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JOURNAL ARTICLE
Noah Gamble, Alexandra Bradu, Jason A Caldwell, Joshua McKeever, Olubusayo Bolonduro, Ebru Ermis, Caroline Kaiser, YeEun Kim, Benjamin Parks, Sandy Klemm, William J Greenleaf, Gerald R Crabtree, Andrew S Koh
Adaptive immunity relies on specialized effector functions elicited by lymphocytes, yet how antigen recognition activates appropriate effector responses through nonspecific signaling intermediates is unclear. Here we examined the role of chromatin priming in specifying the functional outputs of effector T cells and found that most of the cis-regulatory landscape active in effector T cells was poised early in development before the expression of the T cell antigen receptor. We identified two principal mechanisms underpinning this poised landscape: the recruitment of the nucleosome remodeler mammalian SWItch/Sucrose Non-Fermentable (mSWI/SNF) by the transcription factors RUNX1 and PU...
April 17, 2024: Nature Immunology
#2
JOURNAL ARTICLE
Emil Andersson, Ellen V Rothenberg, Carsten Peterson, Victor Olariu
T-cell development provides an excellent model system for studying lineage commitment from a multipotent progenitor. The intrathymic development process has been thoroughly studied. The molecular circuitry controlling it has been dissected and the necessary steps like programmed shut off of progenitor genes and T-cell genes upregulation have been revealed. However, the exact timing between decision-making and commitment stage remains unexplored. To this end, we implemented an agent-based multi-scale model to investigate inheritance in early T-cell development...
April 17, 2024: NPJ Systems Biology and Applications
#3
JOURNAL ARTICLE
Jian Shen, Minzhe Li
Gastric cancer (GC) is highly heterogeneous and influenced by aging-related factors. This study aimed to improve individualized prognostic assessment of GC by identifying aging-related genes and subtypes. Immune scores of GC samples from GEO and TCGA databases were calculated using ESTIMATE and scored as high immune (IS_high) and low immune (IS_low). ssGSEA was used to analyze immune cell infiltration. Univariate Cox regression was employed to identify prognosis-related genes. LASSO regression analysis was used to construct a prognostic model...
2024: Critical Reviews in Immunology
#4
JOURNAL ARTICLE
Kazuaki Matsumoto, Kazuki Okuyama, Tom Sidwell, Motoi Yamashita, Takaho Endo, Naoko Satoh-Takayama, Hiroshi Ohno, Tomohiro Morio, Ellen V Rothenberg, Ichiro Taniuchi
BCL11B is a transcription factor with six C2 H2 -type zinc-finger domains. Studies in mice have shown that Bcl11b plays essential roles in T cell development. Several germline heterozygous BCL11B variants have been identified in human patients with inborn errors of immunity (IEI) patients. Among these, two de novo mis-sense variants cause asparagine (N) to lysine (K) replacement in distinct zinc-finger domains, BCL11BN441K and BCL11BN807K . To elucidate the pathogenesis of the BCL11BN807K variant, we generated a mouse model of BCL11BN807K by inserting the corresponding mutation, Bcl11bN797K , into the mouse genome...
2024: Frontiers in Immunology
#5
REVIEW
José María García-Aznar, Sara Alonso Alvarez, Teresa Bernal Del Castillo
The transcription factor BCL11B plays an essential role in the development of central nervous system and T cell differentiation by regulating the expression of numerous genes involved in several pathways. Monoallelic defects in the BCL11B gene leading to loss-of-function are associated with a wide spectrum of phenotypes, including neurological disorders with or without immunological features and susceptibility to hematological malignancies. From the genetic point of view, the landscape of BCL11B mutations reported so far does not fully explain the genotype-phenotype correlation...
