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tumor sequencing

Yanghao Hou, Jorge Pinheiro, Felix Sahm, David E Reuss, Daniel Schrimpf, Damian Stichel, Belén Casalini, Christian Koelsche, Philipp Sievers, Annika K Wefers, Annekathrin Reinhardt, Azadeh Ebrahimi, Francisco Fernández-Klett, Stefan Pusch, Jochen Meier, Leonille Schweizer, Werner Paulus, Marco Prinz, Christian Hartmann, Karl H Plate, Guido Reifenberger, Torsten Pietsch, Pascale Varlet, Mélanie Pagès, Ulrich Schüller, David Scheie, Karin de Stricker, Stephan Frank, Jürgen Hench, Bianca Pollo, Sebastian Brandner, Andreas Unterberg, Stefan M Pfister, David T W Jones, Andrey Korshunov, Wolfgang Wick, David Capper, Ingmar Blümcke, Andreas von Deimling, Luca Bertero
Papillary glioneuronal tumor (PGNT) is a WHO-defined brain tumor entity that poses a major diagnostic challenge. Recently, SLC44A1-PRKCA fusions have been described in PGNT. We subjected 28 brain tumors from different institutions histologically diagnosed as PGNT to molecular and morphological analysis. Array-based methylation analysis revealed that 17/28 tumors exhibited methylation profiles typical for other tumor entities, mostly dysembryoplastic neuroepithelial tumor and hemispheric pilocytic astrocytoma...
February 13, 2019: Acta Neuropathologica
Alexander R Gawronski, Yen-Yi Lin, Brian McConeghy, Stephane LeBihan, Hossein Asghari, Can Koçkan, Baraa Orabi, Nabil Adra, Roberto Pili, Colin C Collins, S Cenk Sahinalp, Faraz Hach
Motivation: Cancer is a complex disease that involves rapidly evolving cells, often forming multiple distinct clones. In order to effectively understand progression of a patient-specific tumor, one needs to comprehensively sample tumor DNA at multiple time points, ideally obtained through inexpensive and minimally invasive techniques. Current sequencing technologies make the 'liquid biopsy' possible, which involves sampling a patient's blood or urine and sequencing the circulating cell free DNA (cfDNA)...
February 13, 2019: Nucleic Acids Research
Georgia Papachristopoulou, Apostolos Malachias, Marina Devetzi, Evdoxia Kamouza, Andreas Scorilas, Dimitris Xynopoulos, Maroulio Talieri
Background Kallikrein-related peptidases (KLKs) are a subgroup of serine proteases located on chromosome 19q13.3. Most KLKs have been extensively studied as potential biomarkers for several carcinomas and other diseases. KLK5 was originally identified from a keratinocyte library, and its enzyme was purified from the stratum corneum of human skin. KLK5 was shown to be differentially expressed in a variety of endocrine tumors, although it is not as yet examined widely in colorectal cancer (CRC). Methods In this study, we quantitatively assessed the mRNA expression status of KLK5 in 197 colorectal tissues from 133 patients (70 cancerous and their paired normal colonic mucosa for 64 of them, as well as 63 colorectal adenomas) by quantitative real-time PCR (qPCR) using TaqMan probes...
February 13, 2019: Clinical Chemistry and Laboratory Medicine: CCLM
Doenja M J Lambregts, Thierry N Boellaard, Regina G H Beets-Tan
In recent years, neoadjuvant chemoradiotherapy (CRT) has become the standard of care for patients with locally advanced rectal cancer. Until recently, patients routinely proceeded to surgical resection after CRT, regardless of the response. Nowadays, treatment is tailored depending on the response to chemoradiotherapy. In patients that respond very well to CRT, organ-preserving treatments such as watch-and-wait are increasingly considered as an alternative to surgery. To facilitate such personalized treatment planning, there is now an increased demand for more detailed radiological response evaluation after chemoradiation...
February 13, 2019: Insights Into Imaging
María Milagros Otero-García, Alicia Mesa-Álvarez, Olivera Nikolic, Patricia Blanco-Lobato, Marijana Basta-Nikolic, Rafael Menéndez de Llano-Ortega, Laura Paredes-Velázquez, Nikola Nikolic, Magda Szewczyk-Bieda
MRI plays important roles in endometrial and cervical cancer assessment, from detection to recurrent disease evaluation. Endometrial cancer (EC) is the most common malignant tumor of the female genital tract in Western countries. EC patients are divided into risk categories based on histopathological tumor type, grade, and myometrial invasion depth. EC is surgically staged using the International Federation of Gynecology and Obstetrics (FIGO) system. Since FIGO (2009) stage correlates with prognosis, preoperative staging is essential for tailored treatment...
February 13, 2019: Insights Into Imaging
Takashi Yoshida, Tatsuya Yamaguchi, Shinya Maekawa, Shinichi Takano, Toru Kuno, Keisuke Tanaka, Fumihiko Iwamoto, Yuya Tsukui, Shoji Kobayashi, Yukiko Asakawa, Hiroko Shindo, Mitsuharu Fukasawa, Yasuhiro Nakayama, Taisuke Inoue, Tomoyoshi Uetake, Masahiko Ohtaka, Tadashi Sato, Kunio Mochizuki, Nobuyuki Enomoto
BACKGROUND AND AIMS: The recent advancement of next-generation sequencing (NGS) has enabled the identification of cancer-related somatic aberrations in advanced gastric cancer. However, these remain unclear in early gastric cancers, especially in intramucosal gastric cancers. PATIENTS AND METHODS: Thirty-one well-differentiated (tub1) intramucosal gastric cancers obtained by endoscopic submucosal dissection (ESD) from 29 patients were analyzed. After precise collection of tumors and non-tumors from formalin-fixed paraffin-embedded tissues using laser-captured microdissection (LCM), target sequencing analysis of 50 cancer-related genes was performed using an Ion-Proton sequencer...
February 11, 2019: Gastric Cancer
Soo Ki Kim, Haruhiko Takeda, Atsushi Takai, Tomonori Matsumoto, Nobuyuki Kakiuchi, Akira Yokoyama, Kenichi Yoshida, Toshimi Kaido, Shinji Uemoto, Sachiko Minamiguchi, Hironori Haga, Yuichi Shiraishi, Satoru Miyano, Hiroshi Seno, Seishi Ogawa, Hiroyuki Marusawa
BACKGROUND: Hepatocellular carcinoma (HCC) recurrently develops in cirrhotic liver containing a number of regenerative nodules (RNs). However, the biological tumorigenic potential of RNs is still unclear. To uncover the molecular bases of tumorigenesis in liver cirrhosis, we investigated the genetic aberrations in RNs of cirrhotic tissues using next-generation sequencing. METHODS: We isolated 205 RNs and 7 HCC tissues from the whole explanted livers of 10 randomly selected patients who had undergone living-donor liver transplantation...
February 12, 2019: Journal of Gastroenterology
Fengtao You, Yinyan Wang, Licui Jiang, Xuejun Zhu, Dan Chen, Lei Yuan, Gangli An, Huimin Meng, Lin Yang
Chimeric antigen receptor (CAR) immunotherapy has recently shown promise in clinical trials for B-cell malignancies; however, designing CARs for T-cell based diseases remain a challenge since most target antigens are shared between normal and malignant cells, leading to CAR-T cell fratricide. CD7 is highly expressed in T-cell acute lymphoblastic leukemia (T-ALL), but it is not expressed in one small group of normal T lymphocytes. Here, we constructed monovalent CD7-CAR-NK-92MI and bivalent dCD7-CAR-NK-92MI cells using the CD7 nanobody VHH6 sequences from our laboratory...
2019: American Journal of Cancer Research
Ines Block, Carolin Müller, Daniel Sdogati, Henriette Pedersen, Markus List, Aleksandra M Jaskot, Silje Damkjær Syse, Pernille Lund Hansen, Steffen Schmidt, Helle Christiansen, Cinzia Casella, Sidsel Bering Olsen, Monica M Blomstrøm, Angela Riedel, Mads Thomassen, Torben A Kruse, Søren W Karlskov Hansen, Petra Kioschis, Jan Mollenhauer
Breast cancer is a heterogeneous genetic disease driven by the accumulation of individual mutations per tumor. Whole-genome sequencing approaches have identified numerous genes with recurrent mutations in primary tumors. Although mutations in well characterized tumor suppressors and oncogenes are overrepresented in these sets, the majority of the genetically altered genes have so far unknown roles in breast cancer progression. To improve the basic understanding of the complex disease breast cancer and to potentially identify novel drug targets or regulators of known cancer-driving pathways, we analyzed 86 wild-type genes and 94 mutated variants for their effect on cell growth using a serially constructed panel of MCF7 cell lines...
