APOE Christchurch enhances a disease-associated microglial response to plaque but suppresses response to tau pathology

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

APOE4 is the strongest genetic risk factor for late-onset Alzheimer's disease.

“Apolipoprotein E ε4 (APOE4) is the strongest genetic risk factor for late-onset Alzheimer’s disease (LOAD).”

• Also stated in: § Background · boosted

  “APOE4 is the most robust genetic risk factor for sporadic LOAD.”

• cites [9] Serrano-Pozo A, et al. APOEepsilon2 is associated with milder clinical and pathological Alzheimer disease. Ann Neurol. 2015;77(6):917–29. sourceSupported
• cites [10] Corder EH, et al. Gene dose of apolipoprotein E type 4 allele and the risk of Alzheimer’s disease in late onset families. Science. 1993;261(5123):921–3. sourceNot checked — no full text of the source

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

Mouse APOE shares 70% homology with human APOE and is encoded by one major allele that resembles human APOE4 by having arginine at positions 112 and 158.

“By contrast, mouse APOE (mAPOE) shares 70% homology with human APOE and is encoded by one major allele, which resembles the human APOE4 isoform by having arginine at both positions 112 and 158 [11].”

• cites [11] Nguyen D, Dhanasekaran P, Nickel M, et al. Influence of domain stability on the properties of human apolipoprotein E3 and E4 and mouse apolipoprotein E. Biochemistry. 2014;53(24):4025–33. sourcePartly supported

  The Results section, under “Primary Structures of Human and Mouse ApoE Variants” (page unavailable), says the human and mouse sequences are 70% identical. The paper also says human apoE4 has arginine at positions 112 and 158, but our copy does not state that mouse apoE has those residues or is encoded by one major allele. (LLM, conf=0.86)

  Experimental — accuracy not yet measured

May combine two claims.

PET imaging of the proband revealed significant Aβ plaque deposits consistent with FAD carriers, but relatively low and atypical burden of neurofibrillary tau tangles and neurodegeneration.

“Positron emission tomography (PET) imaging revealed significant Aβ plaque deposits in her brain, consistent with carriers of FAD mutations, but a relatively low and atypical burden of neurofibrillary tau tangles and neurodegeneration.”

• cites [15] Arboleda-Velasquez JF, et al. Resistance to autosomal dominant Alzheimer’s disease in an APOE3 Christchurch homozygote: a case report. Nat Med. 2019;25(11):1680–3. sourceSupported

Classified as probably not a substantial claim.

Differences in APOE isoform-specific receptor binding affinity and lipid interactions affect neuroinflammation, tau pathology, and amyloid plaque dynamics.

“Studies indicate that APOE binding is integral to some of these processes [16–20] with differences in APOE isoform-specific receptor binding affinity and lipid interactions affecting neuroinflammation, tau pathology, and amyloid plaque dynamics [21–24].”

• cites [21] Barger SW, Mattson MP. Isoform-specific modulation by apolipoprotein E of the activities of secreted beta-amyloid precursor protein. J Neurochem. 1997;69(1):60–7. sourceNot checked — no full text of the source
• cites [22] Huang YA, et al. ApoE2, ApoE3, and ApoE4 differentially stimulate APP transcription and abeta secretion. Cell. 2017;168(3):427–441 e21. sourcePartly supported

  The Results report that ApoE2, ApoE3, and ApoE4 differ in their ability to stimulate Aβ synthesis in human neurons; the Discussion links that effect to ApoE-receptor signaling. The Introduction also notes an association between ApoE4 and Aβ accumulation. The paper does not establish that differences in receptor-binding affinity or lipid interactions cause these effects, and it does not address effects on neuroinflammation or tau pathology. (LLM, conf=0.85)

  Experimental — accuracy not yet measured
• cites [23] Kloske CM, Wilcock DM. The Important Interface Between Apolipoprotein E and Neuroinflammation in Alzheimer’s Disease. Front Immunol. 2020;11:754. sourcePartly supported

  The “ApoE in the Central Nervous System” section (page not provided) describes isoform differences in LDL-receptor affinity and lipid binding. The “ApoE and Aβ” and “ApoE and Tau” sections (pages not provided) report isoform-related differences in plaque formation and tau-associated neuroinflammation, but do not establish that the receptor-binding and lipid interactions cause those outcomes. (LLM, conf=0.85)

  Experimental — accuracy not yet measured
• cites [24] Rebeck GW, et al. Apolipoprotein E in sporadic Alzheimer’s disease: allelic variation and receptor interactions. Neuron. 1993;11(4):575–80. sourceNot checked — no full text of the source

Classified as probably not a substantial claim.

APOE binding is integral to some processes involving lipoprotein receptors, including Aβ aggregation and neuronal uptake of extracellular tau.

“Studies indicate that APOE binding is integral to some of these processes [16–20] with differences in APOE isoform-specific receptor binding affinity and lipid interactions affecting neuroinflammation, tau pathology, and amyloid plaque dynamics [21–24].”

• cites [16] Fuentealba RA, et al. Low-density lipoprotein receptor-related protein 1 (LRP1) mediates neuronal Abeta42 uptake and lysosomal trafficking. PLoS ONE. 2010;5(7):e11884. sourcePartly supported

  The Introduction says apoE is required for lipoprotein internalization by neuronal apoE receptors, and the Discussion supports a role for apoE in Aβ uptake. The paper does not establish that APOE binding is integral to Aβ aggregation or neuronal uptake of extracellular tau, so it supports only part of the attributed claim. (LLM, conf=0.85)

  Experimental — accuracy not yet measured
• cites [17] Kanekiyo T, et al. Heparan sulphate proteoglycan and the low-density lipoprotein receptor-related protein 1 constitute major pathways for neuronal amyloid-beta uptake. J Neurosci. 2011;31(5):1644–51. sourcePartly supported

  The Introduction identifies APOE as an LRP1 ligand, and the Discussion describes LRP1 and HSPG roles in neuronal Aβ uptake. But the paper does not establish that APOE binding is integral to Aβ aggregation, and it does not address neuronal uptake of extracellular tau. Page numbers are unavailable in our copy. (LLM, conf=0.85)

  Experimental — accuracy not yet measured
• cites [18] Kanekiyo T, Bu G. The low-density lipoprotein receptor-related protein 1 and amyloid-beta clearance in Alzheimer’s disease. Front Aging Neurosci. 2014;6:93. sourcePartly supported

  The Summary and Perspective (page not provided) identifies apoE as an LRP1 ligand that affects Aβ aggregation and cellular uptake. The section on the relationship among LRP1, apoE, and Aβ also discusses apoE binding and receptor-dependent Aβ uptake. The passages found do not address neuronal uptake of extracellular tau. (LLM, conf=0.87)

  Experimental — accuracy not yet measured
• cites [19] Kanekiyo T, et al. Neuronal clearance of amyloid-beta by endocytic receptor LRP1. J Neurosci. 2013;33(49):19276–83. sourcePartly supported

  The Introduction (page unavailable in our copy) identifies APOE as an LRP1 ligand involved in Aβ production or clearance, and the Results report that neuronal LRP1 deletion increases cortical Aβ deposition in amyloid-model mice. These passages connect an APOE-binding receptor to amyloid processes, but do not establish that APOE binding is integral to Aβ aggregation or address neuronal uptake of extracellular tau. (LLM, conf=0.83)

  Experimental — accuracy not yet measured
• cites [20] Rauch JN, et al. LRP1 is a master regulator of tau uptake and spread. Nature. 2020;580(7803):381–5. sourcePartly supported

  The Results (page not available) report that ApoE-containing medium reduced extracellular tau uptake in H4 neuroglioma cells and that LRP1 regulates tau uptake in neurons. They also discuss ApoE4-dependent Aβ pathology, but do not establish an effect on Aβ aggregation or test ApoE’s effect on tau uptake specifically in neurons. (LLM, conf=0.85)

  Experimental — accuracy not yet measured

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

Homozygous APOE4 individuals have a 6 to 18-fold increase in AD risk compared to APOE2/3 individuals.

“Homozygous APOE4 individuals have a 6 to 18-fold increase in AD risk compared to APOE2/3 individuals [9, 10].”

