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JOURNAL ARTICLE
Lei Wan, Guojun Yang, Zhen Yan
Genetic sequencing has identified high-confidence ASD risk genes with loss-of-function mutations. How the haploinsufficiency of distinct ASD risk genes causes ASD remains to be elucidated. In this study, we examined the role of four top-ranking ASD risk genes, ADNP, KDM6B, CHD2, and MED13, in gene expression regulation. ChIP-seq analysis reveals that gene targets with the binding of these ASD risk genes at promoters are enriched in RNA processing and DNA repair. Many of these targets are found in ASD gene database (SFARI), and are involved in transcription regulation and chromatin remodeling...
April 8, 2024: Human Molecular Genetics
#2
Vijay S Ganesh, Kevin Riquin, Nicolas Chatron, Kay-Marie Lamar, Miriam C Aziz, Pauline Monin, Melanie O'Leary, Julia K Goodrich, Kiran V Garimella, Eleina England, Esther Yoon, Ben Weisburd, Francois Aguet, Carlos A Bacino, David R Murdock, Hongzheng Dai, Jill A Rosenfeld, Lisa T Emrick, Shamika Ketkar, Yael Sarusi, Damien Sanlaville, Saima Kayani, Brian Broadbent, Bertrand Isidor, Alisée Pengam, Benjamin Cogné, Daniel G MacArthur, Igor Ulitsky, Gemma L Carvill, Anne O'Donnell-Luria
Genes encoding long non-coding RNAs (lncRNAs) comprise a large fraction of the human genome, yet haploinsufficiency of a lncRNA has not been shown to cause a Mendelian disease. CHASERR is a highly conserved human lncRNA adjacent to CHD2- a coding gene in which de novo loss-of-function variants cause developmental and epileptic encephalopathy. Here we report three unrelated individuals each harboring an ultra-rare heterozygous de novo deletion in the CHASERR locus. We report similarities in severe developmental delay, facial dysmorphisms, and cerebral dysmyelination in these individuals, distinguishing them from the phenotypic spectrum of CHD2 haploinsufficiency...
February 7, 2024: medRxiv
#3
JOURNAL ARTICLE
Philippe Gélisse, Carlos Gallegos, Annacarmen Nilo, Greta Macorig, Pierre Genton, Arielle Crespel
Epilepsy with eyelid myoclonia (EM) or Jeavons syndrome (JS) is an epileptic syndrome related to the spectrum of genetic generalized epilepsies (GGE). We report two untreated children on which EEGs were performed several hours after a generalized tonic-clonic seizure (GTCS). These showed a unilateral, nearly continuous posterior slowing. This slow-wave activity was associated with contralateral epileptiform activity in one case, while in the second case, it was associated with an ipsilateral activity. However, in the latter child, a few months later an independent focus on the contralateral side was observed...
February 28, 2024: Clinical Neurophysiology
#4
JOURNAL ARTICLE
Francesca Cogliati, Letizia Straniero, Valeria Rimoldi, Maura Masciadri, Sara Perego, Berardo Rinaldi, Donatella Milani, Davide Gentilini, Lidia Larizza, Rosanna Asselta, Silvia Russo, Maria Francesca Bedeschi
Loss-of-function CHD2 (chromodomain helicase DNA-binding protein 2) mutations are associated with a spectrum of neurodevelopmental disorders often including early-onset generalized seizures, photosensitivity, and epileptic encephalopathies. Patients show psychomotor delay/intellectual disability (ID), autistic features, and behavior disorders, such as aggression and impulsivity. Most reported cases are sporadic with description of germline mosaicism only in two families. We detect the first case of parental gonosomal CHD2 mosaicism disclosed by two brothers showing mild ID, born to healthy parents...
February 22, 2024: American Journal of Medical Genetics. Part B, Neuropsychiatric Genetics
#5
JOURNAL ARTICLE
Bin Yu, Chengkui Geng, Zhongxiong Wu, Zhongzi Zhang, Aili Zhang, Ze Yang, Jiazheng Huang, Ying Xiong, Huiqin Yang, Zhuoyuan Chen
Osteosarcoma is generally considered a cold tumor and is characterized by epigenetic alterations. Although tumor cells are surrounded by many immune cells such as macrophages, T cells may be suppressed, be inactivated, or not be presented due to various mechanisms, which usually results in poor prognosis and insensitivity to immunotherapy. Immunotherapy is considered a promising anti-cancer therapy in osteosarcoma but requires more research, but osteosarcoma does not currently respond well to this therapy. The cancer immunity cycle (CIC) is essential for anti-tumor immunity, and is epigenetically regulated...
