Ponraj Prabakaran, Abhinav Gupta, Sambasiva P Rao, Deepak Rajpal, Maria Wendt, Yu Qiu, Partha S Chowdhury
{"title":"Unveiling inverted D genes and D-D fusions in human antibody repertoires unlocks novel antibody diversity.","authors":"Ponraj Prabakaran, Abhinav Gupta, Sambasiva P Rao, Deepak Rajpal, Maria Wendt, Yu Qiu, Partha S Chowdhury","doi":"10.1038/s42003-024-07441-6","DOIUrl":"10.1038/s42003-024-07441-6","url":null,"abstract":"<p><p>Antibodies, essential components of adaptive immunity, derive their remarkable diversity primarily from V(D)J gene rearrangements, particularly within the heavy chain complementarity-determining region 3 (CDR-H3) where D genes play a major role. Traditionally, D genes were thought to recombine only in the forward direction, despite having identical recombination signal sequences (12 base pair spacers) at both ends. This observation led us to question whether these symmetrical sequences might enable bidirectional recombination. We identified 25 unique inverted D genes (InvDs) in both naive and memory B cells from antibody repertoires of 13 healthy donors. These InvDs utilize all three reading frames during translation, producing distinct amino acid profiles enriched in histidine, proline, and lysine in CDR-H3s of antibodies with potential functional diversity. Notably, our analysis revealed a broader range of D-D fusions, including D-D, D-InvD, InvD-D, and InvD-InvD configurations, opening new perspectives for antibody engineering and therapeutic development.</p>","PeriodicalId":10552,"journal":{"name":"Communications Biology","volume":"8 1","pages":"133"},"PeriodicalIF":5.2,"publicationDate":"2025-01-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11775173/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143058369","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Hang Lin, Lingzhi Qu, Hudie Wei, Ming Guo, Xiaojuan Chen, Qianmeng Lin, Huajun Zhang, Shuyan Dai, Yongheng Chen
{"title":"Characterization of Bozitinib as a potential therapeutic agent for MET-amplified gastric cancer.","authors":"Hang Lin, Lingzhi Qu, Hudie Wei, Ming Guo, Xiaojuan Chen, Qianmeng Lin, Huajun Zhang, Shuyan Dai, Yongheng Chen","doi":"10.1038/s42003-025-07490-5","DOIUrl":"10.1038/s42003-025-07490-5","url":null,"abstract":"<p><p>Hyperactive c-Met signaling pathway caused by altered MET is a common mechanism underlying gastric cancer and represents an attractive target for the treatment of gastric cancer with MET alterations. However, no c-Met kinase inhibitors are currently approved specifically for the treatment of c-Met-amplified gastric cancer. Recently, bozitinib, a highly selective c-Met kinase inhibitor, has shown remarkable potency in selectively inhibiting MET-altered non-small cell lung cancer and secondary glioblastoma. In this study, we investigate the antitumor activity of bozitinib against MET-amplified gastric cancer and elucidate its molecular mechanism. Bozitinib demonstrates a strong effect on MET-amplified gastric cancer cells by blocking the c-Met signaling pathway, leading to the inhibition of cell proliferation and survival, as well as the induction of G0/G1 phase arrest and apoptosis. Structurally, bozitinib is optimally embedded in the ATP pocket of c-Met and firmly binds via an extensive interaction network. In addition, bozitinib efficiently inhibits c-Met resistance-conferring mutations G1163R and Y1230H, although its potency is significantly decreased against the D1228N and Y1230C mutations. Overall, our study reveals the molecular mechanism of bozitinib against c-Met, highlights its ability to overcome acquired resistance mutations, and provides valuable insights into further design and improvement of selective c-Met inhibitors.</p>","PeriodicalId":10552,"journal":{"name":"Communications Biology","volume":"8 1","pages":"134"},"PeriodicalIF":5.2,"publicationDate":"2025-01-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11775172/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143058337","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Mario Scazzari, Ying Zhang, Anna Moddemann, Sabine Rospert
{"title":"Stalled disomes marked by Hel2-dependent ubiquitin chains undergo Ubp2/Ubp3-mediated deubiquitination upon translational run-off.","authors":"Mario Scazzari, Ying Zhang, Anna Moddemann, Sabine Rospert","doi":"10.1038/s42003-025-07569-z","DOIUrl":"10.1038/s42003-025-07569-z","url":null,"abstract":"<p><p>Stalled ribosomes cause collisions, impair protein synthesis, and generate potentially harmful truncated polypeptides. Eukaryotic cells utilize the ribosome-associated quality control (RQC) and no-go mRNA decay (NGD) pathways to resolve these problems. In yeast, the E3 ubiquitin ligase Hel2 recognizes and polyubiquitinates disomes and trisomes at the 40S ribosomal protein Rps20/uS10, thereby priming ribosomes for further steps in the RQC/NGD pathways. Recent studies have revealed high concentrations of disomes and trisomes in unstressed cells, raising the question of whether and how Hel2 selects long-term stalled disomes and trisomes. This study presents quantitative