11 research outputs found
Mass Spectrometry-Based Pipeline for Identifying RNA Modifications Involved in a Functional Process: Application to Cancer Cell Adaptation
Cancer onset and
progression are known to be regulated
by genetic
and epigenetic events, including RNA modifications (a.k.a. epitranscriptomics).
So far, more than 150 chemical modifications have been described in
all RNA subtypes, including messenger, ribosomal, and transfer RNAs.
RNA modifications and their regulators are known to be implicated
in all steps of post-transcriptional regulation. The dysregulation
of this complex yet delicate balance can contribute to disease evolution,
particularly in the context of carcinogenesis, where cells are subjected
to various stresses. We sought to discover RNA modifications involved
in cancer cell adaptation to inhospitable environments, a peculiar
feature of cancer stem cells (CSCs). We were particularly interested
in the RNA marks that help the adaptation of cancer cells to suspension
culture, which is often used as a surrogate to evaluate the tumorigenic
potential. For this purpose, we designed an experimental pipeline
consisting of four steps: (1) cell culture in different growth conditions
to favor CSC survival; (2) simultaneous RNA subtype (mRNA, rRNA, tRNA)
enrichment and RNA hydrolysis; (3) the multiplex analysis of nucleosides
by LC-MS/MS followed by statistical/bioinformatic analysis; and (4)
the functional validation of identified RNA marks. This study demonstrates
that the RNA modification landscape evolves along with the cancer
cell phenotype under growth constraints. Remarkably, we discovered
a short epitranscriptomic signature, conserved across colorectal cancer
cell lines and associated with enrichment in CSCs. Functional tests
confirmed the importance of selected marks in the process of adaptation
to suspension culture, confirming the validity of our approach and
opening up interesting prospects in the field
Effects of harmine on hepatic SAHH and NQO1 activities, and on plasma Hcy levels in Tg 189N3 mice.
<p>Hepatic SAHH (A) and NQO1 (B) activities are presented as percent of untreated (Vehicle) non-transgenic (Tg â) mice activities. (C) Plasma Hcy level. Data correspond to means ± SEM and the statistical analysis was done with one-way ANOVA followed by Student's unpaired <i>t</i>-test. nâ=ânumber of mice.</p
Hepatic SAHH activity is increased in Tg 189N3 and Ts65Dn transgenic mice.
<p>SAHH activity in (A) Tg 189N3 and (B) Ts65Dn transgenic mice. The values were normalized to the mean of Tg â mice from each line. Data correspond to means ± SEM and the statistical analysis was done by Student's unpaired <i>t</i>-test. nâ=ânumber of mice.</p
Primer sequences for real-time quantitative reverse transcription-polymerase chain reaction (Q-PCR) (all primers are listed 5âČ to 3âČ).
<p>Primer sequences for real-time quantitative reverse transcription-polymerase chain reaction (Q-PCR) (all primers are listed 5âČ to 3âČ).</p
Plasma Hcy level is decreased in 152F7 transgenic mice and in CBS-deficient mice crossbred with 152F7 transgenic mice.
<p>(A) Plasma Hcy level, (B) hepatic CBS, (C) SAHH and (D) NQO1 activity in wild type mice (<i>Cbs</i><sup>+/+</sup> Tg -), heterozygous mice (<i>Cbs</i><sup>+/â</sup> Tg -), 152F7 transgenic mice (<i>Cbs</i><sup>+/+</sup> Tg 152F7), and heterozygous mice crossbred with 152F7 transgenic mice (<i>Cbs</i><sup>+/â</sup> Tg 152F7). The values were normalized to the mean of <i>Cbs</i><sup>+/+</sup> Tg - mice. Data correspond to means ± SEM and the statistical analysis was done with one-way ANOVA followed by Student's unpaired <i>t</i>-tests. nâ=ânumber of mice.</p
Relative expression of DYRK1A, SAHH and NQO1 and SAHH and NQO1 activities obtained from lymphoblastoid cell lines.
