SWI 1 is a member of a new class of tumor DNA-binding proteins named as the AT-rich in- teraction domain family （ARID）, and considered to bind with AT base pairs specifically. Genomic and functional data support ARI...SWI 1 is a member of a new class of tumor DNA-binding proteins named as the AT-rich in- teraction domain family （ARID）, and considered to bind with AT base pairs specifically. Genomic and functional data support ARID1A as a tumor suppressor because AR1D1A/BAF250a （SWI1） subunit of the SWI/SNF chromatin-remodeling complex has emerged as recurrently mutated in a broad array of tumor types. But the crystal structure of SWI1 has not been solved as yet. Using docking and molecular dynamics, we predicted the DNA interaction pattern of human SWI1 ARID and made comparisons with the other two representative ARID family members, human Mrf-2 ARID and Drosophila Dri ARID. Dynamic results revealed that the N-terminal and loop L1 of SWI1 ARID bound with the DNA major groove, while the loop L2 and helix H6 bound with the minor groove. Moreover, it was found that SWI1 ARID bound with DNA apparently in a sequence-nonspecific manner. It was concluded that SWI1 ARID can form stable complex with sequence-nonspecific DNA segment comparing to Mrf-2 ARID/DNA and Dri ARID/DNA sequence-specific complexes.展开更多
AIM: To explore the association between AT-rich interactive domain 1A (ARID1A) protein loss by immunohistochemistry and both clinicopathologic characteristics and prognosis in patients with colorectal cancer.
BACKGROUND Adaptor protein,phosphotyrosine interacting with PH domain and leucine zipper 1(APPL1)plays a crucial role in regulating insulin signaling and glucose metabolism.Mutations in the APPL1 gene have been associ...BACKGROUND Adaptor protein,phosphotyrosine interacting with PH domain and leucine zipper 1(APPL1)plays a crucial role in regulating insulin signaling and glucose metabolism.Mutations in the APPL1 gene have been associated with the development of maturity-onset diabetes of the young type 14(MODY14).Currently,only two mutations[c.1655T>A(p.Leu552*)and c.281G>A p.(Asp94Asn)]have been identified in association with this disease.Given the limited understanding of MODY14,it is imperative to identify additional cases and carry out comprehensive research on MODY14 and APPL1 mutations.AIM To assess the pathogenicity of APPL1 gene mutations in diabetic patients and to characterize the functional role of the APPL1 domain.METHODS Patients exhibiting clinical signs and a medical history suggestive of MODY were screened for the study.Whole exome sequencing was performed on the patients as well as their family members.The pathogenicity of the identified APPL1 variants was predicted on the basis of bioinformatics analysis.In addition,the pathogenicity of the novel APPL1 variant was preliminarily evaluated through in vitro functional experiments.Finally,the impact of these variants on APPL1 protein expression and the insulin pathway were assessed,and the potential mechanism underlying the interaction between the APPL1 protein and the insulin receptor was further explored.RESULTS A total of five novel mutations were identified,including four missense mutations(Asp632Tyr,Arg633His,Arg532Gln,and Ile642Met)and one intronic mutation(1153-16A>T).Pathogenicity prediction analysis revealed that the Arg532Gln was pathogenic across all predictions.The Asp632Tyr and Arg633His variants also had pathogenicity based on MutationTaster.In addition,multiple alignment of amino acid sequences showed that the Arg532Gln,Asp632Tyr,and Arg633His variants were conserved across different species.Moreover,in in vitro functional experiments,both the c.1894G>T(at Asp632Tyr)and c.1595G>A(at Arg532Gln)mutations were found to downregulate the expression of APPL1 on both protein and mRNA levels,indicating their pathogenic nature.Therefore,based on the patient’s clinical and family history,combined with the results from bioinformatics analysis and functional experiment,the c.1894G>T(at Asp632Tyr)and c.1595G>A(at Arg532Gln)mutations were classified as pathogenic mutations.Importantly,all these mutations were located within the phosphotyrosinebinding domain of APPL1,which plays a critical role in the insulin sensitization effect.CONCLUSION This study provided new insights into the pathogenicity of APPL1 gene mutations in diabetes and revealed a potential target for the diagnosis and treatment of the disease.展开更多
