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133 Publications visible to you, out of a total of 133
Annual transcriptomic trajectory of grapevine buds reveals the coordinated regulation of thiamine and stilbenoid biosynthesis during winter dormancy.

Abstract (Expand)

Bud dormancy is a critical survival strategy for perennial plants in temperate climates to endure winter, involving complex transcriptional reprogramming. While previous studies have investigated gene … expression during discrete phases of the grapevine bud annual cycle, a holistic understanding requires an integrated, season-wide analysis. We conducted a meta-analysis by combining and reexamining the transcriptomic data from two seminal studies on grapevine bud development. Using Self-Organizing Maps, we parsed the combined gene expression data into three major clusters corresponding to distinct seasonal activities, which we termed "summer-upregulated," "winter-upregulated," and "intermediate." Our analysis revealed that genes whose expression was predominantly upregulated during the winter months were significantly enriched in Gene Ontology terms related to stilbenoid biosynthesis and thiamine biosynthesis. This finding prompted a deeper investigation into these two pathways. We observed profound and coordinated upregulation of key genes in both pathways during the coldest winter months, suggesting that these genes are integral components of the bud's strategy for surviving low temperatures and maintaining viability. These results confirm the role of stilbenoids as stress-responsive compounds and reveal a novel role for thiamine biosynthesis in the molecular mechanisms of grapevine bud dormancy. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s12870-026-08190-w.

Authors: T. Konecny, A. Asatryan, H. Binder

Date Published: 21st Jan 2026

Publication Type: Journal

Development of biobanking infrastructure in Armenia: opportunities and challenges

Abstract (Expand)

Biobanking has become a cornerstone of biomedical research and precision medicine, enabling population studies, biomarker discovery, and translational research. However, while high-income countries … operate mature biobanking systems, middle-income and transitional economies encounter distinct barriers to establishing sustainable and internationally compatible infrastructures. This mini review examines the development of biobanking in Armenia as a representative middle-income case. It highlights key opportunities, such as strong diaspora scientific networks, a growing biotechnology sector, increasing national interest in precision medicine, and Armenia’s strategic geographic position between Europe and Asia. At the same time, significant challenges persist, including limited funding, regulatory and ethical gaps, infrastructure constraints, shortages in specialized technical personnel, and socio-cultural barriers related to sample donation and data sharing. The review outlines strategic approaches adopted in Armenia, including international collaboration, capacity-building initiatives, and alignment with global best practices. Lessons from Armenia’s experience may guide other middle-income and post-Soviet countries in developing effective and resilient biobanking systems.

Authors: Gohar Mkrtchyan, Kristina Avanesyan, Hovsep Ghazaryan, Merry Mazmanian, Marie-Alexandra Alyanakian, Arsene Mekinian, Arsen Arakelyan

Date Published: 13th Jan 2026

Publication Type: Journal

Integrated analysis of the blood metallome and DNA methylation, gene expression, and protein levels of immune-associated genes in residents from mining region

Abstract (Expand)

Environmental exposure to toxic and essential metals can disrupt host immune function through mechanisms involving epigenetic, transcriptional, and post-transcriptional regulation. Although numerous … studies have investigated these regulatory layers separately, integrative analyses across molecular levels in relation to metallome is missing. In this study, we performed a targeted multi-omics analysis of six immune-associated genes (NFKB1, CDKN2A, IGF2, H19, ESR1, and APOA5) and corresponding proteins in healthy residents from a long-term mining region (MRR, n = 46) and a non-mining region (NMR, n = 48). Transcriptome data were generated by mRNA sequencing, while DNA methylation data were obtained using targeted bisulfite sequencing by analyzing previously identified differentially methylated positions. Plasma protein levels were measured by enzyme-linked immunosorbent assay, and plasma metal concentrations were quantified using inductively coupled plasma mass spectrometry. We observed significantly higher plasma levels of NFKB1 and CDKN2A proteins, along with lower ESR1 transcript levels, in residents of the mining region compared to the non-mining region. NFKB1 protein levels were associated with both promoter methylation and residence in mining region, suggesting a regulatory cascade from DNA methylation to protein expression. IGF2 protein levels were higher in males and showed positive associations with age and the cumulative Z-score of essential metal mixture burden. Our results show that long-term residence in mining regions is associated with changes in NFKB1 at both the DNA methylation and protein levels, which may serve as a sensitive biomarker of metal exposure.

