Proteogenomic analysis of human cerebrospinal fluid identifies neurologically relevant regulation and implicates causal proteins for Alzheimer’s disease

May combine two claims.

Calcineurin (PPP3R1), associated with both phosphorylated tau levels and rate of decline in AD, is genetically regulated by this region.

“Calcineurin (PPP3R1), associated with both phosphorylated tau levels and rate of decline in AD39, is also genetically regulated by this region.”

• cites [39] Cruchaga, C. et al. SNPs associated with cerebrospinal fluid phospho-tau levels influence rate of decline in Alzheimer’s disease. PLoS Genet. 6, e1001101 (2010). sourceSupported

May combine two claims.

The study also observed apoptotic pathways, including activation of BH3-only proteins and apoptosis, suggesting a potential role of APOE in cell death.

“We also observe apoptotic pathways, including activation of BH3-only proteins (Reactome:R-HSA-114452) and apoptosis (Reactome:R-HSA-109581, Supp. Table S36), suggesting a potential role of APOE40–42 in cell death.”

• cites [40] Zhao, J. et al. APOE4 exacerbates synapse loss and neurodegeneration in Alzheimer’s disease patient iPSC-derived cerebral organoids. Nat. Commun. 11, 5540 (2020). sourcePartly supported

  The Results (Fig. 2) report increased apoptosis in APOE4 cerebral organoids, supporting a potential role for APOE4 in cell death. The paper does not report activation of BH3-only proteins or identify the specified Reactome apoptotic pathways; its pathway analysis used MetaCore. (LLM, conf=0.87)

  Experimental — accuracy not yet measured
• cites [41] Wang, C. et al. Gain of toxic apolipoprotein E4 effects in human iPSC-derived neurons is ameliorated by a small-molecule structure corrector. Nat. Med. 24, 647–657 (2018). sourceSupported
• cites [42] Grainger, D. J., Reckless, J. & McKilligin, E. Apolipoprotein E modulates clearance of apoptotic bodies in vitro and in vivo, resulting in a systemic proinflammatory state in apolipoprotein E-deficient mice. J. Immunol. 173, 6366–6375 (2004). sourceSupported

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

GWAS have identified over 75 loci associated with Alzheimer's disease.

“GWAS have identified over 75 loci associated with AD23, but the genes driving the associations for most of them are still unknown, and little research has been done to understand how these genes interact in specific pathways and disease mechanisms.”

• cites [23] Bellenguez, C. et al. New insights into the genetic etiology of Alzheimer’s disease and related dementias. Nat. Genet. 54, 412–436 (2022). sourcePartly supported

  The Discussion reports that the GWAS meta-analysis identified 75 independent loci associated with Alzheimer’s disease and related dementias, supporting the claim’s main point. It does not report over 75 loci, so the stated threshold is not supported. (LLM, conf=0.88)

  Experimental — accuracy not yet measured

May combine two claims.

OSTN is highly expressed in human neurons, regulates dendritic growth in the human brain and is proposed as a candidate gene at this locus.

“We note that OSTN, the gene flanking the 3’ end of this region, is highly expressed in human neurons, regulates dendritic growth in the human brain and is proposed as a candidate gene at this locus17.”

• cites [17] Hansson, O. et al. The genetic regulation of protein expression in cerebrospinal fluid. EMBO Mol. Med. 15, e16359 (2023). sourcePartly supported

  The Results section (‘The GMNC‐OSTN region and CSF trans‐pQTLs’; page unavailable) says OSTN has enhanced expression in the cerebral cortex, encodes a hormone that regulates dendritic growth there, and is a possible causal gene for the region’s CSF trans-pQTLs. It does not establish that OSTN is highly expressed specifically in human neurons; cortical expression is a less specific claim. (LLM, conf=0.86)

  Experimental — accuracy not yet measured

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

Besides AD, APOE has been associated with at least eighteen other diseases, including heart disease and high cholesterol.

“Besides AD43, APOE has been associated with at least eighteen other diseases, including heart disease and high cholesterol44.”

• cites [43] Liu, C.-C., Kanekiyo, T., Xu, H. & Bu, G. Apolipoprotein E and Alzheimer disease: risk, mechanisms and therapy. Nat. Rev. Neurol. 9, 106–118 (2013). sourcePartly supported

  The Introduction states that ApoE4 is associated with hypercholesterolemia and coronary heart disease, supporting both examples. The paper does not state that APOE is associated with at least eighteen other diseases, so it does not support the claimed count. (LLM, conf=0.89)

  Experimental — accuracy not yet measured
• cites [44] Lumsden, A. L., Mulugeta, A., Zhou, A. & Hyppönen, E. Apolipoprotein E (APOE) genotype-associated disease risks: a phenome-wide, registry-based, case–control study utilising the UK Biobank. eBioMedicine 59, 102954 (2020). sourcePartly supported

  The Abstract (Findings) reports APOE associations with 18 distinct diseases, including Alzheimer’s disease, hypercholesterolaemia and ischaemic heart disease. It does not support the claim of at least 18 diseases besides Alzheimer’s disease; the reported total is 18 including it. (LLM, conf=0.90)

  Experimental — accuracy not yet measured

May combine two claims.

The study performed MR and identified 17 unique proteins as putatively causal for AD (FDR-corrected P<0.05) with confirmed directionality using the Steiger test.

“We next performed MR47 and identified 17 unique proteins as putatively causal for AD (Fig. 4A, Supp. Table S40&41, FDR-corrected P<0.05) with confirmed directionality using the Steiger test52 (Supp. Table S42).”

