Biology subjects

Amato, C.

Publications and source records attributed to Amato, C..

6 recordsLinked to original sources

bioRxiv2026

Gonadal PIP-seq reveals genes involved in germ cell development and sexual differentiation in sea lamprey ( Petromyzon marinus )

Vertebrate sex determination is highly diverse, with distinct mechanisms that have evolved repeatedly and independently across phylogeny. The sea lamprey (Petromyzon marinus) is an extant jawless vertebrate that remains sexually labile during its larval stage that lasts around 3-20 years. Their gonad contains bipotential, female, and male germ cells before metamorphosis. To examine the genetic programs in germ cells at different developmental stages, we profiled transcriptomes of dissociated gonadal cells from larvae and recently metamorphosed juvenile (transformers, sex-determined) using fluorescence-activated cell sorting (BD FACS Aria IIu) and PIPseqTM (Fluent BioSciences/Illumina). 66,676 cells were sequenced and classified into 19 cell clusters according to their gene expression profiles. Primordial germ cells differentially expressed genes encoding various heat-shock proteins, hormones, growth factors, and their receptors, and proteins sensitive to iron, nitrogen starvation, sugar and lipid metabolisms, and oxidative stress, providing possible links between environmental factors, cellular functions, and cell fate determinants. Germ cells in larvae had enriched expression of genes involved in DNA replication, transcription, translation, apoptosis, autophagy, cell cycle, cell differentiation, cell adhesion and migration, cell survival, chromatin remodeling, and proliferation. Specifically, female germ cells differentially expressed various transcript isoforms of AEP1, CUZD1, S100A1, and ZP genes, whereas male germ cells differentially expressed BOLL and PIWIL1. Pseudotime trajectory and Gene Ontology (GO) analysis revealed that genes with changing expressions along the female differentiation pathway were involved in binding of sperm to zona pellucida, egg coat formation, prevention of polyspermy and positive regulation of acrosome reaction. On the other hand, genes with changing expressions along the male differentiation pathway were involved in ribosome assembly and translation. Several WNT5 transcripts were differentially expressed in germ cells or somatic cells. Our results suggest that sea lamprey sex determination and sexual differentiation likely involve the coordinated action of numerous genes that interact with various environmental factors and regulate germ cell specification and development.

Developmental Biology↗

bioRxiv2026

Intermittent exposure to high ambient heat during the second half of gestation in mice causes mild alterations of reproductive endpoints in male embryos

Periods of elevated ambient temperature challenge the bodys ability to maintain internal homeostasis, and heat stress poses particular risks during pregnancy. Epidemiological studies associate gestational heat exposure with higher rates of congenital anomalies such as hypospadias, yet the direct link between gestational heat exposure and reproductive anomalies remains unknown. In this study, we examined the effects of intermittent heat exposure on reproductive development in male mouse offspring. Pregnant dams either remained at constant temperature of 22{degrees}C (control) or were exposed to 38{degrees}C for 2 hours daily (experimental) from embryonic day (E)10 to E18, modeling intermittent heat exposure during mid-to-late gestation. Embryos were collected at E18 for analysis. While heat exposure did not affect pregnancy outcomes, including placental development, litter size, sex ratio, or fetal growth, male embryos exhibited significantly reduced anogenital distance and increased hypospadias scores, which are both markers of disrupted androgen signaling. Despite these phenotypic changes, expression of genes involved in androgen synthesis in the fetal testis, as well as gene expression in external genitalia, remained unchanged. Instead, transcriptomic analysis revealed significant alterations in testicular pathways related to RNA splicing and mRNA processing. Together, these findings reveal that maternal heat stress disrupts reproductive development of male offspring, with altered gene regulatory processes being a potential driver.

developmental biology↗

bioRxiv2026

Nuclear plasticity regulates macrophage phagocytic capacity in vivo

Macrophages fine-tune their appetite to fulfil their clearance role, but how they achieve this is incompletely understood. The nucleus can sense and respond to extracellular physical challenges, but whether it can also detect and react to intracellular mechanical inputs is unclear. Here, we tested the hypothesis that phagosomes exert a strain on the nucleus, and that the consequent nuclear mechanoresponse influences macrophage appetite. Combining genetic manipulation and live in vivo imaging, we show that engulfed apoptotic bodies indent the nucleus of Drosophila embryonic macrophages, leading to nuclear deformation and causing an increase in Lamin B levels. We demonstrate that these phagosome-induced nuclear molecular and mechanical adaptations are critical for macrophages to sustain uptake - unveiling a role for nuclear plasticity in the regulation of macrophage phagocytic capacity in vivo.

cell biology↗

bioRxiv2024

Single-nucleus multiomics reveals the gene-regulatory networks underlying sex determination of murine primordial germ cells

