Biology subjects

Alfieri, F.

Publications and source records attributed to Alfieri, F..

7 recordsLinked to original sources

bioRxiv2026

KaryoTap-based scDNA seq assessment of aneuploidy induction by hydroquinone in hematopoietic stem cells

Monosomy 7 is a frequent cytogenetic alteration associated with poor outcomes in myelodysplastic syndrome and acute myeloid leukemia. The benzene metabolite hydroquinone (HQ) has been reported to induce chromosome 7 loss in cultured hematopoietic cells, suggesting a mechanism linking benzene exposure to these diseases. However, these findings were largely based on FISH analysis of selected chromosomes in relatively small numbers of cells. Here, we tested whether HQ increases aneuploidy in primary human CD34+ hematopoietic stem and progenitor cells (HSPCs) using KaryoTap, a single-cell DNA sequencing approach that measures copy number across all 22 autosomes, together with interphase FISH. We first identified 20 uM as the highest HQ concentration tested that preserved sufficient viable cells for single-cell analysis. We then examined cord blood and adult mobilized CD34+ cells, including the MPS1 inhibitor reversine as a positive control in the cord blood experiment. Reversine increased whole-chromosome gains and losses, including those of chromosome 7. HQ did not produce a reproducible increase in aneuploidy across three donors and two sources of CD34+ cells, including two concentrations and two timepoints in the adult donor. A modest increase in chromosome 7 loss in one cord blood donor was not reproduced in the other donors. In the other cord blood donor, the estimated upper bound on the HQ-associated increase was approximately 1.4 percentage points. HSPCs also showed a greater increase in chromosome losses than epithelial cells or melanocytes following the same reversine exposure. These findings do not support a substantial, reproducible increase in whole-chromosome aneuploidy after HQ exposure under the conditions tested. They are consistent with a model in which benzene exposure favors the expansion of pre-existing monosomy 7 clones, although this possibility requires direct testing.

cancer biology↗

bioRxiv2026

ZATELLITE: a toolkit to visualize and manipulate human centromeres in live cells using synthetic zinc fingers

Changes in the number of chromosomes or their spatial organization within the nucleus have critical consequences for cell fate. Yet capturing the karyotype or three-dimensional architecture of chromatin in living cells remains limited by the difficulty in labeling endogenous loci non-invasively. The most widely used tools rely on dCas9, a bulky protein whose persistent DNA binding interferes with DNA and RNA metabolism, causes DNA damage, and is hard to multiplex. We developed ZATELLITE, an AI-enabled tool to target endogenous repetitive sequences with fluorescently-tagged synthetic zinc fingers. ZATELLITE probes have key advantages over dCas9: they are smaller, easier to multiplex and, critically, they do not cause DNA damage or chromosomal abnormalities, even after long-term labeling. We generated a collection of ZATELLITE probes to label the centromeres of nearly all human chromosomes, enabling the capture of genome organization and karyotype alterations in real time in living cells. Finally, we show that ZATELLITE can be used for simultaneous labeling and epigenetic editing of centromeres. Thus, ZATELLITE is a non-toxic, versatile tool for genome visualization and manipulation.

cell biology↗

bioRxiv2026

COATS Identifies Copy-Number-Dependent Drivers and Enablers of Aneuploidy in Cancer

Aneuploidy is a hallmark of most cancers but at the same time has been shown to decrease cellular fitness. Thus, to solve this conundrum, a current hypothesis in the field is that specific SCNAs may promote tolerance to the aneuploid state and/or promote additional chromosomal instability (CIN) and more aneuploidy. In other words, gains or losses of oncogenes (OGs) and tumor suppressor genes (TSGs) can, in turn, drive further CIN, promoting additional somatic alterations, or enhance aneuploid cell survival. Despite their importance, CN-dependent OGs and TSGs associated with aneuploidy remain largely unidentified. Here, we present a new method, Copy-number-dependent Oncogenes And Tumor Suppressors (COATS), to identify pan-cancer and cancer-specific CN-dependent OGs and TSGs associated with aneuploidy (Aneu-OGs and Aneu-TSGs). COATS integrates information theory and statistical tests to analyze gene expression, copy number, and aneuploidy, and incorporates timing analysis to distinguish early drivers of CIN from late tolerance enablers. Interestingly, using the CINner simulation framework, we show that aneuploidy drivers tend to occur earlier than aneuploidy enablers. Applying COATS to 33 TCGA cancer types, we identified 479 pan-cancer amplification-dependent Aneu-OGs and 141 deletion-dependent Aneu-TSGs. For validation, we used shRNA to knock down CCT5, a COATS-identified pan-cancer Aneu-OG predicted to promote aneuploidy tolerance, in isogenic aneuploid and near-diploid cells. Strikingly, CCT5 depletion was selectively toxic in aneuploid cells, supporting its classification as an aneuploidy tolerance enabler gene. Overall, our study defines a set of CN-dependent genes associated with aneuploidy and points to candidate therapeutic targets for chromosomally unstable cancers.