Objective Cisplatin(CDDP)-based chemotherapy is a first-line,drug regimen for muscle-invasive bladder cancer(BC)and metastatic bladder cancer.Clinically,resistance to CDDP restricts the clinical benefit of some bladde...Objective Cisplatin(CDDP)-based chemotherapy is a first-line,drug regimen for muscle-invasive bladder cancer(BC)and metastatic bladder cancer.Clinically,resistance to CDDP restricts the clinical benefit of some bladder cancer patients.AT-rich interaction domain 1A(ARID1A)gene mutation occurs frequently in bladder cancer;however,the role of CDDP sensitivity in BC has not been studied.Methods We established ARID1A knockout BC cell lines using CRISPR/Cas9 technology.IC50 determination,flow cytometry analysis of apoptosis,and tumor xenograft assays were performed to verify changes in the CDDP sensitivity of BC cells losing ARID1A.qRT-PCR,Western blotting,RNA interference,bioinformatic analysis,and ChIP-qPCR analysis were performed to further explore the potential mechanism of ARID1A inactivation in CDDP sensitivity in BC.Results It was found that ARID1A inactivation was associated with CDDP resistance in BC cells.Mechanically,loss of ARID1A promoted the expression of eukaryotic translation initiation factor 4A3(EIF4A3)through epigenetic regulation.Increased expression of EIF4A3 promoted the expression of hsa_circ_0008399(circ0008399),a novel circular RNA(circRNA)identified in our previous study,which,to some extent,showed that ARID1A deletion caused CDDP resistance through the inhibitory effect of circ0008399 on the apoptosis of BC cells.Importantly,EIF4A3-IN-2 specifically inhibited the activity of EIF4A3 to reduce circ0008399 production and restored the sensitivity of ARID1A inactivated BC cells to CDDP.Conclusion Our research deepens the understanding of the mechanisms of CDDP resistance in BC and elucidates a potential strategy to improve the efficacy of CDDP in BC patients with ARID1A deletion through combination therapy targeting EIF4A3.展开更多
Protein evolution proceeds by two distinct processes： 1） individual mutation and selection for adaptive mutations and 2） rearrangement of entire domains within proteins into novel combinations, producing new protei...Protein evolution proceeds by two distinct processes： 1） individual mutation and selection for adaptive mutations and 2） rearrangement of entire domains within proteins into novel combinations, producing new protein families that combine functional properties in ways that previously did not exist. Domain rearrangement poses a challenge to sequence alignment-based search methods, such as BLAST, in predicting homology since the methodology implicitly assumes that related proteins primarily differ from each other by individual mutations. Moreover, there is ample evidence that the evolutionary process has used （and continues to use） domains as building blocks, therefore, it seems fit to utilize computational, domain-based methods to reconstruct that process. A challenge and opportunity for computational biology is how to use knowledge of evolutionary domain recombination to characterize families of proteins whose evolutionary history includes such recombination, to discover novel proteins, and to infer protein-protein interactions. In this paper we review techniques and databases that exploit our growing knowledge of “horizontal” protein evolution, and suggest possible areas of future development. We illustrate the power of the domain-based methods and the possible directions of future development by a case history in progress aiming at facilitating a particular approach to understanding microbial pathogenicity.展开更多
The formation of the ferroelectric domain structure as a result of irradiation by focused ion beam of[100]-cut 0.61Pb(Mg_(1/3)Nb_(2/3)TO_(3)–0.39PbTiO_(3)(PMN–PT)single crystals covered by surface artificial dielect...The formation of the ferroelectric domain structure as a result of irradiation by focused ion beam of[100]-cut 0.61Pb(Mg_(1/3)Nb_(2/3)TO_(3)–0.39PbTiO_(3)(PMN–PT)single crystals covered by surface artificial dielectric layer and with free surface was investigated.The dot irradiation resulted in formation of the wedge-like domains grown along[001]direction.For irradiation of the free surface,the domains are mainly located under the surface,while at the irradiated surface with an artificial dielectric layer the domains are located at the surface.It was shown that the subsurface wedge-shaped part of the domain is unstable and completely disappears after a month due to spontaneous backswitching under the action of the residual depolarization field.The revealed nonlinear dose dependence of the domain sizes was attributed to the distribution of the electric field using the point charge model.The domain interaction for the distance between irradiated dots below 30m has been revealed in all samples.It was shown that the decrease of the distance between irradiated dots in the created domain row leads to an increase in the length of the central domains,which is explained by the contribution of all injected charges to the switching field.展开更多
Objective： To investigate the possible mechanisms in acupuncture analgesia by interaction of δ-opioid receptor with neurotransmitter transport proteins or the Na^＋-K^＋ pump. Methods： Microinjection of respective ...Objective： To investigate the possible mechanisms in acupuncture analgesia by interaction of δ-opioid receptor with neurotransmitter transport proteins or the Na^＋-K^＋ pump. Methods： Microinjection of respective heterologous cRNA into the Xenopus oocytes as a model system, and measurement of steady-state currents under two-electrode voltage clamp. Results： The co-expression of the 8-opioid receptor with GAT1, EAAC 1 or the sodium pump resulted in reducing activity of the respective transporter. Opioid receptor activation affected transporter activity in different ways： 1） GAT1 was further inhibited; 2） EAAC1 was stimulated; 3） Na^＋-K^＋ pump activity interfered with agonist sensitivity of DOR. Pump inhibition led to higher sensitivity for DPDPE. Conclusion： GABA transporter inhibition and glutamate transporter stimulation may counteract pain sensation by affecting the neurotransmitter concentration in the synaptic cleft and, therefore, may contribute synergistically to pain suppression by acupuncture. Sodium pump inhibition by endogenous ouabain may amplify these effects. These synergistic effects may be the molecular mechanism of inhibiting pain sense and/or acupuncture analgesia.展开更多
基金supported by the College Scientific and Technological Innovation Project of Huazhong University of Science and Technology(No.15A263)
文摘SWI 1 is a member of a new class of tumor DNA-binding proteins named as the AT-rich in- teraction domain family （ARID）, and considered to bind with AT base pairs specifically. Genomic and functional data support ARID1A as a tumor suppressor because AR1D1A/BAF250a （SWI1） subunit of the SWI/SNF chromatin-remodeling complex has emerged as recurrently mutated in a broad array of tumor types. But the crystal structure of SWI1 has not been solved as yet. Using docking and molecular dynamics, we predicted the DNA interaction pattern of human SWI1 ARID and made comparisons with the other two representative ARID family members, human Mrf-2 ARID and Drosophila Dri ARID. Dynamic results revealed that the N-terminal and loop L1 of SWI1 ARID bound with the DNA major groove, while the loop L2 and helix H6 bound with the minor groove. Moreover, it was found that SWI1 ARID bound with DNA apparently in a sequence-nonspecific manner. It was concluded that SWI1 ARID can form stable complex with sequence-nonspecific DNA segment comparing to Mrf-2 ARID/DNA and Dri ARID/DNA sequence-specific complexes.
基金Supported by National High Technology Research and Development Program of China(863 Program),No.2012AA02A506National Natural Science Foundation of China,No.81372570+1 种基金the Science and Technology Foundation of Guangdong Province,China,No.2012B031800088the Science and Technology Foundation of Guangdong Province,China,No.C2011019
文摘AIM: To explore the association between AT-rich interactive domain 1A (ARID1A) protein loss by immunohistochemistry and both clinicopathologic characteristics and prognosis in patients with colorectal cancer.
基金Supported by the National Natural Science Foundation,No.81974124and Taishan Scholar Project,No.tsqn20161071.
