Biology subjects

Cuomo, C.

Publications and source records attributed to Cuomo, C..

9 recordsLinked to original sources

bioRxiv2024

Deep conservation of cis-regulatory elements and chromatin organization in echinoderms uncover ancestral regulatory features of animal genomes

Despite the growing abundance of sequenced animal genomes, we only have detailed knowledge of regulatory organization for a handful of lineages, particularly flies and vertebrates. These two groups of taxa show contrasting trends in the molecular mechanisms of 3D chromatin organization and long-term evolutionary dynamics of cis-regulatory element (CREs) conservation. To help us identify shared versus derived features that could be responsible for the evolution of these different regulatory architectures in animals, we studied the evolution and organization of the regulatory genome of echinoderms, a lineage whose phylogenetic position and relatively slow molecular evolution has proven particularly useful for evolutionary studies. First, using PacBio and HiC data, we generated new reference genome assemblies for two species belonging to two different echinoderm classes: the purple sea urchin Strongylocentrotus purpuratus and the bat sea star Patiria miniata. Second, we characterized their 3D chromatin architecture, identifying TAD-like domains in echinoderms that, like in flies, do not seem to be associated with CTCF motif orientation. Third, we systematically profiled CREs during sea star and sea urchin development using ATAC-seq, comparing their regulatory logic and dynamics over multiple developmental stages. Finally, we investigated sea urchin and sea star CRE evolution across multiple evolutionary distances and timescales, from closely related species to other echinoderm classes and deuterostome lineages. This showed the presence of several thousand elements conserved for hundreds of millions of years, revealing a vertebrate-like pattern of CRE evolution that probably constitutes an ancestral property of the regulatory evolution of animals.

evolutionary biology↗

bioRxiv2024

On the recovery of malformed horseshoe crabs across multiple moulting stages

Malformed horseshoe crabs have been documented for over a century. However, most of these records are anecdotal observations of often striking morphologies recorded in isolation. There is therefore little understanding of how malformations are manifested and how they can develop in the group. Here we consider the moult sequences of three extant Limulus polyphemus individuals to explore different patterns of malformation development. One specimen with an injured telson demonstrates a gradual recovery of the telson section over three moulting events. The second individual demonstrates a fused thoracetron-telson articulation with a hole for the telson. This individual shows consistent growth of a reduced telson across moults. The third individual shows a thoracetronic injury incurred during at least moult-stage 7 that shows no evidence of recovery over five moulting stages. These records illustrate that horseshoe crab malformation recovery is far more complicated than previously thought. This also suggests that unless an exoskeletal section has functional morphological importance (i.e., the telson), the region is unlikely to recover from an older malformation. From a conservation standpoint, the ability or inability to fully recover from injury affects a horseshoe crabs ability to survive and/or reproduce in the wild particularly if the injury affects the telson. Given the global decline in horseshoe crab populations and conservation efforts underway, the extent of injuries in extant populations of horseshoe crabs may affect population recovery and should be considered.

ecology↗

bioRxiv2023

An integrative multi-omics approach to draft gene regulatory networks at a cell type resolution

Drafting gene regulatory networks (GRNs) requires embryological knowledge pertaining to the cell type families, information on the regulatory genes, causal data from gene knockdown experiments and validations of the identified interactions by cis-regulatory analysis. We use multi-omics involving next-generation sequencing (-seq) to obtain the necessary information drafting the sea urchin posterior gut GRN. Here we present an update to the GRN using i) a single cell RNA-seq derived cell atlas highlighting the 2 day post fertilization (dpf) sea urchin gastrula cell type families, as well as the genes expressed at single cell level, ii) a set of putative cis-regulatory modules and transcription factor (TF) binding sites obtained from chromatin accessibility ATAC-seq data, and iii) interactions directionality obtained from differential bulk RNA-seq following knockdown of the TF Sp-Pdx1, a key regulator of gut patterning in sea urchins. Combining these datasets, we draft the GRN for the hindgut Sp-Pdx1 positive cells in the 2 dpf gastrula embryo. Overall, our data resolves the complex connectivity of the posterior gut GRN and increases the resolution of gene regulatory cascades operating within it.

developmental biology↗

bioRxiv2020

Amoeba predation of Cryptococcus neoformans results in pleiotropic changes to traits associated with virulence

