1.Fertility Online:A Straightforward Pipeline for Functional Gene Annotation and Disease Mutation Discovery
Gao JIANING ; Zhang HUAN ; Jiang XIAOHUA ; Ali ASIM ; Zhao DAREN ; Bao JIANQIANG ; Jiang LONG ; Iqbal FURHAN ; Shi QINGHUA ; Zhang YUANWEI
Genomics, Proteomics & Bioinformatics 2022;20(3):455-465
		                        		
		                        			
		                        			Exploring the genetic basis of human infertility is currently under intensive investigation.However,only a handful of genes have been validated in animal models as disease-causing genes in infertile men.Thus,to better understand the genetic basis of human spermatogenesis and bridge the knowledge gap between humans and other animal species,we construct the FertilityOnline,a data-base integrating the literature-curated functional genes during spermatogenesis into an existing sper-matogenic database,SpermatogenesisOnline 1.0.Additional features,including the functional annotation and genetic variants of human genes,are also incorporated into FertilityOnline.By searching this database,users can browse the functional genes involved in spermatogenesis and instantly narrow down the number of candidates of genetic mutations underlying male infertility in a user-friendly web interface.Clinical application of this database was exampled by the identifi-cation of novel causative mutations in synaptonemal complex central element protein 1(SYCE1)and stromal antigen 3(STAG3)in azoospermic men.In conclusion,FertilityOnline is not only an integrated resource for spermatogenic genes but also a useful tool facilitating the exploration of the genetic basis of male infertility.
		                        		
		                        		
		                        		
		                        	
2.Hepatic perivascularepithelioid cell tumor (PEComa):report of a case and literature review
Chenni ZHAN ; Daren LIU ; Dike SHI ; Yuanliang XU ; Liping CAO
Chinese Journal of Hepatic Surgery(Electronic Edition) 2014;(5):295-298
		                        		
		                        			
		                        			Objective To discuss the clinical characteristics of hepatic perivascularepithelioid cell tumor (PEComa). Methods Clinical data of one patient with hepatic PEComa in the Second Affiliated Hospital, Zhejiang University School of Medicine in 2011 were analyzed retrospectively. The informed consent of the patient was obtained and the ethical committee approval was received. The patient was a 25-year-old female and was admitted in hospital for the physical examination finding of space occupying lesions in the liver. The results of physical and laboratory examinations were normal. Multiple round-like mass of low density with poorly defined borders were observed in the liver by CT scan. Significant enhancement was observed in the arterial phase by enhancement scan, and homo- or hypo-enhancement in the delayed phase. The liver lesions showed intermediated signal intensity on T1WI by MRI and slightly hyperintense on T2WI. Significant enhancement was observed in the arterial phase after enhancement and degraded in the delayed phase. The patient was primarily diagnosed with liver focal nodular hyperplasia clinically. Results After sufficient preoperative preparation, hepatectomy was performed on the patient under general anesthesia by tracheal intubation on December 8th , 2011. The tumor was observed 
 composed of polygonal morphology cells of epithelial cells without lipocytes or abnormal blood vessels by pathological examination. The tumor was observed with strongly positive human melanoma black-45 (HMB-45), smooth muscle actin (SMA), and positive vimentin, cluster of differentiation (CD) 34. The diagnosis of hepatic PEComa was confirmed pathologically. The patient recovered well and was discharged from hospital 1 week after operation. No recurrence or metastasis was observed during the regular follow-up till the submission date. Conclusions Hepatic PEComa is extremely rare without specific clinical manifestation. The diagnosis depends on the pathological examination. Surgical resection is an effective method for the tumor with a good prognosis.
		                        		
		                        		
		                        		
		                        	
3.Effect of Smad7 antisense oligodeoxynucleotide on the expression of MMP-2, TIMP-2 and proliferation in human pancreatic cancer cells SW1990
Hong YU ; Junxing HUANG ; Chaofu WANG ; Daren SHI
Chinese Journal of Pancreatology 2012;12(1):22-25
		                        		