Authors: Yeva Bareghamyan, Arpine Minasyan, Suren Davitavyan, Anna Petrackova, Jakub Savara, Romana Nesnadna, Eva Kriegova, Jonathan Schug, Arsen Arakelyan, Ani Stepanyan

Date Published: 4th Jan 2026

Publication Type: Journal

Persistence of Western Diet-Associated Pathway Activity Profiles in Ventricular Tissues

Abstract (Expand)

The consumption of a Western diet (WD), characterized by high levels of fats and sugars, is strongly associated with adverse cardiovascular outcomes. In this case-control study, we evaluated long-term … alterations in signaling pathway activities in the left (LV) and right (RV) ventricular tissues of C57Bl/6J mice that were exposed to WD starting at 300 days of age for 125 days before switching to a normal diet (ND). LV and RV tissues were collected at 530 days and subjected to RNA sequencing. Pathway activity for 40 signaling pathways (comprising 709 pathway branches/sinks) was calculated using the topology-aware Pathway Signal Flow (PSF) algorithm, which assesses signal propagation along a pathway based on gene expression levels of its components and their interactions. We observed significant perturbations in 14 pathway branches specifically in LV tissue of male mice, 105 days after the ND switch. These alterations included the downregulation of cardioprotective VEGF signaling and the upregulation of pro-fibrotic TGF-beta signaling, suggesting lasting cardiovascular risks. Furthermore, strong signaling was detected in the cGMP-PKG and FOXO pathways linked to cardiac failure. Finally, pro- and anti-apoptotic signals were simultaneously upregulated, accompanied by the downregulation of cell cycle inhibitors. Notably, no significant gene expression changes were detected in the left ventricular tissue of females, and no significant differences were observed in right ventricular tissue in either sex. These findings suggest that the effects of a Western diet may persist even after transitioning to a healthier diet. Further studies are needed to elucidate the diet-associated risks and develop strategies to mitigate these long-term effects.

Authors: Tamara Sirunyan, Gisane Lazaryan, Siras Hakobyan, Suren Davitavyan, Ani Stepanyan, Agnieszka Brojakowska, Mary Khlgatian, Malik Bisserier, Shihong Zhang, David Goukassian, Arsen Arakelyan

Date Published: 2nd Jan 2026

Publication Type: Journal

Long-Term Impact of Western Diet on Right Ventricular Transcriptome: Uncovering Sex-Specific Patterns in C57BL/6J Mice

Abstract (Expand)

The Western diet (WD) has been linked to various structural and functional alterations in the left ventricle (LV), but the molecular response of the right ventricle (RV) remains largely unknown. Given … the RV’s distinct anatomical and functional characteristics, it is crucial to understand how long-term WD exposure affects RV gene expression, especially in a sex-specific context. Our objective was to perform gene expression profiling of the RV late responses to WD in wild-type mice. Male and female C57BL/6J mice were fed a WD for 125 days from 300 to 425 days of age, and RV tissues were collected at 530 and 640/750 (female/male) days. mRNA sequencing was performed on RV tissues to identify differentially expressed genes (DEGs) between WD-fed and normal diet (ND)-fed groups. Data processing and analysis were conducted using the STAR aligner and DESeq2. WD-induced RV transcriptomic changes were characterized by differential expression of genes associated with cardiac remodeling and transcriptional regulation in both sexes. In females, additional genes showing altered expression were associated with immune response, whereas in males, changes were more limited, primarily involving genes related to circadian rhythm and cardiac remodeling. Echocardiography revealed modest, sex-specific differences: WD-fed females showed a decrease in right-ventricular internal diameter in diastole and a trend toward increased pulmonary trunk diameter, whereas males showed no notable changes. These exploratory results suggest that WD is associated with modest transcriptomic changes in the RV in both sexes, with only minor structural differences observed in females, indicating subtle sex-specific effects after a switch to normal chow.

