNA pathway. By using iterative rounds of screening, we reveal a novel mechanism whereby target engagement by Argonaute 2 (AGO2) triggers its hierarchical, multi-site phosphorylation by CSNK1A1 on a set of highly conserved residues (S824-S834), followed by rapid dephosphorylation by the ANKRD52-PPP6C phosphatase complex...
February 9, 2017: Nature
Naoko Hosono, Hideki Makishima, Reda Mahfouz, Bartlomiej Przychodzen, Kenichi Yoshida, Andres Jerez, Thomas LaFramboise, Chantana Polprasert, Michael J Clemente, Yuichi Shiraishi, Kenichi Chiba, Hiroko Tanaka, Satoru Miyano, Masashi Sanada, Edward Cui, Amit K Verma, Michael A McDevitt, Alan F List, Yogen Saunthararajah, Mikkael A Sekeres, Jacqueline Boultwood, Seishi Ogawa, Jaroslaw P Maciejewski
BACKGROUND: Deletion of chromosome 5q (del(5q)) is the most common karyotypic abnormality in myeloid neoplasms. MATERIALS AND METHODS: To define the pathogenic molecular features associated with del(5q), next-generation sequencing was applied to 133 patients with myeloid neoplasms (MDS; N = 69, MDS/MPN; N = 5, sAML; N = 29, pAML; N = 30) with del(5q) as a sole abnormally or a part of complex karyotype and results were compared to molecular features of patients diploid for chr5...
January 24, 2017: Oncotarget
Leylah Drusbosky, Cindy Medina, Regina Martuscello, Kimberly E Hawkins, Myron Chang, Jatinder K Lamba, Shireen Vali, Ansu Kumar, Neeraj Kumar Singh, Taher Abbasi, Mikkael A Sekeres, Mar Mallo, Francesc Sole, Rafael Bejar, Christopher R Cogle
Although the majority of MDS patients fail to achieve clinical improvement to approved therapies, some patients benefit from treatment. Predicting patient response prior to therapy would improve treatment effectiveness, avoid treatment-related adverse events and reduce healthcare costs. Three separate cohorts of MDS patients were used to simulate drug response to lenalidomide alone, hypomethylating agent (HMA) alone, or HMA plus lenalidomide. Utilizing a computational biology program, genomic abnormalities in each patient were used to create an intracellular pathway map that was then used to screen for drug response...
January 2017: Leukemia Research
Xiang Shu, Yuanqing Ye, Jian Gu, Yonggang He, John W Davis, Timothy C Thompson, Christopher J Logothetis, Jeri Kim, Xifeng Wu
Little is known about the genetic predictors of prostate cancer aggressiveness and reclassification in men with localized prostate cancer undergoing active surveillance. The Wnt signaling pathway is important for prostate cancer development and progression. Identifying genetic variants associated with prostate cancer aggressiveness and reclassification may have a potential role in the management of localized patients. In this study, we used a three-phase design. In phases I and II prostate cancer patient cohort, 578 single nucleotide polymorphisms (SNPs) from 45 genes of the Wnt signaling pathway were analyzed in 1762 localized prostate cancer patients...
October 2016: Carcinogenesis
Jorunn Litlekalsoy, Kari Rostad, Karl-Henning Kalland, Jens G Hostmark, Ole Didrik Laerum
BACKGROUND: The purpose of this study was to evaluate invasive and metastatic potential of urothelial cancer by investigating differential expression of various clock genes/proteins participating in the 24 h circadian rhythms and to compare these gene expressions with transcription of other cancer-associated genes. METHODS: Twenty seven paired samples of tumour and benign tissue collected from patients who underwent cystectomy were analysed and compared to 15 samples of normal bladder tissue taken from patients who underwent cystoscopy for benign prostate hyperplasia (unrelated donors)...
