WO2019237244A1 - Utilisation de l'ubiquitylation de protéine histone 2a - Google Patents
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- WO2019237244A1 WO2019237244A1 PCT/CN2018/090791 CN2018090791W WO2019237244A1 WO 2019237244 A1 WO2019237244 A1 WO 2019237244A1 CN 2018090791 W CN2018090791 W CN 2018090791W WO 2019237244 A1 WO2019237244 A1 WO 2019237244A1
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Definitions
- biomarkers which may be used in the diagnosing, or providing a prognostic indicator of an aging related condition.
- the present disclosure provides a new biomarker for diagnosing, or providing a prognostic indicator of an aging related condition. Further, this disclosure is believed to be the first description of any the correlation between the ubiquitylation of Histone 2A protein and an aging related condition.
- the present disclosure provides a kit for diagnosing, or providing a prognostic indicator of an aging related condition in a mammal comprising an agent to measure the ubiquitylation of Histone 2A protein or functional equivalent thereof.
- the present disclosure firstly demonstrate the correlation between the ubiquitylation of Histone 2A protein and an aging related condition, then the kit described above may be used to diagnose, or provide a prognostic indicator of an aging related condition in a mammal effectively.
- the present disclosure provides the usage of an agent to measure the ubiquitylation of Histone 2A protein (ubH2A) in the preparation of a kit for diagnosing, or providing a prognostic indicator of an aging related condition in a mammal.
- the present disclosure firstly demonstrates the correlation between the ubiquitylation of Histone 2A protein and an aging related condition, then the agent described above can be used in a kit to diagnose, or provide a prognostic indicator of an aging related condition in a mammal effectively.
- the present disclosure provides an agent to measure the ubiquitylation of Histone 2A protein for use in diagnosing, or providing a prognostic indicator of an aging related condition in a mammal.
- the present disclosure firstly demonstrates the correlation between the ubiquitylation of Histone 2A protein and an aging related condition, then the agent described above can be used to diagnose, or provide a prognostic indicator of an aging related condition in a mammal effectively.
- the method described above can be used to diagnose or provide a prognostic indicator of an aging related condition in a mammal effectively, and the inventors found that the higher level of the ubH2A, the more serious of the aging related condition.
- the present disclosure provides a method for screening an agent for the treatment of an aging related condition in a mammal comprising contacting a cell from a subject with the aging related condition with a candidate agent and determining whether the candidate agent reduces the level of the ubiquitylation of Histone 2A protein, wherein a reduction in the level of the ubiquitylation of Histone 2A protein indicates that the candidate agent is suitable for the treatment of the aging related condition.
- the present disclosure demonstrates the correlation between the ubiquitylation of Histone 2A protein and an aging related condition, then the person skilled in the art may understand that the method described above may be used to screen an agent for the treatment of an aging related condition in a mammal effectively.
- the said candidate agent which may decrease the ubiquitylation of Histone 2A protein to a mammal may prevent, manage, treat or lessen disorders or diseases caused by ubH2A, such as aging related condition, in a mammal.
- the present disclosure provides a pharmaceutical composition for treating an aging related condition in a mammal comprising an agent to decrease the ubiquitylation of Histone 2A protein.
- the present disclosure firstly demonstrates the correlation between the ubiquitylation of Histone 2A protein and an aging related condition, then the person skilled in the art may understand that an agent which may decrease the ubiquitylation of Histone 2A protein may be used to treat an aging related condition.
- the said pharmaceutical composition may prevent, manage, treat or lessen disorders or diseases caused by ubH2A in a mammal.
- the present disclosure provides a usage of an agent to decrease the ubiquitylation of Histone 2A protein in the preparation of a pharmaceutical for treating an aging related condition in a mammal.
- the present disclosure firstly demonstrates the correlation between the ubiquitylation of Histone 2A protein and an aging related condition, then the person skilled in the art may understand that an agent which may decrease the ubiquitylation of Histone 2A protein may be used to prepare a pharmaceutical for treating an aging related condition in a mammal effectively.
- the said agent may be used in the preparation of a pharmaceutical which can preventing, managing, treating or lessening disorders or diseases caused by ubH2A in a mammal.
- the present disclosure provides the usage of an agent to decrease the ubiquitylation of Histone 2A protein for use in treating an aging related condition in a mammal.
- an agent which may decrease the ubiquitylation of Histone 2A protein may be used to treat an aging related condition in a mammal effectively.
