4.8 Article

The Snf1-related kinase, Hunk, is essential for mammary tumor metastasis

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NATL ACAD SCIENCES
DOI: 10.1073/pnas.0906993106

Keywords

breast cancer; knockout mice; mouse models; protein kinase

Funding

  1. National Institutes of Health (NIH) [CA105490]
  2. Department of Defense (DOD) [W81XWH05-1-0405]

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We previously identified a SNF1/AMPK-related protein kinase, Hunk, from a mammary tumor arising in an MMTV-neu transgenic mouse. The function of this kinase is unknown. Using targeted deletion in mice, we now demonstrate that Hunk is required for the metastasis of c-myc-induced mammary tumors, but is dispensable for normal development. Reconstitution experiments revealed that Hunk is sufficient to restore the metastatic potential of Hunk-deficient tumor cells, as well as defects in migration and invasion, and does so in a manner that requires its kinase activity. Consistent with a role for this kinase in the progression of human cancers, the human homologue of Hunk is overexpressed in aggressive subsets of carcinomas of the ovary, colon, and breast. In addition, a murine gene expression signature that distinguishes Hunk-wild type from Hunk-deficient mammary tumors predicts clinical outcome in women with breast cancer in a manner consistent with the pro-metastatic function of Hunk in mice. These findings identify a direct role for Hunk kinase activity in metastasis and establish an in vivo function for this kinase.

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Hegde, David Heiman, Zachary Heins, Austin J. Hepperla, Andrea Holbrook, Robert A. Holt, Alan P. Hoyle, Ralph H. Hruban, Jianhong Hu, Mei Huang, David Huntsman, Jason Huse, Christine A. Iacobuzio Donahue, Michael Ittmann, Joy C. Jayaseelan, Stuart R. Jefferys, Corbin D. Jones, Steven J. M. Jones, Hartmut Juhl, Koo Jeong Kang, Beth Karlan, Katayoon Kasaian, Electron Kebebew, Hark Kyun Kim, Viktoriya Korchina, Ritika Kundra, Phillip H. Lai, Eric Lander, Xuan Le, Darlene Lee, Douglas A. Levine, Lora Lewis, Tim Ley, Haiyan Irene Li, Pei Lin, W. M. Linehan, Fei Fei Liu, Yiling Lu, Lisa Lype, Yussanne Ma, Dennis T. Maglinte, Elaine R. Mardis, Jeffrey Marks, Marco A. Marra, Thomas J. Matthew, Michael Mayo, Karen McCune, Samuel R. Meier, Shaowu Meng, Piotr A. Mieczkowski, Tom Mikkelsen, Christopher A. Miller, Gordon B. Mills, Richard A. Moore, Carl Morrison, Lisle E. Mose, Catherine D. Moser, Andrew J. Mungall, Karen Mungall, David Mutch, Donna M. Muzny, Jerome Myers, Yulia Newton, Michael S. Noble, Peter O'Donnell, Brian Patrick O'Neill, Angelica Ochoa, Joong-Won Park, Joel S. Parker, Harvey Pass, Alessandro Pastore, Nathan A. Pennell, Charles M. Perou, Nicholas Petrelli, Olga Potapova, Janet S. Rader, Suresh Ramalingam, W. Kimryn Rathmell, Victor Reuter, Sheila M. Reynolds, Matthew Ringel, Jeffrey Roach, Lewis R. Roberts, A. Gordon Robertson, Sara Sadeghi, Charles Saller, Francisco Sanchez-Vega, Dirk Schadendorf, Jacqueline E. Schein, Heather K. Schmidt, Nikolaus Schultz, Raja Seethala, Yasin Senbabaoglu, Troy Shelton, Yan Shi, Juliann Shih, Ilya Shmulevich, Craig Shriver, Sabina Signoretti, Janae Simons, Samuel Singer, Payal Sipahimalani, Tara J. Skelly, Karen Smith McCune, Nicholas D. Socci, Matthew G. Soloway, Anil K. Sood, Angela Tam, Donghui Tan, Roy Tarnuzzer, Nina Thiessen, R. Houston Thompson, Leigh B. Thorne, Ming Tsao, Christopher Umbricht, David J. Van Den Berg, Erwin G. Van Meir, Umadevi Veluvolu, Douglas Voet, Linghua Wang, Paul Weinberger, Daniel J. Weisenberger, Dennis Wigle, Matthew D. Wilkerson, Richard K. Wilson, Boris Winterhoff, Maciej Wiznerowicz, Tina Wong, Winghing Wong, Liu Xi, Christina Yau, Hailei Zhang, Hongxin Zhang, Jiashan Zhang

NATURE (2020)

Article Multidisciplinary Sciences

Unsupervised class discovery in pancreatic ductal adenocarcinoma reveals cell-intrinsic mesenchymal features and high concordance between existing classification systems

