keyword
https://read.qxmd.com/read/38515689/identification-of-prognostic-models-for-glycosylation-related-subtypes-and-tumor-microenvironment-infiltration-characteristics-in-clear-cell-renal-cell-cancer
#21
JOURNAL ARTICLE
Cheng Shen, Bing Zheng, Zhan Chen, Wei Zhang, Xinfeng Chen, Siyang Xu, Jianfeng Ji, Xingxing Fang, Chunmei Shi
BACKGROUND: One of the most fatal forms of cancer of the urinary system, renal cell carcinoma (RCC), significantly negatively impacts human health. Recent research reveals that abnormal glycosylation contributes to the growth and spread of tumors. However, there is no information on the function of genes related to glycosylation in RCC. METHODS: In this study, we created a technique that can be used to guide the choice of immunotherapy and chemotherapy regimens for RCC patients while predicting their survival prognosis...
March 30, 2024: Heliyon
https://read.qxmd.com/read/38515575/a-systematic-review-of-primary-large-cell-neuroendocrine-carcinoma-of-the-prostate
#22
Ngan Nguyen, Ronald Dean Franz, Omar Mohammed, Richard Huynh, Christine Kim Son, Rida Nusrat Khan, Bilawal Ahmed
BACKGROUND: Large cell neuroendocrine carcinoma (LCNEC) is a rare subtype of prostate cancer. The pathogenesis, clinical manifestation, treatment options, and prognosis are uncertain and underreported. MATERIALS AND METHODS: A systematic search was conducted in April 2022 through PubMed, Embase, and Cochrane. We reviewed cases of LCNEC developed either from de novo or transformation from prostate adenocarcinoma and summarized the relevant pathophysiological course, treatment options, and outcomes...
2024: Frontiers in Oncology
https://read.qxmd.com/read/38513819/skin-cancer-risk-is-increased-by-somatic-mutations-detected-noninvasively-in-healthy-appearing-sun-exposed-skin
#23
JOURNAL ARTICLE
Kulvinder Kaur, Rizi Ai, Allyson G Perry, Bae Riley, Emma L Roberts, Erica N Montano, Jessica Han, Joanna Roacho, Brenda Garcia Lopez, Maral K Skelsey, Maria V Childs, James N Childs, John Dobak, Claudia Ibarra, Burkhard Jansen, Loren E Clarke, Steven Stone, John W Whitaker
Skin cancer risk is increased by exposure to ultraviolet radiation (UVR). Since UVR exposure accumulates over time and lighter skin is more susceptible to UVR, age and skin tone are risk factors for skin cancer. However, measurements of somatic mutations in healthy-appearing skin have not been used to calculate skin cancer risk. Herein, we developed a noninvasive test that quantifies somatic mutations in healthy-appearing sun-exposed skin and applied it to a 1,038-subject cohort. Somatic mutations were combined with other known skin cancer risk factors to train a model to calculate risk...
March 9, 2024: Journal of Investigative Dermatology
https://read.qxmd.com/read/38512527/identification-and-validation-of-neutrophils-related-subtypes-and-prognosis-model-in-triple-negative-breast-cancer
#24
JOURNAL ARTICLE
Shanqi Li, Yuzhou Qian, Wanchen Xie, Xinyu Li, Jiaying Wei, Long Wang, Guosheng Ren, Xuedong Yin
BACKGROUND: Neutrophils are considered to be crucial players in the initiation and progression of cancer. However, the complex relationship between neutrophils and cancer prognosis remains elusive, mainly due to the significant plasticity and diversity exhibited by these immune cells. METHODS: As part of our thorough investigation, we examined 38 Neutrophils-Related Genes (NRGs) and the associated copy number variations (CNV), somatic mutations, and gene expression patterns in relation to triple negative breast cancer (TNBC)...
March 21, 2024: Journal of Cancer Research and Clinical Oncology
https://read.qxmd.com/read/38512513/integrative-analysis-with-machine-learning-identifies-diagnostic-and-prognostic-signatures-in-neuroblastoma-based-on-differentially-dna-methylated-enhancers-between-inss-stage-4-and-4s-neuroblastoma
#25
JOURNAL ARTICLE
Shan Li, Tao Mi, Liming Jin, Yimeng Liu, Zhaoxia Zhang, Jinkui Wang, Xin Wu, Chunnian Ren, Zhaoying Wang, Xiangpan Kong, Jiayan Liu, Junyi Luo, Dawei He
INTRODUCTION: Accumulating evidence demonstrates that aberrant methylation of enhancers is crucial in gene expression profiles across several cancers. However, the latent effect of differently expressed enhancers between INSS stage 4S and 4 neuroblastoma (NB) remains elusive. METHODS: We utilized the transcriptome and methylation data of stage 4S and 4 NB patients to perform Enhancer Linking by Methylation/Expression Relationships (ELMER) analysis, discovering a differently expressed motif within 67 enhancers between stage 4S and 4 NB...
