Genetic and Expression Alterations in Association with the Sarcomatous Change of Cholangiocarcinoma Cells
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Screening and Identification of Key Biomarkers in Clear Cell Renal Cell Carcinoma Based on Bioinformatics Analysis
bioRxiv preprint doi: https://doi.org/10.1101/2020.12.21.423889; this version posted December 23, 2020. The copyright holder for this preprint (which was not certified by peer review) is the author/funder. All rights reserved. No reuse allowed without permission. Screening and identification of key biomarkers in clear cell renal cell carcinoma based on bioinformatics analysis Basavaraj Vastrad1, Chanabasayya Vastrad*2 , Iranna Kotturshetti 1. Department of Biochemistry, Basaveshwar College of Pharmacy, Gadag, Karnataka 582103, India. 2. Biostatistics and Bioinformatics, Chanabasava Nilaya, Bharthinagar, Dharwad 580001, Karanataka, India. 3. Department of Ayurveda, Rajiv Gandhi Education Society`s Ayurvedic Medical College, Ron, Karnataka 562209, India. * Chanabasayya Vastrad [email protected] Ph: +919480073398 Chanabasava Nilaya, Bharthinagar, Dharwad 580001 , Karanataka, India bioRxiv preprint doi: https://doi.org/10.1101/2020.12.21.423889; this version posted December 23, 2020. The copyright holder for this preprint (which was not certified by peer review) is the author/funder. All rights reserved. No reuse allowed without permission. Abstract Clear cell renal cell carcinoma (ccRCC) is one of the most common types of malignancy of the urinary system. The pathogenesis and effective diagnosis of ccRCC have become popular topics for research in the previous decade. In the current study, an integrated bioinformatics analysis was performed to identify core genes associated in ccRCC. An expression dataset (GSE105261) was downloaded from the Gene Expression Omnibus database, and included 26 ccRCC and 9 normal kideny samples. Assessment of the microarray dataset led to the recognition of differentially expressed genes (DEGs), which was subsequently used for pathway and gene ontology (GO) enrichment analysis. -
Systems and Chemical Biology Approaches to Study Cell Function and Response to Toxins
Dissertation submitted to the Combined Faculties for the Natural Sciences and for Mathematics of the Ruperto-Carola University of Heidelberg, Germany for the degree of Doctor of Natural Sciences Presented by MSc. Yingying Jiang born in Shandong, China Oral-examination: Systems and chemical biology approaches to study cell function and response to toxins Referees: Prof. Dr. Rob Russell Prof. Dr. Stefan Wölfl CONTRIBUTIONS The chapter III of this thesis was submitted for publishing under the title “Drug mechanism predominates over toxicity mechanisms in drug induced gene expression” by Yingying Jiang, Tobias C. Fuchs, Kristina Erdeljan, Bojana Lazerevic, Philip Hewitt, Gordana Apic & Robert B. Russell. For chapter III, text phrases, selected tables, figures are based on this submitted manuscript that has been originally written by myself. i ABSTRACT Toxicity is one of the main causes of failure during drug discovery, and of withdrawal once drugs reached the market. Prediction of potential toxicities in the early stage of drug development has thus become of great interest to reduce such costly failures. Since toxicity results from chemical perturbation of biological systems, we combined biological and chemical strategies to help understand and ultimately predict drug toxicities. First, we proposed a systematic strategy to predict and understand the mechanistic interpretation of drug toxicities based on chemical fragments. Fragments frequently found in chemicals with certain toxicities were defined as structural alerts for use in prediction. Some of the predictions were supported with mechanistic interpretation by integrating fragment- chemical, chemical-protein, protein-protein interactions and gene expression data. Next, we systematically deciphered the mechanisms of drug actions and toxicities by analyzing the associations of drugs’ chemical features, biological features and their gene expression profiles from the TG-GATEs database. -
