Biology subjects

Rossi, M.

Publications and source records attributed to Rossi, M..

At least 19 recordsLinked to original sources

bioRxiv2026

The Genome In A Bottle HG002 assembly-based variant benchmark set enables comprehensive benchmarking of small and structural variants.

High-accuracy, high-resolution benchmark data are fundamental to improving the accuracy and generalizability of sequencing technologies and associated algorithms. Most existing benchmarks for DNA sequencing rely on mapping to a single linear reference, omitting inaccessible and highly repetitive complex genomic regions. Here, we present the Genome in a Bottle (GIAB) Consortium's HG002 v5.0q benchmark set, a more comprehensive variant benchmark derived from a fully phased, highly curated, and accurate diploid assembly of HG002. Our approach leverages recent advances in long-read sequencing and assembly to provide confident small- and structural-variant calls across previously inaccessible regions, including segmental duplications, homopolymers, tandem repeats, and complex immune loci. The v5.0 benchmark significantly expands the callable genome relative to v4.2.1, adding x200 Mbp of sequence and increasing variant detection by 18 % for small variants and 3-fold for structural variants compared to previous benchmarks. The benchmark regions include more variants in repetitive regions, including 1.2 x segmental duplications, 1.8 x tandem repeats, and 2.0 x homopolymers, compared to v4.2.1. Separate and combined small- and structural-variant benchmarks are available for three versions of the human reference genome (GRCh37, GRCh38, and CHM13). We validate the reliability of this benchmark set by comparing multiple sequencing technologies and variant calling pipelines and curating differences. The v5.0q benchmark provides a critical resource for the development and validation of next-generation sequencing technologies and analysis methods.

genomics↗

bioRxiv2026

Reduced LANCL1-AS1 in old human skeletal muscle diminishes mitochondrial activity, shortens mt-mRNA poly(A) tails, and suppresses myogenesis

Regeneration of skeletal muscle preserves muscle mass and function, which decline with age. Here, we sought to identify long noncoding (lnc)RNAs involved in skeletal muscle myogenesis and potentially relevant to muscle aging. Cross-sectional analysis of skeletal muscle transcriptomes from healthy 22-through 89-year-old individuals revealed lncRNA LANCL1-AS1 among the top declining transcripts. Conversely, LANCL1-AS1 increased robustly during skeletal myogenesis and promoted myogenic differentiation in culture. Affinity pulldown by ChIRP followed by mass spectrometry revealed that LANCL1-AS1 associated with the mitochondrial protein LRPPRC, enhancing the formation of the chaperone complex LRPPRC-SLIRP, which maintains longer poly(A) tails of mitochondrial (mt-)mRNAs and stabilizes mt-mRNAs. Importantly, while myoblasts from old rhesus monkey muscle expressed lower levels of LANCL1-AS1 and mt-mRNAs, and displayed lower mitochondrial activity than young monkey myoblasts, overexpressing LANCL1-AS1 in old myoblasts restored mitochondrial activity and myogenesis. We propose that the age-associated reduction in LANCL1-AS1 contributes to impaired mitochondrial function and reduced myogenic capacity in aging skeletal muscle.

molecular biology↗

bioRxiv2026

Novel role of the lncRNA EPR as oncosuppressor in intestinal cancer.

We previously reported that the murine lncRNA Epr is essential for maintaining colon mucosal integrity and permeability. Mice lacking Epr in the colon are more susceptible to colitis and tumor development. Additionally, we demonstrated that human EPR expression is reduced in ulcerative colitis and in a small cohort of colon adenocarcinoma patients. Here, we present evidence that human and mouse EPR share several key physiological features: preferential binding to the KH1 domain of their interacting protein, KSRP; specific expression in canonical and immature goblet cells of the large intestine; and a functional role in intestinal goblet cell development. The correlation between EPR levels and survival in large cohorts of metastatic colon adenocarcinoma patients, together with the capacity of human EPR to inhibit cell proliferation and induce apoptosis in two distinct human colon adenocarcinoma cell lines, suggests that EPR may serve as both a valuable prognostic marker for goblet cell-derived adenocarcinomas and a potential therapeutic target.

