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Genes, Chromosomes & Cancer

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https://www.readbyqxmd.com/read/30242938/mechanisms-shaping-the-mutational-landscape-of-the-fra3b-fhit-deficient-cancer-genome
#1
REVIEW
Joshua C Saldivar, Dongju Park
Genome instability is an enabling characteristic of cancer, that facilitates the acquisition of oncogenic mutations that drive tumorigenesis. Underlying much of the instability in cancer is DNA replication stress, which causes both chromosome structural changes and single base-pair mutations. Common fragile sites are some of the earliest and most frequently altered loci in tumors. Notably, the fragile locus, FRA3B, lies within the fragile histidine triad (FHIT) gene, and consequently deletions within FHIT are common in cancer...
September 22, 2018: Genes, Chromosomes & Cancer
https://www.readbyqxmd.com/read/30239046/somatic-mutational-profiles-of-stage-ii-and-iii-gastric-cancer-according-to-tumor-microenvironment-immune-type
#2
Jiwon Koh, Soo Kyung Nam, Hanseong Roh, Jonghyuk Kim, Byung-Chul Lee, Jin Won Kim, Sang-Hoon Ahn, Do Joong Park, Hyung-Ho Kim, Kyoung Un Park, Jin Haeng Chung, Woo Ho Kim, Hye Seung Lee
We aimed to determine somatic mutational profiles of stage II/III gastric cancers (GCs) according to their tumor microenvironment immune types (TMITs), which classify cancer based on co-assessment of PD-L1 expression and CD8+ tumor infiltrating lymphocytes. Eighty stage II/III GC patients were classified as follows: TMIT I (PD-L1+ /CD8High ), TMIT II (PD-L1- /CD8Low ), TMIT III (PD-L1+ /CD8Low ), and TMIT IV (PD-L1- /CD8High ). Deep targeted sequencing using a panel of 170 cancer-related genes was performed on an Illumina HiSeq-2500 system...
September 21, 2018: Genes, Chromosomes & Cancer
https://www.readbyqxmd.com/read/30230086/next-generation-sequencing-of-the-cellular-and-liquid-fraction-of-pancreatic-cyst-fluid-supports-discrimination-of-ipmn-from-pseudocysts-and-reveals-cases-with-multiple-mutated-driver-clones-first-findings-from-the-prospective-zysteus-biomarker-study
#3
Anna-Lena Volckmar, Volker Endris, Matthias M Gaida, Jonas Leichsenring, Fabian Stögbauer, Michael Allgäuer, Moritz von Winterfeld, Roland Penzel, Martina Kirchner, Regine Brandt, Olaf Neumann, Holger Sültmann, Peter Schirmacher, Jochen Rudi, Daniel Schmitz, Albrecht Stenzinger
Half of all pancreatic cysts are neoplastic, mainly comprising intraductal papillary mucinous neoplasms (IPMN), which can progress to cancer. Current Fukuoka guidelines have limited sensitivity and specificity predicting progression of asymptomatic pancreatic cysts. We present first results of the prospective ZYSTEUS biomarker study investigating i) whether detection of driver mutations in IPMN by liquid biopsy is technically feasible, ii) which compartment of IPMN is most suitable for analysis, and iii) implications for clinical diagnostics...
September 19, 2018: Genes, Chromosomes & Cancer
https://www.readbyqxmd.com/read/30203896/improved-cytogenetic-characterization-and-risk-stratification-of-pediatric-acute-lymphoblastic-leukemia-using-single-nucleotide-polymorphism-array-analysis-a-single-center-experience-of-296-cases
#4
Linda Olsson, Kristina B Lundin-Ström, Anders Castor, Mikael Behrendtz, Andrea Biloglav, Ulrika Norén-Nyström, Kajsa Paulsson, Bertil Johansson
Single nucleotide polymorphism array (SNP-A) analyses are increasingly being introduced in routine genetic diagnostics of acute lymphoblastic leukemia (ALL). Despite this, only few studies that have compared the diagnostic value of SNP-A with conventional chromosome banding have been published. We here report such a comparison of 296 ALL cases, the largest series to date. Only genomic imbalances >5 Mb and microdeletions targeting the BTG1, CDKN2A/B, EBF1, ERG, ETV6, IKZF1, PAX5, and RB1 genes and the pseudoautosomal region 1 (PAR1) were ascertained, in agreement with recent guidelines...
