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Wei HS, Qin JH, Cao YZ, Li KB, Yin J. Two classic OBPs modulate the responses of female Holotrichia oblita to three major ester host plant volatiles. INSECT MOLECULAR BIOLOGY 2021; 30:390-399. [PMID: 33822423 DOI: 10.1111/imb.12703] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/16/2020] [Revised: 03/15/2021] [Accepted: 04/01/2021] [Indexed: 06/12/2023]
Abstract
Insects possess a fairly sophisticated olfactory system in their antennae to detect odorants essential for their survival and reproduction. Among them, insect first perceives odour sources by odorant-binding proteins (OBPs) to locate host-plants. Methyl salicylate, (Z)-3-hexenyl acetate and dibutyl phthalate are major volatile components of Ulmus pumila and Ricinus communis and elicit strong responses of the scarab beetle Holotrichia oblita adults. However, olfactory perception of the scarab beetle to these odorant compounds is unclear. In the current study, we cloned the OBP6 and OBP7 of H. oblita. The expression pattern shows that the two genes were highly expressed in the antennae of female beetles. Binding assays verified that the HoblOBP6 had a better binding affinity to methyl salicylate, and so did HoblOBP7 to (Z)-3-hexenyl acetate and dibutyl phthalate. The effect on the responses of female beetles to the three compounds was decreased significantly after these two genes were silenced by RNA interference. These results indicate that HoblOBP6 and HoblOBP7 are essential for female H. oblita perception of methyl salicylate, (Z)-3-hexenyl acetate and dibutyl phthalate. Our study provides important insights into the olfactory mechanism of female H. oblita to ester plant volatiles and could facilitate the development of potential pest control strategies in the field.
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Amenomori M, Bao YW, Bi XJ, Chen D, Chen TL, Chen WY, Chen X, Chen Y, Cui SW, Ding LK, Fang JH, Fang K, Feng CF, Feng Z, Feng ZY, Gao Q, Gomi A, Gou QB, Guo YQ, Guo YY, He HH, He ZT, Hibino K, Hotta N, Hu H, Hu HB, Huang J, Jia HY, Jiang L, Jiang P, Jin HB, Kasahara K, Katayose Y, Kato C, Kato S, Kawata K, Kozai M, Kurashige D, Le GM, Li AF, Li HJ, Li WJ, Li Y, Lin YH, Liu B, Liu C, Liu JS, Liu LY, Liu MY, Liu W, Liu XL, Lou YQ, Lu H, Meng XR, Munakata K, Nakada H, Nakamura Y, Nakazawa Y, Nanjo H, Ning CC, Nishizawa M, Ohnishi M, Ohura T, Okukawa S, Ozawa S, Qian L, Qian X, Qian XL, Qu XB, Saito T, Sakata M, Sako T, Sako TK, Shao J, Shibata M, Shiomi A, Sugimoto H, Takano W, Takita M, Tan YH, Tateyama N, Torii S, Tsuchiya H, Udo S, Wang H, Wang YP, Wu HR, Wu Q, Xu JL, Xue L, Yamamoto Y, Yang Z, Yao YQ, Yin J, Yokoe Y, Yu NP, Yuan AF, Zhai LM, Zhang CP, Zhang HM, Zhang JL, Zhang X, Zhang XY, Zhang Y, Zhang Y, Zhang Y, Zhao SP, Zhou XX. Gamma-Ray Observation of the Cygnus Region in the 100-TeV Energy Region. PHYSICAL REVIEW LETTERS 2021; 127:031102. [PMID: 34328784 DOI: 10.1103/physrevlett.127.031102] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/26/2021] [Revised: 04/30/2021] [Accepted: 06/15/2021] [Indexed: 06/13/2023]
Abstract
We report observations of gamma-ray emissions with energies in the 100-TeV energy region from the Cygnus region in our Galaxy. Two sources are significantly detected in the directions of the Cygnus OB1 and OB2 associations. Based on their positional coincidences, we associate one with a pulsar PSR J2032+4127 and the other mainly with a pulsar wind nebula PWN G75.2+0.1, with the pulsar moving away from its original birthplace situated around the centroid of the observed gamma-ray emission. This work would stimulate further studies of particle acceleration mechanisms at these gamma-ray sources.
