Biology subjects

Oliva, C.

Publications and source records attributed to Oliva, C..

6 recordsLinked to original sources

bioRxiv2025

NanoDel: a long-read sequencing pipeline for identifying large-scale mitochondrial DNA deletions validated in patient samples clinically diagnosed with mitochondrial disease and evaluated in glioblastoma.

MotivationTraditional methods for detecting large-scale mitochondrial DNA (mtDNA) deletions (LSMDs) in cells present challenges, i.e. a priori information, high DNA inputs, poor sensitivity and are not always quantitative. Mitigation can be achieved through high throughput DNA sequencing using e.g. Illumina and Oxford Nanopore Technologies (ONT), in combination with LSMD breakpoint identification and quantification using bioinformatic tools. Splice-aware RNA alignment tools increase the sensitivity for detecting LSMD breakpoints compared with DNA aligners. Long-read sequencing (LRS) also offers potential advantages over short read sequencing, e.g. greater read lengths and capturing variants on single reads. No existing pipelines capture the benefits of both a splice-aware alignment tool and LRS. ResultsWe developed "NanoDel", a LRS pipeline, to sensitively and accurately detect cellular LSMDs. Using artificial datasets, "NanoDel" was more sensitive and accurate than other pipelines. In samples diagnosed with mitochondrial disease, it identified both known and previously uncharacterised (including mixtures) of LSMDs, without a priori information. LSMD breakpoints were found in mt-co1, mt-cyb, mt-nd6 and mt-nd5 genes. Analysis of selected LSMDs revealed proximity to repeat and putative G-quadruplex motifs, and occurrence in a range of healthy and pathological tissues, indicating potential for a shared vulnerability landscape in mtDNA, shaped by sequence motifs and structural constraints. "NanoDel" combined with one-amplicon, not two-amplicon, LR-PCR offers a robust strategy with clinical application for detecting LSMDs across a variety of cell/tissue samples, and its application across a broader range of samples, will yield new mechanistic insights into LSMD formation, and further our understanding of mtDNA instability.

bioinformatics↗

bioRxiv2025

Oncogene SETDB1s Dual Role in Endometrial Cancer: Driving Tumor Progression and Immune Escape

Oncogene SETDB1, an H3K9 methyltransferase, drives tumorigenesis in various cancers. Using endometrial cancer (EC) as a model, we discovered SETDB1s dual mechanisms in driving EC tumorigenesis and mediating immune evasion. SETDB1 knockout (SETDB1-/-) tumor-bearing mice exhibited prolonged survival of up to 100 days. Transcriptomic profiling of SETDB1-/- EC cells revealed decreased expression of oncogenes (POLR2A, MSH6, FLNA) and increased expression of tumor suppressor genes (PGR, RERG, ZNF582), which indicates that SETDB1 intrinsically promotes EC tumor proliferation by regulating these downstream genes. SETDB1 repressed repeat elements and the interferon pathway, mediating immune evasion extrinsically by inhibiting anti-tumor macrophage infiltration. ChIP-seq analysis showed SETDB1 binding at pericentromeric regions on many chromosomes and numerous ZNFs. Loss of SETDB1 resulted in abnormal cell division. SETDB1-/- tumors displayed reduced proliferation markers (Ki67, pHH3) and increased macrophage infiltration. Mechanistically, SETDB1 promotes CD47 (a dont-eat-me signal) and represses CCL5 and CXCL9 (macrophage and T-cell recruiting chemokines), contributing to immune evasion. M1-like macrophages killed more SETDB1-/- cells in co-culture. Additionally, SETDB1 knockout in mouse EC cells reduced tumor growth in C57BL/6 mice, with increased macrophage and CD4+ T-cell infiltration. Our results indicates that elevated SETDB1 and its target genes can predict higher tumor grade and worse survival, suggesting that targeting SETDB1 could be a promising therapeutic strategy for EC.

cancer biology↗

bioRxiv2024

Drospondin, a novel glial-secreted glycoprotein, controls the development and function of the Drosophila nervous system

Reelin is a secreted glycoprotein with roles in the development of the mammalian neocortex, hippocampus and cerebellum. This vertebrate signaling molecule also contributes to adult brain function. Mammalian Reelin increases the complexity of Drosophila Mushroom Body (MB) neurites, an effect mediated by LpR1 and LpR2, the orthologs of mammalian Reelin receptors. Paradoxically, to date, no Reelin ortholog has been described in Drosophila. Here, we report that the protein product of the uncharacterized Drosophila CG17739 gene, which we named Drospondin, shares sequence homology with vertebrate F-spondin and Reelin. We show that Drospondin is expressed in glial cells and is crucial for MB development. Our results also show that Drospondin genetically interacts with LpRs and that human Reelin rescues structural defects in Drospondin-deficient flies. Furthermore, Drospondin-deficient flies exhibit altered sleep homeostasis, locomotion, and social behaviors. Our results reveal that flies express a functional homolog of mammalian Reelin that controls the development and function of the Drosophila nervous system.