analysis of in vivo-formed Hel2•ribosome complexes and the dynamics of Hel2-dependent Rps20 ubiquitination and Ubp2/Ubp3-dependent deubiquitination. Our findings show that Hel2 occupancy progressively increases from translating monosomes to disomes and trisomes. We demonstrate that disomes and trisomes with mono- or di-ubiquitinated Rps20 resolve independently of the RQC component Slh1, while those with tri- and tetra-ubiquitinated Rps20 do not. Based on the results, we propose a model in which Hel2 translates the duration of ribosome stalling into polyubiquitin chain length. This mechanism allows for the distinction between transient and long-term stalling, providing the RQC machinery with a means to select fatally stalled ribosomes over transiently stalled ones.</p>","PeriodicalId":10552,"journal":{"name":"Communications Biology","volume":"8 1","pages":"132"},"PeriodicalIF":5.2,"publicationDate":"2025-01-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11775340/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143058353","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Chenghao Liu, Shuncheng Jia, Hongxing Liu, Xuanle Zhao, Chengyu T Li, Bo Xu, Tielin Zhang
{"title":"Recurrent neural networks with transient trajectory explain working memory encoding mechanisms.","authors":"Chenghao Liu, Shuncheng Jia, Hongxing Liu, Xuanle Zhao, Chengyu T Li, Bo Xu, Tielin Zhang","doi":"10.1038/s42003-024-07282-3","DOIUrl":"10.1038/s42003-024-07282-3","url":null,"abstract":"<p><p>Whether working memory (WM) is encoded by persistent activity using attractors or by dynamic activity using transient trajectories has been debated for decades in both experimental and modeling studies, and a consensus has not been reached. Even though many recurrent neural networks (RNNs) have been proposed to simulate WM, most networks are designed to match respective experimental observations and show either transient or persistent activities. Those few which consider networks with both activity patterns have not attempted to directly compare their memory capabilities. In this study, we build transient-trajectory-based RNNs (TRNNs) and compare them to vanilla RNNs with more persistent activities. The TRNN incorporates biologically plausible modifications, including self-inhibition, sparse connection and hierarchical topology. Besides activity patterns resembling animal recordings and retained versatility to variable encoding time, TRNNs show better performance in delayed choice and spatial memory reinforcement learning tasks. Therefore, this study provides evidence supporting the transient activity theory to explain the WM mechanism from the model designing point of view.</p>","PeriodicalId":10552,"journal":{"name":"Communications Biology","volume":"8 1","pages":"137"},"PeriodicalIF":5.2,"publicationDate":"2025-01-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11775331/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143058351","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"A multilayered regulatory network mediated by protein phosphatase 4 controls carbon catabolite repression and de-repression in Magnaporthe oryzae.","authors":"Zhicheng Huang, Qing Wang, Yan Li, Pengyun Huang, Jian Liao, Jing Wang, Hui Li, Yingying Cai, Jiaoyu Wang, Xiaohong Liu, Fu-Cheng Lin, Jianping Lu","doi":"10.1038/s42003-025-07581-3","DOIUrl":"10.1038/s42003-025-07581-3","url":null,"abstract":"<p><p>Carbon catabolite repression (CCR) and de-repression (CCDR) are critical for fungal development and pathogenicity, yet the underlying regulatory mechanisms remain poorly understood in pathogenic fungi. Here, we identify a serine/threonine protein phosphatase catalytic subunit, Pp4c, as essential for growth, conidiation, virulence, and the utilization of carbohydrates and lipids in Magnaporthe oryzae. We demonstrate that the protein phosphatase 4 complex (Pp4c and Smek1 subunits), the AMP-activated protein kinase (AMPK) Snf1, and the transcriptional regulators CreA (repressor) and Crf1 (activator) collaboratively regulate the utilization of non-preferred carbon sources. Protein interaction and phosphorylation analyses reveal that under glucose-rich conditions, Snf1 and Smek1 directly regulate the phosphorylation status of CreA and Crf1. In contrast, under L-arabinose-rich conditions, Snf1 indirectly modulates the dephosphorylation of these transcription factors via Pp4c and Smek1. Phosphorylation-mediated activation or inactivation of CreA and Crf1 drives CCR and CCDR, thereby governing the metabolism of carbon sources derived from plant cell walls and contributing to fungal pathogenicity. These findings provide deep insights into the regulation of CCR and CCDR, emphasizing their significance in carbon metabolism and pathogenicity in phytopathogenic fungi.</p>","PeriodicalId":10552,"journal":{"name":"Communications Biology","volume":"8 1","pages":"130"},"PeriodicalIF":5.2,"publicationDate":"2025-01-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11775291/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143058333","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Manon Coulée, Alberto de la Iglesia, Mélina Blanco, Clara Gobé, Clémentine Lapoujade, Côme Ialy-Radio, Lucia Alvarez-Gonzalez, Guillaume Meurice, Aurora Ruiz-Herrera, Pierre Fouchet, Julie Cocquet, Laïla El Khattabi
