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Cancer Evolution and Metastasis

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Guest Editors: Christina Curtis and Florian Markowetz

Genomic research has helped us realize that cancer cells are dynamic populations that respond to different cues. Cancer cells can be viewed as diverse individuals, similar to humans within a population, with both intra-tumor heterogeneity and inter-tumor heterogeneity. One population can change to another over time, they evolve and migrate along with the changes of their microenvironment, with or without therapies. These changes happen gradually and understanding this dynamic process is helping us to manage cancer as a chronic disease. Genome Biology has launched the special issue on Cancer Evolution and Metastasis to showcase the recent efforts in understanding the mechanisms driving cancer evolution, heterogeneity, and metastasis.

  1. Lung adenocarcinoma (LUAD) is a highly malignant and heterogeneous tumor that involves various oncogenic genetic alterations. Epigenetic processes play important roles in lung cancer development. However, the ...

    Authors: Chongze Yuan, Haojie Chen, Shiqi Tu, Hsin-Yi Huang, Yunjian Pan, Xiuqi Gui, Muyu Kuang, Xuxia Shen, Qiang Zheng, Yang Zhang, Chao Cheng, Hui Hong, Xiaoting Tao, Yizhou Peng, Xingxin Yao, Feilong Meng…
    Citation: Genome Biology 2021 22:156
    Content type: Research Published on:

  2. The majority of pancreatic ductal adenocarcinomas (PDAC) are diagnosed at the metastatic stage, and standard therapies have limited activity with a dismal 5-year survival rate of only 8%. The liver and lung ar...

    Authors: Won Jin Ho, Rossin Erbe, Ludmila Danilova, Zaw Phyo, Emma Bigelow, Genevieve Stein-O’Brien, Dwayne L. Thomas II, Soren Charmsaz, Nicole Gross, Skylar Woolman, Kayla Cruz, Rebecca M. Munday, Neeha Zaidi, Todd D. Armstrong, Marcelo B. Sztein, Mark Yarchoan…
    Citation: Genome Biology 2021 22:154
    Content type: Research Published on:

  3. Muscle-invasive bladder cancers are characterized by their distinct expression of luminal and basal genes, which could be used to predict key clinical features such as disease progression and overall survival....

    Authors: Tejaswi Iyyanki, Baozhen Zhang, Qixuan Wang, Ye Hou, Qiushi Jin, Jie Xu, Hongbo Yang, Tingting Liu, Xiaotao Wang, Fan Song, Yu Luan, Hironobu Yamashita, Ruby Chien, Huijue Lyu, Lijun Zhang, Lu Wang…
    Citation: Genome Biology 2021 22:105
    Content type: Research Published on:

  4. Millions of nucleotide variants are identified through cancer genome sequencing and it is clinically important to identify the pathogenic variants among them. By introducing base substitutions at guide RNA tar...

    Authors: Changcai Huang, Guangyu Li, Jiayu Wu, Junbo Liang and Xiaoyue Wang
    Citation: Genome Biology 2021 22:80
    Content type: Research Published on:

  5. Frequent activation of the co-transcriptional factor YAP is observed in a large number of solid tumors. Activated YAP associates with enhancer loci via TEAD4-DNA-binding protein and stimulates cancer aggressiv...

    Authors: Li Li, Alejandro P. Ugalde, Colinda L. G. J. Scheele, Sebastian M. Dieter, Remco Nagel, Jin Ma, Abhijeet Pataskar, Gozde Korkmaz, Ran Elkon, Miao-Ping Chien, Li You, Pin-Rui Su, Onno B. Bleijerveld, Maarten Altelaar, Lyubomir Momchev, Zohar Manber…
    Citation: Genome Biology 2021 22:54
    Content type: Research Published on:

  6. Massive genome sequencing data have inspired new challenges in personalized treatments and facilitated oncological drug discovery. We present a comprehensive database, My Personal Mutanome (MPM), for accelerat...