February 12, 2019: Oncogene
Song Wu, Tong Ou, Nianzeng Xing, Jiang Lu, Shengqing Wan, Changxi Wang, Xi Zhang, Feiya Yang, Yi Huang, Zhiming Cai
Bladder cancer is one of the most common and highly vascularized cancers. To better understand its genomic structure and underlying etiology, we conduct whole-genome and targeted sequencing in urothelial bladder carcinomas (UBCs, the most common type of bladder cancer). Recurrent mutations in noncoding regions affecting gene regulatory elements and structural variations (SVs) leading to gene disruptions are prevalent. Notably, we find recurrent ADGRG6 enhancer mutations and FRS2 duplications which are associated with higher protein expression in the tumor and poor prognosis...
February 12, 2019: Nature Communications
Timothy J Robinson, Jennifer A Freedman, Muthana Al Abo, April E Deveaux, Bonnie LaCroix, Brendon M Patierno, Daniel J George, Steven R Patierno
Studies of Alternative RNA Splicing (ARS) have the potential to provide an abundance of novel targets for development of new biomarkers and therapeutics in oncology, which will be necessary to improve outcomes for cancer patients and mitigate cancer disparities. ARS, a key step in gene expression enabling individual genes to encode multiple proteins, is emerging as a major driver of abnormal phenotypic heterogeneity. Recent studies have begun to identify RNA splicing-related genetic and genomic variation in tumors, oncogenes dysregulated by ARS, RNA splice variants driving race-related cancer aggressiveness and drug response, spliceosome-dependent transformation, and RNA splicing-related immunogenic epitopes in cancer...
February 12, 2019: Clinical Cancer Research: An Official Journal of the American Association for Cancer Research
Mengxi Ge, Qiong Zhan, Zhenzhen Zhang, Xiaoyu Ji, Xinli Zhou, Ruofan Huang, Xiaohua Liang
BACKGROUND: The nucleic acid mutation status in intracranial metastasis is markedly significant clinically. The goal of the current study was to explore whether the tumor-associated mutations can be detected by different next-generation sequencing (NGS) pipelines in paired cerebrospinal fluid (CSF) and plasma samples from lung adenocarcinoma (LAC) patients with leptomeningeal metastases (LM). METHODS: Paired CSF cell free DNA (cfDNA), CSF cells, plasma and formalin-fixed and paraffin-embedded (FFPE) samples of primary tumors were collected from 29 LAC patients with LM to detect the mutations by different NGS pipelines...
February 12, 2019: BMC Cancer
Tian Tian, Xiaoyi Li, Jinhua Zhang
The mammalian or mechanistic target of rapamycin (mTOR) pathway plays a crucial role in regulation of cell survival, metabolism, growth and protein synthesis in response to upstream signals in both normal physiological and pathological conditions, especially in cancer. Aberrant mTOR signaling resulting from genetic alterations from different levels of the signal cascade is commonly observed in various types of cancers. Upon hyperactivation, mTOR signaling promotes cell proliferation and metabolism that contribute to tumor initiation and progression...
February 11, 2019: International Journal of Molecular Sciences
Kang Liang, Qing Liu, Pei Li, Hongyan Luo, Haoju Wang, Qingke Kong
Bacteria have been investigated as anti-tumor therapeutic agents for more than a century, since Coley first observed successful curing of a patient with inoperable cancer by injection of streptococcal organisms. Previous studies have demonstrated that some obligate or facultative anaerobes can selectively accumulate and proliferate within tumors and suppress their growth. Developments in molecular biology as well as the complete genome sequencing of many bacterial species have increased the applicability of bacterial organisms for cancer treatment...