March 21, 2024: Journal of Cancer Research and Clinical Oncology
https://read.qxmd.com/read/38512136/antigen-independent-autonomous-b-cell-receptor-signaling-drives-activated-b-cell-dlbcl
#26
JOURNAL ARTICLE
Janneke A Eken, Marvyn T Koning, Kristyna Kupcova, Julieta H Sepúlveda Yáñez, Ruben A L de Groen, Edwin Quinten, Jurriaan Janssen, Cornelis A M van Bergen, Joost S P Vermaat, Arjen Cleven, Marcelo A Navarrete, Bauke Ylstra, Daphne de Jong, Ondrej Havranek, Hassan Jumaa, Hendrik Veelken
Diffuse large B cell lymphoma of activated B cell type (ABC-DLBCL), a major cell-of-origin DLBCL subtype, is characterized by chronic active B cell receptor (BCR) signaling and NF-κB activation, which can be explained by activating mutations of the BCR signaling cascade in a minority of cases. We demonstrate that autonomous BCR signaling, akin to its essential pathogenetic role in chronic lymphocytic leukemia (CLL), can explain chronic active BCR signaling in ABC-DLBCL. 13 of 18 tested DLBCL-derived BCR, including 12 cases selected for expression of IgM, induced spontaneous calcium flux and increased phosphorylation of the BCR signaling cascade in murine triple knockout pre-B cells without antigenic stimulation or external BCR crosslinking...
May 6, 2024: Journal of Experimental Medicine
https://read.qxmd.com/read/38511841/how-i-diagnose-and-manage-vexas-syndrome
#27
JOURNAL ARTICLE
Ashley Hagiya, Imran N Siddiqi, Endi Wang, Chuanyi M Lu
OBJECTIVES: To discuss VEXAS (vacuoles, E1 enzyme, X-linked, autoinflammatory, somatic) syndrome, including the clinical and pathologic features, diagnostic challenges, and treatment options. METHODS: A case-based approach and pertinent literature review were used to highlight the features of VEXAS syndrome, describe how to make the diagnosis, and discuss available therapies. RESULTS: VEXAS syndrome is an adult-onset, progressive systemic inflammatory disorder with overlapping rheumatologic and hematologic manifestations, including an increased risk of myelodysplastic neoplasms and plasma cell neoplasms...
March 21, 2024: American Journal of Clinical Pathology
https://read.qxmd.com/read/38509366/venous-plexus-associated-lymphoid-hubs-support-meningeal-humoral-immunity
#28
JOURNAL ARTICLE
Zachary Fitzpatrick, Nagela Ghabdan Zanluqui, Jared S Rosenblum, Zewen Kelvin Tuong, Colin Y C Lee, Vikram Chandrashekhar, Maria Luciana Negro-Demontel, Andrew P Stewart, David A Posner, Monica Buckley, Kieren S J Allinson, Panagiotis Mastorakos, Prashant Chittiboina, Dragan Maric, Danielle Donahue, Adel Helmy, Tamara Tajsic, John R Ferdinand, Anais Portet, Ana Peñalver, Eleanor Gillman, Zhengping Zhuang, Menna R Clatworthy, Dorian B McGavern
There is increasing interest in how immune cells in the meninges-the membranes that surround the brain and spinal cord-contribute to homeostasis and disease in the central nervous system1,2 . The outer layer of the meninges, the dura mater, has recently been described to contain both innate and adaptive immune cells, and functions as a site for B cell development3-6 . Here we identify organized lymphoid structures that protect fenestrated vasculature in the dura mater. The most elaborate of these dural-associated lymphoid tissues (DALT) surrounded the rostral-rhinal confluence of the sinuses and included lymphatic vessels...