    Authors: Yadi Zhou, Junfei Zhao, Jiansong Fang, William Martin, Lang Li, Ruth Nussinov, Timothy A. Chan, Charis Eng and Feixiong Cheng
    Citation: Genome Biology 2021 22:53
    Content type: Database Published on:

  7. N6-methyladenosine (m6A) and adenosine-to-inosine (A-to-I) RNA editing are two of the most abundant RNA modification events affecting adenosines in mammals. Both these RNA modifications determine mRNA fate and p....

    Authors: Valentina Tassinari, Valeriana Cesarini, Sara Tomaselli, Zaira Ianniello, Domenico Alessandro Silvestris, Lavinia Ceci Ginistrelli, Maurizio Martini, Biagio De Angelis, Gabriele De Luca, Lucia Ricci Vitiani, Alessandro Fatica, Franco Locatelli and Angela Gallo
    Citation: Genome Biology 2021 22:51
    Content type: Research Published on:

  8. Alternative splicing is a rich source of tumor-specific neoantigen targets for immunotherapy. This holds promise for glioblastomas (GBMs), the most common primary tumors of the adult brain, which are resistant...

    Authors: Lin Wang, Karin Shamardani, Husam Babikir, Francisca Catalan, Takahide Nejo, Susan Chang, Joanna J. Phillips, Hideho Okada and Aaron A. Diaz
    Citation: Genome Biology 2021 22:48
    Content type: Research Published on:

  9. Deregulated gene expression is a hallmark of cancer; however, most studies to date have analyzed short-read RNA sequencing data with inherent limitations. Here, we combine PacBio long-read isoform sequencing (...

    Authors: Kie Kyon Huang, Jiawen Huang, Jeanie Kar Leng Wu, Minghui Lee, Su Ting Tay, Vikrant Kumar, Kalpana Ramnarayanan, Nisha Padmanabhan, Chang Xu, Angie Lay Keng Tan, Charlene Chan, Dennis Kappei, Jonathan Göke and Patrick Tan
    Citation: Genome Biology 2021 22:44
    Content type: Research Published on:

  10. Aberrant activation of the Hedgehog pathway drives tumorigenesis of many cancers, including glioblastoma. However, the sensitization mechanism of the G protein-coupled-like receptor smoothened (SMO), a key com...

    Authors: Xujia Wu, Songhua Xiao, Maolei Zhang, Lixuan Yang, Jian Zhong, Bo Li, Fanying Li, Xin Xia, Xixi Li, Huangkai Zhou, Dawei Liu, Nunu Huang, Xuesong Yang, Feizhe Xiao and Nu Zhang
    Citation: Genome Biology 2021 22:33
    Content type: Research Published on:

  11. Metastatic progress is the primary cause of death in most cancers, yet the regulatory dynamics driving the cellular changes necessary for metastasis remain poorly understood. Multi-omics approaches hold great ...

    Authors: Saba Ghaffari, Casey Hanson, Remington E. Schmidt, Kelly J. Bouchonville, Steven M. Offer and Saurabh Sinha
    Citation: Genome Biology 2021 22:19
    Content type: Research Published on:

  12. Crosstalk between genetic, epigenetic, and immune alterations in upper tract urothelial carcinomas and their role in shaping muscle invasiveness and patient outcome are poorly understood.

    Authors: Xiaoping Su, Xiaofan Lu, Sehrish Khan Bazai, Eva Compérat, Roger Mouawad, Hui Yao, Morgan Rouprêt, Jean-Philippe Spano, David Khayat, Irwin Davidson, Nizar N. Tannir, Fangrong Yan and Gabriel G. Malouf
    Citation: Genome Biology 2021 22:7
    Content type: Research Published on:

  13. Pancreatic ductal adenocarcinoma (PDAC) is one of the most lethal cancers due to its high metastasis rate in the liver. However, little is known about the molecular features of hepatic metastases due to diffic...