<p>The values of lymphoblastoid cell lines (LCLs) from patients with DS (T21) were normalized to the mean lymphoblastoid cell lines from control individuals (control). Data correspond to means ± SEM and the statistical analysis was done by Student's unpaired <i>t</i>-tests. nâ=ânumber of LCLs. * <i>p</i><0.05; <b><sup>â </sup></b><i>p</i><0.006.</p
DYRK1A protein expression in liver of CBS-deficient mice crossbred with 152F7 transgenic mice.
<p>(A) Western immunoblots showing DYRK1A expression in liver of wild type mice (<i>Cbs</i><sup>+/+</sup> Tg -), heterozygous mice (<i>Cbs</i><sup>+/â</sup> Tg -), 152F7 transgenic mice (<i>Cbs</i><sup>+/+</sup> Tg 152F7), and heterozygous mice crossbred with 152F7 transgenic mice (<i>Cbs</i><sup>+/â</sup> Tg 152F7). Proteins were subjected to immunoblot analysis using antibodies specific to DYRK1A (85.5 kDa). After stripping, the membranes were reprobed with anti-ÎČ-actin antibody (41.7 kDa) for the control. (B) Relative protein expression was determined by normalization of the density of images from DYRK1A with that of ÎČ-actin of the same blot. The values of <i>Cbs</i><sup>+/â</sup> Tg -, <i>Cbs</i><sup>+/+</sup> Tg 152F7, or <i>Cbs</i><sup>+/â</sup> Tg 152F7 were normalized to the mean of <i>Cbs</i><sup>+/+</sup> Tg - mice. The blots are representative of three independent experiments. Data correspond to means ± SEM and the statistical analysis was done with one-way ANOVA followed by Student's unpaired <i>t</i>-tests. nâ=ânumber of mice.</p
Relative expression of SAHH, BHMT, MS and MTHFR gene based upon Q-PCR data obtained from non-transgenic and Tg189N3 mice.
<p>The values of Tg189N3 were normalized to the mean Tg â mice. Data correspond to means ± SEM and the statistical analysis was done by Student's unpaired <i>t</i>-tests. nâ=ânumber of mice. *<i>p</i>â=â0.068; <b><sup>â </sup></b><i>p</i>< 0.03.</p
Hepatic DYRK1A mRNA and protein expression in liver of transgenic mice.
<p>Relative expression of DYRK1A gene was based on Q-PCR data and protein expression was determined by normalization of the density of images from DYRK1A with that of ÎČ-actin of the same blot. The values of Tg 152F7, Tg189N3 and Ts65Dn were normalized to the mean Tg â mice from each lines. The blots are representative of three independent experiments. Data correspond to means ± SEM and the statistical analysis was done by Student's unpaired <i>t</i>-tests. nâ=ânumber of mice.</p
Plasma Hcy level, DYRK1A protein expression and SAHH activity are correlated.
<p>Hepatic DYRK1A expression and SAHH activity are presented as percent of <i>Cbs</i><sup>+/+</sup> Tg â mice. Correlation of plasma Hcy level vs. (A) hepatic DYRK1A protein expression or (B) hepatic SAHH activity. Increasing levels of plasma Hcy and hepatic DYRK1A protein expression or SAHH activity are negatively correlated at <i>p</i><0.04 and <i>p</i><0.006 with a Ïâ=ââ0.48 and Ïâ=ââ0.61 respectively. Correlation of hepatic DYRK1A protein expression vs. SAHH activity (C). Increasing levels of hepatic DYRK1A protein expression and hepatic SAHH activity are positively correlated at <i>p</i><0.05 with a Ïâ=â0.47. (D) Graph of PCA. The three quantitative variables corresponding of plasma Hcy level, hepatic DYRK1A protein expression and hepatic SAHH activity are represented by vectors.</p