Biology subjects

Ferreira, M. G.

Publications and source records attributed to Ferreira, M. G..

13 recordsLinked to original sources

bioRxiv2026

AI4Life Open Calls and Public Challenges: why, how, and what we have learned.

Within AI4Life, we ran three Open Calls and three Public Challenges (2023-2025), supporting 22 bioimage analysis projects from 151 applications and engaging 225 challenge participants, with the aim of applying FAIR deep learning in the life sciences. Our experience offers a view of the current state of bioimage analysis, the landscape of available tools, as well as the existing gaps between method developers, tool producers and potential users. It highlights that even after careful selection for AI-ready projects, most still require substantial effort to apply deep learning, and that the field still relies heavily on established, well-rounded methods to solve common problems. We come to the conclusion that for scientific AI in biology, the rate-limiting step is not methods and models but data, annotations, and shared infrastructure underneath them.

bioinformatics↗

bioRxiv2025

Telomeric antisense oligonucleotides reduce premature aging phenotypes in telomerase mutant zebrafish

Telomerase activity is restricted in somatic cells, resulting in progressive telomere shortening. Telomere erosion eventually activates the DNA damage response (DDR), inducing cell-cycle arrest and cellular senescence or apoptosis. We previously reported that telomere dysfunction induces the transcription of telomeric non-coding RNAs (tncRNAs) which are critical mediators of DDR activation. Blocking tncRNAs with telomeric antisense oligonucleotides (tASOs) suppresses in vivo DDR signaling and its downstream effects. Here, we show that tASO-mediated inhibition of telomeric DDR in second-generation tert-/- zebrafish embryos with critically short telomeres leads to improved developmental outcomes and rescues premature aging phenotypes, including enhanced survival. Notably, a single tASO treatment administered at the one-cell stage of first-generation tert-/- embryos leads to enhanced fertility observed in 6-month-old adults. Overall, these findings demonstrate that tASO-based inhibition of telomeric DDR is sufficient to effectively rescue premature aging phenotypes in zebrafish.

pathology↗

bioRxiv2025

ReScale4DL: Balancing Pixel and Contextual Information for Enhanced Bioimage Segmentation

Deep learning has established itself as the state-of-the-art approach for segmentation in bioimage analysis. However, these powerful algorithms present an intriguing paradox regarding image resolution: contrary to intuition, lower-resolution images can yield superior performance for specific image analysis carried out by deep learning. This phenomenon is particularly significant in microscopy imaging, where high-resolution acquisitions come with substantial costs in throughput, data storage requirements, and potential photodamage to specimens. Through systematic experimentation, we evaluate how varying image resolution impacts deep learning performance in cellular image segmentation tasks. We trained popular architectures on datasets downsampled to 6-50% of their original resolution, mimicking acquisitions at lower image magnification, and compared their performance against models trained on native-resolution images. Our results show that segmentation accuracy either improves (by up to 25% of mean Intersection over Union (IoU)) or experiences only minimal degradation (< 5% of mean IoU) when using images downsampled by up to a factor of 4 (25% of the original resolution). This downsampling proportionally increases information throughput while reducing data storage requirements and inference time. With these findings, we contribute systematic guidelines to deep learning practitioners in creating efficient experimental pipelines for image-driven discoveries. This approach improves the sustainability and cost-effectiveness of bioimaging studies by reducing data and computing needs while optimising microscopy techniques.

biophysics↗

bioRxiv2024

Zebrafish Avatar-test predicts patient's tumor response to chemotherapy in breast cancer: a co-clinical study towards personalized medicine

Chemotherapy remains the mainstay in most high-risk breast cancer (BC) settings, with several equivalent options of treatment. However, the efficacy of each treatment varies between patients and there is currently no test to determine which option will be the most effective for each individual patient. Here, we developed a fast in-vivo test for BC therapy screening: the zebrafish patient derived xenograft model (zAvatars), where in-vivo results can be obtained in just 10 days. To determine the predictive value of the BC zAvatars we performed a clinical study, where zAvatars were treated with the same therapy as the donor-patient and their response to therapy was compared. Our data shows a 100% correlation between patients clinical response to treatment and its matching zAvatar. Altogether, our results suggest that the zAvatar model constitutes a promising in-vivo assay to optimize cancer treatments in truly personalized manner.

cancer biology↗

bioRxiv2024

cGAS-STING is responsible for aging of telomerase deficient zebrafish.

Telomere shortening occurs in multiple tissues throughout aging. When telomeres become critically short, they trigger DNA damage responses and p53 stabilization, leading to apoptosis or replicative senescence. In vitro, cells with short telomeres activate the cGAS-STING innate immune pathway resulting in type I interferon inflammation and senescence. However, the consequences of these events to the organism are not yet understood. Here, we show that sting is responsible for premature aging of telomerase-deficient zebrafish. We generated sting-/- tert-/- double mutants and observed a thorough rescue of tert-/- phenotypes. At the cellular level, lack of cGAS-STING in ter t mutants resulted in reduced senescence, increased cell proliferation, and low inflammation despite similar short telomeres. Critically, absence of sting function resulted in dampening of the DNA damage response and low p53 levels. At the organism level, sting-/- tert-/- zebrafish regained fertility, delayed cachexia, and cancer incidence, resulting in increased healthspan and lifespan of telomerase mutants.

cell biology↗

bioRxiv2023

DL4MicEverywhere: Deep learning for microscopy made flexible, shareable, and reproducible

Deep learning has revolutionised the analysis of extensive microscopy datasets, yet challenges persist in the widespread adoption of these techniques. Many lack access to training data, computing resources, and expertise to develop complex models. We introduce DL4MicEverywhere, advancing our previous ZeroCostDL4Mic platform, to make deep learning more accessible. DL4MicEverywhere uniquely allows flexible training and deployment across diverse computational environments by encapsulating methods in interactive Jupyter notebooks within Docker containers -a standalone virtualisation of required packages and code to reproduce a computational environment-. This enhances reproducibility and convenience. The platform includes twice as many techniques as originally provided by ZeroCostDL4Mic and enables community contributions via automated build pipelines. DL4MicEverywhere empowers participatory innovation and aims to democratise deep learning for bioimage analysis.

bioinformatics↗

bioRxiv2023

Absence of Telomerase Leads to Immune Response and Tumor Regression in Zebrafish Melanoma

Most cancers reactivate telomerase to maintain telomere length to acquire immortality. The importance of this process is well illustrated by the fact that telomerase promoter mutations are found at a high frequency in many cancer types, including melanoma. However, it is unclear when and if telomerase is strictly required during tumorigenesis. Here, we show that melanoma can occur in the absence of telomerase but is required to sustain later growth and to avoid tumor regression. We combined telomerase mutant zebrafish (tert-/-) with two established melanoma models and found equal melanoma incidence and invasiveness as tumors became visible. Later, however, while tert+/+ fish develop increasing larger tumors, tert-/- tumors stagnate growth and regress. tert-/- tumors showed lower cell proliferation, higher apoptosis and melanocyte differentiation. We also detected an immune response directed at tert-/- tumors. tert-/- tumors exhibited increased immune cell infiltrates and resume growth when transplanted into immunocompromised hosts. We propose that telomerase is required for melanoma in zebrafish, albeit at later stages of progression, to sustain growth while avoiding immune rejection and regression. Thus, absence of telomerase restricts melanoma through tumor-autonomous mechanisms (cell cycle arrest, apoptosis and melanocyte differentiation) and a non-tumor-autonomous mechanisms (immune rejection).

cancer biology↗

bioRxiv2023

Pot1 promotes telomere DNA replication via the Stn1-Ten1 complex in fission yeast

Telomeres are nucleoprotein complexes that protect the chromosome-ends from eliciting DNA repair while ensuring their complete duplication. Pot1 is a subunit of telomere capping complex that binds to the G-rich overhang and inhibits the activation of DNA damage checkpoints. In this study, we explore new functions of fission yeast Pot1 by using a pot1-1 temperature sensitive mutant. We show that pot1 inactivation impairs telomere DNA replication resulting in the accumulation of ssDNA leading to the complete loss of telomeric DNA. Recruitment of Stn1 to telomeres, an auxiliary factor of DNA lagging strand synthesis, is reduced in pot1-1 mutants and overexpression of Stn1 rescues loss of telomeres and cell viability at restrictive temperature. We propose that Pot1 plays a crucial function in telomere DNA replication by recruiting Stn1-Ten1 and Pol-primase complex to telomeres, thus promoting lagging-strand DNA synthesis at stalled replication forks.

genetics↗

bioRxiv2022

Telomere elongation in the gut extends zebrafish lifespan

Telomere shortening is a hallmark of aging and is counteracted by telomerase. The gut is one of the earliest organs to exhibit short telomeres and tissue dysfunction during normal zebrafish aging. This is recapitulated in prematurely aged telomerase mutants (tert-/-). Here, we show that gut-specific telomerase activity in tert-/- zebrafish prevents premature aging. Induction of telomerase rescues gut senescence and low cell proliferation to wild-type levels, while restoring gut tissue integrity, inflammation, and age-dependent gut microbiota dysbiosis. Remarkably, averting gut dysfunction results in a systemic beneficial impact. Gut-specific telomerase activity rescues premature aging markers in remote organs, such as the reproductive (testes) and hematopoietic (kidney marrow) systems. Functionally, it also rescues age-dependent loss of male fertility and testes atrophy. Finally, we show that gut-specific telomerase activity increases the lifespan of telomerase mutants. Our work demonstrates that delaying telomere shortening in the gut is sufficient to systemically counteract aging in zebrafish.

cell biology↗

bioRxiv2020

Environment and sex control lifespan and telomere length in wild-derived African killifish

