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JOURNAL ARTICLE
Servane de Masfrand, Benjamin Cogné, Mathilde Nizon, Wallid Deb, Alice Goldenberg, François Lecoquierre, Gaël Nicolas, Marie Bournez, Antonio Vitobello, Frédéric Tran Mau-Them, Gwenaël le Guyader, Frédéric Bilan, Peter Bauer, Christiane Zweier, Juliette Piard, Laurent Pasquier, Stéphane Bézieau, Bénédicte Gerard, Laurence Faivre, Pascale Saugier-Veber, Amélie Piton, Bertrand Isidor
PURPOSE: Incomplete penetrance is observed for most monogenic diseases. However, for neurodevelopmental disorders, the interpretation of single and multi-nucleotide variants (SNV/MNVs) is usually based on the paradigm of complete penetrance. METHOD: From 2020 to 2022, we proposed a collaboration study with the French molecular diagnosis for intellectual disability network. The aim was to recruit families for whom the index case, diagnosed with a neurodevelopmental disorder, was carrying a pathogenic or likely pathogenic variant for an OMIM morbid gene and inherited from an asymptomatic parent...
March 5, 2024: European Journal of Medical Genetics
#2
JOURNAL ARTICLE
Zhang Dong, Wan Chong, Chen Chen, Li Qi, Li Mengke, Dou Minghui, Yuan Jiawei, Quan Longxi, Liu Hengchao, Jia Liu, Geng Zhimin
BACKGROUNDS: Ampullary adenocarcinoma (AMPAC) is a rare malignancy, treated as pancreatic or intestinal cancer based on its histologic subtype. Little is known about the genomic features of Chinese patients with AMPAC. MATERIALS AND METHODS: We enrolled 145 Chinese AMPAC patients in our local cohort and performed a compressive somatic and germline genetic testing using a 156 gene panel. Expression of PD-L1 (clone 28 - 8) was also assessed in tumor specimens from 64 patients...
March 4, 2024: BMC Cancer
#3
JOURNAL ARTICLE
Majd Al Assaad, Olivier Michaud, Alissa Semaan, Michael Sigouros, Marvel Tranquille, Andy Phan, Max F Levine, Gunes Gundem, Juan S Medina-Martínez, Elli Papaemmanuil, Jyothi Manohar, David Wilkes, Andrea Sboner, Syed A F Hoda, Olivier Elemento, Juan Miguel Mosquera
The molecular characterization of male breast cancer (MaBC) has received limited attention in research, mostly due to its low incidence rate, accounting for only 0.5-1% of all reported cases of breast cancer each year. Managing MaBC presents significant challenges, with most treatment protocols being adapted from those developed for female breast cancer. Utilizing whole-genome sequencing (WGS) and state-of-the-art analyses, the genomic features of ten (n=10) MaBC cases were delineated and correlated with clinical and histopathological characteristics...
February 16, 2024: Modern Pathology
#4
JOURNAL ARTICLE
Favour A Akinjiyan, George Nassief, Jordan Phillipps, Tolulope Adeyelu, Andrew Elliott, Farah Abdulla, Alice Y Zhou, George Souroullas, Kevin B Kim, Ari Vanderwalde, Soo J Park, George Ansstas
ARID genes encode subunits of SWI/SNF chromatin remodeling complexes and are frequently mutated in human cancers. We investigated the correlation between ARID mutations, molecular features, and clinical outcomes in melanoma patients. Cutaneous melanoma samples (n = 1577) were analyzed by next-generation sequencing. Samples were stratified by pathogenic/likely pathogenic mutation in ARID genes (ARID1A/2/1B/5B). PD-L1 expression was assessed using IHC (SP142; positive (+): ≥ 1%)...
