pLoc_Deep-mHum: Predict Subcellular Localization of Human Proteins by Deep Learning

Recently, the life of human beings around the entire world has been endangering by the spreading of pneumonia-causing virus, such as Coronavirus, COVID-19, and H1N1. To develop effective drugs against Coronavirus, knowledge of protein subcellular localization is indispensable. In 2019, a predictor called “pLoc_bal-mHum” was developed for identifying the subcellular localization of human proteins. Its predicted results are significantly better than its counterparts, particularly for those proteins that may simultaneously occur or move between two or more subcellular location sites. However, more efforts are definitely needed to further improve its power since pLoc_bal-mHum was still not trained by a “deep learning”, a very powerful technique developed recently. The present study was devoted to incorporate the “deep-learning” technique and develop a new predictor called “pLoc_Deep-mHum”. The global absolute true rate achieved by the new predictor is over 81% and its local accuracy is over 90%. Both are overwhelmingly superior to its counterparts. Moreover, a user-friendly web-server for the new predictor has been well established at http://www.jci-bioinfo.cn/pLoc_Deep-mHum/, which will become a very useful tool for fighting pandemic coronavirus and save the mankind of this planet.

基于The Human Protein Atlas和TCGA数据库分析SmuG1在人卵巢癌中的表达及预后意义

目的通过数据挖掘分析SmuG1在卵巢癌组织中的表达及预后意义。方法 THPA数据库初步探讨SmuG1在人体的分布以及表达, TCGA数据库分析卵巢癌患者SmuG1 mRNA的表达水平与临床病理特征的相关性,通过生存分析探讨SmuG1 mRNA水平与总体生存期的关系,利用Cox比例风险回归模型分析SmuG1是否为患者总体生存期的独立预后影响因子。结果 THPA数据库发现SmuG1是一种细胞内糖基化酶,在全身各类组织及器官中均有表达,TCGA数据库分析发现SmuG1 mRNA水平与卵巢癌的临床分期呈负相关( P =0.024,相关系数 r =-0.5),而与年龄、肿瘤级别、残留肿瘤大小、耐药性等无关( P >0.05)。生存分析发现SmuG1 mRNA水平高的患者比SmuG1 mRNA水平低的患者存活时间更长差异无统计学意义( P =0.035)。Cox比例风险回归模型分析表明SmuG1的表达水平是卵巢癌患者的显著独立预后指标( HR =0.98,95% CI :0.618 97~1.560 583;P =0.009)。结论人卵巢癌组织中SmuG1水平与临床分期呈负相关。SmuG1表达水平高的卵巢癌患者的总体生存期较长,提示SmuG1可能是卵巢癌显著的独立预后指标。

Establishment of a Multiplex Detection Method for Common Bacteria in Blood Based on Human Mannan-Binding Lectin Protein-Conjugated Magnetic Bead Enrichment Combined with Recombinase-Aided PCR Technology

Objective Recombinase-aided polymerase chain reaction(RAP)is a sensitive,single-tube,two-stage nucleic acid amplification method.This study aimed to develop an assay that can be used for the early diagnosis of three types of bacteremia caused by Staphylococcus aureus(SA),Pseudomonas aeruginosa(PA),and Acinetobacter baumannii(AB)in the bloodstream based on recombinant human mannanbinding lectin protein(M1 protein)-conjugated magnetic bead(M1 bead)enrichment of pathogens combined with RAP.Methods Recombinant plasmids were used to evaluate the assay sensitivity.Common blood influenza bacteria were used for the specific detection.Simulated and clinical plasma samples were enriched with M1 beads and then subjected to multiple recombinase-aided PCR(M-RAP)and quantitative PCR(qPCR)assays.Kappa analysis was used to evaluate the consistency between the two assays.Results The M-RAP method had sensitivity rates of 1,10,and 1 copies/μL for the detection of SA,PA,and AB plasmids,respectively,without cross-reaction to other bacterial species.The M-RAP assay obtained results for<10 CFU/mL pathogens in the blood within 4 h,with higher sensitivity than qPCR.M-RAP and qPCR for SA,PA,and AB yielded Kappa values of 0.839,0.815,and 0.856,respectively(P<0.05).Conclusion An M-RAP assay for SA,PA,and AB in blood samples utilizing M1 bead enrichment has been developed and can be potentially used for the early detection of bacteremia.

