Mutual interactions of the phytohormones cytokinins and auxin determine root or shoot identity during postembryonic de novo organogenesis in plants. However, our understanding to the role of hormonal metabolism and perception during early stages of cell fate reprograming is still elusive. In the hypocotyl explant assay, auxin activated root formation while cytokinins mediated early loss of the root identity, primordia disorganization and initiation of shoot development. Exogenous but also endogenous cytokinins influenced the initiation of newly formed organs as well as the pace of organ developmental sequence. The process of de novo shoot apical meristem establishment was accompanied by accumulation of endogenous cytokinins, differential regulation of genes for individual cytokinin receptors, strong activation of AHK4-mediated signalling and induction of shoot-specific homeodomain regulator WUSCHEL. The latter associated with upregulation of isopentenyladenine-type cytokinins, revealing higher shoot-forming potential when compared with trans-zeatin. Moreover, AHK4-controlled cytokinin signalling negatively regulated root stem cell organizer WUSCHEL RELATED HOMEOBOX 5 in the root quiescent centre. We propose an important role of endogenous cytokinin biosynthesis and AHK4-mediated cytokinin signalling in the control of de novo induced organ identity.

Climate change, with its altered precipitation and extreme temperatures, significantly threatens global viticulture by affecting grapevine growth, yield, and fruit quality. Understanding the molecular underpinnings of grapevine resilience is crucial for developing adaptive strategies. Our aim is to explore the application of multi-omics approaches (integrating genomics, transcriptomics, proteomics, metabolomics, and epigenetics) to investigate grapevine stress responses. Advances in these omics technologies have been pivotal in identifying key stress-response genes, metabolic pathways, and regulatory networks, particularly those contributing to grapevine tolerance to water deficiency, (such as drought and decreased precipitation), extreme temperatures, UV radiation, and salinity. Furthermore, the rich genetic reservoir within grapevines serves as a vital resource for enhancing stress tolerance. While adaptive strategies such as rootstock selection and precision irrigation are important, future research must prioritize integrated multi-omics studies, including those on regional climate adaptation and long-term breeding programs. Such efforts are essential to exploit genetic diversity and ensure the sustainability of viticulture in the evolving climate. In summary, this review demonstrates how utilizing the inherent genetic variability of grapevines and employing multi-omics approaches are critical for understanding and enhancing their resilience to the challenges posed by climate change.

Introduction: The escalating challenge of climate change has underscored the critical need to understand cold defense mechanisms in cultivated grapevine Vitis vinifera. Temperature variations can affect the growth and overall health of vine.Methods: We used Self Organizing Maps machine learning method to analyze gene expression data from leaves of five Vitis vinifera cultivars each treated by four different temperature conditions. The algorithm generated sample-specific “portraits” of the normalized gene expression data, revealing distinct patterns related to the temperature conditions applied.Results: Our analysis unveiled a connection with vitamin B1 (thiamine) biosynthesis, suggesting a link between temperature regulation and thiamine metabolism, in agreement with thiamine related stress response established in Arabidopsis before. Furthermore, we found that epigenetic mechanisms play a crucial role in regulating the expression of stress-responsive genes at low temperatures in grapevines.Discussion: Application of Self Organizing Maps portrayal to vine transcriptomics identified modules of coregulated genes triggered under cold stress. Our machine learning approach provides a promising option for transcriptomics studies in plants.

In the proposed study three major issues have been addressed: Firstly, the diversity of grapevine accessions worldwide and particularly in Armenia, a small country located in the largely volcanic Armenian Highlands, is incredibly rich in cultivated and especially wild grapes; secondly, the information hidden in their (whole) genomes, e.g., about the domestication history of grapevine over the last 11,000 years and phenotypic traits such as cultivar utilization and a putative resistance against powdery mildew, and, thirdly machine learning methods to extract and to visualize this information in an easy to percept way. We shortly describe the Self Origanizing Maps (SOM) portrayal method called “SOMmelier” (as the vine-genome “waiter”) and illustrate its power by applying it to whole genome data of hundreds of grapevine accessions. We also give a short outlook on possible future directions of machine learning in grapevine transcriptomics and ampelogaphy.

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.

Conventional immune checkpoint inhibitors (ICIs) remain largely ineffective in microsatellite-stable metastatic colorectal cancer (MSS mCRC), where low tumor immunogenicity and molecular heterogeneity across metastatic sites underpin therapeutic resistance. We present a comprehensive transcriptomics analysis of metastatic and primary tumor biopsies from MSS mCRC patients treated with botensilimab (BOT; Fc-enhanced anti– CTLA-4 ) ± balstilimab (BAL; anti– PD-1) . Self-organizing map (SOM) machine learning stratified tumors into four molecular types, including a liver-like (LIV) subtype characterized by metabolic reprogramming and immunosuppressive signatures, and proliferative (PRO), inflammatory (INF), and mesenchymal (MES) types concordant with pan-cancer classifications. PRO, INF, and MES types were enriched for epithelial tumor cells, immune cells, and fibroblasts, respectively, defining immune-depleted, immune-enriched, and fibrotic states along a plasticity gradient. We observed treatment-related transcriptomic shifts toward immune-enriched states via upregulation of antigen presentation, T cell recruitment, and cytotoxicity pathways. INF and MES tumor types exhibited improved clinical responses and survival vs PRO and LIV types. This study identified distinct tumor microenvironment states that align along an immunophenotype axis marked by CD74, interferon-γ, and APOBEC3 expression identified previously for primary CRC. Our findings provide novel insights into molecular correlates of immunotherapy response in MSS mCRC, potentially informing future therapeutic strategies to expand ICI efficacy to historically unresponsive tumors.