CCDC15 localizes to the centriole inner scaffold and regulates centriole integrity and ciliogenesis

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   Review Commons

   May 3, 2023

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   Reply to the reviewers

   We thank the reviewers for their comments and constructive suggestions to improve the manuscript. We are encouraged to see that both reviewers acknowledge how the results from our manuscript uses state-of-art technologies to advance molecular underpinnings of centriole length, integrity and function regulation. Both reviewers also highlighted that the manuscript is well laid out and presents clear, rigorous, and convincing data. Reviewer#1 described our manuscript of highest experimental quality and broad interest to the field of centrosome and cell biology form a basic research and genetics/clinical point of view. Here, we explain the revisions, additional …

   Note: This rebuttal was posted by the corresponding author to Review Commons. Content has not been altered except for formatting.

   Learn more at Review Commons

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   Reply to the reviewers

   We thank the reviewers for their comments and constructive suggestions to improve the manuscript. We are encouraged to see that both reviewers acknowledge how the results from our manuscript uses state-of-art technologies to advance molecular underpinnings of centriole length, integrity and function regulation. Both reviewers also highlighted that the manuscript is well laid out and presents clear, rigorous, and convincing data. Reviewer#1 described our manuscript of highest experimental quality and broad interest to the field of centrosome and cell biology form a basic research and genetics/clinical point of view. Here, we explain the revisions, additional experimentations and analyses planned to address the points raised by the referees. We will perform most of the experimentations and corrections requested by the reviewers. We have already made several revisions and are currently working on additional experiments.

   Our responses to each reviewer comment in bold are listed below. References mentioned here are listed in the references section included at the of this document.

   Reviewer #1 (Evidence, reproducibility and clarity (Required)):

   Summary: __In this manuscript, Arslanhan and colleagues use proximity proteomics to identify CCDC15 as a new centriolar protein that co-localizes and interacts with known inner scaffold proteins in cell culture-based systems. Functional characterization using state-of-the-art expansion microscopy techniques reveals defects in centriole length and integrity. The authors further reveal intriguing aberrations in the recruitment of other centriole inner scaffold proteins, such as POC1B and the SFI1/centrin complex, in CCDC15-deficient cells, and observe defects in primary cilia. __

   We thank the reviewer for the accurate summary of the major conclusions of our manuscript.

   Major points:

   1) The authors present a high-quality manuscript that identifies a novel centriolar protein by elegantly revealing and comparing the proximity proteomes of two known centriolar proteins, which represents an important component for the maintenance of centrioles.

   We thank the reviewer for highlighting that our manuscript is of high quality and presents important advances for the field.

   __2) Data are often presented from two independent experiments (n = 2), which is nice, but also the minimum for experiments in biology. It is strongly recommended to perform at least three independent experiments. __

   We agree with the reviewer that analysis of data form three experimental replicates is ideal for statistical analysis. We performed three replicates for the majority of experiments in the manuscript. However, as the reviewer pointed out, we included analysis from two experiments for the following figures:

   • Fig. 4H: quantification of CCDC15 total cellular levels throughout the cell cycle by western blotting
   • Fig. 5A: CCDC15-positive centrioles in control and CCDC15 siRNA-transfected cells
   • Fig. 6B: % centriolar coverage of POC5, FAM161A, POC1B and Centrin-2 in control and CCDC15 siRNA-transfected cells
   • Fig. 6C, 6E: Centrin-2 or SFI1-positive centrioles in control and CCDC15 siRNA-transfected cells
   • Fig. 6J, K: normalized tubulin length and percentage of defective centrioles in cells depleted for CCDC15 or co-depleted for CCDC15 and POC1B
   • Fig. 7F, H: SMO-positive cilia and basal body IFT88 levels in control and CCDC15 siRNA-transfected cells
   • Fig. S3H: centriole amplification in HU-treated control and CCDC15 siRNA-transfected cells (no)
   • Fig. S3A: centrosomal levels upon CCDC15 depletion There are two reasons for why we performed two experimental replicates for these experiments: 1) results from the two experimental replicates were similar, 2) quantification of data by U-ExM is laborious. To address the reviewer’s comments, we will perform the third experimental replicate for the sets of data that led to major conclusions of our manuscript, which are Figures 4H, 6C, 6E, 6J, 6K, 7F, 7H and S3A.

   3) The protein interaction studies presented in Fig. 3 could be of higher quality. While it is great that the authors compared interactions to the centriolar protein SAS6, which is not expected to interact with CCDC15, the presented data raise many questions.

   __a) In most cases, co-expression of tagged CCDC15 stabilizes the tested interaction partners, such that the overall abundance seems to be higher. The increase in protein abundance is substantial for Flag-FAM161A (Fig. 3D) and GFP-Centrin-2 (Fig. 3E) and is even higher for the non-interactor SAS6 (Fig. 3G), while it cannot be assessed for GFP-POC1B (Fig. 3F). Hence, the higher expression levels under these conditions make it more likely that these proteins are "pulled down" and therefore do not represent appropriate controls. __

   We agree with the reviewer that the differences in protein abundance of the prey proteins upon expression of CCDC15 relative to control might impact the interpretation of the interaction data. To address this concern, we will perform the following experiments:

   • To account of the potential stabilizing effects of CCDC15 expression, we will change the relative ratio of plasmids expressing proteins of interest and assess the expression of bait and prey protein levels. We will then repeat the co-immunoprecipitation experiments in conditions where prey expression levels are similar.
   • To avoid the potential stabilizing effects of CCDC15 overexpression, we will perform immunoprecipitation experiments in cells expressing GFP or V5-tagged inner scaffold proteins and assess their potential physical or proximity interaction by blotting for endogenous CCDC15. __b) All Co-IP experiments are lacking negative controls in the form of proteins that are not pulled down under the presented conditions. __

   For the co-IP experiments, we only included a specificity control for the interaction of the bait protein with the tag of the prey protein (i.e. GBP pulldown of GFP or GFP-CCDC15-expressing cells). As the reviewer suggested, we will also include a specificity control for the interaction of bait with the tag of the prey protein for co-immunoprecipitation experiments (i.e. GFP pulldown of cells expressing GFP-CCDC15 with V5-BirA* or V5-BirA*-FAM161A).

   __c) The amounts of co-precipitation of the tested proteins appears very different. Could this reflect strong or weak interactors, or does it reflect the abundance of the respective proteins in centrioles? __

   We agree with the reviewer that the quantity of the co-precipitated prey proteins might be a proxy for the interaction strength if the abundance of the bait proteins is similar. However, the expression levels of bait and prey proteins in co-transfected cells are different and thus, cannot be used to derive a conclusion on the interaction strength. For the revised manuscript, we will repeat the IP experiments and comment on this in the discussion section.

   __4) The observation that IFT88 is supposedly decreased at the base of cilia in CCDC15-depleted cells requires additional experiments/evidence. Fig. 7G shows the results of n = 2 and more importantly, a similar reduction of gamma-tubulin in siCCDC15. Could the observed reduction in IFT88 be explained by a decrease in accessibility to immunofluorescence microscopy? Would the reduction in IFT88 at the base also be apparent when the signals were normalized to gamma-tubulin signals? __

   To address the reviewer’s concern, we quantified the basal body gamma-tubulin and IFT88 levels in control and CCDC15-depleted cells and plotted the basal body IFT88 levels normalized to gamma-tubulin levels in Fig. 7H. Similar to the reduction in IFT88 levels, gamma-tubulin-normalized IFT88 levels was significantly less relative to control cells. Moreover, the gamma-tubulin basal body levels were similar between control and CCDC15 cells. We revised the gamma-tubulin micrographs in Fig. 7G to represent this. These results indicate that the reduction in basal body IFT88 levels upon CCDC15 depletion in specific.

   __5) The observed Hedgehog signaling defects are described as follows: "CCDC15 depletion significantly decreased the percentage of SMO-positive cells". It is similarly described in the figure legend. If this was true, the simplest explanation would be that it reflects the reduction in ciliation rate (which is in a similar range). If SMO-positive cilia (instead of "cells") were determined, the text needs to be changed accordingly. __

   As the reviewer pointed out, we quantified SMO-positive cilia, but not cells. We are sorry for this typo. We corrected SMO-positive cells as SMO-positive cilia in the manuscript text, Fig. 7 and figure legends.

