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Genes, Chromosomes & Cancer

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https://read.qxmd.com/read/30767316/rna-sequencing-identifies-a-novel-usp9x-usp6-promoter-swap-gene-fusion-in-a-primary-aneurysmal-bone-cyst
#1
Patrick R Blackburn, Jaime I Davila, Rory A Jackson, Numrah Fadra, Mazen A Atiq, Beth A Pitel, Asha A Nair, Todd J Van De Walker, Mark G Hessler, Sara K Hovel, Rebecca N Wehrs, Karen J Fritchie, Robert B Jenkins, Kevin C Halling, Katherine B Geiersbach
Primary aneurysmal bone cyst (ABC) is a benign multiloculated cystic lesion of bone that is defined cytogenetically by USP6 gene rearrangements. Rearrangements involving USP6 are promoter swaps, usually generated by fusion of the non-coding upstream exons of different partner genes with exon 1 or 2 of USP6, thus leading to transcriptional upregulation of full-length USP6 coding sequence. Testing for USP6 rearrangements is used diagnostically to distinguish it from secondary ABC and other giant cell-rich primary bone tumors...
February 14, 2019: Genes, Chromosomes & Cancer
https://read.qxmd.com/read/30739374/early-detection-of-the-pax3-foxo1-fusion-gene-in-circulating-tumor-derived-dna-in-a-case-of-alveolar-rhabdomyosarcoma
#2
Minenori Eguchi-Ishimae, Mari Tezuka, Tomoki Kokeguchi, Kozo Nagai, Kyoko Moritani, Sachiko Yonezawa, Hisamichi Tauchi, Kiriko Tokuda, Yasushi Ishida, Eiichi Ishii, Mariko Eguchi
Cell-free DNA (cfDNA), which are small DNA fragments in blood derived from dead cells including tumor cells, could serve as useful biomarkers and provide valuable genetic information about the tumors. cfDNA is now used for the genetic analysis of several types of cancers, as a surrogate for tumor biopsy, designated as "liquid biopsy." Rhabdomyosarcoma (RMS), the most frequent soft tissue tumor in childhood, can arise in any part of the body, and radiological imaging is the only available method for estimating the tumor burden, because no useful specific biological markers are present in the blood...
February 10, 2019: Genes, Chromosomes & Cancer
https://read.qxmd.com/read/30707474/acute-leukemias-harboring-kmt2a-mllt10-fusion-a-10-year-experience-from-a-single-genomics-laboratory
#3
Jess F Peterson, William R Sukov, Beth A Pitel, Stephanie A Smoley, Kathryn E Pearce, Reid G Meyer, Cynthia M Williamson, James B Smadbeck, George Vasmatzis, Nicole L Hoppman, Patricia T Greipp, Linda B Baughn, Rhett P Ketterling
The MLLT10 (formerly AF10) gene is the fourth most common KMT2A fusion partner across all acute leukemias and requires at least three breaks to form an in-frame KMT2A/MLLT10 fusion due to the opposite orientation of each gene. A 10-year retrospective review was performed to identify individuals from all age groups that harbor KMT2A/MLLT10 fusion obtained by our KMT2A/MLLT10 dual-color dual-fusion fluorescence in situ hybridization (D-FISH) assay. Of the 60 unique individuals identified, 31 were male and 29 were female (M:F ratio, 1...
February 1, 2019: Genes, Chromosomes & Cancer
https://read.qxmd.com/read/30706625/pediatric-acute-myeloid-leukemia-with-t-7-21-p22-q22
#4
Prabakaran Paulraj, Steven Diamond, Faisal Razzaqi, Dan Ozeran, Maria Longhurst, Erica F Andersen, Reha M Toydemir, Bo Hong
The t(7;21)(p22;q22) resulting in RUNX1-USP42 fusion, is a rare but recurrent cytogenetic abnormality associated with acute myeloid leukemia (AML) and myelodysplastic syndromes (MDS). The prognostic significance of this translocation has not been well established due to the limited number of patients. Herein, we report three pediatric AML patients with t(7;21)(p22;q22). All three patients presented with pancytopenia or leukopenia at diagnosis, accompanied by abnormal immunophenotypic expression of CD7 and CD56 on leukemic blasts...
