OSov: An Interactive Web Server to Evaluate Prognostic Biomarkers for Ovarian Cancer

Ovarian cancer is one of the most aggressive and highly lethal gynecological cancers. The purpose of our study is to build a free prognostic web server to help researchers discover potential prognostic biomarkers by integrating gene expression profiling data and clinical follow-up information of ovarian cancer. We construct a prognostic web server OSov (Online consensus Survival analysis for Ovarian cancer) based on RNA expression profiles. OSov is a user-friendly web server which could present a Kaplan–Meier plot, forest plot, nomogram and survival summary table of queried genes in each individual cohort to evaluate the prognostic potency of each queried gene. To assess the performance of OSov web server, 163 previously published prognostic biomarkers of ovarian cancer were tested and 72% of them had their prognostic values confirmed in OSov. It is a free and valuable prognostic web server to screen and assess survival-associated biomarkers for ovarian cancer.

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OScc: an online survival analysis web server to evaluate the prognostic value of biomarkers in cervical cancer

Future Oncology ◽

10.2217/fon-2019-0412 ◽

2019 ◽

Vol 15 (32) ◽

pp. 3693-3699 ◽

Cited By ~ 3

Author(s):

Qiang Wang ◽

Lu Zhang ◽

Zhongyi Yan ◽

Longxiang Xie ◽

Yang An ◽

...

Keyword(s):

Cervical Cancer ◽

Web Server ◽

Gene Expression Omnibus ◽

The Cancer Genome Atlas ◽

Prognostic Biomarkers ◽

P Value ◽

Kaplan Meier ◽

Cancer Genome Atlas ◽

The Web

Aim: To establish a web server that can mutually validate prognostic biomarkers of cervical cancer. Methods: Four datasets including expression profiling and relative clinical follow-up data were collected from Gene Expression Omnibus and The Cancer Genome Atlas. The web server was developed by R software. Results: The web server was named OScc including 690 patients and can be accessed at http://bioinfo.henu.edu.cn/CESC/CESCList.jsp . The Kaplan–Meier survival curves with log-rank p-value and hazard ratio will be generated of interested gene in OScc. Compared with previous predictive tools, OScc had the advantages of registration-free, larger sample size and subgroup analysis. Conclusion: The OScc is highly valuable to perform the preliminary assessment and validation of new or interested prognostic biomarkers for cervical cancer.

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Three Years Follow-Up Study Showed Prenatal Methamphetamine Exposure May Cause Chronic Abnormalities In Transcriptomic Pattern

10.21203/rs.3.rs-668566/v1 ◽

2021 ◽

Author(s):

Arvin Haghighatfard ◽

Soha Seifollahi ◽

Pegah Rajabi ◽

Niloofar Rahmani ◽

Rojin Ghannadzadeh

Keyword(s):

Gene Expression ◽

Gene Expression Profiling ◽

Expression Profiling ◽

Expression Profiles ◽

Expression Patterns ◽

Rna Extraction ◽

Childbearing Age ◽

Methamphetamine Use ◽

Methamphetamine Use Disorder

Abstract Background: The high rate of methamphetamine use disorder among young adults and women of childbearing age makes it imperative to clarify the long-term effects of Methamphetamine exposure on the offspring. Behavioral and cognitive problems had been reported in children with parental Methamphetamine exposure (PME). The present study aimed to assess the acute and chronic effects of PME in molecular regulations and gene expression profiles of children during their first years of life.Methods: All subjects were recruited before birth, and sampling was conducted from the first ten days of birth, twelve months, twenty months, and thirty-six months of age. Finally, 2658 children with PME and 3573 normal children had been finished the follow-up. RNA extraction was operated from blood samples and gene expression profiling was conducted by using the Affymetrix GeneChip Human Genome U133 plus 2.0 Array Platform. Gene expression data were confirmed by Real-time PCR. Results: Gene expression profiling during thirty-six months showed several constant mRNA level alterations in children with PME compared with normal. These genes are involved in several gene ontologies and pathways involved with the immune system, neuronal functions, and bioenergetic metabolism. It seems that Methamphetamine use disorder before and during the pregnancy period may affect the expression profile of children, and these changes could remain years after birth. Affected genes have some similarities with the gene expression patterns of addiction, psychiatric disorders, neurodevelopmental disabilities, and immune deficiencies. Conclusion: Findings may shed light on the molecular effects of prenatal methamphetamine exposure and may lead to new psychological and somatic caring protocols for these children based on their potential abnormalities.

