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Assembly and interrogation of Alzheimer's disease genetic networks reveal novel regulators of progression.

Aubry S, Shin W, Crary JF, Lefort R, Qureshi YH, Lefebvre C, Califano A, Shelanski ML - PLoS ONE (2015)

Bottom Line: Our understanding of this disease would thus benefit from an approach that addresses this complexity by elucidating the regulatory networks that are dysregulated in the neural compartment of AD patients, across distinct brain regions.Experimental assays in autopsy-derived human brain tissue showed that three of the top candidate MRs (YY1, p300 and ZMYM3) are indeed biochemically and histopathologically dysregulated in AD brains compared to controls.Our results additionally implicate p53 and loss of acetylation homeostasis in the neurodegenerative process.

View Article: PubMed Central - PubMed

Affiliation: Taub Institute for Research on Alzheimer's Disease & the Aging Brain and the Department of Pathology & Cell Biology, Columbia University, New York, NY, 10032, United States of America.

ABSTRACT
Alzheimer's disease (AD) is a complex multifactorial disorder with poorly characterized pathogenesis. Our understanding of this disease would thus benefit from an approach that addresses this complexity by elucidating the regulatory networks that are dysregulated in the neural compartment of AD patients, across distinct brain regions. Here, we use a Systems Biology (SB) approach, which has been highly successful in the dissection of cancer related phenotypes, to reverse engineer the transcriptional regulation layer of human neuronal cells and interrogate it to infer candidate Master Regulators (MRs) responsible for disease progression. Analysis of gene expression profiles from laser-captured neurons from AD and controls subjects, using the Algorithm for the Reconstruction of Accurate Cellular Networks (ARACNe), yielded an interactome consisting of 488,353 transcription-factor/target interactions. Interrogation of this interactome, using the Master Regulator INference algorithm (MARINa), identified an unbiased set of candidate MRs causally responsible for regulating the transcriptional signature of AD progression. Experimental assays in autopsy-derived human brain tissue showed that three of the top candidate MRs (YY1, p300 and ZMYM3) are indeed biochemically and histopathologically dysregulated in AD brains compared to controls. Our results additionally implicate p53 and loss of acetylation homeostasis in the neurodegenerative process. This study suggests that an integrative, SB approach can be applied to AD and other neurodegenerative diseases, and provide significant novel insight on the disease progression.

No MeSH data available.


Related in: MedlinePlus

Increase in p300 acetyltransferase activity in moderate (mAD) and severe AD (sAD) cases.Immunohistochemistry and immunofluorescence analyses of phosphor-Ser1834-p300 (p-p300) on paraffin sections from the hippocampal area CA1 of human brains from control (Ctrl) (A, D), moderate AD (mAD) (B, E) and severe AD (sAD) (C, F) show cytoplasmic granular labeling resembling granulovacuolar degeneration in pyramidal neurons (B, C, E, F; arrows) in AD tissue, which co-localize with phospho-tau (p-tau) in ~95% of p-p300-positive neurons (E, F; arrows). p-p300-positive threads (A, D, arrowheads) are also observed in affected tissue. Controls are negative for p-tau and p-p300 (A, D). (G) Immunoblots of nuclear and cytoplasmic fractions of temporal neocortex (BA38) from Ctrl, mAD and sAD cases show an increase in Ac-Lys382-p53 (Ac-p53) in AD (n = 7, mAD+sAD) compared to control (n = 5) in both fractions. Quantification using densitometric analysis reveals a significant increase in Ac-p53 in nuclear (H, p = 0.002) and cytoplasmic (I, p = 0.001) fractions compared to controls. (J) Immunoblots of whole tissue extracts from BA38 from Ctrl, mAD and sAD cases also show a significant increase in Ac-Lys14-Histone 3 (Ac-H3) in mAD (n = 7) and sAD (n = 6) compared to Ctrl (n = 7). (K) Quantification reveals a statistically significant increase in Ac-H3 in mAD (p = 0.004) and sAD (p = 0.0003) compared to control. Comparisons were made using a Student’s t-test. Control case 4 is a statistical outlier, more than 3 standard deviations above the mean, and was excluded from the analysis. (A–C) Scale bar = 50 μm, (D–F) scale bar = 50 μm.
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pone.0120352.g005: Increase in p300 acetyltransferase activity in moderate (mAD) and severe AD (sAD) cases.Immunohistochemistry and immunofluorescence analyses of phosphor-Ser1834-p300 (p-p300) on paraffin sections from the hippocampal area CA1 of human brains from control (Ctrl) (A, D), moderate AD (mAD) (B, E) and severe AD (sAD) (C, F) show cytoplasmic granular labeling resembling granulovacuolar degeneration in pyramidal neurons (B, C, E, F; arrows) in AD tissue, which co-localize with phospho-tau (p-tau) in ~95% of p-p300-positive neurons (E, F; arrows). p-p300-positive threads (A, D, arrowheads) are also observed in affected tissue. Controls are negative for p-tau and p-p300 (A, D). (G) Immunoblots of nuclear and cytoplasmic fractions of temporal neocortex (BA38) from Ctrl, mAD and sAD cases show an increase in Ac-Lys382-p53 (Ac-p53) in AD (n = 7, mAD+sAD) compared to control (n = 5) in both fractions. Quantification using densitometric analysis reveals a significant increase in Ac-p53 in nuclear (H, p = 0.002) and cytoplasmic (I, p = 0.001) fractions compared to controls. (J) Immunoblots of whole tissue extracts from BA38 from Ctrl, mAD and sAD cases also show a significant increase in Ac-Lys14-Histone 3 (Ac-H3) in mAD (n = 7) and sAD (n = 6) compared to Ctrl (n = 7). (K) Quantification reveals a statistically significant increase in Ac-H3 in mAD (p = 0.004) and sAD (p = 0.0003) compared to control. Comparisons were made using a Student’s t-test. Control case 4 is a statistical outlier, more than 3 standard deviations above the mean, and was excluded from the analysis. (A–C) Scale bar = 50 μm, (D–F) scale bar = 50 μm.