September 11, 2018: Genes, Chromosomes & Cancer
https://www.readbyqxmd.com/read/30203894/telomere-length-telomerase-reverse-transcriptase-promoter-mutations-and-melanoma-risk
#5
Sivaramakrishna Rachakonda, Haiying Kong, Nalini Srinivas, Zaida Garcia-Casado, Celia Requena, Mahdi Fallah, Barbara Heidenreich, Dolores Planelles, Victor Traves, Dirk Schadendorf, Eduardo Nagore, Rajiv Kumar
Telomere repeats at chromosomal ends, critical for genomic integrity, undergo age-dependent attrition and telomere length has been associated with different disorders including cancers. In this study, based on 1469 patients and 1158 healthy controls, we show a statistically significant (P = 6 × 10-10 ) association between increased telomere length and melanoma risk. Mendelian randomization, using 5 telomere length-associated polymorphisms, ruled out confounding factors or reverse causality and showed association between increased telomere length and melanoma risk with odds ratio of 2...
September 11, 2018: Genes, Chromosomes & Cancer
https://www.readbyqxmd.com/read/30203893/mutational-and-cytogenetic-analyses-of-188-cll-patients-with-trisomy-12-a-retrospective-study-from-the-french-innovative-leukemia-organization-filo-working-group
#6
Damien Roos-Weil, Florence Nguyen-Khac, Sylvie Chevret, Cyrille Touzeau, Clémence Roux, Julie Lejeune, Adrien Cosson, Stéphanie Mathis, Pierre Feugier, Stéphane Leprêtre, Marie-Christine Béné, Marine Baron, Sophie Raynaud, Stéphanie Struski, Virginie Eclache, Laurent Sutton, Claude Lesty, Hélène Merle-Béral, Florence Cymbalista, Loïc Ysebaert, Frédéric Davi, Véronique Leblond
Trisomy 12 (tri12) is the second most frequent chromosomal aberration (15%-20%) in chronic lymphocytic leukemia (CLL). Tri12 confers an intermediate prognosis but is a heterogeneous entity. We examined whether additional mutational or chromosomal alterations might impact tri12 patient outcomes. This retrospective study, carried out by the French Innovative Leukemia Organization, included 188 tri12 patients with comprehensive information on immunoglobulin heavy chain (IGHV) gene status, karyotypic/FISH abnormalities, and NOTCH1, TP53, SF3B1, and MYD88 mutations...
September 11, 2018: Genes, Chromosomes & Cancer
https://www.readbyqxmd.com/read/30203571/kmt2a-mll-rearrangements-observed-in-pediatric-young-adult-t-lymphoblastic-leukemia-lymphoma-a-10-year-review-from-a-single-cytogenetic-laboratory
#7
Jess F Peterson, Linda B Baughn, Kathryn E Pearce, Cynthia M Williamson, Jonna C Benevides Demasi, Renee M Olson, Tony A Goble, Reid G Meyer, Patricia T Greipp, Rhett P Ketterling
T-lymphoblastic leukemia/lymphoma (T-ALL/LBL) accounts for approximately 15% of pediatric and 25% of adult ALL. While the underlying frequency of KMT2A (MLL) gene rearrangements has been identified in approximately 4-8% of T-ALL/LBL cases, a paucity of literature is available to characterize further the KMT2A rearrangements in pediatric/young adult T-ALL/LBL. A 10-year retrospective review was performed to identify KMT2A rearrangements in specimens sent for T-ALL/LBL fluorescence in situ hybridization studies in patients under the age of 30 years...
September 10, 2018: Genes, Chromosomes & Cancer
https://www.readbyqxmd.com/read/30187985/new-advances-in-the-molecular-classification-of-pediatric-mesenchymal-tumors
#8
REVIEW
Albert Jh Suurmeijer, Yu-Chien Kao, Cristina R Antonescu
Pediatric soft tissue tumors are relatively rare and show significant overlap in morphology and immunoprofile, often posing diagnostic and management challenges. Thus their classification remains often subjective or lumped under 'unclassified categories', as a number of lesions lack objective and reproducible criteria in diagnosis. Although in a subset of cases immunohistochemistry has been proved useful to identify a specific line of differentiation, most tumors lack a readily defined histogenesis, being characterized by a rather non-specific immunoprofile...