- the said agent may be used to prevent, manage, treat or lessen disorders or diseases caused by ubH2A, such as an aging related condition in a mammal.
- the present disclosure provides a cell model of an aging related condition with increased ubiquitylation of Histone 2A protein compared with the wild type cell thereof.
- the present disclosure firstly demonstrate the correlation between the ubiquitylation of Histone 2A protein and an aging related condition, then the person skilled in the art may understand that a cell model with an increased ubiquitylation of Histone 2A protein compared with the wild type cell may represent that the said cell model having an aging related condition, thus the said cell model can be used as a research model with an aging related condition.
- the present disclosure provides an animal model of an aging related condition comprising a cell with increased ubiquitylation of Histone 2A protein compared with the wild type cell thereof.
- the present disclosure firstly demonstrate the correlation between the ubiquitylation of Histone 2A protein and an aging related condition, then the person skilled in the art may understand that an animal model with a cell which has an increased ubiquitylation of Histone 2A protein compared with the wild type cell may represent that the said animal model having an aging related condition, thus the said animal model can be used as a research model with an aging related condition.
- Fig. 1 shows a quantification of 15 N%in three tissues after pulse-chase labeling in an example of present disclosure
- the present disclosure is based at least in part on the present discoveries that the correlation between the ubiquitylation of Histone 2A protein and an aging process.
- Histones are proteins that package DNA into nucleosomes. Histones are responsible for maintaining the shape and structure of a nucleosome.
- One chromatin molecule is composed of at least one of each core histones per 100 base pairs of DNA.
- H1/H5 There are five families of histones known to date; these histones are termed H1/H5, H2A, H2B, H3, and H4.
- H2A is considered a core histone, along with H2B, H3 and H4. Core formation first occurs through the interaction of two H2A molecules. Then, H2A forms a dimer with H2B; the core molecule is complete when H3-H4 also attaches to form a tetramer.
- Histone H2A is composed of non-allelic variants.
- the term “Histone H2A” is intentionally no n-specific and refers to a variety of closely related proteins that vary often by only a few amino acids. Notable variants include H2A. 1, H2A. 2, H2A. X, and H2A. Z. H2A variants can be explored using "HistoneDB with Variants"database, which can be obtained from the webs ite of https: //www. ncbi. nlm. nih. gov/research/HistoneDB2.0/index. fcgi/type/H2A/#msa_div_b rowse, or the website of http: //www. uniprot. org/uniprot.
- a prominent feature of aging is a gradual decline in protein homeostasis network, particularly those of long-lived proteins that cannot be efficiently replenished by the protein quality control system.
- long-lived proteins may undergo aberrant chemical modification and damage leading to altered or loss of function over adult lifespan, and their identification is thus important for the present understanding of the aging process.
- the inventors provide a comprehensive analysis of proteins with limited turnover in Drosophila somatic and reproductive tissues.
- the inventors profile the ubiquitin-modified long-lived proteome in fly heads, and identify a new role of ubH2A as an epigenetic modulator of lifespan and potentially a conserved chromatin signature of aging.
- Ubiquitin modification is a critical PTM signal for target proteins.
- the present study extends the scope by profiling the interface between ubiquitylation and aging proteome. Remarkably, the present data reveals a significant preference for old proteins to remain ubiquitylated compared to that of newly synthesized proteins. This evidence may provide a direct support for a decline in UPS and protein turnover during aging as which would manifest a late-onset accumulation of ubiquitin-modified proteins. In addition, long-lived mitochondrial proteins also tend to be ubiquitylated. Since ubiquitin ligase Parkin can target substrates for both proteosomal and autophagic degradation, this finding may implicate a potential link between Parkin and mitochondrial protein quality control during aging.
- Drosophila is still unclear. It has been shown that, in flies and humans, ubH2A resides in the promoter regions of Polycomb-regulated genes, including the Hox genes. Thus, it is possible that ubH2A is involved in transcriptional repression by introducing additional histone marking. Moreover, an emerging crosstalk between ubH2A and methylation on histone H3 at lysine 4 is also reported. Hence, more work will be required to determine the key epigenetic effects of ubH2A underlying fly lifespan modulation.
- the SEQ ID NO: 1 shows the Q99878: Histone H2A type 1-J (Homo sapiens) peptide sequence.
