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JOURNAL ARTICLE
Anthony R P Verkerke, Dandan Wang, Naofumi Yoshida, Zachary H Taxin, Xu Shi, Shuning Zheng, Yuka Li, Christopher Auger, Satoshi Oikawa, Jin-Seon Yook, Melia Granath-Panelo, Wentao He, Guo-Fang Zhang, Mami Matsushita, Masayuki Saito, Robert E Gerszten, Evanna L Mills, Alexander S Banks, Yasushi Ishihama, Phillip J White, Robert W McGarrah, Takeshi Yoneshiro, Shingo Kajimura
Brown adipose tissue (BAT) is best known for thermogenesis. Rodent studies demonstrated that enhanced BAT thermogenesis is tightly associated with increased energy expenditure, reduced body weight, and improved glucose homeostasis. However, human BAT is protective against type 2 diabetes, independent of body weight. The mechanism underlying this dissociation remains unclear. Here, we report that impaired mitochondrial catabolism of branched-chain amino acids (BCAAs) in BAT, by deleting mitochondrial BCAA carriers (MBCs), caused systemic insulin resistance without affecting energy expenditure and body weight...
April 17, 2024: Cell
#2
JOURNAL ARTICLE
Qixing Nie, Xi Luo, Kai Wang, Yong Ding, Shumi Jia, Qixiang Zhao, Meng Li, Jinxin Zhang, Yingying Zhuo, Jun Lin, Chenghao Guo, Zhiwei Zhang, Huiying Liu, Guangyi Zeng, Jie You, Lulu Sun, Hua Lu, Ming Ma, Yanxing Jia, Ming-Hua Zheng, Yanli Pang, Jie Qiao, Changtao Jiang
The gut microbiota has been found to play an important role in the progression of metabolic dysfunction-associated steatohepatitis (MASH), but the mechanisms have not been established. Here, by developing a click-chemistry-based enrichment strategy, we identified several microbial-derived bile acids, including the previously uncharacterized 3-succinylated cholic acid (3-sucCA), which is negatively correlated with liver damage in patients with liver-tissue-biopsy-proven metabolic dysfunction-associated fatty liver disease (MAFLD)...
April 17, 2024: Cell
#3
JOURNAL ARTICLE
Zhi Zong, Feng Xie, Shuai Wang, Xiaojin Wu, Zhenyu Zhang, Bing Yang, Fangfang Zhou
Lysine lactylation is a post-translational modification that links cellular metabolism to protein function. Here, we find that AARS1 functions as a lactate sensor that mediates global lysine lacylation in tumor cells. AARS1 binds to lactate and catalyzes the formation of lactate-AMP, followed by transfer of lactate to the lysince acceptor residue. Proteomics studies reveal a large number of AARS1 targets, including p53 where lysine 120 and lysine 139 in the DNA binding domain are lactylated. Generation and utilization of p53 variants carrying constitutively lactylated lysine residues revealed that AARS1 lactylation of p53 hinders its liquid-liquid phase separation, DNA binding, and transcriptional activation...