   __6) OPTIONAL: While expansion microscopy is slowly becoming one of the standard super-resolution microscopy methods, which is particularly well validated for studying centrioles, the authors should consider confirming part of their findings (as a proof of principle, surely not in all instances) by more established techniques. This could serve to convince critical reviewers that may argue that the expansion process may induce architectural defects of destabilized centrioles, as observed after disruptions of components, such as in Fig. 6. Alternatively, the authors could cite additional work that make strong cases about the suitability of expansion microscopy for their studies, ideally with comparisons to other methods. __

   • SIM imaging was previously successfully applied for nanoscale mapping of other centriole proteins including CEP44, MDM1 and PPP1R35 (Atorino et al., 2020; Sydor et al., 2018; Van de Mark et al., 2015). To complement the U-ExM analysis, we have started imaging cells stained for CCDC15 and different centriole markers (i.e. distal appendage, proximal linker, centriole wall) using a recently purchased 3D-SIM superresolution microscope. We already included the SIM imaging data for CCDC15 localization in centrosome fractions purified from HEK293T cells in Fig. S5B. In the revised manuscript, we will replace confocal imaging data in Fig. 3A and 3B with SIM imaging data.
   • As the reviewer noted, expansion microscopy has been successfully used for the analysis of a wide range of cellular structures and scientific questions including nanoscale mapping of cellular structures across different organisms. In particular, U-ExM of previously characterized centrosome proteins various centriole proteins have significantly advanced our understanding of centriole ultrastructure. In our manuscript, we used the U-ExM protocol that was validated for centrioles by comparative analysis of U-ExM and cryo-ET imaging by our co-authors (Gambarotto et al., 2019; Hamel et al., 2017). To clarify these points, we included the following sentence along with the relevant references in the introduction: “Application of the U-ExM method to investigate known centrosome proteins has started to define the composition of the inner scaffold as well as other centriolar sub-compartments (Chen et al., 2015; Gambarotto et al., 2021; Gambarotto et al., 2019; Kong and Loncarek, 2021; Laporte et al., 2022; Mahen, 2022; Mercey et al., 2022; Odabasi et al., 2023; Sahabandu et al., 2019; Schweizer et al., 2021; Steib et al., 2022; Tiryaki et al., 2022; Tsekitsidou et al., 2023).”

   Minor points:

   1) Text, figures, and referencing are clear and accurate, apart from minor exceptions.

   We clarified and corrected the points regarding text, figures and references as suggested by the two reviewers.

   __

   1. The title suggests a regulator role for CCDC15 in centriole integrity and ciliogenesis, which has formally not been shown. __

   We revised the title as “CCDC15 localizes to the centriole inner scaffold and functions in centriole length control and integrity”.

   __3) As the authors observe changes in centriole lengths in the absence of CCDC15, it would be very insightful to compare these phenotypes to other components that affect centriolar length, such as C2CD3, human Augmin complex components (as HAUS6 is identified in Fig. 1) or others. These could be interesting aspects for discussion, additional experiments are OPTIONAL. __

   We agree with the reviewer that comparative analysis of centriole length phenotypes for CCDC15 and other components that regulate centriole length will provide insight into how these components work together at the centriole inner core. To this end, we phenotypically compared CCDC15 loss-of-function phenotypes to that of other components of the inner scaffold (POC5, POC1B, FAM161A) that interact with CCDC15. In agreement with their previously reported functions in U2OS or RPE1 cells, we found that POC5 depletion resulted in a 4% slight but significant increase in centriole length and POC1B depletion resulted in a 15% significant decrease. In contrast, FAM161A depletion did not alter centriole length (siControl: 447.8±59.7 nm, siFAM161A 436.3±64 nm). Together, our analysis of their centriolar localization dependency and regulatory roles during centriole length suggest that CCDC15 and POC1B might form a functional complex as positive regulators of centriole length. In contrast, POC5 functions as a negative regulator and might be part of a different pathway for centriole length regulation. We integrated the following sub-paragraph in the results section and also included discussion of this data in the discussion section:

   “Moreover, we quantified centriole length in control cells and cells depleted for POC5 or POC1B. While POC5 depletion resulted in longer centrioles, POC1B resulted in shorter centrioles (POC5: siControl: 414.1 nm±38.3, siPOC5: 432.7±44.8 nm, POC1B: siControl: 400.6±36.1 nm, siPOC1B: 341.5±44.39 nm,). FAMA161A depletion did not alter centriole length (siControl: 447.8±59.7 nm, siFAM161A 436.3±64 nm). Together, these results suggest that CCDC15 might cooperate with POC1B and compete with POC5 to establish and maintain proper centriole length.”

   __

   1. While the reduced ciliation rate in the absence of CCDC15 is convincing, the authors did not investigate "ciliogenesis", i.e. the formation of cilia, and hence should re-phrase. The sentence in the discussion that "CCDC15 functions during assembly" should be removed. __

   To clarify that we only investigated the role of CCDC15 in the ability of cells to form cilia, we replaced sentences that indicates “CCDC15 functions in cilium assembly” with “CCDC15 is required for the efficiency of cilia formation”.

   __5) The existence of stably associated CCDC15 pools with centrosomes (Fig. 2) requires further evidence. The recovery of fluorescence after photobleaching in FRAP experiments is strongly dependent on experimental setups and is only semi-quantitative. A full recovery is unrealistic, hence, it is ideally compared to a known static or known mobile component. I personally think this experiment -as it is presented now- is of little value to the overall fantastic study. The authors may consider omitting this piece of data. __

   We agree with the reviewer that FRAP data by itself does not prove the existence of stably associated CCDC15 pool. As controls in these experiments, we use FRAP analysis of GFP-CCDC66, which has a 100% immobile pool at the cilia and 50% immobile pool at the centrosomes as assessed by FRAP (Conkar et al., 2019). To address these points, we toned down the conclusions derived from this experiment by revising the sentence as follows:

   Additionally, we note that the following data provides support for the stable association of CCDC15 at the centrioles:

   • About 49.6% (± 3.96) of the centrioles still had CCDC15 fluorescence signal at one of the centrioles upon CCDC15 siRNA treatment (Fig. 5A, 5B). The inefficient depletion of the mature centriole pool of CCDC15 is analogous to what was observed upon depletion of other centriole lumen and inner scaffold proteins including WDR90 and HAUS6 (Schweizer et al., 2021; Steib et al., 2020). __6) The data that CCDC15 is a cell cycle-regulated protein is not very convincing (see Fig. 3H), as the signals area weak and the experiment has been performed only once (n= 1). This piece of data does not appear to be very critical for the main conclusions of the manuscript and may be omitted. Otherwise, this experiment should be repeated to allow for proper statistical analysis. __

   We will perform these experiments two more times, quantify cellular abundance of CCDC15 in synchronized populations from three experimental replicates and plot it with proper statistical analysis.

   __7) Experimental details on how "defective centrioles" are determined are missing. __

   We included the following experimental details to the methods section:

   “Centrioles were considered as defective when the roundness of the centriole was lost or the microtubule walls were broken or incomplete. In the longitudinal views of centrioles, defective centrioles were visualized as heterogenous acetylated signal along the centriole wall or irregularities in the cylindrical organization of the centriole wall (Fig. 5F). We clarified these points in the methods section.

   __

   1. For figures, in which the focus should be on growing centrioles (see Fig. 4), it could be helpful to guide the reader and indicate the respective areas of the micrographs by arrows. __

   We added arrows to point to the respective areas of the micrographs in Fig. 4F.

   __

   1. Page18: "centriole length shortening" could be changed to "centriole shortening". __

   We corrected this description as suggested.

   __10) It is unclear how the authors determine distal from proximal ends of centrioles in presented micrographs (see Fig. 5D). __

   We determined the proximal and distal ends of the centrioles by taking the centriole pairs as a proxy. Even though we only represent a micrograph containing a single centriole in some of the U-ExM figures including Fig. 5D, the uncropped micrographs contain two centrioles, which are oriented orthogonally and tethered to each other at their proximal ends in interphase cells. We added the following sentence to the methods section to clarify this point:

   *“Since centrioles are oriented orthogonally and tethered to each other at their proximal ends in interphase cells, we also used the orientation of the centriole pairs as a proxy to determine the proximal and distal ends of the centrioles.” *

   __11) Fig. 7A is missing scale bars and Fig.7 overall is lacking rectangle indicators of the areas that are shown at higher magnification in the insets. __

   We added scale bar to Fig. 7A and rectangle indicators for zoomed in regions in Fig. A, E, G.

   12) Fig. 7C displays cilia that appear very short, especially when comparing to the micrographs and bar graphs presented. The authors may want to explain this discrepancy.

   We thank the reviewer for the comment. The zoomed in representative cilia is 4.1 µM in control cells and 1.4 µM in CCDC15-depleted cells. Therefore, the representative cilia is in agreement with the quantification of cilia in Fig. 7C.

