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Cited by 105Renal Diseases and GlomerulopathiesAdvanced Proteomics Techniques and ApplicationsRenal and related cancers

A Multi-layered Quantitative In Vivo Expression Atlas of the Podocyte Unravels Kidney Disease Candidate Genes

Open access
Rinschen, Markus M., Gödel, Markus, Grahammer, Florian, Zschiedrich, Stefan, Helmstädter, Martin, Kretz, Oliver, Zarei, Mostafa, Braun, Daniela A. +19 more·2018·Cell Reports
DOI 10.1016/j.celrep.2018.04.059PMC PMC5986710
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Abstract

Damage to and loss of glomerular podocytes has been identified as the culprit lesion in progressive kidney diseases. Here, we combine mass spectrometry-based proteomics with mRNA sequencing, bioinformatics, and hypothesis-driven studies to provide a comprehensive and quantitative map of mammalian podocytes that identifies unanticipated signaling pathways. Comparison of the in vivo datasets with proteomics data from podocyte cell cultures showed a limited value of available cell culture models. Moreover, in vivo stable isotope labeling by amino acids uncovered surprisingly rapid synthesis of mitochondrial proteins under steady-state conditions that was perturbed under autophagy-deficient, disease-susceptible conditions. Integration of acquired omics dimensions suggested FARP1 as a candidate essential for podocyte function, which could be substantiated by genetic analysis in humans and knockdown experiments in zebrafish. This work exemplifies how the integration of multi-omics datasets can identify a framework of cell-type-specific features relevant for organ health and disease.

AI snapshot

Written from the paper’s full text.

TL;DR

This study combines quantitative in vivo proteomics, mRNA sequencing, and dynamic stable isotope labeling to build a multi-layered atlas of mouse podocytes and glomerular non-podocytes. Integrating these datasets identifies podocyte-enriched proteins, cell-culture artifacts, proteostatic features, and FARP1 as a candidate nephrotic syndrome gene.

Key findings

  • Deep mapping identified more than 9,000 proteins, with absolute quantification of 6,979 proteins; 551 proteins were significantly podocyte-enriched. Disease-associated genes comprised 35 of 7,000 (0.5%) quantified proteins but contributed approximately 4% of podocyte protein mass, and the slit diaphragm complex podocin-Neph1-Nephrin-Fat1 showed a copy-number ratio of ∼10:2:1:0.5.
  • Podocyte mRNA and protein abundances correlated only weakly overall (Pearson’s R = 0.47), though the correlation was stronger for podocytes than non-podocytes; 2D enrichment showed ECM proteins decreased and metabolic proteins stabilized relative to mRNA.
  • In vivo stable isotope labeling revealed rapid synthesis of mitochondrial proteins under steady-state conditions; ATG5 podocyte-specific knockout podocytes showed significantly lower incorporation of ER proteins and significantly higher incorporation of mitochondrial proteins compared with controls.
  • Multi-omics integration nominated FARP1: a homozygous FARP1 mutation was found in one family with nephrotic syndrome, and farp1 knockdown in zebrafish larvae caused pericardial edema and proteinuria.

Methods

  • Podocytes and non-podocyte glomerular cells were isolated by FACS from hNPHS2Cre∗mT/mG mice, then analyzed by mass spectrometry-based proteomics, mRNA sequencing, and bioinformatics; absolute protein quantification used iBAQ and the proteomic ruler.
  • In vivo stable isotope labeling used adult mice fed 13C6-lysine for 1, 2, and 3 weeks, with hierarchical clustering of heavy/light ratios and comparison to ATG5 podocyte-specific knockout mice.
  • Cultured mouse and human podocytes were compared with native podocytes, including growth on soft matrices with an elastic modulus of 12 kPa; human genetic screening used exome sequencing of 430 families with hereditary nephrotic syndrome and a second cohort of 700 patients with nephrotic syndrome.

Limitations

  • Stated: stable isotope incorporation data “do not strictly correlate with a protein ‘half-life’ because of intracellular amino acid recycling”; several known podocyte genes, such as Trpc6, were identified but could not be quantified because of low abundance; the second FARP1 patient’s alleles could not be confirmed to segregate because family DNA was unavailable; and the ATG5-related mitochondrial findings “need further corroboration.”
  • Evident from the text: the human genetic evidence for FARP1 is limited to one homozygous family plus a second heterozygous patient with unclear segregation, and the functional support comes from zebrafish knockdown rather than rescue experiments.
  • Evident from the text: the cell-culture comparison relies on a previously published immortalized mouse podocyte line, and the paper notes that soft-matrix culture does not restore podocyte-specific actin binders or membrane proteins.

