Article
Biochemical Research Methods
Leonardo Pellegrina, Fabio Vandin
Summary: The study presents a new algorithm, MASTRO, for discovering significantly conserved evolutionary trajectories in cancer. The algorithm is applied to lung cancer and acute myeloid leukemia data, confirming and extending previous findings.
Article
Biochemical Research Methods
Kexin Huang, Yun Zhang, Haoran Gong, Zhengzheng Qiao, Tiangang Wang, Weiling Zhao, Liyu Huang, Xiaobo Zhou
Summary: We developed a computational approach to infer the progression trajectory of lung adenocarcinoma (LUAD) and identified molecular events and genetic variations associated with LUAD progression, which have important implications for diagnosis and treatment.
PLOS COMPUTATIONAL BIOLOGY
(2023)
Article
Genetics & Heredity
Joshua T. Lange, John C. Rose, Celine Y. Chen, Yuriy Pichugin, Liangqi Xie, Jun Tang, King L. Hung, Kathryn E. Yost, Quanming Shi, Marcella L. Erb, Utkrisht Rajkumar, Sihan Wu, Sabine Taschner-Mandl, Marie Bernkopf, Charles Swanton, Zhe Liu, Weini Huang, Howard Y. Chang, Vineet Bafna, Anton G. Henssen, Benjamin Werner, Paul S. Mischel
Summary: Random segregation of extrachromosomal DNA contributes to intratumoral heterogeneity and facilitates the rapid adaptation of human tumor cells to anticancer drugs. Oncogene amplification on extrachromosomal DNA (ecDNA) is a common event, driving aggressive tumor growth, drug resistance and shorter survival. Through theoretical models, unbiased image analysis, CRISPR-based ecDNA tagging with live-cell imaging and CRISPR-C, it is shown that random ecDNA inheritance results in extensive intratumoral ecDNA copy number heterogeneity and rapid adaptation to metabolic stress and targeted treatment.
Article
Biochemical Research Methods
Linda K. Sundermann, Jeff Wintersinger, Gunnar Ratsch, Jens Stoye, Quaid Morris
Summary: Tumors are composed of multiple subpopulations of genetically distinct cancer cells. A new method called partial clone tree captures uncertainty in the data more efficiently and can handle large-scale clone trees. SubMARine, an algorithm based on partial clone trees, provides accurate reconstruction of clone trees in a polynomial time and space.
PLOS COMPUTATIONAL BIOLOGY
(2021)
Editorial Material
Multidisciplinary Sciences
Tikvah K. K. Hayes, Matthew Meyerson
Summary: Assessing genetic and cellular changes in human lung cancer during its progression can contribute to the development of treatments, as reported by the TRACERx project.
Article
Multidisciplinary Sciences
Chadi M. Saad-Roy, Sinead E. Morris, C. Jessica E. Metcalf, Michael J. Mina, Rachel E. Baker, Jeremy Farrar, Edward C. Holmes, Oliver G. Pybus, Andrea L. Graham, Simon A. Levin, Bryan T. Grenfell, Caroline E. Wagner
Summary: Given vaccine dose shortages and logistical challenges, various deployment strategies are being proposed to increase population immunity levels to SARS-CoV-2. While focusing on one dose may decrease infections in the short term, the long-term outcomes depend on the relative immune robustness of this approach. Under conditions of partial population immunity, a one-dose policy may increase the potential for antigenic evolution.
Article
Multidisciplinary Sciences
Erik van Dijk, Tom van den Bosch, Kristiaan J. Lenos, Khalid El Makrini, Lisanne E. Nijman, Hendrik F. B. van Essen, Nico Lansu, Michiel Boekhout, Joris H. Hageman, Rebecca C. Fitzgerald, Cornelis J. A. Punt, Jurriaan B. Tuynman, Hugo J. G. Snippert, Geert J. P. L. Kops, Jan Paul Medema, Bauke Ylstra, Louis Vermeulen, Daniel M. Miedema
Summary: Intratumour heterogeneity (ITH) is associated with worse prognosis in cancer, and efficient frameworks to measure it are needed. Here the authors develop a method to estimate copy number heterogeneity, and propose that it is driven by chromosomal instability and can predict pan-cancer survival.