Sarcomatoid Renal Cell Carcinom Atoid Renal Cell Carcinoma
Research Article Sarcomatoid renal cell carcinoma: A case series K Subashree 1*, M Susruthan 2, N Priyathersini 3, Leena Dennis Joseph 4, Sandhya Sundaram 5 1PG Student, 2,3 Assistant Professor, 4,5 Professor, Department of Pathology , Sri Ramachandra Medical College and Research Institute Porur, Chennai-116, Tamil Nadu, INDIA. Email : [email protected] Abstract Introduction: Renal cell carcinoma is the most common form of Renal malignancy. Sarcomatoid renal cell carcinoma represents a high grade dedifferentiation of Renal cell carcinoma. This phenotype can occur in all subtypes of renal cell carcinomas, including clear cell, papillary, chromophob e, and collecting duct carcinoma. Although prognosis in sarcomatoid renal cell carcinoma is known to be extremely poor, little is known about the clinicopathologic information about them. Methods and Methodology: The population of this retrospective study consisted of all patients who underwent surgery for Renal cell carcinoma between January 2010 and February 2013 in the Department of Pathology, Sri Ramachandra university and Research Institute .A total of 64 renal cell carcinoma cases were diagnosed among which 9 had sarcomatoid changes. All 9 cases were reassessed and the diagnosis was confirmed on the basis of morphologic features. Complete baseline and follow -up data were available for analysis for all 9 patients. Conclusion: Present study showed that s arcomatoid changes were seen more commonly in younger age group with male preponderance and ne crosis was a consistent feature. Sarcomatoid areas constitute 1-25% in majority of cases which makes extensive sampling an important measure. Majority of renal cell carcinomas with sarcomatoid changes ha ve a high grade and high stage. -
Rare Sarcomatoid Carcinoma of the Liver in a Patient with No History of Hepatocellular Carcinoma: a Case Report
Rare sarcomatoid carcinoma of the liver in a patient with no history of hepatocellular carcinoma: a case report Abstract Sarcomatoid carcinoma is a rare malignant tumor of unknown pathogenesis characterized by poorly differentiated carcinoma tissue containing sarcoma-like differentiation of either spindle or giant cell and rarely occurs in the gastrointestinal tract and hepatobiliary-pancreatic system.1 Primary hepatic sarcomatoid carcinoma accounts for only 0.2 % of primary malignant liver tumors, and 1.8% of all surgically resected hepatocellular carcinomas.2 The majority of hepatic sarcomatoid carcinoma cases appear to occur simultaneously with hepatocellular or cholangiocellular carcinoma.3 The preferred treatment for hepatic sarcomatoid carcinoma is surgical resection and the overall prognosis is poor.4 This case depicts a 62-year-old female who underwent initial resection of a cavernous hemangioma in 2010. Seven years after her initial diagnosis, she developed what was initially felt to be local recurrence of the hemangioma but additional diagnostic workup with a liver biopsy confirmed primary hepatic sarcomatoid carcinoma. Keywords Sarcomatoid Carcinoma, Hepatocellular Carcinoma, Primary Hepatic Sarcomatoid Carcinoma Case Report A 62-year-old female with past medical history significant for vegan diet, hypothyroidism, iron deficiency anemia, and cavernous liver hemangioma presented with weight loss and abdominal fullness for approximately one month with two days of acute altered mental status, fatigue, and weakness. Patient had a complicated gastrointestinal history and underwent surgical resection of a cavernous hemangioma in 2010. Six years later, she developed abdominal fullness with right upper quadrant pain and an abdominal ultrasound at that time suggested hemangioma recurrence. In 2017, she underwent laparoscopy with unroofing of the hemangioma, drainage of an old organizing hematoma, removal of debris, and placement of an omental patch. -