An overview of human protein databases and their application to functional proteomics in health and disease

Functional proteomics can be defined as a strategy to couple proteomic information with biochemical and physiological analyses with the aim of understanding better the functions of proteins in normal and diseased organs.In recent years,a variety of publicly available bioinformatics databases have been developed to support protein-related information management and biological knowledge discovery.In addition to being used to annotate the proteome,these resources also offer the opportunity to develop global approaches to the study of the functional role of proteins both in health and disease.Here,we present a comprehensive review of the major human protein bioinformatics databases.We conclude this review by discussing a few examples that illustrate the importance of these databases in functional proteomics research.

HPC-Atlas:Computationally Constructing A Comprehensive Atlas of Human Protein Complexes

A fundamental principle of biology is that proteins tend to form complexes to play important roles in the core functions of cells.For a complete understanding of human cellular functions,it is crucial to have a comprehensive atlas of human protein complexes.Unfortunately,we still lack such a comprehensive atlas of experimentally validated protein complexes,which prevents us from gaining a complete understanding of the compositions and functions of human protein complexes,as well as the underlying biological mechanisms.To fill this gap,we built Human Protein Complexes Atlas(HPC-Atlas),as far as we know,the most accurate and comprehensive atlas of human protein complexes available to date.We integrated two latest protein interaction networks,and developed a novel computational method to identify nearly 9000 protein complexes,including many previously uncharacterized complexes.Compared with the existing methods,our method achieved outstanding performance on both testing and independent datasets.Furthermore,with HPC-Atlas we identified 751 severe acute respiratory syndrome coronavirus 2(SARS-CoV-2)-affected human protein complexes,and 456 multifunctional proteins that contain many potential moonlighting proteins.These results suggest that HPC-Atlas can serve as not only a computing framework to effectively identify biologically meaningful protein complexes by integrating multiple protein data sources,but also a valuable resource for exploring new biological findings.The HPCAtlas webserver is freely available at http://www.yulpan.top/HPC-Atlas.

Usefulness of human epididymis protein 4 in predicting cytoreductive surgical outcomes for advanced ovarian tubal and peritoneal carcinoma

Objective： Human epididymis protein 4（HE4） is a promising biomarker of epithelial ovarian cancer（EOC）. But its role in assessing the primary optimal debulking（OD） of EOC remains unknown. The purpose of this study is to elucidate the ability of preoperative HE4 in predicting the primary cytoreductive outcomes in advanced EOC, tubal or peritoneal carcinoma.Methods： We reviewed the records of 90 patients with advanced ovarian, tubal or peritoneal carcinoma who underwent primary cytoreduction at the Department of Obstetrics and Gynecology of Peking University People＇s Hospital between November 2005 and October 2010. Preoperative serum HE4 and CA125 levels were detected with EIA kit. A receiver operating characteristic（ROC） curve was used to determine the most useful HE4 cut-off value. Logistic regression analysis was performed to identify significant preoperative clinical characteristics to predict optimal primary cytoreduction.Results： OD was achieved in 47.7%（43/48） of patients. The median preoperative HE4 level for patients with OD vs. suboptimal debulking was 423 and 820 pmol/L, respectively（P〈0.001）. The areas under the ROC curve for HE4 and CA125 were 0.716 and 0.599, respectively（P=0.080）. The most useful HE4 cut-off value was 473 pmol/L. Suboptimal cytoreduction was obtained in 66.7%（38/57） of cases with HE4 ≥473 pmol/L compared with only 27.3%（9/33） of cases with HE4 〈473 pmol/L. At this threshold, the sensitivity, specificity, positive predictive value（PPV） and negative predictive value（NPV） for diagnosing suboptimal debulking were 81%, 56%, 67%, and 73%, respectively. Logistic regression analysis showed that the patients with HE4 ≥473 pmol/L were less likely to achieve OD（odds ratio =5.044, P=0.002）.Conclusions： Preoperative serum HE4 may be helpful to predict whether optimal cytoreductive surgery could be obtained or whether extended cytoreduction would be needed by an interdisciplinary team.

