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

In the paper

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

What the sources say

• Supported

  The Results identify a PPP3R1 variant associated with CSF phosphorylated tau levels, and the Discussion reports that the variant is also associated with faster AD progression. The citation follows the association claim; the statement that PPP3R1 is genetically regulated by “this region” is the citing authors’ separate assertion. Page numbers were not provided. (LLM, conf=0.92)

  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). source

In the paper

“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.”

What the sources say

• Partly 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)

  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). sourceExperimental — accuracy not yet measured
• Supported

  The citation is attached to APOE’s potential role in cell death, not to the citing authors’ observation of BH3-only pathways. In the Results section on GABAergic neuron degeneration, the source reports more apoptotic cell death in apoE4/4 than apoE3/3 neurons and concludes that apoE4 induces GABAergic neuron death in culture. (LLM, conf=0.90)

  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). source
• Supported

  The Discussion reports that apoE deficiency impairs uptake of apoptotic cells and increases their accumulation in mouse tissues, supporting the hedged suggestion that APOE has a role in cell-death-related processes. The sentence presents BH3-only protein activation as the citing authors’ own observation, not as a finding attributed to this source. (LLM, conf=0.84)

  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). source

In the paper

“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.”

What the sources say

• Partly 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)

  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). sourceExperimental — accuracy not yet measured

In the paper

“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.”

What the sources say

• Partly 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)

  cites [17] Hansson, O. et al. The genetic regulation of protein expression in cerebrospinal fluid. EMBO Mol. Med. 15, e16359 (2023). sourceExperimental — accuracy not yet measured

In the paper

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

What the sources say

• Partly 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)

  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). sourceExperimental — accuracy not yet measured
• Partly 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)

  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). sourceExperimental — accuracy not yet measured

In the paper

“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).”

What the sources say

• Supported

  Citation 47 is attached to “MR,” identifying the method the citing authors used; it is not offered for their finding of 17 proteins or for the Steiger test, which has a separate citation. The source paper’s Introduction (§ Mendelian randomization; page not provided) explains MR as a method for estimating causal effects using genetic variation. (LLM, conf=0.91)

  cites [47] Hemani, G. et al. The MR-Base platform supports systematic causal inference across the human phenome. eLife 7, e34408 (2018). source
• Supported

  Citation 52 is attached to “the Steiger test,” not to the citing authors’ finding of 17 proteins. The cited paper’s Methods (“MR causal test”) describes the Steiger test as indicating the direction of a potential causal relationship and the confidence in that direction. The 17-protein result is not attributed to this source. (LLM, conf=0.92)

  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). source

In the paper

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

What the sources say

• Supported

  Citation 45 is attached to FUSION, identifying the method used, rather than to the citing study’s PWAS results. The source paper’s Results (‘TWAS identifies novel expression-trait associations’) and Online Methods describe its association-testing approach. The 125 pQTL and 108 proteins are the citing study’s findings, not findings attributed to this source. (LLM, conf=0.85)

  cites [45] Gusev, A. et al. Integrative approaches for large-scale transcriptome-wide association studies. Nat. Genet. 48, 245–252 (2016). source
• Supported

  The citation is attached to pleiotropy filtering, rather than to the citing authors’ FUSION analysis or their count of AD associations. In Methods, “Instrumental variable selection for MR” (page unavailable), the source describes removing highly pleiotropic variants when selecting pQTLs. (LLM, conf=0.89)

  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). source
• Supported

  The citation is attached to pleiotropy filtering, not to the citing authors’ FUSION PWAS or their count of 125 pQTLs. In Methods > Instrument validation (page unavailable), the source describes excluding highly pleiotropic instruments from its analyses, supporting the cited methodological point. (LLM, conf=0.89)

  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). source

In the paper

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

What the sources say

• Partly 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)

  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). sourceExperimental — accuracy not yet measured
• Partly 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)

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

In the paper

“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.”