文摘BACKGROUND Adaptor protein,phosphotyrosine interacting with PH domain and leucine zipper 1(APPL1)plays a crucial role in regulating insulin signaling and glucose metabolism.Mutations in the APPL1 gene have been associated with the development of maturity-onset diabetes of the young type 14(MODY14).Currently,only two mutations[c.1655T>A(p.Leu552*)and c.281G>A p.(Asp94Asn)]have been identified in association with this disease.Given the limited understanding of MODY14,it is imperative to identify additional cases and carry out comprehensive research on MODY14 and APPL1 mutations.AIM To assess the pathogenicity of APPL1 gene mutations in diabetic patients and to characterize the functional role of the APPL1 domain.METHODS Patients exhibiting clinical signs and a medical history suggestive of MODY were screened for the study.Whole exome sequencing was performed on the patients as well as their family members.The pathogenicity of the identified APPL1 variants was predicted on the basis of bioinformatics analysis.In addition,the pathogenicity of the novel APPL1 variant was preliminarily evaluated through in vitro functional experiments.Finally,the impact of these variants on APPL1 protein expression and the insulin pathway were assessed,and the potential mechanism underlying the interaction between the APPL1 protein and the insulin receptor was further explored.RESULTS A total of five novel mutations were identified,including four missense mutations(Asp632Tyr,Arg633His,Arg532Gln,and Ile642Met)and one intronic mutation(1153-16A>T).Pathogenicity prediction analysis revealed that the Arg532Gln was pathogenic across all predictions.The Asp632Tyr and Arg633His variants also had pathogenicity based on MutationTaster.In addition,multiple alignment of amino acid sequences showed that the Arg532Gln,Asp632Tyr,and Arg633His variants were conserved across different species.Moreover,in in vitro functional experiments,both the c.1894G>T(at Asp632Tyr)and c.1595G>A(at Arg532Gln)mutations were found to downregulate the expression of APPL1 on both protein and mRNA levels,indicating their pathogenic nature.Therefore,based on the patient’s clinical and family history,combined with the results from bioinformatics analysis and functional experiment,the c.1894G>T(at Asp632Tyr)and c.1595G>A(at Arg532Gln)mutations were classified as pathogenic mutations.Importantly,all these mutations were located within the phosphotyrosinebinding domain of APPL1,which plays a critical role in the insulin sensitization effect.CONCLUSION This study provided new insights into the pathogenicity of APPL1 gene mutations in diabetes and revealed a potential target for the diagnosis and treatment of the disease.
基金This work was supported by grants from the National Natural Science Foundation of China(No.81974396,No.81874091,No.82072840,and No.82102734)the Natural Science Foundation of Hubei Province(No.2020CFB829)the Health Commission of Hubei Province Scientific Research Project(No.WJ2021F081).
文摘Objective Cisplatin(CDDP)-based chemotherapy is a first-line,drug regimen for muscle-invasive bladder cancer(BC)and metastatic bladder cancer.Clinically,resistance to CDDP restricts the clinical benefit of some bladder cancer patients.AT-rich interaction domain 1A(ARID1A)gene mutation occurs frequently in bladder cancer;however,the role of CDDP sensitivity in BC has not been studied.Methods We established ARID1A knockout BC cell lines using CRISPR/Cas9 technology.IC50 determination,flow cytometry analysis of apoptosis,and tumor xenograft assays were performed to verify changes in the CDDP sensitivity of BC cells losing ARID1A.qRT-PCR,Western blotting,RNA interference,bioinformatic analysis,and ChIP-qPCR analysis were performed to further explore the potential mechanism of ARID1A inactivation in CDDP sensitivity in BC.Results It was found that ARID1A inactivation was associated with CDDP resistance in BC cells.Mechanically,loss of ARID1A promoted the expression of eukaryotic translation initiation factor 4A3(EIF4A3)through epigenetic regulation.Increased expression of EIF4A3 promoted the expression of hsa_circ_0008399(circ0008399),a novel circular RNA(circRNA)identified in our previous study,which,to some extent,showed that ARID1A deletion caused CDDP resistance through the inhibitory effect of circ0008399 on the apoptosis of BC cells.Importantly,EIF4A3-IN-2 specifically inhibited the activity of EIF4A3 to reduce circ0008399 production and restored the sensitivity of ARID1A inactivated BC cells to CDDP.Conclusion Our research deepens the understanding of the mechanisms of CDDP resistance in BC and elucidates a potential strategy to improve the efficacy of CDDP in BC patients with ARID1A deletion through combination therapy targeting EIF4A3.