Establishment of a high-resolution 2-D reference map of human spermatozoal proteins from 12 fertile sperm-bank donors

Aim： To extend the analysis of the proteome of human spermatozoa and establish a 2-D gel electrophoresis （2-DE） reference map of human spermatozoal proteins in a pH range of 3.5-9.0. Methods： In order to reveal more protein spots, immobilized pH gradient strips （24 cm） of broad range of pH 3-10 and the narrower range of pH 6-9, as well as different overlapping narrow range pH immobilized pH gradient （IPG） strips, including 3.5-4.5, 4.0-5.0, 4.5-5.5, 5.0-6.0 and 5.5-6.7, were used. After 2-DE, several visually identical spots between the different pH range 2-D gel pairs were cut from the gels and confirmed by mass spectrometry and used as landmarks for computer analysis. Results： The 2-D reference map with pH value from 3.5 to 9.0 was synthesized by using the ImageMaster analysis software. The overlapping spots were excluded, so that every spot was counted only once. A total of 3 872 different protein spots were identified from the reference map, an approximately 3-fold increase compared to the broad range pH 3-10 IPG strip （1 306 spots）. Conclusion： The present 2-D pattern is a high resolution 2-D reference map for human fertile spermatozoal protein spots. A comprehensive knowledge of the protein composition of human spermatozoa is very meaningful in studying dysregulation of male fertility.

Diagnostic value of serum human epididymis protein 4 in esophageal squamous cell carcinoma

BACKGROUND Numerous studies have demonstrated that human epididymis protein 4(HE4)is overexpressed in various malignant tissues including ovarian,endometrial,lung,breast,pancreatic,and gastric cancers.However,no study has examined the diagnostic impact of HE4 in patient with esophageal squamous cell carcinoma(ESCC)until now.AIM To analyze the value of four serum tumor markers for the diagnosis of ESCC,and examine the associations of serum levels of HE4 with ESCC patients’clinicopathological characteristics.METHODS The case group consisted of 80 ESCC patients,which were compared to a control group of 56 patients with benign esophageal disease.Serum levels of HE4,carcinoma embryonic antigen(CEA),alpha fetal protein,and carbohydrate antigen 19-9(CA19-9)were detected by ELISA.The associations of serum HE4 levels with ESCC patients’clinicopathological characteristics such as gender,tumor location,and pathological stage were also examined after operation.RESULTS The result of ELISA showed that serum HE4 level was significantly higher in the patients with ESCC than in the controls,and the staining intensity was inversely correlated with the pathological T and N stages.Serum HE4 levels had a sensitivity of 66.2%and specificity of 78.6%when the cutoff value was set at 3.9 ng/mL.Moreover,the combined HE4 and CA19-9 increased the sensitivity to 83.33%,and interestingly,the combination of HE4 with CEA led to the most powerful sensitivity of 87.5%.Furthermore,A positive correlation was observed between HE4 serum levels and pathological T and N stages(P=0.0002 and 0.0017,respectively),but there was no correlation between HE4 serum levels and ESCC patient gender(P=0.4395)or tumor location(P=0.6777).CONCLUSION The results of this study suggest that detection of serum HE4 levels may be useful in auxiliary diagnosis and evaluation of the progression of ESCC.

Effect of cyclovirobuxine D on human growth-associated protein 43 and neurocan expression in ischemic brain tissue of stroke-prone renovascular hypertensive rats