February 9, 2019: Cancer Letters
Antonio Marcondes Lerario, Kazutaka Nanba, Amy R Blinder, Sachiko Suematsu, Masao Omura, Tetsuo Nishikawa, Thomas J Giordano, William Rainey, Tobias Else
Somatic variants in genes that regulate intracellular ion homeostasis have been identified in aldosterone-producing adenomas (APA). Although the mechanisms leading to an increased aldosterone production in APA cells has been well studied, the molecular events that cause cell proliferation and tumor formation are poorly understood. In the present study, we have performed whole exome sequencing (WES) to characterize the landscape of somatic alterations in a homogeneous series of APA with pathogenic KCNJ5 variants...
February 1, 2019: Endocrine-related Cancer
Jaclyn F Hechtman, David S Klimstra, Gouri Nanjangud, Denise Frosina, Jinru Shia, Achim A Jungbluth
OBJECTIVES: DAXX immunohistochemistry (IHC) is often used as a surrogate for sequencing. We aimed to elucidate the sensitivity of IHC for DAXX mutation. METHODS: All pancreatic neuroendocrine tumors (PanNETs) with DAXX mutations detected by sequencing and a subset of DAXX wild-type PanNETs were analyzed for DAXX expression by IHC. RESULTS: Of 154 PanNETs with MSK-IMPACT testing, 36 (30%) harbored DAXX mutations. DAXX mutations were associated with TSC2 mutations (46% vs 10%, P < 0...
February 8, 2019: Pancreas
Yan Liu, Dongyan Zhu, Hongjian Xing, Yi Hou, Yan Sun
Pancreatic adenocarcinoma (PAC) is the most common type of pancreatic cancer, which commonly has an unfavorable prognosis. The present study aimed to develop a novel prognostic prediction strategy for PAC patients. mRNA sequencing data of PAC (the training dataset) were extracted from The Cancer Genome Atlas database, and the validation datasets (GSE62452 and GSE79668) were acquired from the Gene Expression Omnibus database. The differentially expressed genes (DEGs) between good and poor prognosis groups were analyzed by limma package, and then prognosis‑associated genes were screened using Cox regression analysis...
January 22, 2019: Oncology Reports
Luke K Genutis, Jerneja Tomsic, Ralf Bundschuh, Pamela Brock, Michelle D Williams, Sameek Roychowdhury, Julie W Reeser, Wendy L Frankel, Mohammed Alsomali, Mark J Routbort, Russell R Broaddus, Paul E Wakely, John E Phay, Christopher J Walker, Albert de la Chapelle
BACKGROUND: Inactivation of DNA mismatch repair (MMR) and the resulting microsatellite instability (MSI) are frequently observed in endometrial, stomach and colorectal cancers as well as more rarely in other solid tumor types. The prevalence of MSI in thyroid cancer has not been explored in-depth, although recent studies utilizing data from large cancer sequencing efforts such as The Cancer Genome Atlas indicate MSI is absent or at least very rare in the most common and most well-studied histologic subtype, papillary carcinoma...
February 12, 2019: Thyroid: Official Journal of the American Thyroid Association
Tihana Ibrahimpasic, Ronald Ghossein, Jatin P Shah, Ian Ganly
BACKGROUND: Poorly differentiated thyroid cancer (PDTC) is a rare but clinically highly significant entity because it accounts for most fatalities from non-anaplastic follicular cell-derived thyroid cancer. Due to the relative rarity of the disease and heterogeneous diagnostic criteria, studies on PDTC have been limited. In light of the evolution of ultra deep next-generation sequencing (NGS) technologies and through correlation of clinico-pathological and genomic characteristics of PDTC, an improved understanding of the biology of PDTC has been facilitated...
February 12, 2019: Thyroid: Official Journal of the American Thyroid Association
Jun Wang, Liying Zhu, Xinwei Chen, Ruofei Huang, Shili Wang, Pin Dong
Hypopharyngeal carcinoma is a common malignant tumor of the head and neck with a very poor prognosis; the median survival time for curatively treated patients was 17.2 months in India. However, cell-based gene therapy holds promise to improve patient outcomes. In this study, we investigated whether human bone marrow mesenchymal stem cells (BMSCs) possess potential homing capacity for hypopharyngeal carcinoma. To monitor the efficiency of BMSC transplantation therapy via reporter gene imaging, we employed a hybrid baculovirus vector containing the Luc-P2A-eGFP fusion or sodium iodide symporter (NIS) sequence under the control of the cytomegalovirus promoter...
February 12, 2019: Stem Cells and Development
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