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93 Publications visible to you, out of a total of 93
Dual domestications and origin of traits in grapevine evolution.

Abstract (Expand)

We elucidate grapevine evolution and domestication histories with 3525 cultivated and wild accessions worldwide. In the Pleistocene, harsh climate drove the separation of wild grape ecotypes caused by … continuous habitat fragmentation. Then, domestication occurred concurrently about 11,000 years ago in Western Asia and the Caucasus to yield table and wine grapevines. The Western Asia domesticates dispersed into Europe with early farmers, introgressed with ancient wild western ecotypes, and subsequently diversified along human migration trails into muscat and unique western wine grape ancestries by the late Neolithic. Analyses of domestication traits also reveal new insights into selection for berry palatability, hermaphroditism, muscat flavor, and berry skin color. These data demonstrate the role of the grapevines in the early inception of agriculture across Eurasia.

Authors: Y. Dong, S. Duan, Q. Xia, Z. Liang, X. Dong, K. Margaryan, M. Musayev, S. Goryslavets, G. Zdunic, P. F. Bert, T. Lacombe, E. Maul, P. Nick, K. Bitskinashvili, G. D. Bisztray, E. Drori, G. De Lorenzis, J. Cunha, C. F. Popescu, R. Arroyo-Garcia, C. Arnold, A. Ergul, Y. Zhu, C. Ma, S. Wang, S. Liu, L. Tang, C. Wang, D. Li, Y. Pan, J. Li, L. Yang, X. Li, G. Xiang, Z. Yang, B. Chen, Z. Dai, Y. Wang, A. Arakelyan, V. Kuliyev, G. Spotar, N. Girollet, S. Delrot, N. Ollat, P. This, C. Marchal, G. Sarah, V. Laucou, R. Bacilieri, F. Rockel, P. Guan, A. Jung, M. Riemann, L. Ujmajuridze, T. Zakalashvili, D. Maghradze, M. Hohn, G. Jahnke, E. Kiss, T. Deak, O. Rahimi, S. Hubner, F. Grassi, F. Mercati, F. Sunseri, J. Eiras-Dias, A. M. Dumitru, D. Carrasco, A. Rodriguez-Izquierdo, G. Munoz, T. Uysal, C. Ozer, K. Kazan, M. Xu, Y. Wang, S. Zhu, J. Lu, M. Zhao, L. Wang, S. Jiu, Y. Zhang, L. Sun, H. Yang, E. Weiss, S. Wang, Y. Zhu, S. Li, J. Sheng, W. Chen

Date Published: 3rd Mar 2023

Publication Type: Journal

Transcriptional states of CAR-T infusion relate to neurotoxicity – lessons from high-resolution single-cell SOM expression portraying

Abstract (Expand)

Anti-CD19 CAR-T cell immunotherapy is a hopeful treatment option for patients with B cell lymphomas, however it copes with partly severe adverse effects like neurotoxicity. Single-cell resolved molecular … data sets in combination with clinical parametrization allow for comprehensive characterization of cellular subpopulations, their transcriptomic states, and their relation to the adverse effects. We here present a re-analysis of single-cell RNA sequencing data of 24 patients comprising more than 130,000 cells with focus on cellular states and their association to immune cell related neurotoxicity. For this, we developed a single-cell data portraying workflow to disentangle the transcriptional state space with single-cell resolution and its analysis in terms of modularly-composed cellular programs. We demonstrated capabilities of single-cell data portraying to disentangle transcriptional states using intuitive visualization, functional mining, molecular cell stratification, and variability analyses. Our analysis revealed that the T cell composition of the patient's infusion product as well as the spectrum of their transcriptional states of cells derived from patients with low ICANS grade do not markedly differ from those of cells from high ICANS patients, while the relative abundancies, particularly that of cycling cells, of LAG3-mediated exhaustion and of CAR positive cells, vary. Our study provides molecular details of the transcriptomic landscape with possible impact to overcome neurotoxicity. Keywords: CAR-T cell immunotherapy; bioinformatics workflow; data portraying; single-cell transcriptomics; transcriptional states. Copyright © 2022 Loeffler-Wirth, Rade, Arakelyan, Kreuz, Loeffler, Koehl, Reiche and Binder.