March 12, 2024: Genes and Immunity
#6
JOURNAL ARTICLE
Konrad Grützmann, Theresa Kraft, Matthias Meinhardt, Friedegund Meier, Dana Westphal, Michael Seifert
Melanoma, the deadliest form of skin cancer, can metastasize to different organs. Molecular differences between brain and extracranial melanoma metastases are poorly understood. Here, promoter methylation and gene expression of 11 heterogeneous patient-matched pairs of brain and extracranial metastases were analyzed using melanoma-specific gene regulatory networks learned from public transcriptome and methylome data followed by network-based impact propagation of patient-specific alterations. This innovative data analysis strategy allowed to predict potential impacts of patient-specific driver candidate genes on other genes and pathways...
December 2024: Computational and Structural Biotechnology Journal
#7
JOURNAL ARTICLE
Zhengdao Mao, Yan Qian, Zhiguang Liu, Yujia Shi, Liang Fan, Qian Zhang
Persistent type (T) 2 airway inflammation plays an important role in the development of severe asthma. However, the molecular mechanisms leading to T2 severe asthma have yet to be fully clarified. Human normal lung epithelial cells (BEAS-2B cells) were transfected with LINC00158/BCL11B plasmid/small interfering RNA (siRNA). Levels of epithelial-mesenchymal transition (EMT)-related markers were measured using real-time qPCR (RT-qPCR) and western blot. A dual luciferase reporter assay was used to validate the targeting relationship between LINC00158 and BCL11B...
March 4, 2024: International Immunopharmacology
#8
REVIEW
Franziska Anna Seigfried, Stefan Britsch
Neurodevelopmental disorders (NDDs) comprise a diverse group of diseases, including developmental delay, autism spectrum disorder (ASD), intellectual disability (ID), and attention-deficit/hyperactivity disorder (ADHD). NDDs are caused by aberrant brain development due to genetic and environmental factors. To establish specific and curative therapeutic approaches, it is indispensable to gain precise mechanistic insight into the cellular and molecular pathogenesis of NDDs. Mutations of BCL11A and BCL11B , two closely related, ultra-conserved zinc-finger transcription factors, were recently reported to be associated with NDDs, including developmental delay, ASD, and ID, as well as morphogenic defects such as cerebellar hypoplasia...
February 17, 2024: Biology
#9
JOURNAL ARTICLE
Giovanni A Botten, Yuannyu Zhang, Franklin Fuda, Prasad Koduru, Olga K Weinberg, Tamra L Slone, Ruifang Zheng, Kathryn E Dickerson, Jeffrey R Gagan, Weina Chen
T/myeloid mixed phenotype acute leukaemia (MPAL) is a rare aggressive acute leukaemia with poorly understood pathogenesis. Herein, we report two cases of T/myeloid MPAL harbouring BCL11B-associated structural variants that activate TLX3 (TLX3::BCL11B-TLX3-activation) by genome sequencing and transcriptomic analyses. Both patients were young males with extramedullary involvement. Cooperative gene alterations characteristic of T/myeloid MPAL and T-lymphoblastic leukaemia (T-ALL) were detected. Both patients achieved initial remission following lineage-matched ALL-based therapy with one patient requiring a lineage-switched myeloid-based therapy...
February 22, 2024: British Journal of Haematology
#10
REVIEW
Rong Yang, Yuan Ai, Ting Bai, Xiao-Xi Lu, Guoqian He
BACKGROUND: Williams-Beuren syndrome (WBS) is a rare genetic disorder caused by hemizygous microdeletion of contiguous genes on chromosome 7q11.23. Although the phenotype features extensive heterogeneity in severity and performance, WBS is not considered to be a predisposing factor for cancer development. Currently, hematologic cancers, mainly Burkitt lymphoma, are rarely reported in patients with WBS. Here in, we report a unique case of T-cell acute lymphoblastic leukemia in a male child with WBS...
February 16, 2024: Medicine (Baltimore)
#11
JOURNAL ARTICLE
Artemis Koumoundourou, Märt Rannap, Elodie De Bruyckere, Sigrun Nestel, Carsten Reissner, Alexei V Egorov, Pengtao Liu, Markus Missler, Bernd Heimrich, Andreas Draguhn, Stefan Britsch
The transcription factor Bcl11b has been linked to neurodevelopmental and neuropsychiatric disorders associated with synaptic dysfunction. Bcl11b is highly expressed in dentate gyrus granule neurons and is required for the structural and functional integrity of mossy fiber-CA3 synapses. The underlying molecular mechanisms, however, remained unclear. We show in mice that the synaptic organizer molecule C1ql2 is a direct functional target of Bcl11b that regulates synaptic vesicle recruitment and long-term potentiation at mossy fiber-CA3 synapses in vivo and in vitro...
