Review
Plant Sciences
Fei Gao, Christian Dubos
Summary: Plants tightly control iron uptake, translocation, assimilation, and storage through complex transcriptional regulatory networks, with the bHLH family of transcription factors playing a vital role. Research also involves other classes of transcription factors and post-translational mechanisms. Future research aims to further understand how plants precisely regulate iron homeostasis.
JOURNAL OF EXPERIMENTAL BOTANY
(2021)
Article
Biotechnology & Applied Microbiology
Ruihua Wang, Yuanyuan Li, Minggang Gao, Min Han, Huilian Liu
Summary: A total of 213 RsbHLH (Raphanus sativus L. bHLH) genes were identified in the radish genome, which were grouped into 22 subfamilies. The distribution of these genes was uneven, with 204 genes located on nine chromosomes and nine genes located on the scaffolds. Gene structure analysis showed that 25 genes had no introns. Collineation analysis revealed the syntenic orthologous bHLH gene pairs between radish and Arabidopsis thaliana/Brassica rapa/Brassica oleracea. The RNA-seq results showed a variety of expression patterns for RsbHLH genes at different development stages. Weighted gene co-expression network analysis identified four RsbHLH genes related to chlorophyll content.
Article
Biochemistry & Molecular Biology
Allison T. T. Madsen, Deborah J. J. Good
Summary: Continual advances in our understanding of the human genome have led to exponential increases in known single nucleotide variants. In this study, researchers systematically analyzed all missense mutations in the NHLH2 gene using in silico tools and predicted pathogenicity to narrow down variants for future wet lab analysis. This contributes to the knowledge of the NHLH2 transcription factor and provides a systematic methodology for characterizing variants in other genes.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Review
Biochemistry & Molecular Biology
Yaqi Hao, Xiumei Zong, Pan Ren, Yuqi Qian, Aigen Fu
Summary: The bHLH transcription factor family in plants is involved in regulating various physiological processes such as biosynthesis, metabolism, and plant hormone signaling by forming dimers. They play important roles in plant growth and development, stress responses, and signaling networks.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Review
Plant Sciences
Eun-Deok Kim, Keiko U. Torii
Summary: The formation of stomata is a significant model system for understanding stem cell fate commitment. The regulatory strategies governing cell fate commitment differ between embryonic and postembryonic stomatal development. The interplay of transcription factors and cell cycle machineries is crucial for cell differentiation. Recent studies have provided insights into the molecular mechanisms underlying the interaction between transcription factors and epigenetic machineries.
PLANT CELL AND ENVIRONMENT
(2023)
Article
Multidisciplinary Sciences
Monika Gonczi, Joao M. C. Teixeira, Susana Barrera-Vilarmau, Laura Mediani, Francesco Antoniani, Tamas Milan Nagy, Krisztina Feher, Zsolt Raduly, Viktor Ambrus, Jozsef Tozser, Endre Barta, Katalin E. Kover, Laszlo Csernoch, Serena Carra, Monika Fuxreiter
Summary: The context-dependent higher-order assembly of Mef2D controls muscle lineage development by simultaneously interacting with the basal machinery and myogenic factors. The study found that the alternatively spliced acidic beta-domain enhances the transcription of Mef2D. The beta-domain can serve as an interaction element for higher-order assembly, forming nuclear condensates and solid-like aggregates. These findings suggest that the beta-domain fine-tunes Mef2D assembly and provides a platform for myogenic regulatory factors and transcriptional apparatus during muscle development.
NATURE COMMUNICATIONS
(2023)
Article
Biochemistry & Molecular Biology
Yunyun Cao, Lun Liu, Kangsheng Ma, Wenjing Wang, Hongmei Lv, Ming Gao, Xinman Wang, Xichun Zhang, Shuxin Ren, Na Zhang, Yang-Dong Guo
Summary: This study identified the SlJIG gene in tomato as a direct target of MYC2, involved in JA-induced terpene biosynthesis and resistance against cotton bollworm and B. cinerea. SlJIG knockout plants showed lower terpene contents and weaker expression of JA-responsive defense genes.
JOURNAL OF INTEGRATIVE PLANT BIOLOGY
(2022)
Review
Cell Biology
Martina La Spina, Pablo S. Contreras, Alberto Rissone, Naresh K. Meena, Eutteum Jeong, Jose A. Martina
Summary: Response and adaptation to stress are crucial for survival, and regulation of the transcriptional machinery by the MiT/TFE family of transcription factors is an important aspect of this process. These proteins, conserved through evolution, play key roles in cellular functions in response to various stresses. Their tissue expression and activities are highly regulated by alternative splicing, promoter usage, and posttranslational modifications. The study of MiT/TFE proteins and their transcriptional regulatory mechanisms is important for potential therapeutic targets in human diseases like lysosomal storage disorders, neurodegeneration, and cancer.