Authors: Henry Loeffler-Wirth, Michael Rade, Arsen Arakelyan, Markus Kreuz, Markus Loeffler, Ulrike Koehl, Kristin Reiche, Hans Binder

Date Published: 28th Sep 2022

Publication Type: Journal

Molecular Epidemiology and Virulence of Non-Typhoidal Salmonella in Armenia

Abstract (Expand)

In this work, we analysed human isolates of nontyphoidal Salmonella enterica subsp. enterica (NTS), which were collected from salmonellosis cases in Armenia from 1996 to 2019. This disease became a … leading food-borne bacterial infection in the region, with the younger age groups especially affected. The isolates were characterised by serotyping, Enterobacterial Repetitive Intergenic Consensus (ERIC-PCR) typing, and whole genome sequencing (WGS). The main serotypes were S. Typhimurium, S. Enteritidis, and S. Arizonae. ERIC-PCR indicated a high degree of clonality among S. Typhimurium strains, which were also multidrug-resistant and produced extended spectrum beta-lactamases. During the study period, the frequency of S. Typhimurium and S. Arizonae isolations decreased, but with the increase in S. Enteritidis and other NTS. A total of 42 NTS isolates were subjected to WGS and explored for virulence-related traits and the corresponding genetic elements. Some virulence and genetic factors were shared by all NTS serotypes, while the main differences were attributed to the serotype-specific diversity of virulence genes, SPIs, virulence plasmids, and phages. The results indicated the variability and dynamics in the epidemiology of salmonellosis and a high virulence potential of human NTS isolates circulating in the region.

Authors: Anahit Sedrakyan, Zhanna Ktsoyan, Karine Arakelova, Zaruhi Gevorgyan, Magdalina Zakharyan, Shoghik Hakobyan, Alvard Hovhannisyan, Arsen Arakelyan, Rustam Aminov

Date Published: 18th Aug 2022

Publication Type: Journal

Spaceflight-Associated Changes of snoRNAs in Peripheral Blood Mononuclear Cells and Plasma Exosomes—A Pilot Study

Abstract (Expand)

During spaceflight, astronauts are exposed to various physiological and psychological stressors that have been associated with adverse health effects. Therefore, there is an unmet need to develop novel … diagnostic tools to predict early alterations in astronauts' health. Small nucleolar RNA (snoRNA) is a type of short non-coding RNA (60-300 nucleotides) known to guide 2'-O-methylation (Nm) or pseudouridine (ψ) of ribosomal RNA (rRNA), small nuclear RNA (snRNA), or messenger RNA (mRNA). Emerging evidence suggests that dysregulated snoRNAs may be key players in regulating fundamental cellular mechanisms and in the pathogenesis of cancer, heart, and neurological disease. Therefore, we sought to determine whether the spaceflight-induced snoRNA changes in astronaut's peripheral blood (PB) plasma extracellular vesicles (PB-EV) and peripheral blood mononuclear cells (PBMCs). Using unbiased small RNA sequencing (sRNAseq), we evaluated changes in PB-EV snoRNA content isolated from astronauts (n = 5/group) who underwent median 12-day long Shuttle missions between 1998 and 2001. Using stringent cutoff (fold change > 2 or log2-fold change >1, FDR < 0.05), we detected 21 down-and 9-up-regulated snoRNAs in PB-EVs 3 days after return (R + 3) compared to 10 days before launch (L-10). qPCR validation revealed that SNORA74A was significantly down-regulated at R + 3 compared to L-10. We next determined snoRNA expression levels in astronauts' PBMCs at R + 3 and L-10 (n = 6/group). qPCR analysis further confirmed a significant increase in SNORA19 and SNORA47 in astronauts' PBMCs at R + 3 compared to L-10. Notably, many downregulated snoRNA-guided rRNA modifications, including four Nms and five ψs. Our findings revealed that spaceflight induced changes in PB-EV and PBMCs snoRNA expression, thus suggesting snoRNAs may serve as potential novel biomarkers for monitoring astronauts' health. Keywords: astronaut; biomarker; extracellular vesicles; peripheral blood—mononuclear cells; snoRNA. Copyright © 2022 Rai, Rajan, Bisserier, Brojakowska, Sebastian, Evans, Coleman, Mills, Arakelyan, Uchida, Hadri, Goukassian and Garikipati.

Authors: Amit Kumar Rai, K. Shanmugha Rajan, Malik Bisserier, Agnieszka Brojakowska, Aimy Sebastian, Angela C. Evans, Matthew A. Coleman, Paul J. Mills, Arsen Arakelyan, Shizuka Uchida, Lahouaria Hadri, David A. Goukassian, Venkata Naga Srikanth Garikipati

Date Published: 24th Jun 2022

Publication Type: Journal

Astronauts Plasma-Derived Exosomes Induced Aberrant EZH2-Mediated H3K27me3 Epigenetic Regulation of the Vitamin D Receptor

Abstract (Expand)

