Biology subjects

Martinez-Martin, N.

Publications and source records attributed to Martinez-Martin, N..

6 recordsLinked to original sources

bioRxiv2026

EpiFlow: multidimensional single-cell epigenetic profiling by spectral flow cytometry

The epigenetic landscape of individual cells determines their identity and function, yet current methods for profiling chromatin modifications at single-cell resolution remain low-throughput, costly, or limited in parametric depth. Here we present EpiFlow, a spectral flow cytometry-based platform that enables the simultaneous quantification of 16 epigenetic markers, including histone post-translational modifications, DNA methylation, and hydroxymethylation, at the single-cell level. We demonstrate that EpiFlow is robust across species from yeast to mammals and resolves biologically meaningful epigenetic transitions during the cell cycle, stem cell differentiation, germinal centre B cell maturation, diabetic liver remodelling, and seizure-induced chromatin reprogramming. High-dimensional integration of EpiFlow data enables cell-type classification based solely on epigenetic profiles in liver, brain, blood, and cancer. Furthermore, EpiFlow detects on-target and off-target/indirect effects of epigenetic drugs in a high-throughput-compatible format. Collectively, these results establish EpiFlow as a broadly applicable platform for single-cell epigenetic analysis in basic, pharmaceutical, and translational research.

cell biology↗

bioRxiv2025

Targeting of ibrutinib resistance driving pathways by miR-28 in ABC-DLBCL

Diffuse large B-cell lymphoma (DLBCL) is the most common aggressive B-cell lymphoma. Although many patients respond well to R-CHOP immunochemotherapy, those with the activated B-cell (ABC) subtype are often refractory or relapse. Bruton tyrosine kinase (BTK) inhibitors such as ibrutinib have improved outcomes, but acquired resistance limits their long-term efficacy. Here, we modeled the development of ibrutinib resistance in ABC-DLBCL and investigated whether the BCR-signaling regulator microRNA-28 (miR-28) can block this process. Using flow cytometry-based competition assays, multicolor clonal barcoding, transcriptomic profiling, and xenograft models, we found that miR-28 expression impairs the emergence of ibrutinib-resistant ABC-DLBCL cells. Mechanistically, miR-28 interferes with the clonal selection process triggered by ibrutinib treatment and rewires transcriptional programs by downregulating mitochondrial and mTOR signaling pathways critical for resistance development. Furthermore, the miR-28-repressed gene signature associated with ibrutinib resistance correlates with improved survival in ibrutinib-treated patients from the PHOENIX trial cohort with the MCD genetic subtype, which is associated with ABC-DLBCL. Finally, the targeted therapeutic delivery of miR-28 via aptamer-guided nanoparticles suppresses ibrutinib-resistant tumor growth in vivo. These findings identify miR-28 as an effective inhibitor of ibrutinib resistance, underscoring its translational potential as an adjunct strategy in ABC-DLBCL therapy. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=188 SRC="FIGDIR/small/687947v2_ufig1.gif" ALT="Figure 1"> View larger version (70K): org.highwire.dtl.DTLVardef@8e5913org.highwire.dtl.DTLVardef@17a19c3org.highwire.dtl.DTLVardef@13178f2org.highwire.dtl.DTLVardef@fb5d9b_HPS_FORMAT_FIGEXP M_FIG C_FIG

cancer biology↗

bioRxiv2025

Mitochondria-Lysosomes Crosstalk Shapes Neonatal Metabolic Transition in Neonatal Enterocytes

The neonatal gastrointestinal tract mediates nutrient absorption and the establishment of immune tolerance to commensal microbiota. In early life, lysosome-rich enterocytes (LREs) in the ileum are necessary for the intracellular digestion of maternal milk proteins. However, the molecular mechanisms sustaining their function remain incompletely characterized. Here, we demonstrate that LRE mitochondrial homeostasis and autophagic capacity are critical for efficient nutrient uptake and maintenance of their specialized identity, as disruption of either process leads to premature differentiation into post-weaning enterocytes (PECs) with diminished endolysosomal and metabolic activity. Transcriptomic profiling further revealed that neonatal LREs exhibit a distinctive antioxidant signature, which preserves redox balance and safeguards the expression of the transcriptional regulators MAFB and BLIMP1, both central repressors of the neonatal-to-adult metabolic transition. These findings establish the mitochondria-lysosome axis as a key determinant of LRE function and neonatal metabolic programming. They also provide a mechanistic framework for understanding how organelle dysfunction and redox imbalance may contribute to early-life malnutrition syndromes, such as Kwashiorkor, and suggest therapeutic strategies aimed at preserving mitochondrial and lysosomal integrity.

