Biology subjects

Kaplan, O. I.

Publications and source records attributed to Kaplan, O. I..

8 recordsLinked to original sources

bioRxiv2025

Expanded Catalog of Gold Standard Ciliary Gene List: Integration of Novel Ciliary Genes into the Ciliome

Ciliopathies are rare genetic disorders caused by mutations in genes that encode proteins critical for cilium assembly and function, affecting various subcompartments, including the axoneme, ciliary membrane, transition zone, and basal body. These mutations lead to diverse developmental and degenerative conditions across multiple organ systems. The 2021 ciliary Gold Standard gene list (688 genes) provides a foundational resource, but many ciliary genes remain unidentified or unclassified. We developed CiliaHub (https://theciliahub.github.io/), a scalable and user-friendly platform that integrates automated literature mining with expert manual curation to identify human ciliary genes. The approach combines gene names, synonyms, and targeted keywords (e.g., cilia, flagella, basal body) to extract gene-specific mentions from published studies, followed by rigorous validation through independent expert review. CiliaHub identified 2011 experimentally supported ciliary genes, including 1323 not previously listed in curated databases. Notably, some of these genes are co-found in both cilia and other organelles, such as mitochondria and lysosomes. Cross-referencing with mouse knockout model data revealed strong associations with ciliopathy-relevant phenotypes, such as infertility in Cep70 and renal defects or hearing abnormalities in genes like TMEM145. This work also provides novel ciliopathy candidate genes for further investigation. CiliaHub provides a broad platform for fundamental and translational research, enabling the effective prioritization of candidate disease genes, including recently identified ciliopathy candidates.

bioinformatics↗

bioRxiv2023

CilioGenics: an integrated method and database for predicting novel ciliary genes

Discovering the entire list of human ciliary genes would help in the diagnosis of cilia-related human disorders known as ciliopathy, but at present the genetic diagnosis of many ciliopathies (over 30%) is far from complete (Bachmann-Gagescu et al., 2015; Knopp et al., 2015; Paff et al., 2018). In a theory, many independent approaches may uncover the whole list of ciliary genes, but 30% of the genes on the ciliary gene list are still ciliary candidate genes (van Dam et al., 2019; Vasquez et al., 2021). All of these cutting-edge techniques, however, have relied on a different single strategy to discover ciliary candidate genes. Because different methodologies demonstrated distinct capabilities with varying quality, categorizing the ciliary candidate genes in the ciliary gene list without further evidence has been difficult. Here, we present a method for predicting ciliary capacity of each human gene that incorporates diverse methodologies (single-cell RNA sequencing, protein-protein interactions (PPIs), comparative genomics, transcription factor (TF)-network analysis, and text mining). By integrating multiple approaches, we reveal previously undiscovered ciliary genes. Our method, CilioGenics, outperforms other approaches that are dependent on a single method. Our top 500 gene list contains 256 new candidate ciliary genes, with 31 experimentally validated. Our work suggests that combining several techniques can give useful evidence for predicting the ciliary capability of all human genes.

bioinformatics↗

bioRxiv2023

Matching Variants for functional characterization of genetic variants

Rapid and low-cost sequencing, as well as computer analysis, have facilitated the diagnosis of many genetic diseases, resulting in a substantial rise in the number of disease-associated genes. However, genetic diagnosis of many disorders remains problematic due to the lack of interpretation for many genetic variants, especially missenses, the infeasibility of high-throughput experiments on mammals, and the shortcomings of computational prediction technologies. Additionally, the available mutant databases are not well-utilized. Toward this end, we used Caenorhabditis elegans mutant resources to delineate the functions of eight missense variants (V444I, V517D, E610K, L732F, E817K, H873P, R1105K, and G1205E) and two stop codons (W937stop and Q1434stop), including several matching variants (MatchVar) with human in ciliopathy associated IFT-140 (also called CHE-11)//IFT140 (intraflagellar transport protein 140). Moreover, MatchVars carrying C. elegans mutants, including IFT-140(G680S) and IFT-140(P702A) for the human (G704S) (dbSNP: rs150745099) and P726A (dbSNP: rs1057518064 and a conflicting variation) were created using CRISPR/Cas9. IFT140 is a key component of IFT complex A (IFT-A), which is involved in the retrograde transport of IFT along cilia and the entrance of G protein-coupled receptors (GPCRs) into cilia. Functional analysis of all ten variants revealed that P702A and W937stop, but not others phenocopied the ciliary phenotypes (short cilia, IFT accumulations, mislocalization of membrane proteins, and cilia entry of non-ciliary proteins) of the IFT-140 null mutant, indicating that both P702A and W937stop are phenotypic in C. elegans. Our functional data offered experimental support for interpreting human variants, by using ready-to-use mutants carrying MatchVars and generating MatchVars with CRISPR/Cas9.

