Biology subjects

Florea, L. D.

Publications and source records attributed to Florea, L. D..

10 recordsLinked to original sources

bioRxiv2026

SpliSync: Genomic language model-driven splice site correction of long RNA sequencing reads

Long RNA sequencing reads are rapidly replacing short reads in transcriptomic analyses, enabling full-length transcript sequencing and better identification of isoforms, alternative splicing events, and other transcript variants. However, their higher sequencing error rates can cause misalignments, especially at splice junctions, reducing the accuracy of transcript reconstruction and analysis. We developed SpliSync, a genomic language model-driven method for splice site correction that integrates a pre-trained genomic sequence model (HyenaDNA), alignment data, and a U-net architecture to predict splice sites at nucleotide resolution. SpliSync substantially improved the precision of RNA long-read alignments by 27%-194% across diverse datasets and consistently outperformed competing tools. As a preprocessing step, it increased alternative splicing detection accuracy by 26%-330%. In contrast, its benefit for transcript reconstruction was limited, likely due to the tools built-in correction mechanisms. The code was developed in Python using the PyTorch package, and is freely available at https://github.com/splicebox/SpliSync.

bioinformatics↗

bioRxiv2026

Autism associated Cntnap2 deletion disrupts vestibular sensory signaling and spatial cognition in mice

Autism spectrum disorder (ASD) is frequently accompanied by sensory and motor abnormalities, including impaired balance, postural control, and spatial orientation, that are often attributed largely to altered central circuitry. Emerging evidence, however, suggests that peripheral sensory dysfunction can also shape ASD related behavioral phenotypes. Here, we tested whether loss of the ASD associated gene Cntnap2/Caspr2 alters vestibular signaling in Cntnap2-/- mice. Developmental transcriptomic analysis showed that Cntnap2 is expressed in vestibular sensory organs and increases during the first postnatal month, coincident with vestibular pathway maturation. Vestibular sensory evoked potentials revealed reduced response amplitudes and prolonged latencies in Cntnap2-/- mice, indicating impaired peripheral afferent responses to transient linear acceleration. Cntnap2-/- mice also showed delayed contact righting, reduced ocular counter roll, and increased hindlimb slips and compensatory tail excursions during balance beam walking, whereas rotational vestibulo-ocular reflex gain and phase were preserved. These vestibular and balance abnormalities were accompanied by reduced novel arm preference in the Y maze and severe impairment of Barnes maze acquisition, consistent with impaired spatial learning. Together, these findings identify Cntnap2/Caspr2 as a regulator of vestibular sensory signaling and support a model in which disrupted peripheral vestibular input, likely acting together with central effects of Cntnap2 loss, contributes to sensorimotor and spatial cognitive phenotypes relevant to ASD.

neuroscience↗

bioRxiv2024

Predicting Alu exonization in the human genome with a deep learning model

Alu exonization, or the recruitment of intronic Alu elements into gene sequences, has contributed to functional diversification; however, its extent and the ways in which it influences gene regulation are not fully understood. We developed an unbiased approach to predict Alu exonization events from genomic sequences implemented in a deep learning model, eXAlu, that overcomes the limitations of tissue or condition specificity and the computational burden of RNA-seq analysis. The model captures previously reported characteristics of exonized Alu sequences and can predict sequence elements important for Alu exonization. Using eXAlu, we estimate the number of Alu elements in the human genome undergoing exonization to be between 55-110K, 11-21 fold more than represented in the GENCODE gene database. Using RT-PCR we were able to validate selected predicted Alu exonization events, supporting the accuracy of our method. Lastly, we highlight a potential application of our method to identify polymorphic Alu insertion exonizations in individuals and in the population from whole genome sequencing data.

bioinformatics↗

bioRxiv2023

Regulation of interferon signaling by transposon exonization

SummaryInnate immune signaling is essential for clearing pathogens and damaged cells, and must be tightly regulated to avoid excessive inflammation or autoimmunity. Here, we found that the alternative splicing of exons derived from transposable elements is a key mechanism controlling immune signaling in human cells. By analyzing long-read transcriptome datasets, we identified numerous transposon exonization events predicted to generate functional protein variants of immune genes, including the type I interferon receptor IFNAR2. We demonstrated that the transposon-derived isoform of IFNAR2 is more highly expressed than the canonical isoform in almost all tissues, and functions as a decoy receptor that potently inhibits interferon signaling including in cells infected with SARS-CoV-2. Our findings uncover a primate-specific axis controlling interferon signaling and show how a transposon exonization event can be co-opted for immune regulation.

genomics↗

bioRxiv2022

Overexpression screen of chromosome 21 genes reveals modulators of Sonic hedgehog signaling relevant to Down syndrome

Dysregulation of Sonic hedgehog (SHH) signaling may contribute to multiple Down syndrome-associated phenotypes, including cerebellar hypoplasia, congenital heart defects, craniofacial and skeletal dysmorphologies, and Hirschsprung disease. Granule cell precursors isolated from the developing cerebellum of Ts65Dn mice are less responsive to the mitogenic effects of SHH than euploid cells, and a single postnatal dose of the SHH pathway agonist SAG rescues cerebellar morphology and performance on learning and memory tasks in Ts65Dn mice. SAG treatment also normalizes expression levels of OLIG2 in neural progenitor cells derived from human trisomy 21 iPSCs. However, despite evidence that activating SHH signaling can ameliorate some Down syndrome-associated phenotypes, chromosome 21 does not encode any components of the canonical SHH pathway. Here, we screened 163 chromosome 21 cDNAs in a series of SHH-responsive cell lines to identify chromosome 21 genes that modulate SHH signaling. We confirmed overexpression of trisomic candidate genes using RNA-seq in Ts65Dn and TcMAC21 cerebellum. Our study indicates that some chromosome 21 genes, including DYRK1A, upregulate SHH signaling while others, such as HMGN1 and MIS18A, inhibit SHH signaling. Overexpression of genes involved in chromatin structure and mitosis, but not genes previously implicated in ciliogenesis, regulate the SHH pathway. Our data suggest that cerebellar hypoplasia and other phenotypes related to aberrant SHH signaling arise from the net effect of trisomy for multiple chromosome 21 genes rather than the overexpression of a single trisomic gene. Identifying which chromosome 21 genes modulate SHH signaling may suggest new therapeutic avenues for ameliorating Down syndrome phenotypes. One Sentence SummaryMultiple chromosome 21 genes modulate Sonic hedgehog signaling, which is dysregulated in Down syndrome.

genetics↗

bioRxiv2021

Somatic reversion impacts MDS/AML evolution in the short telomere syndromes

Inherited mutations in telomerase and other telomere maintenance genes manifest in the premature aging short telomere syndromes. Myelodysplastic syndromes and acute myeloid leukemia (MDS/AML) account for 75% of associated malignancies, but how these cancers overcome the germline telomere defect is unknown. We used targeted ultra-deep sequencing to detect candidate somatic reversion mutations hypothesizing they may promote MDS/AML evolution. While no controls carried somatic mutations in telomere maintenance genes (0 of 28), 29% of adults with germline telomere maintenance defects carried at least one (16 of 56, P<0.001). In addition to TERT promoter mutations which were present in 19%, we identified POT1 and TERF2IP mutations in 13%. POT1 mutations impaired telomere binding and in some cases were identical to those found in familial melanoma associated with longer telomere length. Exclusively in patients with germline defects in telomerase RNA (TR), we identified somatic mutations in nuclear RNA exosome genes, RBM7, SKIV2L2, and DIS3, where loss-of-function upregulates mature TR levels. Paradoxically, somatic reversion events were more prevalent in patients who were MDS/AML-free (P=0.01, RR 5.0, 95% CI 1.4-18.9), and no MDS/AML patient had more than one mutant clone (P=0.048). Our data identify diverse somatic adaptive mechanisms in the short telomere syndromes, and raise the possibility that their presence alleviates the telomere crisis that promotes transformation to MDS/AML.

