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JOURNAL ARTICLE
Thai Hoa Tran, Sarah K Tasian
Philadelphia chromosome-like acute lymphoblastic leukemia (Ph-like ALL) represents a high-risk B-lineage ALL subtype characterized by adverse clinical features and poor relapse-free survival despite risk-adapted multi-agent chemotherapy regimens. The advent of next-generation sequencing has unraveled the diversity of kinase-activating genetic drivers in Ph-like ALL that are potentially amenable to 'personalized' molecularly-targeted therapies. Based upon robust preclinical data and promising case series of clinical activity of tyrosine kinase inhibitor (TKI)-based treatment in adults and children with relevant genetic Ph-like ALL subtypes, several clinical trials have investigated the efficacy of JAK- or ABL-directed TKIs in CRLF2/JAK pathway-mutant or ABL-class Ph-like ALL, respectively...
April 24, 2024: Blood
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JOURNAL ARTICLE
Niklas Klümper, Ngoc Khanh Tran, Stefanie Zschäbitz, Oliver Hahn, Thomas Büttner, Florian Roghmann, Christian Bolenz, Friedemann Zengerling, Constantin Schwab, Dora Nagy, Marieta Toma, Glen Kristiansen, Hendrik Heers, Philipp Ivanyi, Günter Niegisch, Camilla Marisa Grunewald, Christopher Darr, Arian Farid, Katrin Schlack, Mahmoud Abbas, Can Aydogdu, Jozefina Casuscelli, Theresa Mokry, Michael Mayr, Dora Niedersüß-Beke, Steffen Rausch, Dimo Dietrich, Jonas Saal, Jörg Ellinger, Manuel Ritter, Abdullah Alajati, Christoph Kuppe, Joshua Meeks, Francisco E Vera Badillo, J Alberto Nakauma-González, Joost Boormans, Kerstin Junker, Arndt Hartmann, Viktor Grünwald, Michael Hölzel, Markus Eckstein
PURPOSE: The anti-NECTIN4 antibody-drug conjugate enfortumab vedotin (EV) is approved for patients with metastatic urothelial cancer (mUC). However, durable benefit is only achieved in a small, yet uncharacterized patient subset. NECTIN4 is located on chromosome 1q23.3, and 1q23.3 gains represent frequent copy number variations (CNVs) in urothelial cancer. Here, we aimed to evaluate NECTIN4 amplifications as a genomic biomarker to predict EV response in patients with mUC. MATERIALS AND METHODS: We established a NECTIN4 -specific fluorescence in situ hybridization (FISH) assay to assess the predictive value of NECTIN4 CNVs in a multicenter EV-treated mUC patient cohort (mUC-EV, n = 108)...
April 24, 2024: Journal of Clinical Oncology
#3
JOURNAL ARTICLE
Rishi Kumar Nageshan, Nevan Krogan, Julia Promisel Cooper
In fission yeast lacking the telomere binding protein, Taz1, replication forks stall at telomeres, triggering deleterious downstream events. Strand invasion from one taz1Δ telomeric stalled fork to another on a separate (non-sister) chromosome leads to telomere entanglements, which are resolved in mitosis at 32°C; however, entanglement resolution fails at ≤20°C, leading to cold-specific lethality. Previously, we found that loss of the mitotic function of Rif1, a conserved DNA replication and repair factor, suppresses cold sensitivity by promoting resolution of entanglements without affecting entanglement formation...
April 25, 2024: G3: Genes—Genomes—Genetics
#4
JOURNAL ARTICLE
Gianno Pannafino, Jun Jie Chen, Viraj Mithani, Lisette Payero, Michael Gioia, J Brooks Crickard, Eric Alani
The accurate segregation of homologous chromosomes during the Meiosis I reductional division in most sexually reproducing eukaryotes requires crossing over between homologs. In baker's yeast approximately 80 percent of meiotic crossovers result from Mlh1-Mlh3 and Exo1 acting to resolve double-Holliday junction (dHJ) intermediates in a biased manner. Little is known about how Mlh1-Mlh3 is recruited to recombination intermediates to perform its role in crossover resolution. We performed a gene dosage screen in baker's yeast to identify novel genetic interactors with Mlh1-Mlh3...