Origins and Functional Impact of Copy Number Variation in the Human Genome
doi:10.1038/nature08516 ARTICLES Origins and functional impact of copy number variation in the human genome Donald F. Conrad1*, Dalila Pinto2*, Richard Redon1,3, Lars Feuk2,4, Omer Gokcumen5, Yujun Zhang1, Jan Aerts1, T. Daniel Andrews1, Chris Barnes1, Peter Campbell1, Tomas Fitzgerald1, Min Hu1, Chun Hwa Ihm5, Kati Kristiansson1, Daniel G. MacArthur1, Jeffrey R. MacDonald2, Ifejinelo Onyiah1, Andy Wing Chun Pang2, Sam Robson1, Kathy Stirrups1, Armand Valsesia1, Klaudia Walter1, John Wei2, Wellcome Trust Case Control Consortium{, Chris Tyler-Smith1, Nigel P. Carter1, Charles Lee5, Stephen W. Scherer2,6 & Matthew E. Hurles1 Structural variations of DNA greater than 1 kilobase in size account for most bases that vary among human genomes, but are still relatively under-ascertained. Here we use tiling oligonucleotide microarrays, comprising 42 million probes, to generate a comprehensive map of 11,700 copy number variations (CNVs) greater than 443 base pairs, of which most (8,599) have been validated independently. For 4,978 of these CNVs, we generated reference genotypes from 450 individuals of European, African or East Asian ancestry. The predominant mutational mechanisms differ among CNV size classes. Retrotransposition has duplicated and inserted some coding and non-coding DNA segments randomly around the genome. Furthermore, by correlation with known trait-associated single nucleotide polymorphisms (SNPs), we identified 30 loci with CNVs that are candidates for influencing disease susceptibility. Despite this, having assessed the completeness of our map and the patterns of linkage disequilibrium between CNVs and SNPs, we conclude that, for complex traits, the heritability void left by genome-wide association studies will not be accounted for by common CNVs. -
Investigation of the Underlying Hub Genes and Molexular Pathogensis in Gastric Cancer by Integrated Bioinformatic Analyses
bioRxiv preprint doi: https://doi.org/10.1101/2020.12.20.423656; this version posted December 22, 2020. The copyright holder for this preprint (which was not certified by peer review) is the author/funder. All rights reserved. No reuse allowed without permission. Investigation of the underlying hub genes and molexular pathogensis in gastric cancer by integrated bioinformatic analyses Basavaraj Vastrad1, Chanabasayya Vastrad*2 1. Department of Biochemistry, Basaveshwar College of Pharmacy, Gadag, Karnataka 582103, India. 2. Biostatistics and Bioinformatics, Chanabasava Nilaya, Bharthinagar, Dharwad 580001, Karanataka, India. * Chanabasayya Vastrad [email protected] Ph: +919480073398 Chanabasava Nilaya, Bharthinagar, Dharwad 580001 , Karanataka, India bioRxiv preprint doi: https://doi.org/10.1101/2020.12.20.423656; this version posted December 22, 2020. The copyright holder for this preprint (which was not certified by peer review) is the author/funder. All rights reserved. No reuse allowed without permission. Abstract The high mortality rate of gastric cancer (GC) is in part due to the absence of initial disclosure of its biomarkers. The recognition of important genes associated in GC is therefore recommended to advance clinical prognosis, diagnosis and and treatment outcomes. The current investigation used the microarray dataset GSE113255 RNA seq data from the Gene Expression Omnibus database to diagnose differentially expressed genes (DEGs). Pathway and gene ontology enrichment analyses were performed, and a proteinprotein interaction network, modules, target genes - miRNA regulatory network and target genes - TF regulatory network were constructed and analyzed. Finally, validation of hub genes was performed. The 1008 DEGs identified consisted of 505 up regulated genes and 503 down regulated genes. -
