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Creighton CJ. Clinical proteomics towards multiomics in cancer. MASS SPECTROMETRY REVIEWS 2024; 43:1255-1269. [PMID: 36495097 DOI: 10.1002/mas.21827] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/17/2023]
Abstract
Recent technological advancements in mass spectrometry (MS)-based proteomics technologies have accelerated its application to study greater and greater numbers of human tumor specimens. Over the last several years, the Clinical Proteomic Tumor Analysis Consortium, the International Cancer Proteogenome Consortium, and others have generated MS-based proteomic profiling data combined with corresponding multiomics data on thousands of human tumors to date. Proteomic data sets in the public domain can be re-examined by other researchers with different questions in mind from what the original studies explored. In this review, we examine the increasing role of proteomics in studying cancer, along with the potential for previous studies and their associated data sets to contribute to improving the diagnosis and treatment of cancer in the clinical setting. We also explore publicly available proteomics and multi-omics data from cancer cell line models to show how such data may aid in identifying therapeutic strategies for cancer subsets.
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Affiliation(s)
- Chad J Creighton
- Dan L. Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, Texas, USA
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas, USA
- Department of Medicine, Baylor College of Medicine, Houston, Texas, USA
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2
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Egeland EV, Seip K, Skourti E, Øy GF, Pettersen SJ, Pandya AD, Dahle MA, Haugen MH, Kristian A, Nakken S, Engebraaten O, Mælandsmo GM, Prasmickaite L. The SRC-family serves as a therapeutic target in triple negative breast cancer with acquired resistance to chemotherapy. Br J Cancer 2024:10.1038/s41416-024-02875-5. [PMID: 39390250 DOI: 10.1038/s41416-024-02875-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2024] [Revised: 09/26/2024] [Accepted: 10/02/2024] [Indexed: 10/12/2024] Open
Abstract
BACKGROUND Resistance to chemotherapy, combined with heterogeneity among resistant tumors, represents a significant challenge in the clinical management of triple negative breast cancer (TNBC). By dissecting molecular pathways associated with treatment resistance, we sought to define patient sub-groups and actionable targets for next-line treatment. METHODS Bulk RNA sequencing and reverse phase protein array profiling were performed on isogenic patient-derived xenografts (PDX) representing paclitaxel-sensitive and -resistant tumors. Pathways identified as upregulated in the resistant model were further explored as targets in PDX explants. Their clinical relevance was assessed in two distinct patient cohorts (NeoAva and MET500). RESULTS Increased activity in signaling pathways involving SRC-family kinases (SFKs)- and MAPK/ERK was found in treatment resistant PDX, with targeted inhibitors being significantly more potent in resistant tumors. Up-regulation of SFKs- and MAPK/ERK-pathways was also detected in a sub-group of chemoresistant patients after neoadjuvant treatment. Furthermore, High SFK expression (of either SRC, FYN and/or YES1) was detected in metastatic lesions of TNBC patients with fast progressing disease (median disease-free interval 27 vs 105 months). CONCLUSIONS Upregulation of SFK-signaling is found in a subset of chemoresistant tumors and is persistent in metastatic lesions. Based on pre-clinical results, these patients may respond favorably to treatment targeting SFKs.
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Affiliation(s)
- Eivind Valen Egeland
- Department of Tumor Biology, Institute for Cancer Research, The Norwegian Radium Hospital, Oslo University Hospital, Oslo, Norway.
| | - Kotryna Seip
- Department of Tumor Biology, Institute for Cancer Research, The Norwegian Radium Hospital, Oslo University Hospital, Oslo, Norway
| | - Eleni Skourti
- Department of Tumor Biology, Institute for Cancer Research, The Norwegian Radium Hospital, Oslo University Hospital, Oslo, Norway
- Insitute for Clinical Medicine, University of Oslo, Oslo, Norway
| | - Geir Frode Øy
- Department of Tumor Biology, Institute for Cancer Research, The Norwegian Radium Hospital, Oslo University Hospital, Oslo, Norway
| | - Solveig J Pettersen
- Department of Tumor Biology, Institute for Cancer Research, The Norwegian Radium Hospital, Oslo University Hospital, Oslo, Norway
| | - Abhilash D Pandya
- Department of Tumor Biology, Institute for Cancer Research, The Norwegian Radium Hospital, Oslo University Hospital, Oslo, Norway
| | - Maria A Dahle
- Department of Tumor Biology, Institute for Cancer Research, The Norwegian Radium Hospital, Oslo University Hospital, Oslo, Norway
- Insitute for Clinical Medicine, University of Oslo, Oslo, Norway
| | - Mads H Haugen
- Department of Tumor Biology, Institute for Cancer Research, The Norwegian Radium Hospital, Oslo University Hospital, Oslo, Norway
- Department of Research and Innovation, Vestre Viken Hospital Trust, Drammen, Norway
| | - Alexander Kristian
- Department of Tumor Biology, Institute for Cancer Research, The Norwegian Radium Hospital, Oslo University Hospital, Oslo, Norway
| | - Sigve Nakken
- Department of Tumor Biology, Institute for Cancer Research, The Norwegian Radium Hospital, Oslo University Hospital, Oslo, Norway
- Centre for Cancer Cell Reprogramming, Institute of Clinical Medicine, Faculty of Medicine, University of Oslo, Oslo, Norway
- Centre for Bioinformatics, Department of Informatics, University of Oslo, Oslo, Norway
| | - Olav Engebraaten
- Department of Tumor Biology, Institute for Cancer Research, The Norwegian Radium Hospital, Oslo University Hospital, Oslo, Norway
- Insitute for Clinical Medicine, University of Oslo, Oslo, Norway
- Department of Oncology, Oslo University Hospital, Oslo, Norway
| | - Gunhild M Mælandsmo
- Department of Tumor Biology, Institute for Cancer Research, The Norwegian Radium Hospital, Oslo University Hospital, Oslo, Norway
- Department of Medical Biology, Faculty of Health Sciences, The Arctic University of Norway-University of Tromsø, Tromsø, Norway
| | - Lina Prasmickaite
- Department of Tumor Biology, Institute for Cancer Research, The Norwegian Radium Hospital, Oslo University Hospital, Oslo, Norway
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3
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Sundaram L, Kumar A, Zatzman M, Salcedo A, Ravindra N, Shams S, Louie BH, Bagdatli ST, Myers MA, Sarmashghi S, Choi HY, Choi WY, Yost KE, Zhao Y, Granja JM, Hinoue T, Hayes DN, Cherniack A, Felau I, Choudhry H, Zenklusen JC, Farh KKH, McPherson A, Curtis C, Laird PW, Demchok JA, Yang L, Tarnuzzer R, Caesar-Johnson SJ, Wang Z, Doane AS, Khurana E, Castro MAA, Lazar AJ, Broom BM, Weinstein JN, Akbani R, Kumar SV, Raphael BJ, Wong CK, Stuart JM, Safavi R, Benz CC, Johnson BK, Kyi C, Shen H, Corces MR, Chang HY, Greenleaf WJ. Single-cell chromatin accessibility reveals malignant regulatory programs in primary human cancers. Science 2024; 385:eadk9217. [PMID: 39236169 DOI: 10.1126/science.adk9217] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2023] [Accepted: 07/03/2024] [Indexed: 09/07/2024]
Abstract
To identify cancer-associated gene regulatory changes, we generated single-cell chromatin accessibility landscapes across eight tumor types as part of The Cancer Genome Atlas. Tumor chromatin accessibility is strongly influenced by copy number alterations that can be used to identify subclones, yet underlying cis-regulatory landscapes retain cancer type-specific features. Using organ-matched healthy tissues, we identified the "nearest healthy" cell types in diverse cancers, demonstrating that the chromatin signature of basal-like-subtype breast cancer is most similar to secretory-type luminal epithelial cells. Neural network models trained to learn regulatory programs in cancer revealed enrichment of model-prioritized somatic noncoding mutations near cancer-associated genes, suggesting that dispersed, nonrecurrent, noncoding mutations in cancer are functional. Overall, these data and interpretable gene regulatory models for cancer and healthy tissue provide a framework for understanding cancer-specific gene regulation.
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Affiliation(s)
- Laksshman Sundaram
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA
- Department of Computer Science, Stanford University, Stanford, CA, USA
- Illumina AI laboratory, Illumina Inc, Foster City, CA, USA
- NVIDIA Bio Research, NVIDIA, Santa Clara, CA, USA
| | - Arvind Kumar
- Illumina AI laboratory, Illumina Inc, Foster City, CA, USA
| | - Matthew Zatzman
- Computational Oncology, Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | | | - Neal Ravindra
- Illumina AI laboratory, Illumina Inc, Foster City, CA, USA
| | - Shadi Shams
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA
- Department of Dermatology, Stanford University School of Medicine, Stanford, CA, USA
- Center for Personal Dynamic Regulomes, Stanford University, Stanford, CA 94305, USA
| | - Bryan H Louie
- Department of Dermatology, Stanford University School of Medicine, Stanford, CA, USA
- Center for Personal Dynamic Regulomes, Stanford University, Stanford, CA 94305, USA
| | - S Tansu Bagdatli
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA
- Department of Dermatology, Stanford University School of Medicine, Stanford, CA, USA
- Center for Personal Dynamic Regulomes, Stanford University, Stanford, CA 94305, USA
| | - Matthew A Myers
- Computational Oncology, Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | | | - Hyo Young Choi
- Department of Preventive Medicine, University of Tennessee Health Science Center, Memphis, TN, USA
- Department of Medicine, University of Tennessee Health Science Center, Memphis, TN, USA
| | - Won-Young Choi
- UTHSC Center for Cancer Research, University of Tennessee Health Science Center, Memphis, TN, USA
| | - Kathryn E Yost
- Department of Dermatology, Stanford University School of Medicine, Stanford, CA, USA
- Center for Personal Dynamic Regulomes, Stanford University, Stanford, CA 94305, USA
| | - Yanding Zhao
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA
- Department of Dermatology, Stanford University School of Medicine, Stanford, CA, USA
- Center for Personal Dynamic Regulomes, Stanford University, Stanford, CA 94305, USA
| | - Jeffrey M Granja
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA
| | - Toshinori Hinoue
- Center for Epigenetics, Van Andel Institute, Grand Rapids, MI 49503, USA
| | - D Neil Hayes
- Department of Preventive Medicine, University of Tennessee Health Science Center, Memphis, TN, USA
- Department of Medicine, University of Tennessee Health Science Center, Memphis, TN, USA
- UTHSC Center for Cancer Research, University of Tennessee Health Science Center, Memphis, TN, USA
| | | | - Ina Felau
- National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Hani Choudhry
- Department of Biochemistry, Faculty of Science, Cancer and Mutagenesis Unit, King Fahd Center for Medical Research, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Jean C Zenklusen
- National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | | | - Andrew McPherson
- Computational Oncology, Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Christina Curtis
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA
- Center for Personal Dynamic Regulomes, Stanford University, Stanford, CA 94305, USA
- Department of Medicine, Stanford University School of Medicine, Stanford, CA, USA
- Department of Biomedical Data Science, Stanford University School of Medicine, Stanford, CA, USA
- Chan Zuckerberg Biohub, San Francisco, CA, USA
| | - Peter W Laird
- Center for Epigenetics, Van Andel Institute, Grand Rapids, MI 49503, USA
| | - John A Demchok
- Center for Cancer Genomics, National Cancer Institute, Bethesda, MD 20892, USA
| | - Liming Yang
- Center for Cancer Genomics, National Cancer Institute, Bethesda, MD 20892, USA
| | - Roy Tarnuzzer
- Center for Cancer Genomics, National Cancer Institute, Bethesda, MD 20892, USA
| | | | - Zhining Wang
- Center for Biomedical Informatics and Information Technology, National Cancer Institute, NIH, 9609 Medical Center Drive, Rockville, MD 20850, USA
| | - Ashley S Doane
- Institute for Computational Biomedicine, Weill Cornell Medicine, New York, NY 10065, USA
| | - Ekta Khurana
- Institute for Computational Biomedicine, Weill Cornell Medicine, New York, NY 10065, USA
- Sandra and Edward Meyer Cancer Center, Weill Cornell Medicine, New York, NY 10065, USA
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY 10065, USA
- Englander Institute for Precision Medicine, Weill Cornell Medicine, New York, NY 10065, USA
| | - Mauro A A Castro
- Bioinformatics and Systems Biology Laboratory, Federal University of Paraná, Curitiba 81520-260, Brazil
| | - Alexander J Lazar
- Departments of Pathology & Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Bradley M Broom
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - John N Weinstein
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
- Department of Systems Biology, University of Texas MD Anderson Cancer Center, Houston, TX 77030
| | - Rehan Akbani
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Shwetha V Kumar
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Benjamin J Raphael
- Department of Computer Science, Princeton University, 35 Olden Street, Princeton, NJ 08540
| | - Christopher K Wong
- Biomolecular Engineering Department, School of Engineering, University of California, Santa Cruz, Santa Cruz, CA 95064, USA
| | - Joshua M Stuart
- Biomolecular Engineering Department, School of Engineering, University of California, Santa Cruz, Santa Cruz, CA 95064, USA
| | - Rojin Safavi
- Biomolecular Engineering Department, School of Engineering, University of California, Santa Cruz, Santa Cruz, CA 95064, USA
| | | | - Benjamin K Johnson
- Center for Epigenetics, Van Andel Institute, Grand Rapids, MI 49503, USA
| | - Cindy Kyi
- Center for Cancer Genomics, National Cancer Institute, Bethesda, MD 20892, USA
| | - Hui Shen
- Center for Epigenetics, Van Andel Institute, Grand Rapids, MI 49503, USA
| | - M Ryan Corces
- Department of Dermatology, Stanford University School of Medicine, Stanford, CA, USA
- Gladstone Institute of Neurological Disease, Gladstone Institutes, San Francisco, CA, USA
- Gladstone Institute of Data Science and Biotechnology, Gladstone Institutes, San Francisco, CA, USA
- Department of Neurology, University of California San Francisco, San Francisco, CA, USA
| | - Howard Y Chang
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA
- Department of Dermatology, Stanford University School of Medicine, Stanford, CA, USA
- Center for Personal Dynamic Regulomes, Stanford University, Stanford, CA 94305, USA
- Howard Hughes Medical Institute, Stanford University, School of Medicine, Stanford, CA, USA
| | - William J Greenleaf
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA
- Center for Personal Dynamic Regulomes, Stanford University, Stanford, CA 94305, USA
- Department of Applied Physics, Stanford University, Stanford, CA, USA
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4
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Li J, Liu W, Mojumdar K, Kim H, Zhou Z, Ju Z, Kumar SV, Ng PKS, Chen H, Davies MA, Lu Y, Akbani R, Mills GB, Liang H. A protein expression atlas on tissue samples and cell lines from cancer patients provides insights into tumor heterogeneity and dependencies. NATURE CANCER 2024:10.1038/s43018-024-00817-x. [PMID: 39227745 DOI: 10.1038/s43018-024-00817-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/04/2023] [Accepted: 08/05/2024] [Indexed: 09/05/2024]
Abstract
The Cancer Genome Atlas (TCGA) and the Cancer Cell Line Encyclopedia (CCLE) are foundational resources in cancer research, providing extensive molecular and phenotypic data. However, large-scale proteomic data across various cancer types for these cohorts remain limited. Here, we expand upon our previous work to generate high-quality protein expression data for approximately 8,000 TCGA patient samples and around 900 CCLE cell line samples, covering 447 clinically relevant proteins, using reverse-phase protein arrays. These protein expression profiles offer profound insights into intertumor heterogeneity and cancer dependency and serve as sensitive functional readouts for somatic alterations. We develop a systematic protein-centered strategy for identifying synthetic lethality pairs and experimentally validate an interaction between protein kinase A subunit α and epidermal growth factor receptor. We also identify metastasis-related protein markers with clinical relevance. This dataset represents a valuable resource for advancing our understanding of cancer mechanisms, discovering protein biomarkers and developing innovative therapeutic strategies.
