Biology subjects

Boulias, K.

Publications and source records attributed to Boulias, K..

7 recordsLinked to original sources

bioRxiv2026

Type 1 immunity linked to CMV exposure improves long-term survival in sepsis without shock

Dysregulated immune responses are at the core of sepsis pathology and can drive both acute organ dysfunction and long-term morbidity and mortality. To better understand the association between specific immune histories, perturbations and sepsis outcomes, we combined immune phenotyping, functional cytokine production assays and antibody repertoire profiling. While sepsis immune profiles were highly heterogeneous, we identified a strong association between the frequency of CXCR3-expressing CD4 memory T cells at time of enrollment and six-month survival in sepsis without shock. Surprisingly, the same population was linked to improved organ function trajectories in septic shock patients but did not influence six-month survival, highlighting the importance of considering physiological states to define immune predictors. Finally, phage display profiling revealed that these Th1 cells were generally expanded in CMV-seropositive individuals, suggesting that previous and latent infections may modulate sepsis outcomes.

immunology↗

bioRxiv2026

Stoichiometric m6A regulation of YY1 orchestrates the metabolic switch during cardiac development

Chemical modifications of RNA provide an additional regulatory layer essential for development. N6A methyladenosine (m6A) is the most abundant internal mRNA mark, but how site specificity, stoichiometry, and cellular context together determine mRNA fate remains unclear. Here, we define these rules in cardiogenesis by combining single-molecule nanopore direct RNA sequencing (DRS) with a CRISPRdCas13 epitranscriptomic editing platform in human induced pluripotent stem cells and a conditional Mettl14 cardiac knockout in mice, integrated with multiomics, to map m6A sites and quantify stoichiometry. We uncover a bimodal m6A code in which low versus high modification ratios are associated with opposite mRNA and protein outcomes. We further show that Mettl14 loss causes developmental cardiomyopathy and embryonic lethality by disrupting the glycolysis to oxidative phosphorylation (OXPHOS) metabolic switch, and identify an m6A YY1 (Yin Yang 1) axis that post transcriptionally controls OXPHOS genes. Finally, targeted installation of m6A at defined sites using CRISPR/dCas13 reveals that m6A effects on YY1 are strongly locus and context dependent. Together, these findings establish m6A as a site and stoichiometry dependent regulatory code interpreted by cellular context to direct cardiac metabolic maturation. These principles are likely to extend to other developmental and physiological contexts in which precise control of metabolic state and gene dosage is required.

developmental biology↗

bioRxiv2026

Reversible m6Am methylation of snRNA by FTO controls morphine reward and tolerance without altering analgesia

Mu opioids, such as morphine, are effective analgesics, but their reward and tolerance drive opioid use disorder. A major goal is to achieve analgesia without these harmful effects. Here we show that morphine reward and tolerance require the RNA demethylase FTO. Genetic depletion and pharmacologic inhibition of FTO each reduced morphine reward, measured by conditioned-place preference, and reduced antinociceptive tolerance to morphine and fentanyl, without altering analgesia. Although FTO is known to erase m6A on mRNA, we found no effect of FTO depletion on m6A sites, but markedly increased levels of m6Am on snRNA. The effects of FTO depletion were suppressed in mice that cannot make m6Am, supporting the role of m6Am in morphine reward and tolerance. We show that FTO depletion regulates a gene expression network linked to morphine signaling. FTO inhibitors may therefore provide useful adjuvants to mu opioids in pain management and treatment of opioid use disorder.

neuroscience↗

bioRxiv2021

Intergenerational hormesis is regulated by heritable 18S rRNA methylation

Heritable non-genetic information can regulate a variety of complex phenotypes. However, what specific non-genetic cues are transmitted from parents to their descendants are poorly understood. Here, we perform metabolic methyl-labelling experiments to track the heritable transmission of methylation from ancestors to their descendants in the nematode Caenorhabditis elegans. We find that methylation is transmitted to descendants in proteins, RNA, DNA and lipids. We further find that in response to parental starvation, fed naive progeny display reduced fertility, increased heat stress resistance, and extended longevity. This intergenerational hormesis is accompanied by a heritable increase in N6-dimethyl adenosine (m6,2A) on the 18S ribosomal RNA at adenosines 1735 and 1736. We identified the conserved DIMT-1 as the m6,2A methyltransferase in C. elegans and find that dimt-1 is required for the intergenerational hormesis phenotypes. This study provides the first labeling and tracking of heritable non-genetic material across generations and demonstrates the importance of rRNA methylation for regulating the heritable response to starvation.

genetics↗

bioRxiv2020

Messenger RNA cap methylation by PCIF1 attenuates the interferon-β induced antiviral state

