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apoptosis next generation sequencing

Sanae Sekihara, Toshio Shibata, Mai Hyakkendani, Shun-Ichiro Kawabata
We recently reported that transglutaminase (TG) suppresses immune deficiency pathway-controlled antimicrobial peptides (IMD-AMPs), thereby conferring immune tolerance to gut microbes, and that RNAi of the TG gene in flies decreases the lifespan compared with non-TG-RNAi flies. Here, analysis of the bacterial composition of the Drosophila gut by next-generation sequencing revealed that gut microbiota comprising one dominant genus of Acetobacter in non-TG-RNAi flies was shifted to that comprising two dominant genera of Acetobacter and Providencia in TG-RNAi flies...
October 19, 2016: Journal of Biological Chemistry
Jun Luo, Junying Liu, Hehe Liu, Tao Zhang, Jiwen Wang, Hua He, Chunchun Han
The bursa of Fabricius (BF) is a central humoral immune organ belonging to avian specifically. Recent studies had suggested that miRNAs were active regulators involved in the immune processes. This study was to investigate the possible differences of the BF at miRNA level between two genetically disparate duck breeds. Using Illumina next-generation sequencing, the data showed that there were 66 differentially expressed miRNAs and 28 novel miRNAs in bursa. A set of abundant miRNAs (i.e., let-7, miR-146a-5p, miR-21-5p, miR-17~92) which involved in immunity and disease were detected and the predicted target genes of the novel miRNAs were associated with duck high anti-adversity ability...
September 16, 2016: Asian-Australasian Journal of Animal Sciences
Maria Ciccone, George Adrian Calin
Chronic lymphocytic leukemia (CLL) is the most common leukemia among adult population in western country. In the last decade, several findings have substantially revolutionized the old concept that CLL is a disease originating from mature, not-dividing cell with indolent clinical course. Notably, next generation sequencing (NGS) have contributed to deepen the knowledge of the cellular networks that imply the onset and the progression of CLL. Among genetic aberrations that are recurrently observed in B-cells from patients with CLL, microRNA deregulation represented the first epigenetic mechanism that has been identified...
August 25, 2016: MicroRNA
S Manteniotis, S Wojcik, P Brauhoff, M Möllmann, L Petersen, J R Göthert, W Schmiegel, U Dührsen, G Gisselmann, H Hatt
The olfactory receptor (OR) family was found to be expressed mainly in the nasal epithelium. In the last two decades members of the OR family were detected to be functional expressed in different parts of the human body such as in liver, prostate or intestine cancer cells. Here, we detected the expression of several ORs in the human chronic myelogenous leukemia (CML) cell line K562 and in white blood cells of clinically diagnosed acute myeloid leukemia (AML) patients by RT-PCR and next-generation sequencing...
2016: Cell Death Discovery
Zhao Li, Wenzhuo Zhu, Liwen Xiong, Xiaobo Yu, Xi Chen, Qiang Lin
Non-small cell type lung cancer (NSCLC) is the most common malignancy and the leading cause of cancer related mortality. In this study, serine/threonine kinase 39 (STK39) was identified as an up-regulated gene in NSCLC tissues by next-generation RNA sequencing. Although STK39 gene polymorphisms may be prognostic of overall survival in patients with early stage NSCLC, the roles of STK39 in NSCLC cancer are poorly understood. In the current study, Genome Set Enrichment Analysis (GSEA) on the RNA-seq data of NSCLC specimens indicated that cancer-related process and pathways, including metastasis, cell cycle, apoptosis and p38 pathway, were significantly correlated with STK39 expression...
August 17, 2016: Oncotarget
Robert L Harrison, Daniel L Rowley, C Joel Funk
The Indianmeal moth, Plodia interpunctella (Lepidoptera: Pyralidae), is a common pest of stored goods with a worldwide distribution. The complete genome sequence for a larval pathogen of this moth, the baculovirus Plodia interpunctella granulovirus (PiGV), was determined by next-generation sequencing. The PiGV genome was found to be 112, 536 bp in length with a 44.2% G+C nucleotide distribution. A total of 123 open reading frames (ORFs) and seven homologous regions (hrs) were identified and annotated. Phylogenetic inference using concatenated alignments of 36 baculovirus core genes placed PiGV in the "b" clade of viruses from genus Betabaculovirus with a branch length suggesting that PiGV represents a distinct betabaculovirus species...
2016: PloS One
Edith Chevret, Jean-Philippe Merlio
Sézary syndrome is probably the most studied cutaneous T-cell lymphoma subtype. Beyond the consensus criteria for Sézary syndrome diagnosis, Sézary cells display heterogeneous phenotypes and differentiation profiles. In the face of SS diversity, the great hope is to develop targeted therapies based on next-generation sequencing to define the genetic landscape of Sézary syndrome. Prasad et al. report on the use of exome sequencing and RNA sequencing to study selected CD4(+) blood cells from 15 patients with erythroderma Sézary syndrome, 14 of whom fulfilled the conventional criteria for diagnosis...
July 2016: Journal of Investigative Dermatology
Cheng-Wei Li, Bor-Sen Chen
Recent studies have demonstrated that cell cycle plays a central role in development and carcinogenesis. Thus, the use of big databases and genome-wide high-throughput data to unravel the genetic and epigenetic mechanisms underlying cell cycle progression in stem cells and cancer cells is a matter of considerable interest. Real genetic-and-epigenetic cell cycle networks (GECNs) of embryonic stem cells (ESCs) and HeLa cancer cells were constructed by applying system modeling, system identification, and big database mining to genome-wide next-generation sequencing data...
June 13, 2016: Cell Cycle
William E Damsky, Jaehyuk Choi
Cutaneous T cell lymphomas (CTCLs) are non-Hodgkin lymphomas of skin homing T cells. Although early-stage disease may be limited to the skin, tumor cells in later stage disease can populate the blood, the lymph nodes, and the visceral organs. Unfortunately, there are few molecular biomarkers to guide diagnosis, staging, or treatment of CTCL. Diagnosis of CTCL can be challenging and requires the synthesis of clinical findings, histopathology, and T cell clonality studies; however, none of these tests are entirely sensitive or specific for CTCL...
July 2016: Current Treatment Options in Oncology
Jinwei Luan, Xianglan Li, Rutao Guo, Shanshan Liu, Hongyu Luo, Qingshan You
BACKGROUND: Next generation sequencing and bio-informatic analyses were conducted to investigate the mechanism of reactivation of p53 and induction of tumor cell apoptosis (RITA)-enhancing X-ray susceptibility in FaDu cells. MATERIALS AND METHODS: The cDNA was isolated from FaDu cells treated with 0 X-ray, 8 Gy X-ray, or 8 Gy X-ray + RITA. Then, cDNA libraries were created and sequenced using next generation sequencing, and each assay was repeated twice. Subsequently, differentially expressed genes (DEGs) were identified using Cuffdiff in Cufflinks and their functions were predicted by pathway enrichment analyses...
June 1, 2016: Radiology and Oncology
Elena Agostoni, Silvia Michelazzi, Marta Maurutto, Alisia Carnemolla, Yari Ciani, Paolo Vatta, Paola Roncaglia, Silvia Zucchelli, Giampiero Leanza, Fiamma Mantovani, Stefano Gustincich, Claudio Santoro, Silvano Piazza, Giannino Del Sal, Francesca Persichetti
Huntington's disease (HD) is a fatal, dominantly inherited, neurodegenerative disorder due to a pathological expansion of the CAG repeat in the coding region of the HTT gene. In the quest for understanding the molecular basis of neurodegeneration, we have previously demonstrated that the prolyl isomerase Pin1 plays a crucial role in mediating p53-dependent apoptosis triggered by mutant huntingtin (mHtt) in vitro. To assess the effects of the lack of Pin1 in vivo, we have bred Pin1 knock-out mice with Hdh(Q111) knock-in mice, a genetically precise model of HD...
2016: Frontiers in Cellular Neuroscience
Preethi Krishnan, Sunita Ghosh, Kathryn Graham, John R Mackey, Olga Kovalchuk, Sambasivarao Damaraju
Piwi-interacting RNAs (piRNAs), whose role in germline maintenance has been established, are now also being classified as post-transcriptional regulators of gene expression in somatic cells. PIWI proteins, central to piRNA biogenesis, have been identified as genetic and epigenetic regulators of gene expression. piRNAs/PIWIs have emerged as potential biomarkers for cancer but their relevance to breast cancer has not been comprehensively studied. piRNAs and mRNAs were profiled from normal and breast tumor tissues using next generation sequencing and Agilent platforms, respectively...
May 10, 2016: Oncotarget
Zixin Ni, Fan Yang, Weijun Cao, Xiangle Zhang, Ye Jin, Ruoqing Mao, Xiaoli Du, Weiwei Li, Jianhong Guo, Xiangtao Liu, Zixiang Zhu, Haixue Zheng
Foot-and-mouth disease virus (FMDV) is the causative agent of a highly contagious disease in livestock. The viral proteinase L(pro) of FMDV is involved in pathogenicity, and mutation of the L(pro) SAP domain reduces FMDV pathogenicity in pigs. To determine the gene expression profiles associated with decreased pathogenicity in porcine cells, we performed transcriptome analysis using next-generation sequencing technology and compared differentially expressed genes in SK6 cells infected with FMDV containing L(pro) with either a wild-type or mutated version of the SAP domain...
June 2016: Virologica Sinica
Darrell Green, William D Fraser, Tamas Dalmay
The cellular lifetime includes stages such as differentiation, proliferation, division, senescence and apoptosis. These stages are driven by a strictly ordered process of transcription dynamics. Molecular disruption to RNA polymerase assembly, chromatin remodelling and transcription factor binding through to RNA editing, splicing, post-transcriptional regulation and ribosome scanning can result in significant costs arising from genome instability. Cancer development is one example of when such disruption takes place...