Model-written summary. Check it against the paper before relying on it.

Integrity signals

Registry

Crossref · 10.1016/j.celrep.2018.04.059

Cites

84 of 84 references verified0 citation errors · 0 not checkable

Statistics

Nothing to recompute.

Claims the paper makes

0 of 53 cited sources checked · 0 supported · 0 flagged

  • Findingown data

    Absolute quantification of 6,979 proteins was performed using iBAQ.

    “We performed absolute quantification of 6,979 proteins using the intensity-based absolute quantification (iBAQ) approach (Table S2).”
    Quote in the paperSubstantial claim
  • Findingown data

    The approach identified more than 9,000 different proteins in total.

    “This approach identified, in total, more than 9,000 different proteins (Tables S1 and S2).”
    Quote in the paperNot a substantial claim
  • Findingown data

    Knockdown of Tsp26A caused overt alterations in nephrocyte ultrastructure.

    “We also found overt alterations in nephrocyte ultrastructure (Figure 3F)”
    Quote in the paperSubstantial claim
  • Findingcitation

    Among the 551 podocyte-enriched proteins were many gene products currently known to be associated with hereditary nephrotic syndrome.

    “among these were many gene products currently known to be associated with hereditary nephrotic syndrome (Sadowski et al., 2015).”
    Quote in the paperNot a substantial claim0 of 1 sources checked
    • cites Sadowski et al., 2015 source

      Not checked in the free run.

  • Findingown data

    ATG5 knockout podocytes had significantly higher incorporation of mitochondrial proteins compared with control podocytes.

    “and, surprisingly a significantly higher incorporation of mitochondrial proteins compared with control podocytes (Figure 5H).”
    Quote in the paperSubstantial claim
  • May combine two claims. 25
  • The quote only partly states this claim. 1
  • Classified as probably not a substantial claim. 25

  • May combine two claims.

    Findingown data

    Significantly enriched protein domains in the 551 podocyte-enriched proteins were Fn3 and IgG-like domains, PDZ domains, i-set domains, CH domain, FERM domain proteins, and tetraspanins.

    “Significantly enriched protein domains were Fn3 and immunoglobulin G (IgG)-like domains (e.g., in Nephrin), PDZ domains (e.g., in ezrin and Par-3), i-set domains (e.g., in nephrin and VCAM/NCAM), CH domain (e.g., in actinin-4), and FERM domain proteins (e.g., in ezrin) or tetraspanins (e.g., CD151).”
    Quote in the paperNot a substantial claim

  • May combine two claims.

    Findingown data

    Podocytes have high mitochondrial protein synthesis but an overall low protein copy number of mitochondrial proteins.

    “An unexpected finding was that podocytes have high mitochondrial protein synthesis but an overall low protein copy number of mitochondrial proteins.”
    Quote in the paperSubstantial claim

  • May combine two claims.

    Findingown data

    The podocyte mRNA-seq dataset was similar to previously published mRNA-seq analyses but demonstrated greater depth when analyzed with the same parameters.

    “Our dataset was similar to previously published mRNA sequencing (mRNA-seq) analyses but demonstrated a greater depth upon analysis with the same parameters (Figure 2A; Table S3; Figure S2).”
    Quote in the paperNot a substantial claim

  • May combine two claims.

    Findingown data

    Disease-associated genes in slit diaphragm and actin-related processes were largely defined by very high Z scores in all four parameters and clustered close to each other.

    “We found that disease-associated genes in slit diaphragm and actin-related processes were largely defined by very high Z scores in all of the four parameters and clustered close to each other (Figures 6A and 6B).”
    Quote in the paperSubstantial claim

  • May combine two claims.

    Findingown data

    Three clusters contained proteins with high abundance in cell lines compared with native podocytes and were enriched for actin cytoskeleton, including stress fibers and focal adhesion proteins.

    “Three clusters contained proteins with high abundance in cell lines compared with the native podocytes and were enriched for proteins related to the actin cytoskeleton, including stress fibers and focal adhesion proteins (Figure 4A).”
    Quote in the paperSubstantial claim

  • May combine two claims.