January 15, 2024: Scientific Reports
#6
JOURNAL ARTICLE
Jennifer M Grants, Christina May, Josh Bridgers, Shujun Huang, Sierra Gillis, Barbara Meissner, Merrill Boyle, Susana Ben-Neriah, Stacy Hung, Gerben Duns, Laura Hilton, Alina S Gerrie, Marco Marra, Robert Kridel, Peter J B Sabatini, Christian Steidl, David W Scott, Aly Karsan
BACKGROUND: Somatic hypermutation (SHM) status of the immunoglobulin heavy variable (IGHV) gene plays a crucial role in determining the prognosis and treatment of patients with chronic lymphocytic leukemia (CLL). A common approach for determining SHM status is multiplex polymerase chain reaction and Sanger sequencing of the immunoglobin heavy locus; however, this technique is low throughput, is vulnerable to failure, and does not allow multiplexing with other diagnostic assays. METHODS: Here we designed and validated a DNA targeted capture approach to detect immunoglobulin heavy variable somatic hypermutation (IGHV SHM) status as a submodule of a larger next-generation sequencing (NGS) panel that also includes probes for ATM, BIRC3, CHD2, KLHL6, MYD88, NOTCH1, NOTCH2, POT1, SF3B1, TP53, and XPO1...
January 4, 2024: Clinical Chemistry
#7
Eleni Angelopoulou, Athina Theodosiou, Ioannis Papaevripidou, Angelos Alexandrou, Thomas Liehr, Yolanda Gyftodimou, Eunice G Stefanou, Carolina Sismani
Chromosomal inversions are usually balanced structural chromosomal rearrangements that do not have an impact on the clinical phenotype of a carrier. The main clinical consequence of inversions is the risk for unbalanced gametes and offspring with severe phenotypes. Rarely though, inversions are associated with a phenotype, mainly due to submicroscopic Copy Number Variants (CNVs) or disruption at the breakpoints of a functionally important gene and/or genomic elements. In this study, a paracentric inversion of chromosome 16 [inv(16)(q22...
December 2023: Heliyon
#8
JOURNAL ARTICLE
Eleni Panagiotakaki, Francesco D Tiziano, Mohamad A Mikati, Lisanne S Vijfhuizen, Sophie Nicole, Gaetan Lesca, Emanuela Abiusi, Agnese Novelli, Lorena Di Pietro, Aster V E Harder, Nicole M Walley, Elisa De Grandis, Anne-Lise Poulat, Vincent Des Portes, Anne Lépine, Marie-Cecile Nassogne, Alexis Arzimanoglou, Rosaria Vavassori, Jan Koenderink, Christopher H Thompson, Alfred L George, Fiorella Gurrieri, Arn M J M van den Maagdenberg, Erin L Heinzen
Alternating hemiplegia of childhood (AHC) is a rare neurodevelopment disorder that is typically characterized by debilitating episodic attacks of hemiplegia, seizures, and intellectual disability. Over 85% of individuals with AHC have a de novo missense variant in ATP1A3 encoding the catalytic α3 subunit of neuronal Na+/ K+ ATPases. The remainder of the patients are genetically unexplained. Here, we used next-generation sequencing to search for the genetic cause of 26 ATP1A3-negative index patients with a clinical presentation of AHC or an AHC-like phenotype...
December 14, 2023: European Journal of Human Genetics: EJHG
#9
JOURNAL ARTICLE
Antonietta Coppola, S Krithika, Michele Iacomino, Dheeraj Bobbili, Simona Balestrini, Irene Bagnasco, Leonilda Bilo, Daniela Buti, Susanna Casellato, Claudia Cuccurullo, Edoardo Ferlazzo, Costin Leu, Lucio Giordano, Giuseppe Gobbi, Laura Hernandez-Hernandez, Nick Lench, Helena Martins, Stefano Meletti, Tullio Messana, Vincenzo Nigro, Michele Pinelli, Tommaso Pippucci, Ravishankara Bellampalli, Barbara Salis, Vito Sofia, Pasquale Striano, Salvatore Striano, Laura Tassi, Aglaia Vignoli, Anna Elisabetta Vaudano, Maurizio Viri, Ingrid E Scheffer, Patrick May, Federico Zara, Sanjay M Sisodiya
OBJECTIVE: Epilepsy with eyelid myoclonia (EEM) spectrum is a generalized form of epilepsy characterized by eyelid myoclonia with or without absences, eye closure-induced seizures with electroencephalographic paroxysms, and photosensitivity. Based on the specific clinical features, age at onset, and familial occurrence, a genetic cause has been postulated. Pathogenic variants in CHD2, SYNGAP1, NEXMIF, RORB, and GABRA1 have been reported in individuals with photosensitivity and eyelid myoclonia, but whether other genes are also involved, or a single gene is uniquely linked with EEM, or its subtypes, is not yet known...
