Biology subjects

Fernandez, E. C.

Publications and source records attributed to Fernandez, E. C..

5 recordsLinked to original sources

bioRxiv2026

Distinct Temporal Responses to Xanthomonas translucens Strains Shape Bacterial Leaf Streak Development in Triticale

Bacterial leaf streak caused by Xanthomonas translucens threatens cereal production, however, the temporal coordination of host transcriptional responses during resistant and susceptible interactions in polyploid crops remains partially understood. Here, we used time-resolved transcriptomics to characterize responses of synthetic hexaploid triticale to two X. translucens pv. undulosa strains that produce contrasting disease outcomes. The resistant interaction with non-virulent LB10 showed a strong early transcriptional response that subsequently declined, whereas responses to the virulent strain P3 progressively intensified as water-soaking symptoms developed. Analysis of syntenic A-, B-, and R-subgenome homoeologs revealed extensive regulatory asymmetry, with R-subgenome homoeologs disproportionately represented among transcriptionally suppressed genes. Despite their conserved coding sequences, homoeologs often showed divergent transcriptional responses during infection, whereas greater similarity in upstream regulatory regions was associated with more coordinated responsive trajectories. We next examined pathogen-mediated transcriptional regulation through transcription activator-like (TAL) effectors. Among eight TAL effector templates identified in LB10 and P3, TAL5-associated predicted targets showed the strongest preferential induction during P3 infection. Disruption of TAL5 in P3 predominantly reduced host gene expression, including genes involved in immune signaling, cell wall-associated defense and photosynthetic function, accompanied by reduced maximum photosystem II quantum efficiency at 72 h post-inoculation. Together, our results show that bacterial leaf streak outcomes are shaped by temporally distinct host responses and pathogen effector-associated transcriptional reprogramming, providing insight into the dynamic regulation underlying cereal-Xanthomonas interactions.

plant biology↗

bioRxiv2025

CD155 regulates tumor growth and immune evasion in diffuse midline glioma.

Diffuse midline glioma (DMG) is a devastating pediatric brain tumor with an unmet need for novel therapies. Immune checkpoint inhibitors have failed to prolong survival for DMG patients. In this study, we analyzed the expression of immune checkpoint molecules in human and murine DMG cells, as well as primary brain tumor samples, and identified CD155 as the most highly expressed. When murine DMG cells were co-cultured with CD8+ T cells, silencing of CD155 led to a marked increase in T cell-mediated killing. Strikingly, CD155-deficient DMG cells failed to grow in immunocompetent mice, and depletion of CD8+ T cells allowed these tumors to grow. CD155 also exerted cell-autonomous effects on tumor cells: silencing of CD155 led to induction of apoptosis of DMG cells and to delayed tumor growth in immunodeficient mice. Transcriptomic analyses identified FOXM1 as a key target of CD155. Notably, FOXM1 silencing also led to reduced proliferation of DMG cells in vitro and in vivo. Finally, treatment of DMG-bearing mice with Thiostrepton, a FOXM1-targeting agent, delayed tumor growth and prolonged survival. These studies demonstrate that CD155 regulates immune evasion and tumor growth in DMG, and suggest that targeting CD155 could be a valuable two-pronged therapeutic strategy for this disease. Conflict-of-interest statementThe authors have declared that no conflict of interest exists.

cancer biology↗

bioRxiv2025

Spatial Coordination between Leaf Gradient and Temperature Response in Barley

The linear shape of cereal leaves creates distinct longitudinal zones that coordinate tissue maturation and resource allocation. Under abiotic stress such as heat, these longitudinal zones may differentially activate protective pathways, revealing hidden heterogeneity in stress response that remains poorly understood. Barley (Hordeum vulgare), a cold-adapted crop particularly sensitive to elevated temperatures, can serve as an ideal model for studying region-specific heat responses in leaves. Using chlorophyll fluorescence imaging, we found that non-photochemical quenching (NPQ) kinetics captured additional physiological changes beyond those detected by SPAD, highlighting the added value of chlorophyll fluorescence-based assessments. NPQ kinetics traits displayed consistent spatial gradients from tip to base, with heat stress reducing NPQ induction across leaf gradients. Genome-wide association analysis of traits derived from chlorophyll fluorescence imaging across leaf gradients identified significant SNPs within multiple candidate genes, including HORVU.MOREX.r3.3HG0262630 that was consistently detected in over 90% resampling iterations under heat stress, suggesting its key role during heat responses. Transcriptomic profiling along the leaf axis revealed both conserved and region-specific heat responses between leaf regions. Conserved activations highlighted conserved heat response pathways, including the reactivation of the Arabidopsis thermomemory module FtsH6-HSP21. In contrast, the region-by-temperature interaction analysis identified 40 genes with spatial responses indicative of resource reallocation from growth to defense, including those involved in growth and transport. The integration between spatially resolved phenotyping and transcriptional profiling underscores region-specific variation in response to heat along the leaf axis, guiding targeted strategies to enhance heat resilience in barley and other cereal crops.

plant biology↗

bioRxiv2024

Elucidation and Pharmacologic Targeting of Master Regulator Dependencies in Coexisting Diffuse Midline Glioma Subpopulations

Diffuse Midline Gliomas (DMGs) are universally fatal, primarily pediatric malignancies affecting the midline structures of the central nervous system. Despite decades of clinical trials, treatment remains limited to palliative radiation therapy. A major challenge is the coexistence of molecularly distinct malignant cell states with potentially orthogonal drug sensitivities. To address this challenge, we leveraged established network-based methodologies to elucidate Master Regulator (MR) proteins representing mechanistic, non-oncogene dependencies of seven coexisting subpopulations identified by single-cell analysis--whose enrichment in essential genes was validated by pooled CRISPR/Cas9 screens. Perturbational profiles of 372 clinically relevant drugs helped identify those able to invert the activity of subpopulation-specific MRs for follow-up in vivo validation. While individual drugs predicted to target individual subpopulations--including avapritinib, larotrectinib, and ruxolitinib--produced only modest tumor growth reduction in orthotopic models, systemic co-administration induced significant survival extension, making this approach a valuable contribution to the rational design of combination therapy.

systems biology↗

bioRxiv2021

Interrogation of genome-wide, experimentally dissected gene regulatory networks reveals mechanisms underlying dynamic cellular state control

Pooled CRISPRi-mediated silencing of >1,000 transcriptional regulators expressed in single colorectal adenocarcinoma cells, followed by single-cell RNA-seq profiling at two timepoints, 1 day and 4 days, allowed reverse engineering the underlying tumor context-specific, causal regulatory network. Furthermore, the availability of experimentally derived, highly multiplexed gene reporter assays for each regulator, as identified by this analysis, allowed accurate assessment of differential protein activity following silencing of each regulator, thus providing proof-of-concept for generating comprehensive, tissue-specific networks of transcriptional and post-translational interactions. Analysis of this causal network allowed elucidation of complex autoregulatory mechanisms that have eluded previous computational approaches and supported systematic elucidation of cooperative mechanisms, where one regulatory protein can modulate the activity of another regulatory protein, as well as transcriptional mimicry, where one regulatory protein can phenocopy others.

systems biology↗