Tau promotes neurodegeneration through global chromatin relaxation

In the paper

“Pan-neuronal transgenic expression of an FTDP-17 mutant form of human tau, tauR406W, in Drosophila causes progressive neurodegeneration and provides a well-characterized in vivo genetic model of tau neurotoxicity7,15,16.”

What the sources say

• Partly supported

  The Introduction describes transgenic human or mutant tau expression in Drosophila as recapitulating progressive neurodegeneration, and the Results document age-dependent degeneration in tau-expressing flies. The methods identify a panneural expression driver. Our copy does not identify the flies showing these findings as expressing tauR406W, however; the Results explicitly name tauV337M for one genetic experiment. (LLM, conf=0.84)

  cites [7] Khurana, V. et al. TOR-mediated cell-cycle activation causes neurodegeneration in a Drosophila tauopathy model. Curr. Biol. 16, 230–241 (2006). sourceExperimental — accuracy not yet measured
• ?Not checked — no full text of the sourcecites [15] Wittmann, C.W. et al. Tauopathy in Drosophila: neurodegeneration without neurofibrillary tangles. Science 293, 711–714 (2001). source
• Supported

  The Introduction describes panneuronal expression of human tau R406W in transgenic Drosophila as an in vivo model for studying tau-induced neurodegeneration. The section on oxidative stress and neurotoxicity reports that tau R406W expression produces progressive neurodegeneration in the fly brain. (LLM, conf=0.91)

  cites [16] Dias-Santagata, D., Fulga, T.A., Duttaroy, A. & Feany, M.B. Oxidative stress mediates tau-induced neurodegeneration in Drosophila. J. Clin. Invest. 117, 236–245 (2007). source

In the paper

“components of the piRNA pathway are associated with stem cell self-renewal and are aberrantly expressed in several types of somatic tumors50”

What the sources say

• Supported

  The Conclusion (page not available in our copy) says the Piwi/piRNA pathway is required for maintaining germline stem cells. “The impact of Piwi proteins on human health” (page not available) reports that ectopic expression of the Piwi proteins hiwi or hili correlates with several cancer types, including breast, gastric, and ovarian cancers and soft tissue sarcomas. (LLM, conf=0.92)

  cites [50] Juliano, C., Wang, J. & Lin, H. Uniting germline and stem cells: the function of Piwi proteins and the piRNA pathway in diverse organisms. Annu. Rev. Genet. 45, 447–469 (2011). source

In the paper

“Indeed, increased expression of a regulatory RNA has already been implicated in the pathogenesis of AD49.”

What the sources say

• Supported

  The Results report elevated BACE1-AS, a regulatory noncoding RNA, in brain samples from people with Alzheimer’s disease compared with controls. The Discussion proposes that this elevation contributes to a feed-forward cycle of disease progression, supporting the claim’s cautious wording, “implicated.” (LLM, conf=0.94)

  cites [49] Faghihi, M.A. et al. Expression of a noncoding RNA is elevated in Alzheimer's disease and drives rapid feed-forward regulation of beta-secretase. Nat. Med. 14, 723–730 (2008). source

In the paper

“and is thought to protect DNA from oxidative damage46-48”

What the sources say

• ?Not checked — no full text of the sourcecites [46] Krylova, S.M. et al. Tau protein binds single-stranded DNA sequence specifically—the proof obtained in vitro with non-equilibrium capillary electrophoresis of equilibrium mixtures. FEBS Lett. 579, 1371–1375 (2005). source
• ?Not checked — no full text of the sourcecites [47] Sjöberg, M.K., Shestakova, E., Mansuroglu, Z., Maccioni, R.B. & Bonnefoy, E. Tau protein binds to pericentromeric DNA: a putative role for nuclear tau in nucleolar organization. J. Cell Sci. 119, 2025–2034 (2006). source
• Supported

  The Results section reports that tau reduced hydroxyl-radical damage to DNA in vitro. The Discussion says this suggests tau protects DNA by blocking hydroxyl-radical attack, while noting that protection in vivo remains untested. (LLM, conf=0.92)

  cites [48] Wei, Y. et al. Binding to the minor groove of the double-strand, tau protein prevents DNA from damage by peroxidation. PLoS ONE 3, e2600 (2008). source

In the paper

“No statistical methods were used to predetermine sample sizes but our sample sizes are similar to those reported in previous publications 7,16,44.”