Lung Equivalent Terms, Definitions, Charts, Tables and Illustrations C340-C349 (Excludes Lymphoma and Leukemia M9590-9989 and Kaposi Sarcoma M9140)
Lung Equivalent Terms, Definitions, Charts, Tables and Illustrations C340-C349 (Excludes lymphoma and leukemia M9590-9989 and Kaposi sarcoma M9140) Introduction Use these rules only for cases with primary lung cancer. Lung carcinomas may be broadly grouped into two categories, small cell and non-small cell carcinoma. Frequently a patient may have two or more tumors in one lung and may have one or more tumors in the contralateral lung. The physician may biopsy only one of the tumors. Code the case as a single primary (See Rule M1, Note 2) unless one of the tumors is proven to be a different histology. It is irrelevant whether the other tumors are identified as cancer, primary tumors, or metastases. Equivalent or Equal Terms • Low grade neuroendocrine carcinoma, carcinoid • Tumor, mass, lesion, neoplasm (for multiple primary and histology coding rules only) • Type, subtype, predominantly, with features of, major, or with ___differentiation Obsolete Terms for Small Cell Carcinoma (Terms that are no longer recognized) • Intermediate cell carcinoma (8044) • Mixed small cell/large cell carcinoma (8045) (Code is still used; however current accepted terminology is combined small cell carcinoma) • Oat cell carcinoma (8042) • Small cell anaplastic carcinoma (No ICD-O-3 code) • Undifferentiated small cell carcinoma (No ICD-O-3 code) Definitions Adenocarcinoma with mixed subtypes (8255): A mixture of two or more of the subtypes of adenocarcinoma such as acinar, papillary, bronchoalveolar, or solid with mucin formation. Adenosquamous carcinoma (8560): A single histology in a single tumor composed of both squamous cell carcinoma and adenocarcinoma. Bilateral lung cancer: This phrase simply means that there is at least one malignancy in the right lung and at least one malignancy in the left lung. -
Growth and Gene Expression Profile Analyses of Endometrial Cancer Cells Expressing Exogenous PTEN
[CANCER RESEARCH 61, 3741–3749, May 1, 2001] Growth and Gene Expression Profile Analyses of Endometrial Cancer Cells Expressing Exogenous PTEN Mieko Matsushima-Nishiu, Motoko Unoki, Kenji Ono, Tatsuhiko Tsunoda, Takeo Minaguchi, Hiroyuki Kuramoto, Masato Nishida, Toyomi Satoh, Toshihiro Tanaka, and Yusuke Nakamura1 Laboratories of Molecular Medicine [M. M-N., M. U., K. O., T. M., T. Ta., Y. N.] and Genome Database [T. Ts.], Human Genome Center, Institute of Medical Science, The University of Tokyo, Tokyo 108-8639, Japan; Department of Obstetrics and Gynecology, School of Medicine, Kitasato University, Sagamihara 228-8555, Japan [H. K.]; Department of Obstetrics and Gynecology, Institute of Clinical Medicine, University of Tsukuba, Tsukuba 305-8576, Japan [M. N.]; and Department of Obstetrics and Gynecology, Ibaraki Seinan Central Hospital, Tsukuba 306-0433, Japan [T. S.] ABSTRACT Akt/protein kinase B, cell survival, and cell proliferation (8). Over- expression of PTEN can decrease cell proliferation and tumorigenicity The PTEN tumor suppressor gene encodes a multifunctional phospha- (9, 10), an observation attributed to the ability of PTEN to induce cell tase that plays an important role in inhibiting the phosphatidylinositol-3- cycle arrest and apoptosis (11, 12). kinase pathway and downstream functions that include activation of Akt/protein kinase B, cell survival, and cell proliferation. Enforced ex- Thus, lack of PTEN expression may affect a complex set of pression of PTEN in various cancer cell lines decreases cell proliferation transcriptional targets. However, no systematic assessment of PTEN- through arrest of the cell cycle, accompanied in some cases by induction regulated targets in cancer cells has been reported to date. -
Transcriptomic and Proteomic Profiling Provides Insight Into