cancer biology↗

bioRxiv2026

SenCat: Cataloging human cell senescence through multiomic profiling of multiple senescent primary cell types

There is an urgent need to comprehensively catalog senescence markers across cell types in an organism in order to characterize senotypes and senescent cell heterogeneity. Here, we profiled the transcriptomes and proteomes in 14 different primary human cell types undergoing over 30 senescence paradigms to create a senescence catalog we termed SenCat. We found that, while senescent cells from all primary tissue types did not share a single unique marker, they did activate shared specific metabolic and damage-response pathways implicated in tissue repair. Machine learning analysis of the SenCat transcriptomic and proteomic datasets successfully identified independent sets of senescent human cells, and senescent-like cells in mouse lung and kidney. In sum, SenCat represents a much-needed resource to identify senescent cells across tissues in the body. HIGHLIGHTSO_LIIdentifying senescent cells in organisms in vivo remains a challenge C_LIO_LIWe created SenCat: a catalog transcriptomes and proteomes of senescent primary cells C_LIO_LIMachine learning (ML) analysis of SenCat identified robust senescence scores C_LIO_LIML-derived senescence scores uncovered senescent-like cell dynamics in vivo C_LI

molecular biology↗

bioRxiv2026

Long-term consequences of fostering: Single egg fostering leads to decreased survival in zebra finch females, but not in males

Cross-Fostering, i.e., the exchange of eggs or hatchlings, is a widely used technique, to disentangle genetic from environmental effects or to manipulate the clutch size. In most bird species, this manipulation is easily accepted by the social parents, leading to the conclusion that fostering has no detrimental effect. Using a dataset of four cohorts (N=298) of zebra finches (Taeniopygia castanotis), in which we fostered routinely a single egg into another nest of zebra finches, we explored potential short- and long-time effects of fostering. Noteworthy, these experiments were not designed to test this hypothesis. The objective of the egg fostering experiments was to test for parental recognition (Caspers et al. 2017) and mate choice decisions (Goluke 2018). Consequently, the aim of the present study is purely explorative. Our study confirmed previous findings that fostering has no short-term effects on the morphology and growth rates of the chicks, neither in males nor in females. However, we found that fostering has a sex-specific long-term effect. Females originating from fostered eggs had a significantly reduced lifespan compared to those from non-fostered eggs. Conversely, the lifespan of fostered males was similar to that of non-fostered males. All birds were housed in large groups, experiencing the same conditions after nutritional independence (day 35). Therefore, we can only speculate that fostering might result in early developmental stress, which may affect the individual fitness of females later in life, ultimately leading to shorter lifespans.

animal behavior and cognition↗

bioRxiv2026

Ketone body beta-hydroxybutyrate restores neuronal Tau proteostasis via ketolysis-independent mechanism

Metabolic interventions that induce ketosis, including ketogenic diets, caloric restriction, intermittent fasting, and exercise, show promise in the treatment of Alzheimers disease (AD) and related tauopathies. {beta}-hydroxybutyrate ({beta}HB), the primary ketone body produced during ketosis, reproduces key features of these metabolic interventions, but the molecular mechanism underlying its neuroprotective properties is not fully understood. Here, we demonstrate that a {beta}HB precursor diet is sufficient to ameliorate Tau pathophysiology in a tauopathy mouse model. Furthermore, across in vitro, ex vivo, and in vivo models, we find that {beta}HB enhances neuronal Tau proteostasis and reduces Tau aggregation and secretion. Importantly, these effects are independent of {beta}HBs oxidation for ATP production, as its ketolysis-resistant enantiomer reproduces these benefits, indicating that ketolysis is dispensable for these effects. Overall, these data position {beta}HB as a novel therapeutic avenue for AD and tauopathy and elucidate a novel mechanism of action of metabolic interventions in neurodegenerative disease.