March 20, 2024: Nature
https://read.qxmd.com/read/38508850/genetic-factors-altering-immune-responses-in-atrial-fibrillation-jacc-review-topic-of-the-week
#29
REVIEW
Sandro Ninni, David Dombrowicz, Menno de Winther, Bart Staels, David Montaigne, Stanley Nattel
Atrial fibrillation (AF) is the most common cardiac arrhythmia worldwide and is associated with a range of adverse clinical outcomes. Accumulating evidence points to inflammatory processes resulting from innate immune responses as a cornerstone in AF pathogenesis. Genetic and epigenetic factors affecting leukocytes have been identified as key modulators of the inflammatory response. Inherited variants in genes encoding proteins involved in the innate immune response have been associated with increased risk for AF recurrence and stroke in AF patients...
March 26, 2024: Journal of the American College of Cardiology
https://read.qxmd.com/read/38508656/circular-rna-as-a-source-of-neoantigens-for-cancer-vaccines
#30
JOURNAL ARTICLE
Yi Ren, Thamizhanban Manoharan, Beijia Liu, Cyrus Zai Ming Cheng, Bei En Siew, Wai-Kit Cheong, Kai Yin Lee, Ian Jse-Wei Tan, Bettina Lieske, Ker-Kan Tan, Gloryn Chia
BACKGROUND: The effectiveness of somatic neoantigen-based immunotherapy is often hindered by the limited number of mutations in tumors with low to moderate mutation burden. Focusing on microsatellite-stable colorectal cancer (CRC), this study investigates the potential of tumor-associated circular RNAs (circRNAs) as an alternative source of neoepitopes in CRC. METHODS: Tumor-associated circRNAs in CRC were identified using the MiOncoCirc database and ribo-depletion RNA sequencing of paired clinical normal and tumor samples...
March 19, 2024: Journal for Immunotherapy of Cancer
https://read.qxmd.com/read/38508103/detection-of-somatic-and-germline-pathogenic-variants-in-adult-cohort-of-drug-resistant-focal-epilepsies
#31
JOURNAL ARTICLE
L Ferri, V Menghi, L Licchetta, P Dimartino, R Minardi, C Davì, L Di Vito, E Cifaldi, C Zenesini, F Gozzo, V Pelliccia, V Mariani, Y C C de Spelorzi, S Gustincich, M Seri, L Tassi, T Pippucci, F Bisulli
OBJECTIVE: This study investigates the prevalence of pathogenic variants in the mechanistic target of rapamycin (mTOR) pathway in surgical specimens of malformations of cortical development (MCDs) and cases with negative histology. The study also aims to evaluate the predictive value of genotype-histotype findings on the surgical outcome. METHODS: The study included patients with drug-resistant focal epilepsy who underwent epilepsy surgery. Cases were selected based on histopathological diagnosis, focusing on MCDs and negative findings...
March 19, 2024: Epilepsy & Behavior: E&B
https://read.qxmd.com/read/38505749/double-somatic-mutations-in-ctnnb1-and-gna11-in-an-aldosterone-producing-adenoma
#32
JOURNAL ARTICLE
Kazutaka Nanba, Amy R Blinder, Aaron M Udager, Yuusuke Hirokawa, Takayoshi Miura, Hiroshi Okuno, Koki Moriyoshi, Yuto Yamazaki, Hironobu Sasano, Akihiro Yasoda, Noriko Satoh-Asahara, William E Rainey, Tetsuya Tagami
Double somatic mutations in CTNNB1 and GNA11/Q have recently been identified in a small subset of aldosterone-producing adenomas (APAs). As a possible pathogenesis of APA due to these mutations, an association with pregnancy, menopause, or puberty has been proposed. However, because of its rarity, characteristics of APA with these mutations have not been well characterized. A 46-year-old Japanese woman presented with hypertension and hypokalemia. She had two pregnancies in the past but had no history of pregnancy-induced hypertension...
2024: Frontiers in Endocrinology
https://read.qxmd.com/read/38504382/somatic-mutations-in-four-novel-genes-contribute-to-homologous-recombination-deficiency-in-breast-cancer-a-real-world-clinical-tumor-sequencing-study
#33
JOURNAL ARTICLE
Yongsheng Huang, Yuntan Qiu, Linxiaoxiao Ding, Shuwei Ren, Yuanling Jiang, Jiahuan Luo, Jinghua Huang, Xinke Yin, Sha Fu, Jianli Zhao, Kaishun Hu, Jianwei Liao
Breast cancers involving mutations in homologous recombination (HR) genes, most commonly BRCA1 and BRCA2 (BRCA1/2), respond well to PARP inhibitors and platinum-based chemotherapy. However, except for these specific HR genes, it is not clear which other mutations contribute to homologous recombination defects (HRD). Here, we performed next-generation sequencing of tumor tissues and matched blood samples from 119 breast cancer patients using the OncoScreen Plus panel. Genomic mutation characteristics and HRD scores were analyzed...
