Integrative Multi-omics Analysis to Characterize Human Brain Ischemia

Stroke is a major cause of death and disability. A better comprehension of stroke pathophysiology is fundamental to reduce its dramatic outcome. The use of high-throughput unbiased omics approaches and the integration of these data might deepen the knowledge of stroke at the molecular level, depicting the interaction between different molecular units. We aimed to identify protein and gene expression changes in the human brain after ischemia through an integrative approach to join the information of both omics analyses. The translational potential of our results was explored in a pilot study with blood samples from ischemic stroke patients. Proteomics and transcriptomics discovery studies were performed in human brain samples from six deceased stroke patients, comparing the infarct core with the corresponding contralateral brain region, unveiling 128 proteins and 2716 genes significantly dysregulated after stroke. Integrative bioinformatics analyses joining both datasets exposed canonical pathways altered in the ischemic area, highlighting the most influential molecules. Among the molecules with the highest fold-change, 28 genes and 9 proteins were selected to be validated in five independent human brain samples using orthogonal techniques. Our results were confirmed for NCDN, RAB3C, ST4A1, DNM1L, A1AG1, A1AT, JAM3, VTDB, ANXA1, ANXA2, and IL8. Finally, circulating levels of the validated proteins were explored in ischemic stroke patients. Fluctuations of A1AG1 and A1AT, both up-regulated in the ischemic brain, were detected in blood along the first week after onset. In summary, our results expand the knowledge of ischemic stroke pathology, revealing key molecules to be further explored as biomarkers and/or therapeutic targets. Graphical abstract: [Figure not available: see fulltext.].This work has been funded by Instituto de Salud Carlos III (PI15/00354, PI18/00804), MINECO (MTM2015-64465-C2-1R) and GRBIO (2014-SGR-464) and co-financed by the European Regional Development Fund (FEDER). Neurovascular Research Laboratory takes part in the Spanish stroke research network INVICTUS + (RD16/0019/0021). L.R is supported by a pre-doctoral fellowship from the Instituto de Salud Carlos III (IFI17/00012).Peer reviewe

Microarray expression analysis in idiopathic and LRRK2-associated Parkinson's disease

LRRK2 mutations are the most common genetic cause of Parkinson's disease (PD). We performed a whole-genome RNA profiling of putamen tissue from idiopathic PD (IPD), LRRK2-associated PD (G2019S mutation), neurologically healthy controls and one asymptomatic LRRK2 mutation carrier, by using the Genechip Human Exon 1.0-ST Array. The differentially expressed genes found in IPD revealed an alteration of biological pathways related to long-term potentiation (LTP), GABA receptor signalling, and calcium signalling pathways, among others. These pathways are mainly related with cell signalling cascades and synaptic plasticity processes. They were also altered in the asymptomatic LRRK2 mutation carrier but not in the LRRK2-associated PD group. The expression changes seen in IPD might be attributed to an adaptive consequence of a dysfunction in the dopamine transmission. The lack of these altered molecular pathways in LRRK2-associated PD patients suggests that these cases could show a different molecular response to dopamine transmission impairment. © 2011 Elsevier Inc.This project was supported by grants from 2001SRG00387 Generalitat de Catalunya, the award 'Distinció per la promoció de la Recerca Universitària de la Generalitat de Catalunya' to Dr. Eduard Tolosa, and grants from Fondo de Investigaciones Sanitarias to Dr. Mario Ezquerra (U-2004-FS041184-O). Dr. Alex Sanchez-Pla is partially supported by grant from the Ministerio de Educación y Ciencia (MTM2008-00642). Teresa Botta-Orfila is recipient of a predoctoral grant from IDIBAPS.Peer Reviewe

Correction: Lymphangioleiomyomatosis Biomarkers Linked to Lung Metastatic Potential and Cell Stemness.

[This corrects the article DOI: 10.1371/journal.pone.0132546.]

Lymphangioleiomyomatosis Biomarkers Linked to Lung Metastatic Potential and Cell Stemness