基金supported by NSF of USA under Grant Nos. 0835718 and 0235792NIH under Grant Nos. 5PN2EY016570-06 and5R01NS063405-02+2 种基金the Beckman Institute for Advanced Science and Technologythe National Center for Supercomputing Applicationsthe Renaissance Computing Institute
文摘Protein evolution proceeds by two distinct processes： 1） individual mutation and selection for adaptive mutations and 2） rearrangement of entire domains within proteins into novel combinations, producing new protein families that combine functional properties in ways that previously did not exist. Domain rearrangement poses a challenge to sequence alignment-based search methods, such as BLAST, in predicting homology since the methodology implicitly assumes that related proteins primarily differ from each other by individual mutations. Moreover, there is ample evidence that the evolutionary process has used （and continues to use） domains as building blocks, therefore, it seems fit to utilize computational, domain-based methods to reconstruct that process. A challenge and opportunity for computational biology is how to use knowledge of evolutionary domain recombination to characterize families of proteins whose evolutionary history includes such recombination, to discover novel proteins, and to infer protein-protein interactions. In this paper we review techniques and databases that exploit our growing knowledge of “horizontal” protein evolution, and suggest possible areas of future development. We illustrate the power of the domain-based methods and the possible directions of future development by a case history in progress aiming at facilitating a particular approach to understanding microbial pathogenicity.
基金the Ministry of Science and Higher Education of the Russian Federation(Project No.075-15-2021-1387)by the National Key R&D Program of China(Grant No.2021YFE0115000)+1 种基金the Ural Center for Shared Use“Modern nanotechnology”Ural Federal University(Reg.No.2968)supported by the Ministry of Science and Higher Education RF(Project No.075-15-2021-677)was used.
文摘The formation of the ferroelectric domain structure as a result of irradiation by focused ion beam of[100]-cut 0.61Pb(Mg_(1/3)Nb_(2/3)TO_(3)–0.39PbTiO_(3)(PMN–PT)single crystals covered by surface artificial dielectric layer and with free surface was investigated.The dot irradiation resulted in formation of the wedge-like domains grown along[001]direction.For irradiation of the free surface,the domains are mainly located under the surface,while at the irradiated surface with an artificial dielectric layer the domains are located at the surface.It was shown that the subsurface wedge-shaped part of the domain is unstable and completely disappears after a month due to spontaneous backswitching under the action of the residual depolarization field.The revealed nonlinear dose dependence of the domain sizes was attributed to the distribution of the electric field using the point charge model.The domain interaction for the distance between irradiated dots below 30m has been revealed in all samples.It was shown that the decrease of the distance between irradiated dots in the created domain row leads to an increase in the length of the central domains,which is explained by the contribution of all injected charges to the switching field.
基金the Science Foundation of Shanghai Municipal Commission of Science and Technology(05DZ19745,06DZ19732,064319053,07DZ19722,07DZ19733)the National Basic Research Program of China(973 Program,2005CB523306)Shanghai Leading Academic Discipline Project(B112 and T0302)
文摘Objective： To investigate the possible mechanisms in acupuncture analgesia by interaction of δ-opioid receptor with neurotransmitter transport proteins or the Na^＋-K^＋ pump. Methods： Microinjection of respective heterologous cRNA into the Xenopus oocytes as a model system, and measurement of steady-state currents under two-electrode voltage clamp. Results： The co-expression of the 8-opioid receptor with GAT1, EAAC 1 or the sodium pump resulted in reducing activity of the respective transporter. Opioid receptor activation affected transporter activity in different ways： 1） GAT1 was further inhibited; 2） EAAC1 was stimulated; 3） Na^＋-K^＋ pump activity interfered with agonist sensitivity of DOR. Pump inhibition led to higher sensitivity for DPDPE. Conclusion： GABA transporter inhibition and glutamate transporter stimulation may counteract pain sensation by affecting the neurotransmitter concentration in the synaptic cleft and, therefore, may contribute synergistically to pain suppression by acupuncture. Sodium pump inhibition by endogenous ouabain may amplify these effects. These synergistic effects may be the molecular mechanism of inhibiting pain sense and/or acupuncture analgesia.
