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RNA Biology Nov 2020Non-coding RNAs occupy a significant fraction of the human genome. Their biological significance is backed up by a plethora of emerging evidence. One of the most robust...
Non-coding RNAs occupy a significant fraction of the human genome. Their biological significance is backed up by a plethora of emerging evidence. One of the most robust approaches to demonstrate non-coding RNA's biological relevance is through their prognostic value. Using the rich gene expression data from The Cancer Genome Altas (TCGA), we designed Advanced Expression Survival Analysis (AESA), a web tool which provides several novel survival analysis approaches not offered by previous tools. In addition to the common single-gene approach, AESA computes the gene expression composite score of a set of genes for survival analysis and utilizes permutation test or cross-validation to assess the significance of log-rank statistic and the degree of over-fitting. AESA offers survival feature selection with post-selection inference and utilizes expanded TCGA clinical data including overall, disease-specific, disease-free, and progression-free survival information. Users can analyse either protein-coding or non-coding regions of the transcriptome. We demonstrated the effectiveness of AESA using several empirical examples. Our analyses showed that non-coding RNAs perform as well as messenger RNAs in predicting survival of cancer patients. These results reinforce the potential prognostic value of non-coding RNAs. AESA is developed as a module in the freely accessible analysis suite MutEx. ACC: Adrenocortical Carcinoma (n = 92); BLCA: Bladder Urothelial Carcinoma (n = 412); BRCA: Breast Invasive Carcinoma (n = 1098); CESC: Cervical Squamous Cell Carcinoma and Endocervical Adenocarcinoma (n = 307); CHOL: Cholangiocarcinoma (n = 51); COAD: Colon Adenocarcinoma (n = 461); DLBC: Lymphoid Neoplasm Diffuse Large B-cell Lymphoma (n = 58); ESCA: Oesophageal Carcinoma (n = 185); GBM: Glioblastoma Multiforme (n = 617); HNSC: Head and Neck Squamous Cell Carcinoma (n = 528); KICH: Kidney Chromophobe (n = 113); KIRC: Kidney Renal Clear Cell Carcinoma (n = 537); KIRP: Kidney Renal Papillary Cell Carcinoma (n = 291); LAML: Acute Myeloid Leukaemia (n = 200); LGG: Brain Lower Grade Glioma (n = 516); LIHC: Liver Hepatocellular Carcinoma (n = 377); LUAD: Lung Adenocarcinoma (n = 585); LUSC: Lung Squamous Cell Carcinoma (n = 504); MESO: Mesothelioma (n = 87); OV: Ovarian Serous Cystadenocarcinoma (n = 608) PAAD: Pancreatic Adenocarcinoma (n = 185); PCPG: Pheochromocytoma and Paraganglioma (n = 179); PRAD: Prostate Adenocarcinoma (n = 500); READ: Rectum Adenocarcinoma (n = 172); SARC: Sarcoma (n = 261); SKCM: Skin Cutaneous Melanoma (n = 470); STAD: Stomach Adenocarcinoma (n = 443); TGCT: Testicular Germ Cell Tumours (n = 150); THCA: Thyroid Carcinoma (n = 507) THYM: Thymoma (n = 124); UCEC: Uterine Corpus Endometrial Carcinoma (n = 560); UCS: Uterine Carcinosarcoma (n = 57); UVM: Uveal Melanoma (n = 80).
Topics: Biomarkers, Tumor; Computational Biology; Databases, Genetic; Gene Expression Profiling; Gene Expression Regulation, Neoplastic; Humans; Neoplasms; Prognosis; RNA, Long Noncoding; RNA, Untranslated
PubMed: 31607216
DOI: 10.1080/15476286.2019.1679585 -
The Tokai Journal of Experimental and... Sep 2019Peritoneal serous papillary carcinoma (PSPC) is a rare disease. It is clinically and histologically similar to progressive ovarian serous adenocarcinoma and involves...
BACKGROUND
Peritoneal serous papillary carcinoma (PSPC) is a rare disease. It is clinically and histologically similar to progressive ovarian serous adenocarcinoma and involves normal-sized ovaries, making it challenging to diagnose. In this report, we describe a case of peritoneal serous papillary carcinoma that was difficult to identify and how we made a correct diagnosis in order to begin a timely course of treatment.