- the SEQ ID NO: 2 shows the Q96KK5: Histone H2A type 1-H (Homo sapiens) peptide sequence.
- the SEQ ID NO: 3 shows the Q16777: Histone H2A type 2-C (Homo sapiens) peptide sequence.
- the SEQ ID NO: 4 shows the A3KPC7: Histone H2A (Homo sapiens) peptide sequence.
- the SEQ ID NO: 5 shows the Q8CGP6: Histone H2A type 1-H (Mus musculus) peptide sequence.
- the SEQ ID NO: 6 shows the Q64523: Histone H2A type 2-C (Mus musculus) peptide sequence.
- the SEQ ID NO: 7 shows the A3KPD0: Histone H2A(Mus musculus) peptide sequence.
- the SEQ ID NO: 8 shows the Q149V4: Histone H2A(Mus musculus) peptide sequence.
- the SEQ ID NO: 9 shows the Q8CGP4: Histone H2A (Mus musculus) peptide sequence.
- the SEQ ID NO: 10 shows the A0AUV1: Histone H2A (Mus musculus) peptide sequence.
- the SEQ ID NO: 11 shows the Q61668: Gene for histone H2a (Mus musculus) peptide sequence.
- the agent is an antibody specific to ubH2A. According to the examples of present disclosure, using an antibody specific to ubH2A to measure the ubH2A is more conveniently and more effectively.
- the antibody is monoclonal antibody.
- the inventors found that the said monoclonal antibody can recognize ubH2A more specifically.
- the antibody is at least one of 05-678 Millipore, #8240 CST and derivatives thereof. The inventors found that the said antibody can recognize ubH2A more specifically and more effectively.
- the aging related condition is at least one of the dementias, neurodegenerative diseases, neurological disorders, and age-related conditions.
- the aging related condition is at least one of atherosclerosis and cardiovascular disease, cancer, arthritis, cataracts, osteoporosis, type 2 diabetes, hypertension , Alzheimer's Disease, Lewy body dementia, vascular dementia, Huntington's Disease, Parkinson's Disease, amyotrophic lateral sclerosis, schizophrenia, depression, Mild Cognitive Impairment, Age-Related Cognitive Decline.
- the kit can diagnose or provide a prognostic indicator of the aging related conditions described above in a mammal more effectively.
- the agent to measure the ubiquitylation is performed by means of Western-Blotting.
- the inventors found that Western blot assays can be used for measuring different histone, and the relative abundance of ubH2A can be normalized by Western blot assays.
- the present disclosure provides the usage of an agent to measure the ubiquitylation of Histone 2A protein in the preparation of a kit for diagnosing, or providing a prognostic indicator of an aging related condition in a mammal.
- the present disclosure firstly demonstrate the correlation between the ubiquitylation of Histone 2A protein and an aging related condition, then the agent described above can be used in a kit to diagnose, or provide a prognostic indicator of an aging related condition in a mammal effectively.
- the ubiquitylation of Histone 2A protein is on the ubiquitylation of Histone 2A protein is on at least one of the following sites:
- the agent is an antibody specific to ubH2A. According to the examples of present disclosure, using an antibody specific to ubH2A to measure the ubH2A is more conveniently and more effectively.
- the antibody is monoclonal antibody.
- the inventors found that the said monoclonal antibody can recognize ubH2A more specifically.
- the antibody is at least one of 05-678 Millipore, #8240 CST and derivatives thereof. The inventors found that the said antibody can recognize ubH2A more specifically and more effectively.
- the aging related condition is at least one of the dementias, neurodegenerative diseases, neurological disorders, and age-related conditions.
- the aging related condition is at least one of atherosclerosis and cardiovascular disease, cancer, arthritis, cataracts, osteoporosis, type 2 diabetes, hypertension , Alzheimer's Disease, Lewy body dementia, vascular dementia, Huntington's Disease, Parkinson's Disease, amyotrophic lateral sclerosis, schizophrenia, depression, Mild Cognitive Impairment, Age-Related Cognitive Decline.
- the kit can diagnose or provide a prognostic indicator of the aging related conditions described above in a mammal effectively.
- the agent to measure the ubiquitylation is performed by means of Western-Blotting.
- the inventors found that Western blot assays can be used for measuring different histone, and the relative abundance of ubH2A can be normalized by Western blot assays.