2016: BMC Cancer
Christopher M Hale, Qingwen Cheng, Danny Ortuno, Ming Huang, Dana Nojima, Paul D Kassner, Songli Wang, Michael M Ollmann, Holly J Carlisle
Autophagy is the primary process for recycling cellular constituents through lysosomal degradation. In addition to nonselective autophagic engulfment of cytoplasm, autophagosomes can recognize specific cargo by interacting with ubiquitin-binding autophagy receptors such as SQSTM1/p62 (sequestosome 1). This selective form of autophagy is important for degrading aggregation-prone proteins prominent in many neurodegenerative diseases. We carried out a high content image-based siRNA screen (4 to 8 siRNA per gene) for modulators of autophagic flux by monitoring fluorescence of GFP-SQSTM1 as well as colocalization of GFP-SQSTM1 with LAMP2 (lysosomal-associated membrane protein 2)-positive lysosomal vesicles...
2016: Autophagy
D F Levey, E M Niculescu, H Le-Niculescu, H L Dainton, P L Phalen, T B Ladd, H Weber, E Belanger, D L Graham, F N Khan, N P Vanipenta, E C Stage, A Ballew, M Yard, T Gelbart, A Shekhar, N J Schork, S M Kurian, G E Sandusky, D R Salomon, A B Niculescu
Women are under-represented in research on suicidality to date. Although women have a lower rate of suicide completion than men, due in part to the less-violent methods used, they have a higher rate of suicide attempts. Our group has previously identified genomic (blood gene expression biomarkers) and clinical information (apps) predictors for suicidality in men. We now describe pilot studies in women. We used a powerful within-participant discovery approach to identify genes that change in expression between no suicidal ideation (no SI) and high suicidal ideation (high SI) states (n=12 participants out of a cohort of 51 women psychiatric participants followed longitudinally, with diagnoses of bipolar disorder, depression, schizoaffective disorder and schizophrenia)...
June 2016: Molecular Psychiatry
Eric S Okerberg, Anna Hainley, Heidi Brown, Arwin Aban, Senait Alemayehu, Ann Shih, Jane Wu, Matthew P Patricelli, John W Kozarich, Tyzoon Nomanbhoy, Jonathan S Rosenblum
We describe the identification of a novel, tumor-specific missense mutation in the active site of casein kinase 1α (CSNK1A1) using activity-based proteomics. Matched normal and tumor colon samples were analyzed using an ATP acyl phosphate probe in a kinase-targeted LC-MS2 platform. An anomaly in the active-site peptide from CSNK1A1 was observed in a tumor sample that was consistent with an altered catalytic aspartic acid. Expression and analysis of the suspected mutant verified the presence of asparagine in the probe-labeled, active-site peptide for CSNK1A1...
2016: PloS One
Tsung-Chieh Lin, Chia-Yi Su, Pei-Yu Wu, Tsung-Ching Lai, Wen-An Pan, Yi-Hua Jan, Yu-Chang Chang, Chi-Tai Yeh, Chi-Long Chen, Luo-Ping Ger, Hong-Tai Chang, Chih-Jen Yang, Ming-Shyan Huang, Yu-Peng Liu, Yuan-Feng Lin, John Y-J Shyy, Ming-Daw Tsai, Michael Hsiao
Nucleolar protein interacting with the FHA domain of pKi-67 (NIFK) is a Ki-67-interacting protein. However, its precise function in cancer remains largely uninvestigated. Here we show the clinical significance and metastatic mechanism of NIFK in lung cancer. NIFK expression is clinically associated with poor prognosis and metastasis. Furthermore, NIFK enhances Ki-67-dependent proliferation, and promotes migration, invasion in vitro and metastasis in vivo via downregulation of casein kinase 1α (CK1α), a suppressor of pro-metastatic TCF4/β-catenin signaling...
March 17, 2016: ELife
Alexander E Smith, Austin G Kulasekararaj, Jie Jiang, Syed Mian, Azim Mohamedali, Joop Gaken, Robin Ireland, Barbara Czepulkowski, Steven Best, Ghulam J Mufti
BACKGROUND: A mechanism for clonal growth advantage in isolated del(5q) disease remains elusive. CSNK1A1 resides on the critically deleted region, and deletion of this gene has been shown in mouse knockout and transplantation studies to produce some characteristics of bone marrow failure, including a proliferative advantage. We aimed to establish the frequency, nature, and clinical association of CSNK1A1 mutations in patients with myelodysplastic syndrome and associated myeloid neoplasms...
May 2015: Lancet Haematology
Jacqueline Boultwood, Andrea Pellagatti
No abstract text is available yet for this article.
May 2015: Lancet Haematology
Alexandra B Lantermann, Dongshu Chen, Kaitlin McCutcheon, Greg Hoffman, Elizabeth Frias, David Ruddy, Daniel Rakiec, Joshua Korn, Gregory McAllister, Frank Stegmeier, Matthew J Meyer, Sreenath V Sharma
Patients with lung tumors harboring activating mutations in the EGF receptor (EGFR) show good initial treatment responses to the EGFR tyrosine kinase inhibitors (TKI) erlotinib or gefitinib. However, acquired resistance invariably develops. Applying a focused shRNA screening approach to identify genes whose knockdown can prevent and/or overcome acquired resistance to erlotinib in several EGFR-mutant non-small cell lung cancer (NSCLC) cell lines, we identified casein kinase 1 α (CSNK1A1, CK1α). We found that CK1α suppression inhibits the NF-κB prosurvival signaling pathway...
November 15, 2015: Cancer Research
Keisuke Kataoka, Yasunobu Nagata, Akira Kitanaka, Yuichi Shiraishi, Teppei Shimamura, Jun-Ichirou Yasunaga, Yasushi Totoki, Kenichi Chiba, Aiko Sato-Otsubo, Genta Nagae, Ryohei Ishii, Satsuki Muto, Shinichi Kotani, Yosaku Watatani, June Takeda, Masashi Sanada, Hiroko Tanaka, Hiromichi Suzuki, Yusuke Sato, Yusuke Shiozawa, Tetsuichi Yoshizato, Kenichi Yoshida, Hideki Makishima, Masako Iwanaga, Guangyong Ma, Kisato Nosaka, Masakatsu Hishizawa, Hidehiro Itonaga, Yoshitaka Imaizumi, Wataru Munakata, Hideaki Ogasawara, Toshitaka Sato, Ken Sasai, Kenzo Muramoto, Marina Penova, Takahisa Kawaguchi, Hiromi Nakamura, Natsuko Hama, Kotaro Shide, Yoko Kubuki, Tomonori Hidaka, Takuro Kameda, Tsuyoshi Nakamaki, Ken Ishiyama, Shuichi Miyawaki, Sung-Soo Yoon, Kensei Tobinai, Yasushi Miyazaki, Akifumi Takaori-Kondo, Fumihiko Matsuda, Kengo Takeuchi, Osamu Nureki, Hiroyuki Aburatani, Toshiki Watanabe, Tatsuhiro Shibata, Masao Matsuoka, Satoru Miyano, Kazuya Shimoda, Seishi Ogawa
Adult T cell leukemia/lymphoma (ATL) is a peripheral T cell neoplasm of largely unknown genetic basis, associated with human T cell leukemia virus type-1 (HTLV-1) infection. Here we describe an integrated molecular study in which we performed whole-genome, exome, transcriptome and targeted resequencing, as well as array-based copy number and methylation analyses, in a total of 426 ATL cases. The identified alterations overlap significantly with the HTLV-1 Tax interactome and are highly enriched for T cell receptor-NF-κB signaling, T cell trafficking and other T cell-related pathways as well as immunosurveillance...
November 2015: Nature Genetics
Erica Bello, Andrea Pellagatti, Jacqueline Shaw, Cristina Mecucci, Rajko Kušec, Sally Killick, Aristoteles Giagounidis, Sophie Raynaud, María J Calasanz, Pierre Fenaux, Jacqueline Boultwood
Mutations of CSNK1A1, a gene mapping to the commonly deleted region of the 5q- syndrome, have been recently described in patients with del(5q) myelodysplastic syndromes (MDS). Haploinsufficiency of Csnk1a1 in mice has been shown to result in β-catenin activation and expansion of haematopoietic stem cells (HSC). We have screened a large cohort of 104 del(5q) MDS patients and have identified mutations of CSNK1A1 in five cases (approximately 5%). We have shown up-regulation of β-catenin target genes in the HSC of patients with del(5q) MDS...