CASE PRESENTATION
A 63-year-old woman with chief complaints of dizziness and abdominal pain was examined, but showed no particular abnormality. Class III cytology of the endometrium was detected through magnetic resonance imaging and a laparotomy was performed on suspicion of endometrial cancer. The patient was finally diagnosed with peritoneal serous papillary carcinoma and was treated with surgical resection and the standard indicated course of chemotherapy.
CONCLUSIONS
The diagnosis and treatment of peritoneal serous papillary carcinoma may be delayed or may not be performed unless Class III findings are detected through uterine mucosal cytology before surgery. Surgeons should not hesitate to perform laparotomy when necessary to identify and appropriately treat patients, even if abnormalities are not detected in the preoperative examination.
Topics: Chemotherapy, Adjuvant; Cystadenocarcinoma, Papillary; Cystadenocarcinoma, Serous; Cytodiagnosis; Diagnosis, Differential; Female; Humans; Laparotomy; Magnetic Resonance Imaging; Middle Aged; Ovarian Neoplasms; Peritoneal Neoplasms
PubMed: 31448396
DOI: No ID Found -
Journal of Ovarian Research Aug 2019The role of calcineurin/NFAT signaling in ovarian cancer has been unknown. NFAT was significantly overexpressed in ovarian cancer tissues and that overexpression of NFAT...
BACKGROUND
The role of calcineurin/NFAT signaling in ovarian cancer has been unknown. NFAT was significantly overexpressed in ovarian cancer tissues and that overexpression of NFAT was significantly associated with metastasis and poor prognosis on clinical tissue level. To investigate whether NFAT upstream protein, calcineurin (CN), affects the prognosis in various histological subtype of ovarian cancer (OC).
METHODS
The association between CN and clinical features was analyzed in 50 OC patients treated from 2007 to 2012. CN expression was examined using immunohistochemistry. We observed the association of CN expression with the prognosis in these patients.
RESULTS
CN expression was significantly increased in later-stage tumor tissue of serous carcinoma compared with those with early-stage. The expression of CN positively correlated with the serum cancer antigen 125 (CA125) level in ovarian clear-cell carcinoma and the serum alpha-fetoprotein (AFP) level in papillary serous cystadenocarcinoma. Particularly, higher CN expression in tumor tissues significantly correlated with reduced overall survival among patients with serous carcinoma. In addition, the serum cancer antigen 72-4 (CA72-4) level, serum carcinoembryonic antigen (CEA) levels, pathological stage, lymph node metastasis, and chemotherapeutic resistance were identified as significant prognostic factors in ovarian clear-cell carcinoma, serous carcinoma, or papillary serous cystadenocarcinoma.
CONCLUSIONS
CN is upregulated in ovarian cancer tissues with later-stage and that the expression of CN, CA72-4, and CEA was remarkably associated with poor prognosis in unique subtype of ovarian cancer. CN levels may be investigated for use as a prognostic biomarker for risk assessment in unique subtype of OC patients.
Topics: Adult; Aged; Biomarkers, Tumor; Calcineurin; Female; Gene Expression; Humans; Immunohistochemistry; Kaplan-Meier Estimate; Middle Aged; Neoplasm Metastasis; Neoplasm Staging; Ovarian Neoplasms; Prognosis; Retrospective Studies; Tumor Burden
PubMed: 31399054
DOI: 10.1186/s13048-019-0550-0 -
Journal of Surgical Case Reports Jul 2019Ovarian cancer (OC) is one of the most commonly diagnosed cancers among women. Regretfully due to its a broad spectrum of clinical behavior and challenging diagnosis...
Ovarian cancer (OC) is one of the most commonly diagnosed cancers among women. Regretfully due to its a broad spectrum of clinical behavior and challenging diagnosis most cases are diagnosed at a late stage. On rare occasions, these tumors can grow to massive sizes if left untreated, worsening the prognosis of the patient. Thanks to the advancement of medicine and diagnostic techniques, these rare cases are less frequent. Timely detection and surgery could avoid all these potentially troublesome scenarios. We report the case of a 64-year-old female with a giant 13 kg high-grade papillary serous ovarian cystadenocarcinoma, the tumor grew during a four year period and was adequately treated with surgery and is under close follow up with the oncologist. To our knowledge, this is the first case of a giant ovarian cystadenocarcinoma ever reported in Ecuador.
PubMed: 31308929
DOI: 10.1093/jscr/rjz207