- the present disclosure provides an agent to measure the ubiquitylation of Histone 2A protein for use in diagnosing, or providing a prognostic indicator of an aging related condition in a mammal.
- the present disclosure firstly demonstrate the correlation between the ubiquitylation of Histone 2A protein and an aging related condition, then the agent described above can be used to diagnose, or provide a prognostic indicator of an aging related condition in a mammal effectively.
- the ubiquitylation of Histone 2A protein is on at least one of the following sites:
- the agent is an antibody specific to ubH2A. According to the examples of present disclosure, using an antibody specific to ubH2A to measure the ubH2A is more conveniently and more effectively.
- the antibody is monoclonal antibody.
- the inventors found that the said monoclonal antibody can recognize ubH2A more specifically.
- the antibody is at least one of 05-678 Millipore, #8240 CST and derivatives thereof. The inventors found that the said antibody can recognize ubH2A more specifically and more effectively.
- the aging related condition is at least one of dementias, neurodegenerative diseases, neurological disorders, and age-related conditions.
- the inventors found that the agent can diagnose or provide a prognostic indicator of the aging related conditions described above in a mammal effectively.
- the aging related condition is at least one of Alzheimer's Disease, atherosclerosis and cardiovascular disease, cancer, arthritis, cataracts, osteoporosis, type 2 diabetes, hypertension, Lewy body dementia, vascular dementia, Huntington's Disease, Parkinson's Disease, amyotrophic lateral sclerosis, schizophrenia, depression, Mild Cognitive Impairment, Age-Related Cognitive Decline.
- the agent to measure the ubiquitylation is performed by means of Western-Blotting.
- the inventors found that Western blot assays can be used for measuring different histone, and the relative abundance of ubH2A can be normalized by Western blot assays.
- the present disclosure provides a method of diagnosing, or providing a prognostic indicator of an aging related condition in a mammal comprising detecting the ubiquitylation of Histone 2A protein in a sample from said mammal, wherein an increase in the level of the ubiquitylation of Histone 2A protein in a cell of said sample, relative to the level of the ubiquitylation of Histone 2A protein in a normal cell indicates said sample is suffering from aging related condition.
- the method described above can be used to diagnose or provide a prognostic indicator of an aging related condition in a mammal effectively, and the inventors found that the higher level of the ubH2A, the more serious of the aging related condition.
- the said method further comprises treating the aging related condition by reducing level of the ubiquitylation of Histone 2A protein in a cell of said sample.
- the inventors found that the method described above may be provide a method of screening an agent which can prevent, manage, treat or lessen disorders or diseases caused by ubH2A, such as aging related condition.
- the level of the ubiquitylation of Histone 2A protein is reduced by site-specific mutagenesis of the Histone 2A protein.
- site-specific mutagenesis to specificity change the site of the ubiquitylation of Histone 2A protein without having a substantial effect on other site of the Histone 2A protein, can reduce the level of the ubiquitylation of Histone 2A protein.
- Histone related diseases such as dementias, neurodegenerative diseases, neurological disorders, and age-related conditions, can be treated using the said site-specific mutagenesis method above.
- the site-specific mutagenesis is performed by means of Crispr-Cas9 method.
- using the Crispr-Cas9 method to specificity change the site of the ubiquitylation of Histone 2A protein without having a substantial effect on other site of the Histone 2A can reduce the level of the ubiquitylation of Histone 2A protein effectively. Therefore, Histone related diseases such as dementias, neurodegenerative diseases, neurological disorders, and age-related conditions, can be treated using the said site-specific mutagenesis method above.
- the level of the ubiquitylation of Histone 2A protein is reduced by inhibiting PRC1.
- inhibiting PRC1 can also reducing the level of the ubH2A, thus compounds which be used to inhibit PRC1 can be performed in preventing, managing, treating or lessening disorders or diseases caused by ubH2A, such as aging related condition.
- the ubiquitylation of Histone 2A protein is at least one of the following sites:
- the said method can diagnose or procide a prognostic indicator of an aging related condition more effectively.
- the detecting is performed with mass spectrometry.
- MS mass spectrometry
- the detecting is performed with an agent, wherein the said agent is an antibody specific to ubH2A.
- the agent is an antibody specific to ubH2A.
- the antibody is monoclonal antibody.
- the inventors found that the said monoclonal antibody can recognize ubH2A more specifically. According to the examples of present disclosure, using the said monoclonal antibody to measure the ubH2A making the method more conveniently and more effectively.
