keyword
https://read.qxmd.com/read/38489371/increased-genomic-instability-and-reshaping-of-tissue-microenvironment-underlie-oncogenic-properties-of-arid1a-mutations
#1
JOURNAL ARTICLE
Alessandro D'Ambrosio, Davide Bressan, Elisa Ferracci, Francesco Carbone, Patrizia Mulè, Federico Rossi, Caterina Barbieri, Elisa Sorrenti, Gaia Fiaccadori, Thomas Detone, Elena Vezzoli, Salvatore Bianchi, Chiara Sartori, Simona Corso, Akihisa Fukuda, Giovanni Bertalot, Andrea Falqui, Mattia Barbareschi, Alessandro Romanel, Diego Pasini, Fulvio Chiacchiera
Oncogenic mutations accumulating in many chromatin-associated proteins have been identified in different tumor types. With a mutation rate from 10 to 57%, ARID1A has been widely considered a tumor suppressor gene. However, whether this role is mainly due to its transcriptional-related activities or its ability to preserve genome integrity is still a matter of intense debate. Here, we show that ARID1A is largely dispensable for preserving enhancer-dependent transcriptional regulation, being ARID1B sufficient and required to compensate for ARID1A loss...
March 15, 2024: Science Advances
https://read.qxmd.com/read/38462571/mutational-immune-microenvironment-and-clinicopathological-profiles-of-diffuse-large-b-cell-lymphoma-and-follicular-lymphoma-with-bcl6-rearrangement
#2
JOURNAL ARTICLE
Joaquim Carreras, Haruka Ikoma, Yara Yukie Kikuti, Masashi Miyaoka, Shinichiro Hiraiwa, Sakura Tomita, Yusuke Kondo, Atsushi Ito, Shunsuke Nagase, Hisanobu Miura, Hiroshi Kawada, Giovanna Roncador, Elias Campo, Rifat Hamoudi, Naoya Nakamura
BCL6-rearrangement (BCL6-R) is associated with a favorable prognosis of follicular lymphoma (FL), but the mechanism is unknown. We analyzed the clinicopathological, immune microenvironment (immune checkpoint, immuno-oncology markers), and mutational profiles of 10 BCL6-R-positive FL, and 19 BCL6-R-positive diffuse large B-cell lymphoma (DLBCL) cases (both BCL2-R and MYC-R negative). A custom-made panel included 168 genes related to aggressive B-cell lymphomas and FL. FL cases were nodal, histological grade 3A in 70%, low Ki67; and had a favorable overall and progression-free survival...
March 11, 2024: Virchows Archiv: An International Journal of Pathology
https://read.qxmd.com/read/38461804/genetic-evaluation-using-next-generation-sequencing-of-children-with-short-stature-a-single-tertiary-center-experience
#3
JOURNAL ARTICLE
Su Jin Kim, Eunyoung Joo, Jisun Park, Chang Ahn Seol, Ji-Eun Lee
PURPOSE: We used next-generation sequencing (NGS) to investigate the genetic causes of suspected genetic short stature in 37 patients, and we describe their phenotypes and various genetic spectra. METHODS: We reviewed the medical records of 50 patients who underwent genetic testing using NGS for suspected genetic short stature from June 2019 to December 2022. Patients with short stature caused by nongenetic factors or common chromosomal abnormalities were excluded...
February 2024: Annals of Pediatric Endocrinology & Metabolism
https://read.qxmd.com/read/38421446/genomic-drivers-in-craniopharyngiomas-analysis-of-the-aacr-project-genie-database
#4
JOURNAL ARTICLE
M Brandon Lehrich, C L Charles Tong, P K Frank Hsu, C Edward Kuan
PURPOSE: Craniopharyngiomas are rare tumors originating in the sellar region, with limited information on their somatic mutational landscape. In this study, we utilized a publicly available genomic database to profile the somatic mutational landscape of craniopharyngioma patients and interrogate differences based on histologic subtype. METHODS: We utilized the American Association for Cancer Research (AACR) Project Genomics Evidence Neoplasia Information Exchange (GENIE)® database accessed from cBioPortal (v13...