What the sources say

• ?Not checked — no full text of the sourcecites [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). source
• Supported

  The cited paper supports the part of the sentence attached to this citation: ephrins are involved in neural development and memory. Its ‘Ephs and Ephrins and Neuronal Morphogenesis’ section describes ephrin-related dendritic development, and ‘Ephrins in Memory Formation’ reports evidence that ephrins are needed for memory formation. The citation is not attached to the region-specific protein count. (LLM, conf=0.90)

  cites [32] Dines, M. & Lamprecht, R. The role of ephs and ephrins in memory formation. Int. J. Neuropsychopharmacol. 19, pyv106 (2016). source
• ?Not checked — no full text of the sourcecites [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). source

In the paper

“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).”

What the sources say

• Partly 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)

  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). sourceExperimental — accuracy not yet measured

In the paper

“We analyzed directionality using MR-Steiger52.”

What the sources say

• Supported

  The Results section, “Using MR Steiger to infer the direction of causality,” identifies MR Steiger as a method for orienting causal direction. The Methods section, “MR causal test,” states that the Steiger test indicates the direction of the causal relationship in an MR analysis. Page numbers were not provided in the passages. (LLM, conf=0.94)

  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). source

In the paper

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

What the sources say

• Partly 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)

  cites [90] Solesio, M. E. et al. Carbonic anhydrase inhibition selectively prevents amyloid β neurovascular mitochondrial toxicity. Aging Cell 17, e12787 (2018). sourceExperimental — accuracy not yet measured

In the paper

“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.”

What the sources say

• Supported

  The Introduction identifies CR1 variants associated with Alzheimer’s disease, including the GWAS-identified rs6656401 variant. This supports the specific statement to which this source is cited: that the association has been linked to CR1. The alternative-candidate nominations are presented as the citing authors’ own analyses, not as findings attributed to this source. (LLM, conf=0.90)

  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). source
• Supported

  The citation is attached to the statement that the AD association at 1q32.2 has been linked to CR1, not to the citing authors’ nomination of alternative candidates. The source’s Results section ('Relationship of CR1-B with flanking SNV alleles'; page unavailable) reports that the CR1-B allele is linked to the AD risk haplotype and could explain the association at nearby SNPs. (LLM, conf=0.91)

  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). source
• Supported

  The citation is attached to the statement that the AD-risk association at 1q32.2 has been linked to CR1, not to the citing authors’ nominations of alternative candidates. The Results section (“CR1 SNP association in Flanders–Belgian cohort”) reports significant associations between SNPs across the CR1 locus and AD risk. (LLM, conf=0.92)

  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). source
• Partly 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)

  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). sourceExperimental — accuracy not yet measured
• Supported

  The citation in the printed sentence is attached to the prior link between the 1q32.2 AD risk association and CR1, not to the citing authors’ nomination of alternative candidates. In Results > Integrative gene prioritization (page unavailable), the source reports that CR1 was top-ranked at its AD risk locus. (LLM, conf=0.90)

  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). source

In the paper

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

What the sources say

• Supported

  The Introduction states that CLN5 mutations cause a variant late-infantile form of neuronal ceroid lipofuscinosis. The Discussion reports that CLN5-deficient human neurons had defects in lysosomal enzyme activity and movement. (LLM, conf=0.94)

  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). source

In the paper

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

What the sources say

• Supported

  The Introduction states that studies of therapies targeting calcium-associated receptors have reversed AD-related pathological changes and describes drug development based on calcium homeostasis as feasible. The AD88 citation is attached to that therapeutic claim; the CASQ1 statement carries a separate identifier. Page numbers were not provided in our copy. (LLM, conf=0.92)

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

In the paper

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

What the sources say

• Supported

  In the “CLN5 localisation and trafficking” section, the Fig. 2 caption states that CLN5 is processed in the ER, transported to the Golgi, and then passes through the early endosome to lysosomes. The statement about enrichment for endosome proteins is the citing authors’ interpretation, not a separate finding attributed to this source. (LLM, conf=0.94)