• cites [9] Serrano-Pozo A, et al. APOEepsilon2 is associated with milder clinical and pathological Alzheimer disease. Ann Neurol. 2015;77(6):917–29. sourcePartly supported

  The Introduction reports that carrying two APOE ε4 alleles increases lifetime AD risk 8–12 times compared with the ε3 allele. It does not give the claimed 6–18-fold range or use APOE ε2/ε3 individuals as the comparator; it separately says ε2 reduces risk relative to ε3. No page number is available in our copy. (LLM, conf=0.90)

  Experimental — accuracy not yet measured
• cites [10] Corder EH, et al. Gene dose of apolipoprotein E type 4 allele and the risk of Alzheimer’s disease in late onset families. Science. 1993;261(5123):921–3. sourceNot checked — no full text of the source

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

The receptor-binding sites (AA136-150) for LDLR, LRP1, and HSPGs are located in a region conserved between mouse and human APOE.

“However, the receptor-binding sites (AA136-150) for lipoprotein receptors such as the low-density lipoprotein receptor (LDLR), lipoprotein-related receptor 1 (LRP1), and heparan sulfate proteoglycans (HSPGs) are located in a region conserved between species (Fig. 1a) [11–14].”

• cites [11] Nguyen D, Dhanasekaran P, Nickel M, et al. Influence of domain stability on the properties of human apolipoprotein E3 and E4 and mouse apolipoprotein E. Biochemistry. 2014;53(24):4025–33. sourcePartly supported

  Results > Structural Characterization (page unavailable) reports that human and mouse apoE sequences are 70% identical, supporting broad conservation between the species. It does not identify residues 136–150 as conserved or locate LDLR, LRP1, and HSPG binding sites there; searches for those residues and receptor-binding terms found no supporting passage. (LLM, conf=0.78)

  Experimental — accuracy not yet measured
• cites [12] Weisgraber KH. Apolipoprotein E: structure-function relationships. Adv Protein Chem. 1994;45:249–302. sourceNot checked — no full text of the source
• cites [13] Futamura M, et al. Two-step mechanism of binding of apolipoprotein E to heparin: implications for the kinetics of apolipoprotein E-heparan sulfate proteoglycan complex formation on cell surfaces. J Biol Chem. 2005;280(7):5414–22. sourcePartly supported

  The paper’s introductory discussion (page unavailable) identifies residues 136–150 as the LDLR-binding region and says the same domain is involved in LRP and HSPG binding. It does not state that this region is conserved between mouse and human APOE; searches for mouse–human conservation found no such passage. (LLM, conf=0.88)

  Experimental — accuracy not yet measured
• cites [14] Libeu CP, et al. New insights into the heparan sulfate proteoglycan-binding activity of apolipoprotein E. J Biol Chem. 2001;276(42):39138–44. sourceNot checked — no full text of the source

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

One representative brain slice from each mouse within identical experimental cohort was subjected to simultaneous staining in the same container.

“One representative brain slice from each mouse within the identical experimental cohort (comprising the same genotype, age, and sex) was subjected to simultaneous staining in the same container as described [25, 27].”

• cites [25] Forner S, et al. Systematic phenotyping and characterization of the 5xFAD mouse model of Alzheimer’s disease. Sci Data. 2021;8(1):270. sourcePartly supported

  The Methods section on Imaris quantitative analysis says comparable sections from each animal were processed at the same time using the same batches of solutions. It does not say that exactly one representative slice per mouse was stained, that mice were grouped by identical genotype, age, and sex, or that slices shared a container. Page numbers are unavailable in our copy. (LLM, conf=0.85)

  Experimental — accuracy not yet measured
• cites [27] Javonillo DI, et al. Systematic phenotyping and characterization of the 3xTg-AD mouse model of Alzheimer’s disease. Front Neurosci. 2021;15:785276. sourceSupported

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

ApoeCh mice exhibited elevated plasma cholesterol (CHOL), mainly contributed by males.

“ApoeCh mice exhibited elevated plasma cholesterol (CHOL), mainly contributed by males (Fig. 1b) [15, 41].”

• cites [15] Arboleda-Velasquez JF, et al. Resistance to autosomal dominant Alzheimer’s disease in an APOE3 Christchurch homozygote: a case report. Nat Med. 2019;25(11):1680–3. sourcePartly supported

  The paper’s Abstract (page unavailable) reports elevated total cholesterol in a human APOE3-Christchurch carrier. It does not report plasma cholesterol in ApoeCh mice or a predominantly male contribution to that finding. (LLM, conf=0.86)

  Experimental — accuracy not yet measured
• cites [41] Chen Y, et al. APOE3ch alters microglial response and suppresses Abeta-induced tau seeding and spread. Cell. 2024;187(2):428–445 e20. sourceNot checked — no full text of the source

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

LAMP1 accumulates in dystrophic neurites around plaques.

“Plaque-induced neuritic damage was assessed by staining for lysosomal-associated membrane protein 1 (LAMP1), which accumulates in dystrophic neurites around plaques [50].”

• cites [50] Condello C, et al. Microglia constitute a barrier that prevents neurotoxic protofibrillar Abeta42 hotspots around plaques. Nat Commun. 2015;6:6176. sourceSupported

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

The APOE3Ch variant is potentially associated with limited tau development and resistance to cognitive decline despite increased Aβ levels.

“The APOE3Ch variant offers a unique opportunity to explore the interplay between Aβ and tau, given its potential association with limited tau development and resistance to cognitive decline despite increased Aβ levels.”

• cites [15] Arboleda-Velasquez JF, et al. Resistance to autosomal dominant Alzheimer’s disease in an APOE3 Christchurch homozygote: a case report. Nat Med. 2019;25(11):1680–3. sourceSupported

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

The 5xFAD mouse model has been reported to exhibit sex-specific differences in phenotype.

“As the 5xFAD mouse model has been reported to exhibit sex-specific differences in phenotype, data separated by sex of significant differences are included in Supp. Figure 3, 4i-x, 6 g-l [25, 49].”

• cites [25] Forner S, et al. Systematic phenotyping and characterization of the 5xFAD mouse model of Alzheimer’s disease. Sci Data. 2021;8(1):270. sourceSupported
• cites [49] Sil A, et al. Sex differences in behavior and molecular pathology in the 5XFAD model. J Alzheimers Dis. 2022;85(2):755–78. sourceSupported

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

TAMPOR removes intra-batch and inter-batch variance while preserving meaningful biological variance.

“TAMPOR is utilized to remove intra-batch and inter-batch variance while preserving meaningful biological variance in protein abundance values, normalizing to the median of selected samples within batch.”

• cites [37] Dammer EB, NT Seyfried, ECB Johnson. Batch correction and harmonization of -Omics datasets with a tunable median polish of ratio. Front Syst Biol. 2023;3:1092341. sourcePartly supported

  The Discussion says TAMPOR minimizes variance across batches while maintaining biological variance and differences between samples within a batch. The Results also describe correcting unequal sample loading, but the source does not support removing intra-batch variance generally; that wording overlooks the within-batch variance TAMPOR is designed to preserve. The Discussion supports the use of the median of selected or all samples for normalization. (LLM, conf=0.86)

  Experimental — accuracy not yet measured

May combine two claims.

In the spatial omics data, there was an expected increase in mRNA and protein APOE level with the presence of amyloid but not tau pathology.

“Consistent with Apoe as a marker for disease-associated microglia (DAM), in the spatial omics data we observed the expected increase in mRNA and protein APOE level with the presence of amyloid but not tau pathology (Fig. 1e, g) [48].”

• cites [48] Keren-Shaul H, et al. A unique microglia type associated with restricting development of Alzheimer’s disease. Cell. 2017;169(7):1276–1290 e17. sourceSupported

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

SCTransform accounts for differences in library size across cell types.

“Datasets were then normalized and scaled using Seurat 5.0.1 SCTransform to account for differences in library size across cell types [31].”

• cites [31] Hao Y, et al. Dictionary learning for integrative, multimodal and scalable single-cell analysis. Nat Biotechnol. 2024;42(2):293–304. sourceCould not verify

  The Results sections on reference mapping and community-scale integration discuss aligning and annotating cell populations, not SCTransform’s normalization behavior. Searches for SCTransform, library size, and sequencing-depth normalization found no passage in our copy addressing whether SCTransform accounts for library-size differences across cell types. (LLM, conf=0.70)

  Experimental — accuracy not yet measured

May combine two claims.

In 5xFAD compared to WT mice, DAM genes (Cst7, Apoe, Ctsb, Ctsd, Ctss, Psen1) are upregulated and homeostatic genes (P2ry12, Tmem119, Csf1r) are downregulated.