neuroscience↗

bioRxiv2025

Tolerance toward foreigners in ants requires chronic exposure for establishment but only sporadic exposure for maintenance

Social insects discriminate between foreigners and members of their own colony via complex olfactory cues. How plastic this discriminatory behavior is, and whether and under what circumstances ants can learn to accept genetically distinct individuals as nestmates, is poorly understood. Here, we study this question in the clonal raider ant, Ooceraea biroi, which provides unparalleled experimental control over the genotype of individuals and the genotypic composition of colonies. Using a cross-fostering design with mixed-genotype colonies of wild-type and transgenically labelled individuals, we show that ants become non-aggressive specifically toward their foster genotype. This tolerance is transient, and aggression resumes after two weeks of being isolated from the foster colony. However, even sporadic re-exposure to individuals from the foster colony is sufficient to maintain tolerance for over a month, while the same paradigm fails to establish tolerance in the first place. This shows that non-nestmate discrimination is remarkably plastic and that, once established, tolerance toward foreigners can be maintained by only intermittent contact. These dynamics echo general principles of social learning and contact-dependent tolerance described in other social species, including humans.

animal behavior and cognition↗

bioRxiv2025

Shedding light on cuticle formation: phytochrome B and downstream signaling events controlling cuticle deposition in tomato fruits

The cuticle is a hydrophobic barrier limiting water loss and pathogen entry. Although light influences cuticle formation, the underlying mechanisms remain poorly understood, particularly in fruits. Here, we show that fruits from tomato (Solanum lycopersicum) plants grown under far-red-enriched light conditions displayed increased cuticle load due to the up-regulation of cutin and wax biosynthetic genes. Both tomato PHYB-encoding genes (SlPHYB1 and SlPHYB2) were implicated as negative regulators of fruit cuticle formation, as revealed by the thinner cuticles, reduced abundance of cutin monomers and cuticular waxes, and downregulation of cuticle-related genes detected in fruits from transgenic plants overexpressing constitutively active alleles of SlPHYB1/B2 (SlYHB1OE and SlYHB2OE). The impaired cuticle of SlYHB1/B2OE fruits resulted in increased susceptibility to Botrytis cinerea, despite their markedly enhanced flavonoid accumulation in the peel. PHYTOCHROME-INTERACTING FACTORs (SlPIF3, SlPIF4) and the B-box protein SlBBX28 were identified as downstream factors of SlPHYB1/B2-mediated regulation of cuticle deposition, synergistically activating the expression of cuticle-related genes. Additionally, SlPHYB1/B2 signaling also downregulated multiple central carbon metabolism-related genes in the fruit peel, likely reducing the pool of activated fatty acids (FAs) feeding into cutin and wax biosynthetic pathways. Together, our results uncover a novel regulatory layer of light signaling in fleshy fruits, revealing that, besides controlling fruit nutritional traits, the PHYB-PIF-BBX regulatory module also shapes the fruit cuticle formation. HighlightsPhytochrome-dependent light signaling regulates cuticle deposition in tomato fruits by controlling downstream transcription factors and the supply of precursors feeding into cutin/wax biosynthetic pathways, thereby affecting postharvest water loss and pathogen susceptibility.

plant biology↗

bioRxiv2025

The anti-cancer drug trametinib suppresses angiotensin-induced cardiac remodelling in mice but is detrimental to function

