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Biology subjects

Pearson, C. G.

Publications and source records attributed to Pearson, C. G..

At least 19 recordsLinked to original sources

Aberrant PCM1 accumulation in Trisomy 21 mislocalizes E3 ligases, delaying primary ciliogenesis

Primary cilia are microtubule-based extracellular signaling structures essential for development and tissue homeostasis, and their defects can cause ciliopathies. Trisomy 21, the cause of Down syndrome, also disrupts cilia formation and function. Here we show that Pericentrin (PCNT), a chromosome 21 resident gene whose protein is elevated in Trisomy 21, impairs primary ciliogenesis by delaying mother centriole uncapping. Elevated PCNT forms pericentrosomal assemblies that promote the accumulation of PCM1 in the pericentrosomal compartment. PCM1 binds and localizes the CP110 E3 ubiquitin ligases HERC2 and MIB1 to the centrosome, so mislocalizing PCM1 depletes these ligases from the centrosome, lowering CP110 ubiquitination and delaying uncapping. Reducing PCNT rescues these defects, whereas elevating PCM1 phenocopies them, establishing PCM1 accumulation as a critical mediator of uncapping. These findings reveal how a dosage-sensitive chromosome 21 gene disrupts ciliogenesis and show that centrosome function depends not only on PCM protein composition but on the spatial partitioning of proteins between the centrosome and pericentrosomal compartments.

cell biology↗

Tet Trim-Away: A conditional rapid protein degradation system for Tetrahymena thermophila

Tetrahymena thermophila is a ciliated protist that has played pivotal roles in biological discovery. Functional studies of Tetrahymena proteins have largely relied on gene knockouts. Because protein depletion upon knockout typically spans multiple cell cycles, compensatory mechanisms can confound phenotypic interpretation. To instead enable rapid and acute protein depletion, we modified and adapted the Trim-Away system for use in Tetrahymena (Tet Trim-Away). Trim-Away is based on the E3 ubiquitin ligase, TRIM21, that binds to antibody-bound proteins and targets them for proteasome mediated degradation. Here, Trim-Away was modified with a fusion of the N-terminal RBCC (RING, B-box, coiled-coil) domains of TRIM21 with an -mCherry (mCh) nanobody sequence that recognizes endogenously tagged mCh proteins of interest (NbmCh). Expression of the RBCC:NbmCh degron, which is controlled by an inducible promotor, promotes rapid target protein depletion within 30 minutes and can be sustained for weeks. Tet Trim-Away is reversible, functions against targets in multiple cellular compartments, and produces loss-of-function phenotypes in Tetrahymena cells.

cell biology↗

Centriolar satellites regulate CEP350 mRNA localization and centrosome amplification

Messenger RNAs (mRNAs) accumulate at centrosomes in mitosis and interphase, yet the mechanisms governing their localization and the functional significance of centrosomal localization remain poorly understood. Here, we investigate the regulation and function of the centrosome-localized mRNA, CEP350. We find that CEP350 mRNA localizes to centrosomes during S phase via the centriolar satellite protein CEP131 and the RNA binding protein (RBP) Unkempt (UNK), in a microtubule (MT)-dependent manner. CEP131 and UNK stabilize CEP350 mRNA to maintain CEP350 mRNA steady-state levels. Furthermore, CEP131 and UNK promote normal CEP350 protein levels at centrosomes. CEP350 is required for PLK4-induced centriole overduplication but is less important for canonical centriole duplication. Moreover, CEP131, UNK, and CEP350 are important for centrosome amplification in triple-negative breast cancer cells. Together, these findings reveal a centriolar satellite-RBP pathway regulating CEP350 mRNA localization to centrosomes. Significance StatementO_LImRNAs encoding centrosomal proteins localize to centrosomes during interphase, though the mechanism and functional significance of this localization remains unclear. C_LIO_LIThis study finds that the centriolar satellite proteins CEP131 and UNK regulate centrosomal localization of CEP350 mRNA and protein during S phase. C_LIO_LICEP131, UNK, and CEP350 are required for centrosome amplification in triple negative breast cancer cells - a dependency that identifies them as potential therapeutic targets. C_LI

