Biology subjects

Fonseca, C.

Publications and source records attributed to Fonseca, C..

8 recordsLinked to original sources

bioRxiv2026

KIF18A Maintains Kinetochore-Microtubule Attachments in CIN Cells by Limiting Microtubule Polymerization

Chromosomal instability (CIN) generates vulnerabilities that can be therapeutically exploited, including sensitivity to inhibition of the kinesin motor KIF18A. However, the mechanistic basis for why a subset of CIN tumor cells depend on KIF18A remains unclear. Here, we compare mitotic phenotypes across KIF18A-sensitive and -insensitive cell models. In sensitive CIN cells, KIF18A inhibition leads to formation of polar chromosomes with unattached kinetochores, recruitment of spindle assembly checkpoint proteins, and prolonged mitotic arrest. Although KIF18A loss reduces kinetochore-microtubule stability in all cell lines, sensitive cells exhibit lower baseline attachment stability and heightened microtubule polymerization rates, predisposing them to attachment failure. Acute KIF18A inhibition disrupts maintenance of attachments after metaphase alignment, while reducing microtubule polymerization suppresses mitotic defects. These findings support a model in which CIN tumor cells rely on KIF18A to restrain excessive microtubule dynamics and maintain attachment.

cancer biology↗

bioRxiv2026

Systemic neoantigen-specific T cells reveal central determinants of PD-(L)1 blockade efficacy

The contribution of neoantigen-specific T cells to PD-(L)1 efficacy has largely been inferred from tumor mutational burden. We functionally profiled circulating T cell responses against 7,038 predicted HLA-I-restricted and 21,453 HLA-II-restricted neopeptides in 27 patients with advanced non-small cell lung cancer treated with anti-PD-(L)1. CD4 responses were frequent and correlated with neoantigen availability but not clinical benefit. In contrast, the magnitude and breadth of neoantigen-specific CD8 T cell responses were associated with clinical benefit, progression-free and overall survival, independently of tumor mutational burden. Patients mounting coordinated CD4 and CD8 responses experienced improved progression-free survival. Tumors from CD8 responders displayed immune signatures indicative of both T cell priming and effector functions. Circulating neoantigen-specific CD8 T cells recognized endogenously processed antigens, trafficked to tumors, and selectively expanded under therapy while retaining CD28, CD226, and CXCR3 expression. These findings identify coordinated, functionally engaged neoantigen-specific T cell responses as central determinants of PD-(L)1 efficacy.

cancer biology↗

bioRxiv2025

TAOK1 regulates chemo- and radiosensitivity in BRCA1/2-deficient tumors

BRCA1/2-deficient cells are hypersensitive to replication stress- and DNA-damage-inducing agents such as poly(ADP-ribose) polymerase inhibitors (PARPi), platinum drugs, and ionizing radiation (IR), largely due to impaired homologous recombination repair and replication fork (RF) protection. The precise mechanisms underlying RF vulnerability in the absence of BRCA1/2 remain incompletely understood, however. Here, we identify Thousand And One Amino Acid Kinase 1 (TAOK1) as a novel regulator of RF dynamics that sensitizes BRCA1/2-deficient cells to both PARPi and IR. Unlike established DNA repair factors, such as PARG or the 53BP1-RIF1-shieldin-CST pathway, which mediate PARPi sensitivity while protecting cells against IR, TAOK1 promotes RF degradation and suppresses post-replicative damage repair. TAOK1 depletion stabilizes RFs and reduces replication-associated DNA damage in BRCA1/2-deficient cells, thereby conferring therapy resistance. Interestingly, we found that TAOK1 functions in RF regulation to be independent of its kinase activity. Instead, it interacts with PCNA and regulates ISG15 levels and thereby affects RF stability. Our findings reveal TAOK1 as a non-canonical mediator of therapy sensitivity in BRCA1/2-deficient tumors. TeaserTAOK1 controls replication fork stability through PCNA and ISG15, affecting therapy response in BRCA1/2-deficient cancers.

cancer biology↗

bioRxiv2024

An operational framework to map Essential Life Support Areas (ELSAs) for biodiversity, climate, and sustainable development

Almost all countries are making increasingly bold commitments to halt and reverse biodiversity loss, minimise the impacts of climate change, and transition to more sustainable development. The effective achievement of many of these commitments relies on integrated spatial planning frameworks that are adaptable to national circumstances, priorities and capabilities. This need is formally recognized by Target 1 of the Kunming-Montreal Global Biodiversity Framework (GBF), which specifies that all areas should be under such planning. Here, we describe the development and application of an operational framework for national-level integrated spatial planning: Essential Life Support Areas (ELSAs). This framework facilitates the identification of areas that - if protected, restored, or sustainably managed - can support the achievement of national commitments to biodiversity, climate, and sustainable development. The process of mapping ELSAs relies heavily on leadership by national experts and stakeholders and the integration of spatial data using systematic conservation planning tools. We showcase the ELSA process carried out for Ecuador, where the use of real-time scenario analyses enabled diverse stakeholder groups to collaborate to assess national priorities for nature, climate, and sustainable development, view trade-offs and synergies, and arrive at a spatial plan to guide national action. ELSA presented an actionable approach for Ecuador, and 12 other pilot countries, to create a spatial plan aimed at fulfilling their national and international commitments to nature, including to the GBF.