• cites [47] Hemani, G. et al. The MR-Base platform supports systematic causal inference across the human phenome. eLife 7, e34408 (2018). sourceSupported
• cites [52] Hemani, G., Tilling, K. & Davey Smith, G. Orienting the causal relationship between imprecisely measured traits using GWAS summary data. PLoS Genet. 13, e1007081 (2017). sourceSupported

May combine two claims.

The study performed a PWAS using FUSION. After FDR correction and pleiotropy filtering, 125 pQTL for 108 proteins were significantly associated with AD.

“We performed a PWAS using FUSION45. After FDR correction and pleiotropy filtering50,51, 125 pQTL for 108 proteins were significantly associated with AD.”

• cites [45] Gusev, A. et al. Integrative approaches for large-scale transcriptome-wide association studies. Nat. Genet. 48, 245–252 (2016). sourceSupported
• cites [50] Yang, C. et al. Mendelian randomization and genetic colocalization infer the effects of the multi-tissue proteome on 211 complex disease-related phenotypes. Genome Med. 14, 140 (2022). sourceSupported
• cites [51] Zheng, J. et al. Phenome-wide Mendelian randomization mapping the influence of the plasma proteome on complex diseases. Nat. Genet. 52, 1122–1131 (2020). sourceSupported

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

cis-pQTL effect sizes correlate with proximity to the protein coding gene.

“We also confirmed previous evidence10,13 that cis-pQTL effect sizes correlate with proximity to the protein coding gene (Fig. 2D; Supp. Fig. 3H).”

• cites [10] Yang, C. et al. Genomic atlas of the proteome from brain, CSF and plasma prioritizes proteins implicated in neurological disorders. Nat. Neurosci. 24, 1302–1312 (2021). sourcePartly supported

  The Results section on functional annotation reports that cis-pQTL association strength (−log10 P) decreased with distance from the transcription start site in all three tissues. Extended Data Fig. 10 likewise plots association significance against distance, but plots effect size (beta) against minor allele frequency instead. The copy therefore supports a proximity relationship for association significance, not specifically for effect size. (LLM, conf=0.84)

  Experimental — accuracy not yet measured
• cites [13] Sun, B. B. et al. Genomic atlas of the human plasma proteome. Nature 558, 73–79 (2018). sourcePartly supported

  The Genetic architecture of the plasma proteome section (page unavailable) reports that cis-pQTL association P values increased with distance from the protein-coding gene’s transcription start site. It does not report a correlation between effect sizes and distance; P values measure statistical significance, not effect size. (LLM, conf=0.82)

  Experimental — accuracy not yet measured

May combine two claims.

Proteins regulated by chr3q28 region included five members of the syntaxin family and five ephrin family members.

“Proteins regulated by this region included five members of the syntaxin family involved in synapse function31 and five ephrin family members involved in neural development and memory32,33.”

• cites [31] Bennett, M. K., Calakos, N. & Scheller, R. H. Syntaxin: a synaptic protein implicated in docking of synaptic vesicles at presynaptic active zones. Science 257, 255–259 (1992). sourceNot checked — no full text of the source
• cites [32] Dines, M. & Lamprecht, R. The role of ephs and ephrins in memory formation. Int. J. Neuropsychopharmacol. 19, pyv106 (2016). sourceSupported
• cites [33] Washburn, H. R., Chander, P., Srikanth, K. D. & Dalva, M. B. Transsynaptic signaling of ephs in synaptic development, plasticity, and disease. Neuroscience 508, 137–152 (2023). sourceNot checked — no full text of the source

May combine two claims.

The study developed a proteomic risk score by selecting PWAS-significant aptamers (n=456) and performing LASSO regression to select predictors of AD status (Npredictors=100) in a training dataset (n=1,325).

“We developed a proteomic risk score91 by selecting PWAS-significant aptamers (n=456) and performing LASSO regression to select predictors of AD status (Npredictors=100) in a training dataset (n=1,325).”

• cites [91] Marigorta, U. M. et al. Transcriptional risk scores link GWAS to eQTLs and predict complications in Crohn’s disease. Nat. Genet. 49, 1517–1521 (2017). sourcePartly supported

  The Introductory Paragraph describes a transcriptional risk score derived from gene expression for predicting Crohn’s disease outcomes, providing a precedent for a molecular risk score. It does not describe a proteomic score, PWAS-significant aptamers, LASSO selection, Alzheimer’s disease status, or the stated predictor and training-set counts; those details concern the citing authors’ study, not this source. (LLM, conf=0.86)

  Experimental — accuracy not yet measured

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

Directionality in the MR analysis was assessed using MR-Steiger.

“We analyzed directionality using MR-Steiger52.”

• cites [52] Hemani, G., Tilling, K. & Davey Smith, G. Orienting the causal relationship between imprecisely measured traits using GWAS summary data. PLoS Genet. 13, e1007081 (2017). sourceSupported

May combine two claims.

CA12 is targeted by carbonic anhydrase inhibitors like acetazolamide, which was shown to reduce Aβ-induced mitochondrial toxicity.

“Finally, CA12 is targeted by carbonic anhydrase inhibitors like acetazolamide (DB00819), which was shown to reduce Aβ-induced mitochondrial toxicity90.”

• cites [90] Solesio, M. E. et al. Carbonic anhydrase inhibition selectively prevents amyloid β neurovascular mitochondrial toxicity. Aging Cell 17, e12787 (2018). sourcePartly supported

  The Introduction identifies acetazolamide as a carbonic anhydrase inhibitor, and the Discussion reports that it reversed Aβ-induced mitochondrial depolarization and H2O2 production in the study’s cell models. The passages identify other carbonic anhydrase isoforms but do not establish that acetazolamide targets CA12 specifically. Page numbers were not supplied. (LLM, conf=0.88)

  Experimental — accuracy not yet measured

May combine two claims.