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Wu PF, Huang XM, Zhang K, Lu ZP, Chen JM, Xi CH, Wei JS, Guo F, Cai BB, Yin J, Jiang KR, Miao Y. [Application of left-sided uncinate process first approach in pancreaticoduodenectomy]. ZHONGHUA WAI KE ZA ZHI [CHINESE JOURNAL OF SURGERY] 2021; 59:624-630. [PMID: 34256464 DOI: 10.3760/cma.j.cn112139-20210218-00088] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
Objective: To evaluate the value of left-sided uncinate process first approach in pancreaticoduodenectomy. Methods: The clinical data of 152 patients who underwent the left-sided uncinate process first approach during pancreaticoduodenectomy at Pancreas Center, the First Affiliated Hospital of Nanjing Medical University from January 2020 to December 2020 were analyzed retrospectively. There were 64 females and 88 males,with age(M(QR)) of 62.0(14.7)years(range:16.0 to 84.0 years). The clinical date of 117 patients who underwent pancreaticoduodenectomy without using left-sided uncinate process first approach in the same period was selected as the control group,including 65 females and 52 males,with age of 64.0(13.0) years(range:13.0 to 84.0 years). Fisher exact probability method and t test were used to compare the data between the two groups,rank sum test was used for comparison of continuous variables between the two groups. Results: Pancreaticoduodenectomy was successfully performed in 152 patients in left-sided uncinate process first approach group. The operation time was 222.5(77.0) minutes(range:117.0 to 480.0 minutes),the time of uncinate process resection from left-side(the time from jejunum dissection to complete dissociation of the uncinate process) was 11.0(4.5) minutes(range:7.5 to 20.0 minutes),the time of pancreatic head resection (the time from jejunum dissection to pancreaticoduodenal specimen removal) was 26.0(8.5) minutes(range:20.0 to 41.0 minutes),the intraoperative blood loss was 200(150) ml(range:50 to 800 ml),and the intraoperative blood transfusion rate was 9.2% (14/152). Postoperative conditions:The postoperative hospital stay was 12 (9) d(range:6 to 55 d),the overall incidence of postoperative complications was 59.9%(91/152),and there was no perioperative death. Pathological results:The R0 resection rate of periampullary malignant tumor was 64.3%(77/112),with negative rate of uncinate process margin was 91.1%(102/112). The R0 resection rate of pancreatic ductal adenocarcinoma was 46.9%,with negative rate of uncinate process margin was 89.1%(57/64). Compared with the non-left-sided uncinate process first approach group(222.5(77.0) minutes, 9.2%(14/152)),the left-sided uncinate process first approach group had shorter operation time(246.0(94.0) minutes) (Z=3.964,P<0.01),less intraoperative blood loss (18.8%(22/117))(Z=4.843,P<0.01),and lower intraoperative blood transfusion rate(χ²=5.248,P=0.029). However,there were no significant differences between two groups in postoperative hospital stay(Z=1.682,P=0.093),postoperative overall complications(P=0.549),R0 resection rate of periampullary malignant tumor(χ²=2.012,P=0.156),and negative rate of uncinate process margin(χ²=2.108,P=0.147). Conclusions: The "left-sided uncinate process first approach" could completely resect uncinate process under a direct vision,especially when the uncinate process was behind the superior mesenteric artery or beyond the left lateral margin of the superior mesenteric artery. The "left-sided uncinate process first approach" might increase the negative rate of uncinate process margin and R0 resection rate for periampullary malignant tumor.
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Hong X, Zhao J, Zhu X, Dai Q, Zhang H, Xuan Y, Yin J, Zhang Y, Yang X, Fang S, Wang Q, Shen H, Zhang Y, Yan D, Wang Y, Peng Z, Zhang Y, Wang B, Ma X. The association between the vaginal microenvironment and fecundability: a register-based cohort study among Chinese women. BJOG 2021; 129:43-51. [PMID: 34258836 DOI: 10.1111/1471-0528.16843] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2020] [Revised: 05/18/2021] [Accepted: 05/27/2021] [Indexed: 12/13/2022]
Abstract
OBJECTIVE To evaluate the association between the vaginal microenvironment and fecundability among women. DESIGN Register-based nationwide cohort study. SETTING Chinese National Free Pre-conception Check-up Project from 2015 to 2018. POPULATION Our study included a total of 3 388 554 eligible women who were attempting to become pregnant. METHOD We assessed the vaginal microenvironment at baseline by considering four indices: vaginal pH, clue cell examination, whiff test and vaginal cleanliness grading. If any of these indicators was abnormal, the vaginal microenvironment was defined as poor. Propensity score matching was used to control for potential confounders and reduce bias. Logistic models were used to estimate the fecundability odds ratios (FORs) after adjustment for covariates. MAIN OUTCOME MEASURES Achievement of a pregnancy within 1 year. RESULTS Of the total study population, 379 718 women (11.2%) had a poor vaginal microenvironment and their pregnancy rate after 1 year was significantly lower than the group with a normal microenvironment (71.8% versus 76.1%, P < 0.001). After adjusting for potential confounders, the women with a poor vaginal microenvironment were associated with a 9% reduction in fecundability compared with the normal microenvironment group (FOR 0.91, 95% CI 0.90-0.92). The adverse effects of a poor vaginal microenvironment were stronger among multipara (FOR 0.89, 95% CI 0.87-0.90) or women with irregular menstruation (FOR 0.86, 95% CI 0.84-0.89). CONCLUSION There was a negative association between a poor vaginal microenvironment and the fecundability of women. These findings highlight the significance of assessing the vaginal microenvironment during pre-pregnancy health examinations. TWEETABLE ABSTRACT Women with a poor vaginal microenvironment were associated with a reduction in fecundability.