   Reviewer #1 (Significance (Required)): • From a technical point of view the authors use two state-of-the-art technologies, namely proximity labeling combined with proteomics and ultrastructure expansion microscopy, that are both challenging and very well suited to address the main questions of this study. ____ • General assessment: The presented study is of highest experimental quality. Despite being very challenging, the expansion microscopy and proximity proteomics experiments have been designed and performed very well to allow solid interpretation. The results of the central data are consistent and allow strong first conclusions about the putative function of the newly identified centriolar protein CCDC15. The study presents a solid foundation for future hypothesis-driven, mechanistic analysis of CCDC15 and inner scaffold proteins in centriole length control and maintaining centriole integrity. The only limitation of the study is that the technically simpler experiments should be repeated to allow proper statistical assessment, which can be addressed easily. • Advance: This is the first study that identifies CCDC15 as a centriolar protein and localizes it to the inner scaffold. It further describes a function for CCDC15 in centriole length control and shows its importance in maintaining centriole integrity with consequences for stable cilia formation in tissue culture. The study provides further functional insights into the interdependence of inner scaffold proteins and the role of CCDC15 in the recruitment of the SFI1/centrin distal complex. • Audience: The manuscript will be of broad interest to the fields of centrosome and cell biology, both from a basic research and genetics/clinical point of view due to the association with human disorders. The state-of-the-art technologies applied will be of interest to a broader cell and molecular biology readership that studies subcellular compartments and microtubules. • Reviewer's field of expertise: Genetics, imaging, and protein-protein interaction studies with a focus on centrosomes and cilia.

   We thank the reviewer for recognizing the importance of our work and for supportive and insightful comments that will further strengthen the conclusions of our manuscript. Our planned revisions will address the only major technical limitation raised by the reviewer that requires adding one more experimental replicate for analysis of the data detailed in major point#1. Notably, we also thank the reviewer to specifying the experiments that are not essential or will be out of the scope of our manuscript as “optional”.

   Reviewer #2 (Evidence, reproducibility and clarity (Required)):

   Summary:

   __In this study, Arslanhan et al. propose CCDC15 as a novel component of the centriole inner scaffold structure with potential roles in centriole length control, stability and the primary cilium formation in cultured epithelial cells. Using proximity labelling they explore the common interactors of Poc5 and Centrin-2, two resident molecules of the centriole inner scaffold, to hunt for novel regulators of this structure. The authors leverage expansion microscopy-based localization and siRNA-dependent loss-of-function experiments to follow up on one such protein they identify, CCDC15, with the aforementioned roles in centriole and cilia biology.

   This study is designed and laid out nicely; however, to be able to support some of the important claims regarding their proximity labelling results and exploration on the roles of CCDC15, there are several major technical and reproducibility concerns that deem major revision. Similarly, the introduction (perhaps inadvertently) omits much of the recent studies on centriole size control that have highlighted the complexity of this biological problem. As such, addressing the following major points will be essential in further considering this work for publication. __

   __We thank the reviewer for recognizing the importance of our work and appreciate the positive reflections on our manuscript and the feedback comments that were well thought-out and articulated and will further strengthen the conclusions of our manuscript. Our planned revisions focus on addressing the reviewer’s comments especially in further supporting our conclusions for proximity-labeling, phenotypic characterization and immunoprecipitation experiments, examining CCDC15 centriole localization in an additional cell line and investigating how CCDC15 works together during centriole length control with known components of the inner scaffold. __

   Major points:

   __1a) The authors use Poc5 and Centrin-2 molecules as joint baits to reveal the interactome of the centriole inner scaffold, however the work lacks appropriate experimental and analytical controls to argue that this is a proximity mapping "at the centriole inner scaffold". In its current state, it is simply an interactome of total Poc5 and Centrin-2, and it might be misleading to call it an interactome at the centriole inner scaffold (the statistical identification of shared interactors cannot do full justice to their biology at the centrosome). Appropriate expression data needed to delineate how large the centrosomal vs. cytoplasmic (or nucleoplasmic) fraction is for either of these molecules, both without and upon the addition of biotin (to see whether the bulk of interaction data stem from the cytoplasm/nucleoplasm or the centrioles themselves). The authors can test this by selectively blotting a lysate fraction containing the centrosomes after centrifugation, and compare them with the simultaneous blot of the supernatant (which were readily used for the blots presented in Fig. 1B). This experiment also becomes very relevant for the case of Centrin-2, as it also heavily localizes to the nucleoplasm as the authors found out (see Fig. 1A and Fig. S1A). __

   __ Additionally, an orthogonal approach should be taken to perform bio-image analysis on their biotin/streptavidin imaging data to demonstrate the exact ratios between the centrosomal vs. cytoplasmic/nucleoplasmic biotin activation with appropriate signal normalization between the biotin/streptavidin images. This is particularly important, as although the authors claim that these cells stably express the V5BirA*, it seems that there is partial clonality to the expression. Some cells in both the Poc5 and Centrin-2 fusion constructs appear to lack the V5/Streptavidin signals upon Biotin addition (such as the two cells in the centre right in Poc5, and again a cell in the centre right for Centrin-2 images). In its current form, Fig. 1A lacks signal quantification and does not report any information about the replicates and distributions of the data. I worry that this may raise concerns on the reproducibility if published in its current form. __a) We agree with the reviewer that the proximity maps of POC5 and

   a) Centrin-2 are not specific to the centriole inner scaffold and thus, do not represent the inner scaffold interactome. The proximity maps identified interactions across different pools of POC5 and Centrin-2 in nucleus, cytoplasm and centrosomes (Fig. 1, S1). To highlight these important points, we already included extensive analysis of the different cellular compartments and biological processes identified by the POC5 and Centrin-2 proximity maps in the results section (pg. 9-10).

   We think that there are two reasons that caused the misinterpretation of the use of these proximity maps as the “inner scaffold interactome”: 1) the way we introduced the motivation for proximity mapping studies, 2) proposing the use of the resulting interactomes as resources for identification of the full repertoire of the inner scaffold proteins. To clarify these points, we revised the manuscript in all relevant parts that might have led to misinterpretation. Following are the specific revisions:

   • To clarify that the proximity maps are not specific to the inner scaffold pools of POC5 and Centrin-2, we revised the title of the results section for Fig. 1 and 2 as follows: “Proximity mapping of POC5 and Centrin-2 identifies new centriolar proteins”.

   • To indicate that POC5 and Centrin-2 localizes to the cytoplasm and/or nucleus in addition to the centrosome, we added the following sentence to the result section: “In addition to centrosomes, both fusion proteins also localized to and induced biotinylation diffusely in the cytoplasm and/or nucleus (Fig. 1A).”

   • In the introduction, we revised the following sentence “Here, we used the known inner scaffold proteins as probes to identify the molecular makeup of the inner scaffold in an unbiased way.” as follows: *“Here, we used the known inner scaffold proteins as probes to identify new components of the inner scaffold”. *

   • To highlight the different cellular pools of POC5 and Centrin-2 and identification of their interactors in these pools, we included the following sentence in the results section: “As shown in Fig. S1, Centrin-2 and POC5 proximity interactomes were enriched for GO categories that are relevant for their published functions during centrosomal, cytoplasmic and/or nuclear biological processes and related cellular compartments (Azimzadeh et al., 2009; Dantas et al., 2013; Heydeck et al., 2020; Khouj et al., 2019; Resendes et al., 2008; Salisbury et al., 2002; Steib et al., 2020; Yang et al., 2010; Ying et al., 2019).”

   • We replaced the “interactome” statement with “proximity interaction maps” or “proximity interactors” throughout the manuscript to prevent the conclusion that the proximity maps represent the inner scaffold interactome. b) As the reviewer noted, most centrosome proteins have multiple different cellular pools including the centrosome. For most proteins like gamma-tubulin and centrin, their cytoplasmic/nucleoplasmic pools are more abundant than their centrosomal pools (Moudjou et al., 1996; Paoletti et al., 1996). For the Firat-Karalar et al. Current Biology 2015 paper, I compared the biotinylation levels of centrosomal fractions versus cytoplasmic fractions and confirmed that this is also true in cells expressing myc-BirA* fusions of CDK5RAP2, CEP192, CEP152 and CEP63 (unpublished) (Firat-Karalar et al., 2014). For the revised manuscript, we will compare the biotinylation level of centrosomal, nuclear and cytoplasmic pools of V5Bir*-POC5 and V5BirA*-Centrin-2 using the stable lines. To this end, we will use published centrosome purification protocols. We will include this data in Fig. S1 to highlight that the proximity interactomes represent the different pools of the bait proteins and to show the relative levels of the baits across their different pools.

   c) BioID approach has been successfully used to probe centrosome interactions by my lab and other labs in the field. In fact, proximity interaction maps of over 50 centrosome proteins were published as resource papers by Pelletier&Gingras labs (Gheiratmand et al., 2019; Gupta et al., 2015). Analogous to our strategy in this manuscript, these studies generated proximity maps of centrosome proteins by creating cell lines that stably express BioID-fusions of centrosome proteins followed by streptavidin pulldowns from whole cell extracts and mass spectrometry analysis. Since majority of centrosome proteins also have pools in multiple cellular locations, the published BioID proximity maps for centrosome proteins are not specific to centrosomes. However, the proximity maps included all known centrosome proteins and identified new proteins, which shows that centrosome interactions are represented in pulldowns form whole cell lysates. Moreover, maps form whole cell lysates are also advantageous as they are are unbiased and can be used in future studies as resources for studying the functions and interactions of the bait proteins in different contexts.