cancer biology↗

bioRxiv2020

Comprehensive and scalable quantification of splicing differences with MntJULiP

Alternative splicing of mRNA is an essential gene regulatory mechanism with important roles in development and disease. We present MntJULiP, a method for comprehensive and accurate quantification of splicing differences between two or more conditions. MntJULiP implements novel Dirichlet-multinomial and zero-inflated negative binomial models within a Bayesian framework to detect both changes in splicing ratios and in absolute splicing levels of introns with high accuracy, and can find classes of variation overlooked by reference tools. Additionally, a mixture model allows multiple conditions to be compared simultaneously. Highly scalable, it processed hundreds of GTEx samples in <1 hour to reveal splicing constituents of tissue differentiation.

bioinformatics↗

bioRxiv2020

Excessive O-GlcNAcylation causes heart failure and sudden death

BackgroundHeart failure is a leading cause of death worldwide and is associated with the rising prevalence of obesity, hypertension and diabetes. O-GlcNAcylation, a post-translational modification of intracellular proteins, serves as a potent transducer of cellular stress. Failing myocardium is marked by increased O-GlcNAcylation, but it is unknown if excessive O-GlcNAcylation contributes to cardiomyopathy and heart failure. The total levels of O-GlcNAcylation are determined by nutrient and metabolic flux, in addition to the net activity of two enzymes, O-GlcNAc transferase (OGT) and O-GlcNAcase (OGA). MethodsWe developed two new transgenic mouse models with myocardial overexpression of OGT and OGA to control O-GlcNAclyation independent of pathological stress. ResultsWe found that OGT transgenic hearts showed increased O-GlcNAcylation, and developed severe dilated cardiomyopathy, ventricular arrhythmias and premature death. In contrast, OGA transgenic hearts had O-GlcNAcylation and cardiac function similar to wild type littermate controls. However, OGA trangenic hearts were resistant to pathological stress induced by pressure overload and had attenuated myocardial O-GlcNAcylation levels, decreased pathological hypertrophy and improved systolic function. Interbreeding OGT with OGA transgenic mice rescued cardiomyopathy and premature death despite persistant elevation of myocardial OGT. Transcriptomic and functional studies revealed disrupted mitochondrial energetics with impairment of complex I activity in hearts from OGT transgenic mice. Complex I activity was rescued by OGA transgenic interbreeding, suggesting an important role for mitochondrial complex I in O-GlcNAc mediated cardiac pathology. ConclusionsOur data provide evidence that excessive O-GlcNAcylation causes cardiomyopathy, at least in part, due to defective energetics. Enhanced OGA activity is well tolerated and attenuation of O-GlcNAcylation is an effective therapy against pressure overload induced heart failure. Attenuation of excessive O-GlcNAcylation may represent a novel therapeutic approach for cardiomyopathy. Clinical PerspectiveO_ST_ABSWhat is new?C_ST_ABSO_LICardiomyopathy from diverse causes is marked by increased O-GlcNAcylation. Here we provide new genetic mouse models to control myocardial O-GlcNAcylation independent of pathological stress. C_LIO_LIGenetically increased myocardial O-GlcNAcylation causes progressive dilated cardiomyopathy and premature death, while genetic reduction of myocardial O-GlcNAcylation is protective against pathological hypertrophy caused by transaortic banding. C_LIO_LIExcessive myocardial O-GlcNAcylation decreases activity and expression of mitochondrial complex I. C_LI What are the clinical implications?O_LIIncreased myocardial O-GlcNAcylation has been shown to be associated with a diverse range of clinical heart failure including aortic stenosis, hypertension, ischemia and diabetes. C_LIO_LIUsing novel genetic mouse models we have provided new proof of concept data that excessive O-GlcNAcylation is sufficient to cause cardiomyopathy. C_LIO_LIWe have shown myocardial over-expression of O-GlcNAcase, an enzyme that reverses O-GlcNAcylation, is well tolerated at baseline, and improves myocardial responses to pathological stress. C_LIO_LIOur findings suggest reversing excessive myocardial O-GlcNAcylation could benefit diverse etiologies of heart failure. C_LI