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Abstract 17607: MicroRNA Expression Profiles in Endomyocardial Biopsies From Patients With Myocarditis - Association With Left Ventricular Function and Clinical Events

Circulation ◽

10.1161/circ.132.suppl_3.17607 ◽

2015 ◽

Vol 132 (suppl_3) ◽

Author(s):

Christian Besler ◽

Daniel Urban ◽

Stefan Watzka ◽

Karin Klingel ◽

Reinhard Kandolf ◽

...

Keyword(s):

Dilated Cardiomyopathy ◽

Expression Profiles ◽

Left Ventricular ◽

Lv Function ◽

Rt Pcr ◽

Skeletal Muscle Function ◽

Cardiovascular Pathology ◽

Clinical Events ◽

Kaplan Meier

Background: Myocarditis represents an important cause of chronic dilated cardiomyopathy. Predicting the clinical course of patients with myocarditis is difficult and the prognostic value of current histological markers remains controversial. We tested whether expression of selected microRNAs (miRNAs) in endomyocardial biopsies is related to left ventricular (LV) function and clinical events in patients with myocarditis. Methods: Endomyocardial biopsies were obtained from patients with non-inflammatory dilated cardiomyopathy (n=22) and histologically proven myocarditis (n=81). Based on literature search, we predefined a set of 6 miRNAs implicated in inflammation (miR-155, miR-146b), heart failure (miR-21, miR-133a), endothelial cell (miR-126) and skeletal muscle function (miR-206). Expression of these miRNAs in endomyocardial biopsies was quantified by RT-PCR. Results: Expression of miR-133a, miR-206 and miR-155 was markedly upregulated in endomyocardial biopsies from patients with myocarditis as compared to patients with dilated cardiomyopathy, irrespective of viral or non-viral etiology. Levels of miR-133a (R=0,68, P<0,01) and miR-155 (R=0,65, P<0,01) significantly correlated with CD68 cell count in endomyocardial biopsies from patients with myocarditis. Patients with myocarditis and preserved LV function at study entry displayed higher endomyocardial expression of miR-133a than patients with reduced LV function. Higher expression levels of miR-133a were associated with improved LV function during a mean follow-up of 3,1 years. Importantly, in a Kaplan-Meier estimate, patients with myocarditis and miR-133a levels above median showed longer survival free of death and malignant arrhythmias. Conclusion: The present study demonstrates that in a predefined set of miRNAs, relevant to cardiovascular pathology, endomyocardial miR-133a levels correlate with macrophage infiltration, improved LV function and clinical outcome in a comparatively large cohort of patients with histologically proven myocarditis. miR-133a may serve as a potential novel biomarker and therapeutic target in human myocarditis.

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Use of microRNA (miR) expression profiling to identify distinct subclasses of triple-negative breast cancers (TNBC).

Journal of Clinical Oncology ◽

10.1200/jco.2012.30.15_suppl.1007 ◽

2012 ◽

Vol 30 (15_suppl) ◽

pp. 1007-1007 ◽

Cited By ~ 1

Author(s):

Charles L. Shapiro ◽

Luciano Cascione ◽

Pierluigi Gasparini ◽

Francesca Lovat ◽

Stefania Carasi ◽

...