The analyses nominate alternative candidates at three AD risk loci: CR2 at 1q32.2, PILRA at 7q22.1, and PRSS8 at 16p11.2.

“Our analyses also nominate alternative candidates at three AD risk loci. First, the association at 1q32.2 has been linked to CR153–55, but we observed a colocalized association for both CR1 and CR2 levels with AD risk (Supp. Fig. 23).”

• Also stated in: § Novel proteins associated with Alzheimer’s disease · hedged

  “At the 7q22.1 AD locus, the nominated genes were ZCWPW1 and NYAP1. Our analyses indicate that PILRA is a functional gene in this locus, identifying a negative association between PILRA levels and AD risk (Supp. Fig. 23).”

• Also stated in: § Novel proteins associated with Alzheimer’s disease · plain

  “At the 16p11.2, KAT8 locus, we nominate PRSS8 as the candidate gene.”

• cites [53] Fonseca, M. I. et al. Analysis of the putative role of CR1 in Alzheimer’s disease: genetic association, expression and function. PLoS ONE 11, e0149792 (2016). sourceSupported
• cites [54] Kucukkilic, E. et al. Complement receptor 1 gene (CR1) intragenic duplication and risk of Alzheimer’s disease. Hum. Genet. 137, 305–314 (2018). sourceSupported
• cites [55] Brouwers, N. et al. Alzheimer risk associated with a copy number variation in the complement receptor 1 increasing C3b/C4b binding sites. Mol. Psychiatry 17, 223–233 (2012). sourceSupported
• cites [58] Rathore, N. et al. Paired immunoglobulin-like type 2 receptor α G78R variant alters ligand binding and confers protection to Alzheimer’s disease. PLoS Genet. 14, e1007427 (2018). sourcePartly supported

  The Results section identifies a PILRA variant associated with protection from Alzheimer’s disease, supporting PILRA as a candidate at one AD risk locus. It calls that locus 7q21, not 7q22.1, and does not support the claim’s CR2 or PRSS8 candidates. No page number is available in our copy. (LLM, conf=0.88)

  Experimental — accuracy not yet measured
• cites [59] Schwartzentruber, J. et al. Genome-wide meta-analysis, fine-mapping and integrative prioritization implicate new Alzheimer’s disease risk genes. Nat. Genet. 53, 392–402 (2021). sourceSupported

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

Mutations in CLN5 contribute to a form of neuronal ceroid lipofuscinosis, while CLN5-deficient neurons showed impaired lysosomal activity and movement.

“Mutations in CLN5 contribute to a form of neuronal ceroid lipofuscinosis78, while CLN5-deficient neurons showed impaired lysosomal activity and movement78.”

• cites [78] Basak, I., Hansen, R. A., Ward, M. E. & Hughes, S. M. Deficiency of the lysosomal protein CLN5 alters lysosomal function and movement. Biomolecules 11, 1412 (2021). sourceSupported

May combine two claims.

CASQ1 is a ligand for calcium and studies suggest targeting calcium receptors may be beneficial in AD.

“CASQ1 is a ligand for calcium (DB11093) and studies suggest that targeting calcium receptors may be beneficial in AD88.”

• cites [88] Ge, M. et al. Role of calcium homeostasis in Alzheimer’s disease. Neuropsychiatr. Dis. Treat. 18, 487–498 (2022). sourceSupported

May combine two claims.

CLN5 is processed through the ER and Golgi before being transported through the early endosome to lysosomes, supporting enrichment for endosome proteins.

“CLN5 is processed through the ER and Golgi before being transported through the early endosome to lysosomes79, supporting enrichment for endosome proteins (Fig. 4F).”

• cites [79] Basak, I. et al. A lysosomal enigma CLN5 and its significance in understanding neuronal ceroid lipofuscinosis. Cell. Mol. Life Sci. 78, 4735–4763 (2021). sourceSupported

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

Captopril, an ACE inhibitor, showed a neuroprotective effect in an AD mouse model.

“Captopril (DB01197), an ACE inhibitor, showed a neuroprotective effect in an AD mouse model89.”

• cites [89] AbdAlla, S., Langer, A., Fu, X. & Quitterer, U. ACE inhibition with captopril retards the development of signs of neurodegeneration in an animal model of Alzheimer’s disease. Int. J. Mol. Sci. 14, 16917–16942 (2013). sourceSupported

May combine two claims.

Increased CTSH mRNA levels were observed in AD, while microglia with CTSH knockouts showed increased Aβ phagocytosis.

“Increased CTSH mRNA levels were observed in AD, while microglia with CTSH knockouts showed increased Aβ phagocytosis75.”

• cites [75] Li, Y. et al. Functional genomics identify causal variant underlying the protective CTSH locus for Alzheimer’s disease. Neuropsychopharmacology 48, 1555–1566 (2023). sourceSupported

May combine two claims.

FCGR3B is targeted by cetuximab, which is associated with decreased risk of AD.

“FCGR3B is targeted by cetuximab (DrugBank accession number DB00002), a chemotherapy agent. Cetuximab is associated with decreased risk of AD85 (Supp. Table S47).”

• cites [85] Akushevich, I., Yashkin, A. P., Kravchenko, J. & Kertai, M. D. Chemotherapy and the risk of Alzheimer’s disease in colorectal cancer survivors: evidence from the medicare system. JCO Oncol. Pract. 17, e1649–e1659 (2021). sourceSupported

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

Glutamic acid targets SLC25A18, a glutamate transporter involved in excitatory signaling in neurons.

“Glutamic acid (DB00142) targets SLC25A18, a glutamate transporter86 and is involved in excitatory signaling in neurons87.”