February 29, 2024: Child's Nervous System: ChNS: Official Journal of the International Society for Pediatric Neurosurgery
https://read.qxmd.com/read/38411299/adult-epithelioid-glioblastoma-exhibits-an-extremely-poor-prognosis-and-high-frequency-of-swi-snf-complex-mutation-insights-from-a-retrospective-study
#5
JOURNAL ARTICLE
Shaoyan Xi, Shimeng Jiang, Hainan Li, Qitao Huang, Jiabin Lu, Xing Zhang, Zhi Li, Jing Zeng
Epithelioid glioblastoma (eGBM) is a rare subtype of GBM. Given the update of the definition of GBM, the understanding of the molecular characteristics and prognosis of "true" adult eGBM remains limited. Herein, we retrospectively analyzed the clinicopathological data of 39 adult eGBM cases. Adult eGBM primarily affected females, with a male-to-female ratio of 1:2.3. The average age of diagnosis was 53 years, and the tumor affected the temporal lobe in 41% of cases (16/39, 41%). Microscopically, the tumors consisted mainly or entirely of epithelioid cells...
February 27, 2024: International Journal of Cancer. Journal International du Cancer
https://read.qxmd.com/read/38393316/large-scale-cancer-genomic-analysis-reveals-significant-disparities-between-microsatellite-instability-and-tumor-mutational-burden
#6
JOURNAL ARTICLE
Jungyoon Choi, Kyong Hwa Park, Yeul Hong Kim, Jason K Sa, Hwa Jung Sung, Yu-Wei Chen, Zhishan Chen, Chao Li, Wanqing Wen, Qingrun Zhang, Xiao-Ou Shu, Wei Zheng, Jung Sun Kim, Xingyi Guo
BACKGROUND: Microsatellite instability (MSI) and tumor mutational burden (TMB) are predictive biomarkers for pan-cancer immunotherapy. The interrelationship between MSI-high (MSI-H) and TMB-high (TMB-H) in human cancers and their predictive value for immunotherapy in lung cancer remain unclear. METHODS: We analyzed somatic mutation data from the Genomics Evidence Neoplasia Information Exchange (n = 46,320) to determine the relationship between MSI-H and TMB-H in human cancers using adjusted multivariate regression models...
February 23, 2024: Cancer Epidemiology, Biomarkers & Prevention
https://read.qxmd.com/read/38347147/protein-destabilization-underlies-pathogenic-missense-mutations-in-arid1b
#7
JOURNAL ARTICLE
Fanny Mermet-Meillon, Samuele Mercan, Beatrice Bauer-Probst, Cyril Allard, Melusine Bleu, Keith Calkins, Judith Knehr, Marc Altorfer, Ulrike Naumann, Kathleen Sprouffske, Louise Barys, Fabian Sesterhenn, Giorgio G Galli
ARID1B is a SWI/SNF subunit frequently mutated in human Coffin-Siris syndrome (CSS) and it is necessary for proliferation of ARID1A mutant cancers. While most CSS ARID1B aberrations introduce frameshifts or stop codons, the functional consequence of missense mutations found in ARID1B is unclear. We here perform saturated mutagenesis screens on ARID1B and demonstrate that protein destabilization is the main mechanism associated with pathogenic missense mutations in patients with Coffin-Siris Syndrome.