Mentions: The p300 protein is a member of the p300/CREB-binding protein (CBP) coactivator family. These proteins interact with numerous transcription factors and participate in various physiological processes including proliferation, differentiation and apoptosis, by coordinating and integrating multiple cellular events to the transcriptional machinery [34,35]. Immunohistochemical staining of control and AD brains for p300 labels perisomatic granules in moderate and AD cases, but no consistent change in staining intensity or distribution is observed (S4C and S4D Fig.). Immunohistochemical staining with an antibody to phospho-Ser1834-p300 (p-p300), which is necessary for p300 acetyl-transferase activity [36], shows AD-specific staining in both CA1 and frontal cortex sections (Fig. 5A-F and S6D Fig.). Cytoplasmic structures, consistent with granulovacuolar degeneration (GVD), are observed in pyramidal neurons from affected tissues (Fig. 5B and 5C). These structures co-localize with phospho-tau (p-tau) in ~95% of p-p300-positive neurons (Fig. 5E and 5F). Many p-p300-positive fine delicate neuritic processes are also observed in affected tissue from human CA1 region as well as in other regions including the frontal cortex (S6D Fig.). Control tissues do not show these staining patterns (Fig. 5A and 5D).


Assembly and interrogation of Alzheimer's disease genetic networks reveal novel regulators of progression.

Aubry S, Shin W, Crary JF, Lefort R, Qureshi YH, Lefebvre C, Califano A, Shelanski ML - PLoS ONE (2015)

Increase in p300 acetyltransferase activity in moderate (mAD) and severe AD (sAD) cases.Immunohistochemistry and immunofluorescence analyses of phosphor-Ser1834-p300 (p-p300) on paraffin sections from the hippocampal area CA1 of human brains from control (Ctrl) (A, D), moderate AD (mAD) (B, E) and severe AD (sAD) (C, F) show cytoplasmic granular labeling resembling granulovacuolar degeneration in pyramidal neurons (B, C, E, F; arrows) in AD tissue, which co-localize with phospho-tau (p-tau) in ~95% of p-p300-positive neurons (E, F; arrows). p-p300-positive threads (A, D, arrowheads) are also observed in affected tissue. Controls are negative for p-tau and p-p300 (A, D). (G) Immunoblots of nuclear and cytoplasmic fractions of temporal neocortex (BA38) from Ctrl, mAD and sAD cases show an increase in Ac-Lys382-p53 (Ac-p53) in AD (n = 7, mAD+sAD) compared to control (n = 5) in both fractions. Quantification using densitometric analysis reveals a significant increase in Ac-p53 in nuclear (H, p = 0.002) and cytoplasmic (I, p = 0.001) fractions compared to controls. (J) Immunoblots of whole tissue extracts from BA38 from Ctrl, mAD and sAD cases also show a significant increase in Ac-Lys14-Histone 3 (Ac-H3) in mAD (n = 7) and sAD (n = 6) compared to Ctrl (n = 7). (K) Quantification reveals a statistically significant increase in Ac-H3 in mAD (p = 0.004) and sAD (p = 0.0003) compared to control. Comparisons were made using a Student’s t-test. Control case 4 is a statistical outlier, more than 3 standard deviations above the mean, and was excluded from the analysis. (A–C) Scale bar = 50 μm, (D–F) scale bar = 50 μm.
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Related In: Results  -  Collection