Aims. Echocardiography is used widely in preclinical mouse studies, but the emphasis remains the histological/pathological/biochemical changes in the myocardium. Analysis/reporting of cardiac function is generally limited, often relying on M-mode assessment of a single plane across the left ventricle. The aim was to determine if global/segmental endocardial speckle-tracking (strain) has greater potential to assess function by distinguishing between mouse lines and identifying regional effects of different drugs. Methods and results. Echocardiograms from male C57Bl/6J (commercially-available) or C57Bl/6(R) (bred in-house) mice treated with vehicle or angiotensin II (AngII; 0.8 mg/kg/d, 7 d) were analysed. Global strain demonstrated different degrees of hypertrophy induced by AngII in the different lines, and variation in function (e.g. stroke volume/cardiac output were reduced in C57Bl/6J mice only, with no effect on global longitudinal strain). For C57Bl/6J mice, segmental strain (radial/longitudinal peak displacement/velocity/strain/strain rate) and frame-to-frame analysis of radial/longitudinal displacement identified more significant effects of AngII in the basal/mid-regions of the left ventricle. Thus, speckle-tracking distinguished between responses in different mouse lines. The methodology was applied to studies of anti-cancer drugs that inhibit extracellular signal-regulated kinase 1/2 signalling. Dabrafenib and/or trametinib inhibited AngII-induced cardiac hypertrophy, but dabrafenib alone caused abnormalities in endocardial movement whilst, for trametinib with AngII, more abnormalities were detected than with AngII alone. For both, the dominant effect was in the basal/mid-regions of the left ventricle. Conclusion. Echocardiography in preclinical studies can be exploited using endocardial segmental strain for greater insight into how drugs affect cardiac function in different regions of the left ventricle.

physiology↗

bioRxiv2025

Esr1-Dependent Signaling and Transcriptional Maturation in the Medial Preoptic Area of the Hypothalamus Shapes the Development of Mating Behavior during Adolescence

Mating and other behaviors emerge during adolescence through the coordinated actions of steroid hormone signaling throughout the nervous system and periphery. In this study, we investigated the transcriptional dynamics of the medial preoptic area (MPOA), a critical region for reproductive behavior, using single-cell RNA sequencing (scRNAseq) and in situ hybridization techniques in male and female mice throughout adolescence development. Our findings reveal that estrogen receptor 1 (Esr1) plays a pivotal role in the transcriptional maturation of GABAergic neurons within the MPOA during adolescence. Deletion of the estrogen receptor gene, Esr1, in GABAergic neurons (Vgat+) disrupted the developmental progression of mating behaviors in both sexes, while its deletion in glutamatergic neurons (Vglut2+) had no observable effect. In males and females, these neurons displayed distinct transcriptional trajectories, with hormone-dependent gene expression patterns emerging throughout adolescence and regulated by Esr1. Esr1 deletion in MPOA GABAergic neurons, prior to adolescence, arrested adolescent transcriptional progression of these cells and uncovered sex-specific gene-regulatory networks associated with Esr1 signaling. Our results underscore the critical role of Esr1 in orchestrating sex-specific transcriptional dynamics during adolescence, revealing gene regulatory networks implicated in the development of hypothalamic controlled reproductive behaviors. One Sentence SummarySingle cell RNA sequencing reveals how adolescent sex hormones sculpt hypothalamic cell types required for mating behavior.

neuroscience↗

bioRxiv2024

A robust benchmark for detecting low-frequency variants in the HG002 Genome In A Bottle NIST reference material.

Somatic mosaicism is an important cause of disease, but mosaic and somatic variants are often challenging to detect because they exist in only a fraction of cells. To address the need for benchmarking subclonal variants in normal cell populations, we developed a benchmark containing mosaic variants in the Genome in a Bottle Consortium (GIAB) HG002 reference material DNA from a large batch of a normal lymphoblastoid cell line. First, we used a somatic variant caller with high coverage (300x) Illumina whole genome sequencing data from the Ashkenazi Jewish trio to detect variants in HG002 not detected in at least 5% of cells from the combined parental data. These candidate mosaic variants were subsequently evaluated using >100x BGI, Element, and PacBio HiFi data. High confidence candidate SNVs with variant allele fractions above 5% were included in the HG002 draft mosaic variant benchmark, with 13/85 occurring in medically relevant gene regions. We also delineated a 2.45 Gbp subset of the previously defined germline autosomal benchmark regions for HG002 in which no additional mosaic variants >2% exist, enabling robust assessment of false positives. The variant allele fraction of some mosaic variants is different between batches of cells, so using data from the homogeneous batch of reference material DNA is critical for benchmarking these variants. External validation of this mosaic benchmark showed it can be used to reliably identify both false negatives and false positives for a variety of technologies and detection algorithms, demonstrating its utility for optimization and validation. By adding our characterization of mosaic variants in this widely-used cell line, we support extensive benchmarking efforts using it in simulation, spike-in, and mixture studies.