February 12, 2024: Nature Structural & Molecular Biology
https://read.qxmd.com/read/38252063/clinical-utility-of-plasma-cell-free-dna-in-pancreatic-neuroendocrine-neoplasms
#8
JOURNAL ARTICLE
Darren Cowzer, Ronak H Shah, Joanne F Chou, Ritika Kundra, Sippy Punn, Laura Fiedler, April DeMore, Marinela Capanu, Michael F Berger, Diane Reidy-Lagunes, Nitya Raj
In advanced pancreatic neuroendocrine neoplasms (PanNEN), there is little data detailing the frequency of genetic alterations identified in cell free DNA (cfDNA), plasma-tissue concordance of detected alterations, and clinical utility of cfDNA. Patients with metastatic PanNENs underwent cfDNA collection in routine practice. Next-generation sequencing (NGS) of cfDNA and matched tissue when available was performed. Clinical actionability of variants was annotated by OncoKB. Thirty-two cfDNA samples were analyzed from 25 patients, the majority who had well differentiated intermediate grade disease (13/25; 52%)...
January 1, 2024: Endocrine-related Cancer
https://read.qxmd.com/read/38243407/arid2-a-milder-cause-of-coffin-siris-syndrome-broadening-the-phenotype-with-17-additional-individuals
#9
JOURNAL ARTICLE
Samantha A Schrier Vergano
Coffin-Siris Syndrome (CSS, MIM 135900) is now a well-described genetic condition caused by pathogenic variants in the Bromocriptine activating factor (BAF) complex, including ARID1B, ARID1A, ARID2, SMARCA4, SMARCE1, SMARCB1, SOX11, SMARCC2, DPF2, and more recently, BICRA. Individuals with CSS have a spectrum of various medical challenges, most often evident at birth, including feeding difficulties, hypotonia, organ-system anomalies, and learning and developmental differences. The classic finding of fifth digit hypo- or aplasia is seen variably...
January 19, 2024: American Journal of Medical Genetics. Part A
https://read.qxmd.com/read/38182156/coffin-siris-syndrome-case-series-of-three-patients-and-a-novel-arid2-variant
#10
JOURNAL ARTICLE
Donghyun Shin, Yoo Jung Lee, Yoon Hee Jo, Juhyun Kong, Yun-Jin Lee, Sang Ook Nam, Bo Lyun Lee, Seung Hwan Oh, Young Mi Kim
Coffin-Siris syndrome (CSS) is a rare congenital disorder characterized by coarse facial features, intellectual disability or developmental delay, and aplasia or hypoplasia of the tips of the fifth finger and/or toes. Mutations in genes affecting the switch/sucrose non-fermenting ATP-dependent chromatin remodeling complex are reported to cause CSS. Here, we describe three CSS patients. Two girls aged 3 and 2 years old presented with global developmental delay, poor growth, and a dysmorphic face. Whole-exome sequencing (WES) was performed and they were diagnosed with CSS due to heterozygous frameshift variants (c...
November 2023: Annals of Clinical and Laboratory Science
https://read.qxmd.com/read/38171562/-genetic-analysis-of-two-children-with-coffin-siris-syndrome-due-to-variants-of-arid1b-gene
#11
JOURNAL ARTICLE
Zhi Li, Fang Liu, Ruihua Wan, Yuanyuan Wu, Jun Liu
OBJECTIVE: To explore the genetic basis of two children with unexplained psychomotor developmental delay and facial dysmorphisms suggestive of Coffin-Siris syndrome (CSS). METHODS: A boy and a girl suspected for CSS at the 980th Hospital of the People's Liberation Army Joint Service Support Force respectively in July 2019 and January 2021, and seven members from their families, were selected as the study subjects. Clinical data and family history of the children were collected, and detailed physical examination was carried out, in addition with laboratory and related auxiliary examinations...
January 10, 2024: Zhonghua Yi Xue Yi Chuan Xue za Zhi, Zhonghua Yixue Yichuanxue Zazhi, Chinese Journal of Medical Genetics
https://read.qxmd.com/read/38167844/genome-wide-association-studies-for-economically-important-traits-in-mink-using-copy-number-variation
#12
JOURNAL ARTICLE
Pourya Davoudi, Duy Ngoc Do, Stefanie Colombo, Bruce Rathgeber, Mehdi Sargolzaei, Graham Plastow, Zhiquan Wang, Guoyu Hu, Shafagh Valipour, Younes Miar
Copy number variations (CNVs) are structural variants consisting of duplications and deletions of DNA segments, which are known to play important roles in the genetics of complex traits in livestock species. However, CNV-based genome-wide association studies (GWAS) have remained unexplored in American mink. Therefore, the purpose of the current study was to investigate the association between CNVs and complex traits in American mink. A CNV-based GWAS was performed with the ParseCNV2 software program using deregressed estimated breeding values of 27 traits as pseudophenotypes, categorized into traits of growth and feed efficiency, reproduction, pelt quality, and Aleutian disease tests...