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Affiliation(s)
- Jun Li
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Wei Liu
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Kamalika Mojumdar
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Hong Kim
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Zhicheng Zhou
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Zhenlin Ju
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Shwetha V Kumar
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Patrick Kwok-Shing Ng
- Institute for Personalized Cancer Therapy, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, USA
- Department of Pediatrics, University of Connecticut Health Center, Farmington, CT, USA
| | - Han Chen
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Michael A Davies
- Department of Melanoma Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Yiling Lu
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Rehan Akbani
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA.
| | - Gordon B Mills
- Knight Cancer Institute and Cell, Developmental and Cancer Biology, Oregon Health and Science University, Portland, OR, USA.
| | - Han Liang
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA.
- Department of Systems Biology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA.
- Institute for Data Science in Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA.
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5
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Wu CC, Huang L, Zhang Z, Ju Z, Song X, Kolb EA, Zhang W, Gill J, Ha M, Smith MA, Houghton P, Morton CL, Kurmasheva R, Maris J, Mosse Y, Lu Y, Gorlick R, Futreal PA, Beird HC. Whole genome and reverse protein phase array landscapes of patient derived osteosarcoma xenograft models. Sci Rep 2024; 14:19891. [PMID: 39191826 PMCID: PMC11350124 DOI: 10.1038/s41598-024-69382-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2023] [Accepted: 08/05/2024] [Indexed: 08/29/2024] Open
Abstract
Osteosarcoma is the most common primary bone malignancy in children and young adults, and it has few treatment options. As a result, there has been little improvement in survival outcomes in the past few decades. The need for models to test novel therapies is especially great in this disease since it is both rare and does not respond to most therapies. To address this, an NCI-funded consortium has characterized and utilized a panel of patient-derived xenograft models of osteosarcoma for drug testing. The exomes, transcriptomes, and copy number landscapes of these models have been presented previously. This study now adds whole genome sequencing and reverse-phase protein array profiling data, which can be correlated with drug testing results. In addition, four additional osteosarcoma models are described for use in the research community.
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Affiliation(s)
- Chia-Chin Wu
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Licai Huang
- Department of Biostatistics, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Zhongting Zhang
- Pediatric Division, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Zhenlin Ju
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Xingzhi Song
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - E Anders Kolb
- Nemours Center for Cancer and Blood Disorders, Alfred I. DuPont Hospital for Children, Wilmington, DE, USA
| | - Wendong Zhang
- Pediatric Division, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Jonathan Gill
- Pediatric Division, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Min Ha
- Department of Biostatistics, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
- Department of Health Informatics and Biostatistics, Yonsei University, Seoul, Korea
| | - Malcolm A Smith
- Cancer Therapy Evaluation Program, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Peter Houghton
- Department of Molecular Medicine, University of Texas Health Science Center at San Antonio, San Antonio, TX, USA
| | | | | | - John Maris
- Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Yael Mosse
- Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Yiling Lu
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Richard Gorlick
- Pediatric Division, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - P Andrew Futreal
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Hannah C Beird
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, USA.
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6
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Tian Y, Liu X, Wang J, Zhang C, Yang W. Antitumor Effects and the Potential Mechanism of 10-HDA against SU-DHL-2 Cells. Pharmaceuticals (Basel) 2024; 17:1088. [PMID: 39204193 PMCID: PMC11357620 DOI: 10.3390/ph17081088] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2024] [Revised: 08/13/2024] [Accepted: 08/16/2024] [Indexed: 09/03/2024] Open
Abstract
10-hydroxy-2-decenoic acid (10-HDA), which is a unique bioactive fatty acid of royal jelly synthesized by nurse bees for larvae and adult queen bees, is recognized for its dual utility in medicinal and nutritional applications. Previous research has indicated that 10-HDA exerts antitumor effects on numerous tumor cell lines, including colon cancer cells, A549 human lung cancer cells, and human hepatoma cells. The present study extends this inquiry to lymphoma, specifically evaluating the impact of 10-HDA on the SU-DHL-2 cell line. Our findings revealed dose-dependent suppression of SU-DHL-2 cell survival, with an IC50 of 496.8 μg/mL at a density of 3 × 106 cells/well after 24 h. For normal liver LO2 cells and human fibroblasts (HSFs), the IC50 values were approximately 1000 μg/mL and over 1000 μg/mL, respectively. The results of label-free proteomics revealed 147 upregulated and 347 downregulated differentially expressed proteins that were significantly enriched in the complement and coagulation cascades pathway (adjusted p-value = 0.012), including the differentially expressed proteins prothrombin, plasminogen, plasminogen, carboxypeptidase B2, fibrinogen beta chain, fibrinogen gamma chain, and coagulation factor V. The top three hub proteins, ribosomal protein L5, tumor protein p53, and ribosomal protein L24, were identified via protein-protein interaction (PPI) analysis. This result showed that the complement and coagulation cascade pathways might play a key role in the antitumor process of 10-HDA, suggesting a potential therapeutic avenue for lymphoma treatment. However, the specificity of the effect of 10-HDA on SU-DHL-2 cells warrants further investigation.
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Affiliation(s)
- Yuanyuan Tian
- College of Bee Science and Biomedicine, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (Y.T.); (X.L.); (J.W.); (C.Z.)
- College of JunCao Science and Ecology (College of Carbon Neutrality), Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Xiaoqing Liu
- College of Bee Science and Biomedicine, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (Y.T.); (X.L.); (J.W.); (C.Z.)
| | - Jie Wang
- College of Bee Science and Biomedicine, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (Y.T.); (X.L.); (J.W.); (C.Z.)
| | - Chuang Zhang
- College of Bee Science and Biomedicine, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (Y.T.); (X.L.); (J.W.); (C.Z.)
| | - Wenchao Yang
- College of Bee Science and Biomedicine, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (Y.T.); (X.L.); (J.W.); (C.Z.)
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7
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Şenbabaoğlu Y, Prabhakar V, Khormali A, Eastham J, Liu E, Warner E, Nabet B, Srivastava M, Ballinger M, Liu K. MOSBY enables multi-omic inference and spatial biomarker discovery from whole slide images. Sci Rep 2024; 14:18271. [PMID: 39107505 PMCID: PMC11303705 DOI: 10.1038/s41598-024-69198-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2024] [Accepted: 08/01/2024] [Indexed: 08/10/2024] Open
Abstract
The utility of deep neural nets has been demonstrated for mapping hematoxylin-and-eosin (H&E) stained image features to expression of individual genes. However, these models have not been employed to discover clinically relevant spatial biomarkers. Here we develop MOSBY (Multi-Omic translation of whole slide images for Spatial Biomarker discoverY) that leverages contrastive self-supervised pretraining to extract improved H&E whole slide images features, learns a mapping between image and bulk omic profiles (RNA, DNA, and protein), and utilizes tile-level information to discover spatial biomarkers. We validate MOSBY gene and gene set predictions with spatial transcriptomic and serially-sectioned CD8 IHC image data. We demonstrate that MOSBY-inferred colocalization features have survival-predictive power orthogonal to gene expression, and enable concordance indices highly competitive with survival-trained multimodal networks. We identify and validate (1) an ER stress-associated colocalization feature as a chemotherapy-specific risk factor in lung adenocarcinoma, and (2) the colocalization of T effector cell vs cysteine signatures as a negative prognostic factor in multiple cancer indications. The discovery of clinically relevant biologically interpretable spatial biomarkers showcases the utility of the model in unraveling novel insights in cancer biology as well as informing clinical decision-making.
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Affiliation(s)
| | | | | | - Jeff Eastham
- Genentech, Inc., South San Francisco, CA, 94080, USA
| | - Evan Liu
- Genentech, Inc., South San Francisco, CA, 94080, USA
| | - Elisa Warner
- Genentech, Inc., South San Francisco, CA, 94080, USA
| | - Barzin Nabet
- Genentech, Inc., South San Francisco, CA, 94080, USA
| | | | | | - Kai Liu
- Genentech, Inc., South San Francisco, CA, 94080, USA.
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8
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Zhang C, Zheng J, Liu J, Li Y, Xing G, Zhang S, Chen H, Wang J, Shao Z, Li Y, Jiang Z, Pan Y, Liu X, Xu P, Wu W. Pan-cancer analyses reveal the molecular and clinical characteristics of TET family members and suggests that TET3 maybe a potential therapeutic target. Front Pharmacol 2024; 15:1418456. [PMID: 39104395 PMCID: PMC11298443 DOI: 10.3389/fphar.2024.1418456] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2024] [Accepted: 05/28/2024] [Indexed: 08/07/2024] Open
Abstract
The Ten-Eleven Translocation (TET) family genes are implicated in a wide array of biological functions across various human cancers. Nonetheless, there is a scarcity of studies that comprehensively analyze the correlation between TET family members and the molecular phenotypes and clinical characteristics of different cancers. Leveraging updated public databases and employing several bioinformatics analysis methods, we assessed the expression levels, somatic variations, methylation levels, and prognostic values of TET family genes. Additionally, we explored the association between the expression of TET family genes and pathway activity, tumor microenvironment (TME), stemness score, immune subtype, clinical staging, and drug sensitivity in pan-cancer. Molecular biology and cytology experiments were conducted to validate the potential role of TET3 in tumor progression. Each TET family gene displayed distinct expression patterns across at least ten detected tumors. The frequency of Single Nucleotide Variant (SNV) in TET genes was found to be 91.24%, primarily comprising missense mutation types, with the main types of copy number variant (CNV) being heterozygous amplifications and deletions. TET1 gene exhibited high methylation levels, whereas TET2 and TET3 genes displayed hypomethylation in most cancers, which correlated closely with patient prognosis. Pathway activity analysis revealed the involvement of TET family genes in multiple signaling pathways, including cell cycle, apoptosis, DNA damage response, hormone AR, PI3K/AKT, and RTK. Furthermore, the expression levels of TET family genes were shown to impact the clinical staging of tumor patients, modulate the sensitivity of chemotherapy drugs, and thereby influence patient prognosis by participating in the regulation of the tumor microenvironment, cellular stemness potential, and immune subtype. Notably, TET3 was identified to promote cancer progression across various tumors, and its silencing was found to inhibit tumor malignancy and enhance chemotherapy sensitivity. These findings shed light on the role of TET family genes in cancer progression and offer insights for further research on TET3 as a potential therapeutic target for pan-cancer.