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pone.0120352.g005: Increase in p300 acetyltransferase activity in moderate (mAD) and severe AD (sAD) cases.Immunohistochemistry and immunofluorescence analyses of phosphor-Ser1834-p300 (p-p300) on paraffin sections from the hippocampal area CA1 of human brains from control (Ctrl) (A, D), moderate AD (mAD) (B, E) and severe AD (sAD) (C, F) show cytoplasmic granular labeling resembling granulovacuolar degeneration in pyramidal neurons (B, C, E, F; arrows) in AD tissue, which co-localize with phospho-tau (p-tau) in ~95% of p-p300-positive neurons (E, F; arrows). p-p300-positive threads (A, D, arrowheads) are also observed in affected tissue. Controls are negative for p-tau and p-p300 (A, D). (G) Immunoblots of nuclear and cytoplasmic fractions of temporal neocortex (BA38) from Ctrl, mAD and sAD cases show an increase in Ac-Lys382-p53 (Ac-p53) in AD (n = 7, mAD+sAD) compared to control (n = 5) in both fractions. Quantification using densitometric analysis reveals a significant increase in Ac-p53 in nuclear (H, p = 0.002) and cytoplasmic (I, p = 0.001) fractions compared to controls. (J) Immunoblots of whole tissue extracts from BA38 from Ctrl, mAD and sAD cases also show a significant increase in Ac-Lys14-Histone 3 (Ac-H3) in mAD (n = 7) and sAD (n = 6) compared to Ctrl (n = 7). (K) Quantification reveals a statistically significant increase in Ac-H3 in mAD (p = 0.004) and sAD (p = 0.0003) compared to control. Comparisons were made using a Student’s t-test. Control case 4 is a statistical outlier, more than 3 standard deviations above the mean, and was excluded from the analysis. (A–C) Scale bar = 50 μm, (D–F) scale bar = 50 μm.
Mentions: The p300 protein is a member of the p300/CREB-binding protein (CBP) coactivator family. These proteins interact with numerous transcription factors and participate in various physiological processes including proliferation, differentiation and apoptosis, by coordinating and integrating multiple cellular events to the transcriptional machinery [34,35]. Immunohistochemical staining of control and AD brains for p300 labels perisomatic granules in moderate and AD cases, but no consistent change in staining intensity or distribution is observed (S4C and S4D Fig.). Immunohistochemical staining with an antibody to phospho-Ser1834-p300 (p-p300), which is necessary for p300 acetyl-transferase activity [36], shows AD-specific staining in both CA1 and frontal cortex sections (Fig. 5A-F and S6D Fig.). Cytoplasmic structures, consistent with granulovacuolar degeneration (GVD), are observed in pyramidal neurons from affected tissues (Fig. 5B and 5C). These structures co-localize with phospho-tau (p-tau) in ~95% of p-p300-positive neurons (Fig. 5E and 5F). Many p-p300-positive fine delicate neuritic processes are also observed in affected tissue from human CA1 region as well as in other regions including the frontal cortex (S6D Fig.). Control tissues do not show these staining patterns (Fig. 5A and 5D).

Bottom Line: Our understanding of this disease would thus benefit from an approach that addresses this complexity by elucidating the regulatory networks that are dysregulated in the neural compartment of AD patients, across distinct brain regions.Experimental assays in autopsy-derived human brain tissue showed that three of the top candidate MRs (YY1, p300 and ZMYM3) are indeed biochemically and histopathologically dysregulated in AD brains compared to controls.Our results additionally implicate p53 and loss of acetylation homeostasis in the neurodegenerative process.

View Article: PubMed Central - PubMed

Affiliation: Taub Institute for Research on Alzheimer's Disease & the Aging Brain and the Department of Pathology & Cell Biology, Columbia University, New York, NY, 10032, United States of America.

ABSTRACT
Alzheimer's disease (AD) is a complex multifactorial disorder with poorly characterized pathogenesis. Our understanding of this disease would thus benefit from an approach that addresses this complexity by elucidating the regulatory networks that are dysregulated in the neural compartment of AD patients, across distinct brain regions. Here, we use a Systems Biology (SB) approach, which has been highly successful in the dissection of cancer related phenotypes, to reverse engineer the transcriptional regulation layer of human neuronal cells and interrogate it to infer candidate Master Regulators (MRs) responsible for disease progression. Analysis of gene expression profiles from laser-captured neurons from AD and controls subjects, using the Algorithm for the Reconstruction of Accurate Cellular Networks (ARACNe), yielded an interactome consisting of 488,353 transcription-factor/target interactions. Interrogation of this interactome, using the Master Regulator INference algorithm (MARINa), identified an unbiased set of candidate MRs causally responsible for regulating the transcriptional signature of AD progression. Experimental assays in autopsy-derived human brain tissue showed that three of the top candidate MRs (YY1, p300 and ZMYM3) are indeed biochemically and histopathologically dysregulated in AD brains compared to controls. Our results additionally implicate p53 and loss of acetylation homeostasis in the neurodegenerative process. This study suggests that an integrative, SB approach can be applied to AD and other neurodegenerative diseases, and provide significant novel insight on the disease progression.

No MeSH data available.


Related in: MedlinePlus