Article
Multidisciplinary Sciences
A. V. Shumilov, P. M. Gotovtsev
Summary: This study demonstrates the application of system biology principles in the dopamine signaling pathway in neurons, presenting a model based on cytomorphic electronic circuits and mathematical modeling. The model accurately captures signal oscillations in biological systems, simplifying calculations and showing pathway dynamics effectively. The proposed changes in calcium channel functioning and the mathematical model of system component interactions align well with existing literature, supporting the validity of the findings.
Article
Agronomy
Fangyu Chen, Yongsheng Wang, Zesen Zhang, Xiaolong Chen, Jinpeng Huang, Zhiming Chen, Jingsheng Zheng, Liangrong Jiang, Yumin Huang, Houcong Wang, Rongyu Huang
Summary: In this study, the role of the LGS1 gene in regulating grain size in rice was investigated using transcriptomic, proteomic, and phosphoproteomic analyses. The study revealed that the regulation of multiple functional clusters and dynamic phosphorylation events are key features of rice grain length development. Additionally, transcriptomic analysis identified alternative splicing events and dynamic gene regulatory networks that contribute to rice grain development.
Article
Chemistry, Analytical
Yanrong Wen, Ge Ge, Dan Xie, Zhen Liu
Summary: A comprehensive analytical platform is lacking for tracking and quantifying cell migration behaviors and molecular dynamics at the single-cell level. In this study, an integrated single living cell analysis platform was developed to address this limitation. It enables long-term observation of migration behavioral phenotypes in single cells and simultaneous analysis of signaling proteins and complexes, providing insights into the molecular mechanism and phenotypes in cell migration.
ANALYTICAL CHEMISTRY
(2023)
Article
Chemistry, Multidisciplinary
Yuki Komoto, Takahito Ohshiro, Masateru Taniguchi
Summary: Single-molecule quantum measurements were utilized to electrically detect cAMP and discriminate its signal from those of ATP, AMP, and ADP with high accuracy using a developed machine learning method. The discrimination was attributed to the structural difference between the ribose of the phosphate site of cAMP and those of ATP, ADP, and AMP.
Article
Oncology
Lauren E. Stopfer, Cameron T. Flower, Aaron S. Gajadhar, Bhavin Patel, Sebastien Gallien, Daniel Lopez-Ferrer, Forest M. White
Summary: SureQuant pTyr is a mass spectrometry-based targeted method that enables sensitive and selective quantitation of several hundred low-abundance tyrosine phosphorylated peptides commonly dysregulated in cancer, improving the robustness and usability of targeted mass spectrometry assays, with potential clinical applications.
Review
Cell Biology
Yifan Wu, Pauline Aegerter, Michael Nipper, Logan Ramjit, Jun Liu, Pei Wang
Summary: The Hippo signaling pathway is crucial for pancreatic development and homeostasis, regulating progenitor cell renewal, proliferation, and differentiation while affecting cell fate decisions. Dysregulation of this pathway can lead to dedifferentiation of pancreatic cells and pancreatitis-like phenotypes.
FRONTIERS IN CELL AND DEVELOPMENTAL BIOLOGY
(2021)
Review
Cell Biology
Harold M. McNamara, Beatrice Ramm, Jared E. Toettcher
Summary: Technological advances have contributed to recent developments in developmental biology, such as light sheet imaging for studying single-cell dynamics and single-cell genomic methods for cataloguing cell types and gene expression states. Synthetic approaches are also emerging to understand development processes from the bottom up, including synthetic circuits for signaling delivery and recording, and synthetic reconstitution of pattern formation on multicellular scales.
SEMINARS IN CELL & DEVELOPMENTAL BIOLOGY
(2023)
Review
Biochemical Research Methods
Peter D. Karp, Peter E. Midford, Richard Billington, Anamika Kothari, Markus Krummenacker, Mario Latendresse, Wai Kit Ong, Pallavi Subhraveti, Ron Caspi, Carol Fulcher, Ingrid M. Keseler, Suzanne M. Paley
Summary: The development of Pathway Tools software enables researchers to construct biological knowledge resources more efficiently, develop metabolic flux models, and interpret high-throughput data using pathway information.