    Findingown data

    iBAQ data correlated with transcriptomic tpm values, but the correlation was rather weak.

    “iBAQ data were correlated with the transcriptomic (tpm) values, but the correlation was rather weak (Figure 2C).”
    Quote in the paperNot a substantial claim

  • The quote only partly states this claim.

    Findingown data

    Cytoskeletal proteins like Actn4 and Arhgdia contributed most to the disease-associated protein mass.

    “with cytoskeletal proteins like Actn4 and Arhgdia contributing most to this amount (Figure 1D).”
    Quote in the paperNot a substantial claim

  • May combine two claims.

    Findingown data

    Disease-associated genes for FSGS or hereditary nephrotic syndrome comprised 35 of 7,000 (0.5%) absolutely quantified proteins and contributed approximately 4% of podocyte protein mass.

    “These “disease-associated genes,” although only comprising 35 of 7,000 (0.5%) absolutely quantified proteins, contributed approximately 4% of the podocyte protein mass”
    Quote in the paperSubstantial claim

  • Probably not a substantial claim: may not pass S3 (load-bearing).

    Findingown data

    Several other known podocyte genes, such as Trpc6, were identified but could not be quantified because of low abundance.

    “Several other known podocyte genes (e.g., Trpc6) were identified but could not be quantified because of their low abundance.”
    Quote in the paperNot a substantial claim

  • May combine two claims.

    Findingown data

    Actin filament proteins and stress fiber proteins were significantly depleted by culturing podocytes on the soft matrix, making them more similar to native podocytes.

    “On a global level, actin filament proteins and stress fiber proteins were significantly depleted by culturing podocytes on the “soft” matrix, which made them, in this regard, “more similar” to the native podocyte (based on the log2 ratio of podocyte/non-podocyte protein expression) (Figure 4D).”
    Quote in the paperSubstantial claim

  • May combine two claims.

    Findingown data

    6,193 proteins were identified in both native podocytes and the mouse podocyte cell line, representing a significant overlap.

    “We could identify 6,193 proteins in both samples, representing a significant overlap between both samples (Figure S4C).”
    Quote in the paperSubstantial claim

  • May combine two claims.

    Findingcitation

    Two clusters showed differences between 33°C and 37°C and native cells; these were related to the cell cycle.

    “Two clusters showed differences between 33°C and 37°C and native cells; these were, as expected (Rinschen et al., 2016b), related to the cell cycle (Figure 4C).”
    Quote in the paperNot a substantial claim0 of 1 sources checked
    • cites Rinschen et al., 2016b

      Not checked in the free run.

  • May combine two claims.

    Findingown data

    On a global level, podocyte-specific proteins were significantly reduced for mitochondria as well as RNA and DNA binding proteins.

    “On a global level, podocyte-specific proteins were significantly reduced for mitochondria as well as RNA and DNA binding proteins (Figure 3C)”
    Quote in the paperNot a substantial claim

  • May combine two claims.

    Findingown data

    In the Exome Aggregation Consortium (ExAC) cohort of 80,000 predominantly healthy individuals, the minor allele frequency of either FARP1 allele is below 0.01%, and neither allele has been reported in the homozygous state.

    “of 80,000 predominantly healthy individuals (Exome Aggregation Consortium [ExAC]), the minor allele frequency of either allele is below 0.01%, and it has not been reported in the homozygous state”
    Quote in the paperSubstantial claim

  • May combine two claims.

    Findingown data

    FARP1 and genes identified in a recent population-based study clustered close to known disease genes and shared high Z scores in at least three of four parameters.

    “This candidate gene, and the genes identified in a recent population-based study (Yu et al., 2016), clustered close to known disease genes (Figure 6A), and all shared high Z scores in at least three of the four parameters analyzed (Figure 6B).”
    Quote in the paperSubstantial claim0 of 1 sources checked
    • cites Yu et al., 2016

      Not checked in the free run.

  • May combine two claims.

    Findingnone given

    Cultivation on soft matrices does not increase the expression of podocyte-specific actin binders or podocyte membrane proteins, which are only minimally expressed under both conditions.