April 24, 2024: Genetics
#5
JOURNAL ARTICLE
Yuta Ito, Amira Marouf, Yasunori Kogure, Junji Koya, Raphaël Liévin, Julie Bruneau, Mariko Tabata, Yuki Saito, Sumito Shingaki, Mitsuhiro Yuasa, Kentaro Yamaguchi, Koichi Murakami, Robert Weil, Manon Vavasseur, Guillaume P Andrieu, Mehdi Latiri, Layla Veleanu, Michaël Dussiot, Isabelle André, Akshay Joshi, Chantal Lagresle-Peyrou, Aude Magerus, Sammara Chaubard, David Lavergne, Emmanuel Bachy, Erika Brunet, Virginie Fataccioli, Chantal Brouzes, Camille Laurent, Laurence De Leval, Alexandra Traverse-Glehen, Céline Bossard, Marie-Cécile Parrens, Véronique Meignin, Laure Philippe, Julien Rossignol, Felipe Suarez, Jean-Marie Michot, Olivier Tournilhac, Gandhi Damaj, François Lemonnier, Christine Bôle-Feysot, Patrick Nitschké, Bruno Tesson, Cécile Laurent, Thierry Molina, Vahid Asnafi, Yosaku Watatani, Kenichi Chiba, Ai Okada, Yuichi Shiraishi, Sachiko Tsukita, Koji Izutsu, Hiroaki Miyoshi, Koichi Ohshima, Seiji Sakata, Akito Dobashi, Kengo Takeuchi, Masashi Sanada, Philippe Gaulard, Arnaud Jaccard, Seishi Ogawa, Olivier Hermine, Keisuke Kataoka, Lucile Couronné
Extranodal NK/T-cell lymphoma (ENKTCL) is an Epstein-Barr virus (EBV)-related neoplasm with male dominance and a poor prognosis. A better understanding of the genetic alterations and their functional roles in ENKTCL could help improve patient stratification and treatments. Here, we performed comprehensive genetic analysis of 177 ENKTCL cases to delineate the landscape of mutations, copy number alterations (CNAs), and structural variations, identifying 34 driver genes including six previously unappreciated ones, namely HLA-B, HLA-C, ROBO1, CD58, POT1, and MAP2K1...
April 24, 2024: Cancer Research
#6
JOURNAL ARTICLE
Qing-Ling Hu, Ji-Chong Zhuo, Gang-Qi Fang, Jia-Bao Lu, Yu-Xuan Ye, Dan-Ting Li, Yi-Han Lou, Xiao-Ya Zhang, Xuan Chen, Si-Liang Wang, Zhe-Chao Wang, Yi-Xiang Zhang, Norida Mazlan, San San Oo, Thet Thet, Prem Nidhi Sharma, Jauharlina Jauharlina, Ir Henik Sukorini, Michael T Ibisate, S M Mizanur Rahman, Naved Ahmad Ansari, Ai-Dong Chen, Zeng-Rong Zhu, Kong Luen Heong, Gang Lu, Hai-Jian Huang, Jun-Min Li, Jian-Ping Chen, Shuai Zhan, Chuan-Xi Zhang
Many insect pests, including the brown planthopper (BPH), undergo windborne migration that is challenging to observe and track. It remains controversial about their migration patterns and largely unknown regarding the underlying genetic basis. By analyzing 360 whole genomes from around the globe, we clarify the genetic sources of worldwide BPHs and illuminate a landscape of BPH migration showing that East Asian populations perform closed-circuit journeys between Indochina and the Far East, while populations of Malay Archipelago and South Asia undergo one-way migration to Indochina...