There are unique stressors in the spaceflight environment. Exposure to such stressors may be associated with adverse effects on astronauts' health, including increased cancer and cardiovascular … disease risks. Small extracellular vesicles (sEVs, i.e., exosomes) play a vital role in intercellular communication and regulate various biological processes contributing to their role in disease pathogenesis. To assess whether spaceflight alters sEVs transcriptome profile, sEVs were isolated from the blood plasma of 3 astronauts at two different time points: 10 days before launch (L-10) and 3 days after return (R+3) from the Shuttle mission. AC16 cells (human cardiomyocyte cell line) were treated with L-10 and R+3 astronauts-derived exosomes for 24 h. Total RNA was isolated and analyzed for gene expression profiling using Affymetrix microarrays. Enrichment analysis was performed using Enrichr. Transcription factor (TF) enrichment analysis using the ENCODE/ChEA Consensus TF database identified gene sets related to the polycomb repressive complex 2 (PRC2) and Vitamin D receptor (VDR) in AC16 cells treated with R+3 compared to cells treated with L-10 astronauts-derived exosomes. Further analysis of the histone modifications using datasets from the Roadmap Epigenomics Project confirmed enrichment in gene sets related to the H3K27me3 repressive mark. Interestingly, analysis of previously published H3K27me3-chromatin immunoprecipitation sequencing (ChIP-Seq) ENCODE datasets showed enrichment of H3K27me3 in the VDR promoter. Collectively, our results suggest that astronaut-derived sEVs may epigenetically repress the expression of the VDR in human adult cardiomyocytes by promoting the activation of the PRC2 complex and H3K27me3 levels.

Authors: Malik Bisserier, Agnieszka Brojakowska, Nathaniel Saffran, Amit Kumar Rai, Brooke Lee, Matthew Coleman, Aimy Sebastian, Angela Evans, Paul J. Mills, Sankar Addya, Arsen Arakelyan, Venkata Naga Srikanth Garikipati, Lahouaria Hadri, David A. Goukassian

Date Published: 16th Jun 2022

Publication Type: Journal

Integrated Multi-Omics Maps of Lower-Grade Gliomas.

Abstract (Expand)

Multi-omics high-throughput technologies produce data sets which are not restricted to only one but consist of multiple omics modalities, often as patient-matched tumour specimens. The integrative … analysis of these omics modalities is essential to obtain a holistic view on the otherwise fragmented information hidden in this data. We present an intuitive method enabling the combined analysis of multi-omics data based on self-organizing maps machine learning. It "portrays" the expression, methylation and copy number variations (CNV) landscapes of each tumour using the same gene-centred coordinate system. It enables the visual evaluation and direct comparison of the different omics layers on a personalized basis. We applied this combined molecular portrayal to lower grade gliomas, a heterogeneous brain tumour entity. It classifies into a series of molecular subtypes defined by genetic key lesions, which associate with large-scale effects on DNA methylation and gene expression, and in final consequence, drive with cell fate decisions towards oligodendroglioma-, astrocytoma- and glioblastoma-like cancer cell lineages with different prognoses. Consensus modes of concerted changes of expression, methylation and CNV are governed by the degree of co-regulation within and between the omics layers. The method is not restricted to the triple-omics data used here. The similarity landscapes reflect partly independent effects of genetic lesions and DNA methylation with consequences for cancer hallmark characteristics such as proliferation, inflammation and blocked differentiation in a subtype specific fashion. It can be extended to integrate other omics features such as genetic mutation, protein expression data as well as extracting prognostic markers.

Authors: H. Binder, M. Schmidt, L. Hopp, S. Davitavyan, A. Arakelyan, H. Loeffler-Wirth

Date Published: 4th Jun 2022

Publication Type: Journal

Space flight associated changes in astronauts’ plasma‐derived small extracellular vesicle microRNA: Biomarker identification

Abstract (Expand)

Dear Editor, This pilot study suggests relatively short (median 12 days long) low-Earth orbit (LEO) spaceflight induces changes in circulating plasma small extracellular vesicle (sEV) microRNA expression. … Normalization of small RNA sequencing (sRNAseq) data and quantitative polymerase chain reaction (qPCR) validation confirmed miR-4732-3p is significantly upregulated up to 3 days post-landing, and enrichment analysis suggests this miRNA is expressed in various central nervous system tissues and hematopoietic cells and may be linked to different organ disorders.

Authors: David Goukassian, Arsen Arakelyan, Agnieszka Brojakowska, Malik Bisserier, Siras Hakobyan, Lahouaria Hadri, Amit Kumar Rai, Angela Evans, Aimy Sebastian, May Truongcao, Carolina Gonzalez, Anamika Bajpai, Zhongjian Cheng, Praveen Kumar Dubey, Sankar Addya, Paul Mills, Kenneth Walsh, Raj Kishore, Matt Coleman, Venkata Naga Srikanth Garikipati

Date Published: 2nd Jun 2022

Publication Type: Journal

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