Interactome Analysis Reveals a Link of the Novel ALMS1-CEP70 Complex to Centrosomal Clusters.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:38122899", "kind": "science-record", "revision": 3, "content_hash": "sha256:1ca364d97d796d74e8844b0a15908b166a9bbea5030609f99c6d79706c3cdf6f", "created_at": "2026-11-01T19:20:03Z", "updated_at": "2026-11-01T22:10:54Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Interactome Analysis Reveals a Link of the Novel ALMS1-CEP70 Complex to Centrosomal Clusters.", "doi": "10.1016/j.mcpro.2023.100701", "pmid": "38122899", "authors": ["Franziska Woerz", "Felix Hoffmann", "Shibu Antony", "Sylvia Bolz", "Mohamed Ali Jarboui", "Katrin Junger", "Franziska Klose", "Isabel F Stehle", "Karsten Boldt", "Marius Ueffing", "Tina Beyer"], "journal": "Molecular & cellular proteomics : MCP", "year": 2024, "abstract": "Alström syndrome (ALMS) is a very rare autosomal-recessive disorder, causing a broad range of clinical defects most notably retinal degeneration, type 2 diabetes, and truncal obesity. The ALMS1 gene encodes a complex and huge ∼0.5 MDa protein, which has hampered analysis in the past. The ALMS1 protein is localized to the centrioles and the basal body of cilia and is involved in signaling processes, for example, TGF-β signaling. However, the exact molecular function of ALMS1 at the basal body remains elusive and controversial. We recently demonstrated that protein complex analysis utilizing endogenously tagged cells provides an excellent tool to investigate protein interactions of ciliary proteins. Here, CRISPR/Cas9-mediated endogenously tagged ALMS1 cells were used for affinity-based protein complex analysis. Centrosomal and microtubule-associated proteins were identified, which are potential regulators of ALMS1 function, such as the centrosomal protein 70 kDa (CEP70). Candidate proteins were further investigated in ALMS1-deficient hTERT-RPE1 cells. Loss of ALMS1 led to shortened cilia with no change in structural protein localization, for example, acetylated and ɣ-tubulin, Centrin-3, or the novel interactor CEP70. Conversely, reduction of CEP70 resulted in decreased ALMS1 at the ciliary basal body. Complex analysis of CEP70 revealed domain-specific ALMS1 interaction involving the TPR-containing C-terminal (TRP-CT) fragment of CEP70. In addition to ALMS1, several ciliary proteins, including CEP135, were found to specifically bind to the TPR-CT domain. Data are available via ProteomeXchange with the identifier PXD046401. Protein interactors identified in this study provide candidate lists that help to understand ALMS1 and CEP70 function in cilia-related protein modification, cell death, and disease-related mechanisms.", "claims": [{"id": "claim-method", "statement": "The Perseus software (version 1.6.14.0) was used for statistical analysis (17). Six biological replicates for each bait/tagged single clone and controls (RAF1 for CEP70, untagged cells for endogenously tagged ALMS1-sfGFP) are available for statistics. Potential contaminants and peptides only identified by side or reverse sequence were excluded for all data. Within the groups, a minimum half +1 of the samples should have valid values. Next, imputation by 0 was done for NaN values, the median values for each group followed by the ratio “specific bait/control” were calculated. Proteins which were significantly more abundant in one group were determined based on two statistical tests and classified in a two Tier system. Tier 1 interactors are stringently filtered with significance A (Benjamini-Hochberg FDR <0.05) and Student’s t test (Permutation-based FDR <0.05). Tier 2 includes additional proteins with a less stringent analysis (Significance A Benjamini Hochberg FDR <0.05 and Student’s t test p-value p < 0.05).", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:38122899", "locator": "sections[13] \"Experimental Design and Statistical Rationale\" paragraph 2", "quote": "The Perseus software (version 1.6.14.0) was used for statistical analysis (17). Six biological replicates for each bait/tagged single clone and controls (RAF1 for CEP70, untagged cells for endogenously tagged ALMS1-sfGFP) are available for statistics. Potential contaminants and peptides only identified by side or reverse sequence were excluded for all data. Within the groups, a minimum half +1 of the samples should have valid values. Next, imputation by 0 was done for NaN values, the median values for each group followed by the ratio “specific bait/control” were calculated. Proteins which were significantly more abundant in one group were determined based on two statistical tests and classified in a two Tier system. Tier 1 interactors are stringently filtered with significance A (Benjamini-Hochberg FDR <0.05) and Student’s t test (Permutation-based FDR <0.05). Tier 2 includes additional proteins with a less stringent analysis (Significance A Benjamini Hochberg FDR <0.05 and Student’s t test p-value p < 0.05)."