April 26, 2024: Science Advances
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JOURNAL ARTICLE
Justin Merondun, Cristiana I Marques, Pedro Andrade, Swetlana Meshcheryagina, Ismael Galván, Sandra Afonso, Joel M Alves, Pedro M Araújo, Gennadiy Bachurin, Jennifer Balacco, Miklós Bán, Olivier Fedrigo, Giulio Formenti, Frode Fossøy, Attila Fülöp, Mikhail Golovatin, Sofia Granja, Chris Hewson, Marcel Honza, Kerstin Howe, Greger Larson, Attila Marton, Csaba Moskát, Jacquelyn Mountcastle, Petr Procházka, Yaroslav Red'kin, Ying Sims, Michal Šulc, Alan Tracey, Jonathan M D Wood, Erich D Jarvis, Mark E Hauber, Miguel Carneiro, Jochen B W Wolf
Sex-limited polymorphism has evolved in many species including our own. Yet, we lack a detailed understanding of the underlying genetic variation and evolutionary processes at work. The brood parasitic common cuckoo ( Cuculus canorus ) is a prime example of female-limited color polymorphism, where adult males are monochromatic gray and females exhibit either gray or rufous plumage. This polymorphism has been hypothesized to be governed by negative frequency-dependent selection whereby the rarer female morph is protected against harassment by males or from mobbing by parasitized host species...
April 26, 2024: Science Advances
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JOURNAL ARTICLE
Yamin Gong, Zhifeng Wang, Wen Zong, Ruifeng Shi, Wenli Sun, Sijia Wang, Bin Peng, Shunichi Takeda, Zhao-Qi Wang, Xingzhi Xu
The S-phase checkpoint involving CHK1 is essential for fork stability in response to fork stalling. PARP1 acts as a sensor of replication stress and is required for CHK1 activation. However, it is unclear how the activity of PARP1 is regulated. Here, we found that UFMylation is required for the efficient activation of CHK1 by UFMylating PARP1 at K548 during replication stress. Inactivation of UFL1, the E3 enzyme essential for UFMylation, delayed CHK1 activation and inhibits nascent DNA degradation during replication blockage as seen in PARP1-deficient cells...
April 30, 2024: Proceedings of the National Academy of Sciences of the United States of America
#9
JOURNAL ARTICLE
Vasileios R Ouzounidis, Mattie Green, Charlotte de Ceuninck van Capelle, Clara Gebhardt, Helena Crellin, Cameron Finlayson, Bram Prevo, Dhanya K Cheerambathur
The KMN (Knl1/Mis12/Ndc80) network at the kinetochore, primarily known for its role in chromosome segregation, has been shown to be repurposed during neurodevelopment. Here, we investigate the underlying neuronal mechanism and show that the KMN network promotes the proper axonal organization within the C. elegans head nervous system. Post-mitotic degradation of KNL-1, which acts as a scaffold for signaling and has microtubule-binding activities at the kinetochore, led to disorganized ganglia and aberrant placement and organization of axons in the nerve ring - an interconnected axonal network...
April 24, 2024: Molecular Biology of the Cell
#10
JOURNAL ARTICLE
Huayun Shi, Oliver W L Carter, Fortuna Ponte, Cinzia Imberti, Miguel A Gomez-Gonzalez, Fernando Cacho-Nerin, Paul D Quinn, Julia E Parker, Emilia Sicilia, Huaiyi Huang, Peter J Sadler
The novel hetero-dinuclear complex trans,trans,trans-[PtIV (py)2 (N3 )2 (OH)(μ-OOCCH2 CH2 CONHCH2 -bpyMe)IrIII (ppy)2 ]Cl (Pt-Ir), exhibits charge transfer between the acceptor photochemotherapeutic Pt(IV) (Pt-OH) and donor photodynamic Ir(III) (Ir-NH2 ) fragments. It is stable in the dark, but undergoes photodecomposition more rapidly than the Pt(IV) parent complex (Pt-OH) to generate Pt(II) species, an azidyl radical and 1 O2 . The Ir(III)* excited state, formed after irradiation, can oxidise NADH to NAD⋅ radicals and NAD+ ...