FRONTIERS IN CELL AND DEVELOPMENTAL BIOLOGY
(2021)
Article
Oncology
Yong-Jae Lee, Eun-Ji Nam, Sunghoon Kim, Young-Tae Kim, Pamela Itkin-Ansari, Sang-Wun Kim
Summary: Ovarian cancer is one of the most fatal gynecological malignancies in women, and although new drugs have been proposed, their efficacy in treating ovarian cancer is limited. This study suggests that modulating the balance of the ID/E2A gene regulators may be a promising approach for treating ovarian cancer.
Article
Biochemistry & Molecular Biology
Hongwoo Lee, Pil Joon Seo
Summary: Research has discovered small 3D chromatin units in plant genomes that are usually established around individual genes and are influenced by chromatin accessibility. Larger contact domains containing multiple genes were also observed, depending on accessible border regions. Computational modeling successfully simulated the formation of these 3D structures.
NUCLEIC ACIDS RESEARCH
(2023)
Article
Computer Science, Artificial Intelligence
Shushan Toneyan, Ziqi Tang, Peter K. Koo
Summary: This study introduces a unified evaluation framework and uses it to compare different binary and quantitative models for predicting chromatin accessibility data. The results show that quantitative modeling improves the generalizability and interpretability of the models, and a robustness metric is introduced to enhance model selection and variant effect predictions.
NATURE MACHINE INTELLIGENCE
(2022)
Article
Multidisciplinary Sciences
Kensuke Toriumi, Yuta Onodera, Toshiyuki Takehara, Tatsufumi Mori, Joe Hasei, Kanae Shigi, Natsumi Iwawaki, Toshifumi Ozaki, Masao Akagi, Mahito Nakanishi, Takeshi Teramura
Summary: In this study, the researchers discovered that the transmembrane protein LRRC15 correlated with the expression of TWIST1 in MSCs, and could be used to estimate the stemness of MSCs. The LRRC15-positive MSC populations expressed stemness-associated transcription factors and therapeutic cytokines, and showed enhanced therapeutic effects in a pulmonary fibrosis mouse model. This study highlights the importance of TWIST1 in MSC stemness and the utility of LRRC15 as a marker for evaluating stem cell quality in MSCs before transplantation.
Article
Chemistry, Multidisciplinary
Edgar M. Faison, Amrita Nallathambi, Qi Zhang
Summary: RNA molecules undergo conformational transitions in response to cellular and environmental stimuli, which can be regulated by site-specific protonation. A new method, pH-differential mutational profiling (PD-MaP) with dimethyl sulfate probing, was developed for high-throughput detection of protonation-coupled conformational ensembles in RNA. The application of this method on microRNA-21 precursor (pre-miR-21) revealed known A(+)-G-coupled conformational ensemble and identified a secondary protonation event involving an A(+)-C mismatch. Validation of these protonation-coupled ensembles was achieved using NMR relaxation dispersion spectroscopy. Furthermore, widespread protonation-coupled conformational ensembles were found in a library of well-annotated human primary microRNAs, suggesting their broad functions in biology.
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
(2023)
Article
Biochemistry & Molecular Biology
Francesco S. Ielasi, Sara Ternifi, Emeline Fontaine, Domenico Iuso, Yohann Coute, Andres Palencia
Summary: Human pre-mRNA processing relies on multi-subunit macromolecular complexes to recognize specific RNA sequence elements. This study reveals how H2AC18 captures two human pre-mRNA processing complexes in a mutually exclusive mode by overlapping a canonical PAS sequence element with a HDE.
NUCLEIC ACIDS RESEARCH
(2022)
Article
Plant Sciences
Mauricio Lopez-Obando, Katarina Landberg, Eva Sundberg, Mattias Thelander
Summary: This study investigates the conservation of regulation of sporogenous cells and nursing cells surrounding them between angiosperm anthers and bryophyte sporangia. It demonstrates that the Clade II bHLH TFs play similar roles in the development of spore precursors in Physcomitrium patens and angiosperms, supporting the hypothesis of their relatedness.
Article
Hematology
Jana Ihlow, Sophia Gross, Leonie Busack, Anne Floercken, Julia Jesse, Michaela Schwarz, Nina Rosa Neuendorff, Ann-Christin Von Bruenneck, Ioannis Anagnostopoulos, Seval Tuerkmen, Igor Wolfgang Blau, Thomas Burmeister, David Horst, Lars Bullinger, Joerg Westermann
Summary: This retrospective study analyzed the prognostic impact of early bone marrow assessment in 1,008 newly diagnosed acute myeloid leukemia patients. It found that early blast persistence had a negative prognostic impact on overall survival, event-free survival, and relapse-free survival. However, patients who achieved at least partial remission and subsequent blast clearance showed improved outcomes. The study suggests that the time slope of remission can inform post-induction therapy decision-making.