		                        			
		                        			ObjectiveTo investigate the effect of Smad7 antisense oligodeoxynucleotide (ASODN) on proliferation in human pancreatic cancer cell line SW1990,with a focus on the expression of matrix metalloproteinase-2(MMP-2) and tissue inhibitor of metalloproteinase-2 (TIMP-2).To explore the underlying mechanism of the role of Smad7 in the pathogenesis and development of pancreatic cancer.MethodsSmad7 ASODN was transfected into SW1990 cells through lipofectamine.Nosense oligodeoxynucleotide (NSODN),ASODN and lipofectamine was used as control. The transfection efficiency was assessed by fluorescence microscopy and flow cytometry.The expressions of Smad7,MMP-2 and TIMP-2 in transfected cells were detectedby RT-PCR and Western blot.Cell viability was assessed by dimethyl thiazoldiphenyltetrazoliumbromide (MTT) method. Results Smad7 was expressed in SW1990 cells.The transfection efficiency of SW1990 was 81.2%.The expressions of Smad7 mRNA were 0.34 ± 0.06,0.95 ±0.07,1.03 ± 0.11 in transfected group,ASODN and lipofectamine group; and the expressions of MMP-2 mRNAwere 0.54 ± 0.08,1.15 ± 0.13,1.27 ± 0.16 ; and the expressions of TIMP - 2 mRNA were 0.26 ±0.07,0.72 ± 0.13,0.78 ± 0.17,the mRNA expressions were significantly reduced in Smad7 ASODN transfected group,compared with other two groups (P <0.01 ).The expressions of Smad7 protein were 0.14 ± 0.03,0.29 ± 0.05,0.28 ± 0.07 in transfected group,ASODN and lipofectamine group; the expressions of MMP-2 protein were 0.17 ±0.02,0.29 ±0.05,0.31 ±0.04,and the expressions of TIMP-2 protein were 0.20 ± 0.03,0.41 ± 0.11,0.43 ± 0.09,the protein expressions were significantly reduced in Smad7 ASODN transfected group,compared with other two groups (P <0.01 ).The A490 values of proliferation were 0.83 ± 0.03,1.02 ±0.02,0.99 ±0.02 in transfected group,ASODN and lipofectamine group,the proliferation were significantly reduced in Smad7 ASODN transfected group,compared with other two groups (P <0.01 ).ConclusionsSmad7 ASODN could effectively inhibit the expressions of Smad7,therefore decrease the expressions of MMP-2,TIMP-2 and reduce the proliferation.
		                        		
		                        		
		                        		
		                        	
4.Clinical implications of positive peritoneal cytology in endometrial cancer
Yulan REN ; Huaying WANG ; Boer SHAN ; Bo PING ; Daren SHI
Chinese Journal of Obstetrics and Gynecology 2011;46(8):595-599
		                        		
		                        			
		                        			Objective To evaluate the clinical significance of positive peritoneal cytology in patients with endometrial cancer.Methods The records of 315 patients with endometrial cancer who were operated at Cancer Hospital, Fudan University between January 1996 and December 2008 were reviewed.Peritoneal cytology were performed and diagnosed in all patients.Factors related with peritoneal cytology were analyzed by correlation analysis.Log-rank test and Cox regression test was used for the analysis of prognosis,respectively.Results (1) Peritoneal cytology were positive in 30 (9.5%) patients.Positive peritoneal cytology was associated with pathological subtype ( P = 0.013 ), stage ( P = 0.000 ), myometrial invasion ( P =0.012), lymph-vascular space invasion ( P = 0.012 ), serosal involvement ( P = 0.004 ), cervical involvement ( P = 0.016), adnexal involvement ( P = 0.000), and omental involvement ( P = 0.000), with no association with grade ( P = 0.152 ) and lymph node metastasis ( P = 0.066 ).( 2 ) Three-year overall survival (OS) and progression-free survival(PFS) were 93.0% and 85.5% ,respectively.Positive peritoneal cytology, surgical stage, pathological subtype, myometrial invasion, grade, and lymph-vascular space invasion were significantly associated with worse prognosis by univariate analysis ( P < 0.05 ), while only surgical-pathology stage and myometrial invasion were independent prognostic factors by multivariate analysis ( P < 0.05 ).For 30 cases with positive peritoneal cytology, the patients with no high risk factors shown significantly prognoses better than those with any risk factors.The results shown that for patients with late stage (stage Ⅲ - Ⅳ ) endometrial cancer with positive peritoneal cytology was significantly associated with the worse OS and PFS by multivariate analysis ( P = 0.006).Conclusions Positive peritoneal cytology was associated with serosal involvement, cervical involvement, adnexal involvement, omental involvement, and late stage.Therefore, peritoneal cytology should be performed and reported separately as a part of full surgical staging procedure.
		                        		