April 24, 2024: Angewandte Chemie
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JOURNAL ARTICLE
Elena Mavridou, Anair Graciela Lema Fernandez, Carlotta Nardelli, Valentina Pierini, Martina Quintini, Silvia Arniani, Danika Di Giacomo, Barbara Crescenzi, Caterina Matteucci, Constantina Sambani, Cristina Mecucci
In myeloid neoplasms, both fusion genes and gene mutations are well-established events identifying clinicopathological entities. In this study, we present a thus far undescribed t(X;21)(p11.4;q22.12) in five cases with myelodysplastic syndrome (MDS) or acute myeloid leukemia (AML). The translocation was isolated or accompanied by additional changes. It did not generate any fusion gene or gene deregulation by aberrant juxtaposition with regulatory sequences. Molecular analysis by targeted next-generation sequencing showed that the translocation was accompanied by at least one somatic mutation in TET2, EZH2, RUNX1, ASXL1, SRSF2, ZRSR2, DNMT3A, and NRAS genes...
April 2024: Genes, Chromosomes & Cancer
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JOURNAL ARTICLE
Maryam Sohrabi, Javad Fathi, Samane Mohebi, Zahra Hashemizadeh, Soudeh Kholdi, Mahtab Hadadi, Kowsar Keshavarz, Zahra Darvishvand
BACKGROUND: Escherichia coli is the most common etiological agent of urinary tract infections (UTIs). Meanwhile, plasmid-mediated quinolone resistance (PMQR) is reported in E. coli isolates producing extended-spectrum β-lactamases (ESBLs). Furthermore, the reservoirs and mechanisms of acquisition of uropathogenic Escherichia coli (UPEC) strains are poorly understood. On the other hand, UTIs are common in pregnant women and the treatment challenge is alarming. METHODS AND RESULTS: In the present study, 54 pregnant women with acute cystitis were included...
April 24, 2024: Molecular Biology Reports
#13
JOURNAL ARTICLE
Matilde Grupe Frost, Kristoffer Jarlov Jensen, Espen Jimenez-Solem, Camilla Qvortrup, Tine Plato Kuhlmann, Jon Lykkegaard Andersen, Estrid Høgdall, Tonny Studsgaard Petersen
OBJECTIVE: This study aims to evaluate the developments in the testing of Kirsten Rat Sarcoma viral oncogene homolog (KRAS) and v-Raf murine sarcoma viral oncogene homolog B1 (BRAF) mutations across different cancer types and regions in Denmark from 2010 to 2022. STUDY DESIGN AND SETTING: Using comprehensive data from the Danish health registries, we linked molecular test results from the Danish Pathology Registry with cancer diagnoses from the Danish National Patient Registry between 2010 and 2022...
April 2024: Genes, Chromosomes & Cancer
#14
JOURNAL ARTICLE
Shuanzeng Wei, Jianming Pei, Paul Belser, Teresa Lee, Jeffrey M Farma, Arthur S Patchefsky, Douglas B Flieder, Elizabeth A Montgomery
Myxoid leiomyosarcoma (MLS) is a rare but well-documented tumor that often portends a poor prognosis compared to the conventional leiomyosarcoma. This rare sarcoma has been reported in the uterus, external female genitalia, soft tissue, and other locations. However, a definite rectal MLS has not been reported. Recently five cases of MLS were reported to harbor PLAG1 fusions (TRPS1::PLAG1, RAD51B::PLAG1, and TRIM13::PLAG1). In this report, we present a case of rectal MLS with a novel MIR143HG::PLAG1 fusion detected by RNA next-generation sequencing...
April 2024: Genes, Chromosomes & Cancer
#15
JOURNAL ARTICLE
Paweł Milczarski, Stefan Stojałowski, Beata Myśków
Genetic maps are an excellent tool for the analysis of important traits, the development of which is the result of the combined expression of several genes, enabling the genomic localization of the factors determining them. Such features, characterized by a normal distribution of values, are referred to as quantitative or polygenic. The analysis of their genetic background using a chromosome map is called the mapping of quantitative traits loci (QTL). QTL analysis is a statistical method of determining the genetic association of phenotypic data (trait measurements) with genotypic data (DNA markers assigned to linkage groups)...