• cites [86] Fiermonte, G. et al. Identification of the mitochondrial glutamate transporter: bacterial expression, reconstitution, functional characterization, and tissue distribution of two human isoforms. J. Biol. Chem. 277, 19289–19294 (2002). sourcePartly supported

  The Discussion (page unavailable) identifies GC1 and GC2 as mitochondrial glutamate carriers, and the substrate-specificity results show that both transport L-glutamate. Our copy does not explicitly identify either isoform as SLC25A18, so it does not fully establish the named target. The neuronal-signaling clause has a separate citation (87) and is not attributed to this source. (LLM, conf=0.78)

  Experimental — accuracy not yet measured
• cites [87] Wang, R. & Reddy, P. H. Role of glutamate and NMDA receptors in Alzheimer’s disease. J. Alzheimers Dis. 57, 1041–1048 (2017). sourceSupported

Classified as probably not a substantial claim. May combine two claims.

In Alzheimer's disease, many genetic loci have been identified, but for some the functional gene is not clear.

“In AD, many genetic loci have been identified, but for some the functional gene is not clear23,59.”

• cites [23] Bellenguez, C. et al. New insights into the genetic etiology of Alzheimer’s disease and related dementias. Nat. Genet. 54, 412–436 (2022). sourceSupported
• cites [59] Schwartzentruber, J. et al. Genome-wide meta-analysis, fine-mapping and integrative prioritization implicate new Alzheimer’s disease risk genes. Nat. Genet. 53, 392–402 (2021). sourceSupported

May combine two claims.

CST8 is part of a protein family that inhibits the activity of cathepsins, offering a potential mechanism for its inverse AD association.

“CST8 is part of a protein family that inhibits the activity of cathepsins77, offering a potential mechanism for its inverse AD association.”

• cites [77] Haves-Zburof, D. et al. Cathepsins and their endogenous inhibitors cystatins: expression and modulation in multiple sclerosis. J. Cell. Mol. Med. 15, 2421–2429 (2011). sourcePartly supported

  The Introduction identifies cystatins B and C as inhibitors of cathepsins, and the Results section on glucocorticoid treatment describes cystatin C as a protease inhibitor. The paper does not identify CST8 as a member of that family or examine its activity; the proposed inverse AD association is the citing authors’ interpretation, not the part directly attached to this citation. Page numbers are unavailable in our copy. (LLM, conf=0.83)

  Experimental — accuracy not yet measured

May combine two claims.

The enrichment of prioritized proteins in microglia and immune pathways supports a strong immunological role in AD, including TREM2, CD33, and IL34.

“supporting a strong immunological role in AD93–95 including TREM27,96, CD33, and IL34.”

• cites [93] Jones, L. et al. Genetic evidence implicates the immune system and cholesterol metabolism in the aetiology of Alzheimer’s disease. PLoS ONE 5, e13950 (2010). sourceSupported
• cites [94] Yokoyama, J. S. et al. Association between genetic traits for immune-mediated diseases and Alzheimer disease. JAMA Neurol. 73, 691–697 (2016). sourceSupported
• cites [95] Haage, V. & De Jager, P. L. Neuroimmune contributions to Alzheimer’s disease: a focus on human data. Mol. Psychiatry 27, 3164–3181 (2022). sourceSupported
• cites [7] Deming, Y. et al. The MS4A gene cluster is a key modulator of soluble TREM2 and Alzheimer’s disease risk. Sci. Transl. Med. 14, eaau2291 (2019). sourceSupported
• cites [96] Jin, S. C. et al. Coding variants in TREM2 increase risk for Alzheimer’s disease. Hum. Mol. Genet. 23, 5838–5846 (2014). sourceSupported

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

Evidence suggests that candidate proteins can be identified for many neurological traits, even with smaller sample sizes.

“Evidence suggests that candidate proteins can be identified for many neurological traits, even with smaller sample sizes10,13”

• cites [10] Yang, C. et al. Genomic atlas of the proteome from brain, CSF and plasma prioritizes proteins implicated in neurological disorders. Nat. Neurosci. 24, 1302–1312 (2021). sourcePartly supported

  The Results (Mendelian randomization and drug repositioning; page unavailable) report identifying proteins implicated in several neurological traits, including Alzheimer’s disease, Parkinson’s disease, ALS and stroke. The paper does not establish the claim that candidate proteins can be identified even with smaller sample sizes; Results (Replication and meta-analyses; page unavailable) instead report substantially more pQTL signals after increasing sample size. (LLM, conf=0.84)

  Experimental — accuracy not yet measured
• cites [13] Sun, B. B. et al. Genomic atlas of the human plasma proteome. Nature 558, 73–79 (2018). sourcePartly supported

  The ‘trans pQTLs identify pathways to disease’ section links plasma proteins to disease-associated genetic variants, supporting the general idea that candidate proteins can be identified for disease traits. The passages do not establish this for many neurological traits or show that it works with smaller sample sizes; the Methods describe an analysis of 3,301 participants, not a smaller-sample comparison. (LLM, conf=0.82)

  Experimental — accuracy not yet measured

May combine two claims.

ITAM- and ITIM-containing proteins regulate processes including microglial phagocytosis and apoptosis, suggesting convergent AD-relevant pathways mediated through microglial surface receptors.

“ITAM- and ITIM-containing proteins regulate processes including microglial phagocytosis and apoptosis74, suggesting convergent AD-relevant pathways mediated through microglial surface receptors.”

• cites [74] Linnartz, B., Wang, Y. & Neumann, H. Microglial immunoreceptor tyrosine-based activation and inhibition motif signaling in neuroinflammation. Int. J. Alzheimers Dis. 2010, 587463 (2010). sourceSupported

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

TREM2 complexes with DAP12, which modulates activation of microglia through its ITAM.

