Elevated TREM2 Gene Dosage Reprograms Microglia Responsivity and Ameliorates Pathological Phenotypes in Alzheimer’s Disease Models

May combine two claims.

The TREM2-GFP transgene is expressed exclusively in Iba1+ microglia, not in astrocytes or neurons.

“Double immunostaining of brain sections from BAC-TREM2-GFP mice demonstrated that the TREM2-GFP transgene was exclusively expressed in the Iba1+ microglia, but not in astrocytes or neurons (Figure 1E–1N).”

May combine two claims.

Murine Trem2 reads are low at baseline and significantly increased in 5xFAD and 5xFAD/TREM2 cortices at 7 months but not at 4 months.

“We observed a low baseline level of murine Trem2 reads that are significantly increased in 5xFAD and 5xFAD/TREM2 cortices at an advanced (7m) but not at early disease stage (4m).”

May combine two claims.

5xFAD/TREM2 mice have 44 and 54 DE genes compared to 5xFAD at 4 and 7 months, respectively.

“5xFAD/TREM2 mice had 44 and 54 DE genes when compared to 5xFAD mice at 4 and 7 months of age respectively.”

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

M11 is enriched for microglia and immune system processes/damage-associated microglia; M12 is enriched for astrocyte genes.

“two of the three modules that were upregulated in 5xFAD and partially rescued in 5xFAD/TREM2 were annotated for microglia-enriched (M11) and astrocyte-enriched genes (M12).”

May combine two claims.

The BAC-TREM2 transgene does not overexpress human TREML1, TREML2, or TREML4.

“we did not observe reads mapping to human TREML1, TREML2 and TREML4 among the BAC-TREM2 transcripts (Figure 1B).”

May combine two claims.

BAC-TREM2 mice express human TREM2 RNA and protein in brain, while murine Trem2 levels remain comparable to wild-type.

“The human TREM2 transcripts are only found in BAC-TREM2 mouse brains but not in wildtype brains at all ages tested.”

• Also stated in: § Generation of BAC-TREM2 mice to increase TREM2 gene dosage under endogenous human regulatory elements · plain

  “BAC-TREM2 mice expressed murine Trem2 transcripts at levels comparable to WT mice (Figure S1).”

• Also stated in: § Generation of BAC-TREM2 mice to increase TREM2 gene dosage under endogenous human regulatory elements · plain

  “we confirmed the expression of human TREM2 protein in BAC-TREM2 mice by Western blot, and showed the expression of murine Trem2 protein is also similar between BAC-TREM2 and wildtype mice (Figure 1C).”

May combine two claims.

In 5xFAD vs WT, downregulated genes are enriched for neurons and synapses, and upregulated genes for top microglia genes and immune system process.

“the top enrichment terms for down-regulated genes in 5xFAD vs WT were “neurons” (p = 7.07E-55) and “synapses” (p = 6.95E-19) at both 4 and 7 months, and the top enrichment for upregulated genes in 5xFAD mice were “top microglia genes” (p = 3.19E-194) and “immune system process” (p = 9.51E-83).”

May combine two claims.

Human TREM2 reads in 5xFAD/TREM2 mice are significantly increased compared to BAC-TREM2 mice at 4 and 7 months, but not at 2 months.

“the human TREM2 reads in 5xFAD/TREM2 mice significantly increased compared to those in BAC-TREM2 mice at 4m and 7m, but not at 2m.”

May combine two claims.

The correlation between DE statistics in male vs female animals is positive and highly significant in all comparisons.

“This correlation between fold changes is positive and highly significant in all cases”

May combine two claims.

The difference in Aβ levels between 5xFAD/TREM2 and 5xFAD is less pronounced and not statistically significant at 7 months.

“However, the difference in Aβ levels was less pronounced and no longer statistically significant at 7 months of age.”

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

Consensus WGCNA identified 28 co-expression modules.

“Our consensus WGCNA analysis identified 28 co-expression modules (Table S4; Figure S6).”

May combine two claims.

Principal component analysis shows separation by 5xFAD genotype at 4 and 7 months but no clear separation by BAC-TREM2 genotype.

“We observed a more defined separation based on 5xFAD genotypes at 4m and 7m only, but did not detect a clear separation based on BAC-TREM2 genotype.”