molecular biology↗

bioRxiv2019

A non-mosaic humanized mouse model of Down syndrome, trisomy of the long arm of human chromosome 21 in mouse chromosome background

Down syndrome (DS) is a complex human condition, and animal models trisomic for human chromosome 21 (HSA21) genes or orthologs provide insights into better understanding and treating DS. However, HSA21 orthologs are distributed into three mouse chromosomes, preventing us from generating mouse models trisomy of a complete set of HSA21 orthologs. The only existing humanized mouse DS model, Tc1, carries a HSA21 with over 20% of protein coding genes (PCGs) disrupted. More importantly, due to the human centromere, Tc1 is mosaic (a mix of euploid and trisomic cells), which makes every mouse unique and compromises interpretation of results. Here, we used mouse artificial chromosome (MAC) technology to "clone" the 34 MB long arm of HSA21 (HSA21q). Through multiple steps of microcell-mediated chromosome transfer we created a new humanized DS mouse model, Tc(HSA21q;MAC)1Yakaz ("TcMAC21"). Constitutive EGFP expression from the transchromosome and fluorescent in situ hybridization validate that TcMAC21, containing a hybrid chromosome of HSA21q and mouse centromere, is not mosaic. Whole genome sequencing shows that TcMAC21 contains a nearly complete copy of HSA21q with 93% of intact PCGs, while RNA-seq and additional mRNA/protein expression analyses confirm that PCGs are transcribed and regulated. A battery of tests show that TcMAC21 recapitulates many DS phenotypes including morphological anomalies in heart, craniofacial skeleton and brain, pathologies at molecular and cellular level, and impairments in learning, memory and synaptic plasticity. TcMAC21 is the most complete mouse model of DS extant and has potential for supporting a wide range of basic and preclinical research. Significance StatementIn the last 25 years, mouse models of trisomy 21 have supported research into Down syndrome, from defining the basis for developmental effects up to support for clinical trials. However, existing models have significant shortfalls, especially for preclinical studies. These deficiencies include incomplete or inappropriate representation of trisomic genes, absence of an extra chromosome, and mosaicism. Using cutting edge technologies we produced a mouse artificial chromosome containing the entire 34Mb long arm of human chromosome 21 and, with assisted reproductive technologies, established it in the germ line of mice. This trisomic mouse manifests developmental and functional features of Down syndrome, including hippocampal-based learning and memory deficits. This is the most complete model of Down syndrome produced to date.

genetics↗

bioRxiv2019

CaMKII oxidation is a performance/disease trade-off in vertebrate evolution

Reactive oxygen species (ROS) contribute to health and disease. CaMKII is a widely expressed enzyme whose activation by oxidation of regulatory domain methionines (ox-CaMKII) contributes to cardiovascular disease, asthma, and cancer. Here we integrate comparative genomic and experimental data to show that CaMKII activation by ROS arose more than half-a-billion years ago on the vertebrate stem lineage where it constituted a bridge between ROS and increased intracellular Ca2+ release, exercise responsive gene transcription, and improved performance in skeletal muscle. These enhancements to fight-or-flight physiology were likely key in facilitating a well-evidenced shift in the behavioural ecology of our immediate chordate ancestors, and, in turn, the evolutionary success of vertebrates. Still, the ox-CaMKII innovation for augmenting performance must be considered a critical evolutionary trade-off, as it rendered us more susceptible to common and often fatal diseases linked to excessive ROS.

evolutionary biology↗