BRIEFINGS IN BIOINFORMATICS
(2021)
Review
Biotechnology & Applied Microbiology
Roberto Di Blasi, Annalise Zouein, Tom Ellis, Francesca Ceroni
Summary: Construction of DNA-encoded programs is crucial in synthetic biology, with Golden Gate toolkits now dominating due to their modular design. Future advances include accessory packs for cloning toolkits to facilitate editing, orthogonality, advanced regulation, and integration into synthetic chromosome construction.
TRENDS IN BIOTECHNOLOGY
(2021)
Article
Oncology
Zhili Xia, Minzhen Li, Meng Hu, Yanyan Lin, Lawrence Lawer Atteh, Wenkang Fu, Long Gao, Mingzhen Bai, Chongfei Huang, Ping Yue, Yu Liu, Wenbo Meng
Summary: This study reveals the mechanism by which CB induces apoptosis of ICC cells through activating the ATM/CHK2/p53 signaling pathway and initiating DNA damage. This finding suggests that CB may serve as a potential chemotherapeutic drug candidate for ICC treatment.
FRONTIERS IN ONCOLOGY
(2022)
Review
Engineering, Biomedical
Payam E. Farahani, Ellen H. Reed, Evan J. Underhill, Kazuhiro Aoki, Jared E. Toettcher
Summary: Cells receive information from their environment and use optogenetic tools to study how they decode signals and produce appropriate responses. Optogenetics helps researchers manipulate protein interactions and activities with precision, leading to a better understanding and engineering of biology.
ANNUAL REVIEW OF BIOMEDICAL ENGINEERING, VOL 23, 2021
(2021)
Article
Cell Biology
Zhipeng Xu, Min Liu, Jin Wang, Kai Liu, Liuyu Xu, Demin Fan, Hui Zhang, Wenxin Hu, Dan Wei, Jianning Wang
Summary: The MYH9 gene is commonly upregulated in clear cell renal cell carcinoma (ccRCC) and its overexpression predicts poor prognosis. Knockdown of MYH9 inhibits the proliferative and metastatic potentials of ccRCC cells, while overexpression enhances these properties. Furthermore, MYH9 plays vital roles through the AKT signaling pathway and determines the response of ccRCC cells to sunitinib treatment.
CELL DEATH DISCOVERY
(2022)
Article
Cell Biology
Susan Olalekan, Bingqing Xie, Rebecca Back, Heather Eckart, Anindita Basu
Summary: Understanding the cellular composition and interactions within the tumor microenvironment is crucial for successful cancer immunotherapies. By performing single-cell RNA sequencing of cells from six ovarian cancer patients, we identified nine major cell types and stratified immune cells into high T cell infiltration and low T cell infiltration groups. The study provides important insights into the immune response in ovarian tumors, highlighting potential anti-tumor responses in the high T cell infiltration group.
Article
Chemistry, Applied
Fang Geng, Xuefei Wen, Yisha Xu, Miao Zhang, Lin Zhou, Dayu Liu, Xiang Li, Jinqiu Wang
Summary: The study revealed significant changes in phosphorylation sites in Dictyophora indusiata during postharvest development, with upregulated phosphoinositide signaling playing a key role in regulating cell wall synthesis. This suggests that targeting the phosphoinositide signaling pathway may be a potential strategy for regulating the postharvest morphological development of D. indusiata.
Article
Biology
Benoit Boulan, Charlotte Ravanello, Amandine Peyrel, Christophe Bosc, Christian Delphin, Florence Appaix, Eric Denarier, Alexandra Kraut, Muriel Jacquier-Sarlin, Alyson Fournier, Annie Andrieux, Sylvie Gory-Faure, Jean-Christophe Deloulme
Summary: Neurodevelopmental axonal pathfinding plays a crucial role in brain wiring and cognitive abilities. Sema3E, through its interaction with MAP6 and CRMP4, is shown to be important in promoting axonal growth and development of the fornix. The study highlights the role of CRMP4 in transducing Sema3E signaling and its importance in understanding psychiatric diseases affecting the fornix.