cell biology↗

Trisomy 21 alters ciliary localization of Sonic Hedgehog signaling proteins

Trisomy 21 (T21), the cause of Down syndrome, impairs cilia-dependent Sonic Hedgehog (SHH) signaling. We investigated how T21 affects SHH signaling at the primary cilium and found that Smoothened (SMO) protein - the main effector of SHH signaling - is diminished in T21 primary cilia. Specifically, T21 cells exhibit both decreased SMO localization to cilia and reduced ciliary SMO phosphorylation (pSMO). Our findings suggest that reduced ciliary SMO in T21 results from defective entry into or maintenance in the cilium rather than impaired transport to centrosomes. Moreover, unlike the ciliogenesis defects observed in T21, the SMO defect does not appear to be associated with increased PCNT protein abundance. We also found that GPR161 (a negative SHH regulator), exhibits increased ciliary localization in T21. Notably, prolonged serum depletion to promote primary cilia maturation equalizes ciliary levels of SMO and GPR161 between T21 cells and D21 controls. We propose that delayed primary cilia maturation contributes to defective SHH signaling in T21. SUMMARYT21 impedes primary cilia assembly and disrupts SHH signaling by diminishing ciliary SMO and increasing GPR161, but extended ciliary maturation equalizes SHH protein localization between D21 and T21.

cell biology↗

SPEF1 mediates assembly of the central pair microtubule complexes in cilia of Tetrahymena.

SPEF1 is a conserved protein that reinforces the seam of central microtubules within the distal segment of motile cilia. We show that in Tetrahymena, loss of SPEF1 destabilized the central pair throughout the cilium length, producing gaps in the microtubule lattice, loss of proximal microtubule portions, and loss of lateral projections. While both central microtubules were affected, C1 suffered more damage than C2 and the defects were already apparent during ciliary assembly. Tetrahymena cells lacking SPEF1 had fewer cilia, which contained an excessively dense ciliary matrix and abnormal densities on the doublet microtubules. Although SPEF1 loss visibly affected only the central microtubules, it localized to all stable microtubules in the cell, both ciliary and non-ciliary. Within cilia, SPEF1 was enriched near the distal tip, but was also present throughout the middle segment, where it was more concentrated along the central than the outer doublet microtubules. In live cilia, SPEF1 particles were mostly stationary and turned over slowly, some diffused but none moved by IFT. We propose that SPEF1 acts as a stabilizer of central microtubules in both the middle and distal segment and its activity contributes to central microtubule assembly.

cell biology↗

Splice-switching antisense oligonucleotides correct cryptic exon inclusion and restore SDCCAG8 protein in Bardet-Biedl Syndrome

Bardet-Biedl Syndrome (BBS) is a ciliopathy often associated with progressive blindness and obesity. A patient presenting with BBS was discovered to have two mutations within 55bp of each other in intron 7 of SDCCAG8 (BBS16). One of the biallelic mutations, c.740+356C>T, causes inclusion of cryptic exon(s) containing premature termination codons, while c.740+301G>A has not been characterized. We hypothesized that antisense oligonucleotides (ASOs) complementary to the patients mutations or to the cryptic exon splice sites would correct the splicing of SDCCAG8 between exons 7 and 8 to prevent cryptic exon inclusion and restore SDCCAG8 expression. We systematically screened 20nt-long ASOs tiled across each mutation and ASOs targeting the 3' splice sites of the cryptic exons in patient-derived fibroblasts, using RT-PCR assays to assess exon 7 and 8 splicing. We identified one ASO for each mutation and a cryptic exon-targeting ASO that restored the splicing pattern to that observed in an unaffected cell line. Lead ASOs were further investigated through RT-PCR, RNA sequencing, and western blotting to confirm ASO-mediated restoration of wild-type transcript and protein. Notably, ASO 20, which targets the cryptic exon 7a/7a' splice site rather than patient-specific mutations, achieved the greatest rescue effect, increasing exon 7-8 splicing from 0% to an average of 26% and restoring SDCCAG8 protein from undetectable levels to approximately 40% of wild-type expression. This mutation-agnostic approach could benefit multiple patients with cryptic exon inclusion in this region of SDCCAG8, expanding therapeutic impact beyond traditional N-of-1 ASO strategies. These findings establish a molecular foundation for clinical development of ASO therapy for BBS caused by SDCCAG8 splicing defects.