NATURE COMMUNICATIONS
(2021)
Article
Biochemistry & Molecular Biology
Tomasz M. Grzywa, Agnieszka A. Koppolu, Wiktor Paskal, Klaudia Klicka, Malgorzata Rydzanicz, Jaroslaw Wejman, Rafal Ploski, Pawel K. Wlodarski
Summary: Melanoma tumors are highly heterogeneous, which leads to challenges in diagnosis and treatment failures. This study revealed significant differences in genetic mutations between high and low proliferation compartments of melanoma tumors, highlighting the functional role of genetic heterogeneity in melanoma.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Article
Biotechnology & Applied Microbiology
Runmin Wei, Siyuan He, Shanshan Bai, Emi Sei, Min Hu, Alastair Thompson, Ken Chen, Savitri Krishnamurthy, Nicholas E. Navin
Summary: CellTrek is a computational method that combines single-cell RNA sequencing and spatial transcriptomics to achieve single-cell spatial mapping. It has demonstrated accuracy and robustness through simulation and experimental validation, and has been successfully applied to tumor tissues.
NATURE BIOTECHNOLOGY
(2022)
Article
Oncology
John H. Lockhart, Hayley D. Ackerman, Kyubum Lee, Mahmoud Abdalah, Andrew John Davis, Nicole Hackel, Theresa A. Boyle, James Saller, Aysenur Keske, Kay Hanggi, Brian Ruffell, Olya Stringfield, W. Douglas Cress, Aik Choon Tan, Elsa R. Flores
Summary: Preclinical genetically engineered mouse models (GEMMs) of lung adenocarcinoma are valuable for studying tumor formation, progression, and therapeutic resistance. To improve histological analysis in these models, researchers developed GLASS-AI, a machine learning tool for grading, segmenting, and analyzing tumors. GLASS-AI showed agreement with expert raters and revealed previously unreported intratumor heterogeneity. Integration of immunohistochemical staining with GLASS-AI analysis identified dysregulation of Mapk/Erk signaling in high-grade lung adenocarcinomas. This study demonstrates the usefulness of GLASS-AI and the power of combining machine learning and molecular biology techniques for cancer research.
NPJ PRECISION ONCOLOGY
(2023)
Article
Multidisciplinary Sciences
Shuhei Aramaki, Shogo Tsuge, Ariful Islam, Fumihiro Eto, Takumi Sakamoto, Soho Oyama, Wenxin Li, Chi Zhang, Shinichi Yamaguchi, Daiki Takatsuka, Yuko Hosokawa, A. S. M. Waliullah, Yutaka Takahashi, Kenji Kikushima, Tomohito Sato, Kei Koizumi, Hiroyuki Ogura, Tomoaki Kahyo, Satoshi Baba, Norihiko Shiiya, Haruhiko Sugimura, Katsumasa Nakamura, Mitsutoshi Setou
Summary: Cancer tissues possess more pathological characteristics than cancer cells, making the evaluation of cancer tissues essential in determining cancer treatment strategies. Mass spectrometry imaging (MSI) provides the ability to assess cancer tissues and identify molecules while preserving spatial information. Cluster analysis of cancer tissues' MSI data has been used to evaluate phenotype heterogeneity, which may not always coincide with genotype heterogeneity. In this study, we explored the phenotype heterogeneity of luminal breast cancer, known to have fewer gene mutations, and successfully identified phenotype heterogeneity based on lipidomics in the tissue samples.
Article
Oncology
Josephine Mun-Yee Ko, Chen Guo, Conghui Liu, Lvwen Ning, Wei Dai, Lihua Tao, Anthony Wing-Ip Lo, Carissa Wing-Yan Wong, Ian Yu-Hong Wong, Fion Siu-Yin Chan, Claudia Lai-Yin Wong, Kwan Kit Chan, Tsz Ting Law, Nikki Pui-Yue Lee, Zhichao Liu, Haoyao Jiang, Zhigang Li, Simon Law, Maria Li Lung
Summary: This study examines the genetic pathogenesis of dual oesophageal squamous cell carcinoma (ESCC) and hypopharyngeal cancer (HPC) through multiple region whole-exome sequencing and clonality analysis. The findings suggest that the two primary tumours have distinct genetic profiles and do not share significant clones. Additionally, high intratumour heterogeneity is associated with relapse and survival.