Keyword(s):

Breast Cancer ◽

Overall Survival ◽

Expression Profiling ◽

Clustering Algorithm ◽

Medical Center ◽

Expression Profiles ◽

Normal Breast ◽

Rank Test ◽

Cancer Data

1007 Background: TNBC is divided into basal and non-basal subclasses. To further subclassify TNBC we performed microRNA (miR) expression profiles and linked them to patient overall survival. Methods: During 1996-2005, 365 consecutive TNBC (phenotypically estrogen, progesterone and HER2 negative by immunohistochemistry [IHC]) were identified from the NCCN Breast Cancer Data Base/Tumor Registry at OSU Medical Center. One hundred fifty-eight (43%) formalin-fixed paraffin embedded (FFPE) breast cancer and 40 normal breast tissue blocks were available and tissue cores were obtained for RNA. RNA was isolated using the Ambion recoverall total nucleic acid isolation kit and the expression of ~700 miRs was assessed for each sample using the nanoString nCounter method. A consensus-clustering algorithm (ConsensusClusterPlus, Bioconductor www.bioconductor.org) was used to identify subclasses of TNBC and Kaplan-Meier overall survival curves were compared using the log-rank test. Censoring occurred at the date of death from causes other than breast cancer or at time of the last known follow-up, whichever occurred first. The median follow-up was 67 mo. (range 4-171 mo.). Results: The median age was 52 yrs. (range 20-84 yrs.); 81% white and 9% African-American; stages I, II, and III were 31%, 54% and 15%, respectively; and most patients received adjuvant anthracycline-based regimens with (25%) or without taxanes (75%). The algorithm identified 5 distinct subclasses; 1 clustering with normal breast miR expression whereas the other 4 each had a unique pattern of deregulated miRs. The median overall survivals were significantly different across the 5 cancer subclasses (log-rank p=0.028) (Table). Conclusions: miR expression profiling identifies and discriminates 5 TNBC subclasses, which do not coincide with those identified as basal and non-basal by IHC. Molecular analyses are ongoing to associate the miR-based subclasses with specific clinical features or the expression of specific pathways. [Table: see text]

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DBtRend: A Web-Server of tRNA Expression Profiles from Small RNA Sequencing Data in Humans

Genes ◽

10.3390/genes12101576 ◽

2021 ◽

Vol 12 (10) ◽

pp. 1576

Author(s):

Jin-Ok Lee ◽

Minho Lee ◽

Yeun-Jun Chung

Keyword(s):

Small Rna ◽

Molecular Subtype ◽

Expression Profiles ◽

Web Server ◽

Gene Expression Omnibus ◽

The Cancer Genome Atlas ◽

Small Rna Sequencing ◽

Sequencing Data ◽

Microrna Sequencing ◽

User Friendly

Transfer RNA (tRNA), a key component of the translation machinery, plays critical roles in stress conditions and various diseases. While knowledge regarding the importance of tRNA function is increasing, its biological roles are still not well understood. There is currently no comprehensive database or web server providing the expression landscape of tRNAs across a variety of human tissues and diseases. Here, we constructed a user-friendly and interactive database, DBtRend, which provides a profile of mature tRNA expression across various biological conditions by reanalyzing the small RNA or microRNA sequencing data from the Cancer Genome Atlas (TCGA) and NCBI’s Gene Expression Omnibus (GEO) in humans. Users can explore not only the expression values of mature individual tRNAs in the human genome, but also those of isodecoders and isoacceptors based on our specific pipelines. DBtRend provides the expressed patterns of tRNAs, the differentially expressed tRNAs in different biological conditions, and the information of samples or patients, tissue types, and molecular subtype of cancers. The database is expected to help researchers interested in functional discoveries of tRNAs.

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The Role of Liver Resection at the Time of Secondary Cytoreduction in Patients With Recurrent Ovarian Cancer

International Journal of Gynecological Cancer ◽

10.1097/igc.0000000000000026 ◽

2014 ◽

Vol 24 (1) ◽

pp. 70-74 ◽

Cited By ~ 12

Author(s):

Valentin Kolev ◽

Elena B. Pereira ◽

Myron Schwartz ◽

Umut Sarpel ◽

Sasan Roayaie ◽

...