genetics↗

Big1 is a cell cycle regulator linking cell size to basal body number

Cell size control in dividing cells coordinates cell growth with cell division. In the ciliated protozoan, Tetrahymena, there is a tight link between cell size and the cytoskeletal assemblies at the cell cortex organized around basal bodies (BBs). BBs dictate the distribution of ciliary units governing cell motility and are organized into 18-22 ciliary rows. The number of BBs per cell remains remarkably consistent even when the number and lengths of ciliary rows vary. big1-1 mutant cells are large and have elevated numbers of BBs, providing a system to investigate links between BB number and cell size control. We discovered BIG1 encodes a protein with an RRM3 RNA-binding domain similar to the fission yeast meiotic entry gene, mei2. The big1-1 mutation is a predicted null allele. By extending the duration of specific cell cycle stages conducive to new BB assembly, big1-1 promotes cell size increases through BB amplification. In contrast, excess Big1 protein localizes to BBs and drives cells into premature cell division, resulting in small cells with fewer BBs. Thus, Tetrahymena Big1 localizes to BBs and controls cell cycle progression, indicating BBs and Big1 link cell growth to the cell division cycle.

cell biology↗

The DNA damage response pathway is required for multiciliated cell differentiation

DNA damage can result from external sources or occur during programmed genome rearrangements in processes like immunity or meiosis. To maintain genome integrity, cells activate DNA repair pathways that prevent harmful outcomes such as cancer or immune dysfunction. In this study, we uncover a novel role for DNA damage during the terminal differentiation of multiciliated cells (MCCs). MCCs, which line the airways, reproductive tracts, and brain ventricles, produce hundreds of motile cilia, each anchored by a centriole. Therefore, MCCs must generate hundreds of centrioles during differentiation. Normally, centriole duplication is tightly linked to the S and G2 phases of the cell cycle, raising questions about how MCCs override numerical and temporal restrictions on centriole duplication. We find that differentiating MCCs accumulate extensive double-stranded DNA breaks during centriole amplification, with damage levels correlating with centriole number. DNA damage response (DDR) kinases are essential for supporting centriole biogenesis and ciliogenesis. We also observe that transcriptional activity, required for the expression of centriole and cilia genes, produces RNA-DNA hybrids (R-loops) that co-localize with DNA damage. This suggests that transcription-coupled DNA damage helps initiate a pseudo-cell cycle program, permitting centriole amplification without triggering full S/G2 phase processes. Our findings indicate that MCCs harness DDR signaling as part of their developmental program, revealing a broader principle in which the canonical cell cycle is adaptively rewired during differentiation.

cell biology↗

Quantification of subcellular RNA localization through direct detection of RNA oxidation

Across cell types and organisms, thousands of RNAs display asymmetric subcellular distributions. The study of this process often requires quantifying abundances of specific RNAs at precise subcellular locations. To analyze subcellular transcriptomes, multiple proximity-based techniques have been developed in which RNAs near a localized bait protein are specifically labeled, facilitating their biotinylation and purification. However, these complex methods are often laborious and require expensive enrichment reagents. To streamline the analysis of localized RNA populations, we developed Oxidation-Induced Nucleotide Conversion sequencing (OINC-seq). In OINC-seq, RNAs near a genetically encoded, localized bait protein are specifically oxidized in a photo-controllable manner. These oxidation events are then directly detected and quantified using high-throughput sequencing and our software package, PIGPEN, without the need for biotin-mediated enrichment. We demonstrate that OINC-seq can induce and quantify RNA oxidation with high specificity in a dose- and light-dependent manner. We further show the spatial specificity of OINC-seq by using it to quantify subcellular transcriptomes associated with the cytoplasm, ER, nucleus, and the inner and outer membranes of mitochondria. Finally, using transgenic zebrafish, we demonstrate that OINC-seq allows proximity-mediated RNA labeling in live animals. In sum, OINC-seq together with PIGPEN provide an accessible workflow for the analysis of localized RNAs across different biological systems.

molecular biology↗

The Structure of Cilium Inner Junctions Revealed by Electron Cryo-tomography

The cilium is a microtubule-based organelle critical for many cellular functions. Its assembly initiates at a basal body and continues as an axoneme that projects out of the cell to form a functional cilium. This assembly process is tightly regulated. However, our knowledge of the molecular architecture and the mechanism of assembly is limited. By applying electron cryo-tomography and subtomogram averaging, we obtained subnanometer resolution structures of the inner junction in three distinct regions of the cilium: the proximal region of the basal body, the central core of the basal body, and the flagellar axoneme. The structures allowed us to identify several basal body and axoneme components. While a few proteins are distributed throughout the entire length of the organelle, many are restricted to particular regions of the cilium, forming intricate local interaction networks and bolstering local structural stability. Finally, by knocking out a critical basal body inner junction component Poc1, we found the triplet MT was destabilized, resulting in a defective structure. Surprisingly, several axoneme-specific components were found to "infiltrate" into the mutant basal body. Our findings provide molecular insight into cilium assembly at its inner junctions, underscoring its precise spatial regulation.

cell biology↗

The Unkempt RNA binding protein reveals a local translation program in centriole overduplication

Excess centrosomes cause defects in mitosis, cell-signaling, and cell migration, and therefore their assembly is tightly regulated. Plk4 controls centriole duplication at the heart of centrosome assembly, and elevation of Plk4 promotes centrosome amplification (CA), a founding event of tumorigenesis. Here, we investigate the transcriptional consequences of elevated Plk4 and find Unkempt, a gene encoding an RNA binding protein with roles in translational regulation, to be one of only two upregulated mRNAs. Unk protein localizes to centrosomes and Cep131-positive centriolar satellites and is required for Plk4-induced centriole overduplication in an RNA-binding dependent manner. Translation is enriched at centrosomes and centriolar satellites with Unk and Cep131 promoting this localized translation. A transient centrosomal downregulation of translation occurs early in Plk4-induced CA. CNOT9, an Unk interactor and component of the translational inhibitory CCR4-NOT complex, localizes to centrosomes at this time. In summary, centriolar satellites and Unk promote local translation as part of a translational program that ensures centriole duplication.

cell biology↗

Poc1 is a basal body inner junction protein that promotes triplet microtubule integrity and interconnections

Basal bodies (BBs) are conserved eukaryotic structures that organize motile and primary cilia. The BB is comprised of nine, cylindrically arranged, triplet microtubules (TMTs) that are connected to each other by inter-TMT linkages which maintain BB structure. During ciliary beating, forces transmitted to the BB must be resisted to prevent BB disassembly. Poc1 is a conserved BB protein important for BBs to resist ciliary forces. To understand how Poc1 confers BB stability, we identified the precise position of Poc1 binding in the Tetrahymena BB and the effect of Poc1 loss on BB structure. Poc1 binds at the TMT inner junctions, stabilizing TMTs directly. From this location, Poc1 also stabilizes inter-TMT linkages throughout the BB, including the cartwheel pinhead and the inner scaffold. Moreover, we identify a molecular response to ciliary forces via a molecular remodeling of the inner scaffold, as determined by differences in Fam161A localization. Thus, while not essential for BB assembly, Poc1 promotes BB interconnections that establish an architecture competent to resist ciliary forces.

cell biology↗

Label-free proteomic comparison reveals ciliary and non- ciliary phenotypes of IFT-A mutants

DIFFRAC is a powerful method for systematically comparing proteome content and organization between samples in a high-throughput manner. By subjecting control and experimental protein extracts to native chromatography and quantifying the contents of each fraction using mass spectrometry, it enables the quantitative detection of alterations to protein complexes and abundances. Here, we applied DIFFRAC to investigate the consequences of genetic loss of Ift122, a subunit of the intraflagellar transport-A (IFT-A) protein complex that plays a vital role in the formation and function of cilia and flagella, on the proteome of Tetrahymena thermophila. A single DIFFRAC experiment was sufficient to detect changes in protein behavior that mirrored known effects of IFT-A loss and revealed new biology. We uncovered several novel IFT-A-regulated proteins, which we validated through live imaging in Xenopus multiciliated cells, shedding new light on both the ciliary and non-ciliary functions of IFT-A. Our findings underscore the robustness of DIFFRAC for revealing proteomic changes in response to genetic or biochemical perturbation.

