Article
Biochemistry & Molecular Biology
Taseef Rahman, Yuanqi Du, Liang Zhao, Amarda Shehu
Summary: The study reveals that current GAN models struggle to capture complex structural patterns in protein molecules, and that mechanisms believed to stabilize training may not be effective. Additionally, performance based solely on loss may not correlate with the quality of generated datasets. The novel contribution of the study is the demonstration that Wasserstein GAN strikes a good balance in capturing both local and distal patterns in protein tertiary structures, paving the way for deeper generative models in exploring diverse protein activities.
Review
Multidisciplinary Sciences
Ton N. Schumacher, Daniela S. Thommen
Summary: This article discusses the current knowledge on TLSs in cancer, focusing on the drivers of TLS formation, the function and contribution of TLSs to the antitumor immune response, and the potential of TLSs as therapeutic targets in human cancers.
Article
Biochemical Research Methods
Lupeng Kong, Fusong Ju, Haicang Zhang, Shiwei Sun, Dongbo Bu
Summary: This study introduces FALCON2, a web server that integrates ProALIGN and ProFOLD for high-quality protein structure prediction service. Evaluation on benchmarks shows that ProALIGN outperforms ProFOLD when high-quality templates are available, while ProFOLD performs better in other cases. By combining these two approaches, FALCON2 outperforms existing methods in performance.
BMC BIOINFORMATICS
(2021)
Article
Biochemistry & Molecular Biology
Fardina Fathmiul Alam, Amarda Shehu
Summary: With the debut of AlphaFold2, it is now possible to obtain a highly-accurate view of the equilibrium tertiary structure of a protein molecule. However, the single-structure view is not sufficient to account for the structural plasticity of protein molecules. This research advances the capabilities of deep learning models to learn from experimentally-available tertiary structures of proteins and explores the role of the composition of the training dataset in learning key patterns. The authors also propose a disentangled latent variable model that improves upon existing models, opening up new avenues of research for computing multi-structure views of protein molecules.
Editorial Material
Immunology
Lisa Schmidleithner, Markus Feuerer
Summary: A recent study reveals that repression of Satb1 in CD4(+) T cells can drive intratumoral TLS formation, resulting in reduced tumor growth.
TRENDS IN IMMUNOLOGY
(2022)
Article
Biochemical Research Methods
F. Adriaan Lategan, Caroline Schreiber, Hugh G. Patterton
Summary: In this study, we developed SeqPredNN, a neural network-based approach to predict the identity of amino acids in a protein structure using only the relative positions, orientations, and backbone dihedral angles of nearby residues. This research is important as it addresses the inverse problem of protein folding and provides valuable insights for protein engineering and biotechnology.
BMC BIOINFORMATICS
(2023)
Article
Multidisciplinary Sciences
Nanda Horeweg, Hagma H. Workel, Dominik Loiero, David N. Church, Lisa Vermij, Alicia Leon-Castillo, Ricki T. Krog, Stephanie M. de Boer, Remi A. Nout, Melanie E. Powell, Linda R. Mileshkin, Helen MacKay, Alexandra Leary, Naveena Singh, Ina M. Juergenliemk-Schulz, Vincent T. H. B. M. Smit, Carien L. Creutzberg, Viktor H. Koelzer, Hans W. Nijman, Tjalling Bosse, Marco de Bruyn
Summary: B-cells and tertiary lymphoid structures (TLS) play critical roles in endometrial cancer (EC). L1CAM is identified as a marker for mature TLS and the presence of TLS is associated with favorable prognosis in EC patients.
NATURE COMMUNICATIONS
(2022)
Review
Oncology
Raj G. Vaghjiani, Joseph J. Skitzki
Summary: Tertiary lymphoid structures (TLS) are anatomical structures similar to but distinct from secondary lymphoid structures, allowing for a more targeted and efficient immune response. TLS are increasingly recognized as markers of prognosis and direct mediators of immunotherapy efficacy in cancer patients. The mechanisms and relationships of TLS in different tumors are being elucidated, with potential for TLS induction as a therapeutic avenue. This review discusses TLS formation, its relationship to malignancies, and its role in immunotherapy.