    Authors: Jianyu Yang, Ping Lin, Minwei Yang, Wei Liu, Xueliang Fu, Dejun Liu, Lingye Tao, Yanmiao Huo, Junfeng Zhang, Rong Hua, Zhigang Zhang, Yixue Li, Liwei Wang, Jing Xue, Hong Li and Yongwei Sun
    Citation: Genome Biology 2021 22:4
    Content type: Research Published on:

  14. Tumor-specific genomic aberrations are routinely determined by high-throughput genomic measurements. It remains unclear how complex genome alterations affect molecular networks through changing protein levels ...

    Authors: Konstantina Charmpi, Tiannan Guo, Qing Zhong, Ulrich Wagner, Rui Sun, Nora C. Toussaint, Christine E. Fritz, Chunhui Yuan, Hao Chen, Niels J. Rupp, Ailsa Christiansen, Dorothea Rutishauser, Jan H. Rüschoff, Christian Fankhauser, Karim Saba, Cedric Poyet…
    Citation: Genome Biology 2020 21:302
    Content type: Research Published on:

    The Protocol to this article has been published in Nature Protocols 2022 17:s41596-022-00727-1

  15. Adult T cell acute lymphoblastic leukemia (T-ALL) is a rare disease that affects less than 10 individuals in one million. It has been less studied than its cognate pediatric malignancy, which is more prevalent...

    Authors: Inés Sentís, Santiago Gonzalez, Eulalia Genescà, Violeta García-Hernández, Ferran Muiños, Celia Gonzalez, Erika López-Arribillaga, Jessica Gonzalez, Lierni Fernandez-Ibarrondo, Loris Mularoni, Lluís Espinosa, Beatriz Bellosillo, Josep-Maria Ribera, Anna Bigas, Abel Gonzalez-Perez and Nuria Lopez-Bigas
    Citation: Genome Biology 2020 21:284
    Content type: Research Published on:

  16. Biological rhythms regulate the biology of most, if not all living creatures, from whole organisms to their constitutive cells, their microbiota, and also parasites. Here, we present the hypothesis that intern...

    Authors: Luis Enrique Cortés-Hernández, Zahra Eslami-S, Antoine M. Dujon, Mathieu Giraudeau, Beata Ujvari, Frédéric Thomas and Catherine Alix-Panabières
    Citation: Genome Biology 2020 21:276
    Content type: Review Published on:

  17. Metastasis is the primary cause of cancer mortality accounting for 90% of cancer deaths. Our understanding of the molecular mechanisms driving metastasis is rudimentary.

    Authors: Won-Chul Lee, Alexandre Reuben, Xin Hu, Nicholas McGranahan, Runzhe Chen, Ali Jalali, Marcelo V. Negrao, Shawna M. Hubert, Chad Tang, Chia-Chin Wu, Anthony San Lucas, Whijae Roh, Kenichi Suda, Jihye Kim, Aik-Choon Tan, David H. Peng…
    Citation: Genome Biology 2020 21:271
    Content type: Research Published on:

  18. Long noncoding enhancer RNAs (lnc-eRNAs) are a subset of stable eRNAs identified from annotated lncRNAs. They might act as enhancer activity-related therapeutic targets in cancer. However, the underlying mecha...

    Authors: Ke Fang, Wei Huang, Yu-Meng Sun, Tian-Qi Chen, Zhan-Cheng Zeng, Qian-Qian Yang, Qi Pan, Cai Han, Lin-Yu Sun, Xue-Qun Luo, Wen-Tao Wang and Yue-Qin Chen
    Citation: Genome Biology 2020 21:269
    Content type: Research Published on:

  19. RNA editing generates modifications to the RNA sequences, thereby increasing protein diversity and shaping various layers of gene regulation. Recent studies have revealed global shifts in editing levels across...