cell biology↗

Intracellular connections between basal bodies promote the coordinated behavior of motile cilia

Hydrodynamic flow produced by multi-ciliated cells is critical for fluid circulation and cell motility. Hundreds of cilia beat with metachronal synchrony for fluid flow. Cilia-driven fluid flow produces extracellular hydrodynamic forces that cause neighboring cilia to beat in a synchronized manner. However, hydrodynamic coupling between neighboring cilia is not the sole mechanism that drives cilia synchrony. Cilia are nucleated by basal bodies (BBs) that link to each other and to the cells cortex via BB-associated appendages. The intracellular BB and cortical network is hypothesized to synchronize ciliary beating by transmitting cilia coordination cues. The extent of intracellular ciliary connections and the nature of these stimuli remain unclear. Moreover, how BB connections influence the dynamics of individual cilia has not been established. We show by FIB-SEM imaging that cilia are coupled both longitudinally and laterally in the ciliate Tetrahymena thermophila by the underlying BB and cortical cytoskeletal network. To visualize the behavior of individual cilia in live, immobilized Tetrahymena cells, we developed Delivered Iron Particle Ubiety Live Light-(DIPULL) microscopy. Quantitative and computer analyses of ciliary dynamics reveal that BB connections control ciliary waveform and coordinate ciliary beating. Loss of BB connections reduces cilia-dependent fluid flow forces. SummarySoh et al investigate whether intracellular connections between basal bodies control ciliary behavior in multi-ciliated cells. Using a Tetrahymena live cell immobilization technique to quantify ciliary dynamics, they show that inter-BB connections are required for effective ciliary waveform and coordinated ciliary beating that promotes fluid flow.

cell biology↗

Trisomy 21 induces pericentrosomal crowding disrupting early stages of primary ciliogenesis and mouse cerebellar development

Primary cilia are signaling organelles essential for development and homeostasis. Loss of primary cilia is lethal, and decreased or defective cilia cause multisystemic conditions called ciliopathies. Down syndrome shares clinical overlap with ciliopathies. We previously showed that trisomy 21 diminishes primary cilia formation and function due to elevated Pericentrin, a centrosome protein encoded on chromosome 21. Pericentrin is mislocalized, creating aggregates that disrupt pericentrosomal trafficking and microtubule organization. Here, we examine the cilia-related molecules and pathways disrupted in trisomy 21 and their in vivo phenotypic relevance. Utilizing ciliogenesis time course experiments, we reveal how Pericentrin, microtubule networks, and components of ciliary vesicles are reorganized for ciliogenesis in euploid cells. Early in ciliogenesis, chromosome 21 polyploidy results in elevated Pericentrin and microtubule networks away from the centrosome that ensnare MyosinVA and EHD1, blocking mother centriole uncapping that is essential for ciliogenesis. Ciliated trisomy 21 cells have persistent trafficking defects that reduce transition zone protein localization, which is critical for Sonic hedgehog signaling. Sonic hedgehog signaling is decreased and anticorrelates with Pericentrin levels in trisomy 21 primary mouse embryonic fibroblasts. Finally, we observe decreased ciliation in vivo. A mouse model of Down syndrome with elevated Pericentrin has fewer primary cilia in cerebellar granule neuron progenitors and thinner external granular layers. Our work reveals that elevated Pericentrin in trisomy 21 disrupts multiple early steps of ciliogenesis and creates persistent trafficking defects in ciliated cells. This pericentrosomal crowding results in signaling defects consistent with the neurological deficits found in individuals with Down syndrome.