<div><p>Lymphangioleiomyomatosis (LAM) is a rare lung-metastasizing neoplasm caused by the proliferation of smooth muscle-like cells that commonly carry loss-of-function mutations in either the tuberous sclerosis complex 1 or 2 (<i>TSC1</i> or <i>TSC2</i>) genes. While allosteric inhibition of the mechanistic target of rapamycin (mTOR) has shown substantial clinical benefit, complementary therapies are required to improve response and/or to treat specific patients. However, there is a lack of LAM biomarkers that could potentially be used to monitor the disease and to develop other targeted therapies. We hypothesized that the mediators of cancer metastasis to lung, particularly in breast cancer, also play a relevant role in LAM. Analyses across independent breast cancer datasets revealed associations between low <i>TSC1/2</i> expression, altered mTOR complex 1 (mTORC1) pathway signaling, and metastasis to lung. Subsequently, immunohistochemical analyses of 23 LAM lesions revealed positivity in all cases for the lung metastasis mediators fascin 1 (FSCN1) and inhibitor of DNA binding 1 (ID1). Moreover, assessment of breast cancer stem or luminal progenitor cell biomarkers showed positivity in most LAM tissue for the aldehyde dehydrogenase 1 (ALDH1), integrin-ß3 (ITGB3/CD61), and/or the sex-determining region Y-box 9 (SOX9) proteins. The immunohistochemical analyses also provided evidence of heterogeneity between and within LAM cases. The analysis of <i>Tsc2</i>-deficient cells revealed relative over-expression of FSCN1 and ID1; however, <i>Tsc2</i>-deficient cells did not show higher sensitivity to ID1-based cancer inhibitors. Collectively, the results of this study reveal novel LAM biomarkers linked to breast cancer metastasis to lung and to cell stemness, which in turn might guide the assessment of additional or complementary therapeutic opportunities for LAM.</p></div

Positivity for breast cancer lung metastasis mediators in LAM tissue.

<p>(A) Representative results for FSCN1 and ID1 in two LAM cases. Arrows mark magnified fields shown in the insets. (B) Representative immunohistochemistry results for CD34 and FSCN1 in LAM tissue. Positivity for FSCN1 is greater and not limited to endothelial cells.</p

Immunohistochemical characterization of biomarkers in normal breast and lung tissue.

<p>(A) Representative hematoxylin-eosin and immunohistochemical staining in normal breast tissue. The observed patterns of positivity were those expected with the exception of ALDH1, which could have showed positivity in the basal and luminal cell layers of the acini; nonetheless, this can only be observed at the growing end and branching of the ducts [<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0132546#pone.0132546.ref048" target="_blank">48</a>], which may be represented by the image shown in the right panel. Expression of ALDH1, CD61, FSCN1 and SOX9 was also seen in spindle-like cells surrounding the terminal extra-lobular ducts as well as in similar cells of the loose specialized intra-lobular stroma (arrows in insets). The results of CD61 are detailed for the basal cell layer in differentiated acini (a) and for spindle-like intra-lobular cells (b). The arrows mark magnified fields. (B) Representative hematoxylin-eosin and immunohistochemical staining in normal lung tissue. ALDH1 and FSCN1 mark the alveolar endothelium, and ALDH1 also marks the basal and luminal layers of the bronchioles. CD61, ID1 and SOX9 are not expressed in differentiated alveoli, and CD61 and SOX9 show positivity in the luminal and/or basal layers of the bronchioles.</p

Positivity for breast cancer stemness biomarkers in LAM tissue.

<p>Representative positive results for ALDH1, CD61 and SOX9 in two LAM cases. Arrows mark magnified fields shown in the insets.</p

Expression of mTOR pathway components and breast cancer metastasis to lung.

<p>(A) Kaplan-Meier lung metastasis-free survival (LMFS) and bone metastasis-free survival (BMFS) curves based on categorization of <i>TSC2</i> expression. The <i>P</i> values of the Cox proportional-hazards regression analysis are shown. (B) Tumor sample and gene expression clustering, and correlations of <i>TSC1/2</i> and genes from the lung metastasis signature, in the seminal breast cancer dataset [<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0132546#pone.0132546.ref027" target="_blank">27</a>]. (C) GSEA results for Cox regression values of the mTOR pathway gene set and LMFS or BMFS. (D) GSEA results for Cox regression values of metabolic pathway gene sets and LMFS or BMFS. (E) Tumor sample and gene expression clustering, and correlations between <i>TSC1/2</i> and genes from lung metastasis signature, in the TCGA dataset [<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0132546#pone.0132546.ref070" target="_blank">70</a>]. (F) GSEA results for the expression difference of the lung metastasis signature between MCF7 cells transduced with control or <i>TSC2</i>-target shRNAs. The left top panel shows the results for absolute expression differences, and the middle and bottom panels show the results for real differences of the up-regulated and down-regulated subsets of the signature, respectively. The right panels show the Western blot results for tuberin, pS6 and control loading, TUBA.</p

Intra-tissue and inter-case heterogeneity in the staining of canonical and novel LAM biomarkers.

<p>(A) Left panels, details of immunohistochemical results for canonical and novel biomarkers (FSNC1 and ID1) in a given LAM lesion, revealing expression heterogeneity. Right panels, evidence of heterogeneity based on the staining of SMA and FSCN1, SMA and ID1, and SMA and HMB-45 in three independent lesions/cases. (B) Top panel, heterogeneity for pS6 staining in a characteristic LAM cystic structure. The arrows mark two different tissue regions (a, b) that are magnified (bottom panels) for the immunohistochemical results of pS6 and the novel biomarkers. (C) Double immunofluorescence staining results also show intra-tissue heterogeneity for the novel biomarkers. (D) In large LAM lesions, pS6 is mostly apparent at the front.</p