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Zhang FH, Wu Q, Yin J, Zhang JR, Yang XF, Chen SN. [Philadelphia chromosome-negative acute promyelocytic leukemia manifesting after long-term treatment for chronic myeloid leukemia: a case report]. ZHONGHUA XUE YE XUE ZA ZHI = ZHONGHUA XUEYEXUE ZAZHI 2021; 42:259. [PMID: 33910315 PMCID: PMC8081947 DOI: 10.3760/cma.j.issn.0253-2727.2021.03.015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 12/02/2022]
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Zhai D, Wang G, Li L, Jia X, Zheng G, Yin J. [LIM-domain binding protein 2 regulated by m 6A modification inhibits lung adenocarcinoma cell proliferation in vitro]. NAN FANG YI KE DA XUE XUE BAO = JOURNAL OF SOUTHERN MEDICAL UNIVERSITY 2021; 41:329-335. [PMID: 33849822 DOI: 10.12122/j.issn.1673-4254.2021.03.03] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
OBJECTIVE To investigate the role and expression pattern of LIM-domain binding protein 2 (LDB2) in lung adenocarcinoma. OBJECTIVE We studied the expression pattern of LDB2 in lung adenocarcinoma based on data from the online databases TCGA, GEO and CPTAC, and the results were verified in lung adenocarcinoma tissues and cells using immunohistochemistry, qRT-PCR and Western blotting. The relationship between LDB2 and the prognosis of patients with lung adenocarcinoma was analyzed using GEPIA and GEO databases. We further analyzed the role of LDB2 in regulating cell behaviors in a H1299 cell model over-expressing LDB2 using cell counting, soft agar colony forming assay and flow cytometry. The m6A binding sites on LDB2 were confirmed by bioinformatics analysis and MeRIP-qPCR assays. The effect of YTHDC2 on LDB2 was examined using qRT-PCR and Western blotting, and the binding of YTHDC2 to the transcript of LDB2 was verified with RIP-qPCR assays. Dual luciferase reporter assay was performed to verify YTHDC2 functioning via m6A sites. OBJECTIVE LDB2 expression was significantly decreased in lung adenocarcinoma in comparison with normal tissues based on data from TCGA, GEPIA and CPTAC, and the same results were obtained from 80 lung adenocarcinoma tissues and 17 adjacent normal tissues. Similarly, LDB2 expression was decreased in lung adenocarcinoma cells as compared with 16HBE cells. The data from Prognoscan and GEPIA suggested that a high LDB2 expression was positively correlated with a more favorable outcome of lung adenocarcinoma patients. LDB2-overexpressing H1299 cells showed a significant inhibition of proliferative activity with cell cycle arrest in S phage. Bioinformatics analysis and MeRIP-qPCR assay confirmed the presence of m6A sites on LDB2. The m6A reader YTHDC2 was positively related with LDB2 in lung adenocarcinoma based on data from GEPIA (r=0.22). Overexpression YTHDC2 significantly enhanced LDB2 expression in H1299 cells by about 19.35 folds. Dual luciferase reporter assay showed that YTHDC2 enhanced the promoter activity in the wild-type group but not in deletion group. OBJECTIVE LDB2 expression can be up-regulated by m6A reader YTHDC2 in lung adenocarcinoma to inhibit the proliferation of the tumor cells in vitro.
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Fang Y, Zhang S, Yin J, Shen YX, Wang H, Chen XS, Tang H. LINC01535 promotes proliferation and inhibits apoptosis in esophageal squamous cell cancer by activating the JAK/STAT3 pathway. EUROPEAN REVIEW FOR MEDICAL AND PHARMACOLOGICAL SCIENCES 2021; 24:3694-3700. [PMID: 32329845 DOI: 10.26355/eurrev_202004_20832] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
OBJECTIVE To detect the expression of long intergenic non-coding ribonucleic acid (LINC) 01535 in esophageal squamous cell cancer (ESCC) tissues and cells, and to investigate the influences of LINC01535 on the proliferation and apoptosis of ESCC cells and the possible mechanism. PATIENTS AND METHODS Quantitative real-time polymerase chain reaction (qRT-PCR) was performed to determine the relative expression of LINC01535 in 43 cases of ESCC tissues and human esophageal cancer cells (KYSE30, EC9706, TE-13, and Ecal09) compared with human esophageal mucosal epithelial cells (HET-1A). The esophageal cancer cells with the highest expression were selected and transfected with small interfering RNA (si)-LINC01535 (experimental group) or si-negative control (NC) (control group). The interference efficiency was measured via qRT-PCR assay. Regulatory effects of LINC01535 on cell proliferative capacity was examined through colony formation assay and cell proliferation assay [Cell Counting Kit-8 (CCK-8)]. Cell cycle and apoptosis influenced by LINC01535 were detected via flow cytometry. Western blotting was applied to determine the expression changes in the molecular markers of the Janus kinase/signal transducer and activator of transcription 3 (JAK/STAT3) signaling pathway. RESULTS LINC01535 expression in ESCC tissues and cells was remarkably higher than that in para-carcinoma tissues and esophageal mucosal epithelial cells. Knockdown of LINC01535 decreased proliferative capacity, arrested cell cycle in G1/G0 phase, and increased apoptotic rate of ESCC cells. The expressions of the molecular markers of the JAK/STAT3 signaling pathway were altered after knockdown of LINC01535. The above results illustrated that LINC01535 accelerated the proliferation but repressed the apoptosis of ESCC cells by regulating the JAK/STAT3 signaling pathway. CONCLUSIONS The expression of LINC01535 is up-regulated in ESCC tissues and cells, and the highly expressed LINC01535 promotes the proliferation and inhibits the apoptosis of ESCC cells by regulating the JAK/STAT3 signaling pathway. Our findings provide new directions for the diagnosis and treatment of esophageal cancer.
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Wang S, He S, Zhang X, Sun J, Huang Q, Liu J, Han C, Yin Z, Ding B, Yin J. Acellular bovine pericardium matrix in immediate breast reconstruction compared with conventional implant-based breast reconstruction. JPRAS Open 2021; 29:1-9. [PMID: 33937472 PMCID: PMC8079238 DOI: 10.1016/j.jpra.2021.03.005] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2020] [Accepted: 03/09/2021] [Indexed: 11/26/2022] Open
Abstract
Background Acellular Bovine Pericardium Matrix (ABPM) is a new material in implant-based breast reconstruction (IBBR). Few studies have reported on its outcome and complications worldwide and most studies were without a control group. Our aim was to compare its use in IBBR with the other two conventional implant-based reconstruction methods. Methods A retrospective review of patients undergoing IBBR from January to December 2018 was performed. Patients were assigned to the ABPM-assisted IBBR (group A), latissimus dorsi-assisted IBBR (group B) and two-stage IBBR (group C). Patients’ post-operative complications, cost-effectiveness and Quality of Life were compared. Results 100 patients with 100 breasts were included in the study. No complications occurred in group C (n = 11). No significant differences were noted between group A (n = 44) and group B (n = 45) in terms of overall complications (9.1% vs 11.1%, p = 0.973). Group B had the longest operative duration (310.8 ± 62.3 min, p<0.001). The cost of hospitalization forthe three groups was $8051.3 ± 849.2, $7566.0 ± 1172.7 and $7896.5 ± 1762.2, respectively (p = 0.128). The postoperative Breast-Q scores were similar across the three groups. Conclusions ABPM demonstrated acceptable complication rates, cost-effectiveness and quality of life outcomes when compared to LD-assisted IBBR and two-stage IBBR.
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Yang HM, Yin J, Li G, Liu XC. [Clinical features and interventional bronchoscopic treatment of primary airway tumor in 8 children]. ZHONGHUA ER KE ZA ZHI = CHINESE JOURNAL OF PEDIATRICS 2021; 59:27-32. [PMID: 33397000 DOI: 10.3760/cma.j.cn112140-20200904-00849] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Objective: To summarize the clinical manifestations and to evaluate the feasibility of therapeutic bronchoscopy in pediatric primary airway tumors. Methods: The clinical data of 8 children presented with airway tumors in Beijing Children's Hospital from November 2016 to March 2018 were retrospectively analyzed. Descriptive analysis was used to summarize the outcome and prognosis of these children after interventional bronchoscopy. Results: Among the 8 children, 5 were male and 3 were female, aged from 4 years and 8 months to 9 years and 2 months. The main clinical manifestations were cough and wheezing in 6 cases, hemoptysis in 3 cases and recurrent pulmonary infection in 2 cases, and none of them had lymph node metastasis and extra-pulmonary metastasis. All 8 children underwent bronchoscopic resection of the tumors, and the 4 children with blood-rich tumors had bronchial artery embolization at the blood supply site before the resection. No major bleeding or pneumothorax occurred during or after the operation. Four cases had low grade malignant bronchial mucoepidermoid carcinoma, 2 had inflammatory myofibroblastoma, and the rest two had pleomorphic adenoma and bronchial smooth muscle spindle cell tumor. Postoperative follow-up lasted 2 to 4 years, and 3 had tumor recured. Among the 3 cases, 2 had inflammatory myofibroblastoma who underwent surgical resection of the lesion and combined chemotherapy, respectively; and one had mucoepidermoid carcinoma who was under follow-up after interventional cryotherapy. Conclusions: The clinical manifestations of primary airway tumors in children are atypical. The main clinical manifestations are dry cough, wheezing, recurrent pulmonary infection and hemoptysis. Interventional bronchoscopy is a feasible choice for the treatment of pediatric airway tumors.
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Zhang X, Liang Y, Li Y, Yin J. Comparative Efficacy and Safety of Different Regimens of Advanced Gastrointestinal Stromal Tumors After Failure Prior Tyrosine Kinase Inhibitors: A Network Meta-Analysis. Adv Ther 2021; 38:399-412. [PMID: 33131035 DOI: 10.1007/s12325-020-01545-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2020] [Accepted: 10/20/2020] [Indexed: 12/24/2022]
Abstract
INTRODUCTION The prospect of targeted therapies for advanced gastrointestinal stromal tumors (GISTs) has been dramatically transformed after encouraging results achieved in recent clinical trials. At present, the number of second- and third-line treatments are increasing, although the challenge is to take into account the differences between these interventions. Therefore, our goal is to evaluate the investigation of different regimens currently used in GISTs based on findings from phase II or phase III randomized controlled trials (RCTs), and then indirectly compare the effectiveness and safety of the available therapies. METHODS The qualified literatures in relevant sources were searched systematically. Studies to identify RCTs of which main endpoints were progression-free survival (PFS), overall survival (OS), and grade 3 or more adverse events (AEs) in patients with GISTs were considered for inclusion. RESULTS Eight RCTs met our inclusion criteria, which involved 2351 patients. For PFS, compared with placebo, imatinib, and sunitinib, regorafenib (HR = 0.12, 95% CI 0.07-0.23; HR = 0.27, 95% CI 0.19-0.39; HR = 0.36, 95% CI 0.19-0.72, respectively) and ripretinib (HR = 0.15, 95% CI 0.09-0.25; HR = 0.33, 95% CI 0.16-0.68; HR = 0.44, 95% CI 0.25-0.78, respectively) were significantly correlated with the improvement of PFS, and regorafenib may be the preferred option according to the analysis of treatment rankings. For OS, compared with placebo, imatinib, and sunitinib, masitinib (HR = 0.13, 95% CI 0.04-0.44; HR = 0.13, 95% CI 0.04-0.51; HR = 0.27, 95%CI 0.09-0.84) and ripretinib (HR = 0.36, 95% CI 0.21-0.62; HR = 0.36, 95% CI 0.16-0.80; HR = 0.18, 95% CI 0.09-0.36, respectively) were significantly more effective, and masitinib may be the best choice according to treatment ranking analysis. Statistically, regorafenib can be considered to be the highest in high-grade AEs, while the rate of severe AEs of ripretinib and masitinib was likely the lowest. CONCLUSION Our results show that ripretinib has the most favorable balance between effectiveness and tolerability among the different treatment regimens for GISTs.