Article
Allergy
Yasutaka Mitamura, Daniel Schulz, Saskia Oro, Nick Li, Isabel Kolm, Claudia Lang, Reihane Ziadlou, Ge Tan, Bernd Bodenmiller, Peter Steiger, Angelo Marzano, Nicolas de Prost, Olivier Caudin, Mitchell Levesque, Corinne Stoffel, Peter Schmid-Grendelmeier, Emanual Maverakis, Cezmi A. Akdis, Marie-Charlotte Bruggen
Summary: This study found that COVID-MDR in COVID-19 patients exhibited a more prominent and phenotypically shifted cellular infiltrate, along with a more robust cytotoxic response in skin, although SARS-CoV-2 was not detected in skin samples at the time of MDR diagnosis. Serum proteomic profiling of COVID-MDR patients revealed upregulation of various inflammatory mediators, indicating a massive systemic cytokine storm.
Article
Multidisciplinary Sciences
Johanna Wagner, Markus Masek, Andrea Jacobs, Charlotte Soneson, Sujana Sivapatham, Nicolas Damond, Natalie de Souza, Mark D. Robinson, Bernd Bodenmiller
Summary: In this study, the EMT transition phenotypes in four non-cancerous human mammary epithelial cell lines were comprehensively profiled and compared to breast cancer cell lines. The results revealed a spectrum of EMT transition phenotypes in each cell line. These findings contribute to a better understanding of the complexity of EMT and provide valuable insights for the design of EMT time course experiments.
Article
Allergy
Patrick Taeschler, Sarah Adamo, Yun Deng, Carlo Cervia, Yves Zurbuchen, Stephane Chevrier, Miro E. Raeber, Sara Hasler, Esther Bachli, Alain Rudiger, Melina Stussi-Helbling, Lars C. Huber, Bernd Bodenmiller, Onur Boyman, Jakob Nilsson
Summary: This study suggests that most patients recover T-cell numbers and function after COVID-19. However, there is evidence of persistent T-cell activation up to 12 months after infection and a subgroup of severe COVID-19 patients exhibit a dysregulated immune response during acute infection.
Article
Genetics & Heredity
Esther Danenberg, Helen Bardwell, Vito R. T. Zanotelli, Elena Provenzano, Suet-Feung Chin, Oscar M. Rueda, Andrew Green, Emad Rakha, Samuel Aparicio, Ian O. Ellis, Bernd Bodenmiller, Carlos Caldas, H. Raza Ali
Summary: Imaging mass cytometry profiling of 693 breast tumors revealed 10 recurrent tumor microenvironment spatial structures, associated with genomic profiles and outcomes. These multicellular structures within the TME, varying in vascular content, stromal activation, and leukocyte composition, could improve patient stratification and link spatial organization to local TME function.
Article
Immunology
Tobias Hoch, Daniel Schulz, Nils Eling, Julia Martinez Gomez, Mitchell P. Levesque, Bernd Bodenmiller
Summary: Intratumoral immune cells play a crucial role in tumor control and antitumor responses during immunotherapy. This study analyzed the chemokine expression and immune infiltration in melanoma using multiplexed mass cytometry-based imaging, and found that tumors lacking immune infiltration had low levels of chemokines, antigen presentation, and markers of inflammation, while infiltrated tumors expressed multiple chemokines.