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The mass spectrometry proteomics data have been deposited to the ProteomeXchange Consortium via the PRIDE partner repository with the dataset identifier PXD046401 (63).", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:38122899", "locator": "sections[26] \"Data Availability\" paragraph 2", "quote": "The mass spectrometry proteomics data have been deposited to the ProteomeXchange Consortium via the PRIDE partner repository with the dataset identifier PXD046401 (63)."}], "state": "complete"}, {"id": "claim-target-result", "statement": "The study identified CEP70 as an ALMS1 interactor and showed that CEP70 knockdown reduces ALMS1 at the ciliary basal body through interaction with the TPR-containing C-terminal domain of CEP70.", "kind": "quantitative", "target": {"value": 0.001, "unit": "p-value", "tolerance": null, "source": "Interestingly, CEP70 KD led to a very high significant reduction of ALMS1 intensity at the BB of cilia, indicating that CEP70 is involved in recruiting ALMS1 to or stabilization of ALMS1 at the BB (normalized intensity mean siCo = 212.9 ± 70.2 (89 cilia), normalized intensity mean siCEP70 = 132.9 ± 84.7 (56 cilia), p < 0.001; Fig. 5, C and D)."}, "evidence": [{"asset": "source:pmid:38122899", "locator": "sections[21] \"Complex Analysis Using Endogenously Tagged Cells Revealed New Interactions of ALMS1\" paragraph 5", "quote": "For the first time, CEP70 has been identified as an interaction partner of ALMS1."}, {"asset": "source:pmid:38122899", "locator": "sections[23] \"Loss of CEP70 led to Reduced ALMS1 at the Basal Body in hTERT-RPE1 Cells\" paragraph 4", "quote": "Interestingly, CEP70 KD led to a very high significant reduction of ALMS1 intensity at the BB of cilia, indicating that CEP70 is involved in recruiting ALMS1 to or stabilization of ALMS1 at the BB (normalized intensity mean siCo = 212.9 ± 70.2 (89 cilia), normalized intensity mean siCEP70 = 132.9 ± 84.7 (56 cilia), p < 0.001; Fig. 5, C and D)."}, {"asset": "source:pmid:38122899", "locator": "sections[24] \"CEP70 Interacts Domain Specific With ALMS1 and Other Centrosomal Proteins\" paragraph 6", "quote": "When analyzing the CEP70 fragments, ALMS1 was identified as a significant interactor in TPR-CT but not in CC1-2 hinting towards an ALMS1-independent localization of CEP70 to the BB (supplemental Fig. S6B)."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "partial", "objective": "The study identified CEP70 as an ALMS1 interactor and showed that CEP70 knockdown reduces ALMS1 at the ciliary basal body through interaction with the TPR-containing C-terminal domain of CEP70.", "steps": [{"id": "read_published_estimate", "order": 1, "name": "Read the published estimate from the source", "kind": "other", "state": "complete", "blocked_on": null, "description": "The claim, method and evidence span published with the source article.", "duration_hours": null, "parameters": {}, "inputs": ["source:pmid:38122899"], "outputs": ["the published estimate and its evidence"], "instruments": [], "reagents": []}, {"id": "obtain_source_data", "order": 2, "name": "Obtain the source data from the named repository", "kind": "data-preparation", "state": "complete", "blocked_on": null, "description": "The GEO series accession resolves and its sample accessions are listed. 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Here, CRISPR/Cas9-mediated endogenously tagged ALMS1 cell"], "order_basis": "paper_text_order:762", "id": "assay:1"}, {"role": "data_generation", "definition_id": "cell_culture", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.99, "evidence": ["urther investigated in ALMS1-deficient hTERT-RPE1 cells. Loss of ALMS1 led to shortened cilia", "l Culture HEK293T (CRL-3216, ATCC) and hTERT-RPE1 (CRL-4000, ATCC) were grown in Dulbecco’s Mo"], "order_basis": "paper_text_order:1103", "id": "assay:2"}, {"role": "analysis", "definition_id": "group_comparison", "definition_version": "f2132e96ae6c7a4e", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"dsl_catalogue": "f2132e96ae6c7a4e"}, "confidence": 1.0, "evidence": ["The Perseus software (version 1.6.14.0) was used for statistical analysis (17). Six biological replicates for each bait/tagged single clone and controls (RAF1 for CEP70, untagged cells for endogenously tagged ALMS1-sfGFP) are available for statistics. Potential contaminants and peptides only identified by side or reverse sequence were excluded for all data. Within the groups, a minimum half +1 of the samples should have valid values. Next, imputation by 0 was done for NaN values, the median values for each group followed by the ratio “specific bait/control” were calculated. Proteins which were significantly more abundant in one group were determined based on two statistical tests and classified in a two Tier system. Tier 1 interactors are stringently filtered with significance A (Benjamini-Hochberg FDR <0.05) and Student’s t test (Permutation-based FDR <0.05). Tier 2 includes additional proteins with a less stringent analysis (Significance A Benjamini Hochberg FDR <0.05 and Student’s t test p-value p < 0.05)."], "order_basis": "consumes_earlier_output", "id": "assay:3"}]}