    “Cultivation on soft matrices does not, however, increase the expression of podocyte-specific actin binders or podocyte membrane proteins, which are only minimally expressed under both conditions.”
    Quote in the paperNot a substantial claim

  • May combine two claims.

    Findingown data

    Knockdown of farp1 mRNA in zebrafish larvae resulted in pericardial edema and proteinuria.

    “knockdown of the farp1 mRNA in zebrafish larvae resulted in a phenotype of pericardial edema as well as proteinuria”
    Quote in the paperSubstantial claim

  • May combine two claims.

    Findingown data

    A significant fraction of these proteins has not been extensively studied and will require further consideration.

    “A significant fraction of these proteins, however, has not been extensively studied and will require further consideration”
    Quote in the paperNot a substantial claim

  • May combine two claims.

    Findingown data

    Podocytes express a high abundance of actin-binding proteins and proteins known to be localizing to the leading edge of the cell.

    “Podocytes express a high abundance of actin-binding proteins and proteins known to be localizing to the leading edge of the cell”
    Quote in the paperNot a substantial claim

  • May combine two claims.

    Findingown data

    Cultivation of either human or mouse podocyte cells on soft matrices resulted in a major shift in the proteome, which partly reduced the actin-related cell culture artefact.

    “the cultivation of either human or mouse podocyte cells on soft matrices resulted in a major shift in the proteome, which partly reduced this actin-related cell culture artefact”
    Quote in the paperSubstantial claim

  • May combine two claims.

    Findingcitation

    Mediators of alternative autophagy (e.g., Rab9 and Becn1) are abundantly expressed in podocytes but not significantly enriched.

    “mediators of alternative autophagy (e.g., Rab9 and Becn1) are abundantly expressed in podocytes but not significantly enriched”
    Quote in the paperNot a substantial claim

  • Probably not a substantial claim: may not pass S3 (load-bearing).

    Premisecitation

    In vivo stable amino acid isotope labeling strategies opened new avenues for quantification of protein dynamics when used in pulse experiments.

    “In addition, in vivo stable amino acid isotope labeling strategies opened new avenues for the quantification of protein dynamics when used in pulse experiments (Krüger et al., 2008, Savas et al., 2012, Toyama et al., 2013).”
    Quote in the paperNot a substantial claim0 of 3 sources checked
    • cites Krüger et al., 2008 source

      Not checked in the free run.

    • cites Savas et al., 2012 source

      Not checked in the free run.

    • cites Toyama et al., 2013 source

      Not checked in the free run.

  • Probably not a substantial claim: may not pass S3 (load-bearing). May combine two claims.

    Premisecitation

    Proteins can be resolved and quantified relatively and absolutely, culminating in a near-comprehensive mass spectrometry-based expression map of the human proteome.

    “As a result, proteins can be resolved and quantified relatively and absolutely, culminating in a near-comprehensive mass spectrometry-based expression map of the human proteome (Kim et al., 2014, Wilhelm et al., 2014).”
    Quote in the paperNot a substantial claim0 of 2 sources checked
    • cites Kim et al., 2014 source

      Not checked in the free run.

    • cites Wilhelm et al., 2014 source

      Not checked in the free run.

  • Probably not a substantial claim: may not pass S3 (load-bearing).

    Premisecitation

    iBAQ is relative to copy numbers in a given sample.

    “This proteomics parameter is relative to copy numbers in a given sample (Kohli et al., 2014, Schwanhäusser et al., 2011).”
    Quote in the paperNot a substantial claim0 of 2 sources checked
    • cites Kohli et al., 2014 source

      Not checked in the free run.

    • cites Schwanhäusser et al., 2011 source

      Not checked in the free run.

  • May combine two claims.

    Premisecitation

    Incorporation of heavy isotope-labeled lysine should correlate with dynamic synthesis rate, although these data do not strictly correlate with protein half-life because of intracellular amino acid recycling.

    “The incorporation of this essential amino acid should correlate with the dynamic synthesis rate (although these data do not strictly correlate with a protein “half-life” because of intracellular amino acid recycling (Krüger et al., 2008)).”
    Quote in the paperSubstantial claim0 of 1 sources checked
    • cites Krüger et al., 2008 source

      Not checked in the free run.

  • Classified as probably not a substantial claim.

    Interpretationreasoning

    Some differences between cultured and native podocytes may be a cell culture artefact due to the mechanical properties of the plastic dish.

