Biology subjects

Rota, I. A.

Publications and source records attributed to Rota, I. A..

4 recordsLinked to original sources

bioRxiv2025

Computational Inference of Metabolic Programs: A Case Study Analyzing the Effect of BRCA1 Loss

Metabolic reprogramming is a hallmark of cancer, yet how oncogenic drivers shape tumor metabolism across disease progression remains incompletely understood. In this study, we present iMSEA (in silico Metabolic State and Enrichment Analysis), a computational framework that infers flux-based metabolic states from omics profiles. Applying iMSEA to isogenic BRCA1-mutant and BRCA1-wild-type ovarian cancer cells, we identified a shift toward glycolysis, nucleotide biosynthesis, and redox imbalance, coupled with impaired oxidative phosphorylation. These predictions were validated with metabolomics, Seahorse, and SCENITH assays, demonstrating the accuracy of our approach. Extending the analysis to homologous recombination deficient patient tumors at single-cell resolution, we found that BRCA1-deficient cancers display heightened metabolic activity and site-specific adaptations, including altered central carbon fluxes, mitochondrial function, nucleotide biosynthesis, and lipid metabolism. By linking transcriptional programs to functional metabolic states, iMSEA reveals hidden metabolic liabilities in BRCA1-deficient ovarian cancer and provides a broadly applicable strategy for dissecting metabolic heterogeneity and therapeutic vulnerabilities in cancer.

systems biology↗

bioRxiv2021

A FOXN1 mutation competitively displaces wild-type FOXN1 from higher order nuclear condensates to cause immunodeficiency

The transcription factor FOXN1 is a master regulator of thymic epithelial cell development and function. Here we demonstrate that FOXN1 expression is differentially regulated during organogenesis and participates in multi-molecular nuclear condensates essential for the factors transcriptional activity. FOXN1s C-terminal sequence regulates the diffusion velocity within these aggregates and modulates the binding to proximal gene regulatory regions. These dynamics are significantly altered in a patient with a mutant FOXN1 which is modified in its C-terminal sequence. This mutant is transcriptionally inactive and acts as a dominant negative factor displacing wild-type FOXN1 from condensates and causing athymia and severe lymphopenia in heterozygotes. Expression of the mutated mouse ortholog, selectively impairs mouse thymic epithelial cell (TEC) differentiation revealing a gene dose dependency for individual TEC subtypes. We have therefore identified the cause for a primary immunodeficiency disease and determined the mechanism by which this FOXN1 gain-of-function mutant mediates its dominant negative effect.

immunology↗

bioRxiv2020

The chaperonin CCT8 controls proteostasis essential for T cell maturation, selection, and function

T cells rely for their development and function on the correct folding and turnover of proteins generated in response to a broad range of molecular cues. In the absence of the eukaryotic type II chaperonin complex, CCT, T cell activation induced changes in the proteome are compromised including the formation of nuclear actin filaments and the formation of a normal cell stress response. Consequently, thymocyte maturation and selection, and T cell homeostatic maintenance and receptor-mediated activation are severely impaired. Additionally, Th2 polarization digresses in the absence of CCT-controlled protein folding resulting paradoxically in continued IFN-{gamma} expression. As a result, CCT-deficient T cells fail to generate an efficient immune protection against helminths as they are unable to sustain a coordinated recruitment of the innate and adaptive immune systems. These findings thus demonstrate that normal T cell biology is critically dependent on CCT-controlled proteostasis and that its absence is incompatible with protective immunity.

immunology↗

bioRxiv2018

The structural basis for forkhead box family specificity revealed by the crystal structure of human FOXN1 in complex with DNA

SignificanceFOXN1 is a transcription factor that is essential for the development of the thymus and the production of T-lymphocytes. It is a member of a large family of transcription factors which recognize DNA sequences through the conserved Forkhead (FH) domain. FOXN1 recognizes a DNA sequence that is different from the common consensus binding sequence of FH domains, although key binding residues are identical. We present crystal structures of the FH domain of FOXN1, free and DNA-bound, which shed light on the different binding specificities; the structure also revelas the basis of the immunocompromised nude mutation, as well as a preferential binding to non-methylated CpG motifs.\n\nAbstractFOXN1 is a member of the forkhead box (FOX) family of transcription factors, and plays an important role in thymic epithelial cell differentiation and function. FOXN1 mutations in humans and mice give rise to the \"nude\" phenotype which is marked by athymia. FOXN1 belongs to a subset of the FOX family that recognize an alternate consensus sequence (GACGC), which is different from the more widely-recognized canonical sequence consensus RYAAAYA. Here, we present the structure of FOXN1 in complex with DNA at 1.6 [A] resolution, in which the DNA sequence is recognised by a mixture of direct and water-mediated contacts provided by residues in an a-helix inserted in the DNA major groove (the recognition helix). Comparisons with other FOX family structures reveal that the canonical and alternate DNA sequences are bound in two distinct modes, with partially different registers for the protein DNA contacts. We identify a single alternate rotamer within the recognition helix itself as an important determinant of DNA specificity, and indicate sequence features in the recognition helix that could be used to predict the specificity of other FOX family members. Finally we demonstrate that FOXN1 has a significantly reduced affinity for DNA containing 5-methylcytosine, which may have implications for the role of FOXN1 in thymic senescence.

biochemistry↗