May combine two claims.

Five modules are significantly upregulated in 5xFAD vs WT at 4 or 7 months, and nine modules are downregulated.

“we identified five modules (M11, M12, M13, M28 and M30) significantly (p < 0.05) upregulated in 5xFAD vs. WT mice at 4 or 7m, and 9 modules (M4, M15, M24, M31, M33, M37, M44, M46 and M48) down-regulated in 5xFAD mice.”

May combine two claims.

Three of the five upregulated 5xFAD modules and five of the nine downregulated modules are partially rescued in 5xFAD/BAC-TREM2 mice.

“three of the five upregulated 5xFAD modules (M11, M12 and M13) and five of the nine downregulated AD modules (M4, M31, M44, M46 and M48) are partially rescued in 5xFAD/BAC-TREM2 mice (Figure 3D).”

May combine two claims.

In contextual fear conditioning, 5xFAD/TREM2 mice performed comparably to WT controls, unlike 5xFAD mice which showed a robust deficit.

“Impressively, unlike the 5xFAD mice that exhibited a robust deficit in this task, the performance of 5xFAD/TREM2 mice is comparable to that of WT controls (Figure 7F).”

May combine two claims.

Plaque-associated microglia in 5xFAD mice exhibit shortened, thickened processes with hypertrophic amoeboid shape, and these phenotypes are attenuated in 5xFAD/TREM2 mice.

“In 5xFAD mice, plaque-associated microglia exhibited shortened and thickened processes with hypertrophic amoeboid shape, representing canonical reactive microglia (Figure 5A–5D). However, these phenotypes were significantly attenuated in 5xFAD/TREM2 mice (Figure 5E–5H).”

May combine two claims.

M11 eigengene is progressively upregulated in 5xFAD vs WT, and this elevation is significantly reduced at 4 months in 5xFAD/TREM2 mice.

“The M11 eigengene was progressively upregulated in 5xFAD compared to WT mice. This elevation was significantly reduced at 4m in the 5xFAD/TREM2 mice (Figure 3D–3E).”

May combine two claims.

TD3 group is modestly enriched for postsynaptic density genes, consistent with partial normalization of neuronal and synaptic genes.

“Finally, the TD3 group is only modestly enriched for postsynaptic density genes (Table S6), consistent with the results of network analyses showing that a subset of neuronal and synaptic genes downregulated in 5xFAD mice were partially normalized with TREM2 overexpression.”

May combine two claims.

In vitro, increased TREM2 gene dosage augmented microglial phagocytic activity, opposite to Trem2 deficiency.

“Functional studies in vitro showed TREM2 gene dosage increase augmented microglia phagocytic activity, a phenotype opposite to that of Trem2 deficiency.”

May combine two claims.

TD1 genes are enriched for upregulated in damage-associated microglia, top human microglia-specific genes, autophagy lysosome, genes upregulated with age in hippocampus, and immune system process.

“The top enrichment terms for TD1 genes are “Upregulated in damage associated microglia” (p = 2.29E-23; Keren-Shaul et al., 2017), “top human microglia-specific genes” (p = 2.15E-16; Galatro et al., 2017), “Autophagy lysosome” (p = 4.90E-09), “genes upregulated with age in hippocampus” (p = 2.89E-08), and “immune system process” (p = 0.000142).”

• cites Keren-Shaul et al., 2017 sourceNot checked yet

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• cites Galatro et al., 2017 sourceNot checked yet

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May combine two claims.

Increased TREM2 gene dosage significantly improves these modules at 4 months, and for M46 the effect extends to 7 months.

“Increased TREM2 gene dosage in 5xFAD/TREM2 mice significantly improved these modules at 4m, and for M46 such effect appeared to be extend to 7m (Figure 3E).”

May combine two claims.

AD models with elevated TREM2 gene dosage showed reduced neuritic pathology and improved memory task.

“We also showed evidence for reduced neuritic pathology and improved memory task in the AD models with elevated TREM2 gene dosage.”

May combine two claims.

M4 is enriched for dendrite and synaptic genes; M46 is enriched for neuronal genes and genes downregulated in AD patient hippocampi.