bioinformatics↗

bioRxiv2024

RNA-seq gene expression profiling of the bladder in a mouse model of urogenital schistosomiasis

Background: Parasitic flatworms of the Schistosoma genus cause schistosomiasis, which affects over 230 million people. Schistosoma haematobium causes the urogenital form of schistosomiasis (UGS), which can lead to hematuria, fibrosis, and increased risk of secondary infections by bacteria or viruses. UGS is also linked to bladder cancer. To understand the bladder pathology during S. haematobium infection, our group previously developed a mouse model that involves the injection of S. haematobium eggs into the bladder wall. Using this model, we studied changes in epigenetics profile, as well as changes in gene and protein expression in the host bladder tissues. In the current study, we expand upon this work by examining the expression level of both host and parasite genes using RNA sequencing (RNA-seq) in the mouse bladder wall injection model of S. haematobium infection. Methods: We used a mouse model of S. haematobium infection in which parasite eggs or vehicle control were injected into the bladder walls of female BALB/c mice. RNA-seq was performed on the RNA isolated from the bladders four days after bladder wall injection. Results/Conclusions: RNA-seq analysis of egg- and vehicle control-injected bladders revealed the differential expression of 1025 mouse genes in the egg-injected bladders, including genes associated with cellular infiltration, immune cell chemotaxis, cytokine signaling, and inflammation We also observed the upregulation of immune checkpoint-related genes, which suggests that while the infection causes an inflammatory response, it also dampens the response to avoid excessive inflammation-related damage to the host. Identifying these changes in host signaling and immune responses improves our understanding of the infection and how it may contribute to the development of bladder cancer. Analysis of the differential gene expression of the parasite eggs between bladder-injected versus uninjected eggs revealed 119 S. haematobium genes associated with transcription, intracellular signaling, and metabolism. The analysis of the parasite genes also revealed fewer transcript reads compared to that found in the analysis of mouse genes, highlighting the challenges of studying parasite egg biology in the mouse model of S. haematobium infection. Author summaryMore than 230 million people worldwide are estimated to carry infection with parasites belonging to the Schistosoma genus, which cause morbidity associated with parasite egg deposition. Praziquantel, the drug of choice to treat the infection, does not prevent reinfection, and its decades-long history as the main treatment raises concerns for drug resistance. Of the schistosome species, Schistosoma haematobium causes urogenital disease and has a strong association with bladder cancer. The possibility for drug resistance and the gap in knowledge with respect to the mechanisms driving S. haematobium-related bladder cancer highlight the need to better understand the biology of the infection to aid in the development of new therapeutic strategies. In this study, we used a mouse model of S. haematobium infection that delivers parasite eggs directly to the host mouse bladder wall, and we examined the changes in the gene expression profile of the host and the parasite by RNA-sequencing. The results corroborated previous findings with respect to the hosts inflammatory responses against the parasite eggs, as well as revealed alterations in other immune response genes that deepen our understanding of the mechanisms involved in urogenital schistosomiasis pathogenesis.

molecular biology↗

bioRxiv2024

Comprehensive and accurate genome analysis at scale using DRAGEN accelerated algorithms