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Affiliation(s)
- Chunyan Zhang
- Department of General Surgery, Tianjin Fifth Central Hospital, Tianjin, China
- Tianjin Key Laboratory of Epigenetics for Organ Development of Premature Infants, Tianjin Fifth Central Hospital, Tianjin, China
- High Altitude Characteristic Medical Research Institute, Huangnan Tibetan Autonomous Prefecture People’s Hospital, Huangnan Prefecture, Qinghai, China
| | - Jie Zheng
- Department of Pathology, Tianjin Fifth Central Hospital, Tianjin, China
| | - Jin Liu
- North China University of Science and Technology, Tangshan, Hebei, China
| | - Yanxia Li
- Tianjin Key Laboratory of Epigenetics for Organ Development of Premature Infants, Tianjin Fifth Central Hospital, Tianjin, China
- High Altitude Characteristic Medical Research Institute, Huangnan Tibetan Autonomous Prefecture People’s Hospital, Huangnan Prefecture, Qinghai, China
| | - Guoqiang Xing
- Department of General Surgery, Tianjin Fifth Central Hospital, Tianjin, China
| | - Shupeng Zhang
- Department of General Surgery, Tianjin Fifth Central Hospital, Tianjin, China
| | - Hekai Chen
- Department of General Surgery, Tianjin Fifth Central Hospital, Tianjin, China
| | - Jian Wang
- Department of General Surgery, Tianjin Fifth Central Hospital, Tianjin, China
| | - Zhijiang Shao
- Department of General Surgery, Tianjin Fifth Central Hospital, Tianjin, China
- High Altitude Characteristic Medical Research Institute, Huangnan Tibetan Autonomous Prefecture People’s Hospital, Huangnan Prefecture, Qinghai, China
| | - Yongyuan Li
- Department of General Surgery, Tianjin Fifth Central Hospital, Tianjin, China
- High Altitude Characteristic Medical Research Institute, Huangnan Tibetan Autonomous Prefecture People’s Hospital, Huangnan Prefecture, Qinghai, China
| | - Zhongmin Jiang
- Department of Pathology, Tianjin Fifth Central Hospital, Tianjin, China
| | - Yingzi Pan
- Department of Ophthalmology, Peking University First Hospital, Beijing, China
| | - Xiaozhi Liu
- Tianjin Key Laboratory of Epigenetics for Organ Development of Premature Infants, Tianjin Fifth Central Hospital, Tianjin, China
- High Altitude Characteristic Medical Research Institute, Huangnan Tibetan Autonomous Prefecture People’s Hospital, Huangnan Prefecture, Qinghai, China
| | - Ping Xu
- High Altitude Characteristic Medical Research Institute, Huangnan Tibetan Autonomous Prefecture People’s Hospital, Huangnan Prefecture, Qinghai, China
- Department of Pharmacy, Tianjin Fifth Central Hospital, Tianjin, China
| | - Wenhan Wu
- Department of General Surgery, Tianjin Fifth Central Hospital, Tianjin, China
- Tianjin Key Laboratory of Epigenetics for Organ Development of Premature Infants, Tianjin Fifth Central Hospital, Tianjin, China
- High Altitude Characteristic Medical Research Institute, Huangnan Tibetan Autonomous Prefecture People’s Hospital, Huangnan Prefecture, Qinghai, China
- Department of General Surgery, Peking University First Hospital, Beijing, China
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9
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Yu K, Tian Q, Feng S, Zhang Y, Cheng Z, Li M, Zhu H, He J, Li M, Xiong X. Integration analysis of cell division cycle-associated family genes revealed potential mechanisms of gliomagenesis and constructed an artificial intelligence-driven prognostic signature. Cell Signal 2024; 119:111168. [PMID: 38599441 DOI: 10.1016/j.cellsig.2024.111168] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2024] [Revised: 03/26/2024] [Accepted: 04/07/2024] [Indexed: 04/12/2024]
Abstract
Cell division cycle-associated (CDCA) gene family members are essential cell proliferation regulators and play critical roles in various cancers. However, the function of the CDCA family genes in gliomas remains unclear. This study aims to elucidate the role of CDCA family members in gliomas using in vitro and in vivo experiments and bioinformatic analyses. We included eight glioma cohorts in this study. An unsupervised clustering algorithm was used to identify novel CDCA gene family clusters. Then, we utilized multi-omics data to elucidate the prognostic disparities, biological functionalities, genomic alterations, and immune microenvironment among glioma patients. Subsequently, the scRNA-seq analysis and spatial transcriptomic sequencing analysis were carried out to explore the expression distribution of CDCA2 in glioma samples. In vivo and in vitro experiments were used to investigate the effects of CDCA2 on the viability, migration, and invasion of glioma cells. Finally, based on ten machine-learning algorithms, we constructed an artificial intelligence-driven CDCA gene family signature called the machine learning-based CDCA gene family score (MLCS). Our results suggested that patients with the higher expression levels of CDCA family genes had a worse prognosis, more activated RAS signaling pathways, and more activated immunosuppressive microenvironments. CDCA2 knockdown inhibited the proliferation, migration, and invasion of glioma cells. In addition, the MLCS had robust and favorable prognostic predictive ability and could predict the response to immunotherapy and chemotherapy drug sensitivity.
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Affiliation(s)
- Kai Yu
- Department of Neurosurgery, Renmin Hospital of Wuhan University, Wuhan 430060, Hubei Province, China
| | - Qi Tian
- Department of Neurosurgery, Renmin Hospital of Wuhan University, Wuhan 430060, Hubei Province, China
| | - Shi Feng
- Department of Neurosurgery, Renmin Hospital of Wuhan University, Wuhan 430060, Hubei Province, China
| | - Yonggang Zhang
- Department of Neurosurgery, Renmin Hospital of Wuhan University, Wuhan 430060, Hubei Province, China
| | - Ziqi Cheng
- Department of Neurosurgery, Renmin Hospital of Wuhan University, Wuhan 430060, Hubei Province, China
| | - Mingyang Li
- Department of Neurosurgery, Renmin Hospital of Wuhan University, Wuhan 430060, Hubei Province, China
| | - Hua Zhu
- Department of Neurosurgery, Renmin Hospital of Wuhan University, Wuhan 430060, Hubei Province, China
| | - Jianying He
- Department of Orthopedics, The First Affiliated Hospital of Nanchang Medical College, Nanchang 330006, Jiangxi Province, China
| | - Mingchang Li
- Department of Neurosurgery, Renmin Hospital of Wuhan University, Wuhan 430060, Hubei Province, China.
| | - Xiaoxing Xiong
- Department of Neurosurgery, Renmin Hospital of Wuhan University, Wuhan 430060, Hubei Province, China.
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10
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Sharma A, Debik J, Naume B, Ohnstad HO, Bathen TF, Giskeødegård GF. Comprehensive multi-omics analysis of breast cancer reveals distinct long-term prognostic subtypes. Oncogenesis 2024; 13:22. [PMID: 38871719 DOI: 10.1038/s41389-024-00521-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2024] [Revised: 05/20/2024] [Accepted: 05/22/2024] [Indexed: 06/15/2024] Open
Abstract
Breast cancer (BC) is a leading cause of cancer-related death worldwide. The diverse nature and heterogeneous biology of BC pose challenges for survival prediction, as patients with similar diagnoses often respond differently to treatment. Clinically relevant BC intrinsic subtypes have been established through gene expression profiling and are implemented in the clinic. While these intrinsic subtypes show a significant association with clinical outcomes, their long-term survival prediction beyond 5 years often deviates from expected clinical outcomes. This study aimed to identify naturally occurring long-term prognostic subgroups of BC based on an integrated multi-omics analysis. This study incorporates a clinical cohort of 335 untreated BC patients from the Oslo2 study with long-term follow-up (>12 years). Multi-Omics Factor Analysis (MOFA+) was employed to integrate transcriptomic, proteomic, and metabolomic data obtained from the tumor tissues. Our analysis revealed three prominent multi-omics clusters of BC patients with significantly different long-term prognoses (p = 0.005). The multi-omics clusters were validated in two independent large cohorts, METABRIC and TCGA. Importantly, a lack of prognostic association to long-term follow-up above 12 years in the previously established intrinsic subtypes was shown for these cohorts. Through a systems-biology approach, we identified varying enrichment levels of cell-cycle and immune-related pathways among the prognostic clusters. Integrated multi-omics analysis of BC revealed three distinct clusters with unique clinical and biological characteristics. Notably, these multi-omics clusters displayed robust associations with long-term survival, outperforming the established intrinsic subtypes.
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Affiliation(s)
- Abhibhav Sharma
- Department of Public Health and Nursing (ISM), Norwegian University of Science and Technology- NTNU, Trondheim, Norway.
| | - Julia Debik
- Department of Public Health and Nursing (ISM), Norwegian University of Science and Technology- NTNU, Trondheim, Norway
- Department of Circulation and Medical Imaging, NTNU, Trondheim, Norway
| | - Bjørn Naume
- Department of Oncology, Division of Cancer Medicine, Oslo University Hospital, Oslo, Norway
- Institute of Clinical Medicine, University of Oslo, Oslo, Norway
| | - Hege Oma Ohnstad
- Department of Oncology, Division of Cancer Medicine, Oslo University Hospital, Oslo, Norway
| | - Tone F Bathen
- Department of Circulation and Medical Imaging, NTNU, Trondheim, Norway
| | - Guro F Giskeødegård
- Department of Public Health and Nursing (ISM), Norwegian University of Science and Technology- NTNU, Trondheim, Norway.
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11
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He Y, Hu Y, Cheng Y, Li X, Chen C, Zhang S, He H, Cao F. Multi-Omics Insights into Disulfidptosis-Related Genes Reveal RPN1 as a Therapeutic Target for Liver Cancer. Biomolecules 2024; 14:677. [PMID: 38927080 PMCID: PMC11201601 DOI: 10.3390/biom14060677] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2024] [Revised: 05/21/2024] [Accepted: 05/22/2024] [Indexed: 06/28/2024] Open
Abstract
Disulfidptosis, a newly identified mode of programmed cell death, is yet to be comprehensively elucidated with respect to its multi-omics characteristics in tumors, specific pathogenic mechanisms, and antitumor functions in liver cancer. This study included 10,327 tumor and normal tissue samples from 33 cancer types. In-depth analyses using various bioinformatics tools revealed widespread dysregulation of disulfidptosis-related genes (DRGs) in pan-cancer and significant associations with prognosis, genetic variations, tumor stemness, methylation levels, and drug sensitivity. Univariate and multivariate Cox regression and LASSO regression were used to screen and construct prognosis-related hub DRGs and predictive models in the context of liver cancer. Subsequently, single cell analysis was conducted to investigate the subcellular localization of RPN1, a hub DRG, in various solid tumors. Western blotting was performed to validate the expression of RPN1 at both cellular and tissue levels. Additionally, functional experiments, including CCK8, EdU, clone, and transwell assays, indicated that RPN1 knockdown promoted the proliferative and invasive capacities of liver cancer cells. Therefore, this study elucidated the multi-omics characteristics of DRGs in pan-cancer and established a prognostic model for liver cancer. Additionally, this study revealed the molecular functions of RPN1 in liver cancer, suggesting its potential as a therapeutic target for this disease.