December 13, 2023: Epilepsia
#10
JOURNAL ARTICLE
Se Hee Kim, Jieun Seo, Soon Sung Kwon, Lip-Yuen Teng, DongJu Won, Saeam Shin, Joon Soo Lee, Seung-Tae Lee, Jong Rak Choi, Hoon-Chul Kang
OBJECTIVE: We aimed to identify common genes and recurrent causative variants in a large group of Asian patients with different epilepsy syndromes and subgroups. METHODS: Patients with unexplained pediatric-onset epilepsy were identified from the in-house Severance Neurodevelopmental Disorders and Epilepsy Database. All patients underwent either exome sequencing or multigene panels from January 2017 to December 2019, at Severance Children's Hospital in Korea. Clinical data were extracted from the medical records...
December 10, 2023: Epilepsia
#11
JOURNAL ARTICLE
Regina Gamirova, Elena Shagimardanova, Takehiro Sato, Takayuki Kannon, Rimma Gamirova, Atsushi Tajima
Many questions remain regarding the genetics of idiopathic generalized epilepsy (IGE), a subset of genetic generalized epilepsy (GGE). We aimed to identify the candidate coding variants of epilepsy panel genes in a cohort of affected individuals, using variant frequency information from a control cohort of the same region. We performed whole-exome sequencing analysis of 121 individuals and 10 affected relatives, focusing on variants of 950 candidate genes associated with epilepsy according to the Genes4Epilepsy curated panel...
November 22, 2023: Journal of Human Genetics
#12
JOURNAL ARTICLE
Dhruv Garg, Steven A Fisher
Smoothelins are cytoskeletal proteins with a single C-terminal calponin homology domain type 2 (CHD2). Little is known about the significance of variation in SMTN CHD2 domains, addressed here through analysis of public databases. A conserved 152 nt penultimate constitutive exon present in all SMTNs encodes helices II-IV of CHD2 with high identity (nt/aa 63/65%). Variable CHD2s of SMTN (helices IV-VI) are generated by alternative splicing of 165 nt exon E20. E20 and the CHD2 it encodes have high homology with the terminal constitutive exon of SMTNL1 (E8; nt/aa 72/75% identity)...
November 2023: Physiological Reports
#13
JOURNAL ARTICLE
Nitin Jain, Lisa J Croner, John N Allan, Tanya Siddiqi, Alessandra Tedeschi, Xavier C Badoux, Karl Eckert, Leo W K Cheung, Anwesha Mukherjee, James P Dean, Edith Szafer-Glusman, John F Seymour
PURPOSE: Mutations in BTK, PLCG2, and BCL2 have been reported in patients with progressive disease (PD) on continuous single-agent BTK or BCL2 inhibitor treatment. We tested for these mutations in samples from patients with PD after completion of first-line treatment with fixed-duration ibrutinib plus venetoclax for chronic lymphocytic leukemia (CLL) in the phase II CAPTIVATE study. PATIENTS AND METHODS: A total of 191 patients completed fixed-duration ibrutinib plus venetoclax (three cycles of ibrutinib then 12-13 cycles of ibrutinib plus venetoclax)...
February 1, 2024: Clinical Cancer Research
#14
JOURNAL ARTICLE
Atefeh Mir, Yongjun Song, Hane Lee, Zakiye Nadeali, Mohammad Amin Tabatabaiefar
BACKGROUND: The chromodomain helicase DNA-binding protein 2 (CHD2) is a member of the ATP-dependent chromatin remodelling family of proteins, which are critical for the assembly and regulation of chromatin. De novo variants and deletions in the CHD2 gene have been associated with childhood-onset developmental and epileptic encephalopathies type 94 (DEE 94). This study reports a novel deleterious de novo heterozygous frameshift insertion variant in the CHD2 gene. METHODS: The causative variant was diagnosed using whole-exome sequencing...
October 25, 2023: Molecular Genetics & Genomic Medicine
#15
Christy W LaFlamme, Cassandra Rastin, Soham Sengupta, Helen E Pennington, Sophie J Russ-Hall, Amy L Schneider, Emily S Bonkowski, Edith P Almanza Fuerte, Miranda Galey, Joy Goffena, Sophia B Gibson, Talia J Allan, Denis M Nyaga, Nico Lieffering, Malavika Hebbar, Emily V Walker, Daniel Darnell, Scott R Olsen, Pandurang Kolekar, Nahdir Djekidel, Wojciech Rosikiewicz, Haley McConkey, Jennifer Kerkhof, Michael A Levy, Raissa Relator, Dorit Lev, Tally Lerman-Sagie, Kristen L Park, Marielle Alders, Gerarda Cappuccio, Nicolas Chatron, Leigh Demain, David Genevieve, Gaetan Lesca, Tony Roscioli, Damien Sanlaville, Matthew L Tedder, Monika Weisz Hubshman, Shamika Ketkar, Hongzheng Dai, Kim Carlyle Worley, Jill A Rosenfeld, Hsiao-Tuan Chao, Geoffrey Neale, Gemma L Carvill, Zhaoming Wang, Samuel F Berkovic, Lynette G Sadleir, Danny E Miller, Ingrid E Scheffer, Bekim Sadikovic, Heather C Mefford
Sequence-based genetic testing currently identifies causative genetic variants in ∼50% of individuals with developmental and epileptic encephalopathies (DEEs). Aberrant changes in DNA methylation are implicated in various neurodevelopmental disorders but remain unstudied in DEEs. Rare epigenetic variations ("epivariants") can drive disease by modulating gene expression at single loci, whereas genome-wide DNA methylation changes can result in distinct "episignature" biomarkers for monogenic disorders in a growing number of rare diseases...