June 18, 2015: British Journal of Haematology
Andrea Pellagatti, Jacqueline Boultwood
The 5q- syndrome is the most distinct of the myelodysplastic syndromes (MDS) and patients with this disorder have a deletion of chromosome 5q [del(5q)] as the sole karyotypic abnormality. Several genes mapping to the commonly deleted region of the 5q- syndrome have been implicated in disease pathogenesis in recent years. Haploinsufficiency of the ribosomal gene RPS14 has been shown to cause the erythroid defect in the 5q- syndrome. Loss of the microRNA genes miR-145 and miR-146a has been associated with the thrombocytosis observed in 5q- syndrome patients...
2015: Mediterranean Journal of Hematology and Infectious Diseases
Katarina Davalieva, Ivana Maleva Kostovska, Sanja Kiprijanovska, Katerina Markoska, Katerina Kubelka-Sabit, Vanja Filipovski, Sotir Stavridis, Oliver Stankov, Selim Komina, Gordana Petrusevska, Momir Polenakovic
BACKGROUND: The key to a more effective diagnosis, prognosis, and therapeutic management of prostate cancer (PCa) could lie in the direct analysis of cancer tissue. In this study, by comparative proteomics analysis of PCa and benign prostate hyperplasia (BPH) tissues we attempted to elucidate the proteins and regulatory pathways involved in this disease. METHODS: The samples used in this study were fresh surgical tissues with clinically and histologically confirmed PCa (n = 19) and BPH (n = 33)...
October 2015: Prostate
Nuala H Simpson, Fabiola Ceroni, Rose H Reader, Laura E Covill, Julian C Knight, Elizabeth R Hennessy, Patrick F Bolton, Gina Conti-Ramsden, Anne O'Hare, Gillian Baird, Simon E Fisher, Dianne F Newbury
An exploratory genome-wide copy number variant (CNV) study was performed in 127 independent cases with specific language impairment (SLI), their first-degree relatives (385 individuals) and 269 population controls. Language-impaired cases showed an increased CNV burden in terms of the average number of events (11.28 vs 10.01, empirical P=0.003), the total length of CNVs (717 vs 513 Kb, empirical P=0.0001), the average CNV size (63.75 vs 51.6 Kb, empirical P=0.0005) and the number of genes spanned (14.29 vs 10...
October 2015: European Journal of Human Genetics: EJHG
Rui Su, Shaoyin Fu, Yanjun Zhang, Ruijun Wang, Yanhong Zhou, Jinquan Li, Wenguang Zhang
MicroRNA (miRNA) is a large class of non-coding RNA which usually acts a fine-tuned regulation in repressing gene expression on transcriptional and post-transcriptional level during ontogenetic development, metabolism, and occurrence of disease. Due to the lateness of goat genome investigation, registered goat microRNAs are little known and the function of it is poorly understood. In this study, we identified 5 novel miRNAs express in cashmere goat skin and longissimus dorsi using comparative genomic approach combined with expression profile analysis...
May 2015: Molecular Biology Reports
Seema Mishra
Glioblastoma (GBM) is the malignant form of glioma, and the interplay of different pathways working in concert in GBM development and progression needs to be fully understood. Wnt signaling and sonic hedgehog (SHH) signaling pathways, having basic similarities, are among the major pathways aberrantly activated in GBM, and hence, need to be targeted. It becomes imperative, therefore, to explore the functioning of these pathways in context of each other in GBM. An integrative approach may help provide new biological insights, as well as solve the problem of identifying common drug targets for simultaneous targeting of these pathways...
2014: Cancer Informatics
Rebekka K Schneider, Vera Ademà, Dirk Heckl, Marcus Järås, Mar Mallo, Allegra M Lord, Lisa P Chu, Marie E McConkey, Rafael Kramann, Ann Mullally, Rafael Bejar, Francesc Solé, Benjamin L Ebert
The casein kinase 1A1 gene (CSNK1A1) is a putative tumor suppressor gene located in the common deleted region for del(5q) myelodysplastic syndrome (MDS). We generated a murine model with conditional inactivation of Csnk1a1 and found that Csnk1a1 haploinsufficiency induces hematopoietic stem cell expansion and a competitive repopulation advantage, whereas homozygous deletion induces hematopoietic stem cell failure. Based on this finding, we found that heterozygous inactivation of Csnk1a1 sensitizes cells to a CSNK1 inhibitor relative to cells with two intact alleles...
October 13, 2014: Cancer Cell
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