2024: Methods in Molecular Biology
#16
JOURNAL ARTICLE
Beata Myśków, Paweł Milczarski, Stefan Stojałowski
Genetic mapping is the determination of the position and relative genetic distance between genes or molecular markers in the chromosomes of a particular species. The construction of genetic maps uses data from the genotyping of the mapping population. Among the different mapping populations used, two are relatively common: the F2 and recombinant inbred lines (RILs) obtained as a result of the controlled crossing of genetically diverse parental forms (e.g., inbred lines). Also, the dihaploid (DH) population is often used in plants, but obtaining DHs in different crops, including rye, is very difficult or even impossible...
2024: Methods in Molecular Biology
#17
JOURNAL ARTICLE
Anna Gasperl, Maria Müller
Our method describes how to collect forest tree root tips in the field, to store them for transfer to the lab, to pretreat root tips in order to arrest cells in metaphase, fix root tips to preserve specific morphological organizations, to stain fixed root tips by Feulgen's Reaction in order to increase contrast, and to prepare the root meristem for analyzing mitotic stages and chromosomal aberrations via light microscopy. We further describe how to classify chromosomal abnormalities and quantify them via aberration indices...
2024: Methods in Molecular Biology
#18
JOURNAL ARTICLE
Rongxing Qin, Lijuan Huang, Wei Xu, Qingchun Qin, Xiaojun Liang, Xinyu Lai, Xiaoying Huang, Minshan Xie, Li Chen
Stroke is a leading cause of death and disability, and genetic risk factors play a significant role in its development. Unfortunately, effective therapies for stroke are currently limited. Early detection and diagnosis are critical for improving outcomes and developing new treatment strategies. In this study, we aimed to identify potential biomarkers and effective prevention and treatment strategies for stroke by conducting transcriptome and single-cell analyses. Our analysis included screening for biomarkers, functional enrichment analysis, immune infiltration, cell-cell communication, and single-cell metabolism...
April 13, 2024: Functional & Integrative Genomics
#19
JOURNAL ARTICLE
Bohui Han, Xiao Wang, Yangyang Sun, Xilu Kang, Meng Zhang, Jiawen Luo, Haiming Han, Shenghui Zhou, Yuqing Lu, Weihua Liu, Xinming Yang, Xiuquan Li, Jinpeng Zhang, Lihui Li
We developed T1AL·1PS and T1AS·1PL Robertsonian translocations by breakage-fusion mechanism based on wheat-A. cristatum 1P(1A) substitution line with smaller leaf area, shorter plant height, and other excellent agronomic traits Agropyron cristatum, a wild relative of wheat, is a valuable germplasm resource for improving wheat genetic diversity and yield. Our previous study confirmed that the A. cristatum chromosome 1P carries alien genes that reduce plant height and leaf size in wheat. Here, we developed T1AL·1PS and T1AS·1PL Robertsonian translocations (RobTs) by breakage-fusion mechanism based on wheat-A...
April 24, 2024: TAG. Theoretical and Applied Genetics. Theoretische und Angewandte Genetik
#20
JOURNAL ARTICLE
Can Hu, Xue-Ting Zhu, Ming-Hong He, Yangyang Shao, Zhongjun Qin, Zhi-Jing Wu, Jin-Qiu Zhou
Telomeres, which are chromosomal end structures, play a crucial role in maintaining genome stability and integrity in eukaryotes. In the baker's yeast Saccharomyces cerevisiae , the X- and Y'-elements are subtelomeric repetitive sequences found in all 32 and 17 telomeres, respectively. While the Y'-elements serve as a backup for telomere functions in cells lacking telomerase, the function of the X-elements remains unclear. This study utilized the S. cerevisiae strain SY12, which has three chromosomes and six telomeres, to investigate the role of X-elements (as well as Y'-elements) in telomere maintenance...
April 24, 2024: ELife
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