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Affiliation(s)
- Yan He
- Vascular Surgery, Department of General Surgery, The First Hospital of Anhui Medical University, Hefei 230001, China
| | - Yue Hu
- Pathology Department, Hefei Cancer Hospital, Chinese Academy of Sciences (CAS), Hefei 230000, China;
| | - Yunsheng Cheng
- Department of General Surgery, The Second Affiliated Hospital of Anhui Medical University, Hefei 230000, China
| | - Xutong Li
- Department of Infectious Diseases, The First Hospital of Anhui Medical University, Hefei 230001, China
| | - Chuanhong Chen
- Vascular Surgery, Department of General Surgery, The First Hospital of Anhui Medical University, Hefei 230001, China
| | - Shijie Zhang
- Department of General Surgery, The Fuyang Hospital of Anhui Medical University, Fuyang 236000, China;
| | - Huihu He
- Department of General Surgery, The Fuyang Hospital of Anhui Medical University, Fuyang 236000, China;
| | - Feng Cao
- Vascular Surgery, Department of General Surgery, The First Hospital of Anhui Medical University, Hefei 230001, China
- Medical Faculty, University Hospital RWTH Aachen, 52074 Aachen, Germany
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12
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Mofunanya A, Cameron ER, Braun CJ, Celeste F, Zhao X, Hemann MT, Scott KL, Li J, Powers S. Simultaneous screening of overexpressed genes in breast cancer for oncogenic drivers and tumor dependencies. Sci Rep 2024; 14:13227. [PMID: 38851782 PMCID: PMC11162420 DOI: 10.1038/s41598-024-64297-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2024] [Accepted: 06/06/2024] [Indexed: 06/10/2024] Open
Abstract
There are hundreds of genes typically overexpressed in breast cancer cells and it's often assumed that their overexpression contributes to cancer progression. However, the precise proportion of these overexpressed genes contributing to tumorigenicity remains unclear. To address this gap, we undertook a comprehensive screening of a diverse set of seventy-two genes overexpressed in breast cancer. This systematic screening evaluated their potential for inducing malignant transformation and, concurrently, assessed their impact on breast cancer cell proliferation and viability. Select genes including ALDH3B1, CEACAM5, IL8, PYGO2, and WWTR1, exhibited pronounced activity in promoting tumor formation and establishing gene dependencies critical for tumorigenicity. Subsequent investigations revealed that CEACAM5 overexpression triggered the activation of signaling pathways involving β-catenin, Cdk4, and mTOR. Additionally, it conferred a growth advantage independent of exogenous insulin in defined medium and facilitated spheroid expansion by inducing multiple layers of epithelial cells while preserving a hollow lumen. Furthermore, the silencing of CEACAM5 expression synergized with tamoxifen-induced growth inhibition in breast cancer cells. These findings underscore the potential of screening overexpressed genes for both oncogenic drivers and tumor dependencies to expand the repertoire of therapeutic targets for breast cancer treatment.
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Affiliation(s)
- Adaobi Mofunanya
- Department of Pathology, Stony Brook Cancer Center, Stony Brook, NY, 11794, USA
| | - Eleanor R Cameron
- Koch Institute for Integrative Cancer Research and Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
| | - Christian J Braun
- Koch Institute for Integrative Cancer Research and Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
| | - Frank Celeste
- Department of Pathology, Stony Brook Cancer Center, Stony Brook, NY, 11794, USA
- Graduate Program in Genetics, Stony Brook University, Stony Brook, NY, 11794, USA
| | - Xiaoyu Zhao
- Department of Pathology, Stony Brook Cancer Center, Stony Brook, NY, 11794, USA
- Graduate Program in Molecular and Cellular Biology, Stony Brook University, Stony Brook, NY, 11794, USA
| | - Michael T Hemann
- Koch Institute for Integrative Cancer Research and Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
| | - Kenneth L Scott
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Jinyu Li
- Department of Pathology, Stony Brook Cancer Center, Stony Brook, NY, 11794, USA
| | - Scott Powers
- Department of Pathology, Stony Brook Cancer Center, Stony Brook, NY, 11794, USA.
- Graduate Program in Genetics, Stony Brook University, Stony Brook, NY, 11794, USA.
- Graduate Program in Molecular and Cellular Biology, Stony Brook University, Stony Brook, NY, 11794, USA.
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13
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Jacobson JC, Qiao J, Cochran ED, McCreery S, Chung DH. Migration, invasion, and metastasis are mediated by P-Rex1 in neuroblastoma. Front Oncol 2024; 14:1336031. [PMID: 38884093 PMCID: PMC11176429 DOI: 10.3389/fonc.2024.1336031] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2023] [Accepted: 05/08/2024] [Indexed: 06/18/2024] Open
Abstract
Neuroblastoma accounts for approximately 15% of pediatric cancer-related deaths despite intensive multimodal therapy. This is due, in part, to high rates of metastatic disease at diagnosis and disease relapse. A better understanding of tumor biology of aggressive, pro-metastatic phenotypes is necessary to develop novel, more effective therapeutics against neuroblastoma. Phosphatidylinositol 3,4,5-trisphosphate-dependent Rac exchanger 1 (P-Rex1) has been found to stimulate migration, invasion, and metastasis in several adult malignancies. However, its role in neuroblastoma is currently unknown. In the present study, we found that P-Rex1 is upregulated in pro-metastatic murine models of neuroblastoma, as well as human neuroblastoma metastases. Correspondingly, silencing of P-Rex1 was associated with decreased migration and invasion in vitro. This was associated with decreased AKT-mTOR and ERK2 activity, dysregulation of Rac, and diminished secretion of matrix metalloproteinases. Furthermore, increased P-Rex1 expression was associated with inferior relapse-free and overall survival via tissue microarray and Kaplan-Meier survival analysis of a publicly available clinical database. Together, these findings suggest that P-Rex1 may be a novel therapeutic target and potential prognostic factor in neuroblastoma.
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Affiliation(s)
- Jillian C Jacobson
- Division of Pediatric Surgery, Department of Surgery, University of Texas Southwestern Medical Center and Children's Health, Dallas, TX, United States
| | - Jingbo Qiao
- Division of Pediatric Surgery, Department of Surgery, University of Texas Southwestern Medical Center and Children's Health, Dallas, TX, United States
| | - Elizabeth D Cochran
- Division of Pediatric Surgery, Department of Surgery, University of Texas Southwestern Medical Center and Children's Health, Dallas, TX, United States
| | - Sullivan McCreery
- Division of Pediatric Surgery, Department of Surgery, University of Texas Southwestern Medical Center and Children's Health, Dallas, TX, United States
| | - Dai H Chung
- Division of Pediatric Surgery, Department of Surgery, University of Texas Southwestern Medical Center and Children's Health, Dallas, TX, United States
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14
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Yu X, Li W, Sun S, Li J. DDIT3 is associated with breast cancer prognosis and immune microenvironment: an integrative bioinformatic and immunohistochemical analysis. J Cancer 2024; 15:3873-3889. [PMID: 38911383 PMCID: PMC11190778 DOI: 10.7150/jca.96491] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2024] [Accepted: 05/12/2024] [Indexed: 06/25/2024] Open
Abstract
DNA damage-inducible transcript 3 (DDIT3) is a transcription factor central to apoptosis, differentiation, and stress response. DDIT3 has been extensively studied in cancer biology. However, its precise implications in breast cancer progression and its interaction with the immune microenvironment are unclear. In this study, we utilized a novel multi-omics integration strategy, combining bulk RNA sequencing, single-cell sequencing, spatial transcriptomics and immunohistochemistry, to explore the role of DDIT3 in breast cancer and establish the correlation between DDIT3 and poor prognosis in breast cancer patients. We identified a robust prognostic signature, including six genes (unc-93 homolog B1, TLR signaling regulator, anti-Mullerian hormone, DCTP pyrophosphatase 1, mitochondrial ribosomal protein L36, nuclear factor erythroid 2, and Rho GTPase activating protein 39), associated with DDIT3. This signature stratified the high-risk patient groups, characterized by increased infiltration of the regulatory T cells and M2-like macrophages and fibroblast growth factor (FGF)/FGF receptor signaling activation. Notably, the high-risk patient group demonstrated enhanced sensitivity to immunotherapy, presenting novel therapeutic opportunities. Integrating multi-omics data helped determine the spatial expression pattern of DDIT3 in the tumor microenvironment and its correlation with immune cell infiltration. This multi-dimensional analysis provided a comprehensive understanding of the intricate interplay between DDIT3 and the immune microenvironment in breast cancer. Overall, our study not only facilitates understanding the role of DDIT3 in breast cancer but also offers innovative insights for developing prognostic models and therapeutic strategies. Identifying the DDIT3-related prognostic signature and its association with the immune microenvironment provided a promising avenue for personalized breast cancer treatment.
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Affiliation(s)
- Xin Yu
- Department of Breast and Thyroid Surgery, Renmin Hospital of Wuhan University, Wuhan, Hubei, P. R. China
| | - Wenge Li
- Department of Oncology, Shanghai GoBroad Cancer Hospital, Shanghai, P. R. China
| | - Shengrong Sun
- Department of Breast and Thyroid Surgery, Renmin Hospital of Wuhan University, Wuhan, Hubei, P. R. China
| | - Juanjuan Li
- Department of Breast and Thyroid Surgery, Renmin Hospital of Wuhan University, Wuhan, Hubei, P. R. China
- Department of general surgery, Taikang Tongji (Wuhan) Hospital, Wuhan, Hubei, P. R. China
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15
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Yan B, Liao P, Liu S, Lei P. Comprehensive pan-cancer analysis of inflammatory age-clock-related genes as prognostic and immunity markers based on multi-omics data. Sci Rep 2024; 14:10468. [PMID: 38714870 PMCID: PMC11076581 DOI: 10.1038/s41598-024-61381-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2024] [Accepted: 05/06/2024] [Indexed: 05/12/2024] Open
Abstract
Inflammatory age (iAge) is a vital concept for understanding the intricate interplay between chronic inflammation and aging in the context of cancer. However, the importance of iAge-clock-related genes (iAge-CRGs) across cancers remains unexplored. This study aimed to explore the mechanisms and applications of these genes across diverse cancer types. We analyzed profiling data from over 10,000 individuals, covering 33 cancer types, 750 small molecule drugs, and 24 immune cell types. We focused on DCBLD2's function at the single-cell level and computed an iAge-CRG score using GSVA. This score was correlated with cancer pathways, immune infiltration, and survival. A signature was then derived using univariate Cox and LASSO regression, followed by ROC curve analysis, nomogram construction, decision curve analysis, and immunocytochemistry. Our comprehensive analysis revealed epigenetic, genomic, and immunogenomic alterations in iAge-CRGs, especially DCBLD2, leading to abnormal expression. Aberrant DCBLD2 expression strongly correlated with cancer-associated fibroblast infiltration and prognosis in multiple cancers. Based on GSVA results, we developed a risk model using five iAge-CRGs, which proved to be an independent prognostic index for uveal melanoma (UVM) patients. We also systematically evaluated the correlation between the iAge-related signature risk score and immune cell infiltration. iAge-CRGs, particularly DCBLD2, emerge as potential targets for enhancing immunotherapy outcomes. The strong correlation between abnormal DCBLD2 expression, cancer-associated fibroblast infiltration, and patient survival across various cancers underscores their significance. Our five-gene risk signature offers an independent prognostic tool for UVM patients, highlighting the crucial role of these genes in suppressing the immune response in UVM.Kindly check and confirm whether the corresponding affiliation is correctly identified.I identified the affiliation is correctly.thank you.Per style, a structured abstract is not allowed so we have changed the structured abstract to an unstructured abstract. Please check and confirm.I confirm the abstract is correctly ,thank you.
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Affiliation(s)
- Bo Yan
- Haihe Laboratory of Cell Ecosystem, Department of Geriatrics, Tianjin Medical University General Hospital, 154 Anshan Road, Heping District, Tianjin, 300052, China
- Tianjin Geriatrics Institute, Tianjin Medical University General Hospital, 154 Anshan Road, Heping District, Tianjin, 300052, China
| | - Pan Liao
- Tianjin Geriatrics Institute, Tianjin Medical University General Hospital, 154 Anshan Road, Heping District, Tianjin, 300052, China
- The School of Medicine, Nankai University, 94 Weijin Road, Tianjin, 300071, China
| | - Shan Liu
- Haihe Laboratory of Cell Ecosystem, Department of Geriatrics, Tianjin Medical University General Hospital, 154 Anshan Road, Heping District, Tianjin, 300052, China
- Tianjin Geriatrics Institute, Tianjin Medical University General Hospital, 154 Anshan Road, Heping District, Tianjin, 300052, China
| | - Ping Lei
- Haihe Laboratory of Cell Ecosystem, Department of Geriatrics, Tianjin Medical University General Hospital, 154 Anshan Road, Heping District, Tianjin, 300052, China.
