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Genes, Chromosomes & Cancer

Tala Achkar, Siraj M Ali, Allison Welsh, Rajiv Dhir, Susanne M Gollin, Rahul A Parikh
Tumor genome sequencing has become an invaluable resource in determining targets for new therapies. In this report, we describe the case of a patient with metastatic urothelial carcinoma with sarcomatoid features. Sarcomatoid differentiation is a rare histologic subtype that confers a more aggressive course. The first-line treatment for patients with urothelial carcinoma is platinum-based chemotherapy. Next generation tumor sequencing performed using the FoundationOne assay revealed loss of one NF2 allele and an unbalanced der(22)t(10;22)(p11...
March 13, 2018: Genes, Chromosomes & Cancer
Nicole Köger, Lea Paulsen, Francisco López-Kostner, Adriana Della Valle, Carlos Alberto Vaccaro, Edenir Inêz Palmero, Karin Alvarez, Carlos Sarroca, Florencia Neffa, Pablo German Kalfayan, Maria Laura Gonzalez, Benedito Mauro Rossi, Rui Manuel Reis, Angela Brieger, Stefan Zeuzem, Inga Hinrichsen, Mev Dominguez-Valentin, Guido Plotz
Inactivating mutations in the MLH1 gene cause the cancer predisposition Lynch syndrome, but for small coding genetic variants it is mostly unclear if they are inactivating or not. Nine such MLH1 variants have been identified in South American colorectal cancer (CRC) patients (p.Tyr97Asp, p.His112Gln, p.Pro141Ala, p.Arg265Pro, p.Asn338Ser, p.Ile501del, p.Arg575Lys, p.Lys618del, p.Leu676Pro), and evidence of pathogenicity or neutrality was not available for the majority of these variants. We therefore performed biochemical laboratory testing of the variant proteins and compared the results to protein in-silico predictions on structure and conservation...
March 9, 2018: Genes, Chromosomes & Cancer
Jyoti Roy, Bibekanand Mallick
Remarkable attempts have been exercised in recent years using high-throughput technologies to identify and decipher the functions of piRNAs in various abnormalities like cancer. However, piRNAs in the oncogenesis of neuroblastoma (NB) has not been reported yet even after their illustrated roles in neurological processes. Therefore, we investigated the piRNA transcriptome in IMR-32 and SH-SY-5Y NB cell lines by employing high-throughput next-generation sequencing after confirming the expression of three associated PIWILs both at mRNAs and protein level by qRT-PCR and immunofluroscence respectively...
March 8, 2018: Genes, Chromosomes & Cancer
Hélène Lasolle, Eudeline Alix, Clémentt Bonnefille, Mad-Hélénie Elsensohn, Jessica Michel, Damien Sanlaville, Pascal Roy, Gérald Raverot, Claire Bardel
Reliable interpretation of comparative genomic hybridization array (aCGH) results requires centralization and normalization of the data. We evaluated the reliability of aCGH centralization by comparing aCGH results (with classical centralization-normalization steps) to fluorescence in situ hybridization (FISH) results. In addition, we propose a method to correct centralization bias. Sixty-six pituitary tumors were analyzed (Agilent aCGH+SNP 4 × 180K microarray). For each tumor, the FISH-based log2 (ratios) of a subset of chromosomes were compared with the corresponding aCGH raw log2 (ratios)...
February 20, 2018: Genes, Chromosomes & Cancer
Danai Fimereli, Debora Fumagalli, David Brown, David Gacquer, Françoise Rothé, Roberto Salgado, Denis Larsimont, Christos Sotiriou, Vincent Detours
The advent of next generation sequencing technologies has boosted the interest in exploring the role of fusion genes in the development and progression of solid tumors. In breast cancer, most of the detected gene fusions seem to be "passenger" events while the presence of recurrent and driver fusions is still under study. We performed RNA sequencing in 55 well-characterized breast cancer samples and 10 adjacent normal breast tissues, complemented by an analysis of SNP array data. We explored the presence of fusion genes and defined their association with breast cancer subtypes, clinical-pathologic characteristics and copy number aberrations...