    “We postulated that some of these differences may have been a cell culture artefact because of the mechanical properties of the plastic dish on which these cells were cultivated.”
    Quote in the paperSubstantial claim

  • Probably not a substantial claim: may not pass S3 (load-bearing).

    Premisecitation

    Podocyte protein homeostasis largely depends on signaling mediated via posttranslational modifications, such as phosphorylation, ubiquitylation, acetylation, and proteolytic processing.

    “Podocyte protein homeostasis largely depends on signaling mediated via posttranslational modifications, such as phosphorylation, ubiquitylation, acetylation, and proteolytic processing (New et al., 2014).”
    Quote in the paperNot a substantial claim0 of 1 sources checked
    • cites New et al., 2014 source

      Not checked in the free run.

  • Probably not a substantial claim: may not pass S3 (load-bearing).

    Premisecitation

    The ATG5 pKO allele makes podocytes extremely susceptible to damage.

    “The ATG5 pKO allele makes podocytes extremely susceptible to damage (Hartleben et al., 2010).”
    Quote in the paperNot a substantial claim0 of 1 sources checked
    • cites Hartleben et al., 2010 source

      Not checked in the free run.

  • May combine two claims.

    Premisecitation

    Proteins synthesized rapidly should exhibit a high heavy amino acid incorporation rate (high H/L ratio), whereas stable, long-lived proteins with slow translation should have a lower incorporation rate.

    “Still, proteins synthesized rapidly should exhibit a high heavy amino acid incorporation rate (and a high heavy/light [H/L] ratio), whereas stable, “long-lived” proteins with slow translation should have a lower incorporation rate (Savas et al., 2012).”
    Quote in the paperSubstantial claim0 of 1 sources checked
    • cites Savas et al., 2012 source

      Not checked in the free run.

  • Probably not a substantial claim: may not pass S3 (load-bearing).

    Study design and conductnone given

    The mass spectrometers were calibrated weekly.

    “The mass spectrometers were calibrated weekly.”
    Quote in the paperNot a substantial claim

  • Probably not a substantial claim: may not pass S3 (load-bearing).

    Study design and conductnone given

    Validated cell lines were regularly tested for mycoplasms using a commercial kit.

    “Validated cell lines were regularly tested for mycoplasms using a commercial kit (VENOR, Sigma).”
    Quote in the paperNot a substantial claim

  • Probably not a substantial claim: may not pass S2 (checkable).

    Interpretationown data

    These data provide a unique resource and starting point for the next level of systematic understanding of podocyte identity, function, and glomerular disease mechanisms, including a systems view of podocyte proteome dynamics.

    “these data provide a unique resource and starting point for the next level of systematic understanding of podocyte identity, function, and glomerular disease mechanisms, including a systems view of podocyte proteome dynamics”
    Quote in the paperNot a substantial claim

  • Probably not a substantial claim: may not pass S3 (load-bearing).

    Premisecitation

    A similar number of proteins has been shown to be expressed in native neurons.

    “a similar number of proteins has been shown to be expressed in native neurons”
    Quote in the paperNot a substantial claim0 of 1 sources checked
    • cites Sharma et al., 2015 source

      Not checked in the free run.

  • Probably not a substantial claim: may not pass S3 (load-bearing).

    Interpretationcitation

    The dysregulation of stress fiber formation proteins in cell cultures could be caused by stiffness of the cell culture dish.

    “a finding that could be caused by stiffness of the cell culture dish”
    Quote in the paperNot a substantial claim0 of 1 sources checked
    • cites Gilbert et al., 2010 source

      Not checked in the free run.

  • Probably not a substantial claim: may not pass S2 (checkable), S3 (load-bearing).

    Interpretationown data

    Based on these global proteomic data, the leading edge paradigm could be further expanded.

    “based on these global proteomic data, this paradigm could be further expanded”
    Quote in the paperNot a substantial claim

  • Probably not a substantial claim: may not pass S3 (load-bearing).

    Premisecitation

    At least 10,000 proteins are suggested to be expressed in a cultured cell line.

    “At least 10,000 proteins are suggested to be expressed in a cultured cell line”
    Quote in the paperNot a substantial claim0 of 3 sources checked
    • cites Kulak et al., 2014 source

      Not checked in the free run.