BACKGROUND： Experimental data indicate that human growth-associated protein 43 mRNA expression coincides with axonal growth during nerve ganglion development; while neurocan, secreted from astrocytes, can inhibit sprouting and elongation of the axonal growth cone. OBJECTIVE： To verify regulatory effects of cyclovirobuxine D （CVB-D） extracted from Chinese box branchlet on human growth-associated protein 43 （GAP-43）, and neurocan expression in brain tissue of stroke-prone renovascular hypertensive （RHRSP） rats, at different time points after cerebral ischemia/reperfusion. DESIGN： Randomized grouping design and controlled animal study. SETTING： This study was performed at the Center of Guangdong Hospital of Traditional Chinese Medicine （a national key laboratory） from March 2003 to September 2006. MATERIALS： 100 healthy male Sprague-Dawley rats, aged 2 3 months and weighing 90-120 g, were selected for this study. CVB-D was provided by Nanjing Xiaoying Pharmaceutical Factory （Batch number： 307701）. METHODS： The initial tip of renal arteries was clamped bilaterally for 10 weeks to establish the RHRSP model. 100 RHRSP rats were randomly divided into 4 groups： naive group （n = 10）, sham surgery group （n = 10）, CVB-D group （n = 40）, and lesion group （n = 40）. Rats in the naive group did not undergo any treatment, and cervical vessels of rats in the sham surgery group were exposed, but not blocked. The right middle cerebral artery of rats in the CVB-D group and lesion group were occluded to establish cerebral ischemia. Rats in the CVB-D group were intraperitoneally injected with CVB-D （6.48 mg/kg） every day and with saline （1.5 mL/injection） twice a day. Rats in the lesion group were intraperitoneally injected with saline （2 mL/injection）. MAIN OUTCOME MEASURES： Immunohistochemistry was applied to detect GAP-43 and neurocan expression in the ischemic penumbra region of CVB-D and lesion brains at 2 hours post-cerebral ischemia and at 1, 7, 14, and 30 days post-perfusion （n = 10 at each time point）. Similarly, GAP-43 and neurocan expression was detected in the right hemisphere of naive and sham-operated animals. The results were expressed as positive cells. RESULTS： A total of 100 rats were included in the final analysis. The number of GAP-43 positive cells increased in the CVB-D group 1, 7, 14, and 30 days post-cerebral ischemia/perfusion compared to the lesion group, as indicated by a significant difference between the CVB-D and lesion group （P 〈 0.054）.01）. The number of neurocan-positive cells decreased in the CVB-D group on the first day compared to the model group; however, there was no significant difference between the two groups （P 〉 0.05）. On post-ischemia days 7, 14, and 30, the number of neurocan-positive cells in the CVB-D group was significantly less than in the lesion group （P 〈 0.05）. Both, GAP-43 and neurocan expression was not detectable in brains of naive and sham-operated animals. CONCLUSION： CVB-D treatment up-regulated GAP-43 expression and down-regulated neurocan expression in the ischemic region of RHRSP rats.

Construction of Adeno-associated Virus System for Human Bone Morphogenetic Protein 7 Gene

To construct the recombinant adeno-associated virus （rAAV） vector with human bone morphogenetic protein 7 （BMP7） and observe the BMP7 mRNA expression in vitro, BMP7 CDS sequence was cloned into expression plasmid pAAV-MCS of AAV Helper Free System. The recombinant plasmid was identified with enzyme digestion and sequencing. The recombinant plasmid, pAAV-RC, pHelper were co-transfected into AAV-293 cells according to the calcium phosphate-based protocol. The viral stock was collected by 4 rounds of freeze/thaw. After purified and concentrated, the recombinant virus titer was determined by dot-blot assay. HEK293 cells were transfected with the recombinant virus at different MOI, and the expression of BMP7 mRNA was detected by RT-PCR. The results showed rAAV-BMP7 was constructed and packaged successfully. The physical particle titer was 2.5×10^11 vector genomes/mL. There was different expression level of BMP7 mRNA after transfecton. These data suggested that recombinant AAV mediated a stable expression of hBMP7 mRNA in 293 cells. The AAV production method may pave the way of an effective strategy for the jaw bone defection around dental implants.

Heterotopic ossification after the use of recombinant human bone morphogenetic protein-7