    Authors: Tracey W. Chan, Ting Fu, Jae Hoon Bahn, Hyun-Ik Jun, Jae-Hyung Lee, Giovanni Quinones-Valdez, Chonghui Cheng and Xinshu Xiao
    Citation: Genome Biology 2020 21:268
    Content type: Research Published on:

  20. CRISPR-Cas9 gene editing has transformed our ability to rapidly interrogate the functional impact of somatic mutations in human cancers. Droplet-based technology enables the analysis of Cas9-introduced gene ed...

    Authors: Elisa ten Hacken, Kendell Clement, Shuqiang Li, María Hernández-Sánchez, Robert Redd, Shu Wang, David Ruff, Michaela Gruber, Kaitlyn Baranowski, Jose Jacob, James Flynn, Keith W. Jones, Donna Neuberg, Kenneth J. Livak, Luca Pinello and Catherine J. Wu
    Citation: Genome Biology 2020 21:266
    Content type: Short Report Published on:

  22. Immune checkpoint blockade (ICB) therapy has improved patient survival in a variety of cancers, but only a minority of cancer patients respond. Multiple studies have sought to identify general biomarkers of IC...

    Authors: Shengqing Stan Gu, Xiaoqing Wang, Xihao Hu, Peng Jiang, Ziyi Li, Nicole Traugh, Xia Bu, Qin Tang, Chenfei Wang, Zexian Zeng, Jingxin Fu, Cliff Meyer, Yi Zhang, Paloma Cejas, Klothilda Lim, Jin Wang…
    Citation: Genome Biology 2020 21:263
    Content type: Research Published on:

  24. RNA-binding proteins (RBPs) function as master regulators of gene expression. Alterations in RBP expression and function are often observed in cancer and influence critical pathways implicated in tumor initiat...

    Authors: Adam Kosti, Patricia Rosa de Araujo, Wei-Qing Li, Gabriela D. A. Guardia, Jennifer Chiou, Caihong Yi, Debashish Ray, Fabiana Meliso, Yi-Ming Li, Talia Delambre, Mei Qiao, Suzanne S. Burns, Franziska K. Lorbeer, Fanny Georgi, Markus Flosbach, Sarah Klinnert…
    Citation: Genome Biology 2020 21:195
    Content type: Research Published on:

  25. Glioma is the most common intrinsic brain tumor and also occurs in the spinal cord. Activating EGFR mutations are common in IDH1 wild-type gliomas. However, the cooperative partners of EGFR driving gliomagenesis ...

    Authors: Imran Noorani, Jorge de la Rosa, Yoon Ha Choi, Alexander Strong, Hannes Ponstingl, M. S. Vijayabaskar, Jusung Lee, Eunmin Lee, Angela Richard-Londt, Mathias Friedrich, Federica Furlanetto, Rocio Fuente, Ruby Banerjee, Fengtang Yang, Frances Law, Colin Watts…
    Citation: Genome Biology 2020 21:181
    Content type: Research Published on:

    The Author Correction to this article has been published in Genome Biology 2020 21:206

  26. Tumors can evolve and adapt to therapeutic pressure by acquiring genetic and epigenetic alterations that may be transient or stable. A precise understanding of how such events contribute to intratumoral hetero...

    Authors: Christine E. Eyler, Hironori Matsunaga, Volker Hovestadt, Samantha J. Vantine, Peter van Galen and Bradley E. Bernstein
    Citation: Genome Biology 2020 21:174
    Content type: Research Published on:

  27. Malignant transformation and progression of cancer are driven by the co-evolution of cancer cells and their dysregulated tumor microenvironment (TME). Recent studies on immunotherapy demonstrate the efficacy i...

    Authors: Jian Chen, Yun Tan, Fenghuan Sun, Likun Hou, Chi Zhang, Tao Ge, Huansha Yu, Chunxiao Wu, Yuming Zhu, Liang Duan, Liang Wu, Nan Song, Liping Zhang, Wei Zhang, Di Wang, Chang Chen…
    Citation: Genome Biology 2020 21:152
    Content type: Research Published on: