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https://www.readbyqxmd.com/read/27905489/the-mammalian-linc-complex-regulates-genome-transcriptional-responses-to-substrate-rigidity
#1
Samer G Alam, Qiao Zhang, Nripesh Prasad, Yuan Li, Srikar Chamala, Ram Kuchibhotla, Birendra Kc, Varun Aggarwal, Shristi Shrestha, Angela L Jones, Shawn E Levy, Kyle J Roux, Jeffrey A Nickerson, Tanmay P Lele
Mechanical integration of the nucleus with the extracellular matrix (ECM) is established by linkage between the cytoskeleton and the nucleus. This integration is hypothesized to mediate sensing of ECM rigidity, but parsing the function of nucleus-cytoskeleton linkage from other mechanisms has remained a central challenge. Here we took advantage of the fact that the LINC (linker of nucleoskeleton and cytoskeleton) complex is a known molecular linker of the nucleus to the cytoskeleton, and asked how it regulates the sensitivity of genome-wide transcription to substratum rigidity...
December 1, 2016: Scientific Reports
https://www.readbyqxmd.com/read/27889481/mitotic-nuclear-envelope-breakdown-and-spindle-nucleation-are-controlled-by-interphase-contacts-between-centromeres-and-the-nuclear-envelope
#2
Alfonso Fernández-Álvarez, Cécile Bez, Eileen T O'Toole, Mary Morphew, Julia Promisel Cooper
Faithful genome propagation requires coordination between nuclear envelope (NE) breakdown, spindle formation, and chromosomal events. The conserved linker of nucleoskeleton and cytoskeleton (LINC) complex connects fission yeast centromeres and the centrosome, across the NE, during interphase. During meiosis, LINC connects the centrosome with telomeres rather than centromeres. We previously showed that loss of telomere-LINC contacts compromises meiotic spindle formation. Here, we define the precise events regulated by telomere-LINC contacts and address the analogous possibility that centromeres regulate mitotic spindle formation...
December 5, 2016: Developmental Cell
https://www.readbyqxmd.com/read/27872710/linc-ror-and-its-spliced-variants-2-and-4-are-significantly-up-regulated-in-esophageal-squamous-cell-carcinoma
#3
Reza Sahebi, Mahshid Malakootian, Baharak Balalaee, Alireza Shahryari, Masoud Khoshnia, Mohammad Reza Abbaszadegan, Abdolvahab Moradi, Seyed Javad Mowla
OBJECTIVES: Similar characteristics of molecular pathways between cellular reprogramming events and tumorigenesis have been accentuated in recent years. Reprogramming-related transcription factors, also known as Yamanaka factors (OCT4, SOX2, KLF4, and c-MYC), are also well-known oncogenes promoting cancer initiation, progression, and cellular transformation into cancer stem cells. Long non-coding RNAs (lncRNAs) are a major class of RNA molecules with emerging roles in stem cell pluripotency, cellular reprogramming, cellular transformation, and tumorigenesis...
October 2016: Iranian Journal of Basic Medical Sciences
https://www.readbyqxmd.com/read/27871198/-it-is-easier-for-me-to-shoot-up-stigma-abandonment-and-why-hiv-positive-drug-users-in-russia-fail-to-link-to-hiv-care
#4
Tetiana Kiriazova, Karsten Lunze, Anita Raj, Natalia Bushara, Elena Blokhina, Evgeny Krupitsky, Carly Bridden, Dmitry Lioznov, Jeffrey H Samet, Allen L Gifford
Many HIV-positive people who inject drugs (PWID) globally are not receiving HIV care. This represents a major challenge among key populations to end the global HIV epidemic. This qualitative study explored the process and associated barriers of linking HIV-positive PWID who are in addiction treatment to HIV care in St. Petersburg, Russia. We conducted three focus groups and seven semi-structured interviews with participants in the LINC ("Linking Infectious and Narcology Care") project at addiction and HIV hospitals in St...
November 22, 2016: AIDS Care
https://www.readbyqxmd.com/read/27858498/sun1-splice-variants-sun1_888-sun1_785-and-predominant-sun1_916-variably-function-in-directional-cell-migration
#5
Yu Nishioka, Hiromasa Imaizumi, Junko Imada, Jun Katahira, Nariaki Matsuura, Miki Hieda
The LINC complex is a multifunctional protein complex that is involved in various processes at the nuclear envelope, such as nuclear migration, mechanotransduction and chromatin tethering in the meiotic phase. However, it remains unknown how these functions are regulated in different cell contexts. An inner nuclear membrane component of the LINC complex, SUN1, is ubiquitously expressed. The human SUN1 gene produces over 10 variants by alternative splicing. Although functions of SUN1 are relatively well characterized, functional differences among SUN1 splice variants are poorly characterized...