BRITISH JOURNAL OF CANCER
(2022)
Article
Multidisciplinary Sciences
Zhi-Nan Xia, Jing-Gen Wu, Wen-Hao Yao, Yu-Yang Meng, Wen-Gang Jian, Teng-Da Wang, Wei Xue, Yi-Peng Yu, Li-Cheng Cai, Xing-Yuan Wang, Peng Zhang, Zhi-Yuan Li, Hao Zhou, Zhi-Cheng Jiang, Jia-Yu Zhou, Cheng Zhang
Summary: This study analyzes single-cell and bulk RNA sequencing data to explore the correlation between the tumor microenvironment, clinical outcomes, and immunotherapeutic responses in renal cell carcinoma (RCC). It identifies distinct differentiation trajectories and molecular subtypes of ccRCC, and constructs a prognostic risk signature and a nomogram for predicting patient prognosis. The study highlights the importance of ccRCC cell differentiation and TME evolution in predicting clinical outcomes and potential immunotherapeutic responses, and provides an accurate method for prognosis prediction.
SCIENTIFIC REPORTS
(2022)
Article
Ecology
Xiao Fu, Yue Zhao, Jose I. Lopez, Andrew Rowan, Lewis Au, Annika Fendler, Steve Hazell, Hang Xu, Stuart Horswell, Scott T. C. Shepherd, Charlotte E. Spencer, Lavinia Spain, Fiona Byrne, Gordon Stamp, Tim O'Brien, David Nicol, Marcellus Augustine, Ashish Chandra, Sarah Rudman, Antonia Toncheva, Andrew J. S. Furness, Lisa Pickering, Santosh Kumar, Dow-Mu Koh, Christina Messiou, Derfel ap Dafydd, Matthew R. Orton, Simon J. Doran, James Larkin, Charles Swanton, Erik Sahai, Kevin Litchfield, Samra Turajlic, Paul A. Bates
Summary: The study examined spatial and temporal features of clonal diversification in clear cell renal cell carcinoma using a combined modelling and real tumour analysis approach, providing insights into predicting tumour evolution patterns and subclone diversification levels.
NATURE ECOLOGY & EVOLUTION
(2022)
Article
Multidisciplinary Sciences
Jack Edwards, Andriy Marusyk, David Basanta
Summary: Cancers are the outcome of eco-evolutionary processes driven by heritable phenotypic diversification and environmental selection. By using agent-based modeling, it was discovered that the interplay between exploring new space and maximizing cell proliferation leads to ecological succession and the emergence of large, heterogeneous populations. Despite both remodeling and proliferation strategies being positively selected in simulations, their interaction can result in sub-clonal architecture that resembles neutral evolution, cautioning against overinterpretation of cancer genome sequencing data.
Article
Biology
Yuki Kanayama, Yoh Iwasa
Summary: Research using life history theory explains the large body size of sauropod dinosaurs. The analysis showed that adult body size increased with food-plant quality and availability but decreased with higher mortality due to predators.
JOURNAL OF THEORETICAL BIOLOGY
(2021)
Article
Biology
Ryo Yamaguchi, Yoh Iwasa, Yuuya Tachiki
Summary: Species diversity in an archipelagic system is determined by the balance of speciation, extinction, and migration. As species numbers increase, average population size per species decreases, leading to higher extinction probabilities. In a study using a multi-species two-island model, it was found that migration plays a crucial role in affecting the rate of recurrent speciation events, potentially stabilizing species numbers at a finite level.
PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES
(2021)
Article
Biology
Shintaro Hishida, Yoh Iwasa
Summary: We investigated the spatial distribution patterns of two microbial strains along the intestinal duct, including the standard pattern, proximal reversion pattern, and distal suppression pattern.
JOURNAL OF THEORETICAL BIOLOGY
(2021)
Article
Multidisciplinary Sciences
Jason Olejarz, Yoh Iwasa, Andrew H. Knoll, Martin A. Nowak
Summary: The Great Oxygenation Event (GOE) 2.4 billion years ago is believed to have been critical for the evolution of complex life. The authors propose a model suggesting that competition between major bacterial groups could have triggered the GOE in a feedback loop with geophysical processes.
NATURE COMMUNICATIONS
(2021)
Article
Biology
Yoh Iwasa, Sachi Yamaguchi
Summary: In species with separate sexes, males provide nuptial gifts containing nutrition to their mates, which can affect the male's reproductive success and bring direct and indirect benefits to the female. By formalizing and analyzing a quantitative genetics model describing the coevolution of nuptial gift size and female's propensity to remate, it was found that various evolutionary equilibriums exist, including scenarios with no nuptial gifts or remating, as well as scenarios where males produce nuptial gifts and females engage in multiple matings.