February 15, 2024: ELife
#12
JOURNAL ARTICLE
Jie Zhang, Qiang Gao, Shiyang Hou, Xiaoqian Chi, Meiliang Zheng, Qijun Zhang, Haifeng Shan, Xiaoyu Zhang, Chunbo Kang
Colorectal cancer is a cancer that arises from the abnormal growth of cells in the colon or rectum. Osteosarcoma (OS) is a common primary bone tumor with high degree of malignancy. The configuration files for colorectal cancer dataset GSE142279 and OS datasets GSE197158 and GSE206448 were downloaded from Gene Expression Omnibus database using the platforms GPL20795, GPL20301, and GPL24676. Differentially expressed genes (DEGs) were screened and weighted gene co-expression network analysis (WGCNA) was performed...
February 2, 2024: Medicine (Baltimore)
#13
JOURNAL ARTICLE
Clemer Abad, Maria C Robayo, Maria Del Mar Muñiz-Moreno, Maria T Bernardi, Maria G Otero, Christina Kosanovic, Anthony J Griswold, Tyler Mark Pierson, Katherina Walz, Juan I Young
GATAD2B (GATA zinc finger domain containing 2B) variants are associated with the neurodevelopmental syndrome GAND, characterized by intellectual disability (ID), infantile hypotonia, apraxia of speech, epilepsy, macrocephaly and distinct facial features. GATAD2B encodes for a subunit of the Nucleosome Remodeling and Histone Deacetylase (NuRD) complex. NuRD controls transcriptional programs critical for proper neurodevelopment by coupling histone deacetylase with ATP-dependent chromatin remodeling activity. To study mechanisms of pathogenesis for GAND, we characterized a mouse model harboring an inactivating mutation in Gatad2b...
January 18, 2024: Translational Psychiatry
#14
JOURNAL ARTICLE
Masayuki Umeda, Jing Ma, Tamara Westover, Yonghui Ni, Guangchun Song, Jamie L Maciaszek, Michael Rusch, Delaram Rahbarinia, Scott Foy, Benjamin J Huang, Michael P Walsh, Priyadarshini Kumar, Yanling Liu, Wenjian Yang, Yiping Fan, Gang Wu, Sharyn D Baker, Xiaotu Ma, Lu Wang, Todd A Alonzo, Jeffrey E Rubnitz, Stanley Pounds, Jeffery M Klco
Recent studies on pediatric acute myeloid leukemia (pAML) have revealed pediatric-specific driver alterations, many of which are underrepresented in the current classification schemas. To comprehensively define the genomic landscape of pAML, we systematically categorized 887 pAML into 23 mutually distinct molecular categories, including new major entities such as UBTF or BCL11B, covering 91.4% of the cohort. These molecular categories were associated with unique expression profiles and mutational patterns. For instance, molecular categories characterized by specific HOXA or HOXB expression signatures showed distinct mutation patterns of RAS pathway genes, FLT3 or WT1, suggesting shared biological mechanisms...
January 11, 2024: Nature Genetics
#15
JOURNAL ARTICLE
Yiannis Petros Dimopoulos, Sanam Loghavi
No abstract text is available yet for this article.