  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). source

In the paper

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

What the sources say

• Supported

  Section 2.10 reports that captopril slowed the development of signs of neuronal degeneration in the Tg2576 mouse model of AD. The Conclusions likewise report retarded Aβ plaque accumulation and signs of neuronal regeneration after treatment with the ACE inhibitor captopril. Page numbers are not provided in the supplied copy. (LLM, conf=0.93)

  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). source

In the paper

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

What the sources say

• Supported

  The section ‘Increased CTSH mRNA expression in brain tissues of AD patients and AD mouse models’ reports significantly higher CTSH mRNA in several brain regions of AD patients than in controls. The CTSH-knockout section reports higher fluorescent Aβ42 uptake in knockout human microglial cells than in wild-type cells and interprets this as increased phagocytic ability. (LLM, conf=0.94)

  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). source

In the paper

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

What the sources say

• Supported

  The Discussion reports that cetuximab was associated with the lowest risk of Alzheimer’s disease in this study of colorectal cancer survivors. The citation is attached to the sentence about AD risk; the preceding FCGR3B targeting statement carries a DrugBank identifier and is not attributed to this paper. (LLM, conf=0.91)

  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). source

In the paper

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

What the sources say

• Partly 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)

  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). sourceExperimental — accuracy not yet measured
• Supported

  The citation to this paper is attached to the excitatory-signaling clause, not the preceding SLC25A18 transporter claim. In “Glutamate and glutamatergic signaling,” the paper describes glutamate as the most abundant excitatory neurotransmitter in the mammalian CNS and discusses its role in synaptic signaling. (LLM, conf=0.91)

  cites [87] Wang, R. & Reddy, P. H. Role of glutamate and NMDA receptors in Alzheimer’s disease. J. Alzheimers Dis. 57, 1041–1048 (2017). source

In the paper

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

What the sources say

• Supported

  The Main section says that many putative AD-associated loci and genes have been reported. The Gene prioritization section says that, for five loci, there was insufficient molecular evidence to prioritize a gene beyond the nearest one, supporting the claim that the functional gene is unclear for some loci. Page numbers are not available in our copy. (LLM, conf=0.93)

  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). source
• Supported

  The Results section reports 37 Alzheimer’s disease risk loci and says the authors analyzed them to identify causal genes and variants. The colocalization results note that multiple genes can be implicated at an individual locus, requiring further evidence to prioritize the relevant gene. Page numbers are not available in our copy. (LLM, conf=0.93)

  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). source

In the paper

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

What the sources say

• Partly 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)

  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). sourceExperimental — accuracy not yet measured

In the paper

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

What the sources say

• Supported

  The Discussion (page unavailable) says the data suggest that genetic variation in the innate immune system is among the primary causes of late-onset AD. That supports the strong immunological role to which this citation is attached; the citing sentence gives TREM2 separate citations. (LLM, conf=0.91)

  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). source
• Supported

  The Discussion reports genetic overlap between Alzheimer disease and immune-mediated diseases and concludes that immune- and inflammation-associated genes likely influence AD pathogenesis and progression. The Conclusions likewise say the findings are consistent with inflammation influencing AD pathogenesis. This supports the broad immunological role attached to this citation; the paper is not cited specifically for enrichment of prioritized proteins. (LLM, conf=0.92)

  cites [94] Yokoyama, J. S. et al. Association between genetic traits for immune-mediated diseases and Alzheimer disease. JAMA Neurol. 73, 691–697 (2016). source
• Supported

  The citation is attached to the claim of a strong immunological role in AD, not to the citing authors’ protein-prioritization result. In “Recent studies renewing interest in the immunological contribution to AD,” the review reports enrichment of immune-response genes among AD susceptibility loci and identifies myeloid-cell genes including CD33 and TREM2. (LLM, conf=0.91)

  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). source
• Supported

  In the citing sentence, this citation is attached to TREM2, not to the enrichment analysis, CD33, or IL34. The source’s Introduction (page not available) describes TREM2 as essential to immune responses in microglia and reports TREM2 variants associated with Alzheimer’s disease risk, supporting its inclusion as an example of an immunological role in AD. (LLM, conf=0.91)

  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). source
• Supported

  The citation is attached to TREM2, not to CD33, IL34, or the citing authors’ protein-enrichment result. The paper’s Discussion identifies TREM2 as primarily expressed on brain microglia and involved in inflammatory regulation; its Abstract reports an association between TREM2 variants and AD risk. (LLM, conf=0.93)

  cites [96] Jin, S. C. et al. Coding variants in TREM2 increase risk for Alzheimer’s disease. Hum. Mol. Genet. 23, 5838–5846 (2014). source

In the paper

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

What the sources say

• Partly 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)

  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). sourceExperimental — accuracy not yet measured
• Partly 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)

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

In the paper

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

What the sources say

• Supported

  Section 2 describes ITAM-associated microglial receptors increasing phagocytosis and ITIM-bearing receptors counter-regulating that signaling. Section 5 says Siglecs participate in the induction of apoptosis, while the paper discusses these receptor pathways in relation to Alzheimer’s disease. The citation supports the attributed processes; the proposed convergence is the citing authors’ inference. (LLM, conf=0.87)

  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). source

In the paper

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

What the sources say

• Supported

  The Introduction (page not supplied) states that TREM2 signaling is required for the transition to stage 2 disease-associated microglia and calls TREM2 a key player in inducing that phenotype. This supports the claim that TREM2 regulates the microglial response to neurodegeneration. (LLM, conf=0.93)

  cites [68] Deczkowska, A. et al. Disease-associated microglia: a universal immune sensor of neurodegeneration. Cell 173, 1073–1081 (2018). source

In the paper

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

What the sources say

• Supported

  The TREM2/DAP12 complex section states that TREM2 binds DAP12 and that phosphorylation of DAP12’s ITAM initiates downstream signaling. It also explains that the complex can either activate or inhibit cellular activation, consistent with ‘modulates.’ No page number is provided in the supplied passages. (LLM, conf=0.93)

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

In the paper

“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.”

What the sources say

• Supported

  The Introduction identifies GRN mutations as a cause of frontotemporal lobar degeneration (FTLD), and the section “TMEM106B is a risk factor for FTLD with GRN mutations” describes TMEM106B’s FTLD association and the proteins’ roles in lysosomal biology. The citing sentence assigns the latest AD risk GWAS finding to a separate citation (23), not to this review. (LLM, conf=0.90)

  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). source
• Supported

  The Discussion ('The role of TMEM106B in FTLD') describes PGRN and TMEM106B as acting in the lysosome and links GRN and TMEM106B to frontotemporal lobar degeneration. In the citing sentence, this source is cited for the proteins’ identification; the AD risk GWAS statement has a separate citation. (LLM, conf=0.90)

  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). source
• Supported

  The Abstract identifies GRN mutations as a cause of FTLD-TDP and reports TMEM106B as a genetic risk factor for FTLD-TDP. This supports the frontotemporal-dementia association attributed to this source; the separate claim about an AD risk GWAS has a different citation in the citing sentence. (LLM, conf=0.92)

  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). source
• ?Not checked — no full text of the sourcecites [83] Baker, M. et al. Mutations in progranulin cause tau-negative frontotemporal dementia linked to chromosome 17. Nature 442, 916–919 (2006). source
• Supported

  The GWAS meta-analysis names GRN and TMEM106B among the loci identified in the AD-risk analysis. The ‘Genetic overlap with other neurodegenerative diseases’ section also identifies both as loci associated with types of frontotemporal dementia; the Discussion links both to endosome/lysosome function. (LLM, conf=0.91)

  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). source

In the paper

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

What the sources say

• Supported

  The Results (Cross-platform comparisons; page not specified) report good agreement between SomaScan and the complementary Olink and mass-spectrometry platforms for proteins measured in CSF and plasma. Median within-subject correlations across platforms were approximately 0.7 in CSF and 0.6 in plasma. (LLM, conf=0.93)

  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). source
• Partly 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)

  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). sourceExperimental — accuracy not yet measured

In the paper

“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).”