November 18, 2016: Nucleus
https://www.readbyqxmd.com/read/27855392/the-emerging-roles-of-long-noncoding-rna-ror-lincrna-ror-and-its-possible-mechanisms-in-human-cancers
#6
Yan Pan, Chen Li, Jing Chen, Kai Zhang, Xiaoyuan Chu, Rui Wang, Longbang Chen
To date, there is only up to 2% of protein-coding genes that are stably transcribed, whereas the vast majority are non-coding RNAs (ncRNAs). These ncRNAs, also known as non-messenger RNAs (nmRNAs) or functional RNAs (fRNAs), include transfer RNAs, ribosomal RNAs, microRNAs and long non-coding RNAs (lncRNAs). With the advance of high-resolution microarrays and massively parallel sequencing technology, lncRNAs have gained extended attentions nowadays and are found to play important roles in tumorigenesis and progression of human cancers...
2016: Cellular Physiology and Biochemistry
https://www.readbyqxmd.com/read/27796074/systematic-quality-control-analysis-of-lincs-data
#7
L Cheng, L Li
The Library of Integrated Cellular Signatures (LINCS) project provides comprehensive transcriptome profiling of human cell lines before and after chemical and genetic perturbations. Its L1000 platform utilizes 978 landmark genes to infer the transcript levels of 14,292 genes computationally. Here we conducted the L1000 data quality control analysis by using MCF7, PC3, and A375 cell lines as representative examples. Before perturbations, a promising 80% correlation in transcriptome was observed between L1000- and Affymetrix HU133A-platforms...
October 31, 2016: CPT: Pharmacometrics & Systems Pharmacology
https://www.readbyqxmd.com/read/27785603/linc-ror-confers-gemcitabine-resistance-to-pancreatic-cancer-cells-via-inducing-autophagy-and-modulating-the-mir-124-ptbp1-pkm2-axis
#8
Chenggang Li, Zhiming Zhao, Zhipeng Zhou, Rong Liu
PURPOSE: In this study, we investigated the regulation of linc-ROR on autophagy and gemcitabine resistance of pancreatic cancer cells and further studied the underlying involvement of the miR-124/PTBP1/PKM2 axis in this regulation. METHODS: Pancreatic cancer cell lines PANC-1 and MIAPaCa-2 cells were used as in vitro model. Autophagy was assessed by western blot of LC3 I/II and observation GFP-LC3 puncta. Cell viability was examined using CCK-8 assay. Cell apoptosis was examined by flow cytometric analysis of Annexin V/PI staining...
October 26, 2016: Cancer Chemotherapy and Pharmacology
https://www.readbyqxmd.com/read/27775378/a-posterior-probability-approach-for-gene-regulatory-network-inference-in-genetic-perturbation-data
#9
William Chad Young, Adrian E Raftery, Ka Yee Yeung
Inferring gene regulatory networks is an important problem in systems biology. However, these networks can be hard to infer from experimental data because of the inherent variability in biological data as well as the large number of genes involved. We propose a fast, simple method for inferring regulatory relationships between genes from knockdown experiments in the NIH LINCS dataset by calculating posterior probabilities, incorporating prior information. We show that the method is able to find previously identified edges from TRANSFAC and JASPAR and discuss the merits and limitations of this approach...
December 1, 2016: Mathematical Biosciences and Engineering: MBE
https://www.readbyqxmd.com/read/27773892/the-significance-of-low-levels-of-linc-rp1130-1-expression-in-human-hepatocellular-carcinoma
#10
Chaohui Xiao, Cheng Wang, Sijie Cheng, Chengcai Lai, Peirui Zhang, Zizheng Wang, Tao Zhang, Shaogeng Zhang, Rong Liu
Hepatocellular carcinoma (HCC) is the most common neoplasms. Little progress has been made in the diagnosis and treatment of HCC and its prognosis remains poor. Studies have increasingly found that long non-coding RNA (lncRNA) is involved in the regulation of the occurrence and development of HCC. To investigate the diagnostic and prognostic value of lncRNA in HCC, the current study examined 25 lncRNAs with differing levels of expression (according to the fold change) in microarray databases. Expression of LINC RP1130-1 was found to be markedly down-regulated in 51 HCC tissues compared to matching adjacent non-tumor liver tissues...