   In the Firat-Karalar et al. Current Biology 2015 paper, I combined centrosome purifications with BioID pulldowns to enrich for the centrosomal interactions in the proximity maps of centriole duplication proteins(Firat-Karalar et al., 2014). However, I started the purification with cells transiently transfected with the BioID-fusion constructs, which resulted in high ectopic expression of the fusions in the cytoplasm and/or nucleus. Therefore, centrosome enrichments were useful as an additional step before mass spectrometry. Comparative analysis of the data for proximity maps of 4 centrosome proteins generated from stable lines or centrosome fractions of transiently transfected cells substantially overlap as compared in the Gupta et al. Cell 2015 study and were more comprehensive (Table S2) (Gupta et al., 2015). Therefore, we are confident that the proximity interactomes we generated for POC5 and Centrin-2 include their centrosomal interactions.

   __1b) Similarly, it is not clear whether the expression of Poc5 and Centrin-2 fusion molecules somehow interfere with their endogenous interactions or function. At least some loss-of-function (e.g., RNAi) experiments should be performed where the depletion of endogenous proteins should be attempted to rescue by the fusion constructs. This will help evaluate whether the fusion proteins can rescue the depletion of their endogenous counterparts and behave as expected from a wild-type scenario. __

   The reviewer raises an important concern regarding the physiological relevance of the POC5 and Centrin-2 proximity maps. In the manuscript, we showed and discussed the validation of their proximity interactomes by two lines of evidence, which are: 1) the interactomes identified the previously described cellular compartments, biological processes or interactors of POC5 and Centrin-2, 2) the interactomes led to the identification of CCDC15 as a new inner scaffold protein.

   As the reviewer indicated, stable expression of POC5 and Centrin-2 in the presence of their endogenous pools might affect cellular physiology and thereby the landscape of the interactomes. We plan to address this using the following experiments:

   a) We will perform a set of functional assays to assess whether stable V5BirA*-Centrin-2 and V5BirA*-POC5 cells behaves like control cells in terms of their centrosome number, cell cycle profiles and mitotic progression. We will specifically quantify:

   • centrosome number (immunofluorescence analysis for gamma-tubulin and centrin)
   • their mitotic index (immunofluorescence analysis by DAPI)
   • spindle polarity and percentage of multinucleation (immunofluoerescence analysis for microtubules, gamma-tubulin and DAPI)
   • cell cycle profiles (flow cytometry and immunofluorescence)
   • apoptosis (immunoblotting for caspase 3) Together, results from these experiments indicate that the V5BirA*-POC5 or Centrin-2-expressing stable lines do not exhibit defects associated with their stable expression.

   b) We will perform expansion microscopy in V5BirA*-Centrin-2 and V5BirA*-POC5 cells to assess whether the fusion protein specifically localizes to the centriole inner scaffold, which will provide support for the presence of inner scaffold proteins in their proximity maps. Specifically, we plan to stain the fusion proteins by V5 or BirA antibodies and include the data for the antibody that works for expansion microscopy. This experiment will address whether their stable expression results in specific localization of these proteins at the centriole inner scaffold.

   1c) Overall, as the entire claim around the proximity mapping revolve around its assumption about the centriole inner scaffold, these controls seem imperative to substantiate the ground truth of the biology presented in the manuscript.

   In the revised manuscript, we toned down and made it clear that Centrin-2 and POC5 proximity maps are not specific to the inner scaffold and do not represent the inner scaffold interactome. Since the maps were generated from the whole cell extract, they will provide a resource for future studies aimed at studying functions and mechanisms of POC5 and Centrin-2 across their different cellular pools including the centrosome.

   We would like to also highlight that the proximity maps of POC5 and Centrin-2 are not the major advances of our manuscript. The major advance of our manuscript is the identification of CCDC15 as a new inner scaffold protein that is required for regulation of centriole size and architectural integrity and thereby, for maintaining the ability of centrioles to template the assembly of functional cilia. Importantly, our results identified CCDC15 as the first dual regulator of centriolar recruitment of inner scaffold protein POC1B and the distal end SFI1/Centrin complex and provided important insight into how inner scaffold proteins work together during centriole integrity and size regulation. The new set of experiments we will perform for the revisions of the paper will strengthen these conclusions.

   __2) I am curious about the choices of the cell lines in this work. The proximity mapping to reveal CCDC15 as a candidate protein for centriole inner scaffold was performed in HEK293T cells (human embryonic kidney), however its immunostaining was performed using RPE1 and U2OS cells (human retinal and osteosarcoma epithelial cells respectively). This raises questions regarding the generality of CCDC15 as a centriole inner scaffold protein. Could CCDC15 be simply unique to the centriole inner scaffold of epithelial cells such as RPE1 and U2OS cells? Or could the authors demonstrate any information/data on whether it's similarly localized to the inner scaffold in embryonic kidney cells or other cell types? If not, the claims should be moderated to reflect this fine detail. __

   To test whether CCDC15 localizes to the inner scaffold in other cell types, we performed U-ExM analysis of CCDC15 localization relative to the centriolar microtubules in differentiating multiciliated epithelial cultures (MTEC). As shown in Fig. S3A, CCDC15 localized to the inner scaffold in the centrioles in MTEC ALI+4 cells. Given that the inner scaffold proteins including CCDC15 and previously characterized ones have not been studied in multiciliated epithelia, this result is important and provides support for potential role of the inner scaffold in ensuring centriole integrity during ciliary beating. Additionally, we examined CCDC15 localization by 3D-SIM in centrosomes purified from HEK293T cells, which showed that CCDC15 localizes between the distal centriole markers CEP164 and Centrin-3 and proximal centriole markers gamma-tubulin and rootletin (Fig. S3B).

   3) Discussions and data on the localization of CCDC15 to centriolar satellites appear anecdotal and not fully convincing (Fig. S2D). Given that the authors test the relevance of PCM1 for CCDC15's centriolar localization, it is key to have quantitative data supporting their claim that centriolar satellites can help recruit CCDC15 to the centriole. Could the authors quantify what proportion of CCDC15 localize to the centriolar satellites? One way to do this could be to quantify the colocalization coefficience of CCDC15 and PCM1 signals.

   We only observed co-localization of CCDC15 with the centriolar satellite marker PCM1 in cells transiently transfected with mNG-CCDC15. In Fig. S2E, we included the quantification of the percentage of U2OS and RPE1 cells that exhibit co-localization of PCM1 (100% of U2OS cells, about 80% of RPE1 cells). Like CCDC15, ectopic expression of WDR90 revealed its centriolar satellite localization, suggesting a potential link between centriolar satellites and inner scaffold proteins that can be investigated in future studies (Steib et al., 2020). We now included these results in the discussion section as follows:

   “As assessed by co-localization with the centriolar satellite marker PCM1, mNG-CCDC15 localized to centriolar satellites in all U2OS cells and in about 80% of RPE1 cells (Fig. S2C-E). Association of CCDC15 with centriolar satellites is further supported by its identification in the centriolar satellite proteomes(Gheiratmand et al., 2019; Quarantotti et al., 2019).”

   Even though endogenous staining for CCDC15 did not reveal its localization to centriolar satellites, following lines of data support the presence of a dynamic and low abundance pool of CCDC15 at the centriolar satellites: 1) CCDC15 was identified in the centriolar satellite proteome and interactome (Gheiratmand et al., 2019; Quarantotti et al., 2019). 2) CCDC15 centrosomal targeting is in part regulated by PCM1 (Fig. S2F, S2G). For majority of the proteins identified in the centriolar satellite proteome, their satellite pool can only be observed upon ectopic expression. This might be because their centriolar satellite pool is of low abundance and transient as satellite interactions are extensively identified only in proximity mapping studies, but not in traditional pulldowns

   __4) Similar to above (#3), there is no quantitative information on the co-localization or partial co-localization of the signal foci in Fig. 3A and 3B. The authors readily study CCDC15's localization in wonderful detail in their expansion microscopy data, so they could actually consider taking out Fig. 3A and 3B, as the data seem redundant without any quantification. __

   To address the reviewer’s concern, we included plot intensity profile analysis of CCDC15 and different centriole markers along a line drawn at the centrioles in Fig. 3A and 3B, which shows the extent of their overlap. As part of our revision plan, we will replace the confocal imaging data in Fig. 3A and 3B with 3D-SIM imaging data of CCDC15 relative to different centriole markers together with plot profile analysis. We already included 3D-SIM imaging of centrosomes purified form HEK293T cells in Fig. S3B. 3D-SIM imaging data will complement the localization data revealed by U-ExM.