SCIENCE IMMUNOLOGY
(2022)
Article
Neurosciences
Mor Kenigsbuch, Pierre Bost, Shahar Halevi, Yuzhou Chang, Shuo Chen, Qin Ma, Renana Hajbi, Benno Schwikowski, Bernd Bodenmiller, Hongjun Fu, Michal Schwartz, Ido Amit
Summary: This study identifies a shared signature of oligodendrocytes in central nervous system pathologies. The researchers discovered a specific oligodendrocyte state, termed disease-associated oligodendrocytes (DOLs), that increased with brain pathology. DOLs were found in various neurodegenerative and inflammatory conditions, indicating a common response to severe pathological conditions.
NATURE NEUROSCIENCE
(2022)
Article
Oncology
Jian Wang, Tobias Weiss, Marian C. Neidert, Nora C. Toussaint, Reza Naghavian, Carla Selles Moreno, Magdalena Foege, Paula Tomas Ojer, Gioele Medici, Ivan Jelcic, Daniel Schulz, Elisabeth Rushing, Susanne Dettwiler, Barbara Schrors, Joo Heon Shin, Ron McKay, Catherine J. Wu, Andreas Lutterotti, Mireia Sospedra, Holger Moch, Erich F. Greiner, Bernd Bodenmiller, Luca Regli, Michael Weller, Patrick Roth, Roland Martin
Summary: The study developed a strategy to design neopeptides with enhanced immunogenicity through single amino acid mutations. Vaccination with these peptides resulted in immune responses from CD8+ T cells and CD4+ T cells upon tumor recurrence.
CLINICAL CANCER RESEARCH
(2022)
Article
Multidisciplinary Sciences
Tyler Funnell, Ciara H. O'Flanagan, Marc J. Williams, Andrew McPherson, Steven McKinney, Farhia Kabeer, Hakwoo Lee, Sohrab Salehi, Ignacio Vazquez-Garcia, Hongyu Shi, Emily Leventhal, Tehmina Masud, Peter Eirew, Damian Yap, Allen W. Zhang, Jamie L. P. Lim, Beixi Wang, Jazmine Brimhall, Justina Biele, Jerome Ting, Vinci Au, Michael Van Vliet, Yi Fei Liu, Sean Beatty, Daniel Lai, Jenifer Pham, Diljot Grewal, Douglas Abrams, Eliyahu Havasov, Samantha Leung, Viktoria Bojilova, Richard A. Moore, Nicole Rusk, Florian Uhlitz, Nicholas Ceglia, Adam C. Weiner, Elena Zaikova, J. Maxwell Douglas, Dmitriy Zamarin, Britta Weigelt, Sarah H. Kim, Arnaud Da Cruz Paula, Jorge S. Reis-Filho, Spencer D. Martin, Yangguang Li, Hong Xu, Teresa Ruiz de Algara, So Ra Lee, Viviana Cerda Llanos, David G. Huntsman, Jessica N. McAlpine, Sohrab P. Shah, Samuel Aparicio
Summary: This study reveals the contribution of cell-to-cell structural variation to the phenotypic and evolutionary diversity in human breast cancer and ovarian cancer, and provides insights into the genomic and mutational states of individual cancer cells.
Article
Biochemical Research Methods
Pierre Bost, Daniel Schulz, Stefanie Engler, Clive Wasserfall, Bernd Bodenmiller
Summary: Recent advances in multiplexed imaging methods have allowed for simultaneous detection of multiple proteins and RNAs, providing a deeper understanding of the spatial characteristics of healthy and diseased tissues. However, optimal design parameters for multiplex imaging studies, particularly in capturing all cell phenotype clusters, are currently lacking. In this study, a statistical framework using a spatial transcriptomic atlas was developed to determine the number and area of fields of view needed to accurately identify all cell phenotypes in a tissue. This strategy, applied to imaging mass cytometry data, identified a measure of tissue spatial segregation that enables optimal experimental design, thus improving the design of multiplexed imaging studies.