November 15, 2016: Bioscience Trends
https://www.readbyqxmd.com/read/27765630/long-non-coding-rna-linc-cdh4-2-inhibits-the-migration-and-invasion-of-hcc-cells-by-targeting-r-cadherin-pathway
#11
Yunzhen Gao, Gaoxiong Wang, Cuilin Zhang, Minjie Lin, Xiaolong Liu, Yongyi Zeng, Jingfeng Liu
Long non-coding RNAs (LncRNAs) have played very important roles in the malignancy behaviors of hepatocellular carcinoma (HCC). Linc-cdh4-2 (TCONS_00027978) is a novel LncRNA that has been identified in HCC tissues from our previous study. Overexpression of linc-cdh4-2 in HCC cell lines (SK-Hep-1 and Huh7) significantly decreases the migration and invasion abilities of these cells, while knockdown the expression of linc-cdh4-2 significantly increases the migration and invasion abilities. Interestingly, neither the over expression nor the knock down of linc-cdh4-2 could affect the viability and proliferation of HCC cells...
October 17, 2016: Biochemical and Biophysical Research Communications
https://www.readbyqxmd.com/read/27756768/linc-maf-4-regulates-th1-th2-differentiation-and-is-associated-with-the-pathogenesis-of-multiple-sclerosis-by-targeting-maf
#12
Fang Zhang, Guiyou Liu, Changjuan Wei, Chao Gao, Junwei Hao
In this study, we strove to substantiate the ability of linc-MAF-4 to act as a regulator of pathogenesis during multiple sclerosis (MS). We recruited 34 patients who were diagnosed with MS according to the revised McDonald Criteria. Six patients with MS and 5 healthy volunteers contributed peripheral blood mononuclear cells for microarray analysis. Subsequent knockdown and overexpression of linc-MAF-4 in naive CD4(+) T cells from the additional 28 patients with MS was performed to track changes in CD4(+) T-cell subsets and their function as well as to confirm results from the prior microarray analysis...
October 18, 2016: FASEB Journal: Official Publication of the Federation of American Societies for Experimental Biology
https://www.readbyqxmd.com/read/27738870/differentially-expressed-long-non-coding-rnas-were-predicted-to-be-involved-in-the-control-of-signaling-pathways-in-pediatric-astrocytoma
#13
Ruth Ruiz Esparza-Garrido, Juan Manuel Rodríguez-Corona, Javier Enrique López-Aguilar, Marco Antonio Rodríguez-Florido, Ana Claudia Velázquez-Wong, Rubí Viedma-Rodríguez, Fabio Salamanca-Gómez, Miguel Ángel Velázquez-Flores
Expression changes for long non-coding RNAs (lncRNAs) have been identified in adult glioblastoma multiforme (GBM) and in a mixture of adult and pediatric astrocytoma. Since adult and pediatric astrocytomas are molecularly different, the mixture of both could mask specific features in each. We determined the global expression patterns of lncRNAs and messenger RNA (mRNAs) in pediatric astrocytoma of different histological grades. Transcript expression changes were determined with an HTA 2.0 array. lncRNA interactions with microRNAs and mRNAs were predicted by using an algorithm and the LncTar tool, respectively...
October 13, 2016: Molecular Neurobiology
https://www.readbyqxmd.com/read/27713136/the-role-of-extracellular-vesicles-in-mediating-progression-metastasis-and-potential-treatment-of-hepatocellular-carcinoma
#14
Naibin Yang, Shanshan Li, Guoxiang Li, Shengguo Zhang, Xinyue Tang, Shunlan Ni, Xiaomin Jian, Cunlai Xu, Jiayin Zhu, Mingqin Lu
Hepatocellular carcinoma (HCC) is a major cause of cancer-related death worldwide. As vectors for intercellular information exchange, the potential role of extracellular vesicles (EVs) in HCC formation, progression and therapy has been widely investigated. In this review, we explore the current status of the researches in this field. Altogether there is undeniable evidence that EVs play a crucial role in HCC development, metastasis. Moreover, EVs have shown great potential as drug delivery systems (DDSs) for the treatment of HCC...
October 4, 2016: Oncotarget
https://www.readbyqxmd.com/read/27708234/plasma-and-tumor-levels-of-linc-pint-are-diagnostic-and-prognostic-biomarkers-for-pancreatic-cancer
#15
Le Li, Guang-Quan Zhang, Hua Chen, Zhong-Jie Zhao, Hong-Ze Chen, Huan Liu, Gang Wang, Yue-Hui Jia, Shang-Ha Pan, Rui Kong, Yong-Wei Wang, Bei Sun
Long intergenic non-protein coding RNA, p53 induced transcript (Linc-pint) is a long noncoding RNA (lncRNA) that regulates tumor cell viability and proliferation. We used qRT-PCR and RNA FISH analysis to evaluate Linc-pint levels in the plasma and tumor tissues of pancreatic cancer (PCa) patients. Our data demonstrate that Linc-pint expression is lower in plasma samples from PCa patients than from healthy individuals, and indicate that plasma Linc-pint levels are more sensitive than CA19-9 for detecting PCa...