January 2, 2024: Scientific Reports
https://read.qxmd.com/read/38139431/dna-copy-number-alterations-and-copy-neutral-loss-of-heterozygosity-in-adult-ph-negative-acute-b-lymphoblastic-leukemia-focus-on-the-genes-involved
#13
JOURNAL ARTICLE
Natalya Risinskaya, Maria Gladysheva, Abdulpatakh Abdulpatakhov, Yulia Chabaeva, Valeriya Surimova, Olga Aleshina, Anna Yushkova, Olga Dubova, Nikolay Kapranov, Irina Galtseva, Sergey Kulikov, Tatiana Obukhova, Andrey Sudarikov, Elena Parovichnikova
The landscape of chromosomal aberrations in the tumor cells of the patients with B-ALL is diverse and can influence the outcome of the disease. Molecular karyotyping at the onset of the disease using chromosomal microarray (CMA) is advisable to identify additional molecular factors associated with the prognosis of the disease. Molecular karyotyping data for 36 patients with Ph-negative B-ALL who received therapy according to the ALL-2016 protocol are presented. We analyzed copy number alterations and their prognostic significance for CDKN2A / B , DMRTA , DOCK8 , TP53 , SMARCA2 , PAX5 , XPA , FOXE1 , HEMGN , USP45 , RUNX1 , NF1 , IGF2BP1 , ERG , TMPRSS2 , CRLF2 , FGFR3 , FLNB , IKZF1 , RUNX2 , ARID1B , CIP2A , PIK3CA , ATM , RB1 , BIRC3 , MYC , IKZF3 , ETV6 , ZNF384 , PTPRJ , CCL20 , PAX3 , MTCH2 , TCF3 , IKZF2 , BTG1 , BTG2 , RAG1 , RAG2 , ELK3 , SH2B3 , EP300 , MAP2K2 , EBI3 , MEF2D , MEF2C , CEBPA , and TBLXR1 genes, choosing t(4;11) and t(7;14) as reference events...
December 18, 2023: International Journal of Molecular Sciences
https://read.qxmd.com/read/38130310/the-stage-dependent-prognostic-role-of-arid1a-in-hepatocellular-carcinoma
#14
JOURNAL ARTICLE
Hai Zhou, Dantong Sun, Chunxiao Miao, Junyan Tao, Chao Ge, Taoyang Chen, Hong Li, Helei Hou
BACKGROUND: Hepatocellular carcinoma (HCC) is one of the most common causes of cancer-related death. Although novel treatment currently achieves a better response, the majority of HCC patients develop resistance and cannot benefit. Hence, novel biomarkers for guiding therapy and predicting the prognosis are needed. METHODS: Tissue microarrays of 206 HCC patients were used, and ARID1A expression was determined by immunohistochemistry. Databases were used for the verification and expansion of our results...