AIM To present the incidence of heterotopic ossification after the use of recombinant human bone morphogenetic protein-7(rhB MP-7) for the treatment of nonunions.METHODS Bone morphogenetic proteins(BMPs) promote bone formation by auto-induction. Recombinant human BMP-7 in combination with bone grafts was used in 84 patients for the treatment of long bone nonunions. All patients were evaluated radiographicaly for the development of heterotopic ossification during the standard assessment for the nonunion healing. In all patients(80.9%) with radiographic signs of heterotopic ossification, a CT scan was performed. Nonunion site palpation and ROM evaluation of the adjacent jointswere also carried out. Factors related to the patient(age, gender), the nonunion(location, size, chronicity, number of previous procedures, infection, surrounding tissues condition) and the surgical procedure(graft and fixation type, amount of rhB MP-7) were correlated with the development of heterotopic ossification and statistical analysis with Pearsons χ~2 test was performed.RESULTS Eighty point nine percent of the nonunions treated with rh BMP-7, healed with no need for further procedures. Heterotopic bone formation occurred in 15 of 84 patients(17.8%) and it was apparent in the routine radiologi-cal evaluation of the nonunion site, in a mean time of 5.5 mo after the rh BMP-7 application(range 3-12). The heterotopic ossification was located at the femur in 8 cases, at the tibia in 6, and at the humerus in οne patient. In 4 patients a palpable mass was present and only in one patient, with a para-articular knee nonunion treated with rhB MP-7, the size of heterotopic ossification affected the knee range of motion. All the patients with heterotopic ossification were male. Statistical analysis proved that patient's gender was the only important factor for the development of heterotopic ossification(P = 0.007). CONCLUSION Heterotopic ossification after the use of rh BMP-7 in nonunions was common but it did not compromise the final clinical outcome in most cases, and affected only male patients.

A study of the relationship between expression level of TRF1 protein and telomerase activity in human acute leukemia

Objective： To study the expression level of TRF1 （telomeric repeat binding factor 1） protein in human acute leukemia and relationship between expression level of TRF1 protein and telomerase, Methods： A quantitative Western±Blot technique was developed using anti±TRF1^33±277 monoclonal antibody and GST±TRFI purity protein as a standard to further determine the expression level of TRF1 protein in total proteins extracted from clinical specimens. Results： Bone marrow tissues of 20 acute leukemia patients were studied, 11 healthy donors＇ bone marrows were taken as a control. The expression level of TRF1 protein was significantly higher （P〈0.01） in normal bone marrow （（2.2174±0.462） μg/μl） than that of acute leukemia patients （（0.7544±0.343） μg/μl）, But there was no remarkable difference between ALL and ANLL patients （（0.6184±0.285） μg/μl vs （0.8454±0.359） μg/μl, P〉0.05）. After chemotherapy, TRFI expression level of patients with complete remission elevated （（0.7724±0.307）/μg/μl vs （1.6834±0,344）μg/μl, P〈0.01 ）, but lower than that of normal （（2.2174±0.462）/μg/μl, P〈0.01）. There was no significantly difference after chemotherapy （（0.7264±0.411） μg/μl vs （0.895±0.339） μg/μl,p〉0.05）. TRF1 expression level of patients with complete remission is higher than that of patients without complete remission （（1,683±0.344）μg/μl vs （0.895±0.339）μg/μl P〈0.01）. All samples were determined for telomerase activity. It was confirmed that the activity of telomerase in normal bone marrow was lower than that of acute leukemia patients （（0.125±0.078） μg/μl vs （0.765±0.284）μg/μl, P〈0.01）. There was no significant difference of expression level ofTRF I protein between ALL and ANLL patients （（0.897±0.290） μg/μl vs （0.677±0.268） μg/μl, P〉0.05）. After chemotherapy, telomerase activity of patients with complete remission decreased （（0.393±0.125） μg/μl）, but was still higher than that of normal （（0.125±0.078） μg/μl, P〈0.01）. Conclusion： The expression level of TRF1 protein has correlativity to the activity of telomerase （P〈0.001）.

Recombinant human zona pellucida proteins ZP1, ZP2 and ZP3 co-expressed in a human cell line

Aim: To produce biologically active recombinant human (rh) ZP proteins in a human cell for use in sperm function tests. Methods: The human embryonic kidney cell line 293T was employed to produce rhZP1, rhZP2 and rhZP3 proteins individually and together by co-expression. Presence of these proteins in the culture medium and cell lysate was assessed by Western blotting analysis. The effect of the recombinant proteins on the human AR was assessed. Results: RhZP2 and rhZP3 were secreted into the culture medium, whereas rhZPl was found only in the cell lysate. Interestingly, when all zona pellucida proteins were co-expressed in the same cells, rhZPl was also secreted into the culture medium. However, despite the presence of all three ZP proteins in sufficient concentration and evidence of heavy glycosylation on gel electrophoresis, biological activity to induce the AR was not observed. Conclusion: RhZP1, rhZP2 and rhZP3 were successfully expressed in the human embryonic kidney cell line 293T. It appears that an interaction amongst these proteins may be required for release of rhZPl from the cell. Although this approach is not satisfactory for producing active human ZP proteins, it makes a significant contribution to the understanding of the structural and functional characteristics of the ZP proteins.