BASIC RESEARCH www.jasn.org Transcriptomic and Proteomic Profiling Provides Insight into Mesangial Cell Function in IgA Nephropathy † † ‡ Peidi Liu,* Emelie Lassén,* Viji Nair, Celine C. Berthier, Miyuki Suguro, Carina Sihlbom,§ † | † Matthias Kretzler, Christer Betsholtz, ¶ Börje Haraldsson,* Wenjun Ju, Kerstin Ebefors,* and Jenny Nyström* *Department of Physiology, Institute of Neuroscience and Physiology, §Proteomics Core Facility at University of Gothenburg, University of Gothenburg, Gothenburg, Sweden; †Division of Nephrology, Department of Internal Medicine and Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, Michigan; ‡Division of Molecular Medicine, Aichi Cancer Center Research Institute, Nagoya, Japan; |Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala, Sweden; and ¶Integrated Cardio Metabolic Centre, Karolinska Institutet Novum, Huddinge, Sweden ABSTRACT IgA nephropathy (IgAN), the most common GN worldwide, is characterized by circulating galactose-deficient IgA (gd-IgA) that forms immune complexes. The immune complexes are deposited in the glomerular mesangium, leading to inflammation and loss of renal function, but the complete pathophysiology of the disease is not understood. Using an integrated global transcriptomic and proteomic profiling approach, we investigated the role of the mesangium in the onset and progression of IgAN. Global gene expression was investigated by microarray analysis of the glomerular compartment of renal biopsy specimens from patients with IgAN (n=19) and controls (n=22). Using curated glomerular cell type–specific genes from the published literature, we found differential expression of a much higher percentage of mesangial cell–positive standard genes than podocyte-positive standard genes in IgAN. Principal coordinate analysis of expression data revealed clear separation of patient and control samples on the basis of mesangial but not podocyte cell–positive standard genes. -
Sarcomatoid Urothelial Carcinoma Arising in the Female Urethral Diverticulum
Journal of Pathology and Translational Medicine 2021; 55: 298-302 https://doi.org/10.4132/jptm.2021.04.23 CASE STUDY Sarcomatoid urothelial carcinoma arising in the female urethral diverticulum Heae Surng Park Department of Pathology, Ewha Womans University Seoul Hospital, Seoul, Korea A sarcomatoid variant of urothelial carcinoma in the female urethral diverticulum has not been reported previously. A 66-year-old woman suffering from dysuria presented with a huge urethral mass invading the urinary bladder and vagina. Histopathological examination of the resected specimen revealed predominantly undifferentiated pleomorphic sarcoma with sclerosis. Only a small portion of conven- tional urothelial carcinoma was identified around the urethral diverticulum, which contained glandular epithelium and villous adenoma. The patient showed rapid systemic recurrence and resistance to immune checkpoint inhibitor therapy despite high expression of pro- grammed cell death ligand-1. We report the first case of urethral diverticular carcinoma with sarcomatoid features. Key Words: Sarcomatoid carcinoma; Urothelial carcinoma; Urethral diverticulum Received: March 9, 2021 Revised: April 16, 2021 Accepted: April 23, 2021 Corresponding Author: Heae Surng Park, MD, PhD, Department of Pathology, Ewha Womans University Seoul Hospital, Ewha Womans University College of Medicine, 260 Gonghang-daero, Gangseo-gu, Seoul 07804, Korea Tel: +82-2-6986-5253, Fax: +82-2-6986-3423, E-mail: [email protected] Urethral diverticular carcinoma (UDC) is extremely rare; the urinary bladder, and vagina with enlarged lymph nodes at both most common histological subtype is adenocarcinoma [1,2]. femoral, both inguinal, and both internal and external iliac areas Sarcomatoid urothelial carcinoma (UC) is also unusual. Due to (Fig. 1B). -
Clinical Impact of Copy Number Variation Changes in Bladder Cancer Samples
EXPERIMENTAL AND THERAPEUTIC MEDICINE 22: 901, 2021 Clinical impact of copy number variation changes in bladder cancer samples VICTORIA SPASOVA1, BORIS MLADENOV2, SIMEON RANGELOV3, ZORA HAMMOUDEH1, DESISLAVA NESHEVA1, DIMITAR SERBEZOV1, RADA STANEVA1,4, SAVINA HADJIDEKOVA1,4, MIHAIL GANEV1, LUBOMIR BALABANSKI1,5, RADOSLAVA VAZHAROVA5,6, CHAVDAR SLAVOV3, DRAGA TONCHEVA1 and OLGA ANTONOVA1 1Department of Medical Genetics, Medical University‑Sofia, 1431 Sofia;2 Department of Urology, UMBALSM N.I. Pirogov, 1606 Sofia; 3Department of Urology, Tsaritsa Yoanna University Hospital, 1527 Sofia; 4Medical Genetics Laboratory, Nadezhda Women's Health Hospital, 1373 Sofia; 5Medical Genetics Laboratory, GARH Malinov, 1680 Sofia; 6Department of Biology, Medical Genetics and Microbiology, Faculty of Medicine, Sofia University St. Kliment Ohridski, 1407 Sofia, Bulgaria Received November 30, 2019; Accepted February 18, 2021 DOI: 10.3892/etm.2021.10333 Abstract. The aim of the present study was to detect copy uroepithelial tumours may lay a foundation for implementing number variations (CNVs) related to tumour progression and molecular CNV profiling of bladder tumours as part of a metastasis of urothelial carcinoma through whole‑genome routine progression risk estimation strategy, thus expanding scanning. A total of 30 bladder cancer samples staged from the personalized therapeutic approach. pTa to pT4 were included in the study. DNA was extracted from freshly frozen tissue via standard phenol‑chloroform extraction Introduction and CNV analysis was performed on two alternative platforms (CytoChip Oligo aCGH, 4x44K and Infinium OncoArray‑500K The most successful approach to treating a disease has BeadChip; Illumina, Inc.). Data were analysed with BlueFuse always been etiological therapy. In the case of bladder Multi software and Karyostudio, respectively. -
Integrated Analysis of Transcriptomic and Proteomic Analyses Reveals Different Metabolic Patterns in the Livers of Tibetan and Yorkshire Pigs
Open Access Anim Biosci Vol. 34, No. 5:922-930 May 2021 https://doi.org/10.5713/ajas.20.0342 pISSN 2765-0189 eISSN 2765-0235 Integrated analysis of transcriptomic and proteomic analyses reveals different metabolic patterns in the livers of Tibetan and Yorkshire pigs Mengqi Duan1,a, Zhenmei Wang1,a, Xinying Guo1, Kejun Wang2, Siyuan Liu1, Bo Zhang3,*, and Peng Shang1,* * Corresponding Authors: Objective: Tibetan pigs, predominantly originating from the Tibetan Plateau, have been Bo Zhang Tel: +86-010-62734852, subjected to long-term natural selection in an extreme environment. To characterize the Fax: +86-010-62734852, metabolic adaptations to hypoxic conditions, transcriptomic and proteomic expression E-mail: [email protected] patterns in the livers of Tibetan and Yorkshire pigs were compared. Peng Shang Tel: +86-0894-5822924, Methods: RNA and protein were extracted from liver tissue of Tibetan and Yorkshire pigs Fax: +86-0894-5822924, (n = 3, each). Differentially expressed genes and proteins were subjected to gene ontology E-mail: [email protected] and Kyoto encyclopedia of genes and genomes functional enrichment analyses. 1 College of Animal Science, Tibet Agriculture Results: In the RNA-Seq and isobaric tags for relative and absolute quantitation analyses, a and Animal Husbandry University, Linzhi, total of 18,791 genes and 3,390 proteins were detected and compared. Of these, 273 and Xizang 86000, China 257 differentially expressed genes and proteins were identified. Evidence from functional 2 College of Animal Sciences and Veterinary Medicine, Henan Agricultural University, enrichment analysis showed that many genes were involved in metabolic processes. The Zhengzhou, Henan 450046, China combined transcriptomic and proteomic analyses revealed that small molecular biosynthesis, 3 National Engineering Laboratory for Animal metabolic processes, and organic hydroxyl compound metabolic processes were the major Breeding/Beijing Key Laboratory for Animal processes operating differently in the two breeds.