- the antibody is at least one of 05-678 Millipore, #8240 CST and derivatives thereof.
- using the said monoclonal antibody to measure the ubH2A making the method more conveniently and more effectively.
- the agent to measure the ubiquitylation is performed by means of Western-Blotting.
- the inventors found that Western blot assays can be used for measuring different histone, and the relative abundance of ubH2A can be normalized by Western blot assays.
- the aging related condition is at least one of dementias, neurodegenerative diseases, neurological disorders, and age-related conditions.
- the inventors found that the said method can diagnose or provide a prognostic indicator of the aging related conditions described above in a mammal effectively.
- the aging related condition is at least one of Alzheimer's Disease, atherosclerosis and cardiovascular disease, cancer, arthritis, cataracts, osteoporosis, type 2 diabetes, hypertension, Lewy body dementia, vascular dementia, Huntington's Disease, Parkinson's Disease, amyotrophic lateral sclerosis, schizophrenia, depression, Mild Cognitive Impairment, Age-Related Cognitive Decline.
- the present disclosure provides a method for screening an agent for the treatment of an aging related condition in a mammal comprising contacting a cell from a subject with the aging related condition with a candidate agent and determining whether the candidate agent reduces the level of the ubiquitylation of Histone 2A protein, wherein a reduction in the level of the ubiquitylation of Histone 2A protein indicates that the candidate agent is suitable for the treatment of the aging related condition.
- the present disclosure demonstrates the correlation between the ubiquitylation of Histone 2A protein and an aging related condition, then the person skilled in the art may understand that the method described above may be used to screen an agent for the treatment of an aging related condition in a mammal effectively.
- the said candidate agent which may decrease the ubiquitylation of Histone 2A protein to a mammal may prevent, manage, treat or lessen disorders or diseases caused by ubH2A, such as aging related condition, in a mammal.
- the present disclosure provides a pharmaceutical composition for treating an aging related condition in a mammal comprising an agent to decrease the ubiquitylation of Histone 2A protein.
- a pharmaceutical composition for treating an aging related condition in a mammal comprising an agent to decrease the ubiquitylation of Histone 2A protein.
- the present disclosure firstly demonstrate the correlation between the ubiquitylation of Histone 2A protein and an aging related condition, then the person skilled in the art may understand that an agent which may decrease the ubiquitylation of Histone 2A protein may be used to treat an aging related condition.
- the said pharmaceutical composition may prevent, manage, treat or lessen disorders or diseases caused by ubH2A in a mammal.
- the present disclosure provides the usage of an agent to decrease the ubiquitylation of Histone 2A protein in the preparation of a pharmaceutical for treating an aging related condition in a mammal.
- an agent which may decrease the ubiquitylation of Histone 2A protein may be used to treat an aging related condition in a mammal effectively.
- the said agent may be used in the preparation of a pharmaceutical which can preventing, managing, treating or lessening disorders or diseases caused by ubH2A in a mammal.
- the present disclosure provides the usage of an agent to decrease the ubiquitylation of Histone 2A protein for use in treating an aging related condition in a mammal.
- an agent which may decrease the ubiquitylation of Histone 2A protein may be used to treat an aging related condition in a mammal effectively.
- the said agent may be used to prevent, manage, treat or lessen disorders or diseases caused by ubH2A, such as an aging related condition in a mammal.
- the present disclosure provides a method of treating an aging related condition in a mammal comprising administrating an agent to decrease ubiquitylation of Histone 2A protein to a subject in need of such treatment.
- the present disclosure firstly demonstrate the correlation between the ubiquitylation of Histone 2A protein and an aging related condition, then the person skilled in the art may understand that administrating an agent which may decrease the ubiquitylation of Histone 2A protein to a mammal may prevent, manage, treat or lessen disorders or diseases caused by ubH2A, such as aging related condition.
- the present disclosure provides a cell model of an aging related condition with increased ubiquitylation of Histone 2A protein compared with the wild type cell thereof.
- the present disclosure firstly demonstrate the correlation between the ubiquitylation of Histone 2A protein and an aging related condition, then the person skilled in the art may understand that a cell model with an increased ubiquitylation of Histone 2A protein compared with the wild type cell may represent that the said cell model having an aging related condition, thus the said cell model can be used as a research model with an aging related condition.