March 2024: Journal of Pathology. Clinical Research
https://read.qxmd.com/read/38504345/epigenetic-mlh1-silencing-concurs-with-mismatch-repair-deficiency-in-sporadic-naturally-occurring-colorectal-cancer-in-rhesus-macaques
#34
JOURNAL ARTICLE
Simon Deycmar, Brendan J Johnson, Karina Ray, George W Schaaf, Declan Patrick Ryan, Cassandra Cullin, Brandy L Dozier, Betsy Ferguson, Benjamin N Bimber, John D Olson, David L Caudell, Christopher T Whitlow, Kiran Kumar Solingapuram Sai, Emily C Romero, Francois J Villinger, Armando G Burgos, Hannah C Ainsworth, Lance D Miller, Gregory A Hawkins, Jeff W Chou, Bruno Gomes, Michael Hettich, Maurizio Ceppi, Jehad Charo, J Mark Cline
BACKGROUND: Naturally occurring colorectal cancers (CRC) in rhesus macaques share many features with their human counterparts and are useful models for cancer immunotherapy; but mechanistic data are lacking regarding the comparative molecular pathogenesis of these cancers. METHODS: We conducted state-of-the-art imaging including CT and PET, clinical assessments, and pathological review of 24 rhesus macaques with naturally occurring CRC. Additionally, we molecularly characterized these tumors utilizing immunohistochemistry (IHC), microsatellite instability assays, DNAseq, transcriptomics, and developed a DNA methylation-specific qPCR assay for MLH1, CACNA1G, CDKN2A, CRABP1, and NEUROG1, human markers for CpG island methylator phenotype (CIMP)...
March 19, 2024: Journal of Translational Medicine
https://read.qxmd.com/read/38503300/expanding-the-praas-spectrum-de-novo-mutations-of-immunoproteasome-subunit-%C3%AE-type-10-in-six-infants-with-scid-omenn-syndrome
#35
JOURNAL ARTICLE
Caspar I van der Made, Simone Kersten, Odelia Chorin, Karin R Engelhardt, Gayatri Ramakrishnan, Helen Griffin, Ina Schim van der Loeff, Hanka Venselaar, Annick Raas Rothschild, Meirav Segev, Janneke H M Schuurs-Hoeijmakers, Tuomo Mantere, Rick Essers, Masoud Zamani Esteki, Amir L Avital, Peh Sun Loo, Annet Simons, Rolph Pfundt, Adilia Warris, Marieke M Seyger, Frank L van de Veerdonk, Mihai G Netea, Mary A Slatter, Terry Flood, Andrew R Gennery, Amos J Simon, Atar Lev, Shirley Frizinsky, Ortal Barel, Mirjam van der Burg, Raz Somech, Sophie Hambleton, Stefanie S V Henriet, Alexander Hoischen
Mutations in proteasome β-subunits or their chaperone and regulatory proteins are associated with proteasome-associated autoinflammatory disorders (PRAAS). We studied six unrelated infants with three de novo heterozygous missense variants in PSMB10, encoding the proteasome β2i-subunit. Individuals presented with T-B-NK± severe combined immunodeficiency (SCID) and clinical features suggestive of Omenn syndrome, including diarrhea, alopecia, and desquamating erythematous rash. Remaining T cells had limited T cell receptor repertoires, a skewed memory phenotype, and an elevated CD4/CD8 ratio...
March 12, 2024: American Journal of Human Genetics
https://read.qxmd.com/read/38503282/contrasting-somatic-mutation-patterns-in-aging-human-neurons-and-oligodendrocytes
#36
JOURNAL ARTICLE
Javier Ganz, Lovelace J Luquette, Sara Bizzotto, Michael B Miller, Zinan Zhou, Craig L Bohrson, Hu Jin, Antuan V Tran, Vinayak V Viswanadham, Gannon McDonough, Katherine Brown, Yasmine Chahine, Brian Chhouk, Alon Galor, Peter J Park, Christopher A Walsh
Characterizing somatic mutations in the brain is important for disentangling the complex mechanisms of aging, yet little is known about mutational patterns in different brain cell types. Here, we performed whole-genome sequencing (WGS) of 86 single oligodendrocytes, 20 mixed glia, and 56 single neurons from neurotypical individuals spanning 0.4-104 years of age and identified >92,000 somatic single-nucleotide variants (sSNVs) and small insertions/deletions (indels). Although both cell types accumulate somatic mutations linearly with age, oligodendrocytes accumulated sSNVs 81% faster than neurons and indels 28% slower than neurons...