What the sources say

• Supported

  The citation points to a previous publication as a sample-size example, not as evidence about how the citing authors chose their own sample sizes. The cited paper’s experimental procedures (indexed as Discussion; page unavailable) report at least four brains per genotype for PCNA quantification and at least eight hemibrains per time point and genotype for TUNEL staining. (LLM, conf=0.85)

  cites [7] Khurana, V. et al. TOR-mediated cell-cycle activation causes neurodegeneration in a Drosophila tauopathy model. Curr. Biol. 16, 230–241 (2006). source
• Supported

  The citation identifies a previous publication with reported sample sizes. In “Histology, immunostaining, and TUNEL analysis,” the source says each graphed data point averaged counts from at least eight hemibrains. The statement about not using statistical methods to predetermine sample sizes describes the citing authors’ own study, not this source. (LLM, conf=0.86)

  cites [16] Dias-Santagata, D., Fulga, T.A., Duttaroy, A. & Feany, M.B. Oxidative stress mediates tau-induced neurodegeneration in Drosophila. J. Clin. Invest. 117, 236–245 (2007). source
• ?Could not verify

  The Experimental Procedures (Immunoblotting; page unavailable) say immunoblots were repeated at least three times, but give no basis for comparing this paper’s sample sizes with those of the citing study. Searches for sample-size planning, sample counts, and comparisons with previous publications found no passage addressing that comparison. The statement about not predetermining sample sizes describes the citing authors’ own methods, not a claim this source can establish. (LLM, conf=0.70)

  cites [44] DuBoff, B., Gotz, J. & Feany, M.B. Tau promotes neurodegeneration via DRP1 mislocalization in vivo. Neuron 75, 618–632 (2012). sourceExperimental — accuracy not yet measured

In the paper

“EIFA4 and CYC1 were selected as internal controls for human RT-PCR based upon their stability in postmortem brain of AD patients54.”

What the sources say

• Partly supported

  The Results identify CYC1 as a stable reference gene in postmortem brain samples from AD patients and controls. The Discussion recommends CYC1 together with EIF4A2 for RT-qPCR normalization, but the claim names EIFA4 instead of EIF4A2. (LLM, conf=0.88)

  cites [54] Penna, I. et al. Selection of candidate housekeeping genes for normalization in human postmortem brain samples. Int. J. Mol. Sci. 12, 5461–5470 (2011). sourceExperimental — accuracy not yet measured

In the paper

“Pathologic tau causes an increase in actin stabilization18 that inhibits association of the fission protein Drp1 with mitochondria, leading to mitochondrial elongation and the production of reactive oxygen species44.”

What the sources say

• ?Not checked — no full text of the sourcecites [18] Fulga, T.A. et al. Abnormal bundling and accumulation of F-actin mediates tau-induced neuronal degeneration in vivo. Nat. Cell Biol. 9, 139–148 (2007). source
• Supported

  The Discussion describes tau-mediated actin stabilization as mislocalizing DRP1 and producing mitochondrial elongation. It also reports excess ROS in tau flies with elongated mitochondria; the Results section ‘Reversing actin stabilization rescues tau-induced mitochondrial defects’ reports that reversing actin stabilization decreases ROS in tau transgenic neurons. (LLM, conf=0.92)

  cites [44] DuBoff, B., Gotz, J. & Feany, M.B. Tau promotes neurodegeneration via DRP1 mislocalization in vivo. Neuron 75, 618–632 (2012). source

In the paper

“In vitro and in cultured cells, tau binds the minor groove of the DNA double helix”

What the sources say

• ?Not checked — no full text of the sourcecites [46] Krylova, S.M. et al. Tau protein binds single-stranded DNA sequence specifically—the proof obtained in vitro with non-equilibrium capillary electrophoresis of equilibrium mixtures. FEBS Lett. 579, 1371–1375 (2005). source
• ?Not checked — no full text of the sourcecites [47] Sjöberg, M.K., Shestakova, E., Mansuroglu, Z., Maccioni, R.B. & Bonnefoy, E. Tau protein binds to pericentromeric DNA: a putative role for nuclear tau in nucleolar organization. J. Cell Sci. 119, 2025–2034 (2006). source
• Partly supported

  The Discussion reports that tau binds the minor groove of double-stranded DNA, supported by competition assays described in the Results. The Introduction reports tau in cell nuclei and prior evidence of nuclear DNA binding, but the paper does not establish minor-groove binding in cultured cells. No page numbers are available in our copy. (LLM, conf=0.87)

  cites [48] Wei, Y. et al. Binding to the minor groove of the double-strand, tau protein prevents DNA from damage by peroxidation. PLoS ONE 3, e2600 (2008). sourceExperimental — accuracy not yet measured

In the paper

“To identify specific genes with reduced H3K9me2 levels, we performed H3K9me2-based ChIP-sequencing (ChIP-seq) in biological duplicate (Fig. 4a, http://genome.ucsc.edu30), and validated significantly H3K9me2 depleted genes with quantitative PCR (qPCR) (Fig. 4b).”

What the sources say

• Supported

  The citation is attached to the genome.ucsc.edu link in the citing sentence, identifying the UCSC Genome Browser rather than attributing the ChIP-seq experiment or qPCR validation to this paper. The paper’s “Using the Browser” section describes displaying genomic annotations as tracks, so it supports that identification. (LLM, conf=0.90)

  cites [30] Kent, W.J. et al. The human genome browser at UCSC. Genome Res. 12, 996–1006 (2002). source

In the paper

“Tau transgenic Drosophila, however, had significantly reduced chromocenter labeling, and instead had diffusely distributed H3K9me2 and HP1α (Fig. 1c, d, Supplementary Fig. 1d).”

