Protein Interaction Maps

Publication Title: 
Cell Cycle (Georgetown, Tex.)

Macroautophagy is a self-cannibalistic process that enables cells to adapt to various stresses and maintain energy homeostasis. Additionally, autophagy is an important route for turnover of misfolded proteins and damaged organelles, with important implications in cancer, neurodegenerative diseases and aging. Resveratrol and spermidine are able to induce autophagy by affecting deacetylases and acetylases, respectively, and have been found to extend the life-span of model organisms.

Author(s): 
Bennetzen, Martin V.
MariÒo, Guillermo
Pultz, Dennis
Morselli, Eugenia
FÊrgeman, Nils J.
Kroemer, Guido
Andersen, Jens S.
Publication Title: 
Molecular and Cellular Biology

The ubiquitin ligase CHIP (carboxyl terminus of Hsp70-interacting protein) regulates protein quality control, and CHIP deletion accelerates aging and reduces the life span in mice. Here, we reveal a mechanism for CHIP's influence on longevity by demonstrating that CHIP stabilizes the sirtuin family member SirT6, a lysine deacetylase/ADP ribosylase involved in DNA repair, metabolism, and longevity.

Author(s): 
Ronnebaum, Sarah M.
Wu, Yaxu
McDonough, Holly
Patterson, Cam
Publication Title: 
BMC genomics

BACKGROUND: Regular smoking is associated with a wide variety of syndromes with prominent inflammatory components such as cancer, obesity and type 2 diabetes. Heavy regular smoking is also associated with changes in the DNA methylation of peripheral mononuclear cells. However, in younger smokers, inflammatory epigenetic findings are largely absent which suggests the inflammatory response(s) to smoking may be dose dependent.

Author(s): 
Dogan, Meeshanthini V.
Shields, Bridget
Cutrona, Carolyn
Gao, Long
Gibbons, Frederick X.
Simons, Ronald
Monick, Martha
Brody, Gene H.
Tan, Kai
Beach, Steven R. H.
Philibert, Robert A.
Publication Title: 
Nature Neuroscience

We used a collection of 708 prospectively collected autopsied brains to assess the methylation state of the brain's DNA in relation to Alzheimer's disease (AD). We found that the level of methylation at 71 of the 415,848 interrogated CpGs was significantly associated with the burden of AD pathology, including CpGs in the ABCA7 and BIN1 regions, which harbor known AD susceptibility variants. We validated 11 of the differentially methylated regions in an independent set of 117 subjects.

Author(s): 
De Jager, Philip L.
Srivastava, Gyan
Lunnon, Katie
Burgess, Jeremy
Schalkwyk, Leonard C.
Yu, Lei
Eaton, Matthew L.
Keenan, Brendan T.
Ernst, Jason
McCabe, Cristin
Tang, Anna
Raj, Towfique
Replogle, Joseph
Brodeur, Wendy
Gabriel, Stacey
Chai, High S.
Younkin, Curtis
Younkin, Steven G.
Zou, Fanggeng
Szyf, Moshe
Epstein, Charles B.
Schneider, Julie A.
Bernstein, Bradley E.
Meissner, Alex
Ertekin-Taner, Nilufer
Chibnik, Lori B.
Kellis, Manolis
Mill, Jonathan
Bennett, David A.
Publication Title: 
Molecular Systems Biology

The closely related transcription factors (TFs), estrogen receptors ERα and ERβ, regulate divergent gene expression programs and proliferative outcomes in breast cancer. Utilizing breast cancer cells with ERα, ERβ, or both receptors as a model system to define the basis for differing response specification by related TFs, we show that these TFs and their key coregulators, SRC3 and RIP140, generate overlapping as well as unique chromatin-binding and transcription-regulating modules.

Author(s): 
Madak-Erdogan, Zeynep
Charn, Tze-Howe
Jiang, Yan
Liu, Edison T.
Katzenellenbogen, John A.
Katzenellenbogen, Benita S.
Publication Title: 
Journal of Translational Medicine

BACKGROUND: Shuanglong formula (SLF), a Chinese medicine composed of panax ginseng and salvia miltiorrhiza exhibited significant effect in the treatment of myocardial infarction (MI) in clinical. Because of the complex nature and lack of stringent quality control, it's difficult to explain the action mechanism of SLF. METHOD: In this study, we present a "system to system" (S2S) mode.

Author(s): 
Liang, Qiong-Lin
Liang, Xiao-Ping
Wang, Yi-Ming
Xie, Yuan-Yuan
Zhang, Rong-Li
Chen, Xi
Gao, Rong
Cheng, Yi-Jun
Wu, Jun
Xu, Qing-Bo
Xiao, Qing-Zhong
Li, Xue
Lv, Shu-Feng
Fan, Xue-Mei
Zhang, Hong-Yang
Zhang, Qing-Li
Luo, Guo-an
Publication Title: 
PloS One

Si-Wu-Tang (SWT) is a Traditional Chinese Medicine (TCM) formula widely used for the treatments of gynecological diseases. To explore the pharmacological mechanism of SWT, we incorporated microarray data of SWT with our herbal target database TCMID to analyze the potential activity mechanism of SWT's herbal ingredients and targets. We detected 2,405 differentially expressed genes in the microarray data, 20 of 102 proteins targeted by SWT were encoded by these DEGs and can be targeted by 2 FDA-approved drugs and 39 experimental drugs.

Author(s): 
Fang, Zhao
Lu, Bingxin
Liu, Mingyao
Zhang, Meixia
Yi, Zhenghui
Wen, Chengping
Shi, Tieliu
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