“In line with other studies, we observe an upregulation in DAM genes (i.e., Cst7, Apoe, Ctsb, Ctsd, Ctss, and Psen1) and downregulation in homeostatic genes (P2ry12, Tmem119, and Csf1r) in 5xFAD compared to WT mice [48, 57, 58].”

• cites [48] Keren-Shaul H, et al. A unique microglia type associated with restricting development of Alzheimer’s disease. Cell. 2017;169(7):1276–1290 e17. sourcePartly supported

  The Results (page unavailable) report a DAM transition in 5XFAD but not WT mice, with increased Apoe and Cst7 and reduced P2ry12 and Tmem119. They also identify Ctsd in an intermediate DAM state. The passages do not establish the claimed directions of change for Ctsb, Ctss, Psen1, or Csf1r. (LLM, conf=0.88)

  Experimental — accuracy not yet measured
• cites [57] Krasemann S, et al. The TREM2-APOE pathway drives the transcriptional phenotype of dysfunctional microglia in neurodegenerative diseases. Immunity. 2017;47(3):566–581 e9. sourcePartly supported

  The Results section on disease-associated microglia reports increased Apoe and decreased P2ry12, Tmem119, and Csf1r in the APP-PS1 Alzheimer’s mouse model. It does not establish the stated changes in 5xFAD versus WT mice or report upregulation of Cst7, Ctsb, Ctsd, Ctss, and Psen1 as claimed. No page number is available in our copy. (LLM, conf=0.88)

  Experimental — accuracy not yet measured
• cites [58] Deczkowska A, et al. Disease-associated microglia: a universal immune sensor of neurodegeneration. Cell. 2018;173(5):1073–81. sourceNot checked — no full text of the source

Probably not a substantial claim: may not pass S1 (asserted), S3 (load-bearing). The quote only partly states this claim.

CELESTA classifies cells based on marker protein expression.

“Cell types were automatically annotated based on marker gene expression using the CELESTA algorithm [34].”

• cites [34] Zhang W, et al. Identification of cell types in multiplexed in situ images by combining protein expression and spatial information using CELESTA. Nat Methods. 2022;19(6):759–69. sourcePartly supported

  The Results (Overview of CELESTA) describe automatic cell-type assignment using marker expression and a cell-type signature matrix. The Extended Data passage identifies the measured markers through image staining, including cytokeratin and CD31. This supports classification based on marker protein expression, but not the citing sentence’s specification of marker gene expression. (LLM, conf=0.87)

  Experimental — accuracy not yet measured

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

Sample sizes were not predetermined using statistical methods.

“The sample sizes are similar to those found in prior studies conducted by MODEL-AD and were not predetermined using statistical methods [25].”

• cites [25] Forner S, et al. Systematic phenotyping and characterization of the 5xFAD mouse model of Alzheimer’s disease. Sci Data. 2021;8(1):270. sourceSupported

May combine two claims.

APOE is involved in the regulation of DAMs and the microglial response to amyloid.

“APOE is involved in the regulation of DAMs and the microglial response to amyloid [57, 64–66].”

• cites [57] Krasemann S, et al. The TREM2-APOE pathway drives the transcriptional phenotype of dysfunctional microglia in neurodegenerative diseases. Immunity. 2017;47(3):566–581 e9. sourceSupported
• cites [64] Shi Y, Holtzman DM. Interplay between innate immunity and Alzheimer disease: APOE and TREM2 in the spotlight. Nat Rev Immunol. 2018;18(12):759–72. sourceSupported
• cites [65] Yin Z, et al. APOE4 impairs the microglial response in Alzheimer’s disease by inducing TGFbeta-mediated checkpoints. Nat Immunol. 2023;24(11):1839–53. sourceSupported
• cites [66] Liu CC, et al. Cell-autonomous effects of APOE4 in restricting microglial response in brain homeostasis and Alzheimer’s disease. Nat Immunol. 2023;24(11):1854–66. sourceSupported

May combine two claims.

In mice homozygous for the Christchurch variant, microglial activation states are suppressed in PS19 mice (tau-associated pathology), promoting a homeostatic or "disease protective" response, whereas they are enhanced in APP/PS1 mice (amyloid-associated pathology), promoting a "disease-associated" state.

“In mice homozygous for the Christchurch variant, these studies indicate that microglial activation states are suppressed in PS19 mice (tau-associated pathology), promoting a homeostatic or “disease protective” response, whereas they are enhanced in APP/PS1 mice (amyloid-associated pathology), promoting a “disease-associated” state.”

• cites [41] Chen Y, et al. APOE3ch alters microglial response and suppresses Abeta-induced tau seeding and spread. Cell. 2024;187(2):428–445 e20. sourceNot checked — no full text of the source
• cites [76] Nelson MR, et al. The APOE-R136S mutation protects against APOE4-driven Tau pathology, neurodegeneration and neuroinflammation. Nat Neurosci. 2023;26(12):2104–21. sourcePartly supported

  Split into 2 atoms — 1 confirmed, 0 partially supported, 0 disputed, 0 misattributed, 1 unverifiable. Expand the claim to see per-atom verdicts.

  Experimental — accuracy not yet measured
• cites [77] Naguib S, Torres ER, Lopez-Lee C, et al. APOE3-R136S mutation confers resilience against tau pathology via cGAS-STING-IFN inhibition. Preprint. bioRxiv. 2024;2024.04.25.591140. sourcePartly supported

  Split into 2 atoms — 0 confirmed, 1 partially supported, 0 disputed, 0 misattributed, 1 unverifiable. Expand the claim to see per-atom verdicts.

  Experimental — accuracy not yet measured

May combine two claims.

Both models rely on transgene overexpression and familial mutations and are not well suited for studying causative events that lead to development of pathology in sporadic AD.

“Both models rely on transgene overexpression and familial mutations (such as ADAD mutations in 5xFAD mice and frontotemporal dementia mutations in PS19 mice) and are not well suited for studying the causative events that lead to the development of pathology in sporadic AD [44–47].”

• cites [44] Moechars D, et al. Expression in brain of amyloid precursor protein mutated in the alpha-secretase site causes disturbed behavior, neuronal degeneration and premature death in transgenic mice. EMBO J. 1996;15(6):1265–74. sourcePartly supported

  The Discussion (page not available) describes a transgenic mouse model in which overexpression of mutant APP causes the observed phenotype. It does not characterize the 5xFAD or PS19 models, establish that their mutations are familial, or assess their suitability for studying the causes of sporadic AD. (LLM, conf=0.85)

  Experimental — accuracy not yet measured
• cites [45] Yoshiyama Y, et al. Synapse loss and microglial activation precede tangles in a P301S tauopathy mouse model. Neuron. 2007;53(3):337–51. sourceNot checked — no full text of the source
• cites [46] Takeuchi H, et al. P301S mutant human tau transgenic mice manifest early symptoms of human tauopathies with dementia and altered sensorimotor gating. PLoS ONE. 2011;6(6):e21050. sourcePartly supported

  The Introduction (page unavailable) identifies the studied mice as transgenic animals expressing human P301S tau, a mutation associated with hereditary frontotemporal dementia. The Materials and Methods, Animals section (page unavailable) confirms the transgenic model. Our copy does not establish that this model overexpresses the transgene or assess whether either model is unsuitable for studying the causes of sporadic Alzheimer’s disease; it also does not describe 5xFAD mice. (LLM, conf=0.85)

  Experimental — accuracy not yet measured
• cites [47] Maruyama M, et al. Imaging of tau pathology in a tauopathy mouse model and in Alzheimer patients compared to normal controls. Neuron. 2013;79(6):1094–108. sourcePartly supported

  The Experimental Procedures (Animal models; page unavailable) identify PS19 mice as transgenic mice expressing human tau with the FTDP-17 P301S mutation. The paper does not address 5xFAD mice or say that either model is poorly suited to studying causative events in sporadic AD. (LLM, conf=0.87)

  Experimental — accuracy not yet measured

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

While this report was being prepared, independent studies reported similar findings.

“While this report was being prepared, independent studies reported similar findings [41, 76, 77].”