{"title":"Chromatin environment-dependent effects of DOT1L on gene expression in male germ cells.","authors":"Manon Coulée, Alberto de la Iglesia, Mélina Blanco, Clara Gobé, Clémentine Lapoujade, Côme Ialy-Radio, Lucia Alvarez-Gonzalez, Guillaume Meurice, Aurora Ruiz-Herrera, Pierre Fouchet, Julie Cocquet, Laïla El Khattabi","doi":"10.1038/s42003-024-07393-x","DOIUrl":"10.1038/s42003-024-07393-x","url":null,"abstract":"<p><p>The H3K79 methyltransferase DOT1L is essential for multiple aspects of mammalian development where it has been shown to regulate gene expression. Here, by producing and integrating epigenomic and spike-in RNA-seq data, we decipher the molecular role of DOT1L during mouse spermatogenesis and show that it has opposite effects on gene expression depending on chromatin environment. On one hand, DOT1L represses autosomal genes that are devoid of H3K79me2 at their bodies and located in H3K27me3-rich/H3K27ac-poor environments. On the other hand, it activates the expression of genes enriched in H3K79me2 and located in H3K27me3-poor/H3K27ac-rich environments, predominantly X chromosome-linked genes, after meiosis I. This coincides with a significant increase in DOT1L expression at this stage and a genome-wide acquisition of H3K79me2, particularly on the sex chromosomes. Taken together, our results show that H3K79me2 positively correlates with male germ cell genetic program throughout spermatogenesis, with DOT1L predominantly inhibiting rather than activating gene expression. Interestingly, while DOT1L appears to directly regulate the (re)activation of X genes following meiotic sex chromosome inactivation, it also controls the timely expression of (autosomal) differentiation genes during spermatogenesis.</p>","PeriodicalId":10552,"journal":{"name":"Communications Biology","volume":"8 1","pages":"138"},"PeriodicalIF":5.2,"publicationDate":"2025-01-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11775102/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143058340","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Célia Rabhi, Nicolas Babault, Céline Martin, Bénédicte Desforges, Alexandre Maucuer, Vandana Joshi, Serhii Pankivskyi, Yitian Feng, Guillaume Bollot, Revital Rattenbach, David Pastré, Ahmed Bouhss
{"title":"TDP-43 nuclear retention is antagonized by hypo-phosphorylation of its C-terminus in the cytoplasm.","authors":"Célia Rabhi, Nicolas Babault, Céline Martin, Bénédicte Desforges, Alexandre Maucuer, Vandana Joshi, Serhii Pankivskyi, Yitian Feng, Guillaume Bollot, Revital Rattenbach, David Pastré, Ahmed Bouhss","doi":"10.1038/s42003-025-07456-7","DOIUrl":"10.1038/s42003-025-07456-7","url":null,"abstract":"<p><p>Protein aggregation is a hallmark of many neurodegenerative disorders, including amyotrophic lateral sclerosis (ALS), in which TDP-43, a nuclear RNA-binding protein, forms cytoplasmic inclusions. Here, we have developed a robust and automated method to assess protein self-assembly in the cytoplasm using microtubules as nanoplatforms. Importantly, we have analyzed specifically the self-assembly of full-length TDP-43 and its mRNA binding that are regulated by the phosphorylation of its self-adhesive C-terminus, which is the recipient of many pathological mutations. We show that C-terminus phosphorylation prevents the recruitment of TDP-43 in mRNA-rich stress granules only under acute stress conditions because of a low affinity for mRNA but not under mild stress conditions. In addition, the self-assembly of the C-terminus is negatively regulated by phosphorylation in the cytoplasm which in turn promotes TDP-43 nuclear import. We anticipate that reducing TDP-43 C-terminus self-assembly in the cytoplasm may be an interesting strategy to reverse TDP-43 nuclear depletion in neurodegenerative diseases.</p>","PeriodicalId":10552,"journal":{"name":"Communications Biology","volume":"8 1","pages":"136"},"PeriodicalIF":5.2,"publicationDate":"2025-01-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11775348/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143058367","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Bo Hu, Yuping Deng, Tao Lu, Miaomiao Ren, Kuitun Liu, Cong Rao, Hailiang Guo, Jianya Su
