Chapter 14: Hereditary Renal Cancer Syndromes
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Genomic and Transcriptomic Alterations Associated with Drug Vulnerabilities and Prognosis in Adenocarcinoma at the Gastroesophageal Junction
ARTICLE https://doi.org/10.1038/s41467-020-19949-6 OPEN Genomic and transcriptomic alterations associated with drug vulnerabilities and prognosis in adenocarcinoma at the gastroesophageal junction Yuan Lin1,8, Yingying Luo 2,8, Yanxia Sun 2,8, Wenjia Guo 2,3,8, Xuan Zhao2,8, Yiyi Xi2, Yuling Ma 2, ✉ ✉ Mingming Shao2, Wen Tan2, Ge Gao 1,4 , Chen Wu 2,5,6 & Dongxin Lin2,5,7 1234567890():,; Adenocarcinoma at the gastroesophageal junction (ACGEJ) has dismal clinical outcomes, and there are currently few specific effective therapies because of limited knowledge on its genomic and transcriptomic alterations. The present study investigates genomic and tran- scriptomic changes in ACGEJ from Chinese patients and analyzes their drug vulnerabilities and associations with the survival time. Here we show that the major genomic changes of Chinese ACGEJ patients are chromosome instability promoted tumorigenic focal copy- number variations and COSMIC Signature 17-featured single nucleotide variations. We provide a comprehensive profile of genetic changes that are potentially vulnerable to existing therapeutic agents and identify Signature 17-correlated IFN-α response pathway as a prog- nostic marker that might have practical value for clinical prognosis of ACGEJ. These findings further our understanding on the molecular biology of ACGEJ and may help develop more effective therapeutic strategies. 1 Beijing Advanced Innovation Center for Genomics (ICG), Biomedical Pioneering Innovation Center (BIOPIC), Peking University, Beijing, China. 2 Department of Etiology and Carcinogenesis, National Cancer Center/National Clinical Research Center/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China. 3 Cancer Institute, Affiliated Cancer Hospital of Xinjiang Medical University, Urumqi, China. -
Paraganglioma (PGL) Tumors in Patients with Succinate Dehydrogenase-Related PCC–PGL Syndromes: a Clinicopathological and Molecular Analysis
T G Papathomas and others Non-PCC/PGL tumors in the SDH 170:1 1–12 Clinical Study deficiency Non-pheochromocytoma (PCC)/paraganglioma (PGL) tumors in patients with succinate dehydrogenase-related PCC–PGL syndromes: a clinicopathological and molecular analysis Thomas G Papathomas1, Jose Gaal1, Eleonora P M Corssmit2, Lindsey Oudijk1, Esther Korpershoek1, Ketil Heimdal3, Jean-Pierre Bayley4, Hans Morreau5, Marieke van Dooren6, Konstantinos Papaspyrou7, Thomas Schreiner8, Torsten Hansen9, Per Arne Andresen10, David F Restuccia1, Ingrid van Kessel6, Geert J L H van Leenders1, Johan M Kros1, Leendert H J Looijenga1, Leo J Hofland11, Wolf Mann7, Francien H van Nederveen12, Ozgur Mete13,14, Sylvia L Asa13,14, Ronald R de Krijger1,15 and Winand N M Dinjens1 1Department of Pathology, Josephine Nefkens Institute, Erasmus MC, University Medical Center, PO Box 2040, 3000 CA Rotterdam, The Netherlands, 2Department of Endocrinology, Leiden University Medical Center, Leiden,The Netherlands, 3Section for Clinical Genetics, Department of Medical Genetics, Oslo University Hospital, Oslo, Norway, 4Department of Human and Clinical Genetics, Leiden University Medical Center, Leiden, The Netherlands, 5Department of Pathology, Leiden University Medical Center, Leiden, The Netherlands, 6Department of Clinical Genetics, Erasmus MC, University Medical Center, Rotterdam, The Netherlands, 7Department of Otorhinolaryngology, Head and Neck Surgery, University Medical Center of the Johannes Gutenberg University Mainz, Mainz, Germany, 8Section for Specialized Endocrinology, -
Modeling Renal Cell Carcinoma in Mice: Bap1 and Pbrm1 Inactivation Drive Tumor Grade
Published OnlineFirst May 4, 2017; DOI: 10.1158/2159-8290.CD-17-0292 RESEARCH ARTICLE Modeling Renal Cell Carcinoma in Mice: Bap1 and Pbrm1 Inactivation Drive Tumor Grade Yi-Feng Gu1,2, Shannon Cohn1,2, Alana Christie2, Tiffani McKenzie2,3, Nicholas Wolff1,2, Quyen N. Do4, Ananth J. Madhuranthakam4, Ivan Pedrosa2,4, Tao Wang2,5, Anwesha Dey6, Meinrad Busslinger7, Xian-Jin Xie2,8, Robert E. Hammer9, Renée M. McKay1,2, Payal Kapur2,3, and James Brugarolas1,2 Downloaded from cancerdiscovery.aacrjournals.org on September 26, 2021. © 2017 American Association for Cancer Research. 17-CD-17-0292_p900-917.indd 900 7/20/17 10:05 AM Published OnlineFirst May 4, 2017; DOI: 10.1158/2159-8290.CD-17-0292 ABSTRACT Clear cell renal cell carcinoma (ccRCC) is characterized by BAP1 and PBRM1 muta- tions, which are associated with tumors of different grade and prognosis. However, whether BAP1 and PBRM1 loss causes ccRCC and determines tumor grade is unclear. We conditionally targeted Bap1 and Pbrm1 (with Vhl ) in the mouse using several Cre drivers. Sglt2 and Villin proximal convoluted tubule drivers failed to cause tumorigenesis, challenging the conventional notion of ccRCC origins. In contrast, targeting with PAX8, a transcription factor frequently overexpressed in ccRCC, led to ccRCC of different grades. Bap1 -defi cient tumors were of high grade and showed greater mTORC1 activation than Pbrm1 -defi cient tumors, which exhibited longer latency. Disrupting one allele of the mTORC1 negative regulator, Tsc1 , in Pbrm1 -defi cient kidneys triggered higher grade ccRCC. This study establishes Bap1 and Pbrm1 as lineage-specifi c drivers of ccRCC and histologic grade, implicates mTORC1 as a tumor grade rheostat, and suggests that ccRCCs arise from Bowman capsule cells. -
Download Via Github on RNA-Seq and Chip-Seq Data Analysis and the University of And/Or Bioconductor [33–35, 38–40]
Kumka and Bauer BMC Genomics (2015) 16:895 DOI 10.1186/s12864-015-2162-4 RESEARCH ARTICLE Open Access Analysis of the FnrL regulon in Rhodobacter capsulatus reveals limited regulon overlap with orthologues from Rhodobacter sphaeroides and Escherichia coli Joseph E. Kumka and Carl E. Bauer* Abstract Background: FNR homologues constitute an important class of transcription factors that control a wide range of anaerobic physiological functions in a number of bacterial species. Since FNR homologues are some of the most pervasive transcription factors, an understanding of their involvement in regulating anaerobic gene expression in different species sheds light on evolutionary similarity and differences. To address this question, we used a combination of high throughput RNA-Seq and ChIP-Seq analysis to define the extent of the FnrL regulon in Rhodobacter capsulatus and related our results to that of FnrL in Rhodobacter sphaeroides and FNR in Escherichia coli. Results: Our RNA-seq results show that FnrL affects the expression of 807 genes, which accounts for over 20 % of the Rba. capsulatus genome. ChIP-seq results indicate that 42 of these genes are directly regulated by FnrL. Importantly, this includes genes involved in the synthesis of the anoxygenic photosystem. Similarly, FnrL in Rba. sphaeroides affects 24 % of its genome, however, only 171 genes are differentially expressed in common between two Rhodobacter species, suggesting significant divergence in regulation. Conclusions: We show that FnrL in Rba. capsulatus activates photosynthesis while in Rba. sphaeroides FnrL regulation reported to involve repression of the photosystem. This analysis highlights important differences in transcriptional control of photosynthetic events and other metabolic processes controlled by FnrL orthologues in closely related Rhodobacter species. -
1 Canonical BAF Complex in Regulatory T Cells 2 3 Chin
bioRxiv preprint doi: https://doi.org/10.1101/2020.02.26.964981; this version posted February 27, 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. 1 A genome-wide CRISPR screen reveals a role for the BRD9-containing non- 2 canonical BAF complex in regulatory T cells 3 4 Chin-San Loo1,3,#, Jovylyn Gatchalian2,#, Yuqiong Liang1, Mathias Leblanc1, Mingjun 5 Xie1, Josephine Ho2, Bhargav Venkatraghavan1, Diana C. Hargreaves2*, and Ye 6 Zheng1* 7 8 1. NOMIS Center for Immunobiology and Microbial Pathogenesis, Salk Institute for 9 Biological Studies 10 2. Molecular and Cellular Biology Laboratory, Salk Institute for Biological Studies 11 3. Division of Biological Sciences, University of California, San Diego 12 # Co-first authors 13 * Co-corresponding authors 14 1 bioRxiv preprint doi: https://doi.org/10.1101/2020.02.26.964981; this version posted February 27, 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. 15 Summary 16 Regulatory T cells (Tregs) play a pivotal role in suppressing auto-reactive T cells 17 and maintaining immune homeostasis. Treg development and function are 18 dependent on the transcription factor Foxp3. Here we performed a genome-wide 19 CRISPR/Cas9 knockout screen to identify the regulators of Foxp3 in mouse 20 primary Tregs. The results showed that Foxp3 regulators are highly enriched in 21 genes encoding SWI/SNF and SAGA complex subunits. Among the three 22 SWI/SNF-related complexes, the non-canonical or ncBAF (also called GBAF or 23 BRD9-containing BAF) complex promoted the expression of Foxp3, whereas the 24 PBAF complex repressed its expression. -
About SDHD Gene Mutations
About SDHD Gene Mutations About Genes Recommendations Genes are in every cell in our bodies. Genes are made Knowing if you have an SDHD mutation can help you of DNA, which gives instructions to cells about how to grow manage your medical care. and work together. We have two copies of each gene in each cell—one from our mother and one from our father. When MEN AND WOMEN genes work right, they help stop cancer cells from developing. If you know you have an SDHD mutation, it is important If one copy of a gene has a mutation, it cannot function as it to find tumors early. It is also important to tell your doctor should. This increases the risk for certain cancers. that you have this mutation before any medical procedures. TheSDH genes have instructions for turning food into energy Recommendations may vary according to your age. and helping fix mistakes in DNA. The four genes involved are Ages 8-18: SDHA, SDHB, SDHC, and SDHD. If there is a mutation in one • MRI of the whole body every 2-3 years of these genes, it can cause cells to grow and divide too much. This • Neck MRI every 2-3 years can lead to tumors called paragangliomas and pheochromocytomas. These tumors are often benign (non-cancerous) but can be Adults: cancer and spread in some cases. This condition is called • PET/CT scan as your doctor recommends hereditary paraganglioma/pheochromocytoma syndrome. All ages: Paragangliomas and Pheochromocytomas • Physical exam every year with blood pressure check Paragangliomas (PGLs) are slow-growing tumors that develop • Blood test every year along nerves or blood vessels. -
Your Kidneys and Kidney Cancer
Your Kidneys and Kidney Cancer DID YOU KNOW? Kidney Disease Kidney Cancer Having advanced Having kidney cancer kidney disease or a can increase your risk About 1/3 of kidney cancer kidney transplant can for kidney disease or patients have or will develop increase your risk for kidney failure. kidney disease.2 kidney cancer. TOP Kidney cancer is among the 10 10 most common cancers in both men and women.1 KIDNEYS Your kidneys’ main job is to About 62,000 kidney cancers clean waste and extra water 62,000 occur in the U.S. each year.1 from your blood. Having kidney disease means your kidneys are damaged and cannot do this job well. KIDNEY CANCER Over time, kidney disease can get worse and lead to kidney failure. Once kidneys fail, treatment with dialysis or a Kidney cancer is a disease that kidney transplant is needed starts in the kidneys. It happens to stay alive. when kidney cells grow out of control and form a lump (called a “tumor”). The cancer may stay in your kidneys or spread to other parts of your body. 1 Your Kidneys and Kidney Cancer SYMPTOMS Most people don’t have symptoms in the early stages of kidney disease or kidney cancer. Advanced Kidney Cancer Advanced Kidney Disease Blood in the urine Feeling tired or short of breath Pain on the sides of the mid-back Loss of appetite A lump in the abdomen Dry, itchy skin (stomach area) Trouble thinking clearly Weight loss, night sweats, unexplained fever Frequent urination Swollen feet and ankles, Tiredness puiness around eyes Talk to Your Healthcare Provider About your risk for kidney cancer About your risk for kidney disease CANCER TREATMENTS Some cancer treatments can increase your risk for kidney disease or kidney failure. -
Swi/Snf Chromatin Remodeling/Tumor Suppressor Complex Establishes Nucleosome Occupancy at Target Promoters