January 31, 2019: Genes, Chromosomes & Cancer
https://read.qxmd.com/read/30677207/comprehensive-molecular-and-clinicopathological-analysis-of-vascular-malformations-a-study-of-319-cases
#5
Roel W Ten Broek, Astrid Eijkelenboom, Carine J M van der Vleuten, Eveline J Kamping, Marleen Kets, Bas H Verhoeven, Katrien Grünberg, Leo J Schultze Kool, Bastiaan B J Tops, Marjolijn J L Ligtenberg, Uta Flucke
Vascular malformations are part of overgrowth syndromes characterized by somatic mosaic mutations or rarely by germline mutations. Due to their similarities and diversity, clinicopathological classification can be challenging. A comprehensive targeted Next Generation Sequencing screen using Unique Molecular Identifiers (UMI's) with a technical sensitivity of 1% mutant alleles was performed for frequently mutated positions in ≥21 genes on 319 formalin-fixed paraffin-embedded samples. In 132 out of 319 cases (likely) pathogenic mosaic mutations were detected affecting genes previously linked to vascular malformations e...
January 24, 2019: Genes, Chromosomes & Cancer
https://read.qxmd.com/read/30675954/newly-diagnosed-multiple-myeloma-patients-carrying-monoallelic-deletion-of-the-whole-locus-of-immunoglobulin-heavy-chain-gene-have-a-better-prognosis-compared-to-those-with-t-4-14-and-t-14-16
#6
Adrian Duek, Luba Trakhtenbrot, Ninette Amariglio, Noam Benyamini, Itay Zilbershats, Chezi Ganzel, Olga Shevetz, Ronit Leiba, Gabriela Rozic, Arnon Nagler, Merav Leiba
The current study evaluated the prognostic significance of the monoallelic deletion of the whole locus of the immunoglobulin heavy-chain (w_del(IGH)) gene compared to translocations t(4;14) and t(14;16) among newly-diagnosed multiple myeloma (MM) patients. We retrospectively analyzed clinical (age, gender, staging) and laboratory data at diagnosis and the overall survival (OS) of 255 newly-diagnosed MM patients carrying w_del(IGH) or translocations t(4;14) or t(14;16). Bone marrow samples were examined by morphological and sequential interphase fluorescense in situ hybridization analyses...
January 24, 2019: Genes, Chromosomes & Cancer
https://read.qxmd.com/read/30664823/novel-tg-fgfr1-and-trim33-ntrk1-transcript-fusions-in-papillary-thyroid-carcinoma
#7
Aleksandra Pfeifer, Dagmara Rusinek, Jadwiga Żebracka-Gala, Agnieszka Czarniecka, Ewa Chmielik, Ewa Zembala-Nożyńska, Bartosz Wojtaś, Bartłomiej Gielniewski, Sylwia Szpak-Ulczok, Małgorzata Oczko-Wojciechowska, Jolanta Krajewska, Joanna Polańska, Barbara Jarząb
Papillary thyroid carcinoma (PTC) is most common among all thyroid cancers. Multiple genomic alterations occur in PTC, and gene rearrangements are one of them. Here we screened 14 tumors for novel fusion transcripts by RNA-Seq. Two samples harboring RET/PTC1 and RET/PTC3 rearrangements were positive controls whereas the remaining ones were negative regarding the common PTC alterations. We used Sanger sequencing to validate potential fusions. We detected two novel potentially oncogenic transcript fusions: TG-FGFR1 and TRIM33-NTRK1...