“TREM2 complexes with DAP12, which modulates activation of microglia through its immunoreceptor tyrosine-based activation motif (ITAM)69.”

• cites [69] Konishi, H. & Kiyama, H. Microglial TREM2/DAP12 signaling: a double-edged sword in neural diseases. Front. Cell. Neurosci. 12, 206 (2018). sourceSupported

May combine two claims.

The study identified two lysosomal proteins, GRN and TMEM106B, that are associated with frontotemporal dementia but were also identified in the latest AD risk GWAS.

“We also identified two lysosomal proteins, GRN and TMEM106B80,81, that are associated with frontotemporal dementia (FTD)82,83 but were also identified in the latest AD risk GWAS23.”

• cites [80] Paushter, D. H., Du, H., Feng, T. & Hu, F. The lysosomal function of progranulin, a guardian against neurodegeneration. Acta Neuropathol. 136, 1–17 (2018). sourceSupported
• cites [81] Feng, T. et al. Loss of TMEM106B and PGRN leads to severe lysosomal abnormalities and neurodegeneration in mice. EMBO Rep. 21, e50219 (2020). sourceSupported
• cites [82] Van Deerlin, V. M. et al. Common variants at 7p21 are associated with frontotemporal lobar degeneration with TDP-43 inclusions. Nat. Genet. 42, 234–239 (2010). sourceSupported
• cites [83] Baker, M. et al. Mutations in progranulin cause tau-negative frontotemporal dementia linked to chromosome 17. Nature 442, 916–919 (2006). sourceNot checked — no full text of the source
• cites [23] Bellenguez, C. et al. New insights into the genetic etiology of Alzheimer’s disease and related dementias. Nat. Genet. 54, 412–436 (2022). sourceSupported

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

SOMAscan-based measurements correlate well with complementary approaches.

“Nonetheless, we note that SOMAscan-based measurements correlate well with complementary approaches26,97.”

• cites [26] Dammer, E. B. et al. Multi-platform proteomic analysis of Alzheimer’s disease cerebrospinal fluid and plasma reveals network biomarkers associated with proteostasis and the matrisome. Alzheimers Res. Ther. 14, 174 (2022). sourceSupported
• cites [97] Timsina, J. et al. Comparative analysis of Alzheimer’s disease cerebrospinal fluid biomarkers measurement by multiplex SOMAscan platform and immunoassay-based approach. J. Alzheimers Dis. 89, 193–207 (2022). sourcePartly supported

  The Results section (“Correlation between SOMAscan and immunoassay measurements”) reports strong correlations for three CSF biomarkers and a weaker but significant correlation for sTREM2. SNAP-25 showed no significant correlation, so the unqualified claim that SOMAscan-based measurements correlate well with complementary approaches overstates these findings. (LLM, conf=0.88)

  Experimental — accuracy not yet measured

May combine two claims.

This dataset represents an expansion of previous CSF pQTL work in both sample size (n=3,506) and number of proteins (n=6,361).

“This dataset represents an expansion of previous CSF pQTL work10,16–19 in both sample size (n=3,506) and number of proteins (n=6,361).”

• cites [10] Yang, C. et al. Genomic atlas of the proteome from brain, CSF and plasma prioritizes proteins implicated in neurological disorders. Nat. Neurosci. 24, 1302–1312 (2021). sourceSupported
• cites [16] Sasayama, D. et al. Genome-wide quantitative trait loci mapping of the human cerebrospinal fluid proteome. Hum. Mol. Genet. 26, 44–51 (2017). sourceSupported
• cites [17] Hansson, O. et al. The genetic regulation of protein expression in cerebrospinal fluid. EMBO Mol. Med. 15, e16359 (2023). sourceSupported
• cites [18] Kaiser, S. et al. A proteogenomic view of Parkinson’s disease causality and heterogeneity. NPJ Parkinsons Dis. 9, 24 (2023). sourceSupported
• cites [19] Kauwe, J. S. K. et al. Genome-wide association study of CSF levels of 59 Alzheimer’s disease candidate proteins: significant associations with proteins involved in amyloid processing and inflammation. PLoS Genet. 10, e1004758 (2014). sourceSupported

May combine two claims.

Of all proteins prioritized by PWAS, COLOC and MR, eight (all cis) were significant in all three and 38 (24 cis, 13 trans, and one cis and trans) were significant through two methods.

“Of all proteins prioritized by PWAS, COLOC and MR, eight (all cis) were significant in all three and 38 (24 cis, 13 trans, and one cis and trans) were significant through two methods (Figs. 4A–D; Supp. Table S45).”

The quote only partly states this claim.

The study identified 3,885 conditionally independent pQTL associations for 1,883 proteins.

“We identified 3,885 associations for 1,883 proteins, including 2,885 novel pQTLs, demonstrating unique genetic regulation in CSF.”

• Also stated in: § Unique genetic architecture of CSF proteomics · plain

  “In total, we identified 3,885 conditionally independent associations (see Supplementary Notes, Supp. Table S8).”

May combine two claims.

These associations were consistent between controls and AD cases, suggesting APOE has an important role regardless of disease status.

“These associations were consistent between controls and AD cases, suggesting APOE has an important role regardless of disease status (see Supplementary Notes).”

May combine two claims.

Of the 648 that overlap, 78.9% (511) colocalize with a neurologically-relevant tissue and 50.8% (329) are unique to neurological tissues.

“Of the 648 that overlap, 78.9% (511) colocalize with a neurologically-relevant tissue and 50.8% (329) are unique to neurological tissues.”

The quote only partly states this claim.

Of the 3,885 associations, 2,885 were novel to CSF.