Swi/Snf chromatin remodeling/tumor suppressor complex establishes nucleosome occupancy at target promoters Michael Y. Tolstorukova,b,1,2, Courtney G. Sansamc,d,e,1, Ping Luc,d,e,1, Edward C. Koellhofferc,d,e, Katherine C. Helmingc,d,e, Burak H. Alvera, Erik J. Tillmanc,d,e, Julia A. Evansc,d,e, Boris G. Wilsonc,d,e, Peter J. Parka,b,3, and Charles W. M. Robertsc,d,e,3 aCenter for Biomedical Informatics, Harvard Medical School, Boston, MA 02115; bDivision of Genetics, Brigham and Women’s Hospital, Boston, MA 02115; cDepartment of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, MA 02115; dDivision of Hematology/Oncology, Boston Children’s Hospital, Boston, MA 02115; and eDepartment of Pediatrics, Harvard Medical School, Boston, MA 02115 Edited by Mark Groudine, Fred Hutchinson Cancer Research Center, Seattle, WA, and approved May 2, 2013 (received for review February 6, 2013) Precise nucleosome-positioning patterns at promoters are thought Brg1 haploinsufficient mice are tumor prone, establishing these to be crucial for faithful transcriptional regulation. However, the subunits of the complex as bona fide tumor suppressors (1, 12–17). mechanisms by which these patterns are established, are dynam- It is noteworthy that recent exome sequencing of 35 human SNF5- ically maintained, and subsequently contribute to transcriptional deficient rhabdoid tumors identified a remarkably low rate of control are poorly understood. The switch/sucrose non-fermentable mutations, with loss of SNF5 being essentially the sole recurrent event (18). Indeed, in two of the cancers, there were no other chromatin remodeling complex, also known as the Brg1 associated fi factors complex, is a master developmental regulator and tumor identi ed mutations. -
Familial Occurrence of Carcinoid Tumors and Association with Other Malignant Neoplasms1
Vol. 8, 715–719, August 1999 Cancer Epidemiology, Biomarkers & Prevention 715 Familial Occurrence of Carcinoid Tumors and Association with Other Malignant Neoplasms1 Dusica Babovic-Vuksanovic, Costas L. Constantinou, tomies (3). The most frequent sites for carcinoid tumors are the Joseph Rubin, Charles M. Rowland, Daniel J. Schaid, gastrointestinal tract (73–85%) and the bronchopulmonary sys- and Pamela S. Karnes2 tem (10–28.7%). Carcinoids are occasionally found in the Departments of Medical Genetics [D. B-V., P. S. K.] and Medical Oncology larynx, thymus, kidney, ovary, prostate, and skin (4, 5). Ade- [C. L. C., J. R.] and Section of Biostatistics [C. M. R., D. J. S.], Mayo Clinic nocarcinomas and carcinoids are the most common malignan- and Mayo Foundation, Rochester, Minnesota 55905 cies in the small intestine in adults (6, 7). In children, they rank second behind lymphoma among alimentary tract malignancies (8). Carcinoids appear to have increased in incidence during the Abstract past 20 years (5). Carcinoid tumors are generally thought to be sporadic, Carcinoid tumors were originally thought to possess a very except for a small proportion that occur as a part of low metastatic potential. In recent years, their natural history multiple endocrine neoplasia syndromes. Data regarding and malignant potential have become better understood (9). In the familial occurrence of carcinoid as well as its ;40% of patients, metastases are already evident at the time of potential association with other neoplasms are limited. A diagnosis. The overall 5-year survival rate of all carcinoid chart review was conducted on patients indexed for tumors, regardless of site, is ;50% (5). -
Renal Transitional Cell Carcinoma: Case Report from the Regional Hospital Buea, Cameroon and Review of Literature Enow Orock GE1*, Eyongeta DE2 and Weledji PE3
Enow Orock, Int J Surg Res Pract 2014, 1:1 International Journal of ISSN: 2378-3397 Surgery Research and Practice Case Report : Open Access Renal Transitional Cell Carcinoma: Case report from the Regional Hospital Buea, Cameroon and Review of Literature Enow Orock GE1*, Eyongeta DE2 and Weledji PE3 1Pathology Unit, Regional Hospital Buea, Cameroon 2Urology Unit, Regional Hospital Limbe, Cameroon 3Surgical Unit, Regional Hospital Buea, Cameroon *Corresponding author: Enow Orock George, Pathology Unit, Regional Hospital Buea, South West Region, Cameroon, Tel: (237) 77716045, E-mail: [email protected] Abstract United States in 2009. Primary renal pelvis and ureteric malignancies, on the other hand, are much less common with an estimated 2,270 