April 17, 2024: Cell
#4
JOURNAL ARTICLE
Mariko Takahashi, Harrison B Chong, Siwen Zhang, Tzu-Yi Yang, Matthew J Lazarov, Stefan Harry, Michelle Maynard, Brendan Hilbert, Ryan D White, Heather E Murrey, Chih-Chiang Tsou, Kira Vordermark, Jonathan Assaad, Magdy Gohar, Benedikt R Dürr, Marianne Richter, Himani Patel, Gregory Kryukov, Natasja Brooijmans, Aliyu Sidi Omar Alghali, Karla Rubio, Antonio Villanueva, Junbing Zhang, Maolin Ge, Farah Makram, Hanna Griesshaber, Drew Harrison, Ann-Sophie Koglin, Samuel Ojeda, Barbara Karakyriakou, Alexander Healy, George Popoola, Inbal Rachmin, Neha Khandelwal, Jason R Neil, Pei-Chieh Tien, Nicholas Chen, Tobias Hosp, Sanne van den Ouweland, Toshiro Hara, Lillian Bussema, Rui Dong, Lei Shi, Martin Q Rasmussen, Ana Carolina Domingues, Aleigha Lawless, Jacy Fang, Satoshi Yoda, Linh Phuong Nguyen, Sarah Marie Reeves, Farrah Nicole Wakefield, Adam Acker, Sarah Elizabeth Clark, Taronish Dubash, John Kastanos, Eugene Oh, David E Fisher, Shyamala Maheswaran, Daniel A Haber, Genevieve M Boland, Moshe Sade-Feldman, Russell W Jenkins, Aaron N Hata, Nabeel M Bardeesy, Mario L Suvà, Brent R Martin, Brian B Liau, Christopher J Ott, Miguel N Rivera, Michael S Lawrence, Liron Bar-Peled
Cysteine-focused chemical proteomic platforms have accelerated the clinical development of covalent inhibitors for a wide range of targets in cancer. However, how different oncogenic contexts influence cysteine targeting remains unknown. To address this question, we have developed "DrugMap," an atlas of cysteine ligandability compiled across 416 cancer cell lines. We unexpectedly find that cysteine ligandability varies across cancer cell lines, and we attribute this to differences in cellular redox states, protein conformational changes, and genetic mutations...
April 17, 2024: Cell
#5
JOURNAL ARTICLE
Alissa C Greenwald, Noam Galili Darnell, Rouven Hoefflin, Dor Simkin, Christopher W Mount, L Nicolas Gonzalez Castro, Yotam Harnik, Sydney Dumont, Dana Hirsch, Masashi Nomura, Tom Talpir, Merav Kedmi, Inna Goliand, Gioele Medici, Julie Laffy, Baoguo Li, Vamsi Mangena, Hadas Keren-Shaul, Michael Weller, Yoseph Addadi, Marian C Neidert, Mario L Suvà, Itay Tirosh
Glioma contains malignant cells in diverse states. Here, we combine spatial transcriptomics, spatial proteomics, and computational approaches to define glioma cellular states and uncover their organization. We find three prominent modes of organization. First, gliomas are composed of small local environments, each typically enriched with one major cellular state. Second, specific pairs of states preferentially reside in proximity across multiple scales. This pairing of states is consistent across tumors. Third, these pairwise interactions collectively define a global architecture composed of five layers...
April 16, 2024: Cell
#6
Manyu Du, Simon Hendrik Stitzinger, Jan-Hendrik Spille, Won-Ki Cho, Choongman Lee, Mohammed Hijaz, Andrea Quintana, Ibrahim I Cissé
No abstract text is available yet for this article.
April 12, 2024: Cell
#7
JOURNAL ARTICLE
Jordan A Hartmann, Marcella R Cardoso, Maria Cecilia Ramiro Talarico, Devin J Kenney, Madison R Leone, Dagny C Reese, Jacquelyn Turcinovic, Aoife K O'Connell, Hans P Gertje, Caitlin Marino, Pedro E Ojeda, Erich V De Paula, Fernanda A Orsi, Licio Augusto Velloso, Thomas R Cafiero, John H Connor, Alexander Ploss, Angelique Hoelzemer, Mary Carrington, Amy K Barczak, Nicholas A Crossland, Florian Douam, Julie Boucau, Wilfredo F Garcia-Beltran
SARS-CoV-2 and other sarbecoviruses continue to threaten humanity, highlighting the need to characterize common mechanisms of viral immune evasion for pandemic preparedness. Cytotoxic lymphocytes are vital for antiviral immunity and express NKG2D, an activating receptor conserved among mammals that recognizes infection-induced stress ligands (e.g., MIC-A/B). We found that SARS-CoV-2 evades NKG2D recognition by surface downregulation of MIC-A/B via shedding, observed in human lung tissue and COVID-19 patient serum...
