similar proteomic analysis of M-PMV virions was performed to
identify host cell proteins that are incorporated into newly formed
particles. Identification of reproducibly incorporated proteins into
the virions could help to clarify the mechanisms of morphogenesis
or virulence of M-PMV. About sixty of host cell proteins were stably identified in whole M-PMV particles produced in human
embryonic kidney cells. From those, the proteins participating in
clathrin-mediated endocytosis, which has been found to be used by
HIV-1 when entering the host cell, or proteins of the ESCRT complex, which HIV-1 uses to bud from the host cell, were identified.
Additionally, another identified proteins are involved in COPI and
COPII mediated endosomal transport, which could be important
for transport of M-PMV proteins within the host cell.
P.24-022-Mon
Discriminating sub-population responses of a
mixture of human cell lines by proteogenomics
C. Almunia1, Y. Cogne1, O. Pible1, C. Lepleux2, F. Chevalier2,
J. Armengaud1
1
CEA/DRF/LI2D, CEA Marcoule PRAE Marcel boiteux, Bagnols
sur C
eze, France, 2CEA/DRF/iRCM/LARIA, Campus Jules
Horowitz, Caen, France
Monitoring proteome dynamics from different human cell types
present concomitantly in a given sample is of great interest and
could be applied to ultra-precise molecular characterization of
complex tissues. Here, we propose a proteogenomics-based strategy to point at cell line molecular signatures. For this, the proteome is analyzed by high-throughput shotgun mass spectrometry
and specific bioinformatics search are performed. First, mRNA
from chondrosarcoma cells (SW1353 cell line) and immortalized
chondrocytes (T/C28A2 cell line) were sequenced by RNAseq for
establishing the most appropriate protein sequence database. For
this an innovative cascade search allows to conciliate de novo and
mapping RNAseq assemblies and the Human SwissProt database.
A set of 2 million of discriminating peptide sequences of the two
cell lines are then identified. From them, 480 peptide sequences
were detected and monitored based on extracted ion chromatogram (XIC) signals recorded by tandem mass spectrometry. A
list of 55 peptides was used for quantitating the ratio of each cell
type in a given co-culture sample with high precision, selected with
cell lines mixed at 2:1, 1:1; and 1:2 ratio. This new methodology
was used to analyze the bystander effect generated by irradiated
chondrosarcoma cells (SW1353 cell line) on immortalized chondrocytes (T/C28A2 cell line) in co-culture conditions. Such strategy
could be applied to investigate intercellular interactions between
different cell types, paving the way to new insights into the molecular mechanisms of crosstalk between human cells.
P.24-023-Tue
Common miRNA signatures in a group of rare
neuromuscular disorders
E. Aksu1, Y. Z. Akkaya-Ulum1, B. Balci-Peynircioglu1,
D. Dayangac-Erden1, A. Yuzbasioglu1, B. Bakir-Gungor2,
B. Talim3, B. Balci-Hayta1
1
Hacettepe University, Faculty of Medicine, Department of
Medical Biology, Sihhiye 06100, Ankara, Turkey, 2Abdullah Gul
University, Faculty of Engineering and Natural Sciences,
Department of Computer Engineering, 38039, KAYSERI, Turkey,
3
Hacettepe University, Faculty of Medicine, Department of
Pediatrics, Pathology Unit, Sihhiye 06100, Ankara, Turkey
Neuromuscular disorders (NMD) are heterogeneous group of
genetic diseases that encompasses many different syndromes and
diseases that either directly or indirectly impairs the function of
FEBS Open Bio 8 (Suppl. S1) (2018) 107–496 DOI: 10.1002/2211-5463.12453
ª 2018 The Authors. Published by FEBS Press and John Wiley & Sons Ltd.
Omics technologies
skeletal muscle. However, there are currently no effective and
common therapeutic approaches to prevent or delay the progression of these diseases. Recent studies revealed important regulatory roles for small noncoding RNAs, called microRNAs
(miRNAs), in skeletal muscle function under physiological and
pathological conditions. In this study, we aim to identify common miRNA signatures associated with etiopathogenesis of different neuromuscular diseases (Duchenne Muscular Dystrophy,
Megaconial Congenital Muscular Dystrophy (CMD), Ullrich
CMD and alpha-dystroglycanopathy), each caused by mutations
in different nuclear genes encoding proteins with distinct roles.
For this purpose, skeletal muscle biopsies from selected NMDs
presenting mitochondrial damage (n = 12, 3 from each group)
and control individuals (n = 3) were analyzed by using Affymetrix GeneChip miRNA 4.0 Array. To identify differentially
expressed miRNAs in patients, raw data was analyzed by two
different programs, MeV-SAM and Affymetrix TAC. Differentially expressed miRNAs whose expression were found to be statistically significant by both programs (miRNAs that showed an
increase/decrease by 2 fold in patient samples compared to the
control group) were identified as candidates. We then identified
potential target genes of these candidate miRNAs by using miRWalk and classified them by using GENE ONTOLOGYPANTHER databases. Our results revealed that 17 miRNAs
were differentially expressed in patients and 5 of these miRNAs
are likely involved in skeletal muscle differentiation. Our commonality approach will provide contribution to the literature by
identifying common potential therapeutic targets and/or
biomarkers related to different rare NMDs.
P.24-024-Wed
Quantitation of drugs using for treatment of
essential hypertension in dried blood spots by
LC-MS/MS and correlation with dried serum
spots
A. Chernonosov1, M. Kasakin1, V. Koval1,2
1
Institute of Chemical Biology & Fundamental Medicine,
Novosibirsk, Russia, 2Novosibirsk State University, Novosibirsk,
Russia
Mortality from cardiovascular diseases in Russia is in the first
place (Russian Statistical Yearbook, 2015). As a rule, the cause
of this is complications of coronary heart disease leading to angina, myocardial infarction, cardiac arrhythmia, sudden cardiac
death (McMurray J. J 2012), slowing of blood flow, formation of
intravascular thrombus (Uster V 1997). In about half the cases,
the disease begins without previous symptoms with unstable angina or myocardial infarction and immediately changes into a
chronic form (RI Litvinenko, 2014). Often the complications lead
to increased physical and psychological stress. The development
of new tests for determining the pathologies of the cardiovascular
system consists in finding new biomarkers and improving existing
methods by increasing the sensitivity and accuracy of the analysis. The ease of collection and storage of samples makes the choice
of dry blood spots (DBS) and dry blood plasma spots (DPS)
attractive as a source of biological material collection for biomedical research and analysis, especially outside the traditional medical
environment (for example, at home, in remote locations, limited
resources) (McDade TW, 2007). Unlike standard blood plasma
samples, samples on dry spots do not require freezing, can be
stored and transported in simple folders or envelopes at room temperature or with cooling to 4°C. If the stability of the substances
is proved, then such samples can be sent by regular mail. In this
study, we propose to develop methods for quantitation of drugs
using for treatment of essential hypertension in dried blood spots
467
22115463, 2018, S1, Downloaded from https://febs.onlinelibrary.wiley.com/doi/10.1002/2211-5463.12453 by Cumhuriyet University, Wiley Online Library on [24/10/2022]. See the Terms and Conditions (https://onlinelibrary.wiley.com/terms-and-conditions) on Wiley Online Library for rules of use; OA articles are governed by the applicable Creative Commons License
POSTERS