January 11, 2024: Blood
#16
JOURNAL ARTICLE
Akira Nishimura, Kazuaki Yokoyama, Takuya Naruto, Chika Yamagishi, Toshihiko Imamura, Hiroto Nakazono, Shunsuke Kimura, Mieko Ito, Maiko Sagisaka, Yukie Tanaka, Jinhua Piao, Yui Namikawa, Masakatsu Yanagimachi, Takeshi Isoda, Akinori Kanai, Hirotaka Matsui, Tomoya Isobe, Aiko Sato-Otsubo, Naoko Higuchi, Akiko Takada, Haruna Okuno, Shoji Saito, Shuhei Karakawa, Shogo Kobayashi, Daisuke Hasegawa, Hiroyuki Fujisaki, Daiichiro Hasegawa, Kazutoshi Koike, Takashi Koike, Shinya Rai, Katsutsugu Umeda, Hideki Sano, Yujin Sekinaka, Atsushi Ogawa, Akitoshi Kinoshita, Norio Shiba, Mizuka Miki, Fumihiko Kimura, Hideki Nakayama, Yozo Nakazawa, Takashi Taga, Tomohiko Taki, Souichi Adachi, Atsushi Manabe, Katsuyoshi Koh, Yasushi Ishida, Junko Takita, Fumihiko Ishikawa, Hiroaki Goto, Tomohiro Morio, Shuki Mizutani, Arinobu Tojo, Masatoshi Takagi
Myeloid/natural killer (NK) cell precursor acute leukemia (MNKPL) has been described on the basis of its unique immunophenotype and clinical phenotype. However, there is no consensus on the characteristics for identifying this disease type because of its rarity and lack of defined distinctive molecular characteristics. In this study, multiomics analysis revealed that MNKPL is distinct from acute myeloid leukemia, T cell acute lymphoblastic leukemia, and mixed-phenotype acute leukemia (MPAL), and NOTCH1 and RUNX3 activation and BCL11B down-regulation are hallmarks of MNKPL...
December 15, 2023: Science Advances
#17
JOURNAL ARTICLE
Cunte Chen, Yuping Zhang, Xiangbo Zeng, Chengwu Zeng, Grzegorz K Przybylski, Yangqiu Li
No abstract text is available yet for this article.
2023: Clinical Medicine Insights. Oncology
#18
JOURNAL ARTICLE
Xiangyu Sui, Guohao Wu
Cachexia, a debilitating condition that worsens patient outcomes, often accompanies gastric cancer, a malignancy that is prevalent worldwide. The extensive research explored the interconnected molecular and immune aspects of stomach cancer, with a particular emphasis on cachexia. By employing the GEO database, we identified genes that were expressed differently in gastric cancer patients suffering from cachexia. Following the analysis of Weighted Gene Co-expression Network (WGCNA), gene modules intricately linked to particular immune cells were revealed, indicating a significantly disrupted tumor microenvironment...
2023: Frontiers in Immunology
#19
JOURNAL ARTICLE
Yajing Wang, Fei Zhang, Ning Gao, Peng Bu, Wei Cui, Yanfeng Xi
Peripheral T-cell lymphoma is a disease that includes multiple T-cell lymphoma subtypes. It is still unclear whether CD30 can be used as a new target molecule and classification standard for PTCL. Differences in the molecular characteristics of CD30-positive PTCL and CD30-negative PTCL have rarely been reported. This study aimed to analyze the expression of BCL11b and CDKN2A in CD30-positive PTCL and CD30-negative PTCL, in order to guide the pathological classification, prognosis, and clinical treatment of PTCL...
November 17, 2023: Medicine (Baltimore)
#20
JOURNAL ARTICLE
Elise Vickridge, Camila C F Faraco, Fanny Lo, Hedyeh Rahimian, Zi Yang Liu, Payman S Tehrani, Billel Djerir, Zubaidah M Ramdzan, Lam Leduy, Alexandre Maréchal, Anne-Claude Gingras, Alain Nepveu
Genetic studies in mice and human cancers established BCL11B as a haploinsufficient tumor suppressor gene. Paradoxically, BCL11B is overexpressed in some human cancers where its knockdown is synthetic lethal. We identified the BCL11B protein in a proximity-dependent biotinylation screen performed with the DNA glycosylase NTHL1. In vitro DNA repair assays demonstrated that both BCL11B and a small recombinant BCL11B213-560 protein lacking transcription regulation potential can stimulate the enzymatic activities of two base excision repair (BER) enzymes: NTHL1 and Pol β...
November 13, 2023: Nucleic Acids Research
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