September 6, 2018: Genes, Chromosomes & Cancer
https://www.readbyqxmd.com/read/30144205/genomic-analysis-reveals-recurrent-deletion-of-jak-stat-signaling-inhibitors-hnrnpk-and-socs1-in-mycosis-fungoides
#9
Armando N Bastidas Torres, Davy Cats, Hailiang Mei, Karoly Szuhai, Rein Willemze, Maarten H Vermeer, Cornelis P Tensen
Mycosis fungoides (MF) is the most common cutaneous T-cell lymphoma (CTCL). Causative genetic alterations in MF are unknown. The low recurrence of pathogenic small-scale mutations (i.e. nucleotide substitutions, indels) in the disease, calls for the study of additional aspects of MF genetics. Here, we investigated structural genomic alterations in tumor-stage MF by integrating whole-genome sequencing and RNA-sequencing. Multiple genes with roles in cell physiology (n=113) and metabolism (n=92) were found to be impacted by genomic rearrangements, including 47 genes currently implicated in cancer...
August 25, 2018: Genes, Chromosomes & Cancer
https://www.readbyqxmd.com/read/30144193/putative-new-childhood-leukemia-cancer-predisposition-syndrome-caused-by-germline-bi-allelic-missense-mutations-in-ddx41
#10
Birgitte R Diness, Lotte Risom, Thomas L Frandsen, Bente Hansen, Mette K Andersen, Kjeld Schmiegelow, Karin A W Wadt
DDX41 has recently been identified as a new autosomal dominantly inherited cancer predisposition syndrome causing increased risk of adult onset acute myeloid leukemia (AML) or myelodysplastic syndrome (MDS). We report for the first time compound heterozygote germline missense DDX41 mutations located in the DEAD-box domain, identified in two siblings by exome sequencing. Both siblings have slight dysmorphic findings, psychomotor delays and intellectual disability, and one developed blastic plasmacytoid dendritic cell neoplasm (BPDCN) at age five...
August 25, 2018: Genes, Chromosomes & Cancer
https://www.readbyqxmd.com/read/30144186/novel-epc1-gene-fusions-in-endometrial-stromal-sarcoma
#11
Brendan C Dickson, Amy Lum, David Swanson, Marcus Q Bernardini, Terrence J Colgan, Patricia A Shaw, Stephen Yip, Cheng-Han Lee
Endometrial stromal sarcoma encompasses a heterogeneous group of uterine mesenchymal neoplasms, which are currently divided into low-grade and high-grade subtypes. Low-grade endometrial stromal sarcoma is morphologically bland; molecularly, these tumors frequently contain JAZF1-SUZ12, JAZF1-PHF1, and EPC1-PHF1 fusions. In contrast, high-grade endometrial stromal sarcoma is characterized by morphologically undifferentiated neoplasms with high-grade nuclear features; these tumors likewise appear to be genetically diverse with YWHAE-NUTM2 and ZC3H7B-BCOR representing the most frequent gene fusions...
August 24, 2018: Genes, Chromosomes & Cancer
https://www.readbyqxmd.com/read/30136738/expanding-the-spectrum-of-translocations-in-sclerosing-epitheloid-fibrosarcoma-a-new-case-with-ewsr1-creb3l3-fusion
#12
LETTER
Fei Dong, Bradley J Quade, Paola Dal Cin, Vickie Y Jo
No abstract text is available yet for this article.
August 23, 2018: Genes, Chromosomes & Cancer
https://www.readbyqxmd.com/read/30136351/clonal-evolution-analysis-of-paired-anaplastic-and-well-differentiated-thyroid-carcinomas-reveals-shared-common-ancestor
#13
Weilai Dong, Norman G Nicolson, Jungmin Choi, Andrea L Barbieri, John W Kunstman, Sara Abou Azar, James Knight, Kaya Bilguvar, Shrikant M Mane, Richard P Lifton, Reju Korah, Tobias Carling
Foci of papillary or follicular thyroid carcinoma are frequently noted in thyroidectomy specimens of anaplastic thyroid carcinoma (ATC). However, whether ATCs evolve from these co-existing well-differentiated thyroid carcinomas (WDTCs) has not been well-understood. To investigate the progression of ATC in patients with co-existing WDTCs, five ATC tumors with co-existing WDTCs and matching normal tissues were whole-exome sequenced. After mapping the somatic alteration landscape, evolutionary lineages were constructed by sub-clone analysis...
August 22, 2018: Genes, Chromosomes & Cancer
https://www.readbyqxmd.com/read/30126017/preoperative-diagnosis-of-clear-cell-sarcoma-of-the-kidney-by-detection-of-bcor-internal-tandem-duplication-in-circulating-tumor-dna
#14
Hitomi Ueno-Yokohata, Hajime Okita, Keiko Nakasato, Tomoro Hishiki, Ryota Shirai, Shinichi Tsujimoto, Tomoo Osumi, Satoshi Yoshimura, Yuji Yamada, Yoko Shioda, Chikako Kiyotani, Keita Terashima, Osamu Miyazaki, Kimikazu Matsumoto, Nobutaka Kiyokawa, Takako Yoshioka, Motohiro Kato
Clear cell sarcoma of the kidney (CCSK) is the second most common renal malignancy in children. The prognosis is poorer in CCSK than in Wilms' tumor, and multimodal treatment including surgery, intensive chemotherapy, and radiation is required to improve the outcome for children with CCSK. Histological evaluation is required for the diagnosis. However, biopsies of tumors to obtain diagnostic specimens are not routinely performed because of the risk of spreading tumor cells during the procedure. Recently, internal tandem duplication (ITD) of BCOR has been recognized as a genetic hallmark of CCSK...
August 20, 2018: Genes, Chromosomes & Cancer
https://www.readbyqxmd.com/read/30107055/driver-mutations-of-young-lung-adenocarcinoma-patients-with-malignant-pleural-effusion
#15
Shang-Gin Wu, Yi-Nan Liu, Chong-Jen Yu, James Chih-Hsin Yang, Jin-Yuan Shih
Young lung cancer patients have several distinct characteristics. However, there are limited epidemiological data of genetic abnormalities in this population. We conducted a prospective cohort study to delineate the various oncogenic driver mutations of lung adenocarcinoma in young Asian patients. We consecutively collected malignant pleural effusions (MPEs) from lung adenocarcinoma patients. RNA was extracted from MPEs for mutation analysis by reverse transcription-polymerase chain reaction and direct sequencing...
August 14, 2018: Genes, Chromosomes & Cancer
https://www.readbyqxmd.com/read/30107050/a-case-of-pediatric-acute-myeloid-leukemia-with-t-11-16-q23-q24-leading-to-a-novel-kmt2a-usp10-fusion-gene
#16
Elena Zerkalenkova, Svetlana Lebedeva, Anna Kazakova, Pavel Baryshev, Claus Meyer, Rolf Marschalek, Galina Novichkova, Michael Maschan, Aleksey Maschan, Yulia Olshanskaya
We present a leukemia case that exhibits a chromosomal translocation t(11;16)(q23;q23), which results in the expression of a novel KMT2A fusion gene. This novel fusion, KMT2A-USP10, was found in a relapse of acute myeloid leukaemia M5a. USP10 belongs to a protein family that deubiquitinates a distinct set of target proteins, and thus, increases the steady state protein levels of its target subproteome. One of the USP10 targets is TP53. Wildtype TP53 is usually rescued from proteasomal degradation by USP10. As most KMT2A leukemias display wildtype p53 alleles, one might argue that the disruption of an USP10 allele can be classified as a pro-oncogenic event...