What the sources say

• Supported

  The Results section (“Discovery of multi-tissue pQTLs”) identifies this as prior CSF pQTL work and reports that 835 CSF samples and 713 proteins were included after quality control. Both are fewer than the citing document’s stated 3,506 samples and 6,361 proteins; those larger figures describe the citing document’s dataset, not this source. (LLM, conf=0.91)

  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). source
• Supported

  The citation identifies this paper as previous CSF pQTL work, not as the source of the new dataset’s figures. The Abstract reports a CSF pQTL study of 133 subjects and 1,126 proteins, both smaller than the citing dataset’s 3,506 subjects and 6,361 proteins. (LLM, conf=0.93)

  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). source
• Supported

  The Discussion identifies this as a previous CSF pQTL study comprising 1,591 individuals and 398 proteins. Those figures are below the citing dataset’s stated 3,506 samples and 6,361 proteins, so the paper supports its use as an example of earlier, smaller CSF pQTL work; it does not itself report the newer dataset’s figures. (LLM, conf=0.91)

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

  The citation identifies this paper as previous CSF pQTL work, not as the source of the citing authors’ dataset counts. The Introduction (Fig. 1; page unavailable) reports a CSF pQTL analysis of 804 participants and proteomic measurement of 4,135 unique proteins—both below the citing dataset’s stated figures of 3,506 and 6,361. (LLM, conf=0.90)

  cites [18] Kaiser, S. et al. A proteogenomic view of Parkinson’s disease causality and heterogeneity. NPJ Parkinsons Dis. 9, 24 (2023). source
• Supported

  The Methods (Subjects) report 266 Knight ADRC and 308 ADNI samples, and Methods (Statistical analysis) describe genome-wide association tests for 59 CSF protein phenotypes. This identifies the cited paper as earlier CSF pQTL work with a smaller sample and fewer proteins. The figures 3,506 and 6,361 describe the citing paper’s new dataset, not this source. (LLM, conf=0.91)

  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). source

In the paper

“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).”

In the paper

“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).”

In the paper

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

In the paper

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

In the paper

“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.”

In the paper

“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).”

In the paper

“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.”

In the paper

“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.”

In the paper

“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).”

What the sources say

• ?Not checked — no full text of the sourcecites [11] Ferkingstad, E. et al. Large-scale integration of the plasma proteome with genetics and disease. Nat. Genet. 53, 1712–1721 (2021). source

In the paper

“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).”

In the paper

“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.”

In the paper

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

In the paper

“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).”

In the paper

“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).”

In the paper

“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.”

In the paper

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

What the sources say

• ?Not checked — no full text of the sourcecites [11] Ferkingstad, E. et al. Large-scale integration of the plasma proteome with genetics and disease. Nat. Genet. 53, 1712–1721 (2021). source

In the paper

“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).”

In the paper

“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.”

In the paper

“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).”

In the paper

“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.”

In the paper

“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.”

In the paper

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

In the paper

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

In the paper

“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).”

In the paper

“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).”

In the paper

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

In the paper

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

In the paper

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

In the paper

“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).”

In the paper

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

In the paper

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

In the paper

“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.”

What the sources say

• ?Not checked — no full text of the sourcecites [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). source

In the paper

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

In the paper

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

In the paper

“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.”

In the paper

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

In the paper

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

In the paper

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

In the paper

“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.”

In the paper

“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.”

In the paper

“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.”

In the paper

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

In the paper

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

In the paper

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

What the sources say

• ?Not checked — no full text of the sourcecites [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). source

In the paper

“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.”

In the paper

“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.”

In the paper

“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.”

In the paper

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

What the sources say

• ?Not matched

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

  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).

In the paper

“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.”

In the paper

“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.”

In the paper

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

In the paper

“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.”

In the paper

“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.”

In the paper

“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.”