February 11, 2024: Scientific Reports
#5
JOURNAL ARTICLE
Nilesh Gardi, Rohan Chaubal, Pallavi Parab, Sunil Pachakar, Suyash Kulkarni, Tanuja Shet, Shalaka Joshi, Yogesh Kembhavi, Pratik Chandrani, Jelmar Quist, Pradnya Kowtal, Anita Grigoriadis, Rajiv Sarin, Raman Govindarajan, Sudeep Gupta
UNLABELLED: We report a deep next-generation sequencing analysis of 13 sequentially obtained tumor samples, eight sequentially obtained circulating tumor DNA (ctDNA) samples and three germline DNA samples over the life history of 3 patients with triple-negative breast cancer (TNBC), 2 of whom had germline pathogenic BRCA1 mutation, to unravel tumor evolution. Tumor tissue from all timepoints and germline DNA was subjected to whole-exome sequencing (WES), custom amplicon deep sequencing (30,000X) of a WES-derived somatic mutation panel, and SNP arrays for copy-number variation (CNV), while whole transcriptome sequencing (RNA-seq) was performed only on somatic tumor...
February 14, 2024: Cancer Res Commun
#6
JOURNAL ARTICLE
Mark Lee, Luc Gt Morris
A subset of thyroid cancers present at advanced stage or with dedifferentiated histology and have limited response to standard therapy. Tumors harboring the BRAF V600E mutation may be treated with BRAF inhibitors; however, tumor response is often short lived due to multiple compensatory resistance mechanisms. One mode of resistance is the transition to an alternative cell state, which on rare occasions can correspond to tumor dedifferentiation. DNA sequencing and RNA expression profiling show that thyroid tumors that dedifferentiate after BRAF inhibition are enriched in known genetic alterations that mediate resistance to BRAF blockade, and may also drive tumor dedifferentiation, including mutations in the PI3K/AKT/MTOR ( PIK3CA , MTOR ), MAP/ERK ( MET , NF2 , NRAS , RASA1 ), SWI/SNF chromatin remodeling complex ( ARID2 , PBRM1 ), and JAK/STAT pathways ( JAK1 )...
January 24, 2024: Oncotarget
#7
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
#8
JOURNAL ARTICLE
Sara Lucila Lorenzo-Guerra, Helena Codina-Martínez, Laura Suárez-Fernández, Virginia N Cabal, Rocío García-Marín, Cristina Riobello, Blanca Vivanco, Verónica Blanco-Lorenzo, Paula Sánchez-Fernández, Fernando López, Jóse Luis Llorente, Mario A Hermsen
Sinonasal teratocarcinosarcoma (TCS) is a rare tumor that displays a variable histology with admixtures of epithelial, mesenchymal, neuroendocrine and germ cell elements. Facing a very poor prognosis, patients with TCS are in need of new options for treatment. Recently identified recurrent mutations in SMARCA4 may serve as target for modern therapies with EZH1/2 and CDK4/6 inhibitors. Here, we present the first in vitro cell line TCS627, established from a previously untreated primary TCS originating in the ethmoid sinus with invasion into the brain...
December 30, 2023: Cells
#9
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
#10
JOURNAL ARTICLE
Runtai Chen, Guogang Zhang, Kun Sun, Alex F Chen
BACKGROUND: Chemotherapy-induced cardiovascular disease is a growing concern in the elderly population who have survived cancer, yet the underlying mechanism remains poorly understood. We investigated the role of ALKBH5 (AlkB homolog 5), a primary N6 -methyladenosine (m6 A) demethylase, and its involvement in m6 A methylation-mediated regulation of targets in aging-associated doxorubicin-induced cardiotoxicity. METHODS AND RESULTS: To validate the relationship between doxorubicin-induced cardiotoxicity and aging, we established young and old male mouse models...