- Tianjin Geriatrics Institute, Tianjin Medical University General Hospital, 154 Anshan Road, Heping District, Tianjin, 300052, China.
- The School of Medicine, Nankai University, 94 Weijin Road, Tianjin, 300071, China.
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16
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Zhao G, Wang Y, Zhou J, Ma P, Wang S, Li N. Pan-cancer analysis of polo-like kinase family genes reveals polo-like kinase 1 as a novel oncogene in kidney renal papillary cell carcinoma. Heliyon 2024; 10:e29373. [PMID: 38644836 PMCID: PMC11033160 DOI: 10.1016/j.heliyon.2024.e29373] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2023] [Revised: 04/02/2024] [Accepted: 04/07/2024] [Indexed: 04/23/2024] Open
Abstract
Background Polo-like kinases (PLKs) are a kinase class of serine/threonine with five members that play crucial roles in cell cycle regulation. However, their biological functions, regulation, and expression remain unclear. This study revealed the molecular properties, oncogenic role, and clinical significance of PLK genes in pan-cancers, particularly in kidney renal papillary cell carcinoma (KIRP). Methods We evaluated the mutation landscape, expression level, and prognostic values of PLK genes using bioinformatics analyses and explored the association between the expression level of PLK genes and tumor microenvironment (TME), immune subtype, cancer immunotherapy, tumor stemness, and drug sensitivity. Finally, we verified the prognostic value in patients with KIRP through univariate and multivariate analyses and nomogram construction. Results PLK genes are extensively altered in pan-cancer, which may contribute to tumorigenesis. These genes are aberrantly expressed in some types of cancer, with PLK1 being overexpressed in 31 cancers. PLK expression is closely associated with the prognosis of various cancers. The expression level of PLK genes is related with sensitivity to diverse drugs and cancer immunity as well as cancer immunotherapy. Importantly, we verified that PLK1 was overexpressed in KIRP tissues and could be an unfavorable prognostic biomarker in patients with KIRP. Hence, PLK1 may serve as an oncogenic gene in KIRP and should be explored in future studies. Conclusions Our study comprehensively reports the molecular characteristics and biological functions of PLK family gens across human cancers and recommends further investigation of these genes as potential biomarkers and therapeutic targets, especially in KIRP.
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Affiliation(s)
| | | | - Jiawei Zhou
- Clinical Trial Center, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100021, China
| | - Peiwen Ma
- Clinical Trial Center, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100021, China
| | - Shuhang Wang
- Clinical Trial Center, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100021, China
| | - Ning Li
- Clinical Trial Center, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100021, China
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17
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Bylicky MA, Shankavaram U, Aryankalayil MJ, Chopra S, Naz S, Sowers AL, Choudhuri R, Calvert V, Petricoin EF, Eke I, Mitchell JB, Coleman CN. Multiomic-Based Molecular Landscape of FaDu Xenograft Tumors in Mice after a Combinatorial Treatment with Radiation and an HSP90 Inhibitor Identifies Adaptation-Induced Targets of Resistance and Therapeutic Intervention. Mol Cancer Ther 2024; 23:577-588. [PMID: 38359816 PMCID: PMC10985469 DOI: 10.1158/1535-7163.mct-23-0796] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2023] [Revised: 01/10/2024] [Accepted: 02/09/2024] [Indexed: 02/17/2024]
Abstract
Treatments involving radiation and chemotherapy alone or in combination have improved patient survival and quality of life. However, cancers frequently evade these therapies due to adaptation and tumor evolution. Given the complexity of predicting response based solely on the initial genetic profile of a patient, a predetermined treatment course may miss critical adaptation that can cause resistance or induce new targets for drug and immunotherapy. To address the timescale for these evasive mechanisms, using a mouse xenograft tumor model, we investigated the rapidity of gene expression (mRNA), molecular pathway, and phosphoproteome changes after radiation, an HSP90 inhibitor, or combination. Animals received radiation, drug, or combination treatment for 1 or 2 weeks and were then euthanized along with a time-matched untreated group for comparison. Changes in gene expression occur as early as 1 week after treatment initiation. Apoptosis and cell death pathways were activated in irradiated tumor samples. For the HSP90 inhibitor and combination treatment at weeks 1 and 2 compared with Control Day 1, gene-expression changes induced inhibition of pathways including invasion of cells, vasculogenesis, and viral infection among others. The combination group included both drug-alone and radiation-alone changes. Our data demonstrate the rapidity of gene expression and functional pathway changes in the evolving tumor as it responds to treatment. Discovering these phenotypic adaptations may help elucidate the challenges in using sustained treatment regimens and could also define evolving targets for therapeutic efficacy.
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Affiliation(s)
- Michelle A. Bylicky
- Radiation Oncology Branch, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, Maryland
| | - Uma Shankavaram
- Radiation Oncology Branch, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, Maryland
| | - Molykutty J. Aryankalayil
- Radiation Oncology Branch, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, Maryland
| | - Sunita Chopra
- Radiation Oncology Branch, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, Maryland
| | - Sarwat Naz
- Radiation Biology Branch, National Cancer Institute, NIH, Bethesda, Maryland
| | - Anastasia L. Sowers
- Radiation Biology Branch, National Cancer Institute, NIH, Bethesda, Maryland
| | - Rajani Choudhuri
- Radiation Biology Branch, National Cancer Institute, NIH, Bethesda, Maryland
| | - Valerie Calvert
- Center for Applied Proteomics and Molecular Medicine, George Mason University, Manassas, Virginia
| | - Emanuel F. Petricoin
- Center for Applied Proteomics and Molecular Medicine, George Mason University, Manassas, Virginia
| | - Iris Eke
- Department of Radiation Oncology, Stanford University Medical School, Stanford, California
| | - James B. Mitchell
- Radiation Biology Branch, National Cancer Institute, NIH, Bethesda, Maryland
| | - C. Norman Coleman
- Radiation Oncology Branch, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, Maryland
- Radiation Research Program, National Cancer Institute, NIH, Rockville, Maryland
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18
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Yu X, Du Z, Zhu P, Liao B. Diagnostic, prognostic, and therapeutic potential of exosomal microRNAs in renal cancer. Pharmacol Rep 2024; 76:273-286. [PMID: 38388810 DOI: 10.1007/s43440-024-00568-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2023] [Revised: 01/22/2024] [Accepted: 01/23/2024] [Indexed: 02/24/2024]
Abstract
Renal cell carcinoma (RCC) arises from the tubular epithelial cells of the nephron. It has the highest mortality rate among urological cancers. There are no effective therapeutic approaches and no non-invasive biomarkers for diagnosis and follow-up. Thus, suitable novel biomarkers and therapeutic targets are essential for improving RCC diagnosis/prognosis and treatment. Circulating exosomes such as exosomal microRNAs (Exo-miRs) provide non-invasive prognostic/diagnostic biomarkers and valuable therapeutic targets, as they can be easily isolated and quantified and show high sensitivity and specificity. Exosomes secreted by an RCC can exhibit alterations in the miRs' profile that may reflect the cellular origin and (patho)physiological state, as a ''signature'' or ''fingerprint'' of the donor cell. It has been shown that the transportation of renal-specific miRs in exosomes can be rapidly detected and measured, holding great potential as biomarkers in RCC. The present review highlights the studies reporting tumor microenvironment-derived Exo-miRs with therapeutic potential as well as circulating Exo-miRs as potential diagnostic/prognostic biomarkers in patients with RCC.
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Affiliation(s)
- Xiaodong Yu
- Department of Urology, Affiliated Hospital of North Sichuan Medical College, Nanchong, 637000, China
| | - Zhongbo Du
- Department of Urology, Affiliated Hospital of North Sichuan Medical College, Nanchong, 637000, China
| | - Pingyu Zhu
- Department of Urology, Affiliated Hospital of North Sichuan Medical College, Nanchong, 637000, China
| | - Bo Liao
- Department of Urology, Affiliated Hospital of North Sichuan Medical College, Nanchong, 637000, China.
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19
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Hu Z, Wu Z, Liu W, Ning Y, Liu J, Ding W, Fan J, Cai S, Li Q, Li W, Yang X, Dou Y, Wang W, Peng W, Lu F, Zhuang X, Qin T, Kang X, Feng C, Xu Z, Lv Q, Wang Q, Wang C, Wang X, Wang Z, Wang J, Jiang J, Wang B, Mills GB, Ma D, Gao Q, Li K, Chen G, Chen X, Sun C. Proteogenomic insights into early-onset endometrioid endometrial carcinoma: predictors for fertility-sparing therapy response. Nat Genet 2024; 56:637-651. [PMID: 38565644 DOI: 10.1038/s41588-024-01703-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2023] [Accepted: 03/05/2024] [Indexed: 04/04/2024]
Abstract
Endometrial carcinoma remains a public health concern with a growing incidence, particularly in younger women. Preserving fertility is a crucial consideration in the management of early-onset endometrioid endometrial carcinoma (EEEC), particularly in patients under 40 who maintain both reproductive desire and capacity. To illuminate the molecular characteristics of EEEC, we undertook a large-scale multi-omics study of 215 patients with endometrial carcinoma, including 81 with EEEC. We reveal an unexpected association between exposome-related mutational signature and EEEC, characterized by specific CTNNB1 and SIGLEC10 hotspot mutations and disruption of downstream pathways. Interestingly, SIGLEC10Q144K mutation in EEECs resulted in aberrant SIGLEC-10 protein expression and promoted progestin resistance by interacting with estrogen receptor alpha. We also identified potential protein biomarkers for progestin response in fertility-sparing treatment for EEEC. Collectively, our study establishes a proteogenomic resource of EEECs, uncovering the interactions between exposome and genomic susceptibilities that contribute to the development of primary prevention and early detection strategies for EEECs.
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Affiliation(s)
- Zhe Hu
- Department of Gynecological Oncology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, P. R. China
- National Clinical Research Center for Obstetrics and Gynecology, Cancer Biology Research Center (Key Laboratory of the Ministry of Education), Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, P. R. China
| | - Zimeng Wu
- Department of Gynecological Oncology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, P. R. China
- National Clinical Research Center for Obstetrics and Gynecology, Cancer Biology Research Center (Key Laboratory of the Ministry of Education), Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, P. R. China
| | - Wei Liu
- Obstetrics and Gynecology Hospital of Fudan University, Shanghai, P. R. China
| | - Yan Ning
- Department of Pathology, Obstetrics and Gynecology Hospital of Fudan University, Shanghai, P. R. China
| | - Jingbo Liu
- Department of Gynecological Oncology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, P. R. China
- National Clinical Research Center for Obstetrics and Gynecology, Cancer Biology Research Center (Key Laboratory of the Ministry of Education), Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, P. R. China
| | - Wencheng Ding
- National Clinical Research Center for Obstetrics and Gynecology, Cancer Biology Research Center (Key Laboratory of the Ministry of Education), Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, P. R. China
| | - Junpeng Fan
- Department of Gynecological Oncology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, P. R. China
- National Clinical Research Center for Obstetrics and Gynecology, Cancer Biology Research Center (Key Laboratory of the Ministry of Education), Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, P. R. China
| | - Shuyan Cai
- Obstetrics and Gynecology Hospital of Fudan University, Shanghai, P. R. China
| | - Qinlan Li
- Department of Gynecological Oncology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, P. R. China
- National Clinical Research Center for Obstetrics and Gynecology, Cancer Biology Research Center (Key Laboratory of the Ministry of Education), Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, P. R. China
| | - Wenting Li
- Department of Gynecological Oncology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, P. R. China
- National Clinical Research Center for Obstetrics and Gynecology, Cancer Biology Research Center (Key Laboratory of the Ministry of Education), Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, P. R. China
| | - Xiaohang Yang
- Department of Gynecological Oncology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, P. R. China
- National Clinical Research Center for Obstetrics and Gynecology, Cancer Biology Research Center (Key Laboratory of the Ministry of Education), Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, P. R. China
| | - Yingyu Dou
- Department of Gynecological Oncology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, P. R. China
- National Clinical Research Center for Obstetrics and Gynecology, Cancer Biology Research Center (Key Laboratory of the Ministry of Education), Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, P. R. China
| | - Wei Wang
- Department of Gynecological Oncology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, P. R. China
- National Clinical Research Center for Obstetrics and Gynecology, Cancer Biology Research Center (Key Laboratory of the Ministry of Education), Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, P. R. China
| | - Wenju Peng
- Department of Gynecological Oncology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, P. R. China
- National Clinical Research Center for Obstetrics and Gynecology, Cancer Biology Research Center (Key Laboratory of the Ministry of Education), Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, P. R. China
| | - Funian Lu
- Department of Gynecological Oncology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, P. R. China
- National Clinical Research Center for Obstetrics and Gynecology, Cancer Biology Research Center (Key Laboratory of the Ministry of Education), Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, P. R. China
| | - Xucui Zhuang
- Department of Gynecological Oncology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, P. R. China
- National Clinical Research Center for Obstetrics and Gynecology, Cancer Biology Research Center (Key Laboratory of the Ministry of Education), Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, P. R. China
| | - Tianyu Qin
- Department of Gynecological Oncology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, P. R. China
- National Clinical Research Center for Obstetrics and Gynecology, Cancer Biology Research Center (Key Laboratory of the Ministry of Education), Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, P. R. China
| | - Xiaoyan Kang
- Department of Gynecological Oncology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, P. R. China
- National Clinical Research Center for Obstetrics and Gynecology, Cancer Biology Research Center (Key Laboratory of the Ministry of Education), Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, P. R. China
| | - Chenzhao Feng
- Department of Gynecological Oncology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, P. R. China
- National Clinical Research Center for Obstetrics and Gynecology, Cancer Biology Research Center (Key Laboratory of the Ministry of Education), Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, P. R. China
| | - Zhiying Xu
- Obstetrics and Gynecology Hospital of Fudan University, Shanghai, P. R. China
| | - Qiaoying Lv
- Obstetrics and Gynecology Hospital of Fudan University, Shanghai, P. R. China
| | - Qian Wang
- Obstetrics and Gynecology Hospital of Fudan University, Shanghai, P. R. China
| | - Chao Wang
- Obstetrics and Gynecology Hospital of Fudan University, Shanghai, P. R. China
| | - Xinyu Wang
- The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, P. R. China
| | - Zhiqi Wang
- Department of Obstetrics and Gynecology, Peking University People's Hospital; Peking University People's Hospital, Xicheng District, Beijing, P. R. China
| | - Jianliu Wang
- Department of Obstetrics and Gynecology, Peking University People's Hospital; Peking University People's Hospital, Xicheng District, Beijing, P. R. China
| | - Jie Jiang
- Department of Obstetrics and Gynecology, Qilu Hospital of Shandong University, Jinan, P. R. China
| | - Beibei Wang
- Department of Gynecological Oncology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, P. R. China
- National Clinical Research Center for Obstetrics and Gynecology, Cancer Biology Research Center (Key Laboratory of the Ministry of Education), Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, P. R. China
| | | | - Ding Ma
- Department of Gynecological Oncology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, P. R. China
- National Clinical Research Center for Obstetrics and Gynecology, Cancer Biology Research Center (Key Laboratory of the Ministry of Education), Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, P. R. China
| | - Qinglei Gao
- Department of Gynecological Oncology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, P. R. China.