“We identified 3,885 associations for 1,883 proteins, including 2,885 novel pQTLs, demonstrating unique genetic regulation in CSF.”

• Also stated in: § Unique genetic architecture of CSF proteomics · plain

  “When analyzing conditional associations 2,885 were novel to CSF, of which 2,007 were CSF-specific and 878 were novel.”

May combine two claims.

303 pathways were enriched for chr3q28 proteins, most-significant almost exclusively neuronal and cell surface pathways.

“In addition, we observed 303 pathways enriched for these proteins. The most-significant were almost exclusively neuronal and cell surface pathways (Fig. 3C, Supp. Fig. 12, Supp. Table S30), including neuron projection development (GO:0031175), cell junction (GO:0030054), axon development (GO:0061564), and SNAP receptor activity (GO:0048812).”

May combine two claims.

The 38 proteins showed overrepresentation in microglia/macrophages (P=1.38×10−4), astrocytes (P=0.012), and neurodegenerative pathways.

“We observed an overrepresentation in microglia/macrophages (P=1.38×10−4, Fig. 4E, Supp. Fig. 13, Supp. Table S29), astrocytes (P=0.012), and neurodegenerative pathways, including late-onset AD and brain atrophy.”

May combine two claims.

In CSF, the APOE region at chr19q13.32 was associated with the largest number of proteins, with eleven unique index variants in three LD blocks associated with the levels of 335 proteins, of which four are in cis.

“In CSF, the APOE region at chr19q13.32 was associated with the largest number of proteins, with eleven unique index variants in three LD blocks (R2>0.5, Supp. Fig. 15) associated with the levels of 335 proteins (Fig. 3I, Supp. Table S27), of which four (three aptamers tagging APOE and APOC2) are in cis.”

May combine two claims.

The same region in plasma contained 1,756 associations, significantly more than CSF (9.71% of all plasma associations vs 6.50% of all CSF associations; P=3.10×10−7).

“The same region in plasma contained 1,756 associations11, significantly more than CSF (9.71% of all plasma associations vs 6.50% of all CSF associations; P=3.10×10−7).”

• cites [11] Ferkingstad, E. et al. Large-scale integration of the plasma proteome with genetics and disease. Nat. Genet. 53, 1712–1721 (2021). sourceNot checked — no full text of the source

May combine two claims.

The study identified 1,861 index CSF pQTL (75.1% of all, 866 cis, 995 trans) that failed to colocalize with any pQTL across tissues (CSF-specific, 1,280) or were associated with newly-measured proteins (true novel, 581).

“We identified 1,861 index CSF pQTL (75.1% of all, 866 cis, 995 trans) that failed to colocalize with any pQTL across tissues (CSF-specific, 1,280) or were associated with newly-measured proteins (true novel, 581).”

May combine two claims.

Among these, inverse associations (higher protein, decreased risk) were observed for ACE, TREM2, and GRN, while CTSH, SHARPIN, and CR1 were associated with increased risk.

“Among these we observed inverse associations (higher protein, decreased risk) for ACE, TREM2, and GRN, while CTSH, SHARPIN, and CR1 were associated with increased risk.”

May combine two claims. The quote only partly states this claim.

The study identified 32 cis associations for 23 unique proteins and 129 trans associations for 47 unique proteins in chr6 region.

“We identified 32 cis associations for 23 unique proteins and 129 trans associations for 47 unique proteins.”

May combine two claims.

Pathway analysis identified 86 enriched pathways using the 70 proteins, highly immune-specific.

“Pathway analysis identified 86 enriched pathways using the 70 proteins (Fig. 3G, Supp. Fig. 14, Supp. Table S32). These were highly immune-specific, including regulation of immune response (GO:0050776), leukocyte mediated immunity (GO:0002443), and antigen processing and presentation (KEGG:hsa04612).”

May combine two claims.

Colocalization with brain and plasma pQTL: 16.8% (72/428) of associations in plasma and 6.7% (35/520) in brain.

“We observed colocalization (PP.H4≥0.8) for 16.8% (72/428) of associations in plasma and 6.7% (35/520) in brain (Fig. 2G).”

May combine two claims.

The study integrated CSF pQTL associations with Alzheimer's disease through PWAS, colocalization and Mendelian Randomization and identified 38 putative causal proteins.

“We integrated our associations with Alzheimer’s disease (AD) through PWAS, colocalization and Mendelian Randomization and identified 38 putative causal proteins, 15 of which have drugs available.”

May combine two claims.

Only one pQTL was observed in chr3q28 region in plasma, suggesting this is a CSF-specific pQTL hotspot.

“Only one pQTL was observed in this region in plasma11, suggesting this is a CSF-specific pQTL hotspot.”

• cites [11] Ferkingstad, E. et al. Large-scale integration of the plasma proteome with genetics and disease. Nat. Genet. 53, 1712–1721 (2021). sourceNot checked — no full text of the source

May combine two claims.

Most proteins (n=1,025, 54.4%) had a single association, but up to 16 independent cis associations were observed for two proteins (SIRPB1 & GSTM1).

“Most proteins (n=1,025, 54.4%) had a single association, but we observed up to 16 independent cis associations for two proteins (SIRPB1 & GSTM1).”

May combine two claims.

QTLs were enriched for protein-altering variants (PAVs) (P<0.001, Fold change=9.78), a trend that persisted after removing potential binding artifacts (P < 0.001, FC = 6.39).

“QTLs were enriched for protein-altering variants (PAVs, see Supplementary Notes, Supp. Fig. 9B, Supp. Table S12, P<0.001, Fold change=9.78), a trend that persisted after removing potential binding artifacts (P < 0.001, FC = 6.39), indicating that pQTL are enriched for coding variants in comparison with non-pQTL variants.”

May combine two claims.

Although proteins with APOE-region associations were enriched in neurons, APOE is mainly expressed in astrocytes.

“Interestingly, although we observed an enrichment of proteins with APOE-region associations in neurons (Fig. 3J, Supp. Fig. 13, Supp. Table S29), APOE is mainly expressed in astrocytes (Supp. Table S28).”

May combine two claims.

The chr3q28 region is intergenic, located between GMNC and OSTN, and consists of twelve index variants corresponding to one LD block associated with 208 unique proteins, all trans.

“The chr3q28 region is intergenic, located between GMNC and OSTN, and consists of twelve index variants corresponding to one LD block (R2>0.5, Supp. Fig. 12I) associated with 208 unique proteins (Fig. 3A, Supp. Table S27), all of them trans.”

May combine two claims.

The performance of the model was consistent across ages and APOE genotypes and the independent Stanford dataset (ProtRS AUC=0.932).

“The performance of the model was consistent across ages and APOE genotypes (Supp. Fig. 25, Supp. Table S50) and the independent Stanford dataset (ProtRS AUC=0.932, Supp. Fig. 26), which only included 65% of the proteins.”

May combine two claims.

The study integrated its pQTL with AD GWAS and prioritized 38 proteins, 24 of which were not nominated by previous studies.

“We integrated our pQTL with AD GWAS and prioritized 38 proteins, 24 of which were not nominated by previous studies.”

May combine two claims.

Many of the study's findings were confirmed using a complementary proteomic platform, showing robustness across cohorts and measurement techniques.

“We confirmed many of our findings using a complementary proteomic platform, highlighting the robustness of our findings across cohorts and measurement techniques.”

May combine two claims.

The model accurately classified participants in the training dataset (AUC=0.949) and testing dataset (AUC=0.902).

“The model accurately classified participants in both the training (AUC=0.949; Supp. Fig. 25, Supp. Table S49) and testing datasets (AUC=0.902, Fig. 4G).”

May combine two claims.

The model performed better than a PRS with covariates or a model incorporating APOE genotype with covariates (P<2.2×10−16).

“The model performed better than a PRS with covariates or a model incorporating APOE genotype with covariates (P<2.2×10−16, Supp. Table S50).”

May combine two claims.

The study highlighted a lysosomal role, with GRN and TMEM106B among others implicated in endosome-lysosome fusion.

“We also highlighted a lysosomal role, with GRN and TMEM106B among others implicated in endosome-lysosome fusion.”

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

In total, 5,750 proteins had genes that were included in the cell-type expression data.

“In total, 5,750 proteins had genes that were included in the cell-type expression data.”

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

There is an instance where aptamers do not correlate with the expected genotype.

“This includes an instance where aptamers do not correlate with the expected genotype (see Supplementary Notes, Supp. Figs. 27&28).”

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

Filtering for cryptic relatedness through identity by descent was performed, and pairs with PI_HAT ≥0.25 were considered related with one sample from each pair removed.

“Filtering for cryptic relatedness through identity by descent (IBD) was performed using PLINK1.998 including variants with MAF≥0.15 or HWE P≥0.001 and R2 of 0.2 (Supplementary Figure 2B). Pairs with PI_HAT≥0.25 were considered related and one sample from each pair was removed to minimize samples lost (n=230).”

May combine two claims.

The binding characteristics of each aptamer are not available, so the study cannot determine which isoform the aptamers are binding to.

“The binding characteristics of each aptamer are not available, so we cannot determine which isoform the aptamers are binding to.”

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

Protein measurement using aptamers can introduce binding artifacts that affect the pQTL associations.

“protein measurement using aptamers can introduce binding artifacts that affect the pQTL associations.”

May combine two claims.

CSF is neurologically relevant because it surrounds the brain and spinal cord, and many CSF proteins are derived from the central nervous system.

“CSF is neurologically relevant as the fluid that surrounds the brain and spinal cord, while many CSF proteins are derived from the central nervous system92.”

• cites [92] Regeniter, A. et al. A modern approach to CSF analysis: pathophysiology, clinical application, proof of concept and laboratory reporting. Clin. Neurol. Neurosurg. 111, 313–318 (2009). sourceNot checked — no full text of the source

Classified as probably not a substantial claim.

After merging all datasets, variants with genotyping rate ≥90%, minor allele count ≥10, and Hardy-Weinberg Equilibrium P ≥1×10−6 were kept.

“All datasets were merged and variants with genotyping rate ≥90%, minor allele count (MAC) ≥10, and HWE P≥1×10−6 were kept.”

Classified as probably not a substantial claim.

The MR analysis harmonized the instrument and outcome datasets to ensure matching effect alleles.

“We extracted the instrument variants then harmonized the two datasets to ensure matching effect alleles.”

Classified as probably not a substantial claim.

A study-wide significant p-value of 5×10−8/1450 (approximately P<3.45×10−11) was used to define trans-pQTL.

“In total 1,450 proteomic PCs were necessary to account for that variance, so a study-wide significant p-value of 5x10−8/1450 (approximately P<3.45x10−11) was used to define trans-pQTL.”

Classified as probably not a substantial claim.

Principal component analysis was performed using PLINK1.9 to account for population stratification.

“Principal component analysis (PCA) was performed using PLINK1.998 to account for population stratification.”

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

The cell-type analyses were derived from healthy individuals and RNA levels, which may correlate poorly with proteins.

“Our cell-type analyses were derived from healthy individuals and RNA levels, which may correlate poorly with proteins.”

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

For all enrichment analyses, an FDR-corrected p-value threshold of 0.05 was used.