Letter
Oncology
Lorenz Bastian, Alina M. Hartmann, Thomas Beder, Sonja Haenzelmann, Jan Kaessens, Miriam Bultmann, Marc P. Hoeppner, Soeren Franzenburg, Michael Wittig, Andre Franke, Inga Nagel, Malte Spielmann, Niklas Reimer, Hauke Busch, Stefan Schwartz, Bjoern Steffen, Andreas Viardot, Konstanze Doehner, Mustafa Kondakci, Gerald Wulf, Knut Wendelin, Andrea Renzelmann, Alexander Kiani, Heiko Trautmann, Martin Neumann, Nicola Goekbuget, Monika Brueggemann, Claudia D. Baldus
Article
Oncology
Laura E. Fischer, Sebastian Stintzing, Volker Heinemann, Ulrich Keilholz, Dietmar Keune, Claudia Vollbrecht, Thomas Burmeister, Andreas Kind, Lena Weiss, David Horst, Thomas Kirchner, Frederick Klauschen, Andreas Jung, Christoph Benedikt Westphalen, Ivan Jelas
Summary: This study retrospectively analyzed the implementation of liquid biopsies (LB) in the clinical management of colorectal cancer (CRC) patients between 2017 and 2021. The results indicate that the potential of LB as a diagnostic tool to drive personalized treatment in CRC patients is not yet fully exploited in everyday clinical practice.
FRONTIERS IN ONCOLOGY
(2022)
Article
Multidisciplinary Sciences
Birgit Burkhardt, Ulf Michgehl, Jonas Rohde, Tabea Erdmann, Philipp Berning, Katrin Reutter, Marius Rohde, Arndt Borkhardt, Thomas Burmeister, Sandeep Dave, Alexandar Tzankov, Martin Dugas, Sarah Sandmann, Falko Fend, Jasmin Finger, Stephanie Mueller, Nicola Goekbuget, Torsten Haferlach, Wolfgang Kern, Wolfgang Hartmann, Wolfram Klapper, Ilske Oschlies, Julia Richter, Udo Kontny, Mathias Lutz, Britta Maecker-Kolhoff, German Ott, Andreas Rosenwald, Reiner Siebert, Arend von Stackelberg, Brigitte Strahm, Wilhelm Woessmann, Martin Zimmermann, Myroslav Zapukhlyak, Michael Grau, Georg Lenz
Summary: This study compares mutational profiles in different age groups of Burkitt lymphoma patients and finds a transition in mutational features between the ages of 25 and 40. There are also differences in the mutation frequencies between pediatric and adult patients. TP53 mutations in pediatric patients are significantly associated with higher relapse incidence.
NATURE COMMUNICATIONS
(2022)
Article
Immunology
Merle Sauer, Joerg Scheffel, Stefan Frischbutter, Niklas Mahnke, Marcus Maurer, Thomas Burmeister, Karoline Krause, Martin Metz
Summary: This study aimed to investigate a possible gain-of-function mutation or activating polymorphism in the STAT3 gene responsible for low IgE levels in patients with CSUaiTIIb. However, no differences were found in the prevalence of tested SNPs or mutations in the relevant exons of STAT3, indicating that the low IgE levels in these patients may not be linked to STAT3 mutations or altered activity. Further research is needed to uncover the cause of low IgE levels in CSUaiTIIb patients.
FRONTIERS IN IMMUNOLOGY
(2022)
Meeting Abstract
Hematology
Sophia Gross, Jana Ihlow, Leonie Busack, Kacper Adamiak, Jens F. Schrezenmeier, Julia Jesse, Michaela Schwarz, Anne Floercken, Kathrin Rieger, Jan Kronke, Philipp le Coutre, Vivien Boldt, Ann-Christin Von Bruenneck, David Horst, Thomas Burmeister, Igor Wolfgang Blau, Ulrich Keller, Lars Bullinger, Joerg Westermann
Article
Multidisciplinary Sciences
Sven Liebig, Martin Neumann, Patricia Silva, Jutta Ortiz-Tanchez, Veronika Schulze, Konstandina Isaakidis, Cornelia Schlee, Michael P. Schroeder, Thomas Beder, Luc G. T. Morris, Timothy A. Chan, Lorenz Bastian, Thomas Burmeister, Stefan Schwartz, Nicola Goekbuget, Liliana H. Mochmann, Claudia D. Baldus
Summary: FAT atypical cadherin 1 (FAT1), a transmembrane protein, is frequently mutated in various cancer types and has been described as context-dependent tumor suppressor or oncogene. FAT1 expression in T-ALL patients is correlated with promoter methylation status, with a subset of TLX1-driven T-ALL patients showing methylation-independent high FAT1 expression.