Telomere length is correlated positively with longevity at the individual level, but negatively when compared across species. Here, we tested the association between lifespan and telomere length in African annual killifish. We analyzed telomere length in 18 Nothobranchius strains derived from diverse habitats and measured the laboratory lifespan of 14 strains of N. furzeri and N. kadleci. We found that males had shorter telomeres than females. The longest telomeres were recorded in strains derived from dry region where male lifespans were shortest. At the individual level, we detected a weak negative association between rapid juvenile growth and shorter telomeres in early adulthood. Overall, average telomere length was a good descriptor of telomere length distribution. However, within-individual telomere length spread was not related to any pattern. This substantial variation in telomere length between strains from different environments provides killifish as powerful tool to understand the evolutionarily adaptive value of telomere length.

evolutionary biology↗

bioRxiv2020

Akt/Foxo pathway activation switches apoptosis to senescence in short telomere zebrafish

Progressive telomere shortening during lifespan is associated with increased genome instability, block to cell proliferation and aging. Apoptosis and senescence are the two main cellular outcomes upon irreversible cell damage. In this study, we show a transition between apoptosis to senescence in cells of two independent tissues in telomerase zebrafish mutants. In young mutants, proliferative tissues exhibit defects in cell proliferation and p53-dependent apoptosis, but no senescence. Progressively, these tissues display signs of tissue dysfunction, loss of cellularity and increased senescence. These alterations are accompanied by an activation of pro-proliferative stimulus mediated by AKT. Consequently, FoxO1 and FoxO4 transcriptional factors are inactivated, reducing SOD2 levels, causing an increase in ROS. These alterations elicit the activation of the zebrafish p16/15 and senescence. Thus, upon telomere shortening in aging, early apoptosis induces compensatory proliferation. However, progressive decline in cell proliferation results in tissue damage and proliferative signals, promoting a switch to senescence.

cell biology↗

bioRxiv2019

Telomere shortening produces an inflammatory environment that promotes tumor invasiveness in zebrafish

Cancer incidence increases exponentially with age, when human telomeres are shorter. Similarly, telomerase mutant zebrafish (tert) have premature short telomeres and anticipate cancer incidence to younger ages. However, because short telomeres constitute a road block to cell proliferation, telomere shortening is currently viewed as a tumor suppressor mechanism and should protect from cancer. This conundrum is not fully understood. In our current study, we report that telomere shortening promotes cancer in a non-cell autonomous manner. Using zebrafish chimeras, we show increased incidence of invasive melanoma when WT tumors are generated in tert mutant zebrafish. tert zebrafish show increased levels of senescence (cdkn2a and ink4a/b) and inflammation (TNF-). In addition, we transferred second generation tert blastula cells into WT to produce embryo chimeras. Cells with very short telomeres induced senescence and increased neutrophil numbers in surrounding larval tissues in a non-cell autonomous manner, creating an inflammatory environment. Considering that inflammation is pro-tumorigenic, we transplanted melanoma-derived cells into second generation tert zebrafish embryos and observed that tissue environment with short telomeres leads to increased micrometastasis. To test if inflammation was necessary for this effect, we treated melanoma transplants with non-steroid anti-inflammatory drugs and show that higher melanoma invasiveness can be averted. Thus, apart from the cell autonomous role of short telomeres in contributing to genome instability, we propose that telomere shortening with age causes systemic chronic inflammation leading to increased tumor incidence. Significance StatementCancer incidence increases exponentially in human midlife. Even though mutation accumulation in somatic tissues results in increased tumorigenesis, it is currently not understood how aging contributes to cancer. Telomeres, the ends of eukaryotic linear chromosomes, shorten with each cell division. Here we show that telomere shortening contributes to cancer in a non-cell autonomous manner. Using embryo chimeras of telomerase deficient zebrafish generated from melanoma-prone fish, we show that tumors arise more frequently and become more invasive in animals with shorter telomeres. Telomere shortening gives rise to increased senescence and systemic inflammation. We observed increased melanoma metastasis dissemination in zebrafish larvae with very short telomeres. Thus, telomere shortening similar to human aging, generates a chronic inflammatory environment that increases cancer incidence.

cancer biology↗

bioRxiv2018

Molecular basis of mitotic decline during human aging

Aneuploidy, an abnormal chromosome number, has been linked to aging and age-associated diseases, but the underlying molecular mechanisms remain unknown. Supported by direct live-cell imaging of young, middle-aged and old-aged primary human dermal fibroblasts, we found that aneuploidy increases with aging due to general dysfunction of the mitotic machinery. Increased chromosome segregation defects in elderly mitotic cells correlated with an early senescence-associated secretory phenotype (SASP) and repression of Forkhead box M1 (FoxM1), the transcription factor that drives expression of most G2/M genes. By restoring FoxM1 levels in elderly and Hutchison-Gilford Progeria Syndrome fibroblasts we prevented aneuploidy and, importantly, ameliorated cellular phenotypes associated with aging. Moreover, senescent fibroblasts isolated from elderly donors cultures were mostly aneuploid, suggesting that aneuploidy is a key player in the progression into full senescence phenotypes. Based on this feedback loop between cellular aging and aneuploidy, we propose modulation of mitotic efficiency through FoxM1 as a potential strategy against aging and progeria syndromes.

cell biology↗