developmental biology↗

bioRxiv2025

The V-ATPase/ATG16L1 axis drives membrane remodeling during epithelial morphogenesis

Epithelial tubulogenesis shapes internal organs by transforming flat epithelial sheets or unpolarized cords into hollow tubes with central lumens. A key example is the formation of the posterior neural tube during secondary neurulation, which requires precise morphogenetic events for de novo lumen formation. Although several studies have highlighted the role of autophagy in specific morphogenetic events, its involvement in epithelial organ development remains unclear. Autophagy operates via canonical and noncanonical pathways. Canonical autophagy is catabolic, requiring double-membrane autophagosomes and the full ATG protein set. Noncanonical autophagy, including the V-ATPase/ATG16L1-dependent Conjugation of ATG8 in Single Membranes (CASM), has both degradative and non-degradative roles and regulates different membrane trafficking processes. Using human neural tube organoids, spheroids, and tube micropatterns deficient in CASM or canonical autophagy, we show that CASM plays a pivotal role in epithelial tube morphogenesis. Specifically, the V-ATPase/ATG16L1 axis is essential for de novo lumen formation by regulating membrane junction remodeling and Rab11-dependent recycling pathways. These findings reveal distinct contributions of autophagy pathways in epithelial development, with potential implications for diseases linked to autophagy dysfunction.

cell biology↗

bioRxiv2025

NSD2 links developmental plasticity to mitochondrial function in muscle and lymphocyte differentiation

Developmental processes require a precise regulation of all the aspects of cellular function to successfully achieve the generation of differentiated cells. This regulation does not only encompass gene expression levels activating the developmental programs, but should also attend the demanding energetic needs of the differentiating cells. Epigenetic regulators are essential for establishing cell-type-specific transcriptional programs, but emerging evidence suggests that they also play a more direct role in regulating metabolism. Nsd2 is a Histone-3-Lysine36 mono- and di-methyltransferase key in the development of several cell types, and is involved in human pathologies both by loss- and gain-of-function alterations. Methylation at H3K36 by proteins of the Nsd family has been shown to be crucial in the maintenance of cell identity by being involved in the establishment and sustained expression of cell-type-specific programs. Here, we demonstrate that Nsd2 is essential for coordinating mitochondrial function and metabolic remodeling during B cell activation and muscle progenitor differentiation. In the terminal differentiation of B cells in the germinal center, the absence of Nsd2 results in defective mitochondrial function, characterized by hyperpolarization of the mitochondrial membrane, elevated reactive oxygen species (ROS) production, and reduced oxygen consumption and ATP production. Similarly, Nsd2 deficiency in myoblasts disrupts metabolic reprogramming during muscle differentiation, leading to impaired mitochondrial respiration and structural abnormalities. In both cell types, these alterations correlate with widespread changes in the expression of genes involved in mitochondrial function and cellular metabolism. These findings highlight Nsd2 as a central mediator linking epigenetic regulation with mitochondrial function, underscoring its critical role in coupling transcriptional programs with metabolic adaptation during cell differentiation.

developmental biology↗

bioRxiv2025

Diacylglycerol kinase zeta dictates CD40-mediated immune synapse formation, mTORC1 signaling and plasma cell fate in B lymphocytes

To mount a robust T-dependent immune response, antigen-specific B lymphocytes require CD40 stimulation through immune synapse formation with CD4+ T follicular helper cells. CD40 triggers the activation of mammalian target of rapamycin complex-1 (mTORC1) and remodels the mitochondria to meet increased bioenergetic and anabolic demands. We show that diacylglycerol-kinase-{zeta} (DGK{zeta}) has a crucial role in activating the mTORC1 pathway and remodeling mitochondria downstream of CD40 signaling in B cells. DGK{zeta} governs organelle translocation to the CD40-mediated immune synapse and the recruitment of mTORC1 to lysosomes. DGK{zeta}-/- B cells exhibited impaired mitochondria function, protein biosynthesis, metabolite transporter expression and cell cycle progression, accompanied by dysregulation of the transcriptional network governing B cell fate. These defects lead to a blockage in the progression of the germinal center response and plasma cell differentiation in vivo. Our findings establish DGK{zeta} as a key mediator of CD40 functions in the B cell response.

immunology↗