Phagocytic amoeboid predators such as amoeba have been proposed to select for survival traits in soil microbes such as Cryptococcus neoformans that can also function in animal virulence by defeating phagocytic immune cells, such as macrophages. Several prior studies have shown that incubation of various fungal species with amoeba can enhance their virulence. However, the mechanisms by which fungi adapt to amoeba and thus change their virulence are unknown. In this study we exposed three strains of C. neoformans (1 clinical and 2 environmental) to predation by Acanthamoeba castellanii for prolonged periods of time and then analyzed surviving colonies phenotypically and genetically. Surviving colonies were comprised of cells that expressed either pseudohyphal or yeast phenotypes, which demonstrated variable expression of such traits associated with virulence such as capsule size, urease production and melanization. Phenotypic changes were associated with aneuploidy and DNA sequence mutations in some amoeba-passaged isolates, but not in others. Mutations in the gene encoding for the oligopeptide transporter (CNAG_03013; OPT1) were observed among amoeba-passaged isolates from each of the three strains. In addition, isolates derived from environmental strains gained the capacity for enhanced macrophage toxicity after amoeba selection and carried mutations on the CNAG_00570 gene, which encodes Pkr1 (AMP-dependent protein kinase regulator) but were less virulence in mice because they elicited more effective fungal-clearing immune responses. Our results indicate that C. neoformans survival under constant amoeba predation involves the generation of strains expressing pleiotropic phenotypic and genetic changes, which confer increase resistance against protozoal predation. Given the myriad of potential predators in soils the diversity observed among amoeba-selected strains suggests a bet-hedging strategy whereby variant diversity increases the likelihood that some will survive predation. Author summaryCryptococcus neoformans is a ubiquitous environmental fungus that is also a leading cause of fatal fungal infection in humans, especially among immunocompromised patients. Cryptococcosis is a worldwide concern due to its high mortality rate. A major question in the field is how an environmental yeast such as C. neoformans becomes a human pathogen when it has no need for animal host in its life cycle. Previous studies showed evidence that C. neoformans increases its pathogenicity after interacting with its environmental predator amoebae. Amoebae behave like macrophages, an important immune cell in human body, so it is considered as a training ground for pathogens to resist macrophages. However, how C. neoformans changes its virulence through interacting with amoebae is unknown. Here, we exposed C. neoformans to amoebae for a long period of time. We found that C. neoformans cells recovered from amoebae manifested numerous changes to phenotypes related to its virulence and one of the amoeba-passaged C. neoformans cells had enhanced ability to kill macrophages. We further analyzed their genome sequences and found various mutations in different cells of amoeba-passaged C. neoformans, showing that DNA mutations may be the major cause of the phenotypic changes after interacting with amoebae. Our study indicates that fungal survival in the face of amoeba predation is associated with the emergence of pleiotropic phenotypic and genomic changes that increase the chance of fungal survival.

microbiology↗

bioRxiv2020

Tracing the evolutionary history and global expansion of Candida auris using population genomic analyses

Candida auris has emerged globally as a multidrug-resistant yeast that can spread via nosocomial transmission. An initial phylogenetic study of isolates from Japan, India, Pakistan, South Africa, and Venezuela revealed four populations (Clades I, II, III, and IV) corresponding to these geographic regions. Since this description, C. auris has been reported in over 30 additional countries. To trace this global emergence, we compared the genomes of 304 C. auris isolates from 19 countries on six continents. We found that four predominant clades persist across wide geographic locations. We observed phylogeographic mixing in most clades; Clade IV, with isolates mainly from South America, demonstrated the strongest phylogeographic substructure. C. auris isolates from two clades with opposite mating types were detected contemporaneously in a single healthcare facility in Kenya. We estimated a Bayesian molecular clock phylogeny and dated the origin of each clade within the last 339 years; outbreak-causing clusters from Clades I, III, and IV originated 34-35 years ago. We observed high rates of antifungal resistance in Clade I, including four isolates resistant to all three major classes of antifungals. Mutations that contribute to resistance varied between the clades, with Y132F in ERG11 as the most widespread mutation associated with azole resistance and S639P in FKS1 for echinocandin resistance. Copy number variants in ERG11 predominantly appeared in Clade III and were associated with fluconazole resistance. These results provide a global context for the phylogeography, population structure, and mechanisms associated with antifungal resistance in C. auris. ImportanceIn less than a decade, C. auris has emerged in healthcare settings worldwide; this species is capable of colonizing skin and causing outbreaks of invasive candidiasis. In contrast to other Candida species, C. auris is unique in its ability to spread via nosocomial transmission and its high rates of drug resistance. As part of the public health response, whole-genome sequencing has played a major role in characterizing transmission dynamics and detecting new C. auris introductions. Through a global collaboration, we assessed genome evolution of isolates of C. auris from 19 countries. Here, we described estimated timing of the expansion of each C. auris clade and of fluconazole resistance, characterized discrete phylogeographic population structure of each clade, and compared genome data to sensitivity measurements to describe how antifungal resistance mechanisms vary across the population. These efforts are critical for a sustained, robust public health response that effectively utilizes molecular epidemiology.

genomics↗

bioRxiv2019

Diversity and complexity of the large surface protein family in the compacted genomes of various Pneumocystis species