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Acharya A, Agarwal R, Baker M, Baudry J, Bhowmik D, Boehm S, Byler KG, Chen S, Coates L, Cooper C, Demerdash O, Daidone I, Eblen J, Ellingson S, Forli S, Glaser J, Gumbart JC, Gunnels J, Hernandez O, Irle S, Kneller D, Kovalevsky A, Larkin J, Lawrence T, LeGrand S, Liu SH, Mitchell J, Park G, Parks J, Pavlova A, Petridis L, Poole D, Pouchard L, Ramanathan A, Rogers D, Santos-Martins D, Scheinberg A, Sedova A, Shen Y, Smith J, Smith M, Soto C, Tsaris A, Thavappiragasam M, Tillack A, Vermaas J, Vuong V, Yin J, Yoo S, Zahran M, Zanetti-Polzi L. Supercomputer-Based Ensemble Docking Drug Discovery Pipeline with Application to Covid-19. J Chem Inf Model 2020; 60:5832-5852. [PMID: 33326239 PMCID: PMC7754786 DOI: 10.1021/acs.jcim.0c01010] [Citation(s) in RCA: 109] [Impact Index Per Article: 27.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2020] [Indexed: 01/18/2023]
Abstract
We present a supercomputer-driven pipeline for in silico drug discovery using enhanced sampling molecular dynamics (MD) and ensemble docking. Ensemble docking makes use of MD results by docking compound databases into representative protein binding-site conformations, thus taking into account the dynamic properties of the binding sites. We also describe preliminary results obtained for 24 systems involving eight proteins of the proteome of SARS-CoV-2. The MD involves temperature replica exchange enhanced sampling, making use of massively parallel supercomputing to quickly sample the configurational space of protein drug targets. Using the Summit supercomputer at the Oak Ridge National Laboratory, more than 1 ms of enhanced sampling MD can be generated per day. We have ensemble docked repurposing databases to 10 configurations of each of the 24 SARS-CoV-2 systems using AutoDock Vina. Comparison to experiment demonstrates remarkably high hit rates for the top scoring tranches of compounds identified by our ensemble approach. We also demonstrate that, using Autodock-GPU on Summit, it is possible to perform exhaustive docking of one billion compounds in under 24 h. Finally, we discuss preliminary results and planned improvements to the pipeline, including the use of quantum mechanical (QM), machine learning, and artificial intelligence (AI) methods to cluster MD trajectories and rescore docking poses.
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Shu Y, Guo J, Ma X, Yan Y, Wang Y, Chen C, Sun X, Wang H, Yin J, Long Y, Yan X, Lu Z, Petersen F, Yu X, Qiu W. Anti-N-methyl-D-aspartate receptor (NMDAR) encephalitis is associated with IRF7, BANK1 and TBX21 polymorphisms in two populations. Eur J Neurol 2020; 28:595-601. [PMID: 33065758 DOI: 10.1111/ene.14596] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2020] [Revised: 10/09/2020] [Accepted: 10/10/2020] [Indexed: 12/20/2022]
Abstract
BACKGROUND AND PURPOSE Autoantibodies targeting the GluN1(NR1) subunit of the anti-N-methyl-D-aspartate receptor (NMDAR) cause encephalitis. Although it has been shown that anti-NMDAR encephalitis is associated with human leukocyte antigen (HLA) loci, susceptibility genes for the disease outside the HLA loci remain unidentified. In this study, we aimed to explore the association of anti-NMDAR encephalitis with non-HLA genes. METHODS Two Chinese anti-NMDAR encephalitis cohorts from Han populations were recruited for this study. The North Chinese case-control set consisted of 98 patients and 460 controls, while the South Chinese case-control set included 78 patients and 541 controls. All participants were genotyped for 28 single nucleotide polymorphisms that are associated with autoimmune disorders or infectious diseases. RESULTS In two independent case-control sets, we identified significant associations of anti-NMDAR encephalitis with IRF7 rs1131665 (odds ratio [OR] 3.34, 95% confidence interval [CI] 1.99-5.63; P < 0.000001, Padjusted = 0.00004), BANK1 rs4522865 (OR 1.44, 95% CI 1.15-1.82; P = 0.0017, Padjusted = 0.0149), and TBX21 rs17244587 (OR 2.03, 95% CI 1.35-3.05; P = 0.00051, Padjusted = 0.0066). Furthermore, analysis of the three polymorphisms with clinical features of the disease revealed that the IRF7 rs1131665 was associated with tumor status. CONCLUSION The present study has for the first time identified non-HLA susceptibility genes for anti-NMDAR encephalitis. The association of IRF7, BANK1 and TBX21 with anti-NMDAR encephalitis suggests that B-cell activation, Th1 responses, virus infection and the type I interferon signaling pathway are involved in the pathogenesis of the disease.