ecology↗

bioRxiv2024

FIGNL1 inhibits homologous recombination in BRCA2 deficient cells by dissociating RAD51 filaments

Homologous recombination (HR) deficiency upon BRCA2 loss arises from defects in the formation of RAD51 nucleoprotein filaments. Here, we demonstrate that loss of the anti-recombinase FIGNL1 retains RAD51 loading at DNA double-stranded breaks (DSBs) in BRCA2-deficient cells, leading to genome stability, HR proficiency, and viability of BRCA2-deficient mouse embryonic stem cells. Mechanistically, we directly show that strand invasion and subsequent HR defects upon BRCA2 loss primarily arises from the unrestricted removal of RAD51 from DSB sites by FIGNL1, rather than from defective RAD51 loading. Furthermore, we identify that the MMS22L-TONSL complex interacts with FIGNL1 and is critical for HR in BRCA2/FIGNL1 double-deficient cells. These findings identify a pathway for tightly regulating RAD51 activity to promote efficient HR, offering insights into mechanisms of chemoresistance in BRCA2-deficient tumors.

genetics↗

bioRxiv2023

DNA Combing versus DNA Spreading and the Separation of Sister Chromatids

DNA combing and DNA spreading are two central approaches for studying DNA replication fork dynamics genome-wide at single-molecule resolution by distributing labeled genomic DNA on coverslips or slides for immunodetection. Perturbations in DNA replication fork dynamics can differentially affect either leading or lagging strand synthesis, for example in instances where replication is blocked by a lesion or obstacle on only one of the two strands. Thus, we sought to investigate whether the DNA combing and/or spreading approaches are suitable for resolving adjacent sister chromatids during DNA replication, thereby enabling the detection of DNA replication dynamics within individual nascent strands. To this end, we developed a thymidine labeling scheme that discriminates between these two possibilities. Our data suggests that DNA combing resolves single chromatids, allowing the detection of strand-specific alterations, whereas DNA spreading does not. These findings have important implications when interpreting DNA replication dynamics from data obtained by these two commonly used techniques.

molecular biology↗

bioRxiv2021

Development of quantitative high-throughput screening methods for identification of antifungal biocontrol strains

Large screens of bacterial strain collections to identify potential biocontrol agents are often time consuming, costly, and fail to provide quantitative results. In this study, we present two quantitative and high-throughput methods to assess the inhibitory capacity of bacterial biocontrol candidates against fungal phytopathogens. One method measures the inhibitory effect of bacterial culture supernatant components on the fungal growth, while the other accounts for direct interaction between growing bacteria and the fungus by co-cultivating the two organisms. The antagonistic supernatant method quantifies the culture components antifungal activity by calculating the cumulative impact of supernatant addition relative to a non-treated fungal control, while the antagonistic co-cultivation method identifies the minimal bacterial cell concentration required to inhibit fungal growth by co-inoculating fungal spores with bacterial culture dilution series. Thereby, both methods provide quantitative measures of biocontrol efficiency and allow prominent fungal inhibitors to be distinguished from less effective strains. The combination of the two methods shed light on the type of inhibition mechanisms and provide the basis for further mode of action studies. We demonstrate the efficacy of the methods using Bacillus spp. with different levels of antifungal activities as model antagonists and quantify their inhibitory potency against classic plant pathogens. ImportanceFungal phytopathogens are responsible for tremendous agricultural losses on annual basis. While microbial biocontrol agents represent a promising solution to the problem, there is a growing need for high-throughput methods to evaluate and quantify inhibitory properties of new potential biocontrol agents for agricultural application. In this study, we present two high-throughput and quantitative fungal inhibition methods that are suitable for commercial biocontrol screening.

microbiology↗

bioRxiv2019

Genetic and molecular mechanism for distinct clinical phenotypes conveyed by allelic truncating mutations implicated in FBN1

The molecular and genetic mechanisms by which different single nucleotide variant (SNV) alleles in specific genes, or at the same genetic locus, bring about distinct disease phenotypes often remain unclear. Allelic truncating mutations of fibrillin-1(FBN1) cause either classical Marfan syndrome (MFS) or a more severe phenotype associated with Marfanoid-progeroid-lipodystrophy syndrome (MPLS). A total of three Marfan syndrome/Marfanoid patients (2 singletons and 1 parent-offspring trio) were recruited. Targeted next-generation sequencing was performed on all the participants. We analyzed the molecular diagnosis, patient clinical features, and the potential molecular mechanism involved in the MPLS subject in our cohort. We investigated a small cohort, consisting of two classical MFS and one MPLS patient from China, whose clinical presentation included scoliosis potentially requiring surgical intervention. We provide evidence that most nonsense and frameshift mutations lead to FBN1 null alleles due to mutant mRNA transcript degradation. In contrast, the more severe disease phenotype, MPLS, is caused by mutant mRNAs that are predicted to escape the nonsense mediated decay (NMD) surveillance pathway, making a mutant protein that exerts a dominant negative interference effect to FBN1 thus generating a gain-of-function (GoF) rather than a loss-of-function (LoF) allele as in MFS. Overall, we provide direct evidence that a dominant negative interaction of FBN1 potentially explains the distinct clinical phenotype in MPLS patients through genetic and functional analysis of the first Chinese patient with MPLS. Moreover, our study expands the mutation spectrum of FBN1 and highlights the potential molecular mechanism for MPLS patients.

genetics↗