Pneumocystis, a major opportunistic pathogen in patients with a broad range of immunodeficiencies, contains abundant surface proteins encoded by a multi-copy gene family, termed the major surface glycoprotein (Msg) gene superfamily. This superfamily has been identified in all Pneumocystis species characterized to date, highlighting its important role in Pneumocystis biology. In this report, through a comprehensive and in-depth characterization of 459 msg genes from 7 Pneumocystis species, we demonstrate, for the first time, the phylogeny and evolution of conserved domains in Msg proteins, and provide detailed description of the classification, unique characteristics and phylogenetic relatedness of five Msg families. We further describe the relative expression levels of individual msg families in two rodent Pneumocystis species, the substantial variability of the msg repertoires in P. carinii from laboratory and wild rats, and the distinct features of the expression site for the classic msg genes in Pneumocystis from 8 mammalian host species. Our analysis suggests a wide variety of functions for this superfamily, not only conferring antigenic variation to allow immune evasion but also mediating life-stage development, optimizing cell mobility and adhesion, and adapting to specific host niches or environmental conditions. This study provides a rich source of information that lays the foundation for the continued experimental exploration of the functions of the Msg superfamily in Pneumocystis biology.

molecular biology↗

bioRxiv2019

Host-pathogen transcriptomics of macrophages, Mucorales and their endosymbionts: a polymicrobial pas de trois

Mucorales spores, the causative agents of mucormycosis, interact with the innate immune system to cause acute, chronic, or resolving infection. Understanding the factors that influence disease initiation and progression is key to understanding mucormycosis and developing new treatments. Complicating this, mucormycosis can be caused by a number of species that span the Mucorales order and may be host to bacterial endosymbionts. This study sets out to examine the differences between two species in the Mucorales order by characterising their differential interactions with the innate immune system, and their interactions with environmental bacterial endosymbionts. Through a holistic approach, this study examines the transcriptional responses of Rhizopus delemar and Rhizopus microsporus, two of the most commonly diagnosed species, to innate immune cells. This study also examines the immune cell response and assesses the variation in these responses, given the presence or absence of bacterial endosymbionts within the fungi. We see that the fungal response is driven by interaction with innate immune cells. Moreover, the effect of the bacterial endosymbiont on the fungus is species-specific and strongly influences fungal transcription during phagocyte stress. The macrophage response varies depending on the infecting fungal species, and depending on endosymbiont status. Macrophages are better able to survive when germination is inhibited, or upon a pro-inflammatory response. This work reveals species-specific host responses to related Mucorales spores and shows that bacterial endosymbionts have an important role to play by impacting both innate immune cell response, and fungal response when under stress.

microbiology↗

bioRxiv2018

Coordinated host-pathogen transcriptional dynamics revealed using sorted subpopulations and single, Candida albicans infected macrophages

The outcome of fungal infections depends on interactions with innate immune cells. Within a population of macrophages encountering C. albicans, there are distinct host-pathogen trajectories; however, little is known about the molecular heterogeneity that governs these fates. We developed an experimental system to separate interaction stages and single macrophage cells infected with C. albicans from uninfected cells and assessed transcriptional variability in the host and fungus. Macrophages displayed an initial up-regulation of pathways involved in phagocytosis and proinflammatory response after C. albicans exposure that declined during later time points. Phagocytosed C. albicans shifted expression programs to survive the nutrient poor phagosome and remodeled the cell wall. The transcriptomes of single infected macrophages and phagocytosed C. albicans revealed a tightly coordinated shift in gene expression co-stages and revealed expression bimodality and differential splicing that may drive infection outcome. This work establishes an approach for studying host-pathogen trajectories to resolve heterogeneity in dynamic populations.

genomics↗

bioRxiv2017

Population Genomics And The Evolution Of Virulence In The Fungal Pathogen Cryptococcus neoformans

Cryptococcus neoformans is an opportunistic fungal pathogen that causes approximately 625,000 deaths per year from nervous system infections. Here, we leveraged a unique, genetically diverse population of C. neoformans from sub-Saharan Africa, commonly isolated from mopane trees, to determine how selective pressures in the environment coincidentally adapted C. neoformans for human virulence. Genome sequencing and phylogenetic analysis of 387 isolates, representing the global VNI and African VNB lineages, highlighted a deep, non-recombining split in VNB (herein VNBI and VNBII). VNBII was enriched for clinical samples relative to VNBI, while phenotypic profiling of 183 isolates demonstrated that VNBI isolates were significantly more resistant to oxidative stress and more heavily melanized than VNBII isolates. Lack of melanization in both lineages was associated with loss-of-function mutations in the BZP4 transcription factor. A genome-wide association study across all VNB isolates revealed sequence differences between clinical and environmental isolates in virulence factors and stress response genes. Inositol transporters and catabolism genes, which process sugars present in plants and the human nervous system, were identified as targets of selection in all three lineages. Further phylogenetic and population genomic analyses revealed extensive loss of genetic diversity in VNBI, suggestive of a history of population bottlenecks, along with unique evolutionary trajectories for mating type loci. These data highlight the complex evolutionary interplay between adaptation to natural environments and opportunistic infections, and that selection on specific pathways may predispose isolates to human virulence.

genomics↗