- the present disclosure provides an animal model of an aging related condition comprising a cell with increased ubiquitylation of Histone 2A protein compared with the wild type cell thereof.
- the present disclosure firstly demonstrate the correlation between the ubiquitylation of Histone 2A protein and an aging related condition, then the person skilled in the art may understand that an animal model with a cell which has an increased ubiquitylation of Histone 2A protein compared with the wild type cell may represent that the said animal model having an aging related condition, thus the said animal model can be used as a research model with an aging related condition.
- Flies were cultured in standard media at 25 °C with 60%humidity in a 12 hours light and 12 hours dark cycle.
- the WT (control) line used was 5905 (FlyBase ID FBst0005905, w1118) . All fly lines used in this study have been backcrossed with 5905 for five consecutive generations for a uniform genetic background, to assure that phenotypes were not associated with any variation in background.
- 3d old male and female flies were crossed on media consisting of 10% (w/v) 15 N labeled Saccharomyces cerevisiae (Silantes GmbH, Germany) , 150 mM sucrose, 6 mM methylparaben, and 0.5 ⁇ propionic acid. Flies were maintained in a 12 hour light/12 hours dark cycle at 25 °C and 60%relative humidity. The parent flies were removed after 5 days. 11 days later, the newborn flies were collected and transferred to a 15 N diet for another 5-day culture. Then the flies were switched to a normal 14 N food until 30d and 60d old of age.
- Head, muscle and testis tissues were homogenized in ice-cold urea lysis buffer containing 8 M urea, 100 mM Tris-HCl, pH 8.5, 150 mm NaCl, and protease inhibitor (Pierce, USA) .
- the homogenate was centrifuged using 14,000 g for 10 minutes, and the protein concentration of the supernatant was determined using the BCA protein assay (Pierce, USA) . Proteins were digested with trypsin by a standard protocol of filter-aided sample preparation.
- Off-line basic RP HPLC fractionation was performed on a XBridge BEH C18 column using an Agilent 1260 HPLC system. 500 ⁇ g or 8 mg of peptide was fractionated by using a 72 min basic RP HPLC gradient for aging proteome or ubiquitylome analysis respectively. Upon sample injection, 72 fractions were collected into 1.5ml Eppendorf tubes (Eppendorf, UK) . The resulting small fractions were then pooled in a non-contiguous manner into 7 -8 large fractions. The original fractions 1, 9, 17, 25, 33, 41, 49, 57 and 65 were combined to generate the first pooled fraction. The remaining seven fractions were created followed by a similar pooling strategy. Fractions were dried to completeness in a vacuum concentrator. Peptides from each fraction were subjected to LC-MS analysis or ubiquitylation enrichment using antibody recognizing K-GG remnant.
- Off-line basic RP HPLC fractionation was performed on a XBridge BEH C 18 column using an Agilent 1260 HPLC system. 500 ⁇ g or 8 mg of peptide was fractionated by using a 72 min basic RP HPLC gradient for aging proteome or ubiquitylome analysis respectively. Upon sample injection, 72 fractions were collected into 1.5ml Eppendorf tubes (Eppendorf, UK) . The resulting small fractions were then pooled in a non-contiguous manner into 7-8 large fractions. The original fractions 1, 9, 17, 25, 33, 41, 49, 57 and 65 were combined to generate the first pooled fraction. The remaining seven fractions were created followed by a similar pooling strategy. Fractions were dried to completeness in a vacuum concentrator. Peptides from each fraction were subjected to LC-MS analysis or ubiquitylation enrichment using antibody recognizing K-GG remnant.
- the peptide mixture about 1 mg each fraction were dissolved in 200 ⁇ l IP buffer (50 mM MOPS pH 7.2, 10 mM sodium phosphate, 50 mM NaCl, and 0.3%NP40) .
- IP buffer 50 mM MOPS pH 7.2, 10 mM sodium phosphate, 50 mM NaCl, and 0.3%NP40.
- Total 80 ⁇ l of K-GG ubiquitin remnant motif antibody bead conjugate PTM-1104 , PTM Biolabs, China
- PTM-1104 K-GG ubiquitin remnant motif antibody bead conjugate
- IP buffer and IP buffer without NP40 were used to wash beads for 2 times separately to remove unspecific-binding peptides and following three times wash with H 2 O by centrifuge force of 200 g.