developmental biology↗

bioRxiv2023

The Sterile Insect Technique can efficiently reduce the reproduction of the spotted wing drosophila (Drosophila suzukii) in strawberry

The spotted wing drosophila (SWD) Drosophila suzukii (Diptera: Drosophilidae) is a pest of soft fruit. Since its introduction in Europe in 2008 farmers struggle to protect their crops. The sterile insect technique (SIT) has proven efficient at controlling numerous fruit fly species and could be deployed to control D. suzukii. In recent years, key elements of SIT applied to D. suzukii have become available. However, field- and field-like experiments are scarce. In this experiment, we assayed the efficacy of a high-performance strain at reducing the reproduction of D. suzukii in complex, yet replicated and controlled conditions. Two ratios of sterile to fertile insects (5:1 and 1:1) using bisexual releases were compared to a control treatment with fertile, wild flies only. The presence of sterile individuals at a 5:1 ratio significantly reduced fly reproduction, measured after 5 days, by an approximate threefold factor. However, the proportion of infested fruits in the treated plots remained unaffected. The number of available berries in the cage appeared an unexpected determinant of fly infestation, suggesting undocumented density-dependent processes. The success of this assay opens the door to larger scales experiments, over several generations, and, in the near future, the field-evaluation of the efficacy of the SIT to control D. suzukii.

ecology↗

bioRxiv2021

Characterizing the genetic basis of trait evolution in the Mexican cavefish

Evolution in response to a change in ecology often coincides with various morphological, physiological, and behavioral traits. For most organisms little is known about the genetic and functional relationship between evolutionarily derived traits, representing a critical gap in our understanding of adaptation The Mexican tetra, Astyanax mexicanus, consists of largely independent populations of fish that inhabit at least 30 caves in Northeast Mexico, and a surface fish population, that inhabits the rivers of Mexico and Southern Texas. The recent application of molecular genetic approaches combined with behavioral phenotyping have established A. mexicanus as a model for studying the evolution of complex traits. Cave populations of A. mexicanus are interfertile with surface populations and have evolved numerous traits including eye degeneration, insomnia, albinism and enhanced mechanosensory function. The interfertility of different populations from the same species provides a unique opportunity to define the genetic relationship between evolved traits and assess the co-evolution of behavioral and morphological traits with one another. To define the relationships between morphological and behavioral traits, we developed a pipeline to test individual fish for multiple traits. This pipeline confirmed differences in locomotor activity, prey capture, and startle reflex between surface and cavefish populations. To measure the relationship between traits, individual F2 hybrid fish were characterized for locomotor behavior, prey-capture behavior, startle reflex and morphological attributes. Analysis revealed an association between body length and slower escape reflex, suggesting a trade-off between increased size and predator avoidance in cavefish. Overall, there were few associations between individual behavioral traits, or behavioral and morphological traits, suggesting independent genetic changes underlie the evolution of behavioral and morphological traits. Taken together, this approach provides a novel system to identify genes that underlie naturally occurring genetic variation in morphological and behavioral traits.

evolutionary biology↗

bioRxiv2021

Lipophorin receptors regulate mushroom bodies development and participate in learning, memory, and sleep in flies

BackgroundDrosophila melanogaster Lipophorin Receptors (LpRs), LpR1 and LpR2, mediate lipid uptake. The orthologs of these receptors in vertebrates, ApoER2 and VLDL-R, bind Reelin, a glycoprotein not present in flies. These receptors are associated with the development and function of the hippocampus and cerebral cortex, important association areas in the mammalian brain. It is currently unknown whether LpRs play similar roles in the Drosophila brain. ResultsWe report that LpR-deficient flies exhibit impaired olfactory memory and sleep patterns, which seem to reflect anatomical defects found in a critical brain association area, the Mushroom Bodies (MB). Moreover, cultured MB neurons respond to mammalian Reelin by increasing the complexity of their neurites. This effect depends on LpRs and Dab, the Drosophila ortholog of the reelin signaling adaptor protein Dab1. In vitro, two of the long isoforms of LpRs allow the internalization of Reelin. ConclusionsThese findings demonstrate that LpRs contribute to MB development and function, supporting the existence of LpR-dependent signaling in Drosophila.

neuroscience↗