Although transitional cell carcinoma is the most common tumour of the renal pelvis, we report the first histologically-confirmed case in cases diagnosed and 790 deaths in 2009 [6]. Worldwide statistics our service in a period of about twenty years. The patient is a mid- vary with the highest incidence found in the Balkans where urothelial aged female African, with no apparent risks for the disease. She cancers account for 40% of all renal cancers and are bilateral in 10% presented with the classical sign of the disease (hematuria) and of cases [7]. We report a first histologically-confirmed case of renal was treated by nephrouretectomy for a pT3N0MX grade II renal pelvic transitional cell carcinoma in 20 years of practice in a mid-aged pelvic tumour. She is reporting well one year after surgery. The case African woman. highlights not only the peculiar diagnosis but also illustrates the diagnostic and management challenges posed by this and similar Case Report diseases in a low- resource setting like ours. -
Inactivation of the PBRM1 Tumor Suppressor Gene Amplifies
Inactivation of the PBRM1 tumor suppressor gene − − amplifies the HIF-response in VHL / clear cell renal carcinoma Wenhua Gaoa, Wei Lib,c, Tengfei Xiaoa,b,c, Xiaole Shirley Liub,c, and William G. Kaelin Jr.a,d,1 aDepartment of Medical Oncology, Dana-Farber Cancer Institute and Brigham and Women’s Hospital, Harvard Medical School, Boston, MA 02115; bCenter for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA 02215; cDepartment of Biostatistics and Computational Biology, Dana-Farber Cancer Institute and Harvard T.H. Chan School of Public Health, Boston, MA 02115; and dHoward Hughes Medical Institute, Chevy Chase, MD 20815 Contributed by William G. Kaelin, Jr., December 1, 2016 (sent for review October 31, 2016; reviewed by Charles W. M. Roberts and Ali Shilatifard) Most clear cell renal carcinomas (ccRCCs) are initiated by somatic monolayer culture and in soft agar (10). These effects were not, inactivation of the VHL tumor suppressor gene. The VHL gene prod- however, proven to be on-target, and were not interrogated in uct, pVHL, is the substrate recognition unit of an ubiquitin ligase vivo. As a step toward understanding the role of BAF180 in that targets the HIF transcription factor for proteasomal degrada- ccRCC, we asked whether BAF180 participates in the canonical tion; inappropriate expression of HIF target genes drives renal car- PBAF complex in ccRCC cell lines and whether loss of BAF180 cinogenesis. Loss of pVHL is not sufficient, however, to cause ccRCC. measurably alters ccRCC behavior in cell culture and in mice. Additional cooperating genetic events, including intragenic muta- tions and copy number alterations, are required. -
Kidney Cancer What You Need to Know
Kidney Cancer What You Need to Know What is it? Signs and symptoms • Kidney cancer is a disease In the early stages, most people don’t have signs that most often starts in the or symptoms. Kidney cancer is usually found by kidneys. It happens when chance during an abdominal (belly) imaging test healthy cells in one or both for other complaints. However, as the tumor grows, kidneys turn cancerous to form you may have: a lump (called a tumor). • Renal cell carcinoma (RCC) is the most common type of kidney cancer in adults. • RCC usually starts in the lining of tiny tubes in the kidney called renal tubules. • RCC often stays in the kidney, but it can spread to Blood in the urine Pain in the lower back other parts of the body, most often the bones, lungs, or brain. • There are many types of RCC tumors. Some types grow and spread fast and others grow more slowly and are less likely to spread. The most common RCC tumors are: clear-cell, chromophobe, and papillary. • Other types of kidney cancer include: transitional cell A lump in the Unexplained weight loss, carcinoma (TCC), renal sarcoma, and Wilms tumor, lower back or side night sweats, fever, which occurs most often in children. of the waist or fatigue How is kidney cancer found? • Medical history, physical exam, and blood and urine tests • Only one or a few of these imaging tests: – Computed tomography (CT) scans use x-rays to make a complete picture of the kidneys and abdomen (belly). They can be done with or without a contrast dye.