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Oxley MP, Yin J, Borodinov N, Somnath S, Ziatdinov M, Lupini AR, Jesse S, Vasudevan RK, Kalinin SV. Deep learning of interface structures from simulated 4D STEM data: cation intermixing vs. roughening. MACHINE LEARNING-SCIENCE AND TECHNOLOGY 2020. [DOI: 10.1088/2632-2153/aba32d] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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Li L, Tang S, Yin J, Pang J, Bao H, Ge H, Liu Y, Wang J, Dong L, Mu D, Yuan S, Wu X, Wang X, Shao Y, Yu J, Yuan S. Molecular Biomarkers for Chemoradiotherapy Response in Unresectable Limited Stage Small Cell Lung Cancer. Int J Radiat Oncol Biol Phys 2020. [DOI: 10.1016/j.ijrobp.2020.07.2074] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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Zheng Z, Yin J, Cheng H, Wang H, Lou F, Cao S, Zhang J. 149P Molecular and clinical characteristics of patients with resectable gastric cancer. Ann Oncol 2020. [DOI: 10.1016/j.annonc.2020.10.170] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
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Hui A, Yin J, Liu W, Zheng K. 18P Prolonged in-use stability of reconstituted atezolizumab in commercial intravenous bags. Ann Oncol 2020. [DOI: 10.1016/j.annonc.2020.08.171] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022] Open
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Ma L, Xu Z, Chen Y, Zhang M, Yin J, Li M, Chen K, Yin P. Sub-nanoscaled Metal Oxide Cluster-Integrated Polymer Network for Quasi-Homogeneous Catalysis. ACS APPLIED MATERIALS & INTERFACES 2020; 12:38655-38661. [PMID: 32846496 DOI: 10.1021/acsami.0c09666] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
The simultaneous improvement of catalytic activity and recyclability of metal oxides is exciting, however challenging, due to the paradox for particle size requirements. Herein, we report the design of polymer nanocomposites (PNCs) by covalently integrating a sub-nanoscaled metal oxide cluster (∼0.7 nm) into a polymer network with superelasticity. Due to the ultrasmall sizes of loaded clusters and the high swelling ratios (SRs) of PNCs, the swelled organogels from PNCs claim similar catalytic efficiencies to homogeneous catalysts, while their recyclability can be simply achieved after the catalytic reactions. Thanks to their robust mechanical properties, the PNCs can be processed into microgel particles for column reactors, enabling large-scale and continuous-flow catalysis.
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Acharya A, Agarwal R, Baker M, Baudry J, Bhowmik D, Boehm S, Byler KG, Coates L, Chen SY, Cooper CJ, Demerdash O, Daidone I, Eblen JD, Ellingson S, Forli S, Glaser J, Gumbart JC, Gunnels J, Hernandez O, Irle S, Larkin J, Lawrence TJ, LeGrand S, Liu SH, Mitchell JC, Park G, Parks JM, Pavlova A, Petridis L, Poole D, Pouchard L, Ramanathan A, Rogers D, Santos-Martins D, Scheinberg A, Sedova A, Shen S, Smith JC, Smith MD, Soto C, Tsaris A, Thavappiragasam M, Tillack AF, Vermaas JV, Vuong VQ, Yin J, Yoo S, Zahran M, Zanetti-Polzi L. Supercomputer-Based Ensemble Docking Drug Discovery Pipeline with Application to Covid-19. CHEMRXIV : THE PREPRINT SERVER FOR CHEMISTRY 2020:12725465. [PMID: 33200117 PMCID: PMC7668744 DOI: 10.26434/chemrxiv.12725465] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Revised: 07/29/2020] [Indexed: 01/18/2023]
Abstract
We present a supercomputer-driven pipeline for in-silico drug discovery using enhanced sampling molecular dynamics (MD) and ensemble docking. We also describe preliminary results obtained for 23 systems involving eight protein targets of the proteome of SARS CoV-2. THe MD performed is temperature replica-exchange enhanced sampling, making use of the massively parallel supercomputing on the SUMMIT supercomputer at Oak Ridge National Laboratory, with which more than 1ms of enhanced sampling MD can be generated per day. We have ensemble docked repurposing databases to ten configurations of each of the 23 SARS CoV-2 systems using AutoDock Vina. We also demonstrate that using Autodock-GPU on SUMMIT, it is possible to perform exhaustive docking of one billion compounds in under 24 hours. Finally, we discuss preliminary results and planned improvements to the pipeline, including the use of quantum mechanical (QM), machine learning, and AI methods to cluster MD trajectories and rescore docking poses.
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Chang X, Hu LF, Ma XJ, Yin J, Liu XY, Li JB. Influence of roflumilast on sepsis mice through the JAK/STAT signaling pathway. EUROPEAN REVIEW FOR MEDICAL AND PHARMACOLOGICAL SCIENCES 2020; 23:1335-1341. [PMID: 30779101 DOI: 10.26355/eurrev_201902_17028] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
OBJECTIVE The aim of this study was to explore the influence of roflumilast on sepsis mice through the Janus kinase/signal transducer and activator of transcription (JAK/STAT) signaling pathway. MATERIALS AND METHODS A total of 36 Sprague-Dawley mice were randomly divided into normal group (n=12), model group (n=12) and roflumilast group (n=12). Mice in the normal group were fed normally. However, mice in the model group and roflumilast group were intraperitoneally injected with endotoxin to establish the sepsis mouse model. Furthermore, mice in the model group and roflumilast group were intraperitoneally injected with 0.9% sodium chloride and roflumilast once a day, respectively. After 7 d of intervention, mice were sampled. Lung tissue morphology was observed via hematoxylin-eosin (HE) staining, and the pathological score was given. The protein expression levels of JAK and STAT-3 were detected via Western blotting. The expression levels of interleukin-6 (IL-6) and tumor necrosis factor-α (TNF-α) were detected via enzyme-linked immunosorbent assay (ELISA). Meanwhile, the mRNA expression levels of JAK, STAT-3, IL-6 and TNF-α were detected via quantitative Polymerase Chain Reaction (qPCR). The number of inflammatory cells in the lavage fluid was counted by a biochemical detector. RESULTS The survival rate of mice in the roflumilast group was significantly higher than that of the model group (p<0.05). The results of HE staining revealed that lung tissue morphology in roflumilast group was significantly improved when compared with the model group. Meanwhile, the pathological score in the roflumilast group was significantly lower than that of the model group (p<0.05). Western blotting showed that the protein expression levels of JAK and STAT-3 in the roflumilast group were markedly lower than those of the model group (p<0.05). According to the results of ELISA, the expression levels of IL-6 and TNF-α in the roflumilast group were remarkably lower than the model group (p<0.05). Further qPCR results manifested that the mRNA expression levels of JAK, STAT-3, IL-6 and TNF-α in the roflumilast group were significantly lower than those of the model group (p<0.05). Moreover, the number of neutrophils, monocytes and lymphocytes in the roflumilast group was significantly smaller than the model group. CONCLUSIONS Roflumilast can improve lung tissue morphology of sepsis mice by inhibiting the JAK/STAT signaling pathway.