Keyword(s):

Ovarian Cancer ◽

Survival Analysis ◽

Liver Resection ◽

Ovarian Carcinoma ◽

Cytoreductive Surgery ◽

Residual Disease ◽

Recurrent Ovarian Cancer ◽

Kaplan Meier

ObjectiveThe aim of this study is to determine the role of liver metastatectomy in the morbidity and survival of patients with recurrent ovarian carcinoma.MethodsWe retrospectively reviewed the records of all patients who had undergone hepatic resection for liver metastases from ovarian carcinoma at the time of cytoreductive surgery at our institution from 1988 to 2012. The Kaplan-Meier method was used for survival analysis. A total of 76 patients met the inclusion criteria and had undergone liver resection as part of cytoreductive surgery for ovarian carcinoma during the study period. Of these 76 patients, 27 underwent liver resection at the time of secondary cytoreduction, and these patients that are the focus of this analysis.ResultsMedian overall survival for the study group from the time of diagnosis to the last follow-up or death was 56 months (range, 12–249 months). Twenty died of the disease with an overall median survival of 12 months from the time of the liver resection (2–190 months), and 7 patients were alive with the disease at the time of the last follow-up. Based on Kaplan-Meier survival analysis, the factors associated with the longest survival after the liver resection (2–190 months) were the interval from the primary surgery of less than 24 months versus more than 24 months (P= 0.044) and secondary cytoreduction to residual disease of less than 1 cm (P= 0.014).ConclusionsBased on our analysis of a single institution’s series of ovarian cancer patients with hepatic metastasis, liver resection is feasible and safe and should be considered as an option in selected patients at the time of secondary cytoreduction.

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Analysis of clinical features of ovarian cancer (OC) and breast cancer (BC) among BRCA-mutated (BRCA+) and sporadic (NH) double tumors.

Journal of Clinical Oncology ◽

10.1200/jco.2012.30.15_suppl.e12037 ◽

2012 ◽

Vol 30 (15_suppl) ◽

pp. e12037-e12037

Author(s):

Maria Ornella Nicoletto ◽

Lucia Borgato ◽

Grazia Artioli ◽

Alessandra Perin ◽

Fable Zustovich ◽

...

Keyword(s):

Breast Cancer ◽

Ovarian Cancer ◽

Locally Advanced ◽

Significant Risk ◽

Rank Test ◽

Pathological Features ◽

Exact Test ◽

Kaplan Meier

e12037 Background: Women BRCA+ are at significant risk of developing both OC and BC. Double tumors could arise also in NH patients. Whether the clinical outcome of double OC and BC is different in BRCA+ and in NH subjects is unknown. Methods: The databases of the Istituto Oncologico Veneto (IOV), Medical Oncology Department of Mirano (VE) and Thiene (VI) were searched to identify the clinical and pathological features of (BC) and (OC) arisen in BRCA+ subjects as well as patients with both malignancy but tested negative/no-tested/unknown for BRCA1/2 mutation (NH). The primary endpoint was to establish if OC instead of BC needs a more intensive follow-up because it principally affects patient’s prognosis. Patients were censored at last follow-up or death (any cause) for determination of overall survival (OS). OS estimates were determined using the Kaplan-Meier method and compared by means of log-rank test. The Fisher’s exact test and the t-test were used to compare frequencies and means between groups, respectively. Results: 24/31 (77%) BRCA+ and 30/49 (61%) NH had BC as their first malignancy (p=0.15). Among NH, 20 were BRCA test negative, 20 were untested and 9 unknown. BRCA+ were younger than NH at diagnosis of first malignancy (mean age 51 vs 56y, p=0.055). Bilateral BC was more frequent in BRCA+ than in NH (78.6% vs 28.6% p=0.001). Stage III-IV OC at diagnosis were 74% in BRCA vs 61% in NH (p=0.34). Locally advanced (stage II-III) BC was significantly more frequent in BRCA+ vs NH (75% vs 42%, p=0.03). No OS difference was observed between BRCA+ and NH subjects (P=0.99). Death for progression of ovarian cancer was observed in 11/31 (35%) in BRCA+ vs 10/49 (20%) patients in NH (p=0.19). No progression of breast cancer was reported in either groups. Conclusions: OC is the killer malignancy among patients affected by OC and BC, both in BRCA+ and in NH subjects. In patients with double tumors, irrespective of their pathological features, a more conserving management for BC and an intensive follow-up for OC are suggested.