Frederike Dijk, Veronique L. Veenstra, Eline C. Soer, Mark P. G. Dings, Lan Zhao, Johannes B. Halfwerk, Gerrit K. Hooijer, Helene Damhofer, Marco Marzano, Anne Steins, Cynthia Waasdorp, Olivier R. Busch, Marc G. Besselink, Johanna A. Tol, Lieke Welling, Lennart B. van Rijssen, Sjors Klompmaker, Hanneke W. Wilmink, Hanneke W. van Laarhoven, Jan Paul Medema, Louis Vermeulen, Sander R. van Hooff, Jan Koster, Joanne Verheij, Marc J. van de Vijver, Xin Wang, Maarten F. Bijlsma

SCIENTIFIC REPORTS (2020)

Article Biochemical Research Methods

PRIME: a probabilistic imputation method to reduce dropout effects in single-cell RNA sequencing

Hyundoo Jeong, Zhandong Liu

BIOINFORMATICS (2020)

Article Biochemical Research Methods

GDASC: a GPU parallel-based web server for detecting hidden batch factors

Xiao Wang, Haidong Yi, Jia Wang, Zhandong Liu, Yanbin Yin, Han Zhang

BIOINFORMATICS (2020)

Article Cell Biology

Antisense oligonucleotide therapy in a humanized mouse model of MECP2 duplication syndrome

Yingyao Shao, Yehezkel Sztainberg, Qi Wang, Sameer S. Bajikar, Alexander J. Trostle, Ying-Wooi Wan, Paymaan Jafar-Nejad, Frank Rigo, Zhandong Liu, Jianrong Tang, Huda Y. Zoghbi

Summary: Research has shown that using ASO therapy can effectively reduce the amount of MeCP2 protein in MDS mouse models and reverse the disease features. By generating an MDS mouse model with two human MECP2 alleles and administering MECP2-ASO through intracerebroventricular injection, it was found to efficiently down-regulate MeCP2 expression throughout the brain and improve disease features without toxicity.

SCIENCE TRANSLATIONAL MEDICINE (2021)

Article Biochemical Research Methods

Single-cell multi-omics integration for unpaired data by a siamese network with graph-based contrastive loss

Chaozhong Liu, Linhua Wang, Zhandong Liu

Summary: The paper proposes a deep learning framework called MinNet for integrating single-cell multi-omics sequencing data, which has high accuracy and generalizability and can effectively remove batch effects. The framework is of great significance in single-cell multi-omics research.

BMC BIOINFORMATICS (2023)

Article Multidisciplinary Sciences

Region-specific denoising identifies spatial co-expression patterns and intra-tissue heterogeneity in spatially resolved transcriptomics data

Linhua Wang, Mirjana Maletic-Savatic, Zhandong Liu

Summary: Spatially resolved transcriptomics is a new technique for mapping transcriptional information within tissues. In this study, the authors present MIST, a computational tool that detects molecular regions and denoises missing gene expression values using region-specific imputation.

NATURE COMMUNICATIONS (2022)

Correction Biochemical Research Methods

Single-cell multi-omics integration for unpaired data by a siamese network with graph-based contrastive loss (vol 24, 5, 2023)

Chaozhong Liu, Linhua Wang, Zhandong Liu

BMC BIOINFORMATICS (2023)

Article Genetics & Heredity

Literature-based predictions of Mendelian disease therapies

Cole A. Deisseroth, Won-Seok Lee, Jiyoen Kim, Hyun-Hwan Jeong, Ryan S. Dhindsa, Julia Wang, Huda Y. Zoghbi, Zhandong Liu

Summary: Correcting the underlying molecular imbalance may be more effective than symptomatic treatment for Mendelian disorders. PARMESAN is a computational tool that searches PubMed and PubMed Central to assemble drug-gene and gene-gene relationships into a central knowledge base. It predicts novel drug-gene relationships and assigns evidence-based scores to each prediction.

AMERICAN JOURNAL OF HUMAN GENETICS (2023)

Article Biochemical Research Methods

Unravelling spatial gene associations with SEAGAL: a Python package for spatial transcriptomics data analysis and visualization

Linhua Wang, Chaozhong Liu, Yang Gao, Xiang H. -F Zhang, Zhandong Liu

Summary: In the era of single-cell and spatial transcriptome profiling, traditional co-expression analysis is insufficient for exploring spatial gene associations. The SEAGAL Python package presented in this study allows for detecting and visualizing spatial gene correlations at both single-gene and gene-set levels. By inputting spatial transcriptomics datasets containing gene expression and spatial coordinates, SEAGAL enables the analysis and visualization of both gene-gene and cell-type colocalization within the precise spatial context. The output can be easily transformed into volcano plots and heatmaps, providing a user-friendly tool for mining spatial gene associations.

BIOINFORMATICS (2023)

Article Biotechnology & Applied Microbiology

A benchmark for RNA-seq deconvolution analysis under dynamic testing environments

Haijing Jin, Zhandong Liu

Summary: The study investigates the pitfalls and challenges of deconvolution analysis by examining various technical and biological factors using three benchmarking frameworks. These frameworks compare 11 popular deconvolution methods under 1766 conditions, providing new insights for researchers in the future application, standardization, and development of deconvolution tools on RNA-seq data.

GENOME BIOLOGY (2021)

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