- TFA trifluoroacetic acid
- On-line LC-MS/MS analysis was performed on a tribrid Orbitrap fusion mass spectrometer coupled to a NanoLC-1000 HPLC system (Thermo Fisher Scientific, USA) .
- the peptide mixture was separated by an in-house manufactured 15-cm fritless column packed with C 18 resin (1.9- ⁇ m, Dr. Maisch GmbH, Germany) at a flow rate of 300 nl/min.
- 60d aged flies’ head, muscle and testis were used to identify long-lived proteins.
- Raw data of different fractions belong to one sample were searched together against Uniprot Drosophila database (download date: Feb 2016) using Integrated Proteomics Pipeline -IP2 (Integrated Proteomics Applications, San Diego, CA) . http: //www. integratedproteomics. com/) , with 20 ppm and 400 ppm were set for precursor and fragment mass tolerance respectively. Trypsin was set as the enzyme, and maximum allowed cleavage was 1 and 2 for tissue lysate or ubiquitin enriched sample.
- Equal amount of tissues were lysed in RIPA buffer containing 50 mM Tris (pH 7.4) , 150 mM NaCl, 1%NP-40, 0.25%sodium deoxycholate and protease inhibitor (Pierce, USA) with motor pestle. Protein mixture was centrifuged at 16000 g, for 10 min at 4 °C to remove undissolved ceratine, and then separated on a NuPAGE 12%Bis-Tris gel (GeneScript, China) . The separated proteins were then transferred to a polyvinylidene fluoride membrane (Millipore, USA) .
- the respective primary antibodies were diluted 1: 1000 (anti-ubH2A, 05-678, mouse host, Millipore, USA) for mouse brain samples, 1: 2000 (anti-ubH2A, #8240, rabbit host, CST, USA) for Drosophila head and human brain samples, and 1: 2000 (anti-H2A, 07-146, rabbit host, Millipore, USA) for Drosophila, mouse, and human samples, with overnight incubation at 4 °C.
- the HRP-conjugated secondary antibodies, anti-mouse (31430, Pierce, USA) and anti-rabbit (31460, Pierce, USA) were diluted 1: 10000 and incubated for 1 hour at room temperature.
- the signal intensity was quantified by ImageQuant TL (GE Healthcare, UK) .
- the relative abundance of histone modification was normalized to histone H2A signal intensity, and statistical analysis was using a student’s t-test.
- CRISPR/Cas9 mutagenesis was performed as previously described. Two sgRNA plasmids for target gene were injected into fly embryo. Single-fly-PCR assays were used to screen for mutants. To do this, single fly was homogenized in 50 ⁇ l squashing buffer (10 mM Tris buffer (pH 8.5) , 25 mM NaCl, 1 mM EDTA, 200 ⁇ g/ml Proteinase K) , then incubated at 37 °C for 30 minutes, followed by 95 °C, 10 minutes for inactivation.
- 50 ⁇ l squashing buffer (10 mM Tris buffer (pH 8.5) , 25 mM NaCl, 1 mM EDTA, 200 ⁇ g/ml Proteinase K
- Ten male flies were transferred to an empty vial for 30 minutes adaption in dark. Flies were tapped to the bottom of the vial; the percentage of flies abled to climb up to a mark at 2 cm from the bottom within 5 seconds was scored. Ten biological replicates were done for each genotype at given age.
- RNA isolation was followed in accordance with manufacturer’s instruction.
- RNA was re-suspended in DEPC-treated RNase free water (Thermo Fisher Scientific, USA) .
- TURBO DNA free kit was used to remove residual DNA contamination according to manufacturer’s instruction (Thermo Fisher Sicentific, USA) .
- 1 ⁇ g of total RNA was used for reverse transcription by random primers using SuperScript III First-strand synthesis system for RT-PCR (Thermo Fisher Scientific, USA) .
- Analysis was performed using the QuantStudio 6 Flex real-time PCR system with SYBR selected master mix (Thermo Fisher Scientific, USA) .
- the 2 - ⁇ CT method was used for quantification upon normalization to the RP49 gene as internal control.
- R 5'-GCTCGTCCAGATATTCACAAATC-3'. (SEQ ID NO: 17) .
- R 5'-ATCTCGCCGCAGTAAACGC-3' (SEQ ID NO: 19) .
- RNA isolation was followed in accordance with manufacturer’s instruction.
- RNA was re-suspended in DEPC-treated RNase free water (Invitrogen, USA) .