SCIENTIFIC REPORTS
(2023)
Article
Oncology
C. Meyer, P. Larghero, B. Almeida Lopes, T. Burmeister, D. Groeger, R. Sutton, N. C. Venn, G. Cazzaniga, L. Corral Abascal, G. Tsaur, L. Fechina, M. Emerenciano, M. S. Pombo-de-Oliveira, T. Lund-Aho, T. Lundan, M. Montonen, V. Juvonen, J. Zuna, J. Trka, P. Ballerini, H. Lapillonne, V. H. J. van der Velden, E. Sonneveld, E. Delabesse, R. R. C. de Matos, M. L. M. Silva, S. Bomken, K. Katsibardi, M. Keernik, N. Grardel, J. Mason, R. Price, J. Kim, C. Eckert, L. Lo Nigro, C. Bueno, P. Menendez, U. zur Stadt, P. Gameiro, L. Sedek, T. Szczepanski, A. Bidet, V. Marcu, K. Shichrur, S. Izraeli, H. O. Madsen, B. W. Schaefer, S. Kubetzko, R. Kim, E. Clappier, H. Trautmann, M. Brueggemann, P. Archer, J. Hancock, J. Alten, A. Moericke, M. Stanulla, J. Lentes, A. K. Bergmann, S. Strehl, S. Koehrer, K. Nebral, M. N. Dworzak, O. A. Haas, C. Arfeuille, A. Caye-Eude, H. Cave, R. Marschalek
Summary: This study analyzed the genomic breakpoints in 3401 acute leukemia patients and identified 107 KMT2A gene fusions and other rearrangements. The study also found seven common fusion genes and partial tandem duplications, which are important for understanding the pathogenesis of acute leukemia and monitoring minimal residual disease.
Article
Oncology
Viktoria Ingwersen, Joerg Hofmann, Marion Muche, Philipp Le Coutre, Thomas Schneider, Corinna Leng, Thomas Burmeister, Georg Maschmeyer, Ulrich Keller, Stefan Schwartz
Summary: This study retrospectively analyzed 22 immunocompromised patients and found that hepatitis E virus (HEV) could cause chronic infections in these patients. Some patients achieved viral clearance with ribavirin therapy, but others still could not clear the virus and may develop liver failure.
ONCOLOGY RESEARCH AND TREATMENT
(2023)
Article
Oncology
Katherine A. Janeway, Luis Gros, Stefan Schwartz, Claire Daugherty, Eva Gallardo, Christon Hill, Emma Thomas, Suzanne Ward, Carmelo Rizzari
Summary: Delayed elimination of methotrexate can occur in cancer treatment. Compassionate-use trials showed the effectiveness of glucarpidase in rapidly reducing methotrexate concentrations. This study analyzed pediatric and young adult patients and confirmed the efficacy and safety of glucarpidase in this population.
PEDIATRIC BLOOD & CANCER
(2023)
Article
Multidisciplinary Sciences
Thomas Burmeister, Daniela Groeger, Nicola Goekbuget, Bernd Spriewald, Michael Starck, Ahmet Elmaagacli, Dieter Hoelzer, Ulrich Keller, Stefan Schwartz
Summary: The translocation t(1;19)(q23;p13) with the resulting chimeric TCF3::PBX1 gene is the third most prevalent recurrent chromosomal translocation in acute lymphoblastic leukemia. This study provides extensive molecular data on the chromosomal breakpoints of this translocation in adult patients and explores the feasibility of using patient-specific chromosomal break sites as molecular markers for detecting measurable residual disease (MRD). A highly sensitive generic real-time PCR for MRD assessment using these breakpoint sequences was established, offering a potential alternative to the classical method utilizing rearranged immune gene loci.
SCIENTIFIC REPORTS
(2023)
Article
Hematology
Thomas Burmeister, Lars Bullinger, Philipp le Coutre
Summary: Atypical BCR-ABL1 transcripts, present in approximately 2% of chronic myeloid leukemia cases, should be detected as patients with these transcripts can benefit from tyrosine kinase inhibitor therapy. In the e8a2 atypical BCR-ABL1 transcript, two out-of-frame exons are fused, typically with interposed nucleotides to restore the reading frame. This study analyzes a specific e8a2 BCR-ABL1 translocation, identifies the genomic chromosomal breakpoint, explains the formation of this transcript, and provides recommendations for molecular analysis of future e8a2 BCR-ABL1 cases.
ACTA HAEMATOLOGICA
(2023)
Meeting Abstract
Oncology
S. Gross, J. Ihlow, L. Busack, K. Adamiak, J. Jesse, M. Schwarz, K. Rieger, J. Kroenke, P. le Coutre, A. C. von Bruenneck, D. Horst, T. Burmeister, I. W. Blau, U. Keller, L. Bullinger, J. Westermann
ONCOLOGY RESEARCH AND TREATMENT
(2022)