• cites [41] Chen Y, et al. APOE3ch alters microglial response and suppresses Abeta-induced tau seeding and spread. Cell. 2024;187(2):428–445 e20. sourceNot checked — no full text of the source
• cites [76] Nelson MR, et al. The APOE-R136S mutation protects against APOE4-driven Tau pathology, neurodegeneration and neuroinflammation. Nat Neurosci. 2023;26(12):2104–21. sourceSupported
• cites [77] Naguib S, Torres ER, Lopez-Lee C, et al. APOE3-R136S mutation confers resilience against tau pathology via cGAS-STING-IFN inhibition. Preprint. bioRxiv. 2024;2024.04.25.591140. sourceSupported

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

JAG1 has been shown to regulate microglial function and inflammatory responses.

“JAG1 has been shown to regulate microglial function and inflammatory responses [75].”

• cites [75] Peruzzotti-Jametti L, et al. Mitochondrial complex I activity in microglia sustains neuroinflammation. Nature. 2024;628(8006):195–203. sourceCould not verify

  The Main section reports changes in microglial states and neuroinflammation associated with mitochondrial complex I activity, but does not connect those findings to JAG1. Searches for “JAG1,” “Jag1,” and “Jagged1 Notch signaling” found no passage in our copy showing that JAG1 regulates microglial function or inflammatory responses. (LLM, conf=0.74)

  Experimental — accuracy not yet measured

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

Autophagy plays an important role in regulating microglial activation (i.e., DAM phenotype induction).

“A recent report provides evidence that autophagy plays an important role in regulating microglial activation (i.e., DAM phenotype induction)”

• cites [78] Choi I, et al. Autophagy enables microglia to engage amyloid plaques and prevents microglial senescence. Nat Cell Biol. 2023;25(7):963–74. sourceSupported

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

Deficiency in autophagy leads to senescence, reduces DAMs, impairs Aβ clustering around plaques, and aggravates AD pathology.

“deficiency in autophagy leads to senescence, reduces DAMs, impairs Aβ clustering around plaques, and aggravates AD pathology [78].”

• cites [78] Choi I, et al. Autophagy enables microglia to engage amyloid plaques and prevents microglial senescence. Nat Cell Biol. 2023;25(7):963–74. sourceSupported

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

Disease associated microglia upregulate mitochondrial complex 1 activity to sustain the response to pathology.

“but it is known that disease associated microglia upregulate mitochondrial complex 1 activity to sustain the response to pathology [75], in line with our pathway analyses of ApoeCh in 5xFAD mice.”

• cites [75] Peruzzotti-Jametti L, et al. Mitochondrial complex I activity in microglia sustains neuroinflammation. Nature. 2024;628(8006):195–203. sourceSupported

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

Activated microglia, via C1q release, have been implicated as potential mediators of neurotoxic effects, resulting in reactive astrocyte-mediated neuronal and oligodendrocyte death.

“Activated microglia, via C1q release, have been implicated as potential mediators of neurotoxic effects, resulting in reactive astrocyte-mediated neuronal and oligodendrocyte death [87].”

• cites [87] Liddelow SA, et al. Neurotoxic reactive astrocytes are induced by activated microglia. Nature. 2017;541(7638):481–7. sourceSupported

Classified as probably not a substantial claim.

The current consensus is that the microglial response to plaques confers protection.

“The current consensus is that the microglial response to plaques confers protection.”

• cites [99] Fassler M, C Benaim, J George. TREM2 agonism with a monoclonal antibody attenuates Tau pathology and neurodegeneration. Cells. 2023;12(11):1549. sourcePartly supported

  The Introduction (section 1; page unavailable) describes a protective role for TREM2-mediated microglial encircling of amyloid plaques, associated with more compact plaques and attenuated neuritic pathology. But it also calls the evidence from transgenic mouse models inconclusive; it does not establish a general consensus that the microglial response to plaques is protective. (LLM, conf=0.86)

  Experimental — accuracy not yet measured
• cites [100] Zhao P, et al. A tetravalent TREM2 agonistic antibody reduced amyloid pathology in a mouse model of Alzheimer’s disease. Sci Transl Med. 2022;14(661):eabq0095. sourceNot checked — no full text of the source

Classified as probably not a substantial claim.

The DAM (DAM/MGnD) signature is dependent on the TREM2-APOE pathway.

“Krasemann et al. showed that the DAM (DAM/MGnD) signature is dependent on the TREM2-APOE pathway [57].”

• cites [57] Krasemann S, et al. The TREM2-APOE pathway drives the transcriptional phenotype of dysfunctional microglia in neurodegenerative diseases. Immunity. 2017;47(3):566–581 e9. sourceSupported

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

Genetic association data implicate microglial expressed genes, and hence microglia, with altered risk for developing the disease, but the underlying mechanisms are not yet fully understood.

“Genetic association data implicate microglial expressed genes, and hence microglia, with altered risk for developing the disease, but the underlying mechanisms are not yet fully understood [93–95].”

• cites [93] Mosher KI, Wyss-Coray T. Microglial dysfunction in brain aging and Alzheimer’s disease. Biochem Pharmacol. 2014;88(4):594–604. sourceSupported
• cites [94] Bellenguez C, et al. New insights into the genetic etiology of Alzheimer’s disease and related dementias. Nat Genet. 2022;54(4):412–36. sourceSupported
• cites [95] Efthymiou AG, Goate AM. Late onset Alzheimer’s disease genetics implicates microglial pathways in disease risk. Mol Neurodegener. 2017;12(1):43. sourceSupported

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

Overexpression of LDLR in PS19 mice suppresses microglial activation, enlarges pools of oligodendrocyte progenitor cells, and enhances preservation of myelin integrity.

“Shi et al. [86] report that overexpression of LDLR in PS19 mice suppresses microglial activation, enlarges pools of oligodendrocyte progenitor cells, and enhances preservation of myelin integrity.”

• cites [86] Shi Y, et al. Overexpressing low-density lipoprotein receptor reduces tau-associated neurodegeneration in relation to apoE-linked mechanisms. Neuron. 2021;109(15):2413–2426 e7. sourceSupported

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

APOE2 or Apoe KO protects against, and APOE4 exacerbates, tauopathy-induced neurodegeneration.

“while APOE2 or Apoe KO protects against, and APOE4 exacerbates, tauopathy-induced neurodegeneration [29].”

• cites [29] Shi Y, et al. ApoE4 markedly exacerbates tau-mediated neurodegeneration in a mouse model of tauopathy. Nature. 2017;549(7673):523–7. sourcePartly supported

  The paper reports that ApoE4 worsens tau-mediated neurodegeneration and ApoE knockout is protective. Its Extended Data Figure 9 places E2 at approximately the same level of neurodegeneration as E3, well above knockout; the Abstract also reports neuronal damage with recombinant E2. Thus the claim overstates the evidence that E2 itself is protective, although E2 fares better than E4. (LLM, conf=0.88)

  Experimental — accuracy not yet measured

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

APOE-TREM2 interactions facilitate phagocytosis of apoptotic neurons and increased uptake of Aβ.

“APOE-TREM2 interactions have been found to facilitate phagocytosis of apoptotic neurons and increased uptake of Aβ [80–83].”

• cites [80] Bailey CC, DeVaux LB, Farzan M. The triggering receptor expressed on myeloid cells 2 binds apolipoprotein E. J Biol Chem. 2015;290(43):26033–42. sourceNot checked — no full text of the source
• cites [81] Atagi Y, et al. Apolipoprotein E is a ligand for Triggering Receptor Expressed on Myeloid Cells 2 (TREM2). J Biol Chem. 2015;290(43):26043–50. sourcePartly supported

  The Results and Discussion (page numbers not supplied) report that apoE increased TREM2-mediated phagocytosis of apoptotic neuronal N2a cells by mouse microglia. The Discussion mentions earlier evidence for apoE-facilitated uptake of soluble Aβ, but only proposes that TREM2 may help phagocytose apoE-coated Aβ aggregates; it does not establish increased Aβ uptake through the apoE–TREM2 interaction. (LLM, conf=0.90)

  Experimental — accuracy not yet measured
• cites [82] Jendresen C, et al. The Alzheimer’s disease risk factors apolipoprotein E and TREM2 are linked in a receptor signaling pathway. J Neuroinflammation. 2017;14(1):59. sourcePartly supported

  The Results report ApoE–TREM2 binding and signaling in reporter cells. The Discussion proposes that this interaction might participate in clearance and could activate phagocytosis, but does not establish phagocytosis of apoptotic neurons or increased Aβ uptake. The latter finding appears in a cited study’s title in the References, not as a result demonstrated by this paper. (LLM, conf=0.88)

  Experimental — accuracy not yet measured
• cites [83] Yeh FL, et al. TREM2 binds to apolipoproteins, including APOE and CLU/APOJ, and thereby facilitates uptake of amyloid-beta by microglia. Neuron. 2016;91(2):328–40. sourceNot checked — no full text of the source

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

Microglial elimination from PS19 mice or suppression of inflammation prevents tau-induced neurodegeneration.