   __5) Do the authors also feel that CCDC15 localize to the core lumen in a somehow helical manner (Fig. 1A, Fig. 1F top and bottom panels, Fig. 5A etc.)? Le Guennec et al. 2020's helical lattice proposal for the inner scaffold further reaffirms that CCDC15 is indeed a likely major component of the inner scaffold. In my view, authors should state this physical similarity explicitly to further support their findings on CCDC15. __

   As the reviewer indicated, cryo–electron tomography and subtomogram averaging of centrioles from four evolutionarily distant species showed that centriolar microtubules are bound together by a helical inner scaffold covering ~70% of the centriole length (Le Guennec et al., 2020). Although U-ExM data do not have enough resolution to show that CCDC15 localizes in a helical manner, we agree with the reviewer that the discussion of this possibility is important and thus we included the following sentence in the results:

   “Longitudinal views suggest potential helical organization of CCDC15 at the inner scaffold, which is consistent with its reported periodic, helical structure (Le Guennec et al., 2020).”

   __6a) The data on the link between the CCDC15 recruitment and the centriole growth (Fig. 4F) or the G2 phase of the cell cycle (Fig. 4H) are not fully convincing without quantitative data. For Fig. 4F, the authors should consider plotting the daughter centriole length vs the daughter CCDC15 intensities against each another, to see whether more elongated daughters truly tend to have more CCDC15. __

   To address the reviewer’s concern, we will plot the daughter centriole length versus CCDC15 intensity at different stages of centriole duplication. In asynchronous cultures that we analyzed with U-ExM, we were not able to find enough cells to perform such quantification. To overcome this limitation, we will perform U-ExM analysis of cells fixed at different points after mitotic shake-off and stained for CCDC15 and tubulin. We will include minimum 10 different representative U-ExM data for different stages of centriole duplication in the revised manuscript along with quantification of length versus signal.

   As detailed in the results section, the goal of these experiments was to determine when CCDC15 is recruited to the procentrioles during centriole duplication, but not to suggest a role for CCDC15 in centriole growth. We clarified this by including the following sentence:

   “To investigate the timing of CCDC15 centriolar recruitment during centriole biogenesis, we examined CCDC15 localization relative to the length of procentrioles that represent cells at different stages of centriole duplication (Fig. 4F).”

   __6b) For Fig. 4H, the argument regarding the cell cycle regulation requires quantification of the bands from several WB repeats, normalized to the expression of GAPDH within each blot (this is particularly relevant, as the bands of CCDC15 do not look dramatically different enough to draw conclusions by eye). __

   We will perform these experiments two more times, quantify cellular abundance of CCDC15 in synchronized populations from three experimental replicates and plot it with proper statistical analysis.

   __7a) The authors find herein that CCDC15 depletion lead to centrioles that are ~10% shorter than the controls. With the depletion of Poc5 and Wdr90 (other proposed components of the inner scaffold), the centrioles end up larger however (Steib et al., 2020). If the role of inner scaffold in promoting centriole elongation is structural, why are these two results the opposite of each other? I realize there is a brief discussion about this at the end of the paper, however, this requires a detailed discussion and speculation on the relevance of these findings. It would be key to clarify whether the inner scaffold as a structure inhibits or promotes centriole growth - or somehow both? If so, how? __

   We agree with the reviewer that comparative analysis of centriole length phenotypes for CCDC15 and other components that regulate centriole length will provide insight into how these components work together at the centriole inner core. To this end, we phenotypically compared CCDC15 loss-of-function phenotypes to that of other components of the inner scaffold (POC5, POC1B, FAM161A) that interact with CCDC15. In agreement with their previously reported functions in U2OS or RPE1 cells, we found that POC5 depletion resulted in a 4% slight but significant increase in centriole length and POC1B depletion resulted in a 15% significant decrease. In contrast, FAM161A depletion did not alter centriole length (siControl: 447.8±59.7 nm, siFAM161A 436.3±64 nm). Together, our analysis of their centriolar localization dependency and regulatory roles during centriole length suggest that CCDC15 and POC1B might form a functional complex as positive regulators of centriole length. In contrast, POC5 functions as a negative regulator and might be part of a different pathway for centriole length regulation. We integrated the following sub-paragraph in the results section in pg. 19 and also included discussion of this data in the discussion section in pg. 23:

   “Moreover, we quantified centriole length in control cells and cells depleted for POC5 or POC1B. While POC5 depletion resulted in longer centrioles, POC1B resulted in shorter centrioles (POC5: siControl: 414.1 nm±38.3, siPOC5: 432.7±44.8 nm, POC1B: siControl: 400.6±36.1 nm, siPOC1B: 341.5±44.39 nm,). FAMA161A depletion did not alter centriole length (siControl: 447.8±59.7 nm, siFAM161A 436.3±64 nm). Together, these results suggest that CCDC15 might cooperate with POC1B and compete with POC5 to establish and maintain proper centriole length.”

   __7b) There might be some intriguing opposing regulatory action of Poc5 and CCDC15 as demonstrated here, where CCDC15 depletion leads to slightly over-recruitment of Poc5, and vice versa. Does this suggest that a tug-of-war going on between different molecules that localize to the inner scaffold? Does this provide some dynamicity to this structure, which might in turn regulate centriole length both positively and negatively? This may be analogous to how opposing forces of dyneins and kinesins provide robust length control for mitotic spindles. I am speculating here, but hopefully these may provide some useful grounds for further discussion in the paper. If the authors deem it interesting experimentally, they can test whether the two molecules indeed regulate centriole length by opposing each other's action, by a double siRNA of CCDC15 and Poc5 to see if this retains the centriole length at its control siRNA size (like how they do a similar test for Poc1's potential co-operativity with CCDC15 in Fig. 6J). __

   We thank the reviewer for proposing excellent ideas on how inner scaffold proteins work together to regulate centriole length. As proposed by the reviewer, different proteins oppose each other analogous to how dynein and kinesin regulate mitotic spindle length. Loss-of-function and localization dependency data support that CCDC15 cooperates with POC1B, which was supported by phenotypic characterization of co-depleted cells (Fig. 6I-K).

   The increase in POC5 levels and coverage at the centrioles upon CCDC15 depletion and vice versa (Fig. 7B, 7G) suggest that CCDC15 and POC5 compete with each other in centriole length regulation. As suggested by the reviewer, we attempted to test this by comparing centriole length in cells co-depleted for CCDC15 and POC5 relative to their individual depletions. Although we tried different depletion workflows, we were not able to co-deplete CCDC15 and POC5. Specifically, we tried transfecting cells with CCDC15 and POC5 siRNAs at the same time or sequentially for 48 h or 96 h. The centrioles in cells that survived co-depletion were positive for both CCDC15 and POC5. This might be because co-depletion of both proteins is toxic to cells. Since CCDC15 and POC5 are likely part of two different pathway in regulation of centrioles and also have other cellular functions, this might have caused cell death. We included the following statement in the discussion to address the excellent model proposed by the reviewer:

   “Taken together, our results suggest that CCDC15 cooperates with POC1B and competes with POC5 during centriole length regulation. Moreover, they also raise the exciting possibility that centriole length can be regulated by opposing activities of inner scaffold proteins. Future studies that explore the relationship among centriole core proteins are required to uncover the precise mechanisms by which they regulate centriole integrity and size.”