November 30, 2023: Translational Cancer Research
https://read.qxmd.com/read/38117302/delineation-of-the-adult-phenotype-of-coffin-siris-syndrome-in-35-individuals
#15
JOURNAL ARTICLE
Ariane Schmetz, Hermann-Josef Lüdecke, Harald Surowy, Sugirtahn Sivalingam, Ange-Line Bruel, Roseline Caumes, Perrine Charles, Nicolas Chatron, Krystyna Chrzanowska, Marta Codina-Solà, Cindy Colson, Ivon Cuscó, Anne-Sophie Denommé-Pichon, Patrick Edery, Laurence Faivre, Andrew Green, Solveig Heide, Tzung-Chien Hsieh, Alexander Hustinx, Lotte Kleinendorst, Cordula Knopp, Florian Kraft, Peter M Krawitz, Amaia Lasa-Aranzasti, Gaetan Lesca, Vanesa López-González, Julien Maraval, Cyril Mignot, Teresa Neuhann, Christian Netzer, Barbara Oehl-Jaschkowitz, Florence Petit, Christophe Philippe, Renata Posmyk, Audrey Putoux, André Reis, María José Sánchez-Soler, Julia Suh, Tinatin Tkemaladze, Frédéric Tran Mau Them, André Travessa, Laura Trujillano, Irene Valenzuela, Mieke M van Haelst, Georgia Vasileiou, Catherine Vincent-Delorme, Mona Walther, Pablo Verde, Nuria C Bramswig, Dagmar Wieczorek
Coffin-Siris syndrome (CSS) is a rare multisystemic autosomal dominant disorder. Since 2012, alterations in genes of the SWI/SNF complex were identified as the molecular basis of CSS, studying largely pediatric cohorts. Therefore, there is a lack of information on the phenotype in adulthood, particularly on the clinical outcome in adulthood and associated risks. In an international collaborative effort, data from 35 individuals ≥ 18 years with a molecularly ascertained CSS diagnosis (variants in ARID1B, ARID2, SMARCA4, SMARCB1, SMARCC2, SMARCE1, SOX11, BICRA) using a comprehensive questionnaire was collected...
January 2024: Human Genetics
https://read.qxmd.com/read/38114583/de-novo-variants-underlying-monogenic-syndromes-with-intellectual-disability-in-a-neurodevelopmental-cohort-from-india
#16
JOURNAL ARTICLE
Shruti Pande, Purvi Majethia, Karthik Nair, Lakshmi Priya Rao, Selinda Mascarenhas, Namanpreet Kaur, Michelle C do Rosario, Kausthubham Neethukrishna, Ankur Chaurasia, Bhagesh Hunakunti, Nalesh Jadhav, Sruthy Xavier, Jeevan Kumar, Vivekananda Bhat, Gandham SriLakshmi Bhavani, Dhanya Lakshmi Narayanan, B L Yatheesha, Siddaramappa J Patil, Sheela Nampoothiri, Nutan Kamath, Shrikiran Aroor, Ramesh Bhat Y, Leslie E Lewis, Suvasini Sharma, Shruti Bajaj, Naveen Sankhyan, Shahyan Siddiqui, Shalini S Nayak, Stephanie Bielas, Katta Mohan Girisha, Anju Shukla
The contribution of de novo variants as a cause of intellectual disability (ID) is well established in several cohorts reported from the developed world. However, the genetic landscape as well as the appropriate testing strategies for identification of de novo variants of these disorders remain largely unknown in low-and middle-income countries like India. In this study, we delineate the clinical and genotypic spectrum of 54 families (55 individuals) with syndromic ID harboring rare de novo variants. We also emphasize on the effectiveness of singleton exome sequencing as a valuable tool for diagnosing these disorders in resource limited settings...
December 20, 2023: European Journal of Human Genetics: EJHG
https://read.qxmd.com/read/38113761/prioritizing-de-novo-potential-non-canonical-splicing-variants-in-neurodevelopmental-disorders
#17
JOURNAL ARTICLE
Kuokuo Li, Jifang Xiao, Zhengbao Ling, Tengfei Luo, Jingyu Xiong, Qian Chen, Lijie Dong, Yijing Wang, Xiaomeng Wang, Zhaowei Jiang, Lu Xia, Zhen Yu, Rong Hua, Rui Guo, Dongdong Tang, Mingrong Lv, Aojie Lian, Bin Li, GuiHu Zhao, Xiaojin He, Kun Xia, Yunxia Cao, Jinchen Li
BACKGROUND: Genomic variants outside of the canonical splicing site (±2) may generate abnormal mRNA splicing, which are defined as non-canonical splicing variants (NCSVs). However, the clinical interpretation of NCSVs in neurodevelopmental disorders (NDDs) is largely unknown. METHODS: We investigated the contribution of NCSVs to NDDs from 345,787 de novo variants (DNVs) in 47,574 patients with NDDs. We performed functional enrichment and protein-protein interaction analysis to assess the association between genes carrying prioritised NCSVs and NDDs...