October 12, 2023: medRxiv
#16
JOURNAL ARTICLE
Mariem Ben Said, Olfa Jallouli, Abir Ben Aissa, Amal Souissi, Fatma Kamoun, Faiza Fakhfakh, Saber Masmoudi, Ikhlas Ben Ayed, Chahnez Charfi Triki
OBJECTIVE: To develop a high throughput sequencing panel for the diagnosis of developmental and epileptic encephalopathy in Tunisia and to clarify the frequency of disease-causing genes in this region. METHODS: We developed a custom panel for next generation sequencing of the coding sequences of 116 genes in individuals with developmental and epileptic encephalopathy from the Tunisian population. Segregation analyses as well as in silico studies have been conducted to assess the identified variants' pathogenicity...
October 23, 2023: Epilepsia Open
#17
JOURNAL ARTICLE
Tahir Muhammad, Stephen F Pastore, Katrina Good, Juan Ausió, John B Vincent
Chromatin, a protein-DNA complex, is a dynamic structure that stores genetic information within the nucleus and adapts to molecular/cellular changes in its structure, providing conditional access to the genetic machinery. ATP-dependent chromatin modifiers regulate access of transcription factors and RNA polymerases to DNA by either "opening" or "closing" the structure of chromatin, and its aberrant regulation leads to a variety of neurodevelopmental disorders. The chromodomain helicase DNA-binding (CHD) proteins are ATP-dependent chromatin modifiers involved in the organization of chromatin structure, act as gatekeepers of genomic access, and deposit histone variants required for gene regulation...
October 16, 2023: Psychiatric Genetics
#18
JOURNAL ARTICLE
Juho Aaltio, Anna Etula, Simo Ojanen, Virginia Brilhante, Tuula Lönnqvist, Pirjo Isohanni, Anu Suomalainen
BACKGROUND: The aim of the study was to characterize molecular diagnoses in patients with childhood-onset progressive neurological disorders of suspected genetic etiology. METHODS: We studied 48 probands (age range from newborn to 17 years old) with progressive neurological disorders of unknown etiology from the largest pediatric neurology clinic in Finland. Phenotypes included encephalopathy (54%), neuromuscular disorders (33%), movement disorders (11%), and one patient (2%) with hemiplegic migraine...
August 10, 2023: Pediatric Research
#19
JOURNAL ARTICLE
Jing Lv, Jiayue Yang, Dong Zhang, Florian Blauert, Bo Jiang, Dongxu Dai, Weiqing Zhang, Guorong Wu, Wenshao Yang, Quan Shuai, Xueming Yang
The vibrationally excited reaction O(1D) + CHD3(ν1 = 1) has been investigated by crossed-molecular-beam experiments with a time-sliced velocity map imaging technique. Detailed and quantitative information is extracted on the C-H stretching excitation effects on the reactivity and dynamics of the title reaction, with the help of preparation of C-H stretching excited CHD3 molecules by direct infrared excitation. Experimental results show that the vibrational stretching excitation of the C-H bond almost does not affect the relative contributions between different dynamical pathways for all product channels...
July 14, 2023: Journal of Chemical Physics
#20
JOURNAL ARTICLE
Micaela Lasser, Nawei Sun, Yuxiao Xu, Sheng Wang, Sam Drake, Karen Law, Silvano Gonzalez, Belinda Wang, Vanessa Drury, Octavio Castillo, Yefim Zaltsman, Jeanselle Dea, Ethel Bader, Kate E McCluskey, Matthew W State, A Jeremy Willsey, Helen Rankin Willsey
Gene ontology analyses of high-confidence autism spectrum disorder (ASD) risk genes highlight chromatin regulation and synaptic function as major contributors to pathobiology. Our recent functional work in vivo has additionally implicated tubulin biology and cellular proliferation. As many chromatin regulators, including ASD risk genes ADNP and CHD3, are known to directly regulate both tubulins and histones, we studied the five chromatin regulators most strongly associated with ASD (ADNP, CHD8, CHD2, POGZ, and KMT5B) specifically with respect to tubulin biology...
June 27, 2023: Development
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