Research and medical genomics require comprehensive and scalable solutions to drive the discovery of novel disease targets, evolutionary drivers, and genetic markers with clinical significance. This necessitates a framework to identify all types of variants independent of their size (e.g., SNV/SV) or location (e.g., repeats). Here we present DRAGEN that utilizes novel methods based on multigenomes, hardware acceleration, and machine learning based variant detection to provide novel insights into individual genomes with [~]30min computation time (from raw reads to variant detection). DRAGEN outperforms all other state-of-the-art methods in speed and accuracy across all variant types (SNV, indel, STR, SV, CNV) and further incorporates specialized methods to obtain key insights in medically relevant genes (e.g., HLA, SMN, GBA). We showcase DRAGEN across 3,202 genomes and demonstrate its scalability, accuracy, and innovations to further advance the integration of comprehensive genomics for research and medical applications.

genomics↗

bioRxiv2023

M1-derived extracellular vesicles polarize recipient macrophages into M2 and alter skeletal muscle homeostasis in a hyper-glucose environment

BackgroundMacrophages release not only cytokines but also extracellular vesicles (EVs). EVs are small lipid-derived vesicles with virus-like properties transferring lipids, RNA and proteins between cells. Until now, the consequences of macrophage plasticity on the release and the composition of EVs have been poorly explored. In this study, we determined the impact of high-glucose (HG) concentrations on macrophage metabolism, and characterized their derived EV subpopulations. Finally, we determined whether HG-treated macrophage-derived EVs participate in immune responses and in metabolic alterations of skeletal muscle cells. MethodsTHP1-macrophages (M0) were treated with 15mM (MG15) or 30mM (MG30) glucose. M1 or M2 canonical markers, pro- and anti-inflammatory cytokines and lactate production were evaluated. Macrophage-derived EVs were characterized by TEM, flow cytometry, and 1H-Nuclear magnetic resonance spectroscopy for lipid composition. M0 macrophages or C2C12 muscle cells were used as recipients of MG15 and MG30-derived EVs. The lipid profiles of recipient cells were determined, as well as protein and mRNA levels of relevant genes for macrophage polarization or muscle metabolism. ResultsM0 released 2 populations of small and large EVs (sEVs, lEVs) with specific lipid profiles. Proportionally to the glucose concentration, glucose-treatment induced glycolysis in M0 macrophages which consequently shifted into a pro-inflammatory M1 phenotype, containing increased triacylglycerol and cholesterol content. Glucose also affected macrophage sphingolipid and phospholipid compositions. The lipid profile differences between sEVs and lEVs were abolished and represented the lipid profile alterations of MG15 and MG30 macrophages. Both sEVs and lEVs from M15 and M30 macrophages polarized M0 into anti-inflammatory M2, with increased contents of triacylglycerol and cholesterol. MG15 lEVs and sEVs induced insulin-induced AKT hyper-phosphorylation and accumulation of triacylglycerol in muscle cells, a state observed in pre-diabetes. Conversely, MG30 lEVs and sEVs induced insulin resistance in myotubes. ConclusionsAs inflammation involves first M1 macrophages, then the activation of M2 macrophages to attenuate inflammation, this study demonstrates that the dialog between macrophages through the EV route is an intrinsic part of the inflammatory response. In a hyperglycemic context, EV macrophages could participate in the development of muscle insulin-resistance and chronic inflammation.

cell biology↗

bioRxiv2023

Yerba mate (Ilex paraguariensis) genome provides new insights into convergent evolution of caffeine biosynthesis