- National Clinical Research Center for Obstetrics and Gynecology, Cancer Biology Research Center (Key Laboratory of the Ministry of Education), Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, P. R. China.
| | - Kezhen Li
- Department of Gynecological Oncology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, P. R. China.
- National Clinical Research Center for Obstetrics and Gynecology, Cancer Biology Research Center (Key Laboratory of the Ministry of Education), Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, P. R. China.
| | - Gang Chen
- Department of Gynecological Oncology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, P. R. China.
- National Clinical Research Center for Obstetrics and Gynecology, Cancer Biology Research Center (Key Laboratory of the Ministry of Education), Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, P. R. China.
| | - Xiaojun Chen
- Obstetrics and Gynecology Hospital of Fudan University, Shanghai, P. R. China.
| | - Chaoyang Sun
- Department of Gynecological Oncology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, P. R. China.
- National Clinical Research Center for Obstetrics and Gynecology, Cancer Biology Research Center (Key Laboratory of the Ministry of Education), Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, P. R. China.
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20
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Shen LP, Jiang HT. Pan-cancer and single-cell analysis of actin cytoskeleton genes related to disulfidptosis. Open Med (Wars) 2024; 19:20240929. [PMID: 38584831 PMCID: PMC10997004 DOI: 10.1515/med-2024-0929] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2023] [Revised: 03/03/2024] [Accepted: 03/06/2024] [Indexed: 04/09/2024] Open
Abstract
Disulfidptosis was recently reported to be caused by abnormal disulfide accumulation in cells with high SLC7A11 levels subjected to glucose starvation, suggesting that targeting disulfidptosis was a potential strategy for cancer treatment. We analyzed the relationships between gene expression and mutations and prognoses of patients. In addition, the correlation between gene expression and immune cell infiltration was explored. The potential regulatory mechanisms of these genes were assessed by investigating their related signaling pathways involved in cancer, their expression patterns, and their cellular localization. Most cancer types showed a negative correlation between the gene-set variation analysis (GSVA) scores and infiltration of B cells and neutrophils, and a positive correlation between GSVA scores and infiltration of natural killer T and induced regulatory T cells. Single-cell analysis revealed that ACTB, DSTN, and MYL6 were highly expressed in different bladder urothelial carcinoma subtypes, but MYH10 showed a low expression. Immunofluorescence staining showed that actin cytoskeleton proteins were mainly localized in the actin filaments and plasma membrane. Notably, IQGAP1 was localized in the cell junctions. In conclusion, this study provided an overview of disulfidptosis-related actin cytoskeleton genes in pan-cancer. These genes were associated with the survival of patients and might be involved in cancer-related pathways.
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Affiliation(s)
- Li-ping Shen
- Department of Clinical Laboratory, Taizhou Hospital of Zhejiang Province affiliated to Wenzhou Medical University, Taizhou, 318000, Zhejiang Province, China
| | - Han-tao Jiang
- Department of Orthopedics, Taizhou Hospital of Zhejiang Province affiliated to Wenzhou Medical University, Taizhou, 318000, Zhejiang Province, China
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21
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Chowdhury D, Mistry A, Maity D, Bhatia R, Priyadarshi S, Wadan S, Chakraborty S, Haldar S. Pan-cancer analyses suggest kindlin-associated global mechanochemical alterations. Commun Biol 2024; 7:372. [PMID: 38548811 PMCID: PMC10978987 DOI: 10.1038/s42003-024-06044-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2022] [Accepted: 03/11/2024] [Indexed: 04/01/2024] Open
Abstract
Kindlins serve as mechanosensitive adapters, transducing extracellular mechanical cues to intracellular biochemical signals and thus, their perturbations potentially lead to cancer progressions. Despite the kindlin involvement in tumor development, understanding their genetic and mechanochemical characteristics across different cancers remains elusive. Here, we thoroughly examined genetic alterations in kindlins across more than 10,000 patients with 33 cancer types. Our findings reveal cancer-specific alterations, particularly prevalent in advanced tumor stage and during metastatic onset. We observed a significant co-alteration between kindlins and mechanochemical proteome in various tumors through the activation of cancer-related pathways and adverse survival outcomes. Leveraging normal mode analysis, we predicted structural consequences of cancer-specific kindlin mutations, highlighting potential impacts on stability and downstream signaling pathways. Our study unraveled alterations in epithelial-mesenchymal transition markers associated with kindlin activity. This comprehensive analysis provides a resource for guiding future mechanistic investigations and therapeutic strategies targeting the roles of kindlins in cancer treatment.
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Affiliation(s)
- Debojyoti Chowdhury
- Department of Chemical and Biological Sciences, S.N. Bose National Centre for Basic Sciences, Kolkata, West Bengal, 700106, India.
| | - Ayush Mistry
- Department of Biology, Trivedi School of Biosciences, Ashoka University, Sonepat, Haryana, 131029, India
| | - Debashruti Maity
- Department of Chemical and Biological Sciences, S.N. Bose National Centre for Basic Sciences, Kolkata, West Bengal, 700106, India
| | - Riti Bhatia
- Department of Biology, Trivedi School of Biosciences, Ashoka University, Sonepat, Haryana, 131029, India
| | - Shreyansh Priyadarshi
- Department of Biology, Trivedi School of Biosciences, Ashoka University, Sonepat, Haryana, 131029, India
| | - Simran Wadan
- Department of Biology, Trivedi School of Biosciences, Ashoka University, Sonepat, Haryana, 131029, India
| | - Soham Chakraborty
- Department of Biology, Trivedi School of Biosciences, Ashoka University, Sonepat, Haryana, 131029, India
| | - Shubhasis Haldar
- Department of Chemical and Biological Sciences, S.N. Bose National Centre for Basic Sciences, Kolkata, West Bengal, 700106, India.
- Department of Biology, Trivedi School of Biosciences, Ashoka University, Sonepat, Haryana, 131029, India.
- Technical Research Centre, S.N. Bose National Centre for Basic Sciences, Kolkata, West Bengal, 700106, India.
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22
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Zhao Z, Zobolas J, Zucknick M, Aittokallio T. Tutorial on survival modeling with applications to omics data. Bioinformatics 2024; 40:btae132. [PMID: 38445722 PMCID: PMC10973942 DOI: 10.1093/bioinformatics/btae132] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2023] [Revised: 02/22/2024] [Accepted: 03/04/2024] [Indexed: 03/07/2024] Open
Abstract
MOTIVATION Identification of genomic, molecular and clinical markers prognostic of patient survival is important for developing personalized disease prevention, diagnostic and treatment approaches. Modern omics technologies have made it possible to investigate the prognostic impact of markers at multiple molecular levels, including genomics, epigenomics, transcriptomics, proteomics and metabolomics, and how these potential risk factors complement clinical characterization of patient outcomes for survival prognosis. However, the massive sizes of the omics datasets, along with their correlation structures, pose challenges for studying relationships between the molecular information and patients' survival outcomes. RESULTS We present a general workflow for survival analysis that is applicable to high-dimensional omics data as inputs when identifying survival-associated features and validating survival models. In particular, we focus on the commonly used Cox-type penalized regressions and hierarchical Bayesian models for feature selection in survival analysis, which are especially useful for high-dimensional data, but the framework is applicable more generally. AVAILABILITY AND IMPLEMENTATION A step-by-step R tutorial using The Cancer Genome Atlas survival and omics data for the execution and evaluation of survival models has been made available at https://ocbe-uio.github.io/survomics.
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Affiliation(s)
- Zhi Zhao
- Oslo Centre for Biostatistics and Epidemiology (OCBE), Department of Biostatistics, Faculty of Medicine, University of Oslo, Oslo 0372, Norway
- Department of Cancer Genetics, Institute for Cancer Research, Oslo University Hospital, Oslo 0310, Norway
| | - John Zobolas
- Oslo Centre for Biostatistics and Epidemiology (OCBE), Department of Biostatistics, Faculty of Medicine, University of Oslo, Oslo 0372, Norway
- Department of Cancer Genetics, Institute for Cancer Research, Oslo University Hospital, Oslo 0310, Norway
| | - Manuela Zucknick
- Oslo Centre for Biostatistics and Epidemiology (OCBE), Department of Biostatistics, Faculty of Medicine, University of Oslo, Oslo 0372, Norway
- Oslo Centre for Biostatistics and Epidemiology (OCBE), Research Support Services, Oslo University Hospital, Oslo 0372, Norway
| | - Tero Aittokallio
- Oslo Centre for Biostatistics and Epidemiology (OCBE), Department of Biostatistics, Faculty of Medicine, University of Oslo, Oslo 0372, Norway
- Department of Cancer Genetics, Institute for Cancer Research, Oslo University Hospital, Oslo 0310, Norway
- Institute for Molecular Medicine Finland (FIMM), HiLIFE, University of Helsinki, Helsinki FI-00014, Finland
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23
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Shi H, Tan Z, Duan B, Guo C, Li C, Luan T, Li N, Huang Y, Chen S, Gao J, Feng W, Xu H, Wang J, Fu S, Wang H. LASS2 enhances chemosensitivity to cisplatin by inhibiting PP2A-mediated β-catenin dephosphorylation in a subset of stem-like bladder cancer cells. BMC Med 2024; 22:19. [PMID: 38191448 PMCID: PMC10775422 DOI: 10.1186/s12916-023-03243-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/01/2023] [Accepted: 11/01/2023] [Indexed: 01/10/2024] Open
Abstract
BACKGROUND The benefits of first-line, cisplatin-based chemotherapy for muscle-invasive bladder cancer are limited due to intrinsic or acquired resistance to cisplatin. Increasing evidence has revealed the implication of cancer stem cells in the development of chemoresistance. However, the underlying molecular mechanisms remain to be elucidated. This study investigates the role of LASS2, a ceramide synthase, in regulating Wnt/β-catenin signaling in a subset of stem-like bladder cancer cells and explores strategies to sensitize bladder cancer to cisplatin treatment. METHODS Data from cohorts of our center and published datasets were used to evaluate the clinical characteristics of LASS2. Flow cytometry was used to sort and analyze bladder cancer stem cells (BCSCs). Tumor sphere formation, soft agar colony formation assay, EdU assay, apoptosis analysis, cell viability, and cisplatin sensitivity assay were used to investigate the functional roles of LASS2. Immunofluorescence, immunoblotting, coimmunoprecipitation, LC-MS, PCR array, luciferase reporter assays, pathway reporter array, chromatin immunoprecipitation, gain-of-function, and loss-of-function approaches were used to investigate the underlying mechanisms. Cell- and patient-derived xenograft models were used to investigate the effect of LASS2 overexpression and a combination of XAV939 on cisplatin sensitization and tumor growth. RESULTS Patients with low expression of LASS2 have a poorer response to cisplatin-based chemotherapy. Loss of LASS2 confers a stem-like phenotype and contributes to cisplatin resistance. Overexpression of LASS2 results in inhibition of self-renewal ability of BCSCs and increased their sensitivity to cisplatin. Mechanistically, LASS2 inhibits PP2A activity and dissociates PP2A from β-catenin, preventing the dephosphorylation of β-catenin and leading to the accumulation of cytosolic phospho-β-catenin, which decreases the transcription of the downstream genes ABCC2 and CD44 in BCSCs. Overexpression of LASS2 combined with a tankyrase inhibitor (XAV939) synergistically inhibits tumor growth and restores cisplatin sensitivity. CONCLUSIONS Targeting the LASS2 and β-catenin pathways may be an effective strategy to overcome cisplatin resistance and inhibit tumor growth in bladder cancer patients.