“microglial elimination from PS19 mice or suppression of inflammation prevents tau-induced neurodegeneration [101–103]”

• cites [101] Asai H, et al. Depletion of microglia and inhibition of exosome synthesis halt tau propagation. Nat Neurosci. 2015;18(11):1584–93. sourcePartly supported

  The Results (‘Depletion of microglia suppresses tau propagation’; page unavailable) show that depleting microglia in PS19 mice reduced phosphorylated tau, and the Discussion says tau propagation and accompanying neurotoxicity were sensitive to microglial depletion. But the PS19 mice were studied before appreciable neuronal loss, so the paper does not show that depletion prevented neurodegeneration. It also reports reduced basal cytokine expression after depletion, not that suppressing inflammation independently prevented neurodegeneration. (LLM, conf=0.88)

  Experimental — accuracy not yet measured
• cites [102] Wang C, et al. Microglial NF-kappaB drives tau spreading and toxicity in a mouse model of tauopathy. Nat Commun. 2022;13(1):1969. sourcePartly supported

  The Discussion (page unavailable) says that inhibiting microglial NF-κB in PS19 mice rescues learning and memory deficits and suggests protection against tau-induced neuronal toxicity. The Fig. 4 passage (page unavailable) describes microglial depletion in a tau-seeding experiment, but does not show that depletion prevents neurodegeneration. The claim also states prevention more strongly than the reported protective effects establish. (LLM, conf=0.84)

  Experimental — accuracy not yet measured
• cites [103] Yoshiyama Y, et al. Anti-inflammatory action of donepezil ameliorates tau pathology, synaptic loss, and neurodegeneration in a tauopathy mouse model. J Alzheimers Dis. 2010;22(1):295–306. sourceNot checked — no full text of the source

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

Previous studies provide evidence that the Christchurch variant reduces AD pathology and associated CNS damage at least in part through alterations in receptor binding to LRP1, LDLR and/or HSPGs.

“Previous studies provide evidence that the Christchurch variant reduces AD pathology and associated CNS damage at least in part through alterations in receptor binding to LRP1, LDLR and/or HSPGs [15, 41, 76].”

• cites [15] Arboleda-Velasquez JF, et al. Resistance to autosomal dominant Alzheimer’s disease in an APOE3 Christchurch homozygote: a case report. Nat Med. 2019;25(11):1680–3. sourceSupported
• cites [41] Chen Y, et al. APOE3ch alters microglial response and suppresses Abeta-induced tau seeding and spread. Cell. 2024;187(2):428–445 e20. sourceNot checked — no full text of the source
• cites [76] Nelson MR, et al. The APOE-R136S mutation protects against APOE4-driven Tau pathology, neurodegeneration and neuroinflammation. Nat Neurosci. 2023;26(12):2104–21. sourceSupported

May combine two claims.

Apoe deletion rescued brain atrophy and altered microglia and T cells, tying together the role of APOE and the innate and adaptive immune responses to tau vs. plaques via microglia.

“Moreover, Apoe deletion rescued brain atrophy and altered microglia and T cells, tying together the role of APOE and the innate and adaptive immune responses to tau vs. plaques via microglia [88].”

• cites [88] Chen X, et al. Microglia-mediated T cell infiltration drives neurodegeneration in tauopathy. Nature. 2023;615(7953):668–77. sourceSupported

May combine two claims.

HSPGs are responsible for neuronal uptake of tau and the R136S mutation causes impaired binding affinity of APOE to HSPGs, leading to reduced tau pathology.

“HSPGs are responsible for neuronal uptake of tau and the R136S mutation causes impaired binding affinity of APOE to HSPGs, leading to reduced tau pathology [15, 41, 76, 84, 85].”

• cites [15] Arboleda-Velasquez JF, et al. Resistance to autosomal dominant Alzheimer’s disease in an APOE3 Christchurch homozygote: a case report. Nat Med. 2019;25(11):1680–3. sourcePartly supported

  The paper’s Abstract says HSPGs have been suggested to promote neuronal uptake of extracellular tau, and reports that ApoE3-Christchurch had the lowest heparin-binding ability among the ApoE isoforms tested. It also reports relatively limited tau burden in one APOE3-Christchurch homozygote. It does not establish that impaired APOE–HSPG binding caused the reduced tau pathology; it presents that protective mechanism as a possibility. (LLM, conf=0.87)

  Experimental — accuracy not yet measured
• cites [41] Chen Y, et al. APOE3ch alters microglial response and suppresses Abeta-induced tau seeding and spread. Cell. 2024;187(2):428–445 e20. sourceNot checked — no full text of the source
• cites [76] Nelson MR, et al. The APOE-R136S mutation protects against APOE4-driven Tau pathology, neurodegeneration and neuroinflammation. Nat Neurosci. 2023;26(12):2104–21. sourceSupported
• cites [84] Mahley RW, Y Huang, SC Rall Jr. Pathogenesis of type III hyperlipoproteinemia (dysbetalipoproteinemia). Questions, quandaries, and paradoxes. J Lipid Res. 1999;40(11):1933–49. sourceNot checked — no full text of the source
• cites [85] Holmes BB, et al. Heparan sulfate proteoglycans mediate internalization and propagation of specific proteopathic seeds. Proc Natl Acad Sci U S A. 2013;110(33):E3138–47. sourcePartly supported

  The Discussion (page unavailable) reports that HSPGs mediate uptake of tau aggregates into primary hippocampal neurons, supporting the first part of the sentence. The copy does not address the APOE R136S mutation, its binding affinity for HSPGs, or a resulting reduction in tau pathology (searched: R136S and APOE). (LLM, conf=0.90)

  Experimental — accuracy not yet measured

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

The microglial responses to plaques, tangles, and dying neurons are prominent in the human AD brain as well as in animal models, while aberrant microglial activity is associated with synaptic and neuronal loss.

“Further, the microglial responses to plaques, tangles, and dying neurons are prominent in the human AD brain as well as in animal models, while aberrant microglial activity is associated with synaptic and neuronal loss [96–98].”

• cites [96] Rajendran L, Paolicelli RC. Microglia-mediated synapse loss in Alzheimer’s disease. J Neurosci. 2018;38(12):2911–9. sourcePartly supported

  The Introduction (page unavailable) documents microglia around amyloid plaques in humans and AD mouse models. The “Microglia-mediated synapse loss in AD” section (page unavailable) links dysfunctional or activated microglia to synapse loss. The passages do not establish prominent microglial responses to tangles or dying neurons, or an association with neuronal loss distinct from synapse loss. (LLM, conf=0.87)

  Experimental — accuracy not yet measured
• cites [97] Zhan Y, et al. Deficient neuron-microglia signaling results in impaired functional brain connectivity and social behavior. Nat Neurosci. 2014;17(3):400–6. sourceNot checked — no full text of the source
• cites [98] Paolicelli RC, et al. Synaptic pruning by microglia is necessary for normal brain development. Science. 2011;333(6048):1456–8. sourcePartly supported

  The introductory passage labeled Abstract (page unavailable) says microglia respond to neurodegenerative insults and clear debris after neuronal death; the paper also demonstrates synaptic pruning in developing mice. It does not describe responses to plaques or tangles in human AD brains or animal AD models, or establish that aberrant microglial activity is associated with synaptic and neuronal loss in AD. Its conclusion instead reports that reduced microglial numbers delayed pruning and left excess synapses in developing mice. (LLM, conf=0.84)

  Experimental — accuracy not yet measured

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

A prior investigation highlighted the higher inflammatory reactivity (i.e., microglial MHC II + proteins and T cells) associated with tau-induced neurodegeneration, but not those with amyloid deposition.

“A prior investigation highlighted the higher inflammatory reactivity (i.e., microglial MHC II + proteins and T cells) associated with tau-induced neurodegeneration, but not those with amyloid deposition [88].”

• cites [88] Chen X, et al. Microglia-mediated T cell infiltration drives neurodegeneration in tauopathy. Nature. 2023;615(7953):668–77. sourceSupported

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

Cst7-expressing cells cluster around plaques.

“Visualization of cellular expression of the DAM gene Cst7 (Fig. 4f) shows that Cst7-expressing cells cluster around plaques (yellow-green Cst7 expressing cells surround a white plaque; Fig. 4g), as expected.”

May combine two claims.

Reduced LAMP1 volume was observed in 5xFAD;ApoeCh compared to 5xFAD mice at both time points, with the effect driven mainly by female mice at 4 mo.

“Reduced LAMP1 volume was observed in 5xFAD;ApoeCh compared to 5xFAD mice at both time points, with the effect driven mainly by female mice at 4 mo, which is consistent with lowered amyloid plaque load (Fig. 2n-p, Supp. Figure 3j, k).”

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

ApoeCh mice showed no change in plasma triglyceride (TRIG) or very low-density lipid (VLDL).

“However, we observed no change in plasma triglyceride (TRIG) or very low-density lipid (VLDL) in our mouse model (Supp. Figure 2a, b).”

May combine two claims.

Each of MHCII, CD11c, CD68, and APOE is upregulated in microglia surrounding plaques.

“we next visualized and measured intensity of several of the DAM markers included in the panel, including MHCII, CD11c, CD68, and APOE (Fig. 3i-l; inserts show localization of these markers around plaques), and found that each marker was upregulated in microglia surrounding plaques.”

May combine two claims.

All microglia (combined DAM and microglia clusters) are strongly impacted by plaques, with the highest number of DEGs (48 DEGs, padj < 0.05 and absolute average difference > 0.3) between 5xFAD and WT mice.

“Consistent with previous sequencing studies, all microglia (combined DAM and microglia clusters, as there are no DAMs in WT and ApoeCh genotypes) appear strongly impacted by plaques, as seen by the highest number of DEGs (with 48 DEGs, defined as padj < 0.05 and absolute average difference > 0.3) between 5xFAD and WT mice.”

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

mAPOE and hAPOE show only partial homology between positions 112 and 158.

“However, mAPOE and hAPOE show only partial homology between these sites (Fig. 1a), suggesting there could be differences in how this region of APOE functions between the species.”

May combine two claims.

The proportion of cells in disease-associated astrocyte (DAA) and DAM clusters is increased in both 5xFAD and 5xFAD;ApoeCh mice, with no change among other cell types.

“We observe an increased proportion of cells in the disease associated astrocyte (DAA) and disease-associated microglia (DAM) clusters in both 5xFAD and 5xFAD;ApoeCh mice, although no change was found among the other cell types.”

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

Male mice had higher plasma CHOL, TRIG, and VLDL than females.

“Male mice had higher plasma CHOL (Fig. 1b), TRIG (Supp. Figure 2a), and VLDL (Supp. Figure 2b) than females, as previously reported [42].”

• cites [42] Bruell JH, Daroczy AF, Hellerstein HK. Strain and sex differences in serum cholesterol levels of mice. Science. 1962;135(3508):1071–2. sourceNot checked — no full text of the source

May combine two claims.

AmyloGlo staining revealed a reduced brain-wide dense core plaque load in 5xFAD;ApoeCh compared to 5xFAD mice at 4-mo, driven by female mice, and 12 mo of age.

“AmyloGlo staining revealed a reduced brain-wide dense core plaque load in 5xFAD;ApoeCh compared to 5xFAD mice at 4-mo, driven by female mice, and 12 mo of age (Fig. 2a-e, Supp. Figure 3f-i).”

May combine two claims.

The overall decrease in plaque load was accompanied by increased soluble and insoluble Aβ40 and Aβ42 in the cortex and hippocampus at 4 mo of age in 5xFAD;ApoeCh compared to 5xFAD mice, which is partially resolved by 12 mo.

“The overall decrease in plaque load was accompanied by increased soluble and insoluble Aβ40 and Aβ42 in the cortex and hippocampus via MULTI-ARRAY assay (Meso Scale Discovery) at 4 mo of age in 5xFAD;ApoeCh compared to 5xFAD mice, which is partially resolved by 12 mo (Fig. 2f-m, Supp. Figure 4).”

May combine two claims.

Protein levels of APOE, GFAP, and VIM in astrocytes are increased in both 5xFAD genotypes but do not differ between 5xFAD;ApoeCh and 5xFAD brains.

“Plotting protein levels of APOE, GFAP, and VIM in astrocytes shows increases in both 5xFAD genotypes but no difference between 5xFAD;ApoeCh and 5xFAD brains (Fig. 3h).”

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

Twelve potential off-target sites on mouse chromosome 7 were identified.

“Twelve potential off-target sites on mouse chromosome 7 were identified (Supp. Table 1).”

May combine two claims.

No apparent changes were detected in neuronal, neuroepithelial, or vascular populations between WT and 5xFAD mice or between 5xFAD and 5xFAD;ApoeCh mice.

“We detected no apparent changes in neuronal, neuroepithelial, or vascular populations between WT and 5xFAD mice or 5xFAD and 5xFAD;ApoeCh mice (Fig. 3g).”

May combine two claims.

Several ODC 1 genes were upregulated by ApoeCh independent of PS19 background, including Mbp, Myrf, Slc44a1; Mbp was restored to WT levels in PS19;ApoeCh.

“We also found several ODC 1 genes were upregulated by ApoeCh, independent of PS19 background, including Mbp, Myrf and Slc44a1, of which Mbp was restored to WT levels in PS19;ApoeCh mice.”

May combine two claims.

Plasma NfL is dramatically elevated in PS19 compared to WT mice at 9 mo of age, with no difference between PS19 and PS19;ApoeCh mice.

“We next measured plasma NfL, as a surrogate for axonal damage, and as expected found a dramatic elevation in NfL in PS19 compared to WT mice at 9 mo of age, although no difference was found between PS19 and PS19;ApoeCh mice (Supp. Figure 13 k, l).”

May combine two claims.

Microglia and astrocyte populations are expanded in PS19 brains, but unchanged in WT, ApoeCh, and PS19;ApoeCh brains.

“Quantification of cell proportions between genotypes revealed that microglia and astrocyte populations were expanded in PS19 brains, but unchanged in WT, ApoeCh, and PS19;ApoeCh brains.”

May combine two claims.

Several ODC 1 cluster genes altered by PS19 (vs WT) show reverse directionality upon ApoeCh: Sgk1, Gsn, Ptgds down in PS19 vs WT and up in PS19;ApoeCh vs PS19; Tmsb4x, Apoe, Scd2, Pllp up in PS19 vs WT and reduced in PS19;ApoeCh.

“These data reveal that several ODC 1 cluster genes altered by PS19 (compared to WT) show a reverse in directionality of expression upon introduction of the ApoeCh variant. These genes include Sgk1, Gsn, and Ptgds (downregulated in PS19 compared to WT and upregulated in PS19;ApoeCh compared to PS19), Tmsb4x, Apoe, Scd2, and Pllp (upregulated in PS19 compared to WT and reduced in PS19;ApoeCh).”

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

CA1 cluster localized spatially exclusively in the CA1.

“We focused initially on the changes in the CA1 cluster, which localized spatially exclusively in the CA1 (Fig. 8b).”

May combine two claims.

Numbers of DAM-1 were unchanged between 5xFAD;ApoeCh and 5xFAD, while DAM-2 was significantly increased in 5xFAD;ApoeCh compared to 5xFAD.

“Furthermore, while numbers of DAM-1 were unchanged between 5xFAD;ApoeCh and 5xFAD, DAM-2 (Fig. 4l) was significantly increased in 5xFAD;ApoeCh compared to 5xFAD, supporting the increased DAM response in 5xFAD;ApoeCh seen in our proteomics data.”

May combine two claims.

In PS19 vs WT comparison, large numbers of significantly upregulated genes were observed in inhibitory neurons (5), astrocytes (14), and microglia (27), while oligodendrocytes exhibited both up- (8) and down-regulated (4) genes.

“Overall, we observed large numbers of significantly upregulated genes in inhibitory neurons (5 upregulated DEGs, defined as padj < 0.05 and average difference > 0.3), astrocytes (14 upregulated), and microglia (27 upregulated), while oligodendrocytes exhibited both up- (8 upregulated) and down-regulated (4 downregulated) genes.”

May combine two claims.

When grouped, excitatory neurons showed few significant changes, and inhibitory neurons showed upregulation of Gsk3b, Penk, Pcp4, Ppp1r1b, and Adora2a.

“When grouped together, excitatory neurons showed few significant changes, and inhibitory neurons showed upregulation of Gsk3b, a kinase implicated in tau phosphorylation, along with Penk, Pcp4, Ppp1r1b, and Adora2a”

May combine two claims.

Western blot analyses confirmed an increase in pThr231 tau level in the cortical RIPA-soluble fraction in PS19;ApoeCh compared to PS19 mice at 9 months, while no significant change was detected using AT8.

“Additionally, western blot analyses confirmed the increase in pThr231 tau level in the cortical RIPA-soluble fraction in PS19;ApoeCh compared to PS19 mice at 9 months while no significant change was detected using AT8, which recapitulates the histology findings (Fig. 5m, p).”

May combine two claims.

In PS19;ApoeCh mice, IBA1+ microglia total volume is decreased, despite no change in overall microglia number.

“In PS19;ApoeCh mice, IBA1 + microglia total volume was decreased, despite no change in overall microglia number (Fig. 6c, d, Supp. Figure 16f), suggesting an altered microglial response to the pathology.”

May combine two claims.

No change was observed in the proportions of neurons overall across the four genotypes, suggesting no neuronal loss in PS19 mice at this age.

“No change was observed in the proportions of neurons overall across the four genotypes suggesting no neuronal loss is observed in PS19 mice at this age (Fig. 6f).”

May combine two claims.

The number of cells (i.e., plaques) in the Aβ plaque core subcluster is reduced in 5xFAD;ApoeCh compared to 5xFAD, in line with IHC findings that ApoeCh reduces plaque load.

“While there was no difference in cell proportions of homeostatic microglia between 5xFAD;ApoeCh and 5xFAD, the number of cells (i.e., plaques) in the Aβ plaque core subcluster was reduced in 5xFAD;ApoeCh compared to 5xFAD, in line with our IHC findings that the presence of ApoeCh reduces plaque load in 5xFAD mice.”

May combine two claims.

Significant reductions in Homer1 postsynaptic puncta and colocalized Homer-Bassoon pre- and post-synaptic puncta were observed in PS19 mice compared to WT, but no reduction was observed between ApoeCh and PS19;ApoeCh brains.

“Significant reductions in both Homer1 postsynaptic puncta and colocalized Homer-Bassoon pre- and post-synaptic puncta were observed in PS19 mice compared to WT, but no reduction was observed between ApoeCh and PS19;ApoeCh brains (Fig. 8f, g)”

May combine two claims.

DAM genes (Cd74, Cst7, Gpnmb, Spp1, H2-Aa, H2-Ab1) are further upregulated in DAMs in 5xFAD:ApoeCh, while homeostatic microglial genes (Csf1r, Cst3) are further downregulated.

“Consistent with the protein expression data, DAM genes were further upregulated in DAMs in 5xFAD:ApoeCh (i.e., Cd74, Cst7, Gpnmb, Spp1, H2-Aa, and H2-Ab1; Fig. 4h) while homeostatic microglial genes were further downregulated (i.e., Csf1r, Cst3).”

May combine two claims.

In L2/L3, several genes (Malat1, Olfm1, Nell2, Snap25) are upregulated in 5xFAD relative to WT and then downregulated with 5xFAD;ApoeCh.

“For L2/L3, several genes were upregulated in 5xFAD mice relative to WT, and then downregulated with 5xFAD;ApoeCh (i.e., Malat1, Olfm1, Nell2, and Snap25).”

May combine two claims.

An increase in HT7-detected total tau level was observed in PS19;ApoeCh vs PS19, while no difference was observed using DAKO tau antibodies.

“While we observed an increase in HT7-detected (recognizes human tau AA159-163) total tau level in PS19;ApoeCh vs PS19, no difference was observed using DAKO tau antibodies, which recognizes the 4-repeat section of tau (Fig. 5l, o; see Supp. Figure 15 for full blot images).”

May combine two claims.

Among all cell types, microglia surrounding plaques (DAMs) exhibit the greatest differential upregulation (DU) score between 5xFAD;ApoeCh and 5xFAD, implicating an important effect of ApoeCh on the DAM response to plaques.

“Among all the cell types, microglia surrounding plaques (i.e., DAMs) exhibited the greatest differential upregulation (DU) score between 5xFAD;ApoeCh and 5xFAD, implicating an important effect of ApoeCh on the DAM response to plaques (Fig. 4i).”

May combine two claims.

In PS19;ApoeCh vs PS19, genes in inhibitory neurons (9 down), DAM (13 down), and microglia (17 down) were downregulated, while genes in astrocytes (9 up) and vascular cells (10 up) were mostly upregulated.

“PS19;ApoeCh mice exhibit downregulated genes in inhibitory neurons (9 downregulated), DAM (13 downregulated), and microglia (17 downregulated), while genes in astrocytes (9 upregulated), and vascular cells (10 upregulated) were mostly upregulated compared to PS19 mice.”

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

Weight loss was observed in both PS19 and ApoeCh;PS19 mice at 9 mo of age, while no difference was observed between ApoeCh and WT mice.

“As anticipated, weight loss was observed in both PS19 and ApoeCh;PS19 mice at 9 mo of age while no difference was observed between ApoeCh and WT mice (Supp. Figure 13a, b).”

May combine two claims.

In CA1, most changes appear in ApoeCh mice regardless of 5xFAD transgene array, with similar effects in both ApoeCh and 5xFAD;ApoeCh brains (Nell2, Penk, Mid1, Cck, Dnm1, Nnat, Gap43, Atp2b1).

“For CA1, most of the changes appeared in ApoeCh mice regardless of 5xFAD transgene array, with similar effects seen in both ApoeCh and 5xFAD;ApoeCh brains (i.e., Nell2, Penk, Mid1, Cck, Dnm1, Nnat, Gap43, and Atp2b1).”

May combine two claims.

Upregulated proteins in 5xFAD brains were highly concordant with known increases in gene expression, with many inflammatory proteins overexpressed, including GFAP, CST7, TREM2, complement proteins C1QA-C, APOE, LGALS3 and GPNMB.

“Upregulated proteins in 5xFAD brains were highly concordant with known increases in gene expression, with many inflammatory proteins overexpressed, including GFAP, CST7, TREM2, complement proteins C1QA-C, APOE, LGALS3 and GPNMB.”

May combine two claims.

Few overlapping DAPs with ApoeCh in the two mouse models, with concordant upregulation in SHE, FRAS1, INHBA, KDM5B among others, and concordant downregulation in YEATS4, NPHP1, DRG1.

“Indeed, there are few overlapping DAPs with ApoeCh in the two mouse models, with concordant upregulation in SHE, the extracellular matrix protein FRAS1, the TGF-beta family member INHBA, and the lysine demethylase KDM5B among others, and concordant downregulation in the NuA4 histone acetyltransferase complex component YEATS4, and microtubule associated proteins NPHP1 and DRG1.”

May combine two claims.

JAG1 was highly discordant, highly upregulated by ApoeCh in 5xFAD but highly downregulated by ApoeCh in PS19.

“Notably, the notch signaling ligand JAG1 was highly discordant, being highly upregulated by ApoeCh in 5xFAD mice, but highly downregulated by ApoeCh in PS19 mice.”

May combine two claims.

In response to amyloid and tau, microglia exhibit downregulation in similar homeostatic genes and upregulation in many DAM genes (Ctsd, Apoe, Cst7, etc.).

“In response to amyloid and tau, microglia exhibit down regulation in similar homeostatic genes, and an upregulation in many DAM genes (i.e., Ctsd, Apoe, Cst7, etc.).”

May combine two claims.

Several genes showed differential regulation: C1qa-c, Ctss, Cd74, H2-Ab1, H2-Aa were more upregulated in PS19 vs WT compared to 5xFAD vs WT; Apoe and Cst7 were more upregulated in 5xFAD vs WT; Hexb and Csf1r were downregulated in 5xFAD vs WT but unchanged or upregulated in PS19 vs WT.

“However, several genes showed differential regulation between the responses. For example, C1qa-c, Ctss, Cd74, H2-Ab1, and H2-Aa were more upregulated in the PS19 vs. WT response compared to the 5xFAD vs. WT response. Conversely, Apoe and Cst7 were more upregulated in the 5xFAD vs. WT response. Homeostatic genes Hexb and Csf1r were downregulated in 5xFAD mice compared to WT, but unchanged or up”

May combine two claims.

Several genes also correlated positively with those upregulated with ApoeCh in PS19 mice, including CX3CR1, ALDOC, CALM2, but as a whole there was no statistical correlation between human data and PS19 data.

“Several genes also correlated positively with those upregulated with ApoeCh in PS19 mice, including CX3CR1, ALDOC, CALM2, but as a whole there was no statistical correlation between the human data and PS19 data (Fig. 9k, Supp. Figure 21c).”

May combine two claims.

Pathway analyses show large upregulation of network of mitochondrial associated proteins with ApoeCh in 5xFAD mice, while mitochondrial and ribosomal/translation associated proteins are downregulated in PS19 mice.

“For example, pathway analyses show a large upregulation of a network of mitochondrial associated proteins with ApoeCh in 5xFAD mice (Fig. 10g, i), while mitochondrial and ribosomal/translation associated proteins are downregulated in PS19 mice (Fig. 10h, j).”

May combine two claims.

PS19 mice show reduction in proportion of several homeostatic microglial clusters compared to WT (MGL-2,3,4,7,8) and marked increase in DAMs.

“PS19 mice show a reduction in the proportion of several homeostatic microglial clusters compared to WT (MGL-2,3,4,7,8) and a marked increase in DAMs.”

May combine two claims.

Many genes were upregulated in PS19 DAMs compared to 5xFAD DAMs; antigen presentation genes Cd74, H2Ab1, H2-Aa were highly upregulated in PS19 vs 5xFAD DAMs.

“we observed that many genes were upregulated in PS19 DAMs compared to 5xFAD. Antigen presentation-associated genes were highly upregulated in PS19 compared to 5xFAD DAMs, including Cd74, H2Ab1, and H2-Aa (Fig. 9g).”

May combine two claims.

Gene expression changes from 5xFAD;ApoeCh vs 5xFAD and PS19;ApoeCh vs PS19 were inversely correlated, with most genes upregulated in 5xFAD;ApoeCh vs 5xFAD but downregulated in PS19;ApoeCh vs PS19.

“As expected, gene expression changes were inversely correlated to each other, with most genes being upregulated in 5xFAD;ApoeCh vs. 5xFAD microglia/DAM, but downregulated in PS19;ApoeCh vs. PS19 microglia/DAM, reinforcing the opposing effects of ApoeCh on the microglial response to the two pathologies.”

May combine two claims.

Despite a reduction in glial numbers in the pathology-rich subiculum, spatial proteomics and transcriptomics reveal a significant brain-wide upregulation of disease-associated microglia and astrocytes in 5xFAD;ApoeCh compared to 5xFAD mice.

“Despite a reduction in glial numbers in the pathology rich subiculum, spatial proteomics and transcriptomics reveal a significant brain wide upregulation of disease-associated microglia and astrocytes in 5xFAD;ApoeCh compared to 5xFAD mice.”

May combine two claims.

Homeostatic microglia are expressed throughout the brain, while cells in DAM cluster are localized to hippocampus in PS19 mice.

“Plotting these microglial subclusters in space identifies that while homeostatic microglia are expressed throughout the brain, cells in the DAM cluster are localized to the hippocampus in PS19 mice (Fig. 8n).”

May combine two claims.

Spatial proteomics shows only minor changes in IBA1 expression, but strong upregulation of DAM marker proteins such as APOE and CD11C in 5xFAD;ApoeCh.

“spatial proteomics shows only minor changes in IBA1 expression, but strong upregulation of DAM marker proteins such as APOE and CD11C.”

May combine two claims.

In 5xFAD, DAMs make up ~75% of microglial population, expanded in 5xFAD;ApoeCh to ~82%.

“These data show the pronounced number and proportion of DAMs that make up the microglial population in 5xFAD (~ 75%), which appears expanded in 5xFAD;ApoeCh (~ 82%) mice”

May combine two claims.

DGE analysis of all microglia in human dataset revealed elevated microglial reactivity in PSEN1-E280A heterozygote, APOECh homozygote compared to PSEN1-E280A heterozygote individuals, with upregulation of complement and inflammatory genes C1QA, C1QB, C1QC; CTSD, B2M; and APOE.

“DGE analysis of all microglia (i.e., homeostatic and disease-associated) in the human dataset revealed elevated microglial reactivity in the PSEN1-E280A heterozygote, APOECh homozygote compared to PSEN1-E280A heterozygote individuals, with upregulation of complement and inflammatory genes such as C1QA, C1QB, C1QC; CTSD, B2M; and APOE (Fig. 9j)”

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

Merged spatial transcriptomic datasets from 5xFAD;ApoeCh and PS19;ApoeCh yielded 41,790 Microglia/DAM cells.

“we first merged our spatial transcriptomic datasets from both the 5xFAD;ApoeCh and PS19;ApoeCh mice, yielding 41,790 Microglia/DAM cells (Fig. 9a).”

May combine two claims.

Overall, few inflammatory proteins were significantly impacted by ApoeCh in either model and vast number of changes detected were in metabolism associated proteins, showing highly differential effects in 5xFAD vs PS19.

“Overall, few inflammatory proteins were significantly impacted by ApoeCh in either model and the vast number of changes detected were in metabolism associated proteins, and these showed highly differential effects in 5xFAD mice vs. PS19 mice.”

May combine two claims.

In PS19, DAMs are ~20% of microglial population, nearly absent in PS19;ApoeCh.

“In PS19 mice, we observe a much smaller number and proportion of DAMs (~ 20%), which are nearly absent in PS19;ApoeCh mice (Fig. 9b-c).”

May combine two claims.

DAMs in PS19 are specifically enriched in Cd74, H2-Ab1, H2-Aa, while Trem2 and Cst7 are enriched in DAMs found in 5xFAD mice.

“Visualization of Cd74, H2-Ab1, and H2-Aa on the UMAP show that DAMs in PS19 are specifically enriched in these genes, while Trem2 and Cst7 are enriched in DAMs found in 5xFAD mice (Fig. 9c).”

May combine two claims.

PS19 mice exhibit an upregulation in several MHC II-antigen presentation-related genes, which is dampened by ApoeCh.

“Our spatial transcriptomics data also reveals that PS19 mice exhibit an upregulation in several MHC II-antigen presentation-related genes, which is dampened by ApoeCh.”

May combine two claims.

Introduction of ApoeCh in PS19 mice leads to a downregulation in DAM and disease associated astrocytes (DAA), coupled with the upregulation of oligodendrocyte-related genes and rescue of myelin loss.

“We show that introduction of ApoeCh in PS19 mice leads to a downregulation in DAM and disease associated astrocytes (DAA), coupled with the upregulation of oligodendrocyte-related genes and rescue of myelin loss.”

May combine two claims.

ApoeCh diminishes DAM and astrocyte response to tau.

“In line with humanized APOECh observations, we demonstrate a diminished DAM and astrocyte response to tau [76, 77].”

May combine two claims.

In our study, ApoeCh does not rescue tau pathology or functional deficits.

“Contrary to studies in humanized mice [76, 77], our study does not show that ApoeCh rescues tau pathology or functional deficits.”

May combine two claims.

Introduction of ApoeCh in PS19 mice reduces microglia and reactive astrocytes.

“We show that introduction of ApoeCh reduces microglia and reactive astrocytes, similar to 5xFAD mice”

May combine two claims.

By independently crossing with a model of amyloidosis and a model of tauopathy, the murine APOECh variant effects the microglial response to both pathologies, but in opposite directions.

“By independently crossing with a model of amyloidosis and a model of tauopathy, we show that the murine APOECh variant effects the microglial response to both pathologies, but in opposite directions.”

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

All experiments involving mice were approved by the UC Irvine Institutional Animal Care and Use Committee and conducted in compliance with relevant ethical regulations.

“All experiments involving mice were approved by the UC Irvine Institutional Animal Care and Use Committee and were conducted in compliance with all relevant ethical regulations for animal testing and research.”

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

Quantitative comparisons between experimental groups were carried out in sections stained simultaneously.

“Quantitative comparisons between experimental groups were carried out in sections stained simultaneously.”

• Also stated in: § Imaris quantitative analysis · plain

  “Quantitative comparisons between experimental groups were carried out in sections stained simultaneously with the same imaging settings.”

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

Hindlimb clasping scoring was done by observers blinded to genotype.

“Scoring was done by observers blinded to genotype.”