December 29, 2023: Journal of the American Heart Association
#11
JOURNAL ARTICLE
Chikako Hozumi, Akira Iizuka, Tomoatsu Ikeya, Haruo Miyata, Chie Maeda, Tadashi Ashizawa, Takeshi Nagashima, Kenichi Urakami, Yuji Shimoda, Keiichi Ohshima, Koji Muramatsu, Takashi Sugino, Akio Shiomi, Yasuhisa Ohde, Etsuro Bando, Kenichiro Furukawa, Teiichi Sugiura, Takashi Mukaigawa, Seiichiro Nishimura, Yasuyuki Hirashima, Koichi Mitsuya, Shusuke Yoshikawa, Yasuhiro Tsubosa, Hirohisa Katagiri, Masashi Niwakawa, Ken Yamaguchi, Hirotsugu Kenmotsu, Yasuto Akiyama
BACKGROUND/AIM: Recently, inactivating somatic mutations of SWI/SNF chromatin-remodeling genes in cancers have been reported. However, few studies have been performed regarding the immunological analysis of the tumor microenvironment (TME) in chromatin remodeling complex gene-mutated tumors. In the present study, we identified cancer patients harboring various mammalian SWI/SNF complex mutations and investigated the immunological features in those mutated cancers. PATIENTS AND METHODS: Cancer patients harboring any type of chromatin remodeling complex gene mutation were selected and clinicopathological features were compared between chromatin remodeling complex gene expression-low and expression-high groups...
2024: Cancer Genomics & Proteomics
#12
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
#13
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
#14
JOURNAL ARTICLE
Jinwei Yang, Sihui Zhao, Junyan Su, Siyao Liu, Zaozao Wu, Wei Ma, Ming Tang, Jingcui Wu, Erdong Mao, Li Han, Mengyuan Liu, Jiali Zhang, Lei Cao, Jingyi Shao, Yun Shang
BACKGROUND: Colorectal cancer (CRC) is a prevalent malignancy with diverse molecular characteristics. The NGS-based approach enhances our comprehension of genomic landscape of CRC and may guide future advancements in precision oncology for CRC patients. METHOD: In this research, we conducted an analysis using Next-Generation Sequencing (NGS) on samples collected from 111 individuals who had been diagnosed with CRC. We identified somatic and germline mutations and structural variants across the tumor genomes through comprehensive genomic profiling...
2023: Frontiers in Oncology
#15
JOURNAL ARTICLE
Xiaojian Li, Yun Huo, Zhenchang Wang
Systemic lupus erythematosus (SLE) is an autoimmune disease involving multiple systems. Its recurrent episodes and fluctuating disease courses have a severe impact on patients. Biomarkers to predict disease prognosis and remission are still lacking in SLE. We downloaded the GSE50772 dataset from the Gene Expression Omnibus database and identified differentially expressed genes (DEGs) between SLE and healthy controls. Weighted gene co-expression network analysis was used to identify key gene modules and corresponding genes in SLE...
November 24, 2023: Medicine (Baltimore)
#16
JOURNAL ARTICLE
Sebastián Morales-Pison, Julio C Tapia, Sarai Morales-González, Edio Maldonado, Mónica Acuña, Gloria M Calaf, Lilian Jara
Cancer is a genomic disease, with driver mutations contributing to tumorigenesis. These potentially heritable variants influence risk and underlie familial breast cancer (BC). This study evaluated associations between BC risk and 13 SNPs in driver genes MAP3K1 , SF3B1 , SMAD4 , ARID2 , ATR , KMT2C , MAP3K13 , NCOR1 , and TBX3 , in BRCA1/2 -negative Chilean families. SNPs were genotyped using TaqMan Assay in 492 cases and 1285 controls. There were no associations between rs75704921:C>T ( ARID2 ); rs2229032:A>C ( ATR ); rs3735156:C>G ( KMT2C ); rs2276738:G>C, rs2293906:C>T, rs4075943T:>A, rs13091808:C>T ( MAP3K13 ); rs178831:G>A ( NCOR1 ); or rs3759173:C>A ( TBX3 ) and risk...