{"title":"Inhibition of transcriptional regulation of detoxification genes contributes to insecticide resistance management in Spodoptera exigua.","authors":"Bo Hu, Yuping Deng, Tao Lu, Miaomiao Ren, Kuitun Liu, Cong Rao, Hailiang Guo, Jianya Su","doi":"10.1038/s42003-025-07560-8","DOIUrl":"10.1038/s42003-025-07560-8","url":null,"abstract":"<p><p>Synthetic insecticides have been widely used for the prevention and control of disease vectors and agricultural pests. However, frequent uses of insecticides have resulted in the development of insecticide resistance in these insect pests. The resistance adversely affects the efficacy of insecticides, and seriously reduces the lifespan of insecticides. Therefore, resistance management requires new strategies to suppress insecticide resistance. Here, we confirm that CncC/Maf are the key regulators of various detoxification genes involved in insecticide resistance in Spodoptera exigua. Then, we develop a cell screening platform to identify the natural compound inhibitors of CncC/Maf and determine that sofalcone can act as a CncC/Maf inhibitor in vitro and in vivo. Bioassay results showed that sofalcone significantly enhanced the toxicity (more than 3-fold) of chlorpyrifos and lambda-cyhalothrin against S. exigua larvae. Finally, we demonstrate that sofalcone can greatly improve the susceptibility of S. exigua larvae to insecticides by inhibiting the activity of the ROS/CncC-dependent detoxifying enzymes and downregulating the expression levels of detoxification genes. CncC/Maf inhibitors can be used as broad-spectrum synergists to overcome insecticide resistance in pest populations. Altogether, our results demonstrate that reduced expression of detoxification genes resulting from suppression of transcriptional regulation of these genes contributes to controlling insecticide resistance, which provides a very novel and high-efficiency green resistance management strategy.</p>","PeriodicalId":10552,"journal":{"name":"Communications Biology","volume":"8 1","pages":"128"},"PeriodicalIF":5.2,"publicationDate":"2025-01-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11772755/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143058342","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"How the tulip breaking virus creates striped tulips.","authors":"Aidan A Wong, Gustavo Carrero, Thomas Hillen","doi":"10.1038/s42003-025-07507-z","DOIUrl":"10.1038/s42003-025-07507-z","url":null,"abstract":"<p><p>The beauty of tulips has enchanted mankind for centuries. The striped variety has attracted particular attention for its intricate and unpredictable patterns. A good understanding of the mechanism driving the striped pattern formation of broken tulips has been missing since the 17th century. It has been known since 1928 that these patterned tulips suffer from a viral infection by the tulip breaking virus. Here, we present a mathematical model to understand how a virus infection of the petals can lead to stripes, thereby providing a possible explanation of a 350 year-old mystery. The model, which describes the viral inhibition of pigment expression (anthocyanins) and their interaction with viral reproduction, incorporates a pattern formation mechanism identified as an activator-substrate mechanism, similar to the well-known Turing instability, working together with Wolpert's positional information mechanism. The model is solved on a growing tulip petal-shaped domain, whereby we introduce a new method to describe the tulip petal growth explicitly. This work shows how a viral infection that inhibits pigment production can lead to beautiful tulip patterns.</p>","PeriodicalId":10552,"journal":{"name":"Communications Biology","volume":"8 1","pages":"129"},"PeriodicalIF":5.2,"publicationDate":"2025-01-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11772565/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143051645","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Ashwin G Ramayya, Vivek Buch, Andrew Richardson, Timothy Lucas, Joshua I Gold
{"title":"Human response times are governed by dual anticipatory processes with distinct neural signatures.","authors":"Ashwin G Ramayya, Vivek Buch, Andrew Richardson, Timothy Lucas, Joshua I Gold","doi":"10.1038/s42003-025-07516-y","DOIUrl":"10.1038/s42003-025-07516-y","url":null,"abstract":"<p><p>Human behavior is strongly influenced by anticipation, but the underlying neural mechanisms are poorly understood. We obtained intracranial electrocephalography (iEEG) measurements in neurosurgical patients as they performed a simple sensory-motor task with variable (short or long) foreperiod delays that affected anticipation of the cue to respond. Participants showed two forms of anticipatory response biases, distinguished by more premature false alarms (FAs) or faster response times (RTs) on long-delay trials. These biases had distinct neural signatures in prestimulus neural activity modulations that were distributed and intermixed across the brain: the FA bias was most evident in preparatory motor activity immediately prior to response-cue presentation, whereas the RT bias was most evident in visuospatial activity at the beginning of the foreperiod. These results suggest that human anticipatory behavior emerges from a combination of motor-preparatory and attention-like modulations of neural activity, implemented by anatomically widespread and intermixed, but functionally identifiable, brain networks.</p>","PeriodicalId":10552,"journal":{"name":"Communications Biology","volume":"8 1","pages":"124"},"PeriodicalIF":5.2,"publicationDate":"2025-01-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11762298/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143037373","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}