cell biology↗

Trisomy 21 increases microtubules and disrupts centriolar satellite localization

Trisomy 21, the cause of Down syndrome, causes a 0.5-fold protein increase of the chromosome 21-resident gene Pericentrin (PCNT) and reduces primary cilia formation and signaling. Here we investigate the mechanisms by which PCNT imbalances disrupt cilia. Using isogenic RPE-1 cells with increased chromosome 21 dosage, we find PCNT protein accumulates around the centrosome as a pericentrosomal cluster of enlarged cytoplasmic puncta that localize along and at MT ends. Cytoplasmic PCNT puncta impact the intracellular MT trafficking network required for primary cilia, as the PCNT puncta sequester cargo peripheral to centrosomes in what we call pericentrosomal crowding. The centriolar satellite proteins, PCM1, CEP131 and CEP290, important for ciliogenesis, accumulate at sites of enlarged PCNT puncta in trisomy 21 cells. Reducing PCNT when chromosome 21 ploidy is elevated is sufficient to decrease PCNT puncta, reestablish a normal density of MTs around the centrosome, restore ciliogenesis to wild type levels and decrease pericentrosomal crowding. A transient reduction in MTs also decreases pericentrosomal crowding and partially rescues ciliogenesis in trisomy 21 cells, indicating that increased PCNT leads to defects in the microtubule network deleterious to normal centriolar satellite distribution. We propose that chromosome 21 aneuploidy disrupts MT-dependent intracellular trafficking required for primary cilia. TOCMcCurdy et al explore why elevated Pericentrin in trisomy 21 negatively impacts primary cilia formation and signaling. They find that elevated Pericentrin produces more pericentrosomal puncta that associates with and increases microtubules. Changes to Pericentrin and microtubules mislocalizes centriolar satellites in a pericentrosomal crowd.

cell biology↗

Plastic cell morphology changes during dispersal

Dispersal is the movement of organisms from one habitat to another that potentially results in gene flow. It is often found to be plastic, allowing organisms to adjust dispersal movements depending on environmental conditions. A fundamental aim in ecology is to understand the determinants underlying dispersal and its plasticity. We utilized 22 strains of the ciliate Tetrahymena thermophila to determine if different phenotypic dispersal strategies co-exist within a species and which mechanisms underlie this variability. We quantified the cell morphologies impacting cell motility and dispersal. Distinct differences in innate cellular morphology and dispersal rates were detected, but no universally utilized combinations of morphological parameters correlate with dispersal. Rather, multiple distinct and plastic morphological changes impact cilia-dependent motility during dispersal, especially in proficient dispersing strains facing challenging environmental conditions. Combining ecology and cell biology experiments, we show that dispersal can be promoted through a panel of plastic motility-associated changes to cell morphology and motile cilia. Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=152 SRC="FIGDIR/small/448130v1_ufig1.gif" ALT="Figure 1"> View larger version (45K): org.highwire.dtl.DTLVardef@1aad069org.highwire.dtl.DTLVardef@158adbdorg.highwire.dtl.DTLVardef@f6570forg.highwire.dtl.DTLVardef@cdc249_HPS_FORMAT_FIGEXP M_FIG C_FIG HighlightsO_LITetrahymena thermophila exhibits intra-specific diversity in morphology and dispersal. C_LIO_LICell motility behavior during dispersal changes with cilia length and cell shape. C_LIO_LICells from proficient dispersing strains transiently change basal body and cilia position. C_LIO_LIStarvation-induced dispersal triggers increased basal body and cilia density and caudal cilium formation in rapid-swimming cells. C_LI

cell biology↗

A semi-automated machine learning-aided approach to quantitative analysis of centrosomes and microtubule organization

Microtubules (MTs) perform important cellular functions including migration, intracellular trafficking, and chromosome segregation. The centrosome, comprised of two centrioles surrounded by the pericentriolar material (PCM), is the cells central MT organizing center. The PCM proteins, including{gamma} -tubulin and Pericentrin, promote MT nucleation and organization. Centrosomes in cancer cells are commonly numerically amplified. However, the question of how amplification of centrosomes alters the MT organization capacity is not well-studied. We developed a quantitative image-processing and machine learning-aided approach for the automated analysis of MT organization. We designed a convolutional neural network-based approach for detecting centrosomes and an automated pipeline for analyzing MT organization around centrosomes, encapsulated in a semi-automatic graphical tool. Using this tool, we analyzed the spatial distribution of PCM proteins, the growing ends of MTs and the total MT density in breast cancer cells. We find that breast cancer cells with supernumerary centrosomes not only have increased PCM protein but also exhibit expansion in PCM size. Moreover, centrosome amplified cells have a greater MT density and more growing MT ends near centrosomes than unamplified cells. The semi-automated approach developed here enables facile, unbiased and quantitative measurements of centrosome aberrations. We show that these aberrations increase MT nucleation and promote changes to MT density and the spatial distribution of MTs around amplified centrosomes.

cell biology↗