April 11, 2024: Cell
#8
JOURNAL ARTICLE
Jinnan He, Xiangru Huo, Gaofeng Pei, Zeran Jia, Yiming Yan, Jiawei Yu, Haozhi Qu, Yunxin Xie, Junsong Yuan, Yuan Zheng, Yanyan Hu, Minglei Shi, Kaiqiang You, Tingting Li, Tianhua Ma, Michael Q Zhang, Sheng Ding, Pilong Li, Yinqing Li
Precise control of gene expression levels is essential for normal cell functions, yet how they are defined and tightly maintained, particularly at intermediate levels, remains elusive. Here, using a series of newly developed sequencing, imaging, and functional assays, we uncover a class of transcription factors with dual roles as activators and repressors, referred to as condensate-forming level-regulating dual-action transcription factors (TFs). They reduce high expression but increase low expression to achieve stable intermediate levels...
April 10, 2024: Cell
#9
JOURNAL ARTICLE
Gabriela Prus, Shankha Satpathy, Brian T Weinert, Takeo Narita, Chunaram Choudhary
Ubiquitylation regulates most proteins and biological processes in a eukaryotic cell. However, the site-specific occupancy (stoichiometry) and turnover rate of ubiquitylation have not been quantified. Here we present an integrated picture of the global ubiquitylation site occupancy and half-life. Ubiquitylation site occupancy spans over four orders of magnitude, but the median ubiquitylation site occupancy is three orders of magnitude lower than that of phosphorylation. The occupancy, turnover rate, and regulation of sites by proteasome inhibitors are strongly interrelated, and these attributes distinguish sites involved in proteasomal degradation and cellular signaling...
April 8, 2024: Cell
#10
JOURNAL ARTICLE
Li Ren Kong, Komal Gupta, Andy Jialun Wu, David Perera, Roland Ivanyi-Nagy, Syed Moiz Ahmed, Tuan Zea Tan, Shawn Lu-Wen Tan, Alessandra Fuddin, Elayanambi Sundaramoorthy, Grace Shiqing Goh, Regina Tong Xin Wong, Ana S H Costa, Callum Oddy, Hannan Wong, C Pawan K Patro, Yun Suen Kho, Xiao Zi Huang, Joan Choo, Mona Shehata, Soo Chin Lee, Boon Cher Goh, Christian Frezza, Jason J Pitt, Ashok R Venkitaraman
Knudson's "two-hit" paradigm posits that carcinogenesis requires inactivation of both copies of an autosomal tumor suppressor gene. Here, we report that the glycolytic metabolite methylglyoxal (MGO) transiently bypasses Knudson's paradigm by inactivating the breast cancer suppressor protein BRCA2 to elicit a cancer-associated, mutational single-base substitution (SBS) signature in nonmalignant mammary cells or patient-derived organoids. Germline monoallelic BRCA2 mutations predispose to these changes. An analogous SBS signature, again without biallelic BRCA2 inactivation, accompanies MGO accumulation and DNA damage in Kras-driven, Brca2-mutant murine pancreatic cancers and human breast cancers...
April 8, 2024: Cell
#11
JOURNAL ARTICLE
(no author information available yet)
For Cell's 50th anniversary Focus on Immunology, scientific editor Cheri Sirois asked science communicator Liz Neeley, founding partner of Liminal and cofounder of Solving for Science, to discuss strategies for tackling technical complexity and for engaging effectively with broad audiences. A lightly edited transcript of their conversation is shared here.
April 6, 2024: Cell
#12
JOURNAL ARTICLE
Xian Xia, Po-Yu Sung, Michael W Martynowycz, Tamir Gonen, Polly Roy, Z Hong Zhou
Unlike those of double-stranded DNA (dsDNA), single-stranded DNA (ssDNA), and ssRNA viruses, the mechanism of genome packaging of dsRNA viruses is poorly understood. Here, we combined the techniques of high-resolution cryoelectron microscopy (cryo-EM), cellular cryoelectron tomography (cryo-ET), and structure-guided mutagenesis to investigate genome packaging and capsid assembly of bluetongue virus (BTV), a member of the Reoviridae family of dsRNA viruses. A total of eleven assembly states of BTV capsid were captured, with resolutions up to 2...