Accurate specification of female and male germ cells during embryonic development is critical for sexual reproduction. Primordial germ cells (PGCs) are the bipotential precursors of mature gametes that commit to an oogenic or spermatogenic fate in response to sex-determining cues from the fetal gonad. The critical processes required for PGCs to integrate and respond to signals from the somatic environment in gonads are not understood. In this study, we developed the first single-nucleus multiomics map of chromatin accessibility and gene expression during murine PGC development in both XX and XY embryos. Profiling of cell-type specific transcriptomes and regions of open chromatin from the same cell captured the molecular signatures and gene networks underlying PGC sex determination. Joint RNA and ATAC data for single PGCs resolved previously unreported PGC subpopulations and cataloged a multimodal reference atlas of differentiating PGC clusters. We discovered that regulatory element accessibility precedes gene expression during PGC development, suggesting that changes in chromatin accessibility may prime PGC lineage commitment prior to differentiation. Similarly, we found that sexual dimorphism in chromatin accessibility and gene expression increased temporally in PGCs. Combining single-nucleus sequencing data, we computationally mapped the cohort of transcription factors that regulate the expression of sexually dimorphic genes in PGCs. For example, the gene regulatory networks of XX PGCs are enriched for the transcription factors, TFAP2c, TCFL5, GATA2, MGA, NR6A1, TBX4, and ZFX. Sex-specific enrichment of the forkhead-box and POU6 families of transcription factors was also observed in XY PGCs. Finally, we determined the temporal expression patterns of WNT, BMP, and RA signaling during PGC sex determination, and our discovery analyses identified potentially new cell communication pathways between supporting cells and PGCs. Our results illustrate the diversity of factors involved in programming PGCs towards a sex-specific fate.

developmental biology↗

bioRxiv2022

PhenoComb: A discovery tool to assess complex phenotypes in high-dimension, single-cell datasets

MotivationHigh-dimension cytometry assays can simultaneously measure dozens of markers, enabling the investigation of complex phenotypes. However, as manual gating relies on previous biological knowledge, few marker combinations are often assessed. This results in complex phenotypes with potential for biological relevance being overlooked. Here we present PhenoComb, an R package that allows agnostic exploration of phenotypes by assessing all combinations of markers. DesignPhenoComb uses signal intensity thresholds to assign markers to discrete states (e.g. negative, low, high) and then counts the number of cells per sample from all possible marker combinations in a memory-safe manner. Time and disk space are the only constraints on the number of markers evaluated. PhenoComb also provides several approaches to perform statistical comparisons, evaluate the relevance of phenotypes, and assess the independence of identified phenotypes. PhenoComb allows users to guide analysis by adjusting several function arguments such as identifying parent populations of interest, filtering of low-frequency populations, and defining a maximum complexity of phenotypes to evaluate. We have designed PhenoComb to be compatible with local computer or server-based use. ResultsIn testing of PhenoCombs performance on synthetic datasets, computation on 16 markers was completed in the scale of minutes and up to 26 markers in hours. We applied PhenoComb to two publicly available datasets: an HIV flow cytometry dataset (12 markers and 421 samples) and the COVIDome CyTOF dataset (40 markers and 99 samples). In the HIV dataset, PhenoComb identified immune phenotypes associated with HIV seroconversion, including those highlighted in the original publication. In the COVID dataset, we identified several immune phenotypes with altered frequencies in infected individuals relative to healthy individuals. Collectively, PhenoComb represents a powerful discovery tool for agnostically assessing high-dimension, single-cell data. AvailabilityThe PhenoComb R package can be downloaded from https://github.com/SciOmicsLab/PhenoComb

bioinformatics↗

bioRxiv2019

WASP restricts active Rac to maintain cells’ front-rear polarisation

Efficient motility requires polarised cells, with anterior pseudopods and a retracting rear. This polarisation requires that the pseudopod catalyst Rac is restricted to the front. Here we show that the Arp2/3 complex regulator WASP is important for maintaining front-rear polarity, using a mechanism that limits where active Rac localises. Dictyostelium cells lacking WASP inappropriately activate Rac and SCAR/WAVE at their rears, leading to reduced cell speed. WASP facilitates the internalisation of clathrin-coated pits, and its Rac-binding CRIB motif is considered essential for its localisation and activity. However, WASP mutants with deleted CRIB domains, or harbouring a new mutation that prevents Rac binding, localise normally, recruit Arp2/3 complex, and drive actin polymerisation. Similarly, Rac inhibitors do not block WASP localisation or activation. Despite this, WASP CRIB mutants cannot restore polarisation of active Rac. Thus, WASPs interaction with Rac regulates Rac activity and cell polarity, but is dispensable for activating actin polymerization.

cell biology↗