Article
Biochemistry & Molecular Biology
Michael Silk, Douglas E. Pires, Carlos H. M. Rodrigues, Elston N. D'Souza, Moshe Olshansky, Natalie Thorne, David B. Ascher
Summary: The study introduces a new method that combines sequence- and spatial-based scores to accurately identify pathogenic variants in the human genome, providing a valuable tool for large-scale analysis.
NUCLEIC ACIDS RESEARCH
(2021)
Review
Immunology
Roger Li, Anders Berglund, Logan Zemp, Jasreman Dhillon, Ryan Putney, Youngchul Kim, Rohit K. Jain, G. Daniel Grass, Jose Conejo-Garcia, James J. Mule
Summary: The study highlights the importance of tertiary lymphoid structures in the tumor microenvironment, their association with favorable outcomes in tumors, and predictability of response to immune checkpoint blockade. The 12-CK score has been validated as a prognostic marker for survival in various tumor types, including melanoma, breast cancer, and bladder cancer.
FRONTIERS IN IMMUNOLOGY
(2021)
Review
Plant Sciences
Lewis H. Ziska
Summary: While CO2 is widely recognized as a greenhouse gas contributing to global warming, it is also found to have a significant impact on plant biology, including stimulating photosynthesis and growth but potentially affecting plant nutrition. This aspect of anthropogenic climate change is crucial yet often overlooked.
Review
Immunology
Weili Jia, Tianchen Zhang, Qianyun Yao, Jianhui Li, Ye Nie, Xinjun Lei, Zhenzhen Mao, Yanfang Wang, Wen Shi, Wenjie Song
Summary: Tertiary lymphoid structures (TLSs) are organized aggregates of immune cells found in the tumor microenvironment and play an important role in the occurrence and treatment of primary hepatic carcinoma (PHC). The location and cellular composition of TLSs can influence the growth and prognosis of PHC, and TLSs can also serve as markers for immunotherapy to predict treatment response.
FRONTIERS IN IMMUNOLOGY
(2022)
Review
Immunology
Anna Johansson-Percival, Ruth Ganss
Summary: Improving the effectiveness of anti-cancer immunotherapy is a major clinical challenge due to the suppressive tumor microenvironment. The presence of tertiary lymphoid structures (TLS) in some human cancers is associated with better prognosis and responsiveness to immune checkpoint blockade. Inducing and shaping TLS in the tumor microenvironment could provide innovative opportunities to enhance immunotherapies.
FRONTIERS IN IMMUNOLOGY
(2021)
Review
Immunology
Xinlei Zou, Canghai Guan, Jianjun Gao, Wujiang Shi, Yunfu Cui, Xiangyu Zhong
Summary: Pancreatic cancer is highly malignant and has limited response to immunotherapies due to its hypoxic and immunosuppressive tumor microenvironment. The formation of tertiary lymphoid structures (TLSs) induced by immune cells can be found in both intra- and peritumor tissues of pancreatic cancer. Intratumoral TLSs are associated with a good prognosis and can be used as an indicator to assess treatment effectiveness. Targeted induction of TLS formation may open up new possibilities for immunotherapy of pancreatic cancer.
FRONTIERS IN IMMUNOLOGY
(2023)
Review
Immunology
Alessandra Vaccaro, Tiarne van de Walle, Mohanraj Ramachandran, Magnus Essand, Anna Dimberg
Summary: Tertiary lymphoid structures (TLS) are lymph node-like aggregates that form in association with chronic inflammation or cancer. They have been shown to have a positive prognosis and increased sensitivity to cancer immunotherapy. However, a comprehensive understanding of their role in anti-tumor immunity and the mechanisms involved in their formation and function is still lacking. Further research in relevant cancer models is needed to evaluate the impact of TLS on cancer therapies and develop new treatment approaches that promote their formation in cancer.
FRONTIERS IN IMMUNOLOGY
(2023)