February 13, 2018: Genes, Chromosomes & Cancer
Mathieu Roussy, Mélanie Bilodeau, Loubna Jouan, Pauline Tibout, Louise Laramée, Emmanuelle Lemyre, Sophie Cardin, Camille Sauvageau, Françoise Couture, Aurélien Choblet, Natalie Patey, Patrick Gendron, Michel Duval, Pierre Teira, Josée Hébert, Brian T Wilhelm, John K Choi, Tanja A Gruber, Henrique Bittencourt, Sonia Cellot
The advent of large scale genomic sequencing technologies significantly improved the molecular classification of acute megakaryoblastic leukaemia (AMKL). AMKL represents a subset (∼10%) of high fatality pediatric acute myeloid leukemia (AML). Recurrent and mutually exclusive chimeric gene fusions associated with pediatric AMKL are found in 60-70% of cases and include RBM15-MKL1, CBFA2T3-GLIS2, NUP98-KDM5A and MLL rearrangements. In addition, another 4% of AMKL harbor NUP98 rearrangements (NUP98r), with yet undetermined fusion partners...
February 10, 2018: Genes, Chromosomes & Cancer
Raju Kumar, Viswakalyan Kotapalli, Ashmala Naz, Swarnalata Gowrishankar, Satish Rao, Jonathan R Pollack, Murali Dharan Bashyam
Canonical Wnt/β-catenin signaling plays important roles in embryonic development and adult tissue regeneration while aberrant Wnt activation is the major driver of sporadic colorectal cancer (CRC). Thus, it is important to characterize the complete β-catenin target transcriptome. We previously performed microarray-based mRNA profiling of rectal cancer samples stratified for Wnt status. In addition to AXIN2 and EPHB2, XPNPEP3 transcripts were significantly elevated in tumors exhibiting activated Wnt/β-catenin signaling, validated by Q-PCR...
January 31, 2018: Genes, Chromosomes & Cancer
Hyein Ahn, Jeong Mi Yang, Yoon Kyung Jeon, Jin Ho Paik
The A20/Tumor necrosis factor-alpha-induced protein 3 (A20/TNFAIP3) is a negative regulator of NF-κB signaling. We analyzed the clinicopathologic implications of A20 deletions in extranodal NK/T-cell lymphoma (NKTL). Fluorescence in situ hybridization analysis of the A20 gene was performed using archived formalin-fixed tissues in 49 cases of NKTL. Among the 49 NKTL patients (median age, 48 years [10-79]), stage I-II (75% [36/48]) and upper aerodigestive tract (UAT)-origin (84% [41/49]) were predominant. All A20 deletions were monoallelic and found in cases with UAT-origin, accounting for 18% (9/49) of all NKTLs and 22% (9/41) of UAT-origin...
January 30, 2018: Genes, Chromosomes & Cancer
Miguel López-Lázaro
Recent evidence indicates that the risk of being diagnosed with cancer in a tissue is strongly correlated (0.80) with the number of stem cell divisions accumulated by the tissue. Since cell division can generate random mutations during DNA replication, this correlation has been used to propose that cancer is largely caused by the accumulation of unavoidable mutations in driver genes. However, no correlation between the number of gene mutations and cancer risk across tissues has been reported. Because many somatic mutations in cancers originate prior to tumor initiation and the number of cell divisions occurring during tumor growth is similar among tissues, I use whole genome sequencing information from 22,086 cancer samples and incidence data from the largest cancer registry in each continent to study the relationship between the number of gene mutations and the risk of cancer across 33 tissue types...
January 29, 2018: Genes, Chromosomes & Cancer
Sou-Yi Chang, Chih-Chi Kuo, Chang-Chieh Wu, Cheng-Wen Hsiao, Je-Ming Hu, Chih-Hsiung Hsu, Yu-Ching Chou, Yu-Lueng Shih, Ya-Wen Lin
Colorectal cancer (CRC) is a common malignancy worldwide. CRC patients in the same stage often present with dramatically different clinical scenarios. Thus, robust prognostic biomarkers are urgently needed to guide therapies and improve treatment outcomes. The NKX6.1 gene has been identified as a hypermethylation marker in cervical cancer, functioning as a metastasis suppressor by regulating epithelial-mesenchymal transition. Here, we investigated whether hypermethylation of NKX6.1 might be a prognostic biomarker for CRC...