- TURBO DNA free kit was used to remove residual DNA contamination according to manufacturer’s instruction (Invitrogen, USA) .
- 1 ⁇ g of total RNA was used to generate sequencing library using VAHTS mRNA-seq v2 library Prep Kit for Illumina. The library quality was checked by Bioanalyzer 2100 (Agilent, USA) . The quantification was performed by qRT-PCR with a reference to a standard library.
- the libraries were pooled together in equimolar amounts to a final 2 nM concentration.
- the normalized libraries were denatured with 0.1 M NaOH (Sigma, USA) . Pooled denature libraries were sequenced on the illumina NextSeq 550 platforms with single end 100 bps. Sequencing reads were mapped to the reference genome dm6 with STAR2.3.0e by default parameter. The read counts for each gene were calculated by HTSeq-0.5.4e htseq-count with parameters “-m intersection-strict -s no” . The count files were used as input to R package DESeq for normalization and the differential expression genes were set at a p value smaller than 0.05.
- MS data have been deposited under the accession number IPX0001204000 at iProX and the Illumina RNA-seq data have been deposited in the Sequence Read Archive (SRA) , using the NCBI portal, under the BioProject accession number PRJNA453196 and SRA accession number SRR7059190.
- SRA Sequence Read Archive
- the inventors adapted the pulse-SILAM method (stable isotope labeling with amino acids in mammals) in Drosophila (Fig. 1a) . Briefly, flies were fed with 15 N-labeled diet started in utero. For young animals at 5d post-eclosion, fly diet was switched from 15 N-labeled heavy form to natural 14 N-labeled light form, such that newly synthesized proteins during adult lifespan could incorporate 14 N, allowing the separation of the newer proteome from older proteome by mass spectrometry. Using this method, the inventors characterized the Drosophila age-dependent changes in proteomes.
- muscle proteome had the highest proportion of long-lived proteins, with 1,502 out of 1,903 (78.9%) proteins being LLPs; in comparison, 1,715 out of 3,074 (55.8%) proteins in the head proteome were LLPs (Supplementary Fig. 1c) .
- testis of Drosophila germline, where cells are mitotically active had only 928 LLPs, accounting for 30.6%of identified testicular proteins.
- Gene Ontolgoy (GO) analysis found that LLPs shared by all three tissues were associated with energy generation (Supplementary Fig. 1d) .
- the inventors next clustered proteins according to the proportion of 15 N using the Fuzz C-means method.
- This analysis identified a cluster of proteins that retained more than 70%of 15 N forms at 60d, thus representing the extremely long-lived proteins (ELLPs) in Drosophila (Fig. 1c) .
- this study cataloged 276, 503, and 306 ELLPs in head, muscle, and testis, respectively (Fig. 1c) .
- Fig. 1c the extremely long-lived proteins shared by all three tissues.
- 4 were laminin proteins (Supplementary Fig. 1f) . This finding in Drosophila is consistent with a previous LLP study in rat, suggesting that laminin of the nuclear proteins are evolutionarily conserved ELLPs.
- ubiquitylation might differentially modify old versus newly synthesized proteins.
- Analysis of peptide-spectrum matches (PSMs) determined that while 15 N-labeled old forms accounted for 28%of the entire proteome at 60d, they represented 59%of the ubiquitylated proteome (Fig. 2a) .
- older proteomes showed increased modification by ubiquitylation.
- ubiquitylation of individual proteins were also comparatively increased in the older proteins than their young counterparts.
- H2A119K in mammals is a conserved site for histone mono-ubiquitylation
- the inventors asked whether this modification might be also changed with age in different species (Fig. 3a) .
- the inventors first examined the level of ubH2A by western blot and revealed an increase in aged Drosophila (Fig. 3b) .
- the inventors then analyzed young and aged mice (32 weeks and 104 weeks, respectively) and found increased accumulation of ubH2A in the brain of aged mice as compared to that of young animals (Fig. 3c) . More strikingly, the abundance of ubH2A was substantially increased in the prefrontal cortex samples from older human (Fig. 3d) . Combined, these data demonstrate that age-modulated increase of ubH2A is a highly conserved hallmark of aging.
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Abstract
L'invention concerne l'utilisation de l'ubiquitylation de protéine histone 2A en tant qu'indicateur de pronostic d'une affection liée au vieillissement chez un mammifère.
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