March 11, 2024: Cell
https://read.qxmd.com/read/38501975/origins-of-second-malignancies-in-children-and-mutational-footprint-of-chemotherapy-in-normal-tissues
#37
JOURNAL ARTICLE
Mònica Sánchez-Guixé, Ferran Muiños, Morena Pinheiro-Santin, Víctor González-Huici, Carlos J Rodriguez-Hernandez, Alexandra Avgustinova, Cinzia Lavarino, Abel González-Pérez, Jaume Mora, Núria López-Bigas
UNLABELLED: Pediatric cancers are rare diseases, and children without known germline predisposing conditions who develop a second malignancy during developmental ages are extremely rare. We present four such clinical cases and, through whole-genome and error-correcting ultra-deep duplex sequencing of tumor and normal samples, we explored the origin of the second malignancy in four children, uncovering different routes of development. The exposure to cytotoxic therapies was linked to the emergence of a secondary acute myeloid leukemia...
March 19, 2024: Cancer Discovery
https://read.qxmd.com/read/38501656/recurrent-tuberous-sclerosis-complex%C3%A2-%C3%A2-%C3%A2-%C3%A2-%C3%A2-mammalian-target-of-rapamycin-mutations-define-primary-renal-hemangioblastoma-as-a-unique-entity-distinct-from-its-central-nervous-system-counterpart
#38
JOURNAL ARTICLE
Xiao-Tong Wang, Ru Fang, Hui-Ying He, Wei Zhang, Qing Li, Su-An Sun, Xuan Wang, Ru-Song Zhang, Xiao-Dong Teng, Xiao-Jun Zhou, Qiu-Yuan Xia, Ming Zhao, Qiu Rao
Renal hemangioblastoma (HB) is a rare subset of HBs arising outside of the central nervous system (CNS), with its molecular drivers remaining entirely unknown. There were no significant alterations detected in previous studies, including von Hippel-Lindau gene alterations, which are commonly associated with CNS-HB. This study aimed to determine the real molecular identity of renal HB and better understand its relationship with CNS-HB. A cohort of 10 renal HBs was submitted for next-generation sequencing technology...
March 19, 2024: American Journal of Surgical Pathology
https://read.qxmd.com/read/38499737/investigating-the-potential-roles-of-intra-colonial-genetic-variability-in-pocillopora-corals-using-genomics
#39
JOURNAL ARTICLE
Nicolas Oury, Hélène Magalon
Intra-colonial genetic variability (IGV), the presence of more than one genotype in a single colony, has been increasingly studied in scleractinians, revealing its high prevalence. Several studies hypothesised that IGV brings benefits, but few have investigated its roles from a genetic perspective. Here, using genomic data (SNPs), we investigated these potential benefits in populations of the coral Pocillopora acuta from Reunion Island (southwestern Indian Ocean). As the detection of IGV depends on sequencing and bioinformatics errors, we first explored the impact of the bioinformatics pipeline on its detection...
March 18, 2024: Scientific Reports
https://read.qxmd.com/read/38498036/a-lineage-specific-stat5bn642h-mouse-model-to-study-nk-cell-leukemia
#40
JOURNAL ARTICLE
Klara Klein, Sebastian Kollmann, Angela Hiesinger, Julia List, Jonatan Kendler, Thorsten Klampfl, Mehak Randhawa, Jana Trifinopoulos, Barbara Maurer, Reinhard Grausenburger, Christof A Bertram, Richard H Moriggl, Thomas Rülicke, Charles G Mullighan, Agnieszka Witalisz-Siepracka, Wencke Walter, Gregor Hoermann, Veronika Sexl, Dagmar Gotthardt
Patients with T- and NK-cell neoplasms frequently have somatic STAT5B gain-of-function mutations. The most frequent STAT5B mutation is STAT5BN642H, which is known to drive murine T-cell leukemia although its role in NK-cell malignancies is unclear. Introduction of the STAT5BN642H mutation into human NK-cell lines enhances their potential to induce leukemia in mice. We have generated a mouse model that enables tissue-specific expression of STAT5BN642H and have selectively expressed the mutated STAT5B in hematopoietic cells (N642Hvav/+) or exclusively in NK cells (N642HNK/NK)...
March 18, 2024: Blood
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