Correction
Neurosciences
Mor Kenigsbuch, Pierre Bost, Shahar Halevi, Yuzhou Chang, Shuo Chen, Qin Ma, Renana Hajbi, Benno Schwikowski, Bernd Bodenmiller, Hongjun Fu, Michal Schwartz, Ido Amit
NATURE NEUROSCIENCE
(2023)
Article
Multidisciplinary Sciences
Sandra Tietscher, Johanna Wagner, Tobias Anzeneder, Claus Langwieder, Martin Rees, Bettina Sobottka, Natalie de Souza, Bernd Bodenmiller
Summary: Immune checkpoint therapy in breast cancer is limited to triple negative patients and shows rare long-term clinical benefit. This study explores the immune environments of human breast tumors with or without exhausted T cells, focusing on luminal subtypes. The presence of a PD-1(high) exhaustion-like T cell phenotype is associated with an inflammatory immune environment, increased myeloid cell activation, elevated immunomodulatory and cytokine signaling, accumulation of natural killer T cells, and altered spatial organization. PD-1 and CXCL13 expression on T cells, and MHC-I expression on tumor cells are distinguishing features between the immune environments.
NATURE COMMUNICATIONS
(2023)
Article
Biology
Sophia A. Wild, Ian G. Cannell, Ashley Nicholls, Katarzyna Kania, Dario Bressan, Gregory J. Hannon, Kirsty Sawicka
Summary: This study utilizes clonal transcriptomics with WILD-seq to analyze mouse models of TNBC and identifies NRF2 as a major mechanism of taxane resistance. It also discovers the collateral sensitivity of tumor models to asparagine deprivation therapy using L-asparaginase after docetaxel treatment.
Article
Oncology
Ossia M. Eichhoff, Corinne I. Stoffel, Jan Kasler, Luzia Briker, Patrick Turko, Gergely Karsai, Nina Zila, Verena Paulitschke, Phil F. Cheng, Alexander Leitner, Andrea Bileck, Nicola Zamboni, Anja Irmisch, Zsolt Balazs, Aizhan Tastanova, Susana Pascoal, Pal Johansen, Rebekka Wegmann, Julien Mena, Alaa Othman, Vasanthi S. Viswanathan, Judith Wenzina, Andrea Aloia, Annalisa Saltari, Andreas Dzung, Michael Krauthammer, Stuart L. Schreiber, Thorsten Hornemann, Martin Distel, Berend Snijder, Reinhard Dummer, Mitchell P. Levesque
Summary: The clinical management of NRAS-mutated melanomas is challenging due to resistance that arises through genetic, transcriptional, and metabolic adaptation. However, the adoption of a mesenchymal phenotype with a quiescent metabolic program in NRAS-mutated melanoma cells confers sensitivity to reactive oxygen species (ROS) induction, which can be inhibited by ROS inducers in combination with MAPK pathway inhibitors. The findings suggest that targeting both metabolic reprogramming and MAPK signaling could improve patient treatment in melanoma and other cancers.
Article
Cell Biology
Jana Raja Fischer, Hartland Warren Jackson, Natalie de Souza, Zsuzsanna Varga, Peter Schraml, Holger Moch, Bernd Bodenmiller
Summary: Although breast cancer mortality is caused by metastasis, clinical decisions are not based on the phenotype of disseminated cells. This study compares single-cell phenotypes of primary breast tumors and matched lymph node metastases using multiplex imaging mass cytometry. The researchers observe extensive phenotypic variability between primary and metastatic sites, and identify single-cell phenotypes and spatial organizations of disseminated tumor cells associated with patient survival. They also find that p53 and GATA3 in lymph node metastases provide prognostic information beyond clinical classifiers.
CELL REPORTS MEDICINE
(2023)
Article
Oncology
Laura Kuett, Raul Catena, Alaz Ozcan, Alex Pluss, Peter Schraml, Holger Moch, Natalie de Souza, Bernd Bodenmiller
Summary: The article introduces a new imaging mass cytometry technology that allows for multiplexed tissue analysis in three dimensions. The study shows that this technology can reveal the complexity of cells and microenvironments, as well as phenomena occurring in three-dimensional space, such as tumor cell invasion.