January 21, 2019: Genes, Chromosomes & Cancer
https://read.qxmd.com/read/30664813/characterization-of-human-telomerase-reverse-transcriptase-promoter-methylation-and-transcription-factor-binding-in-differentiated-thyroid-cancer-cell-lines
#8
Brittany A Avin, Yongchun Wang, Timothy Gilpatrick, Rachael E Workman, Isac Lee, Winston Timp, Christopher B Umbricht, Martha A Zeiger
Telomerase reverse transcriptase (TERT) activation plays an important role in cancer development by enabling the immortalization of cells. TERT regulation is multifaceted, and its promoter methylation has been implicated in controlling expression through alteration in transcription factor binding. We have characterized TERT promoter methylation, transcription factor binding, and TERT expression levels in five differentiated thyroid cancer (DTC) cell lines and six normal thyroid tissue samples by targeted bisulfite sequencing, ChIP-qPCR, and qRT-PCR...
January 21, 2019: Genes, Chromosomes & Cancer
https://read.qxmd.com/read/30664301/chromosome-territories-and-the-global-regulation-of-the-genome
#9
REVIEW
Andrew J Fritz, Nitasha Sehgal, Artem Pliss, Jinhui Xu, Ronald Berezney
Spatial positioning is a fundamental principle governing nuclear processes. Chromatin is organized as a hierarchy from nucleosomes to Mbp chromatin domains (CD) or topologically associating domains (TADs) to higher level compartments culminating in chromosome territories (CT). Microscopic and sequencing techniques have substantiated chromatin organization as a critical factor regulating gene expression. For example, enhancers loop back to interact with their target genes almost exclusively within TADs, distally located coregulated genes reposition into common transcription factories upon activation and Mbp CD exhibit dynamic motion and configurational changes in vivo...
January 21, 2019: Genes, Chromosomes & Cancer
https://read.qxmd.com/read/30664300/tumor-mutational-burden-tmb-standardization-initiatives-recommendations-for-consistent-tmb-assessment-in-clinical-samples-to-guide-immunotherapy-treatment-decisions
#10
Albrecht Stenzinger, Jeffrey D Allen, Jörg Maas, Mark D Stewart, Diana M Merino, Madison M Wempe, Manfred Dietel
Characterization of tumors utilizing next-generation sequencing methods, including assessment of the number of somatic mutations (tumor mutational burden [TMB]), is currently at the forefront of the field of personalized medicine. Recent clinical studies have associated high TMB with improved patient response rates and survival benefit from immune checkpoint inhibitors; hence, TMB is emerging as a biomarker of response for these immunotherapy agents. However, variability in current methods for TMB estimation and reporting is evident, demonstrating a need for standardization and harmonization of TMB assessment methodology across assays and centers...
January 21, 2019: Genes, Chromosomes & Cancer
https://read.qxmd.com/read/30623509/5q21-deletion-is-often-heterogeneous-in-prostate-cancer
#11
Martina Kluth, Zaid Abdelaziz, Cansu Özden, Khakan Hussein, Sohall Frogh, Christina Möller-Koop, Eike Burandt, Stefan Steurer, Franziska Büscheck, Frank Jacobsen, Andreas M Luebke, Sarah Minner, Maria Christina Tsourlakis, Doris Hoeflmayer, Corinna Wittmer, Thorsten Schlomm, Guido Sauter, Ronald Simon, Waldemar Wilczak
Cancer heterogeneity represents a challenge for the analysis of prognostic molecular markers but can be used to study the evolution of molecular events in tumors. To assess the degree of heterogeneity of 5q21 deletions and their relationship with TMPRSS2:ERG status and 6q15 deletions in prostate cancer, a heterogeneity tissue microarray including 10 tissue spots from 10 different areas of 317 cancers was analyzed by fluorescence in situ hybridization for 5q21 deletion. Data on 6q and ERG were available from earlier studies...