June 2016: Pflügers Archiv: European Journal of Physiology
M Wagle, A M Eiring, M Wongchenko, S Lu, Y Guan, Y Wang, M Lackner, L Amler, G Hampton, M W Deininger, T O'Hare, Y Yan
Chronic myeloid leukemia (CML) patients who relapse on imatinib due to acquired ABL1 kinase domain mutations are successfully treated with second-generation ABL1-tyrosine kinase inhibitors (ABL-TKIs) such as dasatinib, nilotinib or ponatinib. However, ~40% of relapsed patients have uncharacterized BCR-ABL1 kinase-independent mechanisms of resistance. To identify these mechanisms of resistance and potential treatment options, we generated ABL-TKI-resistant K562 cells through prolonged sequential exposure to imatinib and dasatinib...
July 2016: Leukemia: Official Journal of the Leukemia Society of America, Leukemia Research Fund, U.K
Chi Lam Au Yeung, Ngai-Na Co, Tetsushi Tsuruga, Tsz-Lun Yeung, Suet-Ying Kwan, Cecilia S Leung, Yong Li, Edward S Lu, Kenny Kwan, Kwong-Kwok Wong, Rosemarie Schmandt, Karen H Lu, Samuel C Mok
Advanced ovarian cancer usually spreads to the visceral adipose tissue of the omentum. However, the omental stromal cell-derived molecular determinants that modulate ovarian cancer growth have not been characterized. Here, using next-generation sequencing technology, we identify significantly higher levels of microRNA-21 (miR21) isomiRNAs in exosomes and tissue lysates isolated from cancer-associated adipocytes (CAAs) and fibroblasts (CAFs) than in those from ovarian cancer cells. Functional studies reveal that miR21 is transferred from CAAs or CAFs to the cancer cells, where it suppresses ovarian cancer apoptosis and confers chemoresistance by binding to its direct novel target, APAF1...
2016: Nature Communications
O Lindblad, E Cordero, A Puissant, L Macaulay, A Ramos, N N Kabir, J Sun, J Vallon-Christersson, K Haraldsson, M T Hemann, Å Borg, F Levander, K Stegmaier, K Pietras, L Rönnstrand, J U Kazi
Therapy directed against oncogenic FLT3 has been shown to induce response in patients with acute myeloid leukemia (AML), but these responses are almost always transient. To address the mechanism of FLT3 inhibitor resistance, we generated two resistant AML cell lines by sustained treatment with the FLT3 inhibitor sorafenib. Parental cell lines carry the FLT3-ITD (tandem duplication) mutation and are highly responsive to FLT3 inhibitors, whereas resistant cell lines display resistance to multiple FLT3 inhibitors...
September 29, 2016: Oncogene
Napol Kaewkascholkul, Kulwadee Somboonviwat, Shuichi Asakawa, Ikuo Hirono, Anchalee Tassanakajon, Kunlaya Somboonwiwat
MicroRNAs are short noncoding RNAs of RNA interference pathways that regulate gene expression through partial complementary base-pairing to target mRNAs. In this study, miRNAs that are expressed in white spot syndrome virus (WSSV)-infected Penaeus monodon, were identified using next generation sequencing. Forty-six miRNA homologs were identified from WSSV-infected shrimp hemocyte. Stem-loop real-time RT-PCR analysis showed that 11 out of 16 selected miRNAs were differentially expressed upon WSSV infection. Of those, pmo-miR-315 and pmo-miR-750 were highly responsive miRNAs...
July 2016: Developmental and Comparative Immunology
Martin Sokol, Karen Margrethe Jessen, Finn Skou Pedersen
Several studies have shown that human endogenous retroviruses and endogenous retrovirus-like repeats (here collectively HERVs) impose direct regulation on human genes through enhancer and promoter motifs present in their long terminal repeats (LTRs). Although chimeric transcription in which novel gene isoforms containing retroviral and human sequence are transcribed from viral promoters are commonly associated with disease, regulation by HERVs is beneficial in other settings; for example, in human testis chimeric isoforms of TP63 induced by an ERV9 LTR protect the male germ line upon DNA damage by inducing apoptosis, whereas in the human globin locus the γ- and β-globin switch during normal hematopoiesis is mediated by complex interactions of an ERV9 LTR and surrounding human sequence...
January 2016: APMIS: Acta Pathologica, Microbiologica, et Immunologica Scandinavica
Panagiotis G Adamopoulos, Christos K Kontos, Panagiotis Tsiakanikas, Andreas Scorilas
The next-generation sequencing (NGS) technology has enabled genome-wide studies, providing massively parallel DNA sequencing. NGS applications constitute a revolution in molecular biology and genetics and have already paved new ways in cancer research. BCL2L12 is an apoptosis-related gene, previously cloned from members of our research group. Like most members of the BCL2 gene family, it is highly implicated in various types of cancer and hematological malignancies. In the present study, we used NGS to discover novel alternatively spliced variants of the apoptosis-related BCL2L12 gene in many human cancer cell lines, after 3'-RACE nested PCR...
April 1, 2016: Cancer Letters
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