The gene expression changes in darkcd4 apoptosis-deficient mutant flies
Ontology highlight
ABSTRACT:
ORGANISM(S): Drosophila melanogaster
PROVIDER: GSE47853 | GEO | 2014/06/26
SECONDARY ACCESSION(S): PRJNA208081
REPOSITORIES: GEO
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Project description:Apoptosis is required not only for proper morphogenesis and tissue size regulation during development, but also for removing damaged or unwanted cells to maintain homeostasis. Apoptosis is mainly executed by evolutionally-conserved signaling process including caspases and its activator, dark. We performed microarray analysis of darkcd4 mutant flies to reveal the changes in gene expression. We found the elevated immune reaction, suggesting that inflammatory response was triggered by necrosis in darkcd4 . We collected total RNA from day 5 adult of darkcd4 mutant flies backcrossed six generations to w1118. w1118 was used as control. N=4 for each sample.
2014-06-26 | E-GEOD-47853 | biostudies-arrayexpress
Project description:Obesity has emerged as a major health risk on a global scale. Natural small molecules, such as hinokiflavone (HF) extracted from plants like cypress, exhibit diverse chemical structures and low synthesis costs. Using HFD-induced obese mice models, we found that HF suppresses obesity by inducing apoptosis in adipose tissue. Adipocyte apoptosis helps maintain tissue health by removing aging, damaged, or excess fat cells, crucial in preventing obesity and metabolic diseases. We found that HF can specifically bind to insulin-like growth factor 2 mRNA binding protein 2 (IGF2BP2) to promote the stability of N6-methyladenosine (m6A) -modified Bim, inducing mitochondrial outer membrane permeabilization (MOMP). MOMP leads to Caspase9/3-mediated adipocyte mitochondrial pathway apoptosis, alleviating obesity induced by a high-fat diet. HF offers a controlled means of adipocyte apoptosis for weight loss. This study reveals the potential of small molecules like HF in developing new therapeutic approaches in drug development and biomedical research.
2024-10-16 | GSE270326 | GEO
Project description:This model is from the article:
Systems biology analysis of programmed cell death
Shani Bialik, Einat Zalckvar, Yaara Ber, Assaf D. Rubinstein, Adi Kimchi Trends in Biochemical Sciences
Volume 35, Issue 10, 556-564, 27 May 2010 20537543
,
Abstract:
Systems biology, a combined computational and experimental approach to analyzing complex biological systems, has recently been applied to understanding the pathways that regulate programmed cell death. This approach has become especially crucial because recent advances have resulted in an expanded view of the network, to include not just a single death module (apoptosis) but multiple death programs, including programmed necrosis and autophagic cell death. Current research directions in the systems biology field range from quantitative analysis of subprocesses of individual death pathways to the study of interconnectivity among the various death modules of the larger network. These initial studies have provided great advances in our understanding of programmed cell death and have important clinical implications for drug target research.
Brief Note about the model:
This model is an export of 26 SPIKE
Apoptosis Networks to SBML format.
This is a pathway model (not quantitative model) of Apoptosis.
Apoptosis, or type I cell death, is a form of programmed cell death
characterized by fragmentation of the cytoplasm and nucleus, chromatin
condensation and fragmentation, cytoskeletal collapse, membrane
blebbing, and finally, disintegration of the cell into apoptotic
bodies, which are engulfed by adjacent cells, thereby avoiding an
inflammatory response. It serves to model tissues during embryonic
development, to regulate cell number by eliminating excess cells, and
to remove damaged, mutated or infected cells. Defective or excessive
apoptosis can lead to cancer or autoimmune and degenerative diseases,
respectively. Apoptosis is executed by a family of cysteine proteases,
the caspases, which function in a proteolytic cascade that is
initiated by either the intrinsic mitochondrial-based pathway leading
to apoptosome formation, or the extrinsic pathway, which involves
activation of death receptors by their extracellular ligands to form
the DISC. The most distal caspases, known as the executioner caspases,
cleave numerous cellular substrates, thereby leading to specific
dismantling of the cell. Apoptosis is regulated by multiple proteins
at several levels, including the Bcl-2 family, which regulate the
release of apoptogenic factors from the mitochondria, and the IAP
family, which regulate caspase activity, and is countered by survival
signals eminating from the NF-kB signaling pathway. Although most of
the regulation occurs at the post-translational level, involving
protein-protein interactions, proteolysis, changes in subcellular
localization and phosphorylation, transcriptional control, such as by
p53, can also modulate the expression levels of several key apoptotic
proteins.
This model originates from BioModels Database: A Database of Annotated Published Models (http://www.ebi.ac.uk/biomodels/). It is copyright (c) 2005-2011 The BioModels.net Team.
To the extent possible under law, all copyright and related or neighbouring rights to this encoded model have been dedicated to the public domain worldwide. Please refer to CC0 Public Domain Dedication
for more information.