		                        		
		                        		
		                        	
5.Clinical significance of Her-2/neu status in patients with uterine papillary serous carcinoma
Yulan REN ; Huaying WANG ; Xiaoyan ZHOU ; Boer SHAN ; Wentao YANG ; Lei SHEN ; Daren SHI
Chinese Journal of Obstetrics and Gynecology 2010;45(5):367-371
		                        		
		                        			
		                        			Objective The purpose of this study was to evaluate gene amplification by chromogenic in situ hybridization (CISH) and the protein expression of Her-2/neu gene in patients with uterine papillary serous carcinoma ( UPSC) and to determine its prognostic value.Methods Thirty-six patients with confirmed pathologic diagnosis of UPSC in Cancer Hospital of Fudan University from Jan.1996 to Jan.2006,were analysed retrospectively.CISH was performed to assess Her-2/neu gene amplification,and protein expression was evaluated by immunohistochemistry (IHC).The prognostic factors were analyzed by log-rank test or Cox proportional hazard model.Results Among 36 cases with UPSC,13 patients (36.1% ) showed moderate staining (++) to strong staining (+++) for Her-2/neu protein,while amplification of the Her-2/neu gene by CISH was observed in 4 of the 36 (11.1% ) cases.Her-2/neu protein over-expression was significantly associated with advanced surgical stage and worse prognosis by univariate analysis ( P = 0.030 and P = 0.002,respectively),while the multivariate analysis shown that only Her-2/neu protein over-expression and deep myometrial invasion were associated with a poor prognosis ( P < 0.05 ).In 13patients with Her-2/neu protein over-expression,the mean survival period with chemotherapy was shorter than those without chemotherapy (20 vs.42 months,P = 0.370 ).Conclusion Her-2/neu protein over-expression is significantly associated with advanced surgical stage UPSC and poor survival outcome,and might reduce the chemotherapy sensitivity.
		                        		
		                        		
		                        		
		                        	
6.BCL10 expression and chromosomal aberration in primary cutaneous marginal zone B-cell lymphoma
Baizhou LI ; Yunyi KONG ; Wentao YANG ; Xiaoyan ZHOU ; Yuezhen FAN ; Hongfen LU ; Daren SHI
Chinese Journal of Dermatology 2008;41(6):374-376
		                        		
		                        			
		                        			Objective To study the expression of BCL10 and associated chromosomal aberration in primary cutaneous marginal zone B-cell lymphoma (PCMZL). Methods Tissue specimens were collected from 17 patients with PCMZL. Immunohistochemistry was used to detect the expression of BCL10. Fluorescence in situ hybridization (FISH) was performed to examine the presence of API2-MALT1 fusion gene and chromosomal aberration in BCL10, MALT1 as well as IgH genes in these cases. Results Of these patients,94.1% (16/17) expressed BCL10 protein. The cytoplasmic expression of BCL10 was observed in 64.7% (11/17) of the patients, and nuclear expression in 29.4% (5/17). As shown by FISH test, neither API2-MALT1 fusion gene nor chromosomal aberration in BCL10, MALT1 or IgH genes was present in these patients. Conclusions Compared with MALT lymphomas originating from tissues other than skin, PCMZL is uncommonly associated with chromosomal abnormalities; it is possible that there are unknown factors contributing to its tumorigenesis. Nuclear BCL10 is unrelated to the presence of chromosomal aberration in BCL10, MALT1 or IgH genes. Further follow-up is required to clarify the association between nucle ar BCL10 and poor prognosis of PCMZL.
		                        		
		                        		
		                        		
		                        	
7.Combined treatment and prognostic factors for stage Ⅲ and Ⅳ endometrial carcinoma
Yulan REN ; Hnaying WANG ; Daren SHI ; Wentao YANG ; Zhi SUN ; Yun CHEN
Chinese Journal of Obstetrics and Gynecology 2008;43(7):523-527
		                        		
		                        			
		                        			Objective To evaluate prognostic factors and treatment of patients with advanced stage endometrial cancer. Methods One hundred and eighteen patients with advanced stage endometrial cancer were treated in our hospital between January 1996 and December 2006. The treatment and prognosis were retrospectively analyzed. The mean follow-up time was 26 months. Results During the follow-up, 33 cases (28.0%) died and 25 patients(21.2% ) had disease progression. The 3-year overall survival for patients with stage Ⅲ and stage Ⅳ was 78. 3% and 39. 4%, and for endometrioid and nonendometrioid endometrial carcinoma was 69. 3% and 42. 0%, respectively. Four patients with positive cytology only were followed closely after surgery and were free of disease up to the report time. Patients with late stages, deep myometrial invasion, nonendometrioid endometrial cancer, poor differentiation, without lymphadenectomy and without radiochemotherapy after surgery were associated with a worse prognosis by univariate analysis (P < 0. 05 ),while in a multivariate analysis only late stages and deep myometrial invasion were associated with a poor prognosis ( P < 0. 05 ). The patients who received lymphadenectomy and whose residual disease after the surgery was less than 1 cm had better prognoses than those otherwise(P <0. 05). The patients who received postoperative radiochemotherapy had better prognoses than those who did not ( P <0. 05 ). Conclusions Pathological stage and myometrial invasion are independent prognostic factors for late stage endometrial cancer. Satisfactory cytoreduction surgery and lymphadenectomy, followed by postoperative radiochemotherapy, except for stage Ⅲa patients with positive cytology only, are recommended in order to improve prognosis.
		                        		