   __8) In their introduction section, the authors discuss how relatively little is known about the size control of centrioles, however they fail to mention a series of recent primary literature that uncover striking, new mechanisms and novel molecular players that highlight the complexity of centriole size control. This complexity appears to arise from the existence of multitude of length control mechanisms that influence the cartwheel or the microtubule length individually, or simultaneously via yet-to-be further explored crosstalk mechanisms. a. As such, when the authors talk about the procentriole size control in the introduction, they should discuss and refer to the following studies, in terms of: • How theoretical and experimental work demonstrate that procentriole length may vary dependent on the levels of its building block Sas-6 in animals (Dias Louro et al., 2021 PMID: 33970906; Grzonka and Bazzi, 2022 bioRxiv). • How a homeostatic Polo-like kinase 4 clock regulates centriole size during the cell cycle (Aydogan et al., 2018 JCB PMID: 29500190), and how biochemistry and genetics coupled with mathematical modelling unravel a conserved negative feedback loop between Cep152 and Plk4 that constitutes the oscillations of this clock in flies (Boese et al., 2018 PMID: 30256714; Aydogan et al., 2020 PMID: 32531200) and human cells (Takao et al., 2019 PMID: 31533936). __

   __b. Similarly, when the authors refer to centriole size control induced by microtubule-related proteins, they should highlight the further complexity of this process by referring to: • How a molecule located at the microtubule wall, Cep295/Ana1, can regulate centriole length in flies (Saurya et al., 2016 PMID:27206860) and human cells (Chang et al., 2016 PMID:27185865) - like all the other centriolar MT molecules that the authors discuss in the manuscript. • How a crosstalk between Cep97 and Cep152 influences centriole growth in fly spermatids (Galletta et al., 2016 PMID:27185836). • How a crosstalk between CP110-Cep97 and Plk4 influences centriole growth in flies (Aydogan et al., 2022 PMID:35707992), and this molecular crosstalk is conserved, at least biochemically, in human cells (Lee et al., 2017 PMID:28562169). __

   We thank the reviewer for highlighting the papers that uncovered new mechanisms and players of centriole size and integrity control as well as for the detailed explanation of how different studies led to these discoveries in different organisms. We should have discussed these proteins, functional complexes and mechanisms in our manuscript and cited the relevant literature. We inadvertently focused on literature that uncovered centriole length regulation by MAPs and the inner scaffold. In the introduction section of the revised manuscript where we introduced centriole size regulation in pg. 5, we summarized the major findings on the role of different MAPs, cartwheel and PLK4 homeostatic clock in ensuring formation of centrioles at the correct size in different organisms.

   __Minor points: __

   __1) Introduction section: Literature reference missing for the sentence starting with "Importantly, the stable nature of centrioles enables them to withstand...". __

   We cited research articles that show the importance of centriole motility during ciliary motility and cell division.

   “Importantly, the stable nature of centrioles enables them to withstand mechanical forces during cell division and upon ciliary and flagellar motility (Abal et al., 2005; Bayless et al., 2012; Meehl et al., 2016; Pearson et al., 2009).

   __2) Fig. S1 legend: A typo as follows: CRAPome banalysis should read CRAPome analysis. __

   We corrected this typo.

   __3) Fig. S2: Info on the scale bar in the legend is missing in Fig. S2A. Scale bars for different panels are missing in general in Fig. S2A. __

   We added scale bar information for Fig. S2A and to all other supplementary figure legends that lack scale bar information.

   __4) Fig. 3A and 3B: When displaying the data, coloured cartoon diagrams would be beneficial to guide the reader who are not fully familiar with the spatial orientation of these proteins. __

   As suggested by the reviewer, we will remove the confocal imaging data for CCDC15 localization from Fig. 3A and 3B. For the revised version, we will include 3D-SIM imaging data along with a diagram that represents the spatial orientation of CCDC15 relative to the chosen centriole markers.

   __5) Fig. 3H: No information about the sample number (number of cells or technical repeats examined) reported. __

   We included information on the number of experimental replicates and cells analyzed.

   __6) Fig. S3B legend: A typo as follows: CCD15-depelted RPE1 cells should read CCDC15-depleted RPE1 cells. __

   We corrected this typo.

   __7) Fig. S3B legend: A typo as follows: cellswere fixed with should read cells were fixed with. __

   We corrected this typo.

   __8) There are many spelling mistakes and typos throughout the paper. I have listed a few examples above, but please carefully read through the manuscript to correct all the errors. __

   Thank you for indicating the spelling mistakes we missed to correct for initial submission. In the revised manuscript, we carefully read through the manuscript to correct the mistakes.

   __9) Fig. S3E: The orange columns depicting % of cells with Sas-6 dots look awkward. Why the columns look larger than the mean line? Please correct as appropriate. __

   The total percentage of cells in the two categories (orange and purple) we counted is 100%, which corresponds to the column value at the y-axis. Therefore, the value for each experimental replicate for the orange category is less than 100% and is marked below the 100% line.

   __10) Although authors provide microscopy information for the U-ExM and FRAP experiments, there is no information about the microscopy on regular confocal imaging experiments which should be detailed in Materials and Methods. Also, there is no information about the lenses, laser lines and the filter sets that were used in the imaging experiments. These should be provided as well. __

   In the methods section, we now included detailed information for the microscopes we used and imaging setup (lenses, laser lines, filter sets, detectors, z-stack size, resolution).

   11)

   • __ Fig. 2A: lacks a scale bar. __
   • __ Fig. 2C legend: lacks info on the scale bar length. __
   • __ Fig. 5A legend: lacks info on the scale bar length. __
   • __ Fig. 7A: lacks a scale bar. __
   • __ Fig. 7G legend: lacks info on the scale bar length. __
   • __ Fig. S2C-E: lack scale bars. __
   • __ Fig. S3D, F and H: lack scale bars. (Fig. S4 in the revised manuscript)__
   • __ Fig. S3J legend: lacks info on the scale bar length. (Fig. S4 in the revised manuscript)__
   • __ Fig. S4A, B, D and E: lack scale bars. (Fig. S5 in the revised manuscript)__
   • __ Fig. S4C legend: lacks info on the scale bar length. (Fig. S5 in the revised manuscript)__
   • __ Fig. S4G legend: lacks info on the scale bar length. (Fig. S5 in the revised manuscript)__ We added the scale bars and the size information to the figures and figure legends for the above figures.

   Reviewer #2 (Significance (Required)): __The findings of this study join among the relatively new literature (e.g., Steib et al., 2020 and Le Guennec et al. 2020) on the nature of centriole inner scaffold and its potential roles in centriole formation, integrity and its propensity to form the primary cilium. Therefore, it will be of interest to a group of scientists studying these topics in the field of centrosomes/cilia.

   My expertise is on the biochemistry and genetics of centriole formation in animals.__

   We thank the reviewer for his/her comments and constructive feedback to improve our manuscript. We are encouraged to see that the reviewer acknowledges how the results from our manuscript advances our understanding of centriole length, integrity and function regulation.

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   Yang, C.H., C. Kasbek, S. Majumder, A.M. Yusof, and H.A. Fisk. 2010. Mps1 phosphorylation sites regulate the function of centrin 2 in centriole assembly. Mol Biol Cell. 21:4361-4372.

   Ying, G., J.M. Frederick, and W. Baehr. 2019. Deletion of both centrin 2 (CETN2) and CETN3 destabilizes the distal connecting cilium of mouse photoreceptors. J Biol Chem. 294:3957-3973.

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   Referee #2

   Evidence, reproducibility and clarity

   Summary:

   In this study, Arslanhan et al. propose CCDC15 as a novel component of the centriole inner scaffold structure with potential roles in centriole length control, stability and the primary cilium formation in cultured epithelial cells. Using proximity labelling they explore the common interactors of Poc5 and Centrin-2, two resident molecules of the centriole inner scaffold, to hunt for novel regulators of this structure. The authors leverage expansion microscopy-based localization and siRNA-dependent loss-of-function experiments to follow up on one such protein they identify, CCDC15, with the aforementioned roles in centriole …

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   Referee #2

   Evidence, reproducibility and clarity

   Summary:

   In this study, Arslanhan et al. propose CCDC15 as a novel component of the centriole inner scaffold structure with potential roles in centriole length control, stability and the primary cilium formation in cultured epithelial cells. Using proximity labelling they explore the common interactors of Poc5 and Centrin-2, two resident molecules of the centriole inner scaffold, to hunt for novel regulators of this structure. The authors leverage expansion microscopy-based localization and siRNA-dependent loss-of-function experiments to follow up on one such protein they identify, CCDC15, with the aforementioned roles in centriole and cilia biology.

   This study is designed and laid out nicely; however, to be able to support some of the important claims regarding their proximity labelling results and exploration on the roles of CCDC15, there are several major technical and reproducibility concerns that deem major revision. Similarly, the introduction (perhaps inadvertently) omits much of the recent studies on centriole size control that have highlighted the complexity of this biological problem. As such, addressing the following major points will be essential in further considering this work for publication.

   Major comments:

   1. The authors use Poc5 and Centrin-2 molecules as joint baits to reveal the interactome of the centriole inner scaffold, however the work lacks appropriate experimental and analytical controls to argue that this is a proximity mapping "at the centriole inner scaffold". In its current state, it is simply an interactome of total Poc5 and Centrin-2, and it might be misleading to call it an interactome at the centriole inner scaffold (the statistical identification of shared interactors cannot do full justice to their biology at the centrosome). Appropriate expression data needed to delineate how large the centrosomal vs. cytoplasmic (or nucleoplasmic) fraction is for either of these molecules, both without and upon the addition of biotin (to see whether the bulk of interaction data stem from the cytoplasm/nucleoplasm or the centrioles themselves). The authors can test this by selectively blotting a lysate fraction containing the centrosomes after centrifugation, and compare them with the simultaneous blot of the supernatant (which were readily used for the blots presented in Fig. 1B). This experiment also becomes very relevant for the case of Centrin-2, as it also heavily localizes to the nucleoplasm as the authors found out (see Fig. 1A and Fig. S1A).