“M4 is significantly enriched in terms including “dendrite” and “synaptic genes” (e.g. Atp2b2, Grik2, Grin1, Mapt), and M46 (347 genes) is enriched in “neuronal genes” and “genes downregulated in the hippocampi of AD patients” (Figure 3D and 3E; Table S4).”

May combine two claims.

The TREM2 BAC selectively drives reporter transgene expression in microglia in mouse brain and elevates human TREM2 RNA and protein expression.

“We showed that TREM2 BAC can selectively drive reporter transgene expression in microglia in the mouse brain, and elevated human TREM2 RNA and protein expression.”

May combine two claims.

TD2 genes are enriched for negative regulation of T cell activation and innate immune response.

“the other top enrichment terms for TD2 genes were GO terms such as “Negative regulation of T cell activation” (p = 4.96E-09) and “Innate immune response” (p = 8.87E-07).”

May combine two claims.

BAC-TREM2 and Trem2-deficient microglia show dichotomous cellular and molecular phenotypes in AD mouse models, including plaque compaction, microglial process ramification, activated marker expression, and phagocytosis.

“For example, we showed several dichotomous cellular and molecular phenotypes between BAC-TREM2 and Trem2-deficient microglia in mouse models of AD (Jay et al., 2017; Ulrich et al., 2017; Yuan et al., 2016). These include the compaction of amyloid plaques, the ramification of plaque-associated microglial processes, the expression of certain activated microglial markers, and phagocytosis.”

• cites Jay et al., 2017 sourceNot checked yet

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• cites Ulrich et al., 2017 sourceNot checked yet

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• cites Yuan et al., 2016 sourceNot checked yet

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

The outlier removal procedure resulted in the removal of one sample, a 7-month-old female 5xFAD mouse.

“This procedure resulted in the removal of a single sample (7 month old, female 5xFAD).”

Classified as probably not a substantial claim.

The TREM2 genotype is overall not different from wild type.

“We left the TREM2 genotype out of the network analysis since it is overall not different from WT and we wanted to focus the network analysis on the effects of BAC-TREM2 in the 5xFAD background (5xFAD vs. 5xFAD/TREM2).”

May combine two claims.

In 5xFAD/TREM2 mice, microglial and astrocyte module genes are reduced and neuronal and synaptic genes are upregulated.

“Our transcriptome-wide rescue/exacerbation analyses and network analyses show unbiased evidence for partial normalization of the disease-associated gene expression in the 5xFAD/TREM2 mice, with reduction of expression of microglial and astrocyte module genes and upregulation of neuronal and synaptic genes.”

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

The consensus network analysis identified 28 co-expression modules, with module sizes ranging from 52 to 1767 genes.

“This analysis identified 28 co-expression modules ranging from 52 to 1767 genes per module (Table S4; Figure S4).”

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

The fraction of slices exhibiting no LTP did not differ among groups (Chi-square with Yates' correction = 0.6994; p = 0.4030).

“The fraction of slices exhibiting no LTP was not different among groups (Chi-square with Yates’ correction = 0.6994; p = 0.4030).”

May combine two claims.

Transcriptomic changes occur earlier and more robustly in female than male 5xFAD mice, and the effect of increased TREM2 gene dosage is more apparent in females.

“Thus, we conclude that transcriptomic changes occur earlier and more robustly in female than male 5xFAD mice, and that the effect of TREM2 increased gene dosage is also more apparent in female than male 5xFAD mice.”

May combine two claims.

Trem2 in plaque-associated microglia promotes plaque compaction and insulation, reducing neuritic toxicity of fibrillary Aβ.

“Trem2 in plaque-associated microglia plays an important role in plaque compaction and insulation to reduce the neuritic toxicity of fibrillary Aβ (Wang et al., 2016; Yuan et al., 2016).”

• cites Wang et al., 2016 sourceNot checked yet

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• cites Yuan et al., 2016 sourceNot checked yet

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May combine two claims.

Trem2 deficiency has stage-dependent effects on amyloid plaque load: reduced at early disease stage, increased at advanced stages.

“At an early disease stage, the plaque load is reduced in an AD model crossed to Trem2 knockout mouse (Jay et al., 2015), while in more advanced disease stages, the plaque load increased in multiple AD models (Jay et al., 2017; Wang et al., 2015).”