    • cites Mann et al., 2013 source

      Not checked in the free run.

    • cites Nagaraj et al., 2011 source

      Not checked in the free run.

  • May combine two claims.

    Premisecitation

    Several of the proteins, but by far not all of them, have already been studied in podocytes and have been linked in part by dramatic phenotypes in conditional and targeted mouse models or human patients.

    “Several of the proteins, but by far not all of them, have already been studied in podocytes and have been linked in part by dramatic phenotypes in conditional and targeted mouse models (e.g., protein kinase C) (Huber et al., 2009) or human patients (e.g., MAGI2; Bierzynska et al., 2016).”
    Quote in the paperNot a substantial claim0 of 2 sources checked
    • cites Huber et al., 2009 source

      Not checked in the free run.

    • cites Bierzynska et al., 2016 source

      Not checked in the free run.

  • May combine two claims.

    Interpretationreasoning

    The podocyte has an overall low abundance of mitochondrial proteins but high mitochondrial resynthesis and, assuming a steady-state equilibrium, also turnover.

    “Therefore, the podocyte has an overall low abundance of mitochondrial proteins but high mitochondrial resynthesis and, assuming a steady-state equilibrium, also turnover.”
    Quote in the paperSubstantial claim
    • The authors state this as an assumption: The podocyte is in a steady-state equilibrium with respect to mitochondrial protein synthesis and degradation.

  • Probably not a substantial claim: may not pass S2 (checkable).

    Interpretationown data

    This opens the door for a potential integrative "reverse genetic" approach to predict functionally relevant candidate genes associated with human podocyte diseases and prioritize them for further functional testing.

    “This opens the door for a potential integrative “reverse genetic” approach to predict functionally relevant candidate genes associated with human podocyte diseases (Figure 6; Table S7) and prioritize them for further functional testing”
    Quote in the paperNot a substantial claim

  • Probably not a substantial claim: may not pass S2 (checkable), S3 (load-bearing).

    Interpretationown data

    The discovered signaling molecules may be directly translated to novel experimental studies.

    “which may be directly translated to novel experimental studies”
    Quote in the paperNot a substantial claim

  • Probably not a substantial claim: may not pass S3 (load-bearing). May combine two claims.

    Premisecitation

    Cultured podocytes are widely used to investigate podocyte damage and serve as a model to study the regulation of the cytoskeleton and many other aspects of podocyte biology.

    “Cultured podocytes are widely used to investigate podocyte damage and serve as a model to study the regulation of the cytoskeleton and many other aspects of podocyte biology”
    Quote in the paperNot a substantial claim0 of 3 sources checked
    • cites Lee et al., 2015a

      Not checked in the free run.

    • cites Shankland, 2006 source

      Not checked in the free run.

    • cites Yu et al., 2013

      Not checked in the free run.

  • Classified as probably not a substantial claim.

    Premisecitation

    ATG5 is a protein essential for autophagy.

    “ATG5, a protein essential for autophagy”
    Quote in the paperSubstantial claim0 of 1 sources checked
    • cites Hartleben et al., 2010 source

      Not checked in the free run.

  • Probably not a substantial claim: may not pass S3 (load-bearing).

    Premisecitation

    The leading edge is a long-established model to study the cell biology of podocyte foot processes, and eventual slit diaphragm signaling.

    “The leading edge is a long-established model to study the cell biology of podocyte foot processes, and eventual slit diaphragm signaling”
    Quote in the paperNot a substantial claim0 of 3 sources checked
    • cites Garg and Holzman, 2012

      Not checked in the free run.

    • cites Garg et al., 2010 source

      Not checked in the free run.

    • cites Moeller et al., 2004 source

      Not checked in the free run.

  • Probably not a substantial claim: may not pass S3 (load-bearing).

    Premisecitation

    Many of these proteins oppose the formation of stress fibers by promoting actin branching to promote a "motile" phenotype.

    “many of these proteins oppose the formation of stress fibers by promoting actin branching to promote a “motile” phenotype”
    Quote in the paperNot a substantial claim0 of 1 sources checked
    • cites Higgs and Pollard, 2001

      Not checked in the free run.

  • Probably not a substantial claim: may not pass S2 (checkable).

    Interpretationreasoning

    The concept presented here will be advantageous for understanding cell-type-specific function in health and disease.