Authors: Ani Stepanyan, Siras Hakobyan, Agnieszka Brojakowska, Malik Bisserier, Roksana Zakharyan, Suren Davitavyan, Tamara Sirunyan, Gisane Khachatryan, Mary K. Khlgatian, Shihong Zhang, Ania Baghoomian, Susmita Sahoo, Lahouaria Hadri, Venkata Naga Srikanth Garikipati, Arsen Arakelyan, David A. Goukassian

Date Published: 26th Dec 2025

Publication Type: Journal

Long-term Pathway Activation in Cardiac Ventricular Tissues after Gamma and simGCRsim Irradiation.

Abstract (Expand)

Space radiation represents a significant health risk for deep-space exploration, yet its long-term effects on cardiovascular function remain poorly understood. While our previous studies have highlighted … persistent transcriptional changes in left ventricular (LV) and right ventricular (RV) tissues after a single whole-body irradiation in mice, a systems-level understanding of pathway activity deregulation is lacking. To address this gap, we applied the Pathway Signal Flow (PSF) algorithm to analyze long-term pathway activity alterations in LV and RV tissues of C57Bl/6J mice exposed to gamma radiation (100 cGy 137Cs) or the simplified Galactic Cosmic Ray simulation (simGCRsim, 50 cGy 500 MeV/n) composition of ion beams. RNA sequencing data were analyzed to assess pathway activity changes, sex-specific effects, and ventricular differences 440 days post-irradiation. We observed marked sex- and ventricle-specific differences in pathway deregulation. Left ventricular tissues in females exhibited broad signaling pathway alterations after simGCRsim exposure, particularly in immune response, cytoskeletal remodeling, and survival-related pathways (e.g., NF-κB, VEGF, and MAPK). In contrast, male RV tissues demonstrated higher pathway deregulation than LV, particularly in PPAR, NF-κB, and HIF-1 pathways, implicating metabolic disruption and survival adaptations. Furthermore, simGCRsim exposure induced greater long-term pathway perturbations than gamma rays. Our findings suggest that sex-dependent and ventricle-specific signaling alterations contribute to long-term cardiovascular risks following space irradiation. Notably, VEGF and NF-κB signaling emerge as key regulators of cardiac adaptation in females. Future studies in larger cohorts, incorporating early-stage molecular responses and broader pathway analyses, are needed to refine cardiovascular risk assessments for space travel.

Authors: Gisane Khachatryan, Tamara Sirunyan, Siras Hakobyan, Suren Davitavyan, Roksana Zakharyan, Ani Stepanyan, Agnieszka Brojakowska, Mary K Khlgatian, Malik Bisserier, Shihong Zhang, David A Goukassian, Arsen Arakelyan

Date Published: 25th Sep 2025

Publication Type: Journal

Spatial transcriptome analysis of the human eyelid depicts meibomian gland cell differentiation: A pilot study.

Abstract (Expand)

Meibomian glands (MGs) are an integral component of the ocular defense system, as their secretion product, meibum, is essential for protecting the eye surface. To characterize the transcriptional program … underlying meibum production, we employed spatial transcriptomics (ST) analysis of the human eyelid from a sample from a 60-year-old male. We resolved 18 distinct eyelid clusters, representing structures such as the conjunctiva, epidermis, hair-associated sebaceous glands, and MGs. Focusing on the MG, we distinguished basal (MEI-B cluster) and differentiating (MEI-DIFF cluster) meibocytes, as well as a third, duct-related cluster (MEI-DUCT). Self-organizing maps (SOM) portrayal of ST images and pseudotime analysis confirmed progress from MEI-B to MEI-DIFF and further to MEI-DUCT, as the latter turned out to include terminally differentiated meibocytes. Accordingly, gene set enrichment analysis associated early/intermediate meibocyte maturation with energy and lipid metabolism, and later stages with barrier functions. We also identified significant differences between the MG and sebaceous gland transcriptomes. The MG-specific signature included transcripts such as AQP9, MMP3, and PITX1, and selective expression of PITX1 in the MG compared to the sebaceous gland was confirmed by immunohistochemistry on the same sample and samples from three other elderly adults. We deliver the first spatial portrait of the human MG transcriptional landscape. Besides enhancing our understanding of MG physiology, our study identifies novel targets for regulating MG homeostasis in health and disease.

Authors: H. Binder, U. Hampel, H. Loeffler-Wirth, F. Hansmann, H. Pfannkuche, M. Schmidt, M. R. Schneider

Date Published: 19th Sep 2025

Publication Type: Journal

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