April 5, 2024: Cell
#13
JOURNAL ARTICLE
Shouyan Deng, Yibo Zhang, Huanbin Wang, Wenhua Liang, Lu Xie, Ning Li, Yuan Fang, Yiting Wang, Jiayang Liu, Hao Chi, Yufan Sun, Rui Ye, Lishen Shan, Jiawei Shi, Zan Shen, Yonggang Wang, Shuhang Wang, Jean-Philippe Brosseau, Feng Wang, Grace Liu, Yingfei Quan, Jie Xu
Cancer immunotherapy has transformed treatment possibilities, but its effectiveness differs significantly among patients, indicating the presence of alternative pathways for immune evasion. Here, we show that ITPRIPL1 functions as an inhibitory ligand of CD3ε, and its expression inhibits T cells in the tumor microenvironment. The binding of ITPRIPL1 extracellular domain to CD3ε on T cells significantly decreased calcium influx and ZAP70 phosphorylation, impeding initial T cell activation...
April 5, 2024: Cell
#14
JOURNAL ARTICLE
Xiaoyi Li, Wei Chen, Beth K Martin, Diego Calderon, Choli Lee, Junhong Choi, Florence M Chardon, Troy A McDiarmid, Riza M Daza, Haedong Kim, Jean-Benoît Lalanne, Jenny F Nathans, David S Lee, Jay Shendure
We set out to exhaustively characterize the impact of the cis-chromatin environment on prime editing, a precise genome engineering tool. Using a highly sensitive method for mapping the genomic locations of randomly integrated reporters, we discover massive position effects, exemplified by editing efficiencies ranging from ∼0% to 94% for an identical target site and edit. Position effects on prime editing efficiency are well predicted by chromatin marks, e.g., positively by H3K79me2 and negatively by H3K9me3...
April 5, 2024: Cell
#15
JOURNAL ARTICLE
Marine H Laporte, Davide Gambarotto, Éloïse Bertiaux, Lorène Bournonville, Vincent Louvel, José M Nunes, Susanne Borgers, Virginie Hamel, Paul Guichard
Centriole biogenesis, as in most organelle assemblies, involves the sequential recruitment of sub-structural elements that will support its function. To uncover this process, we correlated the spatial location of 24 centriolar proteins with structural features using expansion microscopy. A time-series reconstruction of protein distributions throughout human procentriole assembly unveiled the molecular architecture of the centriole biogenesis steps. We found that the process initiates with the formation of a naked cartwheel devoid of microtubules...
April 5, 2024: Cell
#16
JOURNAL ARTICLE
Thomas W Battaglia, Iris L Mimpen, Joleen J H Traets, Arne van Hoeck, Laurien J Zeverijn, Birgit S Geurts, Gijs F de Wit, Michaël Noë, Ingrid Hofland, Joris L Vos, Sten Cornelissen, Maartje Alkemade, Annegien Broeks, Charlotte L Zuur, Edwin Cuppen, Lodewyk Wessels, Joris van de Haar, Emile Voest
Microbial communities are resident to multiple niches of the human body and are important modulators of the host immune system and responses to anticancer therapies. Recent studies have shown that complex microbial communities are present within primary tumors. To investigate the presence and relevance of the microbiome in metastases, we integrated mapping and assembly-based metagenomics, genomics, transcriptomics, and clinical data of 4,160 metastatic tumor biopsies. We identified organ-specific tropisms of microbes, enrichments of anaerobic bacteria in hypoxic tumors, associations between microbial diversity and tumor-infiltrating neutrophils, and the association of Fusobacterium with resistance to immune checkpoint blockade (ICB) in lung cancer...
April 5, 2024: Cell
#17
JOURNAL ARTICLE
Liron David, Jazlyn P Borges, L Robert Hollingsworth, Allen Volchuk, Isabelle Jansen, Evelyn Garlick, Benjamin E Steinberg, Hao Wu
The membrane protein NINJ1 mediates plasma membrane rupture in pyroptosis and other lytic cell death pathways. Here, we report the cryo-EM structure of a NINJ1 oligomer segmented from NINJ1 rings. Each NINJ1 subunit comprises amphipathic (⍺1, ⍺2) and transmembrane (TM) helices (⍺3, ⍺4) and forms a chain of subunits, mainly by the TM helices and ⍺1. ⍺3 and ⍺4 are kinked, and the Gly residues are important for function. The NINJ1 oligomer possesses a concave hydrophobic side that should face the membrane and a convex hydrophilic side formed by ⍺1 and ⍺2, presumably upon activation...
April 2, 2024: Cell
#18
JOURNAL ARTICLE
Paolo Cadinu, Kisha N Sivanathan, Aditya Misra, Rosalind J Xu, Davide Mangani, Evan Yang, Joseph M Rone, Katherine Tooley, Yoon-Chul Kye, Lloyd Bod, Ludwig Geistlinger, Tyrone Lee, Randall T Mertens, Noriaki Ono, Gang Wang, Liliana Sanmarco, Francisco J Quintana, Ana C Anderson, Vijay K Kuchroo, Jeffrey R Moffitt, Roni Nowarski
Gut inflammation involves contributions from immune and non-immune cells, whose interactions are shaped by the spatial organization of the healthy gut and its remodeling during inflammation. The crosstalk between fibroblasts and immune cells is an important axis in this process, but our understanding has been challenged by incomplete cell-type definition and biogeography. To address this challenge, we used multiplexed error-robust fluorescence in situ hybridization (MERFISH) to profile the expression of 940 genes in 1...
April 1, 2024: Cell
#19
JOURNAL ARTICLE
Ya Cui, Wenbin Ye, Jason Sheng Li, Jingyi Jessica Li, Eric Vilain, Tamer Sallam, Wei Li
The Genome Aggregation Database (gnomAD), widely recognized as the gold-standard reference map of human genetic variation, has largely overlooked tandem repeat (TR) expansions, despite the fact that TRs constitute ∼6% of our genome and are linked to over 50 human diseases. Here, we introduce the TR-gnomAD (https://wlcb.oit.uci.edu/TRgnomAD), a biobank-scale reference of 0.86 million TRs derived from 338,963 whole-genome sequencing (WGS) samples of diverse ancestries (39.5% non-European samples). TR-gnomAD offers critical insights into ancestry-specific disease prevalence using disparities in TR unit number frequencies among ancestries...
March 28, 2024: Cell
#20
JOURNAL ARTICLE
Celeste Parra Bravo, Alice Maria Giani, Jesus Madero Perez, Zeping Zhao, Yuansong Wan, Avi J Samelson, Man Ying Wong, Alessandro Evangelisti, Ethan Cordes, Li Fan, Pearly Ye, Daphne Zhu, Tatyana Pozner, Maria Mercedes, Tark Patel, Allan Yarahmady, Gillian K Carling, Fredrik H Sterky, Virginia M Y Lee, Edward B Lee, Michael DeTure, Dennis W Dickson, Manu Sharma, Sue-Ann Mok, Wenjie Luo, Mingrui Zhao, Martin Kampmann, Shiaoching Gong, Li Gan
Tauopathies are age-associated neurodegenerative diseases whose mechanistic underpinnings remain elusive, partially due to a lack of appropriate human models. Here, we engineered human induced pluripotent stem cell (hiPSC)-derived neuronal lines to express 4R Tau and 4R Tau carrying the P301S MAPT mutation when differentiated into neurons. 4R-P301S neurons display progressive Tau inclusions upon seeding with Tau fibrils and recapitulate features of tauopathy phenotypes including shared transcriptomic signatures, autophagic body accumulation, and reduced neuronal activity...
March 28, 2024: Cell
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