October 2018: Genes, Chromosomes & Cancer
https://www.readbyqxmd.com/read/29923647/13q-deletion-is-linked-to-an-adverse-phenotype-and-poor-prognosis-in-prostate-cancer
#17
Martina Kluth, Sekander Scherzai, Franziska Büschek, Christoph Fraune, Katharina Möller, Doris Höflmayer, Sarah Minner, Cosima Göbel, Christina Möller-Koop, Andrea Hinsch, Emily Neubauer, Maria Christina Tsourlakis, Guido Sauter, Hans Heinzer, Markus Graefen, Waldemar Wilczak, Andreas M Luebke, Eike Burandt, Stefan Steurer, Thorsten Schlomm, Ronald Simon
Deletions of chromosome arm 13q belong to the most frequent molecular alterations in prostate cancer. To better understand the role of 13q deletion in prostate cancer we took advantage of our large prostate cancer tissue microarray comprising more than 12 000 cancer samples with full pathological and clinical follow-up data. Fluorescence in situ hybridization with probes for ENOX1 (13q14.11) and the retinoblastoma gene (RB1, 13q14.2) was employed. A 13q deletion was found in 21% of 7375 analyzable cancers...
October 2018: Genes, Chromosomes & Cancer
https://www.readbyqxmd.com/read/29901254/novel-intra-genic-large-deletions-of-ctnnb1-gene-identified-in-wt-desmoid-type-fibromatosis
#18
Chiara Colombo, Milena Urbini, Annalisa Astolfi, Paola Collini, Valentina Indio, Antonino Belfiore, Nicholas Paielli, Federica Perrone, Giuseppe Tarantino, Elena Palassini, Marco Fiore, Andrea Pession, Silvia Stacchiotti, Maria Abbondanza Pantaleo, Alessandro Gronchi
A wait and see approach for desmoid tumors (DT) has become part of the routine treatment strategy. However, predictive factors to select the risk of progressive disease are still lacking. A translational project was run in order to identify genomic signatures in patients enrolled within an Italian prospective observational study. Among 12 DT patients (10 CTNNB1-mutated and 2 wild type) enrolled from our institution only two patients (17%) showed a progressive disease. Tumor biopsies were collected for whole exome sequencing...
October 2018: Genes, Chromosomes & Cancer
https://www.readbyqxmd.com/read/29790226/comparative-analysis-of-akt-and-the-related-biomarkers-in-uterine-leiomyomas-with-med12-hmga2-and-fh-mutations
#19
Jia Xie, Julianne Ubango, Yanli Ban, Debabrata Chakravarti, J Julie Kim, Jian-Jun Wei
Uterine leiomyomas (ULM) are histologically and molecularly heterogeneous and clinically they grow at vastly different rates. Several driver gene mutations have been identified in ULM, including MED12 mutations, HMGA2 overexpression, and biallelic FH inactivation. ULM with different driver mutant genes may use different molecular pathways, but currently no clear correlation between gene mutations and growth related pathways has been established. To better define this relationship, we collected ULM with MED12 (n = 25), HMGA2 (n = 15), and FH (n = 27) mutations and examined the sex steroid hormone, cell cycle, and AKT pathway genes by immunohistochemistry...
October 2018: Genes, Chromosomes & Cancer
https://www.readbyqxmd.com/read/30014607/dermatofibrosarcoma-protuberans-with-a-novel-col6a3-pdgfd-fusion-gene-and-apparent-predilection-for-breast
#20
Brendan C Dickson, Jason L Hornick, Christopher D M Fletcher, Elizabeth G Demicco, David J Howarth, David Swanson, Lei Zhang, Yun-Shao Sung, Cristina R Antonescu
Dermatofibrosarcoma protuberans is a locally aggressive superficial mesenchymal neoplasm. It typically occurs in adulthood, and has been reported to have a slight male predilection. Tumors have a characteristic histopathologic appearance, including: storiform architecture, infiltrative "honeycomb" growth within subcutaneous adipose tissue, and immunoreactivity for CD34. Virtually all molecularly characterized cases to date have been found to harbor a COL1A1-PDGFB fusion product. Following identification of an index patient with a novel COL6A3-PDGFD fusion gene, we undertook a molecular investigation, using a combination of RNA sequencing and fluorescence in situ hybridization (FISH), to assess the prevalence of PDGFD rearrangement in dermatofibrosarcoma protuberans (N = 63)...
September 2018: Genes, Chromosomes & Cancer
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