• cites Jay et al., 2015 sourceNot checked yet

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• cites Jay et al., 2017 sourceNot checked yet

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• cites Wang et al., 2015 sourceNot checked yet

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May combine two claims.

The BAC-TREM2 transgene drives early low-level human TREM2 overexpression in 5xFAD brains, with a surge as disease progresses, recapitulating disease-associated murine Trem2 upregulation.

“Together, our results suggest the BAC-TREM2 transgene drives early low level overexpression of human TREM2 in 5xFAD mouse brains, and there is a surge in the TREM2 transgene expression as disease progresses, recapitulating the disease-associated upregulation of murine Trem2 in this model.”

Classified as probably not a substantial claim.

In APP mouse models, Trem2 clusters microglia around Aβ plaques.

“In APP mouse models, Trem2 plays a role in clustering microglia around Aβ plaques (Jay et al., 2015; Wang et al., 2015).”

• cites Jay et al., 2015 sourceNot checked yet

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• cites Wang et al., 2015 sourceNot checked yet

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May combine two claims.

TREM2 signals through DAP12 to promote phagocytosis, suppress proinflammatory response, and support cell survival.

“TREM2 signals through its binding partner DAP12 (TYROBP) to elicit responses including phagocytosis, suppression of proinflammatory response, and promoting cell survival (Poliani et al., 2015; Takahashi et al., 2005).”

• cites Poliani et al., 2015 sourceNot checked yet

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• cites Takahashi et al., 2005 sourceNot checked yet

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

Complete loss of TREM2 or DAP12 causes Nasu-Hakola disease, a recessive disorder with bone cysts and early dementia.

“Complete loss of TREM2 or DAP12 leads to Nasu-Hakola disease, a recessive disorder characterized by bone cysts and early dementia (Paloneva et al., 2002)”

• cites Paloneva et al., 2002 sourceNot checked yet

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

TREM2 binds anionic and zwitterionic lipids on damaged neurons and AD-associated proteins APOE and Clusterin.

“TREM2 has been shown to bind anionic and zwitterionic lipids found on damaged neurons (Wang et al., 2015) and AD-associated proteins APOE and Clusterin (Atagi et al., 2015; Bailey et al., 2015; Yeh et al., 2016).”

• cites Wang et al., 2015 sourceNot checked yet

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• cites Atagi et al., 2015 sourceNot checked yet

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• cites Bailey et al., 2015 sourceNot checked yet

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Classified as probably not a substantial claim.

Rare TREM2 variants increase risk for late-onset Alzheimer's disease.

“Rare variants in the microglia-enriched gene TREM2 confer high risk for LOAD (Guerreiro et al., 2013a; Jonsson et al., 2013; Sims et al., 2017).”

• Also stated in: § Abstract · plain

  “Variants of TREM2 are associated with Alzheimer’s disease (AD).”

• cites Guerreiro et al., 2013aNot checked yet

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• cites Jonsson et al., 2013 sourceNot checked yet

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• cites Sims et al., 2017 sourceNot checked yet

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May combine two claims.

Elevated TREM2 gene dosage can mediate microglial reprogramming, reduced neuropathology, and improved cognitive performance in AD mouse models.

“Together, our study reveals that elevated TREM2 gene dosage can mediate microglia reprogramming, reduced neuropathology, and improved cognitive performance in AD mouse models.”

May combine two claims.

Microglial expression of BAC-TREM2 reprograms microglial responsivity and ameliorates disease-associated behavioral impairment in a second AD mouse model.

“The results suggest that microglial expression of the BAC-TREM2 transgene reprograms microglial responsivity and ameliorates the disease-associated behavioral impairment in a second AD mouse model.”

• AssumptionRests on an assumption: The APP/PS1 mouse model has a slower onset of amyloid pathology that affects both hippocampus and cortex.

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

The study used a limited sample size (N=3 per sex/genotype/age group; except N=2 for 5xFAD females at 7m).

“notwithstanding the limited sample size (N=3 per sex/genotype/age group; except N=2 for 5xFAD females at 7m)”

May combine two claims.

A genomic-transgene driven increase in TREM2 expression reprograms microglia responsivity and ameliorates neuropathological and behavioral deficits in AD mouse models.