In summary, you are entitled to use this encoded model in absolutely any manner you deem suitable, verbatim, or with modification, alone or embedded it in a larger context, redistribute it, commercially or not, in a restricted way or not.
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To cite BioModels Database, please use: Li C, Donizelli M, Rodriguez N, Dharuri H, Endler L, Chelliah V, Li L, He E, Henry A, Stefan MI, Snoep JL, Hucka M, Le Novère N, Laibe C (2010) BioModels Database: An enhanced, curated and annotated resource for published quantitative kinetic models. BMC Syst Biol., 4:92.
2005-01-01 | MODEL1107050000 | BioModels
Project description:Proteins encoded by the herpesviridae family members interfere with apoptotic pathways helping the viruses to evade immune surveillance. The aim of the study is to reveal mRNA markers which could be clinically relevant for monitoring of the herpesvirus infections. Majority of the genes being investigated fall within the following categories - death receptors, adaptors, caspases, mitochondrial proteins associated with apoptosis, kinanses involved in apoptosis regulation and execution, splicing factors, transcription factors.
2018-01-31 | GSE109961 | GEO
Project description:Hemolymph samples were collected from 80-100 control or apoptosis-deficient male flies in three biological replicates. Hemolymph samples were subjected to trypsin-digestion. Digested-peptides were desalinated and purified using GL-tip SDB. Purified peptides were subjected to LC-MS/MS analysis.
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Project description:Here we use an integrated systems-level examination of transcription, translation, and proteolysis to explore how cancer cells struggle with a chemotherapeutic drug prior to succumbing to apoptosis. As a model system we study myeloma cells exposed to the proteasome inhibitor bortezomib, a first-line clinical treatment. Despite robust transcriptional changes, unbiased quantitative proteomics detects production of only a few critical anti-apoptotic proteins against a background of general translation inhibition. Ribosome profiling further reveals potential translational regulation of stress response genes following bortezomib treatment. Once the apoptotic machinery is engaged, degradation by caspases is largely independent of changes at the transcriptional level. Moreover, previously uncharacterized non-caspase proteolytic events also participate in cellular deconstruction. As suggested by these data, we find that inhibition of the anti-apoptotic response regulator HSF1 promotes cell death by bortezomib. Thus, monitoring global cellular dynamics after chemotherapy offers in-depth insight into apoptosis and can also guide potential therapeutic combinations.
2013-10-17 | GSE48785 | GEO
Project description:Here we use an integrated systems-level examination of transcription, translation, and proteolysis to explore how cancer cells struggle with a chemotherapeutic drug prior to succumbing to apoptosis. As a model system we study myeloma cells exposed to the proteasome inhibitor bortezomib, a first-line clinical treatment. Despite robust transcriptional changes, unbiased quantitative proteomics detects production of only a few critical anti-apoptotic proteins against a background of general translation inhibition. Ribosome profiling further reveals potential translational regulation of stress response genes following bortezomib treatment. Once the apoptotic machinery is engaged, degradation by caspases is largely independent of changes at the transcriptional level. Moreover, previously uncharacterized non-caspase proteolytic events also participate in cellular deconstruction. As suggested by these data, we find that inhibition of the anti-apoptotic response regulator HSF1 promotes cell death by bortezomib. Thus, monitoring global cellular dynamics after chemotherapy offers in-depth insight into apoptosis and can also guide potential therapeutic combinations. We examined MM1.S myeloma cells exposed to 20 nM bortezomib across a time course with independent samples of poly(A) mRNA and ribosome footprints isolated at each of six time points (0h (untreated), 1.5h, 3h, 6h, 9h, 12h). Sequencing was performed on a Illumina HiSeq 2000 with single-end.
2013-10-17 | E-GEOD-48785 | biostudies-arrayexpress
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Project description:RNA silencing is a post-transcriptional gene-silencing mechanism mediated by microRNAs (miRNAs). However, the regulatory mechanism of RNA silencing during viral infection is unclear. TAR RNA-binding protein (TRBP) is an enhancer of RNA silencing that induces miRNA maturation by interacting with the ribonuclease Dicer. TRBP interacts with a virus sensor protein, laboratory of genetics and physiology 2 (LGP2), in the early stage of viral infection of human cells. Next, it induces apoptosis by inhibiting the maturation of miRNAs, thereby upregulating the expression of apoptosis regulatory genes. In this study, we show that TRBP undergoes a functional conversion in the late stage of viral infection. Viral infection resulted in the activation of caspases that proteolytically processed TRBP into two fragments. The N-terminal fragment did not interact with Dicer but interacted with type I interferon (IFN) signaling modulators, such as protein kinase R (PKR) and LGP2, and induced ER stress. The end results were irreversible apoptosis and suppression of IFN signaling. Our results demonstrate that the processing of TRBP enhances apoptosis, reducing IFN signaling during viral infection.
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