   Additionally, an orthogonal approach should be taken to perform bio-image analysis on their biotin/streptavidin imaging data to demonstrate the exact ratios between the centrosomal vs. cytoplasmic/nucleoplasmic biotin activation with appropriate signal normalization between the biotin/streptavidin images. This is particularly important, as although the authors claim that these cells stably express the V5BirA*, it seems that there is partial clonality to the expression. Some cells in both the Poc5 and Centrin-2 fusion constructs appear to lack the V5/Streptavidin signals upon Biotin addition (such as the two cells in the centre right in Poc5, and again a cell in the centre right for Centrin-2 images). In its current form, Fig. 1A lacks signal quantification and does not report any information about the replicates and distributions of the data. I worry that this may raise concerns on the reproducibility if published in its current form.

   Similarly, it is not clear whether the expression of Poc5 and Centrin-2 fusion molecules somehow interfere with their endogenous interactions or function. At least some loss-of-function (e.g., RNAi) experiments should be performed where the depletion of endogenous proteins should be attempted to rescue by the fusion constructs. This will help evaluate whether the fusion proteins can rescue the depletion of their endogenous counterparts and behave as expected from a wild-type scenario.

   Overall, as the entire claim around the proximity mapping revolve around its assumption about the centriole inner scaffold, these controls seem imperative to substantiate the ground truth of the biology presented in the manuscript.

   1. I am curious about the choices of the cell lines in this work. The proximity mapping to reveal CCDC15 as a candidate protein for centriole inner scaffold was performed in HEK293T cells (human embryonic kidney), however its immunostaining was performed using RPE1 and U2OS cells (human retinal and osteosarcoma epithelial cells respectively). This raises questions regarding the generality of CCDC15 as a centriole inner scaffold protein. Could CCDC15 be simply unique to the centriole inner scaffold of epithelial cells such as RPE1 and U2OS cells? Or could the authors demonstrate any information/data on whether it's similarly localized to the inner scaffold in embryonic kidney cells or other cell types? If not, the claims should be moderated to reflect this fine detail.
   2. Discussions and data on the localization of CCDC15 to centriolar satellites appear anecdotal and not fully convincing (Fig. S2D). Given that the authors test the relevance of PCM1 for CCDC15's centriolar localization, it is key to have quantitative data supporting their claim that centriolar satellites can help recruit CCDC15 to the centriole. Could the authors quantify what proportion of CCDC15 localize to the centriolar satellites? One way to do this could be to quantify the colocalization coefficience of CCDC15 and PCM1 signals.
   3. Similar to above (#3), there is no quantitative information on the co-localization or partial co-localization of the signal foci in Fig. 3A and 3B. The authors readily study CCDC15's localization in wonderful detail in their expansion microscopy data, so they could actually consider taking out Fig. 3A and 3B, as the data seem redundant without any quantification.
   4. Do the authors also feel that CCDC15 localize to the core lumen in a somehow helical manner (Fig. 1A, Fig. 1F top and bottom panels, Fig. 5A etc.)? Le Guennec et al. 2020's helical lattice proposal for the inner scaffold further reaffirms that CCDC15 is indeed a likely major component of the inner scaffold. In my view, authors should state this physical similarity explicitly to further support their findings on CCDC15.
   5. The data on the link between the CCDC15 recruitment and the centriole growth (Fig. 4F) or the G2 phase of the cell cycle (Fig. 4H) are not fully convincing without quantitative data. For Fig. 4F, the authors should consider plotting the daughter centriole length vs the daughter CCDC15 intensities against each another, to see whether more elongated daughters truly tend to have more CCDC15. For Fig. 4H, the argument regarding the cell cycle regulation requires quantification of the bands from several WB repeats, normalized to the expression of GAPDH within each blot (this is particularly relevant, as the bands of CCDC15 do not look dramatically different enough to draw conclusions by eye).
   6. The authors find herein that CCDC15 depletion lead to centrioles that are ~10% shorter than the controls. With the depletion of Poc5 and Wdr90 (other proposed components of the inner scaffold), the centrioles end up larger however (Steib et al., 2020). If the role of inner scaffold in promoting centriole elongation is structural, why are these two results the opposite of each other? I realize there is a brief discussion about this at the end of the paper, however, this requires a detailed discussion and speculation on the relevance of these findings. It would be key to clarify whether the inner scaffold as a structure inhibits or promotes centriole growth - or somehow both? If so, how?

   There might be some intriguing opposing regulatory action of Poc5 and CCDC15 as demonstrated here, where CCDC15 depletion leads to slightly over-recruitment of Poc5, and vice versa. Does this suggest that a tug-of-war going on between different molecules that localize to the inner scaffold? Does this provide some dynamicity to this structure, which might in turn regulate centriole length both positively and negatively? This may be analogous to how opposing forces of dyneins and kinesins provide robust length control for mitotic spindles. I am speculating here, but hopefully these may provide some useful grounds for further discussion in the paper. If the authors deem it interesting experimentally, they can test whether the two molecules indeed regulate centriole length by opposing each other's action, by a double siRNA of CCDC15 and Poc5 to see if this retains the centriole length at its control siRNA size (like how they do a similar test for Poc1's potential co-operativity with CCDC15 in Fig. 6J).

   1. In their introduction section, the authors discuss how relatively little is known about the size control of centrioles, however they fail to mention a series of recent primary literature that uncover striking, new mechanisms and novel molecular players that highlight the complexity of centriole size control. This complexity appears to arise from the existence of multitude of length control mechanisms that influence the cartwheel or the microtubule length individually, or simultaneously via yet-to-be further explored crosstalk mechanisms.

   a. As such, when the authors talk about the procentriole size control in the introduction, they should discuss and refer to the following studies, in terms of:

   • How theoretical and experimental work demonstrate that procentriole length may vary dependent on the levels of its building block Sas-6 in animals (Dias Louro et al., 2021 PMID: 33970906; Grzonka and Bazzi, 2022 bioRxiv).
   • How a homeostatic Polo-like kinase 4 clock regulates centriole size during the cell cycle (Aydogan et al., 2018 JCB PMID: 29500190), and how biochemistry and genetics coupled with mathematical modelling unravel a conserved negative feedback loop between Cep152 and Plk4 that constitutes the oscillations of this clock in flies (Boese et al., 2018 PMID: 30256714; Aydogan et al., 2020 PMID: 32531200) and human cells (Takao et al., 2019 PMID: 31533936).

   b. Similarly, when the authors refer to centriole size control induced by microtubule-related proteins, they should highlight the further complexity of this process by referring to:

   • How a molecule located at the microtubule wall, Cep295/Ana1, can regulate centriole length in flies (Saurya et al., 2016 PMID:27206860) and human cells (Chang et al., 2016 PMID:27185865) - like all the other centriolar MT molecules that the authors discuss in the manuscript.
   • How a crosstalk between Cep97 and Cep152 influences centriole growth in fly spermatids (Galletta et al., 2016 PMID:27185836).
   • How a crosstalk between CP110-Cep97 and Plk4 influences centriole growth in flies (Aydogan et al., 2022 PMID:35707992), and this molecular crosstalk is conserved, at least biochemically, in human cells (Lee et al., 2017 PMID:28562169).

   Minor comments:

   • Introduction section: Literature reference missing for the sentence starting with "Importantly, the stable nature of centrioles enables them to withstand...".
   • Fig. S1 legend: A typo as follows: CRAPome banalysis should read CRAPome analysis.
   • Fig. S2: Info on the scale bar in the legend is missing in Fig. S2A. Scale bars for different panels are missing in general in Fig. S2A.
   • Fig. 3A and 3B: When displaying the data, coloured cartoon diagrams would be beneficial to guide the reader who are not fully familiar with the spatial orientation of these proteins.
   • Fig. 3H: No information about the sample number (number of cells or technical repeats examined) reported.
   • Fig. S3B legend: A typo as follows: CCD15-depelted RPE1 cells should read CCDC15-depleted RPE1 cells.
   • Fig. S3B legend: A typo as follows: cellswere fixed with should read cells were fixed with.
   • There are many spelling mistakes and typos throughout the paper. I have listed a few examples above, but please carefully read through the manuscript to correct all the errors.
   • Fig. S3E: The orange columns depicting % of cells with Sas-6 dots look awkward. Why the columns look larger than the mean line? Please correct as appropriate.
   • Although authors provide microscopy information for the U-ExM and FRAP experiments, there is no information about the microscopy on regular confocal imaging experiments which should be detailed in Materials and Methods. Also, there is no information about the lenses, laser lines and the filter sets that were used in the imaging experiments. These should be provided as well.
   • Fig. 2A: lacks a scale bar.
   • Fig. 2C legend: lacks info on the scale bar length.
   • Fig. 5A legend: lacks info on the scale bar length.
   • Fig. 7A: lacks a scale bar.
   • Fig. 7G legend: lacks info on the scale bar length.
   • Fig. S2C-E: lack scale bars.
   • Fig. S3D, F and H: lack scale bars.
   • Fig. S3J legend: lacks info on the scale bar length.
   • Fig. S4A, B, D and E: lack scale bars.
   • Fig. S4C legend: lacks info on the scale bar length.
   • Fig. S4G legend: lacks info on the scale bar length.