“In summary, our study shows that a genomic-transgene driven increase in TREM2 expression reprograms microglia responsivity and ameliorates neuropathological and behavioral deficits in AD mouse models.”

May combine two claims.

Increasing TREM2 gene dosage selectively upregulates a subset of disease-associated microglial genes to promote phagocytosis and suppress over-activation of innate immune response in AD mouse brain.

“These analyses suggest increasing TREM2 gene dosage selectively upregulates an interesting subset of “disease-associated microglial genes” to promote certain aspects of their function, such as phagocytosis and suppression of over-activation of the innate immune response in the AD mouse brain.”

May combine two claims.

The findings indicate a reprogrammed microglial response in 5xFAD/BAC-TREM2 mice, such that fewer and less activated microglia per plaque still effectively limit amyloid plaque size and diffusion.

“We interpret these findings as evidence for reprogrammed microglial response in 5xFAD/BAC-TREM2 mice, so that fewer and less activated microglia per plaque are still able to function effectively in limiting the size and diffusion of the amyloid plaque in 5xFAD cortices.”

May combine two claims.

The BAC transgene design deletes essential exons in three other TREM-like genes, which have important innate immunity functions and may play distinct roles in AD.

“An important aspect of our BAC transgene design is the deletion of essential exons in three other TREM-like genes on the BAC, which are known to have important innate immunity function (Colonna, 2003; Ford and McVicar, 2009), and may play distinct roles in AD (Carrasquillo et al., 2017).”

• cites Colonna, 2003 sourceNot checked yet

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• cites Ford and McVicar, 2009 sourceNot checked yet

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• cites Carrasquillo et al., 2017 sourceNot checked yet

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May combine two claims.

The BAC transgene is properly expressed in microglia, as shown with the BAC-TREM2-GFP reporter line, and TREM2 is functional in complementing Trem2 deficiency in the in vitro phagocytosis assay.

“We obtained strong evidence that our BAC transgene is properly expressed in microglia cells using our novel BAC-TREM2-GFP reporter line, and showed the TREM2 is functional in complementing the Trem2 deficiency in the in vitro phagocytosis assay (Figure 6G).”

May combine two claims.

TD1 genes are key microglial genes involved in microglia activation in diseased brain and are significantly reversed with increased TREM2 gene dosage.

“These annotations suggest TD1 genes are key microglial genes normally involved in microglia activation in diseased brain, and are significantly reversed with increased TREM2 gene dosage.”

May combine two claims.

Seven TD2 genes are down-regulated in 5xFAD in the absence of Trem2 but upregulated in 5xFAD with increased TREM2 gene dosage, and may be transcriptional targets of Trem2 dosage-dependent signaling.

“Of these genes, the seven TD2 genes are potentially interesting, as they were down-regulated in 5xFAD mice in the absence of Trem2 but upregulated in 5xFAD mice with increased TREM2 gene dosage. They may constitute transcriptional targets of Trem2 gene dosage-dependent signaling in the context of disease-associated microglia.”

May combine two claims.

Trem2 function in regulating microglial phagocytosis is preserved and elevated in the BAC-TREM2 transgene.

“Furthermore, the rescue assay showed that Trem2 function in regulating microglia phagocytosis is preserved and elevated in the BAC-TREM2 transgene.”

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

TD2 genes are known to regulate phagocytosis, microglial activation, survival, M2 activation, and lysosomal proton pump.

“TD2 genes were well characterized for regulation of phagocytosis and microglial activation (e.g. Lgasl3; Rotshenker, 2009), microglial survival (e.g. Spp1; Rabenstein et al., 2016), alternative M2 activation of microglia (Zhou et al., 2015), and lysosomal proton pump (Atp6v0d2).”

• cites Rotshenker, 2009 sourceNot checked yet

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• cites Rabenstein et al., 2016 sourceNot checked yet

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• cites Zhou et al., 2015 sourceNot checked yet

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May combine two claims.

The BAC-TREM2 transgene improves both neuritic pathology and cognitive performance in an AD mouse model.

“Thus, we conclude that the BAC-TREM2 transgene is improving both the neuritic pathology and cognitive performance in an AD mouse model.”

May combine two claims.