		                        		
		                        		
		                        	
8.Detection of bone marrow involvement using flow cytometry in B cell lymphoma
Zhiyu CHEN ; Xiaoyan ZHOU ; Xiangqin WENG ; Daren SHI
China Oncology 2006;0(07):-
		                        		
		                        			
		                        			0.05).(4) The subtypes of 4 cases of B-cell lymphoma diagnosed by cytology originally were determined by analyzing immunophenotype of their bone marrow involvement.Conclusions:Flow cytometry is an effective method for detecting bone marrow involvement in B-cell lymphoma and is superior to cytomorphology;Bone marrow involvement detected by FCM can be useful for helping diagnosis.The relevance of bone marrow involvement in different types of untreated B-cell lymphoma patients with clinical presentations and response to treatment should be further studied in more patients.
		                        		
		                        		
		                        		
		                        	
9.Clinical signifi cance of 3 different approaches in the detection of bone marrow involvement in B cell lymphoma
Zhiyu CHEN ; Xiaoyan ZHOU ; Taiming ZHANG ; Daren SHI
China Oncology 2006;0(10):-
		                        		
		                        			
		                        			Background and purpose:Bone marrow cytomorphology is the main approach for determination of bone marrow involvement in patients with malignant lymphomas. In recent years, with the development of detection of cellular surface markers and molecular biology, flow cytometry (FCM) and polymerase chain reaction (PCR) were gradually applied in the detection of bone marrow in malignant lymphomas. Because such systematic research has not been done domestically , we performed a study to compare diagnostic value and clinipathological signifi cance of cytomorphology of bone marrow aspirates, immunophenotype detected by flow cytometry and immunoglobulin heavy chain gene rearrangement detected by polymerase chain reaction in bone marrow of B cell lymphomas. Methods: Bone marrow cytomorphology, FCM and PCR were simultaneously carried out in 75 bone marrows of B cell lymphoma and compared with each other. Results:(1)16 were demonstrated by cytomorphology, 36 by FCM, 33 by PCR. The positive rates were 21.3%, 48% and 44% respectively. The differences among these three methods have statistical signifi cance (P
		                        		
		                        		
		                        		
		                        	
10.The structure, expression and function prediction of DAZAP2, a down-regulated gene in multiple myeloma.
Yiwu SHI ; Saiqun LUO ; Jianbin PENG ; Chenghan HUANG ; Daren TAN ; Weixin HU
Genomics, Proteomics & Bioinformatics 2004;2(1):47-54
		                        		
		                        			
		                        			In our previous studies, DAZAP2 gene expression was down-regulated in untreated patients of multiple myeloma (MM). For better studying the structure and function of DAZAP2, a full-length cDNA was isolated from mononuclear cells of a normal human bone marrow, sequenced and deposited to Genbank (AY430097). This sequence has an identical ORF (open reading frame) as the NM_014764 from human testis and the D31767 from human cell line KG-1. Phylogenetic analysis and structure prediction reveal that DAZAP2 homologues are highly conserved throughout evolution and share a polyproline region and several potential SH2/SH3 binding sites. DAZAP2 occurs as a single-copy gene with a four-exon organization. We further noticed that the functional DAZAP2 gene is located on Chromosome 12 and its pseudogene gene is on Chromosome 2 with electronic location of human chromosome in Genbank, though no genetic abnormalities of MM have been reported on Chromosome 12. The ORF of human DAZAP2 encodes a 17-kDa protein, which is highly similar to mouse Prtb. The DAZAP2 protein is mainly localized in cytoplasm with a discrete pattern of punctuated distribution. DAZAP2 may associate with carcinogenesis of MM and participate in yet-to-be identified signaling pathways to regulate proliferation and differentiation of plasma cells.
		                        		
		                        		
		                        		
		                        			Amino Acid Sequence
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		                        			Base Sequence
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		                        			Chromosomes, Human, Pair 12
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		                        			genetics
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		                        			Chromosomes, Human, Pair 2
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		                        			genetics
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		                        			Cytoplasm
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		                        			metabolism
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		                        			DNA Primers
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		                        			DNA, Complementary
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		                        			genetics
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		                        			Down-Regulation
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		                        			Gene Components
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		                        			Humans
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		                        			Likelihood Functions
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		                        			Models, Genetic
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		                        			Molecular Sequence Data
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		                        			Multiple Myeloma
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		                        			genetics
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		                        			metabolism
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		                        			Phylogeny
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		                        			Pseudogenes
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		                        			genetics
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		                        			RNA-Binding Proteins
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		                        			genetics
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		                        			metabolism
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		                        			Sequence Alignment
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		                        			Sequence Analysis, DNA
		                        			
		                        		
		                        	
            
Result Analysis
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