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Affiliation(s)
- Hongjin Shi
- Department of Urology, the Second Affiliated Hospital of Kunming Medical University, Kunming, China
- Yunnan Clinical Medical Center of Urological Disease, Kunming, China
- Kunming Medical University, Kunming, China
| | - Zhiyong Tan
- Department of Urology, the Second Affiliated Hospital of Kunming Medical University, Kunming, China
- Yunnan Clinical Medical Center of Urological Disease, Kunming, China
- Kunming Medical University, Kunming, China
| | - Bowen Duan
- Kunming Medical University, Kunming, China
| | - Chunming Guo
- School for Life Science, Yunnan University, Kunming, China
| | - Chong Li
- Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
| | - Ting Luan
- Department of Urology, the Second Affiliated Hospital of Kunming Medical University, Kunming, China
- Yunnan Clinical Medical Center of Urological Disease, Kunming, China
| | - Ning Li
- Department of Urology, the Second Affiliated Hospital of Kunming Medical University, Kunming, China
- Yunnan Clinical Medical Center of Urological Disease, Kunming, China
| | - Yinglong Huang
- Department of Urology, the Second Affiliated Hospital of Kunming Medical University, Kunming, China
- Yunnan Clinical Medical Center of Urological Disease, Kunming, China
| | - Shi Chen
- Department of Urology, the Second Affiliated Hospital of Kunming Medical University, Kunming, China
- Yunnan Clinical Medical Center of Urological Disease, Kunming, China
- Kunming Medical University, Kunming, China
| | - Jixian Gao
- Department of Urology, the Second Affiliated Hospital of Kunming Medical University, Kunming, China
- Yunnan Clinical Medical Center of Urological Disease, Kunming, China
- Kunming Medical University, Kunming, China
| | - Wei Feng
- Department of Urology, the Second Affiliated Hospital of Kunming Medical University, Kunming, China
- Yunnan Clinical Medical Center of Urological Disease, Kunming, China
- Kunming Medical University, Kunming, China
| | - Haole Xu
- Department of Urology, the Second Affiliated Hospital of Kunming Medical University, Kunming, China
- Yunnan Clinical Medical Center of Urological Disease, Kunming, China
- Kunming Medical University, Kunming, China
| | - Jiansong Wang
- Department of Urology, the Second Affiliated Hospital of Kunming Medical University, Kunming, China
- Yunnan Clinical Medical Center of Urological Disease, Kunming, China
| | - Shi Fu
- Department of Urology, the Second Affiliated Hospital of Kunming Medical University, Kunming, China.
- Yunnan Clinical Medical Center of Urological Disease, Kunming, China.
| | - Haifeng Wang
- Department of Urology, the Second Affiliated Hospital of Kunming Medical University, Kunming, China.
- Yunnan Clinical Medical Center of Urological Disease, Kunming, China.
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24
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Liu CH, Lai YL, Shen PC, Liu HC, Tsai MH, Wang YD, Lin WJ, Chen FH, Li CY, Wang SC, Hung MC, Cheng WC. DriverDBv4: a multi-omics integration database for cancer driver gene research. Nucleic Acids Res 2024; 52:D1246-D1252. [PMID: 37956338 PMCID: PMC10767848 DOI: 10.1093/nar/gkad1060] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2023] [Revised: 10/12/2023] [Accepted: 10/25/2023] [Indexed: 11/15/2023] Open
Abstract
Advancements in high-throughput technology offer researchers an extensive range of multi-omics data that provide deep insights into the complex landscape of cancer biology. However, traditional statistical models and databases are inadequate to interpret these high-dimensional data within a multi-omics framework. To address this limitation, we introduce DriverDBv4, an updated iteration of the DriverDB cancer driver gene database (http://driverdb.bioinfomics.org/). This updated version offers several significant enhancements: (i) an increase in the number of cohorts from 33 to 70, encompassing approximately 24 000 samples; (ii) inclusion of proteomics data, augmenting the existing types of omics data and thus expanding the analytical scope; (iii) implementation of multiple multi-omics algorithms for identification of cancer drivers; (iv) new visualization features designed to succinctly summarize high-context data and redesigned existing sections to accommodate the increased volume of datasets and (v) two new functions in Customized Analysis, specifically designed for multi-omics driver identification and subgroup expression analysis. DriverDBv4 facilitates comprehensive interpretation of multi-omics data across diverse cancer types, thereby enriching the understanding of cancer heterogeneity and aiding in the development of personalized clinical approaches. The database is designed to foster a more nuanced understanding of the multi-faceted nature of cancer.
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Affiliation(s)
- Chia-Hsin Liu
- Cancer Biology and Precision Therapeutics Center, China Medical University, Taichung 404328, Taiwan
| | - Yo-Liang Lai
- Department of Radiation Oncology, China Medical University, Taichung 404328, Taiwan
| | - Pei-Chun Shen
- Cancer Biology and Precision Therapeutics Center, China Medical University, Taichung 404328, Taiwan
| | - Hsiu-Cheng Liu
- Cancer Biology and Precision Therapeutics Center, China Medical University, Taichung 404328, Taiwan
| | - Meng-Hsin Tsai
- Cancer Biology and Precision Therapeutics Center, China Medical University, Taichung 404328, Taiwan
| | - Yu-De Wang
- Graduate Institute of Biomedical Sciences, China Medical University, Taichung 404328, Taiwan
- Department of Urology, China Medical University, Taichung 404328, Taiwan
| | - Wen-Jen Lin
- Cancer Biology and Precision Therapeutics Center, China Medical University, Taichung 404328, Taiwan
- School of Medicine, China Medical University, Taichung 404328, Taiwan
| | - Fang-Hsin Chen
- Institute of Nuclear Engineering and Science, National Tsing Hua University, Hsinchu 300044, Taiwan
| | - Chia-Yang Li
- Graduate Institute of Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung 80708, Taiwan
| | - Shu-Chi Wang
- Department of Medical Laboratory Science and Biotechnology, Kaohsiung Medical University, Kaohsiung 80708, Taiwan
| | - Mien-Chie Hung
- Cancer Biology and Precision Therapeutics Center, China Medical University, Taichung 404328, Taiwan
- Graduate Institute of Biomedical Sciences, China Medical University, Taichung 404328, Taiwan
- Institute of Biochemistry and Molecular Biology, China Medical University, Taichung 404328, Taiwan
- Molecular Medicine Center, China Medical University Hospital, China Medical University, Taichung 404328, Taiwan
- Department of Biotechnology, Asia University, Taichung 413305, Taiwan
| | - Wei-Chung Cheng
- Cancer Biology and Precision Therapeutics Center, China Medical University, Taichung 404328, Taiwan
- Graduate Institute of Biomedical Sciences, China Medical University, Taichung 404328, Taiwan
- The Ph.D. program for Cancer Biology and Drug Discovery, China Medical University and Academia Sinica, Taichung 404328, Taiwan
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25
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Jeong E, Yoon S. Current advances in comprehensive omics data mining for oncology and cancer research. Biochim Biophys Acta Rev Cancer 2024; 1879:189030. [PMID: 38008264 DOI: 10.1016/j.bbcan.2023.189030] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2023] [Revised: 09/05/2023] [Accepted: 11/19/2023] [Indexed: 11/28/2023]
Abstract
The availability of a large amount of multiomics data enables data-driven discovery studies on cancers. High-throughput data on mutations, gene/protein expression, immune scores (tumor-infiltrating cells), drug screening, and RNAi (shRNAs and CRISPRs) screening are major integrated components of patient samples and cell line datasets. Improvements in data access and user interfaces make it easy for general scientists to carry out their data mining practices on integrated multiomics data platforms without computational expertise. Here, we summarize the extent of data integration and functionality of several portals and software that provide integrated multiomics data mining platforms for all cancer studies. Recent progress includes programming interfaces (APIs) for customized data mining. Precalculated datasets assist noncomputational users in quickly browsing data associations. Furthermore, stand-alone software provides fast calculations and smart functions, guiding optimal sampling and filtering options for the easy discovery of significant data associations. These efforts improve the utility of cancer omics big data for noncomputational users at all levels of cancer research. In the present review, we aim to provide analytical information guiding general scientists to find and utilize data mining tools for their research.
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Affiliation(s)
- Euna Jeong
- Research Institute of Women's Health, Sookmyung Women's University, Seoul 04310, Republic of Korea
| | - Sukjoon Yoon
- Research Institute of Women's Health, Sookmyung Women's University, Seoul 04310, Republic of Korea; Department of Biological Sciences, Sookmyung Women's University, Seoul 04310, Republic of Korea.
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26
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Lingjærde C, Richardson S. StabJGL: a stability approach to sparsity and similarity selection in multiple-network reconstruction. BIOINFORMATICS ADVANCES 2023; 3:vbad185. [PMID: 38152341 PMCID: PMC10751232 DOI: 10.1093/bioadv/vbad185] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/28/2023] [Revised: 11/23/2023] [Accepted: 12/18/2023] [Indexed: 12/29/2023]
Abstract
Motivation In recent years, network models have gained prominence for their ability to capture complex associations. In statistical omics, networks can be used to model and study the functional relationships between genes, proteins, and other types of omics data. If a Gaussian graphical model is assumed, a gene association network can be determined from the non-zero entries of the inverse covariance matrix of the data. Due to the high-dimensional nature of such problems, integrative methods that leverage similarities between multiple graphical structures have become increasingly popular. The joint graphical lasso is a powerful tool for this purpose, however, the current AIC-based selection criterion used to tune the network sparsities and similarities leads to poor performance in high-dimensional settings. Results We propose stabJGL, which equips the joint graphical lasso with a stable and well-performing penalty parameter selection approach that combines the notion of model stability with likelihood-based similarity selection. The resulting method makes the powerful joint graphical lasso available for use in omics settings, and outperforms the standard joint graphical lasso, as well as state-of-the-art joint methods, in terms of all performance measures we consider. Applying stabJGL to proteomic data from a pan-cancer study, we demonstrate the potential for novel discoveries the method brings. Availability and implementation A user-friendly R package for stabJGL with tutorials is available on Github https://github.com/Camiling/stabJGL.