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Chen J, Yin J, Liu J, Zhu RX, Zheng Y, Wang XL. MiR-202-3p functions as a tumor suppressor and reduces cell migration and invasion in papillary thyroid carcinoma. EUROPEAN REVIEW FOR MEDICAL AND PHARMACOLOGICAL SCIENCES 2020; 23:1145-1150. [PMID: 30779083 DOI: 10.26355/eurrev_201902_17005] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
OBJECTIVE MicroRNAs (miRNAs) are recently identified as key regulators of tumor development and progression. MiR-202-3p functions as tumor suppressor in some cancer types. The aim of the study is to determine its expression pattern and explore the functions underlying the mechanism of miR-202-3p in papillary thyroid carcinoma (PTC). PATIENTS AND METHODS By using quantitative RT-PCR (QRT-PCR) analyses, we detected miR-202-3p expression in PTC tissues and cell lines. Transwell migration and invasion assays were performed to measure the migration and invasion ability of tumor cells transfected with miR-202-3p mimic. Western blot analysis was used to detect the protein expression. RESULTS Our results showed that miR-202-3p expression was frequently downregulated in 96 cases PTC tissues compared to adjacent normal tissues. Lower expression of miR-202-3p associated with lymph node metastasis of patients with PTC. Overexpression of miR-202-3p inhibited cell migration and invasion in TPC-1 and BCPAP cells. Furthermore, enforced expression of miR-202-3p inhibited WNT signaling by downregulating β-catenin expression in TPC-1 and BCPAP cells. CONCLUSIONS Our findings indicated that miR-202-3p may represent a novel therapeutic target of in PTC.
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96
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Wu ZD, Zhang Q, Yin J, Wang XM, Zhang ZJ, Wu WF, Li FJ. Interactions of Mutiple Biological Fields in Stored Grain Ecosystems. Sci Rep 2020; 10:9302. [PMID: 32518259 PMCID: PMC7283473 DOI: 10.1038/s41598-020-66130-6] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2019] [Accepted: 05/15/2020] [Indexed: 12/02/2022] Open
Abstract
Biological entities such as fungi in stored grain evolve and interact with the environment in similar fashions as physical fields. An experiment was conducted to study the behavior of the biological field of fungi in stored grain, as well as the interactions between the biological field of fungi and the physical fields of temperature and moisture. A framework of the biological field is presented to describe biological systems in which multiple biological entities co-exist and interact among themselves and with the surrounding environment. The proposed biological field describes the spatio-temporal distribution of a biological entity and its ability of influencing (or being influenced by) the surrounding biotic and abiotic entities through exchange of energy, matter, and/or information. The strength of a biological field of fungi was quantified as the rate of energy conversion by fungi from grain starch to heat. The experimental data showed that the strength of biological field of fungi in stored grain varied in both space and time, with the maximum field strength of 120-133 W m-3 occurred at the location where the biological field of fungi interacted strongly with the temperature and moisture fields.
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Krishnamoorthy HNS, Adamo G, Yin J, Savinov V, Zheludev NI, Soci C. Infrared dielectric metamaterials from high refractive index chalcogenides. Nat Commun 2020; 11:1692. [PMID: 32245976 PMCID: PMC7125163 DOI: 10.1038/s41467-020-15444-0] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2019] [Accepted: 02/28/2020] [Indexed: 11/09/2022] Open
Abstract
High-index dielectric materials are in great demand for nanophotonic devices and applications, from ultrathin optical elements to metal-free sub-diffraction light confinement and waveguiding. Here we show that chalcogenide topological insulators are particularly apt candidates for dielectric nanophotonics architectures in the infrared spectral range, by reporting metamaterial resonances in chalcogenide crystals sustained well inside the mid-infrared, choosing Bi2Te3 as case study within this family of materials. Strong resonant modulation of the incident electromagnetic field is achieved thanks to the exceptionally high refractive index ranging between 7 and 8 throughout the 2-10 μm region. Analysis of the complex mode structure in the metamaterial allude to the excitation of circular surface currents which could open pathways for enhanced light-matter interaction and low-loss plasmonic configurations by coupling to the spin-polarized topological surface carriers, thereby providing new opportunities to combine dielectric, plasmonic and magnetic metamaterials in a single platform.