“For all enrichment analyses, an FDR-corrected p-value threshold of 0.05 was used.”

Classified as probably not a substantial claim.

The MR analysis selected instrument variants by clumping all variants that reached genome-wide significance (P<5×10−8) in cis for each aptamer, using predefined default clumping thresholds.

“We performed clumping on all variants that reached genome-wide significance (P<5×10−8) in cis for each aptamer, using the predefined default clumping thresholds.”

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

Before imputation, high-quality directly sequenced variants were filtered for genotyping rate ≥98% per SNP or individual, MAF ≥0.01, and Hardy-Weinberg Equilibrium P ≥1×10−6.

“Before imputation, high-quality directly sequenced variants were filtered based on the following criteria: (1) genotyping rate ≥98% per SNP or individual; (2) MAF≥0.01; and (3) Hardy-Weinberg Equilibrium (HWE) P≥1×10−6.”

May combine two claims.

The prioritization was limited to proteins in the panel, excluding genes from many AD-associated regions and limiting the search space for those where a protein is included.

“In addition, the prioritization was limited to proteins in the panel, excluding genes from many AD-associated regions and limiting the search space for those where a protein is included.”

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

In the external replication analysis, associations were corrected for age, sex, and population structure (gPC 1-4).

“Analyses were corrected for age, sex, and population structure (gPC 1-4).”

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

Quality control was also performed on the PPMI SOMAscan 5k data.

“Quality control was also performed on the PPMI SOMAscan 5k data.”

Classified as probably not a substantial claim.

The MR analysis applied multiple test correction using Benjamini-Hochberg false discovery rate with an adjusted p-value threshold of 0.05.

“We performed multiple test correction using Benjamini-Hochberg112 false discovery rate, with an adjusted p-value threshold of 0.05.”

• cites [112] Benjamini, Y. & Hochberg, Y. Controlling the false discovery rate: a practical and powerful approach to multiple testing. J. R. Stat. Soc. Series B Stat. Methodol. 57, 289–300 (1995). sourceNot checked — no full text of the source

Classified as probably not a substantial claim.

To account for pleiotropy, the MR analysis removed variants in pleiotropic regions that regulated two or more proteins, so only variants associated with a single protein were included.

“To account for pleiotropy in the analysis, we first removed all variants for each aptamer including any variant in a pleiotropic region (as identified above) that regulated two or more proteins – so only variants associated with a single protein were included.”

Classified as probably not a substantial claim.

For each aptamer, age, self-reported sex, ten genetic principal components, and cohortArray variables were included as covariates in an additive linear model.

“For each aptamer, age, self-reported sex, ten genetic principal components, and cohortArray variables (for example ADNI_OmniEx) were included as covariates in an additive linear model.”

Classified as probably not a substantial claim.

To account for sample size differences across cohorts, only aptamers present in the largest dataset were kept for analysis.

“To account for sample size differences across the cohorts, only aptamers present in the largest dataset (that consisting of ADNI, DIAN, Knight-ADRC (Oct 2021), FACE, and Barcelona-1, Naptamers=7,008) were kept for analysis.”

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

This dataset has been applied to identify proteogenomic links between the LRRK2 locus and Parkinson's disease.

“and this dataset has been applied to identify proteogenomic links between the LRRK2 locus and Parkinson’s disease21.”

• cites [21] Phillips, B. et al. Proteome wide association studies of LRRK2 variants identify novel causal and druggable proteins for Parkinson’s disease. NPJ Parkinsons Dis. 9, 107 (2023).Not matched

  Couldn’t be matched to a paper in Crossref, so it can’t be checked.

Classified as probably not a substantial claim. May combine two claims.

Aptamers that overlapped between at least two of PWAS, COLOC, and MR were determined and used for subsequent pathway and cell-type analyses.

“We then determined the aptamers that overlapped between at least two of PWAS, COLOC, and MR and performed pathway and cell-type analyses as described below.”

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

The individuals used in the prediction models were also used when identifying the PWAS-significant proteins, so further analysis is needed in independent cohorts to validate the models.

“We note that the individuals used in the prediction models were also used when identifying the PWAS-significant proteins, so further analysis is needed in independent cohorts to validate the models.”

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

TREM2 regulates microglial response to neurodegeneration.

“Immune-relevant proteins included TREM2, which regulates microglial response to neurodegeneration68.”

• cites [68] Deczkowska, A. et al. Disease-associated microglia: a universal immune sensor of neurodegeneration. Cell 173, 1073–1081 (2018). sourceNot checked — no full text of the source

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

Ambiguous SNPs were removed from the analyses to avoid false-positive results due to genotyping array strand differences.

“Ambiguous SNPs were removed from the analyses to avoid false-positive results due to genotyping array strand differences.”

May combine two claims.

In MR analyses, the study attempted to control for horizontal pleiotropy by utilizing only cis-pQTL and removing variants associated with multiple proteins, but it was limited to the proteins in the panel.

“while we attempted to control for horizontal pleiotropy in our MR analyses by utilizing only cis -pQTL and removing any variants associated with multiple proteins, we are limited to the proteins in the panel.”

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

Further quality control was performed on the normalized proteomics data according to an in-house protocol for samples from all cohorts except PPMI.

“Further quality control was performed on the normalized proteomics data provided by Somalogic, according to an in-house protocol, for samples from all cohorts except PPMI.”

Classified as probably not a substantial claim.

The ability to extract CSF from living individuals and its shared biology with the brain highlights its relevance for studying neurological disorders and diseases.

“The ability to extract CSF from living individuals and its shared biology with the brain highlights its relevance for the study of neurological disorders and diseases.”

• AssumptionRests on an assumption: Proteins often directly contribute to disease because of their active participation in biological processes.