Biology subjects

Chatuverdi, P.

Publications and source records attributed to Chatuverdi, P..

4 recordsLinked to original sources

bioRxiv2021

ELeFHAnt: A supervised machine learning approach for label harmonization and annotation of single cell RNA-seq data

Annotation of single cells has become an important step in the single cell analysis framework. With advances in sequencing technology thousands to millions of cells can be processed to understand the intricacies of the biological system in question. Annotation through manual curation of markers based on a priori knowledge is cumbersome given this exponential growth. There are currently ~200 computational tools available to help researchers automatically annotate single cells using supervised/unsupervised machine learning, cell type markers, or tissue-based markers from bulk RNA-seq. But with the expansion of publicly available data there is also a need for a tool which can help integrate multiple references into a unified atlas and understand how annotations between datasets compare. Here we present ELeFHAnt: Ensemble learning for harmonization and annotation of single cells. ELeFHAnt is an easy-to-use R package that employs support vector machine and random forest algorithms together to perform three main functions: 1) CelltypeAnnotation 2) LabelHarmonization 3) DeduceRelationship. CelltypeAnnotation is a function to annotate cells in a query Seurat object using a reference Seurat object with annotated cell types. LabelHarmonization can be utilized to integrate multiple cell atlases (references) into a unified cellular atlas with harmonized cell types. Finally, DeduceRelationship is a function that compares cell types between two scRNA-seq datasets. ELeFHAnt can be accessed from GitHub at https://github.com/praneet1988/ELeFHAnt.

bioinformatics↗

bioRxiv2021

TBX5 drives Aldh1a2 expression to regulate a RA-Hedgehog-Wnt gene regulatory network coordinating cardiopulmonary development

The gene regulatory networks that coordinate the development of the cardiac and pulmonary systems are essential for terrestrial life but poorly understood. The T-box transcription factor Tbx5 is critical for both pulmonary specification and heart development, but how these activities are mechanistically integrated remains unclear. We show that Tbx5 regulates an evolutionarily conserved retinoic acid (RA)-Hedgehog-Wnt signaling cascade coordinating cardiopulmonary development. We demonstrate that Tbx5 directly maintains expression of the RA-synthesizing enzyme Aldh1a2 in the foregut lateral plate mesoderm via an intronic enhancer that is evolutionarily conserved among terrestrial vertebrates. Tbx5 promotes posterior second heart field identity in a positive feedback loop with RA, antagonizing a Fgf8-Cyp regulatory module and restricting FGF activity to the anterior. Tbx5/Aldh1a2-dependent RA signaling also directly activates Shh transcription in the adjacent foregut endoderm through the conserved MACS1 enhancer. Epithelial Hedgehog then signals back to the mesoderm, where together with Tbx5 it activates expression of Wnt2/2b that ultimately induce pulmonary fate in the foregut endoderm. These results provide mechanistic insight into the interrelationship between heart and lung development informing cardiopulmonary evolution and birth defects. KEY FINDINGSO_LITbx5 regulates second heart field patterning and pulmonary development via retinoic acid (RA) and Hedgehog (Hh) signaling. C_LIO_LITbx5 directly maintains transcription of the RA-synthesizing enzyme Aldh1a2 in the posterior second heart field mesoderm via an evolutionarily conserved intronic enhancer. C_LIO_LIDownstream of Tbx5, RA directly promotes Shh transcription through the evolutionarily conserved MACS1 endoderm enhancer. C_LIO_LIDownstream of Tbx5, RA suppresses FGF signaling to pattern the second heart field while promoting a Hedgehog-Wnt2/2b signaling cascade that induces pulmonary fate. C_LI SUMMARY STATEMENTTbx5-dependent Retinoic Acid signaling regulates an evolutionarily conserved gene regulatory network that coordinates cardiac and pulmonary development.

developmental biology↗

bioRxiv2020

Gli3 utilizes Hand2 to synergistically regulate tissue-specific transcriptional networks

Despite a common understanding that Gli TFs are utilized to reiterate a Hh morphogen gradient, genetic analyses suggest craniofacial development does not completely fit this paradigm. We demonstrated that rather than being driven by a Hh threshold, robust Gli3 transcriptional activity during skeletal and glossal development required interaction with the bHLH TF Hand2. Not only did genetic and expression data support a co-factorial relationship, but genomic analysis further revealed that Gli3 and Hand2 were enriched at regulatory elements for genes essential for mandibular patterning and development. Interestingly, motif analysis at sites co-occupied by Gli3 and Hand2 uncovered mandibular-specific, low-affinity, divergent Gli binding motifs (dGBMs). Functional validation revealed these dGBMs conveyed synergistic activation of Gli targets essential for mandibular patterning and development. In summary, this work elucidates a novel, sequence-dependent mechanism for Gli transcriptional activity within the craniofacial complex that is independent of a graded Hh signal.

developmental biology↗

bioRxiv2019

Nubp2 is required for cranial neural crest survival in the mouse.

The N-ethyl-N-nitrosourea (ENU) forward genetic screen is a useful tool for the unbiased discovery of novel mechanisms regulating developmental processes. We recovered the dorothy mutation in such a screen designed to recover recessive mutations affecting craniofacial development in the mouse. Dorothy embryos die prenatally and exhibit many striking phenotypes commonly associated with ciliopathies, including a severe midfacial clefting phenotype. We used exome sequencing to discover a missense mutation in Nucleotide Binding Protein 2 (Nubp2) to be causative. This finding was confirmed with a complementation analysis between the dorothy allele and a Nubp2 null allele (Nubp2Null). We demonstrate that Nubp2 is indispensable for embryogenesis. NUBP2 is implicated in both the Cytosolic Iron/Sulfur cluster Assembly (CIA) pathway and in the negative regulation of ciliogenesis. Conditional ablation of Nubp2 in the neural crest lineage with Wnt1-cre recapitulates the dorothy craniofacial phenotype. Using this model, we found that the proportion of ciliated cells in the craniofacial mesenchyme was unchanged, and that markers of the Shh, Fgf, and Bmp signaling pathways are unaltered. Finally, we show that the phenotype results from a marked increase in apoptosis within the craniofacial mesenchyme.\n\nSummary StatementAn ENU screen identifies a novel allele of Nubp2 which is then demonstrated to be required for cranial neural crest survival and proper midfacial development.

developmental biology↗