December 18, 2023: EBioMedicine
https://read.qxmd.com/read/38113031/smarca4-brg1-deficient-uterine-neoplasm-with-hybrid-adenosarcoma-and-carcinoma-features-expanding-the-molecular-morphologic-spectrum-of-smarca4-driven-gynecologic-malignancies
#18
JOURNAL ARTICLE
Christina H Wei, Evita Sadimin, Mark Agulnik, Susan E Yost, Teri A Longacre, Oluwole Fadare
SMARCA4 gene encodes BRG1, a member of the SWItch/sucrose non-fermentable protein family involved in epigenetic transcriptional regulation of important cellular processes. In the uterine corpus, SMARCA4/BRG1 deficiency is associated with a novel class of undifferentiated uterine sarcomas, characterized by younger age onset, rhabdoid histology, focal phyllodiform architecture, high-risk pathologic findings, and dismal prognosis. Herein, we report a case of a 34-year-old Asian woman with a SMARCA4/BRG1-deficient uterine tumor fulfilling the clinicopathologic features of an undifferentiated uterine sarcoma...
December 12, 2023: International Journal of Gynecological Pathology
https://read.qxmd.com/read/38085333/smarcb1-deficient-sinonasal-adenocarcinoma-a-rare-variant-of-swi-snf-deficient-malignancy-often-misclassified-as-high-grade-non-intestinal-type-sinonasal-adenocarcinoma-or-myoepithelial-carcinoma
#19
JOURNAL ARTICLE
Alena Skálová, Touraj Taheri, Martina Bradová, Tomáš Vaněček, Alessandro Franchi, David Slouka, Tomáš Kostlivý, Gisele de Rezende, Jaroslav Michálek, Natálie Klubíčková, Nicola Ptáková, Antónia Nemcová, Michal Michal, Abbas Agaimy, Ilmo Leivo
SMARCB1-deficient sinonasal adenocarcinoma is a rare variant of SWI/SNF-deficient malignancies with SMARCB1 loss and adenocarcinoma features. More than 200 high-grade epithelial sinonasal malignancies were retrieved. A total of 14 cases exhibited complete SMARCB1 (INI1) loss and glandular differentiation. SMARCA2 and SMARCA4 were normal, except for one case with a loss of SMARCA2. Next-generation sequencing (NGS) and/or fluorescence in situ hybridization (FISH) revealed an alteration in the SMARCB1 gene in 9/13 cases, while 2/13 were negative...
December 12, 2023: Virchows Archiv: An International Journal of Pathology
https://read.qxmd.com/read/37944749/clinicopathological-features-of-a-rare-cancer-intrahepatic-lymphoepithelioma-like-cholangiocarcinoma-with-epstein-barr-virus-infection
#20
JOURNAL ARTICLE
Lingnan Zheng, Nan Zhou, Xi Yang, Yuanfeng Wei, Cheng Yi, Hongfeng Gou
PURPOSE: Epstein-Barr virus-related lymphoepithelioma-like cholangiocarcinoma (EBV-LELCC), a subtype of intrahepatic cholangiocarcinoma (IHCC), is an extremely rare cancer. To date, only few cases have been reported. Therefore, more studies are needed to provide new insights into its clinicopathological characteristics and treatment. METHODS: We retrospectively collected data from 16 EBV-LELCC patients admitted to our hospital between January 2013 and February 2022...
November 7, 2023: Clinics and Research in Hepatology and Gastroenterology
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