Effect of senescence marker protein 30 on the proliferation and apoptosis of human lens epithelial cells SRA01/04

AIM： To study the effect of senescence marker protein 30（SMP30） on the proliferation and apoptosis of human lens epithelial cell（HLEC） SRA01/04.METHODS： SMP30 overexpression（OE） and knock down（KD） type cell lines were cultivated by using two groups regucalcin（RGN; SMP30） lentiviral vectors（LVRGN, LV-RGN-RNAi） and the respective negative control virus infect SRA01/04 cells. Western blot and real-time quantitative polymerase chain reaction（q-PCR） analysis were used to determine RGN overexpression and knock down efficiency. We use cell counting kit-8（CCK8） assay to measure cell viability and 5-bromodeoxyuridine（Brd U） assay to test cell proliferation. Cell cycle was measured by PI FACS assay and cell apoptosis was tested by Annexin V-APC assay through flow cytometry. We use Western blot to measure the content of caspase-3 in SRA01/04.RESULTS： We used PCR and Western blot techniques to determine the successful transfection of SMP30 OE and KD SRA01/04 cell lines. By CCK8, Brdu and PI FACS cell cycle assay, it was found that the SMP30 OE group promoted cell proliferation（P〈0.05） compared with the control group, and the KD group inhibited cell proliferation（P〈0.05）. The results of Annexin V-APC signal staining detection indicated that compared with respective control group, the cell apoptosis rate was higher in KD group（P〈0.05） but lower in OE group（P〈0.01）. The expression of caspase-3 was down-regulated in OE group through Western blot assay and up-regulated in KD group compared with respective control group. CONCLUSION： Proliferation of SRA01/04 was promoted by SMP30 OE and apoptosis was suppressed. Increasing the expression of SMP30 may protect HLEC SRA01/04 against apoptosis in cataract.

Trichloroethylene Induces Biphasic Concentration-dependent Changes in Cell Proliferation and the Expression of SET-Associated Proteins in Human Hepatic L-02 Cells

Trichloroethylene （TCE） is a major pollutant that affects both occupational and general environments. The liver is an important target organ of TCEE. Substantial efforts and remarkable progress into understanding TCE cytotoxicity have been made in cultured liver cells. However, the molecular mechanisms by which TCE induces hepatotoxicity are not well understood. SET （also known as protein phosphatase 2A inhibitor, 12PP2A, or template-activating factor-I, TAF-D is a nuclear protein that regulates histone modification, gene transcription, DNA replication, nucleosome assembly,

Use of recombinant human bone morphogenetic protein-2 in spine surgery

Bone morphogenetic proteins are osteoinductive factors which have gained popularity in orthopaedicsurgery and especially in spine surgery. The use of recombinant human bone morphogenetic protein-2 has been officially approved by the United States Food and Drug Administration only for single level anterior lumbar interbody fusion, nevertheless it is widely used by many surgeons with off-label indications. Despite advantages in bone formation, its use still remains a controversial issue and several complications have been described by authors who oppose their wide use.

Expression of serum human epididymal secretory protein E4 at low grade and high grade serous carcinomas

Objective:To investigate the value of serum human epididymis protein 4(HE4) in differential diagnosis of patients with low-grade serous(LGSC) and high-grade serous carcinoma(HGSC) serous ovarian cancer.Methods:LGSC and HGSC serous ovarian cancer were diagnosed by the two-tier grade system,serum levels of HE4 and carbohydrate antigen 12S(CA125) were measured by ELBA and radioisotope method,respectively in 60 serous ovarian cancer patients. HE4 and TPS3 protein in cancer tissue were measured by immunohistochemical method. Results:The difference in density of HE4 and TP53 protein was significant between LGSC and HGSC tissue,while serum CA12S did not show significant difference between different serum samples.There was significant difference in serum HE4 levels between LGSC and HGSC and the result was different within FIGO(Ⅰ+Ⅱ) stage,suggesting HE4 was not a reliable biomarker for the discrimination between LGSC and HCSC.HE4 had potential as a biomarker for the discrimination between LGSC and HGSC but the role in early diagnosis was limited.Conclusions:HE4 may be a reliable marker for differential diagnosis of LGSC and HGSC.But its role in early diagnosis of LGSC and HGSC need to be confirmed from the perspective of two-tier grade system.