January 9, 2019: Genes, Chromosomes & Cancer
https://read.qxmd.com/read/30614587/jumping-translocations-short-telomeres-or-pathogenic-tp53-variants-as-underlying-mechanism-in-acute-myeloid-leukemia-and-myelodysplastic-syndrome
#12
Yvonne Lisa Behrens, Kathrin Thomay, Maike Hagedorn, Juliane Ebersold, Gunnar Schmidt, Jana Lentes, Claudia Davenport, Brigitte Schlegelberger, Gudrun Göhring
Chromosomal rearrangements involving one donor chromosome and two or more recipient chromosomes are called jumping translocations. To date only few cases of acute myeloid leukemia (AML) and myelodysplastic syndrome (MDS) with jumping translocations have been described and the underlying mechanisms remain unclear. Here, we analyzed 11 AML and 5 MDS cases with jumping translocations. The cases were analyzed by karyotyping, FISH, telomere length measurement, and next-generation sequencing with an AML/MDS gene panel...
January 7, 2019: Genes, Chromosomes & Cancer
https://read.qxmd.com/read/30597651/further-evidence-that-full-gene-deletions-of-dicer1-predispose-to-dicer1-syndrome
#13
LETTER
Leanne de Kock, Morten Hillmer, Rabea Wagener, Dorothée Bouron-Dal Soglio, Nelly Sabbaghian, Reiner Siebert, John R Priest, Michal Miller, William D Foulkes
No abstract text is available yet for this article.
December 30, 2018: Genes, Chromosomes & Cancer
https://read.qxmd.com/read/30597648/integrative-analysis-of-copy-number-and-gene-expression-data-identifies-potential-oncogenic-drivers-that-promote-mammary-tumor-recurrence
#14
Robert A Jones, Roger A Moorehead
Tumor recurrence represents a significant clinical challenge in the treatment and management of breast cancer. To investigate whether copy number aberrations (CNAs) facilitate the re-emergence of tumor growth from residual disease we performed array comparative genomic hybridization (aCGH) on primary and recurrent mammary tumors from an inducible mouse model of type-I insulin-like growth factor receptor (IGF-IR) driven breast cancer. This genome-wide analysis revealed primary and recurrent tumors harbored distinct copy number aberrations (CNAs) with relapsed tumors containing an increased number of gene-level gains and losses...
December 30, 2018: Genes, Chromosomes & Cancer
https://read.qxmd.com/read/30597645/frequent-mutations-of-genes-encoding-vacuolar-h-atpase-components-in-granular-cell-tumors
#15
Masaya Sekimizu, Akihiko Yoshida, Sachiyo Mitani, Naofumi Asano, Makoto Hirata, Takashi Kubo, Fumito Yamazaki, Hiromi Sakamoto, Mamoru Kato, Naohiro Makise, Taisuke Mori, Naoya Yamazaki, Shigeki Sekine, Ichiro Oda, Shun-Ichi Watanabe, Hiroaki Hiraga, Tsukasa Yonemoto, Teruya Kawamoto, Norifumi Naka, Yuki Funauchi, Yoshihiro Nishida, Kanya Honoki, Hirotaka Kawano, Hiroyuki Tsuchiya, Toshiyuki Kunisada, Koichi Matsuda, Katsunori Inagaki, Akira Kawai, Hitoshi Ichikawa
Granular cell tumors (GCTs) are rare mesenchymal tumors that exhibit a characteristic morphology and a finely granular cytoplasm. The genetic alterations responsible for GCT tumorigenesis had been unknown until recently, when loss-of-function mutations of ATP6AP1 and ATP6AP2 were described. Thus, we performed whole-exome sequencing, RNA sequencing, and targeted sequencing of 51 GCT samples. From these genomic analyses, we identified mutations in genes encoding vacuolar H+ -ATPase (V-ATPase) components, including ATP6AP1 and ATP6AP2, in 33 (65%) GCTs...