   Significance

   The findings of this study join among the relatively new literature (e.g., Steib et al., 2020 and Le Guennec et al. 2020) on the nature of centriole inner scaffold and its potential roles in centriole formation, integrity and its propensity to form the primary cilium. Therefore, it will be of interest to a group of scientists studying these topics in the field of centrosomes/cilia.

   My expertise is on the biochemistry and genetics of centriole formation in animals.

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   Referee #1

   Evidence, reproducibility and clarity

   Summary:

   In this manuscript, Arslanhan and colleagues use proximity proteomics to identify CCDC15 as a new centriolar protein that co-localizes and interacts with known inner scaffold proteins in cell culture-based systems. Functional characterization using state-of-the-art expansion microscopy techniques reveals defects in centriole length and integrity. The authors further reveal intriguing aberrations in the recruitment of other centriole inner scaffold proteins, such as POC1B and the SFI1/centrin complex, in CCDC15-deficient cells, and observe defects in primary cilia.

   Major comments:

   • The authors present a high-quality …

   Note: This preprint has been reviewed by subject experts for Review Commons. Content has not been altered except for formatting.

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   Referee #1

   Evidence, reproducibility and clarity

   Summary:

   In this manuscript, Arslanhan and colleagues use proximity proteomics to identify CCDC15 as a new centriolar protein that co-localizes and interacts with known inner scaffold proteins in cell culture-based systems. Functional characterization using state-of-the-art expansion microscopy techniques reveals defects in centriole length and integrity. The authors further reveal intriguing aberrations in the recruitment of other centriole inner scaffold proteins, such as POC1B and the SFI1/centrin complex, in CCDC15-deficient cells, and observe defects in primary cilia.

   Major comments:

   • The authors present a high-quality manuscript that identifies a novel centriolar protein by elegantly revealing and comparing the proximity proteomes of two known centriolar proteins, which represents an important component for the maintenance of centrioles.
   • Data are often presented from two independent experiments (n = 2), which is nice, but also the minimum for experiments in biology. It is strongly recommended to perform at least three independent experiments.
   • The protein interaction studies presented in Fig. 3 could be of higher quality. While it is great that the authors compared interactions to the centriolar protein SAS6, which is not expected to interact with CCDC15, the presented data raise many questions. 1) In most cases, co-expression of tagged CCDC15 stabilizes the tested interaction partners, such that the overall abundance seems to be higher. The increase in protein abundance is substantial for Flag-FAM161A (Fig. 3D) and GFP-Centrin-2 (Fig. 3E) and is even higher for the non-interactor SAS6 (Fig. 3G), while it cannot be assessed for GFP-POC1B (Fig. 3F). Hence, the higher expression levels under these conditions make it more likely that these proteins are "pulled down" and therefore do not represent appropriate controls. 2) All Co-IP experiments are lacking negative controls in the form of proteins that are not pulled down under the presented conditions. 3) The amounts of co-precipitation of the tested proteins appears very different. Could this reflect strong or weak interactors, or does it reflect the abundance of the respective proteins in centrioles?
   • The observation that IFT88 is supposedly decreased at the base of cilia in CCDC15-depleted cells requires additional experiments/evidence. Fig. 7G shows the results of n = 2 and more importantly, a similar reduction of gamma-tubulin in siCCDC15. Could the observed reduction in IFT88 be explained by a decrease in accessibility to immunofluorescence microscopy? Would the reduction in IFT88 at the base also be apparent when the signals were normalized to gamma-tubulin signals?
   • The observed Hedgehog signaling defects are described as follows: "CCDC15 depletion significantly decreased the percentage of SMO-positive cells". It is similarly described in the figure legend. If this was true, the simplest explanation would be that it reflects the reduction in ciliation rate (which is in a similar range). If SMO-positive cilia (instead of "cells") were determined, the text needs to be changed accordingly.
   • OPTIONAL: While expansion microscopy is slowly becoming one of the standard super-resolution microscopy methods, which is particularly well validated for studying centrioles, the authors should consider confirming part of their findings (as a proof of principle, surely not in all instances) by more established techniques. This could serve to convince critical reviewers that may argue that the expansion process may induce architectural defects of destabilized centrioles, as observed after disruptions of components, such as in Fig. 6. Alternatively, the authors could cite additional work that make strong cases about the suitability of expansion microscopy for their studies, ideally with comparisons to other methods.

   Minor points:

   • Text, figures, and referencing are clear and accurate, apart from minor exceptions.
   • The title suggests a regulator role for CCDC15 in centriole integrity and ciliogenesis, which has formally not been shown.
   • As the authors observe changes in centriole lengths in the absence of CCDC15, it would be very insightful to compare these phenotypes to other components that affect centriolar length, such as C2CD3, human Augmin complex components (as HAUS6 is identified in Fig. 1) or others. These could be interesting aspects for discussion, additional experiments are OPTIONAL.
   • While the reduced ciliation rate in the absence of CCDC15 is convincing, the authors did not investigate "ciliogenesis", i.e. the formation of cilia, and hence should re-phrase. The sentence in the discussion that "CCDC15 functions during assembly" should be removed.
   • The existence of stably associated CCDC15 pools with centrosomes (Fig. 2) requires further evidence. The recovery of fluorescence after photobleaching in FRAP experiments is strongly dependent on experimental setups and is only semi-quantitative. A full recovery is unrealistic, hence, it is ideally compared to a known static or known mobile component. I personally think this experiment -as it is presented now- is of little value to the overall fantastic study. The authors may consider omitting this piece of data.
   • The data that CCDC15 is a cell cycle-regulated protein is not very convincing (see Fig. 3H), as the signals area weak and the experiment has been performed only once (n= 1). This piece of data does not appear to be very critical for the main conclusions of the manuscript and may be omitted. Otherwise, this experiment should be repeated to allow for proper statistical analysis.
   • Experimental details on how "defective centrioles" are determined are missing.
   • For figures, in which the focus should be on growing centrioles (see Fig. 4), it could be helpful to guide the reader and indicate the respective areas of the micrographs by arrows.
   • Page18: "centriole length shortening" could be changed to "centriole shortening".
   • It is unclear how the authors determine distal from proximal ends of centrioles in presented micrographs (see Fig. 5D).
   • Fig. 7A is missing scale bars and Fig.7 overall is lacking rectangle indicators of the areas that are shown at higher magnification in the insets.
   • Fig. 7C displays cilia that appear very short, especially when comparing to the micrographs and bar graphs presented. The authors may want to explain this discrepancy.

   Significance

   • From a technical point of view the authors use two state-of-the-art technologies, namely proximity labeling combined with proteomics and ultrastructure expansion microscopy, that are both challenging and very well suited to address the main questions of this study.
   • General assessment: The presented study is of highest experimental quality. Despite being very challenging, the expansion microscopy and proximity proteomics experiments have been designed and performed very well to allow solid interpretation. The results of the central data are consistent and allow strong first conclusions about the putative function of the newly identified centriolar protein CCDC15. The study presents a solid foundation for future hypothesis-driven, mechanistic analysis of CCDC15 and inner scaffold proteins in centriole length control and maintaining centriole integrity. The only limitation of the study is that the technically simpler experiments should be repeated to allow proper statistical assessment, which can be addressed easily.
   • Advance: This is the first study that identifies CCDC15 as a centriolar protein and localizes it to the inner scaffold. It further describes a function for CCDC15 in centriole length control and shows its importance in maintaining centriole integrity with consequences for stable cilia formation in tissue culture. The study provides further functional insights into the interdependence of inner scaffold proteins and the role of CCDC15 in the recruitment of the SFI1/centrin distal complex.
   • Audience: The manuscript will be of broad interest to the fields of centrosome and cell biology, both from a basic research and genetics/clinical point of view due to the association with human disorders. The state-of-the-art technologies applied will be of interest to a broader cell and molecular biology readership that studies subcellular compartments and microtubules.
   • Reviewer's field of expertise: Genetics, imaging, and protein-protein interaction studies with a focus on centrosomes and cilia.

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   Version published to 10.1101/2023.02.16.528810v1 on bioRxiv

   Feb 18, 2023