Human antigen R mediated post-transcriptional regulation of inhibitors of apoptosis proteins in pancreatic cancer

AIM To determine the association of human antigen R(HuR) and inhibitors of apoptosis proteins(IAP1, IAP2) and prognosis in pancreatic cancer.METHODS Protein and mRNA expression levels of IAP1, IAP2 and HuR in pancreatic ductal adenocarcinoma(PDAC) were compared with normal pancreatic tissue. The correlations among IAP1/IAP2 and HuR as well as their respective correlations with clinicopathological parameters were analyzed. The Kaplan-Meier method and log-rank tests were used for survival analysis. Immunoprecipitation assay was performed to demonstrate HuR binding to IAP1, IAP2 mRNA. PANC1 cells were transfected with either anti-HuR siRNA or control siRNA for 72 h and quantitative reverse transcription polymerase chain reaction(RT-PCR), western blot analysis was carried out.RESULTS RT-PCR analysis revealed that HuR, IAP1, IAP2 mRNA expression were accordingly 3.3-fold, 5.5-fold and 8.4 higher in the PDAC when compared to normal pancreas(P < 0.05). Expression of IAP1 was positively strongly correlated with HuR expression(P < 0.05, r = 0.783). Western blot analysis confirmed RTPCR results. High IAP1 expression, tumor resection status, T stage, lymph-node metastases, tumor differentiation grade, perineural and lymphatic invasion were identified as significant factors for shorter survival in PDAC patients(P < 0.05).Immunohistological analysis showed that HuR was mainly expressed in the ductal cancer cell's nucleus and less so in cytoplasm. RNA immunoprecipitation analysis confirmed IAP1 and IAP2 post-transcriptional regulation by HuR protein. Following siHuR transfection, IAP1 mRNA and protein levels were decreased, however IAP2 expression levels were increased.CONCLUSION HuR mediated overexpression of IAP1 significantly correlates with poor outcomes and early progression of pancreatic cancer. Further studies are needed to assess the underlying mechanisms.

Structural analysis of tumor-relatedsingle amino acid mutations in human MxA protein

Background:Human myxovirus resistant protein A(MxA),encoded by the myxovirus resistance 1(Mx1) gene,is an interferon(IFN)-triggered dynamin-like multi-domain GTPase involved in innate immune responses against viral infections.Recent studies suggest that MxA is associated with several human cancers and may be a tumor suppressor and a promising biomarker for IFN therapy.Mxl gene mutations in the coding region for MxA have been discovered in many types of cancer,suggesting potential biological associations between mutations in MxA protein and corresponding cancers.In this study,we performed a systematic analysis based on the crystal structures of MxA and elucidated how these mutations specifically affect the structure and therefore the function of MxA protein.Methods:Cancer-associated Mxl mutations were collected and screened from the COSMIC database.Twenty-two unique mutations that cause single amino acid alterations in the MxA protein were chosen for the analysis.Amino acid sequence alignment was performed using Clustal W to check the conservation level of mutation sites in Mx proteins and dynamins.Structural analysis of the mutants was carried out with Coot.Structural models of selected mutants were generated by the SWISS-MODEL server for comparison with the corresponding non-mutated structures.All structural figures were generated using PyMOL.Results:We analyzed the conservation level of the single-point mutation sites and mapped them on different domains of MxA.Through individual structural analysis,we found that some mutations severely affect the stability and function of MxA either by disrupting the intraVinter-molecular interactions supported by the original residues or by incurring unfavorable configuration alterations,whereas other mutations lead to gentle or no interference to the protein stability and function because of positions or polarity features.The potential clinical value of the mutations that lead to drastic influence on MxA protein is also assessed.Conclusions:Among all of the reported tumor-associated single-point mutations,seven of them notably affect the structure and function of MxA and therefore deserve more attention with respect to potential clinical applications.Our research provides an example for systematic analysis and consequence evaluation of single-point mutations on a given cancer-related protein.