November 8, 2023: International Journal of Molecular Sciences
#17
S Gourisankar, W Wenderski, J A Paulo, S H Kim, K Roepke, C Ellis, S P Gygi, G R Crabtree
Genes encoding subunits of the SWI/SNF or BAF ATP-dependent chromatin remodeling complex are among the most enriched for deleterious de novo mutations in intellectual disabilities and autism spectrum disorder, but the causative molecular pathways are not fully known 1,2 . Synaptic activity in neurons is critical for learning and memory and proper neural development 3 . Neural activity prompts calcium influx and transcription within minutes, facilitated in the nucleus by various transcription factors (TFs) and chromatin modifiers 4 ...
October 14, 2023: bioRxiv
#18
JOURNAL ARTICLE
Bin Xu, Kartik Viswanathan, Mahsa S Ahadi, Sara Ahmadi, Bayan Alzumaili, Mohamed-Amine Bani, Eric Baudin, David Blake Behrman, Marzia Capelletti, Nicole G Chau, Federico Chiarucci, Angela Chou, Roderick Clifton-Bligh, Sara Coluccelli, Dario de Biase, Antonio De Leo, Snjezana Dogan, James A Fagin, Talia Fuchs, Anthony Robert Glover, Julien Hadoux, Ludovic Lacroix, Livia Lamartina, Daniel J Lubin, Catherine Luxford, Kelly Magliocca, Thais Maloberti, Abhinita S Mohanty, Fedaa Najdawi, Aradhya Nigam, Alexander James Papachristos, Andrea Repaci, Bruce Robinson, Jean-Yves Scoazec, Qiuying Shi, Stan Sidhu, Erica Solaroli, Mark Sywak, R Michael Tuttle, Brian R Untch, Justine A Barletta, Abir Al Ghuzlan, Anthony J Gill, Ronald Ghossein, Giovanni Tallini, Ian Ganly
PURPOSE: The prognostic importance of RET and RAS mutations and their relationship to clinicopathologic parameters and outcomes in medullary thyroid carcinoma (MTC) needs to be clarified. EXPERIMENTAL DESIGN: A multicenter retrospective cohort study was performed utilizing data from 290 patients with MTC. The molecular profile was determined and associations were examined with clinicopathologic data and outcomes. RESULTS: RET germline mutations were detected in 40 patients (16...
October 16, 2023: Thyroid: Official Journal of the American Thyroid Association
#19
JOURNAL ARTICLE
Mitchell S Stark, Richard A Sturm, Yan Pan, Darren J Smit, Varsha Kommajosyula, Katie J Lee, Kasturee Jagirdar, Catriona McLean, David L Duffy, H Peter Soyer, Victoria J Mar
BACKGROUND: Nodular melanoma (NM) is a challenge to diagnose early due to its rapid growth and more atypical clinical presentation, making it the largest contributor to melanoma mortality. OBJECTIVES: Our study aimed to perform a rare variant allele analysis of whole exome sequenced NM and non-NM patients (minor allele frequency ≤1% Non- Finnish European) for a set of 500 candidate genes potentially implicated in melanoma. METHODS: This study recruited 131 NM and 194 non-NM participants from South-east Queensland and NM patients from Victoria to perform a comparative analysis of possible genetic differences or similarities between the two melanoma cohorts...
September 28, 2023: British Journal of Dermatology
#20
JOURNAL ARTICLE
Beyhan Tüysüz, Büşra Kasap, Dilek Uludağ Alkaya, Zeynep Alp Ünkar, Pınar Köseoğlu, Filiz Geyik, Emre Özer, Hasan Önal, Alper Gezdirici, Oya Ercan
Intrauterine onset syndromic short stature constitutes a group of diseases that pose challenges in differential diagnosis due to their rarity and clinical as well as molecular heterogeneity. The aim of this study was to investigate the presence of (epi)genetic causes in children born small for gestational age (SGA) and manifesting clinically undiagnosed syndromic short stature. The study group comprised twenty-nine cases selected from the syndromic SGA cohort. Various analyses were performed, including chromosomal microarray (CMA), methylation-specific-multiple ligation probe amplification for chromosomes 6,14 and 20, and whole exome sequencing (WES)...
September 25, 2023: European Journal of Medical Genetics
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