In the paper

“Furthermore, loss of ash1 function or RNAi-mediated reduction of NURF301 significantly silenced expression of the heterochromatin-embedded reporter in tau transgenic flies (Fig. 2d).”

In the paper

“While PIWIL1 levels were very low in control mice, we observed approximately double the levels of PIWIL1 staining in motor neurons of tau transgenic mice (Fig. 5d).”

In the paper

“In pyramidal hippocampal neurons from postmortem control brains, H3K9me2 was concentrated in perinucleolar chromocenters. In AD, however, H3K9me2 staining was diffuse (Fig. 6a)”

In the paper

“RNAi transgenes targeted to ash1, NURF301, and NURF38 were not toxic in the absence of tau, nor was loss of ash1 function.”

In the paper

“and PCNA positive foci (Fig. 2m) compared to tau expressed alone.”

In the paper

“Transgenic RNAi targeted to Ago3 did not affect levels of transgenic tau or tau phosphorylation (Supplementary Fig. 2b)”

In the paper

“Ago3/PIWIL1 was overexpressed in tau transgenic Drosophila and mice, and in human AD.”

In the paper

“There were eleven genes that were identified as significant in both experiments”

In the paper

“For the first experiment, we found 2,456 significant regions covering 167 different genes, and for the biological replicate we found 143 significant regions covering 22 different genes.”

In the paper

“Similar results were obtained with both internal controls.”

In the paper

“Together, these findings suggest that tau-induced heterochromatin loss permits aberrant gene expression that is coincident with tau neurotoxicity, cell cycle reentry, and subsequent apoptosis of postmitotic neurons.”

In the paper

“confirming that these genetic manipulations damage DNA (Fig. 3c, d).”

In the paper

“These tau transgenic mice undergo progressive neurodegeneration, and develop neurofibrillary tangles in the brain and spinal cord35.”

What the sources say

• ?Not checked — no full text of the sourcecites [35] Lewis, J. et al. Neurofibrillary tangles, amyotrophy and progressive motor disturbance in mice expressing mutant (P301L) tau protein. Nat. Genet. 25, 402–405 (2000). source

In the paper

“suggesting that dysregulation of the piRNA pathway leads to loss of proliferative control”

In the paper

“Experiments were carried out in biological duplicates.”

In the paper

“Each data point is the result of at least three biological replicates each composed of three technical replicates.”

In the paper

“We have found that oxidative stress causes DNA damage, heterochromatin loss and consequent aberrant gene expression in Drosophila.”

In the paper

“Ago3 regulates PIWI-interacting RNAs, or piRNAs, a large class of highly conserved small noncoding RNAs that are responsible for silencing transposons33,34.”

What the sources say

• ?Not checked — no full text of the sourcecites [33] Aravin, A. et al. A novel class of small RNAs bind to MILI protein in mouse testes. Nature 442, 203–207 (2006). source
• ?Not checked — no full text of the sourcecites [34] Girard, A., Sachidanandam, R., Hannon, G.J. & Carmell, M.A. A germline-specific class of small RNAs binds mammalian Piwi proteins. Nature 442, 199–202 (2006). source

In the paper

“Data were collected and processed side by side in randomized order for all experiments.”

In the paper

“For experiments in mice and human tissue, sample sizes were based on power analysis calculations, which demonstrated that a 30% difference between 6 cases and controls will achieve a power of 80%.”

In the paper

“In cultured rat embryonic fibroblasts and in the adult rat liver, metabolic stress induced by caloric restriction increases Suv39h1, the mammalian homolog of Su(var)3-945.”

What the sources say

• ?Not checked — no full text of the sourcecites [45] Bosch-Presegué, L. et al. Stabilization of Suv39H1 by SirT1 is part of oxidative stress response and ensures genome protection. Mol. Cell 42, 210–223 (2011). source

In the paper

“heterochromatin loss likely permits increased expression of non-protein coding RNA transcripts”

In the paper

“We used RT-PCR to confirm RNAi-mediated knockdown of Su(var)205 and Su(var)3-9 (Supplementary Fig. 2a).”

In the paper

“Our data suggest that DNA-damage induced heterochromatin loss causes a global shift in gene expression towards a more developmental state that results from neuronal dedifferentiation, triggering inappropriate cell cycle reentry and subsequent apoptosis”

In the paper

“Data collection and analysis were not routinely performed blind to the conditions of the experiments.”

In the paper

“JNPL3 mice are housed 2-5 per cage in a vivarium with a 12 hour off/on light/dark cycle and are used compliance with ethical guidelines and regulations.”

In the paper

“This non-parametric test is the most appropriate to use when the underlying distribution is unknown and the sample size is small.”

In the paper

“human control and AD brains with a postmortem interval of less than 24 hours were collected through the autopsy service at Brigham and Women’s Hospital under the appropriate IRB.”

In the paper

“This procedure ensures that the input is minimally informative about the normalized ChIP.”

In the paper

“We tested for independence between both expression and chromatin states with a large sample size, and thus fulfilled the criteria for this non-parametric test.”