    “The concept presented here will be advantageous for understanding cell-type-specific function in health and disease.”
    Quote in the paperNot a substantial claim
    • Rests on an assumption: The podocyte is a central gatekeeper to prevent proteinuria and renal failure.
    • Rests on an assumption: Interrogation of individual cell types at multiple omics levels can yield insights into both essential molecular components and preventive strategies.

  • Probably not a substantial claim: may not pass S3 (load-bearing).

    Premisecitation

    Specific members of the tetraspanin family were confirmed in Drosophila nephrocyte studies as highly conserved functional regulators of filtering cells.

    “specific members of the tetraspanin family, which were confirmed in Drosophila nephrocyte studies as highly conserved functional regulators of filtering cells”
    Quote in the paperNot a substantial claim0 of 1 sources checked
    • cites Sachs et al., 2012 source

      Not checked in the free run.

  • Classified as probably not a substantial claim.

    Study design and conductnone given

    For large-scale data, correction for multiple testing was performed as described in the respective bioinformatics method sections.

    “For large-scale data, correction for multiple testing was performed as described in the respective bioinformatics method sections.”
    Quote in the paperSubstantial claim

  • Probably not a substantial claim: may not pass S3 (load-bearing).

    Study design and conductnone given

    In general, p < 0.05 was considered significant.

    “In general, p < 0.05 was considered significant.”
    Quote in the paperNot a substantial claim

  • Classified as probably not a substantial claim.

    Premisecitation

    Parkin2 is a key molecule controlling mitophagy.

    “a key molecule controlling mitophagy”
    Quote in the paperSubstantial claim0 of 1 sources checked
    • cites Narendra et al., 2008 source

      Not checked in the free run.

49 of 49

  • The paper relies on this without support.

    Damage to and loss of glomerular podocytes is the culprit lesion in progressive kidney diseases.

    “Damage to and loss of glomerular podocytes has been identified as the culprit lesion in progressive kidney diseases.”

  • The paper relies on this without support.

    Deterioration of podocyte function and subsequent proteinuria are critical accelerators of renal functional decline in disease states.

    “deterioration of podocyte function and subsequent proteinuria are critical accelerators of renal functional decline in disease states.”

  • The paper relies on this without support.

    The molecular identity of the podocyte is not defined.

    “the molecular identity of the podocyte is not defined”

  • The paper relies on this without support.

    It is unclear how podocyte function could be targeted therapeutically.

    “it is unclear how its function could be targeted therapeutically.”

  • The paper relies on this without support.

    The podocyte needs to maintain its proteome because of considerable metabolic and mechanical stress, and this is a prerequisite to maintain its architecture, cytoskeletal integrity, signal transduction, and metabolic function.

    “Because of considerable metabolic and mechanical stress, the podocyte needs to maintain its proteome—a prerequisite to maintain its architecture, cytoskeletal integrity, signal transduction, and metabolic function.”

  • The paper relies on this without support.

    Most genes mutated in genetic forms of proteinuria or nephrotic syndrome encode podocyte-enriched genes.

    “Most of the genes mutated in genetic forms of proteinuria or nephrotic syndrome encode for podocyte-enriched genes.”

  • The paper relies on this without support.

    Podocyte cell cultures are a commonly used tool in podocyte research.

    “a commonly used tool in podocyte research.”

  • The authors state this as an assumption.

    The podocyte is in a steady-state equilibrium with respect to mitochondrial protein synthesis and degradation.

    “assuming a steady-state equilibrium”

  • The paper relies on this without support.

    The podocyte is a central gatekeeper to prevent proteinuria and renal failure.

    “the podocyte has emerged as a central gatekeeper to prevent proteinuria and renal failure, two unmet and frequent clinical symptoms associated with dramatically increased cardiovascular risk.”

  • The paper relies on this without support.

    Interrogation of individual cell types at multiple omics levels can yield insights into both essential molecular components and preventive strategies.

    “Interrogation of individual cell types at multiple omics levels can yield insights into both essential molecular components and preventive strategies.”
10 of 10

Claims other papers make about this one

Each is checked against this paper’s own text: does it say what the citing paper says it does?

  • Unbiased research evidence, for example from omics studies, on autophagy dysfunction in kidney diseases is still missing.