JOURNAL OF THEORETICAL BIOLOGY
(2022)
Article
Biology
Yoh Iwasa, Akane Hara, Shihomi Ozone
Summary: The study investigates the relationship between viral replication in the host and immune response control, as well as the impact of viral virulence and various factors. The results show that enhancing memory cells can effectively suppress viral virulence, which is important in designing drugs to suppress viruses.
JOURNAL OF THEORETICAL BIOLOGY
(2021)
Article
Behavioral Sciences
Yoh Iwasa, Sachi Yamaguchi
Summary: This study investigated the reasons why subordinate individuals in most sex-changing fishes choose to be female or are forced to give up their male function, finding that subordinates are only evicted by dominant males when there is a significant difference in reproductive resources.
BEHAVIORAL ECOLOGY AND SOCIOBIOLOGY
(2022)
Article
Biology
Yuka Uchiyama, Yoh Iwasa, Sachi Yamaguchi
Summary: This study developed a dynamic optimization model to investigate the chloride cell composition of individuals living in an environment with fluctuating salinity. The research found that the optimal fraction of generalist chloride cells is influenced by the frequency of salinity changes, the time needed for new cell functionality, and the maintenance cost.
JOURNAL OF THEORETICAL BIOLOGY
(2022)
Article
Biology
Rena Hayashi, Shingo Iwami, Yoh Iwasa
Summary: After infecting a host, a viral strain may rapidly increase and produce mutants with a faster proliferation rate than the original virus. However, most mutants become extinct due to the stochasticity caused by a small number of infected cells. The study calculated the fraction of mutants that could escape stochastic extinction based on a continuous-time branching process with a time-dependent growth rate.
JOURNAL OF THEORETICAL BIOLOGY
(2022)
Article
Biology
Yoh Iwasa, Yoichi Yusa, Sachi Yamaguchi
Summary: This paper develops an evolutionary game to examine the conditions for different life-cycle types to succeed in a seasonal environment. The study finds that planktotrophy is favored when the planktonic stages are more efficient in terms of biomass gain, while lecithotrophy or direct development is more advantageous under specific conditions.
JOURNAL OF THEORETICAL BIOLOGY
(2022)
Article
Biology
Yoh Iwasa, Rena Hayashi
Summary: This study presents a simple model that couples social and epidemiological dynamics, revealing the relationship between people's activities and waves of infection. The model shows different oscillation patterns and variations, as well as the control conditions of infection.
JOURNAL OF THEORETICAL BIOLOGY
(2023)
Review
Biology
Yoh Iwasa, Sachi Yamaguchi
Summary: Marine animals exhibit diverse and flexible sexual systems. This review focuses on theoretical studies in the last decade, highlighting advancements in understanding sex change in coral fishes, diverse sexual patterns in barnacles, larval production strategies, and temperature-based sex determination in fish and reptiles. The game model provides a valuable framework to comprehend the diversity of sexual patterns, considering various constraints and incorporating physiological and molecular mechanisms.
PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES
(2023)
Review
Cell Biology
Yoh Iwasa
Summary: We reviewed mathematical models and concepts in developmental biology, including the feedback vertex set in ascidian embryos, tissue deformation in chick limb bud formation, mechanobiology and its impact on cell shape and gene expression, and the adaptive design of development in response to fluctuating environments.
DEVELOPMENT GROWTH & DIFFERENTIATION
(2023)
Article
Genetics & Heredity
Yoh Iwasa, Sou Tomimoto, Akiko Satake
Summary: Genomic sequencing reveals that somatic mutations cause genetic differentiation of cells within a single tree. A mathematical model for stem cell proliferation in the shoot apical meristem (SAM) was studied. Phylogenetic distance between cells sampled from different parts of a shoot was evaluated, indicating genetic differences due to mutations accumulated during shoot elongation. The tissue's cell walls suppress cell location exchange, resulting in genetic differentiation according to shoot angle and increased genetic variance among cells.
Article
Biology
Rena Hayashi, Yoh Iwasa
Summary: A high mutation rate of the RNA virus can result in the emergence of novel mutants that may evade the immunity of the original strain. However, many of these mutants go extinct due to the stochasticity of initial infected cell numbers. This study examines the impact of escaping host immune reactions and concludes that the chance of a mutant strain being established decreases with time since the wild-type infection.
BULLETIN OF MATHEMATICAL BIOLOGY
(2023)