December 30, 2018: Genes, Chromosomes & Cancer
https://read.qxmd.com/read/30582658/an-update-of-molecular-pathology-of-bone-tumors-lessons-learned-from-investigating-samples-by-next-generation-sequencing
#16
REVIEW
Daniel Baumhoer, Fernanda Amary, Adrienne M Flanagan
The last decade has seen the majority of primary bone tumor subtypes become defined by molecular genetic alteration. Examples include giant cell tumour of bone (H3F3A p.G34W), chondroblastoma (H3F3B p.K36M), mesenchymal chondrosarcoma (HEY1-NCOA2), chondromyxoid fibroma (GRM1 rearrangements), aneurysmal bone cyst (USP6 rearrangements), osteoblastoma/osteoid osteoma (FOS/FOSB rearrangements), and synovial chondromatosis (FN1-ACVR2A and ACVR2A-FN1). All such alterations are mutually exclusive. Many of these have been translated into clinical service using immunohistochemistry or FISH...
December 24, 2018: Genes, Chromosomes & Cancer
https://read.qxmd.com/read/30578714/non-leukemic-pediatric-mixed-phenotype-acute-leukemia-lymphoma-genomic-characterization-and-clinical-outcome-in-a-prospective-trial-for-pediatric-lymphoblastic-lymphoma
#17
Idoia Martin-Guerrero, Itziar Salaverria, Birgit Burkhardt, Catherine Chassagne-Clement, Monika Szczepanowski, Susanne Bens, Wolfram Klapper, Martin Zimmermann, Edita Kabickova, Yves Bertrand, Alfred Reiter, Reiner Siebert, Ilske Oschlies
Rare cases of hematological precursor neoplasms fulfill the diagnostic criteria of mixed phenotype acute leukemia (MPAL), characterized by expression patterns of at least two hematopoietic lineages, for which a highly aggressive behavior was reported. We present a series of 11 pediatric non-leukemic MPAL identified among 146 precursor lymphoblastic lymphomas included in the prospective trial Euro-LBL 02. Paraffin embedded biopsies of 10 cases were suitable for molecular analyses using OncoScan assay (n=7), fluorescence in situ hybridization (FISH) (n=7) or both (n=5)...
December 22, 2018: Genes, Chromosomes & Cancer
https://read.qxmd.com/read/30578699/role-of-mirnas-in-immune-responses-and-immunotherapy-in-cancer
#18
REVIEW
Maria Angelica Cortez, Simone Anfossi, Rishab Ramapriyan, Hari Menon, Semra Cemre Atalar, Maureen Aliru, James Welsh, George A Calin
In the past decade, the study of mechanisms of cancer immunity has seen a prominent boom, which paralleled the increased amount of research on the clinical efficacy of immune checkpoint blockade in several lethal types of cancers. This conspicuous effort has led to the development of successful immunotherapy treatment strategies, whose medical impact has been recognized by the awarding of 2018 Nobel Prize in Physiology or Medicine to the two pioneers of check point inhibitor research, Tasuku Honjo and James Allison...
December 22, 2018: Genes, Chromosomes & Cancer
https://read.qxmd.com/read/30578698/the-intersection-of-fragile-chromosome-loci-replication-stress-and-genome-instability
#19
REVIEW
Kay Huebner
No abstract text is available yet for this article.
December 22, 2018: Genes, Chromosomes & Cancer
https://read.qxmd.com/read/30578689/bcc-developing-independently-from-bap1-tumor-predisposition-syndrome-in-a-patient-with-bilateral-uveal-melanoma-diagnostic-challenges-to-identify-patients-with-bap1-tpds
#20
Charlotte Melzer, Amit Sharma, Sophia Peters, Stefan Aretz, Arijit Biswas, Frank G Holz, Karin U Loeffler, Martina C Herwig-Carl
Basal cell carcinomas (BCC) have been recently included into the spectrum of BAP1-tumor predisposition syndrome (TPDS). Uveal melanoma (UM) is also a tumor often observed in patients with this hereditary tumor syndrome, in particular bilateral UM is highly suspicious for BAP1-TPDS although no patient has been reported yet. Based on our index patient with BAP1-TPDS with bilateral uveal melanoma (iris OS, choroid OD), several BCCs and thyroid cancer as well as a family history for cancer, this paper analyzes hints and pitfalls to diagnose this syndrome clinically and histologically...
December 22, 2018: Genes, Chromosomes & Cancer
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