Yerba mate (Ilex paraguariensis) is an economically important crop marketed for the elaboration of mate, the third-most widely consumed caffeine-containing infusion worldwide. Here we report the first genome assembly of this species, which has a total length of 1.06 Gb and contains 53,390 protein-coding genes. Comparative analyses revealed that the large yerba mate genome size is partly due to a whole-genome duplication (Ip-) during the early evolutionary history of Ilex, in addition to the hexaploidization event ({gamma}) shared by core eudicots. Characterization of the genome allowed us to clone the genes encoding methyltransferase enzymes that catalyse multiple reactions required for caffeine production. To our surprise, this species has converged upon a different biochemical pathway compared to that of its relatives, coffee and tea. In order to gain insight into the structural basis for the convergent enzyme activities, we obtained a crystal structure for the terminal enzyme in the pathway that forms caffeine. The structure reveals that convergent solutions have evolved for substrate positioning because different amino acid residues facilitate a different substrate orientation such that efficient methylation occurs in the independently evolved enzymes in yerba mate and coffee. While our results show phylogenomic constraint limits the genes coopted for convergence of caffeine biosynthesis, the x-ray diffraction data suggests structural constraints are minimal for the convergent evolution of individual reactions.

plant biology↗

bioRxiv2023

Adaptive introgression of a visual preference gene

Visual preferences are important drivers of mate choice and sexual selection, but little is known of how they evolve at the genetic level. Here we take advantage of the diversity of bright warning patterns displayed by Heliconius butterflies, which are also used during mate choice. We show that two Heliconius species have evolved the same visual mating preferences for females with red patterns by exchanging genetic material through hybridization. Extensive behavioral experiments reveal that male preferences are associated with a genomic region of increased admixture between these two species. Variation in neural expression of regucalcin1, located within this introgressed region, correlates with visual preference across populations, and disruption of regucalcin1 with CRISPR/Cas9 impairs courtship towards conspecific females, proving a direct link between gene and behavior. Our results support a role for hybridization during behavioral evolution, and show how visually-guided behaviors contributing to adaptation and speciation are encoded within the genome.

evolutionary biology↗

bioRxiv2023

Identification of allele-specific KIV-2 repeats and impact on Lp(a) measurements for cardiovascular disease risk

The abundance of Lp(a) protein holds significant implications for the risk of cardiovascular disease (CVD), which is directly impacted by the copy number (CN) of KIV-2, a 5.5 kbp sub-region. KIV-2 is highly polymorphic in the population and accurate analysis is challenging. In this study, we present the DRAGEN KIV-2 CN caller, which utilizes short reads. Data across 166 WGS show that the caller has high accuracy, compared to optical mapping and can further phase [~]50% of the samples. We compared KIV-2 CN numbers to 24 previously postulated KIV-2 relevant SNVs, revealing that many are ineffective predictors of KIV-2 copy number. Population studies, including USA-based cohorts, showed distinct KIV-2 CN, distributions for European-, African-, and Hispanic-American populations and further underscored the limitations of SNV predictors. We demonstrate that the CN estimates correlate significantly with the available Lp(a) protein levels and that phasing is highly important.

genomics↗

bioRxiv2023

Frizzled2 receives the WntA morphogen during butterfly wing pattern formation

Butterfly color patterns provide visible and biodiverse phenotypic readouts of the patterning processes that occur in a developing epithelium. While the secreted ligand WntA was shown to instruct the color pattern formation in butterflies, its modes of reception and signal transduction remain elusive. Butterfly genomes encode four homologues of the Frizzled-family of Wnt receptors. Here we show that CRISPR mosaic knock-outs of frizzled2 (fz2) phenocopy the color pattern effects of WntA loss-of-function in multiple nymphalids. While WntA mosaic clones result in intermediate patterns of reduced size, consistently with a morphogen function, fz2 clones are cell-autonomous. Shifts in pupal expression in WntA crispants show that WntA and fz2 are under positive and negative feedback, respectively. Fz1 is required for Wnt-independent planar cell polarity (PCP) in the wing epithelium. Fz3 and Fz4 show phenotypes consistent with Wnt competitive-antagonist functions in vein formation (Fz3 and Fz4), wing margin specification (Fz3), and color patterning in the Discalis and Marginal Band Systems (Fz4). Overall, these data show that the WntA/Frizzled2 morphogen-receptor pair forms a signaling axis that instructs butterfly color patterning, and shed light on the functional diversity of insect Frizzled receptors.

developmental biology↗