Interferons induce cell intrinsic responses associated with resistance to viral infection. To overcome the suppressive action of interferons and their downstream effectors viruses have evolved diverse mechanisms. Working with vesicular stomatitis virus (VSV) we report a role for the host cell N6-adenosine mRNA cap-methylase, phosphorylated C-terminal domain interacting factor 1 (PCIF1), in attenuating the antiviral activity of interferon-{beta}. Using cell based and in vitro biochemical assays we demonstrate that PCIF1 efficiently modifies VSV mRNA cap structures to m7Gpppm6Am, and we identify the cis-acting elements required for this modification. Under basal conditions, N6-methylation of VSV mRNA cap structures is functionally inert with regard to mRNA stability, translation and viral infectivity. Induction of an antiviral state by treatment of cells with interferon-{beta} prior to infection uncovered a functional role for PCIF1 in attenuation of the antiviral response. Cells lacking PCIF1 or expressing a catalytically inactive PCIF1, exhibit an augmented effect of interferon-{beta} in the inhibition of viral replication and gene expression. This work identifies a function of PCIF1 and cap-proximal m6Am in attenuation of the host response to VSV infection that likely extends to other viruses. SignificanceThe cap structure present at the 5 end of eukaryotic mRNAs regulates RNA stability, translation, and marks mRNA as self, thereby impeding recognition by the innate immune system. Cellular transcripts beginning with adenosine are additionally modified at the N6 position of the 2-O methylated cap-proximal residue by the methyltransferase PCIF1 to m7Gpppm6Am. We define a function for this N6-adenosine methylation in attenuating the interferon-{beta} mediated suppression of viral infection. Cells lacking PCIF1, or defective in its enzymatic activity, augment the cell intrinsic suppressive effect of interferon-{beta} treatment on vesicular stomatitis virus gene expression. VSV mRNAs are efficiently methylated by PCIF1, suggesting this contributes to viral evasion of innate immune suppression.

microbiology↗

bioRxiv2020

Coping with darkness: The adaptive response of marine picocyanobacteria to repeated light energy deprivation

The picocyanobacteria Prochlorococcus and Synechococcus are found throughout the oceans euphotic zone, where the daily light:dark cycle drives their physiology. Periodic deep mixing events can, however, move cells below this zone, depriving them of light for extended periods of time. Here we demonstrate that Prochlorococcus and Synechococcus can adapt to tolerate repeated periods of light energy deprivation. Cyanobacterial cultures kept in the dark for 3 days and then returned to the light initially required 18-26 days to resume growth, but after multiple rounds of dark exposure the strains began to regrow after only 1-2 days. This dark-tolerant phenotype was stable and heritable; cultures retained the trait across at least 18-21 generations even when grown in a standard 13:11 light:dark cycle. We found no genetic differences between the dark-tolerant and parental strains of Prochlorococcus NATL2A, indicating that an epigenetic change is responsible for the adaptation. To begin to explore this possibility, we asked whether DNA methylation - an epigenetic mechanism in bacteria - occurs in Prochlorococcus. LC-MS/MS analysis showed that while DNA methylations, including 6mA and 5mC, are found in some other Prochlorococcus strains, no methylations were detected in either the parental or dark-tolerant strain used in our experiments -i.e. the NATL2A strain. These findings suggest that Prochlorococcus utilizes a yet-to-be-determined epigenetic mechanism to adapt to the stress of extended light energy deprivation.

microbiology↗

bioRxiv2018

Identification of the m6Am methyltransferase PCIF1 reveals the location and functions of m6Am in the transcriptome

mRNAs are regulated by nucleotide modifications that influence their cellular fate. Two of the most abundant modified nucleotides are N6-methyladenosine (m6A), found within mRNAs, and N6,2-O-dimethyladenosine (m6Am), which is found at the first-transcribed nucleotide. A long-standing challenge has been distinguishing these similar modifications in transcriptome-wide mapping studies. Here we identify and biochemically characterize, PCIF1, the methyltransferase that generates m6Am. We find that PCIF1 binds and is dependent on the m7G cap. By depleting PCIF1, we definitively identified m6Am sites and generated transcriptome-wide maps that are selective for m6Am and m6A. We find that m6A and m6Am misannotations largely arise from mRNA isoforms with alternate transcription-start sites. These isoforms contain m6Am that appear to map to \"internal\" sites, increasing the likelihood of misannotation. Using the new m6Am annotations, we find that depleting m6Am does not affect mRNA translation but reduces the stability of a subset of m6Am-annotated mRNAs. The discovery of PCIF1 and our accurate mapping technique will facilitate future studies to characterize m6Ams function.

molecular biology↗