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Salem ME, Yin J, Goldberg RM, Pederson LD, Wolmark N, Alberts SR, Taieb J, Marshall JL, Lonardi S, Yoshino T, Kerr RS, Yothers G, Grothey A, Andre T, De Gramont A, Shi Q. Evaluation of the change of outcomes over a 10-year period in patients with stage III colon cancer: pooled analysis of 6501 patients treated with fluorouracil, leucovorin, and oxaliplatin in the ACCENT database. Ann Oncol 2020; 31:480-486. [PMID: 32085892 PMCID: PMC10688027 DOI: 10.1016/j.annonc.2019.12.007] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2019] [Revised: 12/16/2019] [Accepted: 12/17/2019] [Indexed: 01/05/2023] Open
Abstract
BACKGROUND Since 2004, adjuvant 5-fluorouracil, leucovorin, and oxaliplatin (FOLFOX or FLOX) have been the standard of care for patients with resected colon cancer. Herein we examine the change of outcomes over a 10-year period in patients with stage III colon cancer who received this regimen. PATIENTS AND METHODS Individual patient data from the ACCENT database was used to compare the outcomes in older (1998-2003) and newer (2004-2009) treatment eras for patients with stage III colon cancer who received adjuvant FOLFOX or FLOX. The outcomes were compared between the two groups by the multivariate Cox proportional-hazards model adjusting for age, sex, performance score, T stage, N stage, tumor sidedness, and histological grade. RESULTS A total of 6501 patients with stage III colon cancer who received adjuvant FOLFOX or FLOX in six randomized trials were included in the analysis. Patients enrolled in the new era group experienced statistically significant improvement in time to recurrence [3-year rate, 76.1% versus 73.0%; adjusted hazard ratio (HRadj) = 0.83 (95% CI, 0.74-0.92), P = 0.0008], disease-free survival (DFS) [3-year rate, 74.7% versus 72.3%; HRadj = 0.88 (0.79-0.98), P = 0.024], survival after recurrence (SAR) [median time, 27.0 versus 17.7 months; HRadj = 0.65 (0.57-0.74), P < 0.0001], and overall survival (OS) [5-year rate, 80.9% versus 75.7%; HRadj = 0.78 (0.69-0.88), P < 0.0001]. The improved outcomes remained in patients diagnosed at 45 years of age or older, low-risk patients (T1-3 and N1), left colon, mismatch repair proficient (pMMR), BRAF, and KRAS wild-type tumors. CONCLUSION Improved outcomes were observed in patients with stage III colon cancer enrolled in clinical trials who received adjuvant FOLFOX/FLOX therapy in 2004 or later compared with patients in the older era. Prolonged SAR calls for revalidation of 3-year DFS as the surrogate endpoint of OS in adjuvant clinical trials and reevaluation of optimal follow-up of OS to confirm the trial findings based on the DFS endpoints. CLINICAL TRIALS NUMBERS NCT00079274; NCT00096278; NCT00004931; NCT00275210; NCT00265811; NCT00112918.
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He YX, Yin J, Liu TT, Gao HM, Zhang R, Yao JF, Liu XY, Jia XL, Li XL, Li SL, Wu RH. [FGA gene variation causing congenital dysfibrinogenemia with recurrent arteriovenous thrombosis]. ZHONGHUA ER KE ZA ZHI = CHINESE JOURNAL OF PEDIATRICS 2020; 58:236-238. [PMID: 32135598 DOI: 10.3760/cma.j.issn.0578-1310.2020.03.016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
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Yin J, Cao Y, Zhou JF, Zhang YC. [Prediction of acute graft-versus-host disease after allogeneic hematopoietic stem cell transplantation by the level of galectin-9 in peripheral blood]. ZHONGHUA XUE YE XUE ZA ZHI = ZHONGHUA XUEYEXUE ZAZHI 2020; 41:23-27. [PMID: 32023750 PMCID: PMC7357916 DOI: 10.3760/cma.j.issn.0253-2727.2020.01.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
Objective: To evaluate possible effects of Gelctin-9 on acute graft versus host disease (aGVHD) development and clinical outcomes in patients before and afer allogeneic hematopoietic stem cell transplantation (allo-HSCT) . Methods: Peripheral blood samples were obtained from 29 patients and 15 healthy volunteers with heparin anticoagulant tubes. Samples were analyzed using ELISA kits to measure the serum concentrations of Galectin-9. Results: Patients developing aGVHD had significantly lower level of Galectin-9 [ (7.96±1.18) μg/L] before allo-HSCT compared with those not developing aGVHD [ (12.37±0.97) μg/L, P<0.001]. And after allo-HSCT, the consentration of Galectin-9 increased markedly in patients developing aGVHD [ (17.78±1.78) μg/L] compared with those not developing aGVHD [ (9.45±0.80) μg/L, P<0.001]. Patients developing 3-4 grade aGVHD had significantly higher level of Galectin-9 [ (23.25±2.59) μg/L] compared with those developing 1-2 grade aGVHD [ (14.37±1.45) μg/L, P=0.008] and those without aGVHD [ (9.45±0.80) μg/L, P<0.001]. The patients with lower level of Galectin-9 after allo-HSCT (<13.61 μg/L) showed more favorable clinical outcomes compared with those with higher level of Galectin-9 (≥13.61 μg/L) . The 3-year overall survival rates were (100.00±6.05) % and (69.23±12.80) %, respectively (P=0.009) . The cumulative incidence of non-relapse mortality was significantly higher in high Galectin-9 group [ (23.08±11.69) %] in comparison with low Gaelctin-9 group [ (0.00±7.39) %] (P=0.023) . There was no significant difference between the two groups in terms of the cumulative incidence of relapse. The cumulative incidence of relapse at 3 years were (8.33±7.98) % and (12.50±8.27) % in high and low Galectin-9 groups, respectively (P=0.708) . Conclusions: The serum concentration of Galectin-9 at the time of engraftment after allo-HSCT may be used as a predictor for the development and severity of aGVHD. Galectin-9 might be considered as a potential new approach to regulate transplant rejection to achieve desirable survival.
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