BAC transgenes drive more accurate, endogenous-like transgene expression and are suitable for studying effects of gene dosage increase in intact animals.

“BAC transgenes are known to drive more accurate, endogenous-like transgene expression (Gong et al., 2002b; Yang et al., 1997), and are suitable for studying the effects of gene dosage increase in intact animals (Yang et al., 1999).”

• cites Gong et al., 2002bNot checked yet

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• cites Yang et al., 1997 sourceNot checked yet

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• cites Yang et al., 1999 sourceNot checked yet

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May combine two claims.

The higher CD68 protein in plaque-associated microglia of 5xFAD/TREM2 mice may result from post-transcriptional regulation, because CD68 transcript levels are comparable between 5xFAD and 5xFAD/TREM2 at this age.

“This result suggests that a post-transcriptional mechanism may be involved in the upregulation of CD68 in 5xFAD/TREM2 microglia surrounding the plaque, as transcript amounts are comparable between 5xFAD and 5xFAD/TREM2 at this age (Table S1).”

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

For outlier removal and network analysis, mRNA profiles with observed counts of at least 5 in at least one-quarter of samples were retained, and raw counts were variance-stabilized.

“For outlier removal and for network analysis using WGCNA, we retained mRNA profiles whose observed counts are 5 or more in at least one-quarter of the samples and transformed the raw counts using variance stabilization.”

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

DESeq2 models observed counts using negative binomial generalized linear models with dispersion estimated from the data.

“DESeq2 models observed counts using Negative Binomial General Linear Models with dispersion estimated from data.”

• cites Love et al., 2014 sourceNot checked yet

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

Lgals3 is a critical regulator of microglia activation and facilitates phagocytosis.

“Lgals3 is a critical regulator of microglia activation (Rotshenker, 2009), and it facilitates phagocytosis (Sano et al., 2003).”

• cites Rotshenker, 2009 sourceNot checked yet

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• cites Sano et al., 2003 sourceNot checked yet

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

Sex was used as a covariate in differential expression testing between genotypes.

“For differential expression testing between genotypes, sex was used as a covariate.”

Probably not a substantial claim: may not pass S1 (asserted), S3 (load-bearing).

A subset of TD2 genes could be transcriptional targets positively regulated by TREM2 levels or signaling.

“A subset of TD2 genes show transcriptional changes that are bidirectional in Trem2 knockout and our BAC-TREM2 mice crossed to 5xFAD (Figure 4F), which could be transcriptional targets that are positively regulated by TREM2 levels (or signaling), a hypothesis that can be tested.”

May combine two claims.

Microglial molecular reprogramming led to reduced plaque load, enhanced plaque compaction, reduced dystrophic neurites, and improved behavioral outcomes.

“Such microglia molecular reprogramming led to reduced plaque load and enhanced plaque compaction, reduced dystrophic neurites, and improved behavioral outcomes.”

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

All genotypes were generated and analyzed in the F1 hybrid background (C56BL6J;FvB/NJ F1), which is suitable for phenotypic study of genetically engineered mutant mice.

“Thus, all genotypes of mice used in the current study were generated and analyzed in the F1 hybrid background (C56BL6J;FvB/NJ F1), which is suitable for phenotypic study of genetically engineered mutant mice (Silva et al., 1997).”

• cites Silva et al., 1997 sourceNot checked yet

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

Image acquisition and quantification were performed in a blinded manner.

“The image acquisition and quantification described above were performed in a blinded manner.”

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

Eigengenes were tested for differential expression between genotypes using standard linear models with sex as a covariate.

“Eigengenes were tested for DE between genotypes using standard linear models with sex as a covariate.”

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

Spp1 regulates cytokine expression and promotes microglia survival, similar to Trem2.

“Spp1 regulates cytokine expression and promotes microglia survival (Rabenstein et al., 2016), a function similar to that of Trem2 (Yeh et al., 2017).”

• cites Rabenstein et al., 2016 sourceNot checked yet

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• cites Yeh et al., 2017 sourceNot checked yet

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

Morphological and behavioral studies were subjected to power analysis to determine the number of biological replicates needed to reach greater than 80% confidence.

“Morphological and behavioral studies were subjected to Power analysis to determine the biological replicates (n) needed to reach >80% confidence level.”

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

The module eigengene explains most of the variance of the genes in its module.

“Since genes in each module are co-expressed, it is advantageous to represent each module by a single representative expression profile (i.e. the module eigengene, which explains most of the variance of the module genes) (Horvath and Dong, 2008).”

• cites Horvath and Dong, 2008Not checked yet

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

Matched numbers of mice in both genders were used in the study.

“Matched number of mice in both genders were used in the study.”

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

All BAC modification products were confirmed using established methods such as PCR and restriction mapping.

“All the BAC modification products were confirmed using established methods (e.g. PCR, restriction mapping, etc; Gong and Yang, 2005).”

• cites Gong and Yang, 2005Not checked yet

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May combine two claims.

The mouse models used are only partial models of AD but are useful for showing in vivo neuronal and microglial responses to amyloid pathology.

“We are cognizant of the fact that the mouse models used in the study are only partial models of AD, but they are useful to show the in vivo neuronal and microglial responses to the amyloid pathology.”

Classified as probably not a substantial claim.

The TREM2 gene in the BAC was confirmed by Sanger sequencing of PCR products covering the entire gene.

“The fidelity of the TREM2 gene was confirmed with Sanger sequencing of PCR products covering the entirety of the gene.”

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

An increase in secreted extracellular fragment of TREM2 appears to be a CSF biomarker of disease progression in AD.

“Moreover, an increase in secreted extracellular fragment of TREM2 appears to be a CSF biomarker of disease progression in AD (Suárez-Calvet et al., 2016).”

• cites Suárez-Calvet et al., 2016 sourceNot checked yet

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Classified as probably not a substantial claim.

A consensus analysis identifies modules that group together genes correlated in both data sets, with respect to both time point and genotype.

“The rationale is that a consensus analysis identifies modules that group together genes correlated in both data sets, i.e., both with respect to time point as well as genotype.”

• cites Langfelder and Horvath, 2007 sourceNot checked yet

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

Both TD1 and TD2 genes could play a role in TREM2 gene dosage effects in AD mice, but TD2 genes are favored as prime candidates to investigate first.

“Although we cannot currently rule out that both down-regulated microglial genes (TD1) and upregulated microglial genes (TD2) could both play a role in the TREM2 gene dosage effect in the AD mice, we favor the latter group of genes as prime candidates to investigate first.”

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

Recordings in which LTP was not induced were excluded from the overall LTP averages.

“Presence or absence of an LTP at 40 minutes was determined as previously described (Fernado et al., 2016) and recordings in which LTP was not induced were not included in the overall LTP averages.”

• cites Fernado et al., 2016Not checked yet

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Outlier samples were removed using a Euclidean distance-based sample connectivity Z.k threshold of −6, as described by Oldham et al., 2012.

“Outlier samples were removed as described (Oldham et al., 2012), using the Euclidean distance-based sample connectivity Z.k threshold of −6.”

• cites Oldham et al., 2012 sourceNot checked yet

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

Periostin (Postn) is required for alternative, less inflammatory activation of microglia in brain tumors.

“Periostin (Postn) is shown to be required for alternative (less inflammatory) activation of microglia in brain tumors (Zhou et al., 2015).”

• cites Zhou et al., 2015 sourceNot checked yet

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

All animal studies were carried out in accordance with National Institutes of Health guidelines and approved by the UCLA Institutional Animal Care and Use Committees.

“All animal studies were carried out in strict accordance with National Institutes of Health guidelines and approved by the UCLA Institutional Animal Care and Use Committees.”

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

Lgals3 is an "eat-me" signal linking phagocytic receptor Mertk to its cargo.

“Interestingly, Lgals3 is shown to be an “eat-me” signal linking phagocytic receptor Mertk to its cargo (Caberoy et al., 2012).”

• cites Caberoy et al., 2012 sourceNot checked yet

  Not checked in the free run.

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

A positive linear correlation between gene-wise DE Z statistics of two genotype contrasts indicates broadly similar effects, while a negative correlation indicates broadly opposing effects.

“A positive linear trend (correlation) indicates that the effects of the two genotype contrasts are broadly similar, whereas a negative correlation indicates broadly opposing effects.”