September 30, 2016: Oncotarget
https://www.readbyqxmd.com/read/27706150/immediate-blood-draw-for-cd4-cell-count-is-associated-with-linkage-to-care-in-durban-south-africa-findings-from-pathways-to-engagement-in-hiv-care
#16
Susie Hoffman, Theresa M Exner, Naomi Lince-Deroche, Cheng-Shiun Leu, Jessica L Phillip, Elizabeth A Kelvin, Anisha D Gandhi, Bruce Levin, Dinesh Singh, Joanne E Mantell, Kelly Blanchard, Gita Ramjee
BACKGROUND: Timely linkage to care by newly-diagnosed HIV+ individuals remains a significant challenge to achieving UNAIDS 90-90-90 goals. Current World Health Organization (WHO) guidelines recommend initiating anti-retroviral treatment (ART) regardless of CD4+ count, with priority given to those with CD4+ <350 cells/μl. We evaluated the impact of not having a day-of-diagnosis CD4+ count blood draw, as recommended by South African guidelines, on time to linkage, using data from a prospective cohort study...
2016: PloS One
https://www.readbyqxmd.com/read/27697922/nuclear-envelope-rupture-is-induced-by-actin-based-nucleus-confinement
#17
Emily M Hatch, Martin W Hetzer
Repeated rounds of nuclear envelope (NE) rupture and repair have been observed in laminopathy and cancer cells and result in intermittent loss of nucleus compartmentalization. Currently, the causes of NE rupture are unclear. Here, we show that NE rupture in cancer cells relies on the assembly of contractile actin bundles that interact with the nucleus via the linker of nucleoskeleton and cytoskeleton (LINC) complex. We found that the loss of actin bundles or the LINC complex did not rescue nuclear lamina defects, a previously identified determinant of nuclear membrane stability, but did decrease the number and size of chromatin hernias...
October 10, 2016: Journal of Cell Biology
https://www.readbyqxmd.com/read/27697906/nuclei-migrate-through-constricted-spaces-using-microtubule-motors-and-actin-networks-in-c-elegans-hypodermal-cells
#18
Courtney R Bone, Yu-Tai Chang, Natalie E Cain, Shaun P Murphy, Daniel A Starr
Cellular migrations through constricted spaces are a crucial aspect of many developmental and disease processes including hematopoiesis, inflammation and metastasis. A limiting factor in these events is nuclear deformation. Here, we establish an in vivo model in which nuclei can be visualized while moving through constrictions and use it to elucidate mechanisms for nuclear migration. C. elegans hypodermal P-cell larval nuclei traverse a narrow space that is about 5% their width. This constriction is blocked by fibrous organelles, structures that pass through P cells to connect the muscles to cuticle...
November 15, 2016: Development
https://www.readbyqxmd.com/read/27696511/the-long-non-coding-rna-ror-promotes-the-resistance-of-radiotherapy-for-human-colorectal-cancer-cells-by-targeting-the-p53-mir-145-pathway
#19
Pengxiang Yang, Yue Yang, Weiwei An, Jianyu Xu, Gan Zhang, Jing Jie, Qingyuan Zhang
BACKGROUND AND AIM: LincRNAs have critical roles in elevating efficacy of anticancer therapy and tumor progression. Recent studies show that long intergenic noncoding RNA-ROR (lincRNA-ROR) is aberrantly expressed in several types of cancer, including colorectal cancer (CRC). Radiotherapy is considered as a standard preoperative treatment. However, a considerable number of CRCs are resistant to radiotherapy. In this study, we evaluated the role of lincRNA-ROR in radiotherapy for CRC and detected the underlying molecular mechanism...
October 3, 2016: Journal of Gastroenterology and Hepatology
https://www.readbyqxmd.com/read/27690270/hepatotoxicity-prediction-by-systems-biology-modeling-of-disturbed-metabolic-pathways-using-gene-expression-data
#20
Pablo Carbonell, Oriol Lopez, Alexander Amberg, Manuel Pastor, Ferran Sanz
The present study applies a systems biology approach for the in silico predictive modeling of drug toxicity on the basis of high-quality preclinical drug toxicity data with the aim of increasing the mechanistic understanding of toxic effects of compounds at different levels (pathway, cell, tissue, organ). The model development has been carried out using 77 compounds for which gene expression data are available in the LINCS database for primary human hepatocytes treated with the compounds, as well as rodent in vivo hepatotoxicity information is available in the eTOX database...
September 30, 2016: ALTEX
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