January 24, 2018: Genes, Chromosomes & Cancer
Meriem Benfodda, Steven Gazal, Vincent Descamps, Nicole Basset-Seguin, Lydia Deschamps, Luc Thomas, Philippe Saiag, Roberto Zanetti, Lidia Sacchetto, Giovanna Chiorino, Maria Scatolini, Bernard Grandchamp, Nadem Soufir
Genetic predisposition to cutaneous malignant melanoma (CMM) involves highly penetrant predisposing genes and low and intermediate penetrant predisposing alleles. However, the missing heritability in (CMM) is still high. For such and in order to identify new genetic factors for CMM, we conducted an exome sequencing study in high-risk CMM patients. Two rounds of exome sequencing were successively performed in 33 and 27 high-risk patients. We focused on genes carrying rare nonsense, frameshift, and splice variants (allelic frequency <1%) that were present in both series of exomes...
January 23, 2018: Genes, Chromosomes & Cancer
Karen A Dun, Louise A Riley, Giuseppe Diano, Leanne B Adams, Eleanor Chiu, Archna Sharma
Chromosome abnormalities detected during cytogenetic investigations for B-cell malignancy offer prognostic information that can have wide ranging clinical impacts on patients. These impacts may include monitoring frequency, treatment type and disease staging level. The use of the synthetic oligonucleotide DSP30 combined with interleukin 2 (IL2) has been described as an effective mitotic stimulant in B-cell disorders, predominantly in chronic lymphocytic leukaemia (CLL) but also a range of other B-cell malignancies...
January 19, 2018: Genes, Chromosomes & Cancer
Nicole Naumann, Mohamad Jawhar, Juliana Schwaab, Sebastian Kluger, Johannes Lübke, Georgia Metzgeroth, Henning D Popp, Nada Khaled, Hans-Peter Horny, Karl Sotlar, Peter Valent, Claudia Haferlach, Gudrun Göhring, Brigitte Schlegelberger, Manja Meggendorfer, Wolf-Karsten Hofmann, Nicholas C P Cross, Andreas Reiter, Alice Fabarius
The clinical behavior of systemic mastocytosis (SM) is strongly associated with activating mutations in KIT (D816V in >80% of cases), with the severity of the phenotype influenced by additional somatic mutations, e.g. in SRSF2, ASXL1 or RUNX1. Complex molecular profiles are frequently associated with the presence of an associated hematologic neoplasm (AHN) and an unfavorable clinical outcome. However, little is known about the incidence and prognostic impact of cytogenetic aberrations. We analyzed cytogenetic and molecular characteristics of 109 patients (KIT D816V+, n=102, 94%) with indolent (ISM, n=26) and advanced SM (n=83) with (n=73, 88%) or without AHN...
January 17, 2018: Genes, Chromosomes & Cancer
Farhadul Islam, Vinod Gopalan, Suja Pillai, Cu-Tai Lu, Kais Kasem, Alfred King-Yin Lam
The present study aims to examine promoter methylation status of FAM134B in a large cohort of patients with colorectal adenocarcinomas. The clinical significances and correlations of FAM134B promoter methylation with its expression are also analysed. Methylation-specific high-resolution melt-curve analysis followed by sequencing was used to identify FAM134B promoter methylation in colorectal adenomas (n=32), colorectal adenocarcinomas (n=164), matched adjacent non-neoplastic colorectal mucosae (n=83) and colon cancer cell lines (n=4)...
January 10, 2018: Genes, Chromosomes & Cancer
Leanne de Kock, Dominique Geoffrion, Barbara Rivera, Rabea Wagener, Nelly Sabbaghian, Susanne Bens, Benjamin Ellezam, Dorothée Bouron-Dal Soglio, Jessica Ordóñez, Stephanie Sacharow, Jose Fernando Polo Nieto, R Paul Guillerman, Gordan M Vujanic, John R Priest, Reiner Siebert, William D Foulkes
Germ-line interstitial deletions involving the 14q32 chromosomal region, resulting in 14q32 deletion syndrome, are rare. DICER1 is a recently described cancer-predisposition gene located at 14q32.13. We report the case of a male child with an approximately 5.8 Mbp 14q32.13q32.2 germ-line deletion, which included the full DICER1 locus. We reviewed available clinical and pathological material, and conducted genetic analyses. In addition to having congenital dysmorphic features, the child developed multiple DICER1 syndrome-related tumors before age 5 years: a pediatric cystic nephroma (pCN), a ciliary body medulloepithelioma (CBME), and a small lung cyst (consistent with occult pleuropulmonary blastoma Type I/Ir cysts seen in DICER1 mutation carriers)...
January 9, 2018: Genes, Chromosomes & Cancer
Liping Liu, Han Liu, Di Shao, Zu Liu, Jingjing Wang, Qiuhua Deng, Hailing Tang, Haihong Yang, Yalei Zhang, Yuan Qiu, Fei Cui, Meihua Tan, Pan Zhang, Zhilong Li, Jilong Liu, Wenhua Liang, Yuying Wang, Zhiyu Peng, Jian Wang, Huanming Yang, Mao Mao, Karsten Kristiansen, Mingzhi Ye, Jianxing He
Molecular analysis of potentially actionable mutations has become routine practice in oncological pathology. However, testing a wide range of oncogenes and mutations can be technically challenging because of limitations associated with tumor biopsy. Circulating tumor DNA (ctDNA) is a potential tool for the noninvasive profiling of tumors. In this study, we developed a next-generation sequencing (NGS)-based test for the detection of clinically relevant mutations in ctDNA and evaluated the feasibility of using this ctDNA NGS-based assay as an alternative to tissue genotyping...
December 26, 2017: Genes, Chromosomes & Cancer
Lila E Mullany, Jennifer S Herrick, Roger K Wolff, John R Stevens, Wade Samowitz, Martha L Slattery
Transcription factors (TFs) and microRNAs (miRNAs) regulate gene expression: TFs by influencing messenger RNA (mRNA) transcription and miRNAs by influencing mRNA translation and transcript degradation. Additionally, miRNAs and TFs alter each other's expression, making it difficult to ascertain the effect either one has on target gene (TG) expression. In this investigation, we use a two-way interaction model with the TF and miRNA as independent variables to investigate whether miRNAs and TFs work together to influence TG expression levels in colon cancer subjects...
April 2018: Genes, Chromosomes & Cancer
Marta Brunetti, Ioannis Panagopoulos, Ludmila Gorunova, Ben Davidson, Sverre Heim, Francesca Micci
Sarcomas account for 3% of all uterine malignancies and many of them are characterized by acquired, specific fusion genes whose detection has increased pathogenetic knowledge and diagnostic precision. We describe a novel fusion gene, GREB1-NCOA2, detected by transcriptome sequencing and validated by reverse transcriptase polymerase chain reaction and Sanger sequencing in an undifferentiated uterine sarcoma. The chimeric transcript was an in-frame fusion between exon 3 of GREB1 and exon 15 of NCOA2. The fusion is reported here for the first time, but it involves the GREB1 gene, an important promoter of tumor growth and progression, and NCOA2 which is known to be involved in transcriptional regulation...
April 2018: Genes, Chromosomes & Cancer
Pratima Basak, Heather Leslie, Rachelle L Dillon, William J Muller, Afshin Raouf, Michael R A Mowat
Overexpression of dominant oncogenes and the loss of tumor suppressor genes are basic genetic events in the acquisition of the malignant phenotype. The erb-b2 receptor tyrosine kinase 2 (ERBB-2) proto-oncogene is overexpressed in 20-30% of human breast cancers. The StAR related lipid transfer domain containing 13 gene (STARD13), also known as Deleted in Liver Cancer-2 (DLC-2), maps to chromosome band 13q12.3 and is frequently downregulated in human cancers, including 72% of breast cancers. It encodes a RhoGAP protein with sterile α motif (SAM) and StAR-related lipid transfer (START) domains...
April 2018: Genes, Chromosomes & Cancer
Johanna Oltmann, Kerstin Heselmeyer-Haddad, Leanora S Hernandez, Rüdiger Meyer, Irianna Torres, Yue Hu, Natalie Doberstein, J Keith Killian, David Petersen, Yuelin Jack Zhu, Daniel C Edelman, Paul S Meltzer, Russell Schwartz, E Michael Gertz, Alejandro A Schäffer, Gert Auer, Jens K Habermann, Thomas Ried
The clinical course of breast cancer varies from one patient to another. Currently, the choice of therapy relies on clinical parameters and histological and molecular tumor features. Alas, these markers are informative in only a subset of patients. Therefore, additional predictors of disease outcome would be valuable for treatment stratification. Extensive studies showed that the degree of variation of the nuclear DNA content, i.e., aneuploidy, determines prognosis. Our aim was to further elucidate the molecular basis of aneuploidy...
April 2018: Genes, Chromosomes & Cancer
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