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OSucs: An Online Prognostic Biomarker Analysis Tool for Uterine Carcinosarcoma

Genes ◽

10.3390/genes11091040 ◽

2020 ◽

Vol 11 (9) ◽

pp. 1040

Author(s):

Yang An ◽

Qiang Wang ◽

Fengjie Sun ◽

Guosen Zhang ◽

Fengling Wang ◽

...

Keyword(s):

Molecular Subtype ◽

Expression Profiles ◽

Gene Expression Profiles ◽

Prognostic Biomarkers ◽

Analysis Tool ◽

Uterine Carcinosarcoma ◽

Biomarker Analysis ◽

Therapy Strategies ◽

Transcription Factor 4

Background: Uterine carcinosarcoma (UCS) is a type of rare and aggressive tumor. The standard treatment for UCS involves surgical treatment followed by radiochemotherapy. Clinical outcomes of UCS patients are poor due to high metastasis and relapse rate. Therefore, new targeted therapy strategies for UCS are needed. Because UCS is highly heterogenous, it is critical to identify and develop prognostic biomarkers to distinguish molecular subtypes of UCS for better treatment guidance. Methods: Using gene expression profiles and clinical follow-up data, we developed an online consensus survival analysis tool named OSucs. This web tool allows researchers to conveniently analyze the prognostic abilities of candidate genes in UCS. Results: To test the reliability of this server, we analyzed five previously reported prognostic biomarkers, all of which showed significant prognostic impacts. In addition, ETV4 (ETS variant transcription factor 4), ANGPTL4 (Angiopoietin-like protein 4), HIST1H1C (Histone cluster 1 H1 family member c) and CTSV (Cathepsin V) showed prognostic potential in a molecular subtype-specific manner. Conclusion: We built a platform for researchers to analyze if genes have prognostic potentials in UCS.

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Intraperitoneal Chemotherapy for Ovarian Carcinoma: Results of Long-Term Follow-Up

Journal of Clinical Oncology ◽

10.1200/jco.2002.20.3.694 ◽

2002 ◽

Vol 20 (3) ◽

pp. 694-698 ◽

Cited By ~ 41

Author(s):

Richard R. Barakat ◽

Paul Sabbatini ◽

Dharmendra Bhaskaran ◽

Margarita Revzin ◽

Alex Smith ◽

...

Keyword(s):

Ovarian Cancer ◽

Prognostic Factors ◽

Residual Disease ◽

Term Survival ◽

Long Term Survival ◽

Cox Proportional Hazard ◽

Kaplan Meier ◽

Long Term Follow Up

PURPOSE: To determine long-term survival and predictors of recurrence in a retrospective cohort of patients with epithelial ovarian cancer treated with intraperitoneal (IP) chemotherapy. PATIENTS AND METHODS: Records were reviewed of 433 patients who received IP therapy for ovarian cancer between 1984 and 1998; follow-up data were available for 411 patients. IP therapy was provided as consolidation therapy (n = 89), or for treatment of persistent (n = 310) or recurrent (n = 12) disease after surgery and initial systemic therapy; therapy usually consisted of platinum-based combination therapy. Statistical analysis included tests for associations between potential prognostic factors, and between prognostic factors and survival. Survival probabilities were estimated by Kaplan-Meier methods, and prognostic factors for survival were evaluated by a Cox proportional hazard model. RESULTS: The mean age of patients was 52 years (range, 25 to 76 years). Distribution by stage and grade was as follows: stage I, 7; II, 24; III, 342; IV, 52; not available (NA), 8; and grade 1, 30; 2, 99; and 3, 289; NA, 15. The median survival from initiation of IP therapy by residual disease was none, 8.7 years; microscopic, 4.8 years; less than 1 cm, 3.3 years; more than 1 cm, 1.2 years. In a multivariate analysis, the only significant predictors of long-term survival were grade and size of residual disease at initiation of IP therapy. CONCLUSION: Prolonged survival was observed in selected patients receiving IP platinum-based therapy. It is not possible to determine the contribution of IP therapy to survival in this study. A relationship between size of disease at the initiation of IP therapy and long-term survival was demonstrated.

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