genetics↗

bioRxiv2022

CiliaMiner: an integrated database for Ciliopathy Genes and Ciliopathies

Cilia are found in eukaryotic species ranging from single-celled organisms, such as Chlamydomonas reinhardtii, to humans, but not in plants. The ability to respond to repellents and/or attractants, regulate cell proliferation and differentiation, and provide cellular mobility are just a few examples of how crucial cilia are to cells and organisms. Over 30 distinct rare disorders generally known as ciliopathy are caused by abnormalities or functional impairments in cilia and cilia-related compartments. Because of the complexity of ciliopathies and the rising number of ciliopathies and ciliopathy genes, a ciliopathy-oriented and up-to-date database is required. In addition, disorders not yet known as ciliopathy but have genes that produce cilia localizing proteins have yet to be classified. Here we present CiliaMiner, a manually curated ciliopathy database that includes ciliopathy lists collected from articles and databases. Analysis reveals that there are 55 distinct disorders likely related to ciliopathy, with over 4000 clinical manifestations. Based on comparative symptom analysis and subcellular localization data, diseases are classified as primary, secondary, or atypical ciliopathies. CiliaMiner provides easy access to all of these diseases and disease genes, as well as clinical features and gene-specific clinical features, as well as subcellular localization of each protein. Additionally, the orthologs of disease genes are also provided for mice, zebrafish, Xenopus, Drosophila, and C. elegans. CiliaMiner (https://kaplanlab.shinyapps.io/ciliaminer) aims to serve the cilia community with its comprehensive content, and highly enriched interactive heatmaps, and will be continually updated.

bioinformatics↗

bioRxiv2022

Development of Polymer/DNA Polyplexes System for Nucleic Acid Delivery to the Multicellular Organism C. elegans

Gene therapy studies have been of great importance in the elimination of genetic diseases, and the capability of the CRISPR/Cas9 genome editing technique to correct genetic defects has shown great promise. As DNA-based Cas9 nuclease delivery is preferable because of its low cost and higher stability, effective vector-based CRISPR/Cas9 administration is urgently needed. Here, we used the multicellular organism Caenorhabditis elegans to optimize the polymer-mediated DNA delivery system to generate mutants with CRISPR/Cas9. Toward this end, the cationically quaternized polymer of POEGMA-b-P4VP (POEGMA-b-QP4VP) as a carrier of CRISPR/Cas9 components was first synthesized, followed by the formation of plasmid DNA-polymer complex called polyplexes. 1H NMR, Zeta-Sizer, Scanning Electron Microscopy (SEM) analysis, and gel retardation experiments confirmed the polyplexes formation, including pRF4 (Roller) and sgRNA dpy-10, which were then incubated with C. elegans. The polymer-mediated delivery system facilitated the generation of transgenic Roller animals and heritable Dumpy mutants with CRISPR/Cas9. Our study for the first time demonstrated optimized administration of CRISPR/Cas 9 components to C. elegans.

genetics↗

bioRxiv2021

WDR31 is a novel ciliopathy protein displaying functional redundancy with GTPase-activating proteins ELMOD and RP2 in recruiting BBSome to cilium

The correct intraflagellar transport (IFT) assembly at the ciliary base and the IFT turnaround at the ciliary tip are key for the IFT to perform its function, but we still have poor understanding about how these processes are regulated. Here, we identify WDR31 as a new ciliary protein, and analysis from zebrafish and Caenorhabditis elegans reveals the role of WDR31 in regulating the cilia morphology. We find that loss of WDR-31 together with RP-2 and ELMD-1 (the sole ortholog ELMOD1-3) results in ciliary accumulations of IFT Complex B components and KIF17 kinesin, with fewer IFT/BBSome particles traveling along cilia in both anterograde and retrograde directions, suggesting that the IFT/BBSome entry into cilia and exit from cilia are impacted. Furthermore, anterograde IFT in the middle segment travel at increased speed in wdr-31;rpi-2;elmd-1. Remarkably, a non-ciliary protein leaks into cilia of wdr-31;rpi-2;elmd-1 possible due to IFT defects. This work reveals WDR31-RP-2-ELMD-1 as IFT and BBSome trafficking regulators.

genetics↗

bioRxiv2021

MSABrowser: dynamic and fast visualization of sequence alignments, variations, and annotations

Sequence alignment is an excellent way to visualize the similarities and differences between DNA, RNA, or protein sequences, yet it is currently difficult to jointly view sequence alignment data with genetic variations, modifications such as post-translational modifications, and annotations (i.e. protein domains). Here, we develop the MSABrowser tool that makes it easy to co-visualize genetic variations, modifications, and annotations on the respective positions of amino acids or nucleotides in pairwise or multiple sequence alignments. MSABrowser is developed entirely in JavaScript and works on any modern web browser at any platform, including Linux, Mac OS X, and Windows systems without any installation. MSABrowser is also freely available for the benefit of the scientific community. Availability and implementationMSABrowser is released as open-source and web-based software under GNU General Public License, version 3.0 (GPLv3). The visualizer, documentation, all source codes, and examples are available at http://thekaplanlab.github.io/ and GitHub repository https://github.com/thekaplanlab/msabrowser. Supplementary informationSupplementary data are available online.

bioinformatics↗

bioRxiv2021

ConVarT: a search tool for orthologous variants: A method and server for functional inference of human genetic variants

The availability of genetic variants, together with phenotypic annotations from model organisms, facilitates comparing these variants with equivalent variants in humans. However, existing databases and search tools do not make it easy to scan for equivalent variants, namely "matching variants" (MatchVars) between humans and other organisms. Therefore, we developed an integrated search engine called ConVarT (http://www.convart.org/) for matching variants between humans, mice, and C. elegans. ConVarT incorporates annotations (including phenotypic and pathogenic) into variants, and these previously unexploited phenotypic MatchVars from mice and C. elegans can give clues about the functional consequence of human genetic variants. Our analysis shows that many phenotypic variants in different genes from mice and C. elegans, so far, have no counterparts in humans, and thus, can be useful resources when evaluating a relationship between a new human mutation and a disease.

genetics↗