Cancer Biology↗

bioRxiv2025

The locomotor behavior of subfossil Malagasy sloth-lemurs (Strepsirrhini: Palaeopropithecidae) and koala-lemurs (Strepsirrhini: Megaladapidae): new insights from limb trabecular bone

The locomotion of Malagasy Quaternary subfossil lemurs--including palaeopropithecids ( sloth-lemurs) and megaladapids ( koala-lemurs)--has been investigated on abundant postcranial remains. Proposed strategies include some without living primate parallels, including sloth-like suspensory arboreality in palaeopropithecids, although the degree of suspensory behaviour in palaeopropithecids, or locomotor diversity in koala-lemurs are poorly understood. Differently from external morphology, internal bone structure in these taxa is largely unexplored. We compared the humeral and femoral trabecular architecture of sloth- and koala-lemurs to several extant mammals, studying spherical trabecular samples extracted from high-resolution scans. After defining locomotor categories from quantitative data, we tested links between trabecular parameters and locomotor modes through exploratory and multivariate analyses, accounting for body size and phylogeny. In extant mammals, only femoral trabecular traits--particularly Degree of Anisotropy and Bone Volume Fraction--were significantly associated with locomotion, distinguishing suspensory and bridging arboreal taxa from others. Using this model, we inferred suspensory adaptations in palaeopropithecids, especially Palaeopropithecus--confirming earlier reconstructions--but also in Megaladapis edwarsi, a striking result that would make M. edwarsi the largest mammal ever known to adopt such habits, approached only by extant orangutans. This work highlights the potential of internal bone structure for reconstructing primate locomotor evolution.

paleontology↗

bioRxiv2025

Trabecular structure correlates with leaping distance in tamarins

ObjectivesThe intricate trabecular architecture of long-bone epiphyses underpins functional adaptations for diverse mammalian locomotion. Despite extensive study in other mammals, tamarin trabecular structure and fine-grained differences among leaping taxa remain poorly characterized. Materials and MethodsWe examined humeral and tibial trabecular networks in four tamarin species representing short- and long-distance leapers using {micro}CT-scans and a whole-epiphysis approach. We quantified network complexity with topological indices (node density, tortuosity, trabecular length, fractal dimension) alongside traditional metrics (degree of anisotropy [DA], bone volume fraction [BV/TV]) to capture both geometric and topological features. ResultsLong leapers exhibit significantly higher node density in both humeral and tibial epiphyses and increased trabecular tortuosity in the distal humerus. Elevated node density localizes beneath the humero-scapular joint, within the proximal humerus, and in variable regions across other epiphyses. Other parameters (DA, BV/TV, trabecular length, fractal dimension) showed no leaping-related differences, instead correlating with sex and captivity. DiscussionIncreased mechanical strain during longer leaps likely drives higher node density and, to a lesser extent, tortuosity in humeral and tibial epiphyses, with node density showing the strongest functional signal. While sex and captivity influence other trabecular traits, patterns in these key metrics support locomotor adaptation. Integrating whole-epiphysis analyses with novel topological indices enhances detection of subtle functional signals and complements VOI-based and traditional frameworks in comparative trabecular bone studies.

zoology↗

bioRxiv2025

Constrained variation in the internal architecture of avian wing bones

Extant birds exhibit remarkable ecological disparity accompanied by widespread skeletal convergence driven by functional adaptation. Investigations of morphofunctional associations with ecological factors have frequently focused on the external morphology of avian wing bones; however, the extent to which such associations also apply to the internal structure of the wing skeleton remains understudied. Here, we investigate disparity of the internal epiphyseal and diaphyseal structure of the avian humerus and ulna, and explore its correlates with ecology. Our dataset of 140 species spans extant bird diversity, and demonstrates that the internal structure of avian wing bones exhibits limited ecological signal beyond expected secondary trends related to flightlessness and marine habits. Our work instead shows that variation is primarily determined by body size, suggesting that functional constraints on internal wing bone structure imposed by flight are essentially universal across flying birds irrespective of most ecological habits and flight styles. Despite this broad lack of ecological signal, distinctive aspects of forelimb internal structure may facilitate the identification of flightless bird taxa in the fossil record.

evolutionary biology↗

bioRxiv2020

Evolution of bone cortical compactness in slow arboreal mammals

Lifestyle convergences and related phenotypes are a major topic in evolutionary biology. Low bone cortical compactness (CC), shared by the two genera of tree sloths, has been linked to their convergently evolved slow arboreal ecology. The proposed relationship of low CC with tree sloths lifestyle suggests a potential convergent acquisition of this trait in other slow arboreal mammals. Tree sloths, Lorisidae, Palaeopropithecidae, Megaladapis and koalas were included in a phylogenetically informed CC analysis of the humerus and femur, as well as closely related but ecologically distinct taxa. We found that tree sloths are unparalleled by any analysed clade, in featuring an extremely low CC. A tendency for low CC was however found in palaeopropithecids (especially Palaeopropithecus) and Megaladapis. On the other hand, low CC was not found in Lorisidae. Koalas, although deviating from the compact structure generally observed in mammals, are not clearly distinct from their sister taxon (wombats) and show humeral CC that is higher than femoral CC. Multiple factors seem to influence CC, preventing the recognition of a simple relationship between slow arborealism and low CC. Highly compact cortical bone in extinct sloths confirms that low CC in tree sloths likely represents a recent convergence.

evolutionary biology↗