    “evidence from unbiased research, such as omics studies201, is still lacking”

    From Autophagy in kidney homeostasis and disease (2020) · cites this paper as [201]

Self-check

Percentages, sums and reported differences re-computed from the paper’s own numbers.

Each contradiction between two passages listed here was confirmed by an independent check.

  • Figure 4B reverses which sample has lower protein abundance

    Minor

    The results text says the Figure 4B clusters have lower abundance in cultured cells than in native podocytes. The caption says abundance is lower in native podocytes than in cultured podocytes.

  • Figure 3D is described as both enriched and de-enriched

    Minor

    The results text assigns enriched protein categories to Figure 3D, whereas the caption describes Figure 3D as showing significantly de-enriched terms.

  • Figure 3C is described as both reduced and overrepresented

    Minor

    The results text assigns reduced mitochondrial and RNA/DNA-binding protein representation to Figure 3C, but the caption says Figure 3C shows overrepresented terms.

3 of 3

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Authors
Rinschen, M. M., Gödel, M., Grahammer, F., Zschiedrich, S., Helmstädter, M., Kretz, O., Zarei, M., Braun, D. A., Dittrich, S., Pahmeyer, C., Schroder, P., Teetzen, C., Gee, H., Daouk, G., Pohl, M., Kuhn, E., Schermer, B., Küttner, V., Boerries, M., Busch, H., Schiffer, M., Bergmann, C., Krüger, M., Hildebrandt, F., Dengjel, J., Benzing, T., & Huber, T. B.
Affiliations
  • University of Cologne (DE)
  • University of Freiburg (DE)
  • Boston Children's Hospital (US)
  • Mount Desert Island Biological Laboratory (US)
Corresponding author
  • Rinschen, Markus M.
  • Benzing, Thomas
  • Huber, Tobias B.
ORCID
Venue
Cell Reports
Publisher
Elsevier BV
Published
2018-05
Volume
23
Issue
8
Pages
2495-2508
ISSN
2211-1247 (ISSN-L)
DOI
10.1016/j.celrep.2018.04.059
PMC
PMC5986710
OpenAlex
W2803593737
Cited by
105
References
84
Citations by year
2026: 6 · 2025: 10 · 2024: 12 · 2023: 12 · 2022: 12 · 2021: 20 · 2020: 18 · 2019: 11 · 2018: 3 · 2015: 1
FWCI
10.66
Type
journal article
Language
en
Open access
Licence
Locations
  • Cell Reports (publishedVersion, cc-by-nc-nd)
  • Europe PMC (PubMed Central) (publishedVersion, cc-by-nc-nd)
  • PubMed Central (publishedVersion, cc-by-nc-nd)
  • PubMed (publishedVersion)
  • Kölner Universitäts PublikationsServer (Universität zu Köln) (publishedVersion)
  • RERO DOC (Universität Bern) (submittedVersion)
  • DOAJ (DOAJ: Directory of Open Access Journals) (submittedVersion, cc-by-sa)
  • YUHSpace (Yonsei University Medical Library) (submittedVersion, cc-by-nc-nd)
Funders
  • National Institutes of Health (R01-DK076683)
  • Deutsche Forschungsgemeinschaft (KFO 329, Ri 2811/1-1, HU 1016/8-1, CRC 1140, HU 1016/5-1)
  • Bundesministerium für Bildung und Forschung (01GM1515C, FKZ 01ZX1409B, STOP-FSGS 01GM1518C)
  • American Society of Nephrology
  • Else Kröner-Fresenius-Stiftung
  • Fritz Thyssen Stiftung (01GM1518A, 10.16.2.026MN)
  • Center for Mendelian Genomics, University of Washington (U54HG006504)
  • European Research Council
Topics
  • Health Sciences › Medicine › Nephrology › Renal Diseases and Glomerulopathies
  • Physical Sciences › Chemistry › Spectroscopy › Advanced Proteomics Techniques and Applications
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Renal and related cancers
Keywords
podocytes, glomerular disease, kidney disease, multi-omics integration, stable isotope labeling, mitochondrial translation, autophagy, cell type-specific gene expression, zebrafish knockdown, cell culture model
MeSH terms
Animals, Base Sequence, Cells, Cultured, Gene Expression Regulation, Humans, Kidney Diseases, Zebrafish, Proteome, Podocytes, Mice, Genetic Association Studies, Transcriptome

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Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.

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