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Affiliation(s)
- Camilla Lingjærde
- MRC Biostatistics Unit, University of Cambridge, Cambridge CB2 0SR, United Kingdom
| | - Sylvia Richardson
- MRC Biostatistics Unit, University of Cambridge, Cambridge CB2 0SR, United Kingdom
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27
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Mukhopadhyay S, Huang HY, Lin Z, Ranieri M, Li S, Sahu S, Liu Y, Ban Y, Guidry K, Hu H, Lopez A, Sherman F, Tan YJ, Lee YT, Armstrong AP, Dolgalev I, Sahu P, Zhang T, Lu W, Gray NS, Christensen JG, Tang TT, Velcheti V, Khodadadi-Jamayran A, Wong KK, Neel BG. Genome-Wide CRISPR Screens Identify Multiple Synthetic Lethal Targets That Enhance KRASG12C Inhibitor Efficacy. Cancer Res 2023; 83:4095-4111. [PMID: 37729426 PMCID: PMC10841254 DOI: 10.1158/0008-5472.can-23-2729] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2023] [Revised: 09/16/2023] [Accepted: 09/18/2023] [Indexed: 09/22/2023]
Abstract
Non-small lung cancers (NSCLC) frequently (∼30%) harbor KRAS driver mutations, half of which are KRASG12C. KRAS-mutant NSCLC with comutated STK11 and/or KEAP1 is particularly refractory to conventional, targeted, and immune therapy. Development of KRASG12C inhibitors (G12Ci) provided a major therapeutic advance, but resistance still limits their efficacy. To identify genes whose deletion augments efficacy of the G12Cis adagrasib (MRTX-849) or adagrasib plus TNO155 (SHP2i), we performed genome-wide CRISPR/Cas9 screens on KRAS/STK11-mutant NSCLC lines. Recurrent, potentially targetable, synthetic lethal (SL) genes were identified, including serine-threonine kinases, tRNA-modifying and proteoglycan synthesis enzymes, and YAP/TAZ/TEAD pathway components. Several SL genes were confirmed by siRNA/shRNA experiments, and the YAP/TAZ/TEAD pathway was extensively validated in vitro and in mice. Mechanistic studies showed that G12Ci treatment induced gene expression of RHO paralogs and activators, increased RHOA activation, and evoked ROCK-dependent nuclear translocation of YAP. Mice and patients with acquired G12Ci- or G12Ci/SHP2i-resistant tumors showed strong overlap with SL pathways, arguing for the relevance of the screen results. These findings provide a landscape of potential targets for future combination strategies, some of which can be tested rapidly in the clinic. SIGNIFICANCE Identification of synthetic lethal genes with KRASG12C using genome-wide CRISPR/Cas9 screening and credentialing of the ability of TEAD inhibition to enhance KRASG12C efficacy provides a roadmap for combination strategies. See related commentary by Johnson and Haigis, p. 4005.
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Affiliation(s)
- Suman Mukhopadhyay
- Laura and Isaac Perlmutter Cancer Center, NYU Grossman School of Medicine, NYU Langone Health, New York, United States
| | - Hsin-Yi Huang
- Laura and Isaac Perlmutter Cancer Center, NYU Grossman School of Medicine, NYU Langone Health, New York, United States
| | - Ziyan Lin
- Applied Bioinformatics Laboratories, Office of Science and Research, New York University Grossman School of Medicine, New York, United States
| | - Michela Ranieri
- Laura and Isaac Perlmutter Cancer Center, NYU Grossman School of Medicine, NYU Langone Health, New York, United States
| | - Shuai Li
- Laura and Isaac Perlmutter Cancer Center, NYU Grossman School of Medicine, NYU Langone Health, New York, United States
| | - Soumyadip Sahu
- Laura and Isaac Perlmutter Cancer Center, NYU Grossman School of Medicine, NYU Langone Health, New York, United States
| | - Yingzhuo Liu
- Laura and Isaac Perlmutter Cancer Center, NYU Grossman School of Medicine, NYU Langone Health, New York, United States
| | - Yi Ban
- Laura and Isaac Perlmutter Cancer Center, NYU Grossman School of Medicine, NYU Langone Health, New York, United States
| | - Kayla Guidry
- Laura and Isaac Perlmutter Cancer Center, NYU Grossman School of Medicine, NYU Langone Health, New York, United States
| | - Hai Hu
- Laura and Isaac Perlmutter Cancer Center, NYU Grossman School of Medicine, NYU Langone Health, New York, United States
| | - Alfonso Lopez
- Laura and Isaac Perlmutter Cancer Center, NYU Grossman School of Medicine, NYU Langone Health, New York, United States
| | - Fiona Sherman
- Laura and Isaac Perlmutter Cancer Center, NYU Grossman School of Medicine, NYU Langone Health, New York, United States
| | - Yi Jer Tan
- Laura and Isaac Perlmutter Cancer Center, NYU Grossman School of Medicine, NYU Langone Health, New York, United States
| | - Yeuan Ting Lee
- Laura and Isaac Perlmutter Cancer Center, NYU Grossman School of Medicine, NYU Langone Health, New York, United States
| | - Amanda P. Armstrong
- Laura and Isaac Perlmutter Cancer Center, NYU Grossman School of Medicine, NYU Langone Health, New York, United States
| | - Igor Dolgalev
- Laura and Isaac Perlmutter Cancer Center, NYU Grossman School of Medicine, NYU Langone Health, New York, United States
| | - Priyanka Sahu
- Laura and Isaac Perlmutter Cancer Center, NYU Grossman School of Medicine, NYU Langone Health, New York, United States
| | - Tinghu Zhang
- Department of Chemical and Systems Biology, ChEM-H, Stanford Cancer Institute, School of Medicine, Stanford University, California, United States
| | - Wenchao Lu
- Department of Chemical and Systems Biology, ChEM-H, Stanford Cancer Institute, School of Medicine, Stanford University, California, United States
| | - Nathanael S. Gray
- Department of Chemical and Systems Biology, ChEM-H, Stanford Cancer Institute, School of Medicine, Stanford University, California, United States
| | | | - Tracy T. Tang
- Vivace Therapeutics, Inc., San Mateo, California, United States
| | - Vamsidhar Velcheti
- Laura and Isaac Perlmutter Cancer Center, NYU Grossman School of Medicine, NYU Langone Health, New York, United States
| | - Alireza Khodadadi-Jamayran
- Applied Bioinformatics Laboratories, Office of Science and Research, New York University Grossman School of Medicine, New York, United States
| | - Kwok-Kin Wong
- Laura and Isaac Perlmutter Cancer Center, NYU Grossman School of Medicine, NYU Langone Health, New York, United States
| | - Benjamin G. Neel
- Laura and Isaac Perlmutter Cancer Center, NYU Grossman School of Medicine, NYU Langone Health, New York, United States
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28
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Yan B, Liao P, Shi L, Lei P. Pan-cancer analyses of senescence-related genes in extracellular matrix characterization in cancer. Discov Oncol 2023; 14:208. [PMID: 37985530 PMCID: PMC10660488 DOI: 10.1007/s12672-023-00828-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/05/2023] [Accepted: 11/13/2023] [Indexed: 11/22/2023] Open
Abstract
PURPOSE The aged microenvironment plays a crucial role in tumor onset and progression. However, it remains unclear whether and how the aging of the extracellular matrix (ECM) influences cancer onset and progression. Furthermore, the mechanisms and implications of extracellular matrix senescence-related genes (ECM-SRGs) in pan-cancer have not been investigated. METHODS We collected profiling data from over 10,000 individuals, covering 33 cancer types, 750 small molecule drugs, and 24 immune cell types, for a thorough and systematic analysis of ECM-SRGs in cancer. RESULTS We observed a significant correlation between immune cell infiltrates and Gene Set Variation Analysis enrichment scores of ECM-SRGs in 33 cancer types. Moreover, our results revealed significant differences in immune cell infiltration among patients with copy number variations (CNV) and single nucleotide variations (SNV) in ECM-SRGs across various malignancies. Aberrant hypomethylation led to increased ECM-SRGs expression, and in specific malignancies, a connection between ECM-SRGs hypomethylation and adverse patient survival was established. The frequency of CNV and SNV in ECM-SRGs was elevated. We observed a positive correlation between CNV, SNV, and ECM-SRGs expression. Furthermore, a correlation was found between the high frequency of CNV and SNV in ECM-SRGs and poor patient survival in several cancer types. Additionally, the results demonstrated that ECM-SRGs expression could serve as a predictor of patient survival in diverse cancers. Pathway analysis unveiled the role of ECM-SRGs in activating EMT, apoptosis, and the RAS/MAPK signaling pathway while suppressing the cell cycle, hormone AR, and the response to DNA damage signaling pathway. Finally, we conducted searches in the "Genomics of Drug Sensitivity in Cancer" and "Genomics of Therapeutics Response Portal" databases, identifying several drugs that target ECM-SRGs. CONCLUSIONS We conducted a comprehensive evaluation of the genomes and immunogenomics of ECM-SRGs, along with their clinical features in 33 solid tumors. This may provide insights into the relationship between ECM-SRGs and tumorigenesis. Consequently, targeting these ECM-SRGs holds promise as a clinical approach for cancer treatment.
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Affiliation(s)
- Bo Yan
- Haihe Laboratory of Cell Ecosystem, Department of Geriatrics, Tianjin Medical University General Hospital, 154 Anshan Road, Heping District, Tianjin, 300052, China
- Tianjin Geriatrics Institute, Tianjin Medical University General Hospital, 154 Anshan Road, Heping District, Tianjin, 300052, China
| | - Pan Liao
- Haihe Laboratory of Cell Ecosystem, Department of Geriatrics, Tianjin Medical University General Hospital, 154 Anshan Road, Heping District, Tianjin, 300052, China
- Tianjin Geriatrics Institute, Tianjin Medical University General Hospital, 154 Anshan Road, Heping District, Tianjin, 300052, China
- The School of Medicine, Nankai University, 94 Weijin Road, Tianjin, 300071, China
| | - Liqiu Shi
- Inner Mongolia Forestry General Hospital, 81 Lincheng North Road, Yakeshi, 022150, Inner Mongolia, China
| | - Ping Lei
- Haihe Laboratory of Cell Ecosystem, Department of Geriatrics, Tianjin Medical University General Hospital, 154 Anshan Road, Heping District, Tianjin, 300052, China.
- Tianjin Geriatrics Institute, Tianjin Medical University General Hospital, 154 Anshan Road, Heping District, Tianjin, 300052, China.
- The School of Medicine, Nankai University, 94 Weijin Road, Tianjin, 300071, China.
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29
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Juan-Guadarrama DG, Beltrán-Navarro YM, Reyes-Cruz G, Vázquez-Prado J. Ephexin3/ARHGEF5 Together with Cell Migration Signaling Partners within the Tumor Microenvironment Define Prognostic Transcriptional Signatures in Multiple Cancer Types. Int J Mol Sci 2023; 24:16427. [PMID: 38003617 PMCID: PMC10671824 DOI: 10.3390/ijms242216427] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2023] [Revised: 11/08/2023] [Accepted: 11/15/2023] [Indexed: 11/26/2023] Open
Abstract
Cancer cell migration involves a repertoire of signaling proteins that lead cytoskeleton reorganization as a critical step in metastatic dissemination. RhoGEFs are multidomain effectors that integrate signaling inputs to activate the molecular switches that orchestrate actin cytoskeleton reorganization. Ephexins, a group of five RhoGEFs, play oncogenic roles in invasive and metastatic cancer, leading to a mechanistic hypothesis about their function as signaling nodes assembling functional complexes that guide cancer cell migration. To identify clinically significant Ephexin signaling partners, we applied three systematic data mining strategies, based on the screening of essential Ephexins in multiple cancer cell lines and the identification of coexpressed signaling partners in the TCGA cancer patient datasets. Based on the domain architecture of encoded proteins and gene ontology criteria, we selected Ephexin signaling partners with a role in cytoskeletal reorganization and cell migration. We focused on Ephexin3/ARHGEF5, identified as an essential gene in multiple cancer cell types. Based on significant coexpression data and coessentiality, the signaling repertoire that accompanies Ephexin3 corresponded to three groups: pan-cancer, cancer-specific and coessential. To further select the Ephexin3 signaling partners likely to be relevant in clinical settings, we first identified those whose high expression was statistical linked to shorter patient survival. The resulting Ephexin3 transcriptional signatures represent significant accumulated risk, predictive of shorter survival, in 17 cancer types, including PAAD, LUAD, LGG, OSC, AML, KIRC, THYM, BLCA, LIHC and UCEC. The signaling landscape that accompanies Ephexin3 in various cancer types included the tyrosine kinase receptor MET and the tyrosine phosphatase receptor PTPRF, the serine/threonine kinases MARK2 and PAK6, the Rho GTPases RHOD, RHOF and RAC1, and the cytoskeletal regulator DIAHP1. Our findings set the basis to further explore the role of Ephexin3/ARHGEF5 as an essential effector and signaling hub in cancer cell migration.
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Affiliation(s)
- Dante Gustavo Juan-Guadarrama
- Department of Pharmacology, Cinvestav-IPN, Av. Instituto Politécnico Nacional 2508, Col. San Pedro Zacatenco, Mexico City 07360, Mexico
| | - Yarely Mabell Beltrán-Navarro
- Department of Pharmacology, Cinvestav-IPN, Av. Instituto Politécnico Nacional 2508, Col. San Pedro Zacatenco, Mexico City 07360, Mexico
| | - Guadalupe Reyes-Cruz
- Department of Cell Biology, Cinvestav-IPN, Av. Instituto Politécnico Nacional 2508, Col. San Pedro Zacatenco, Mexico City 07360, Mexico
| | - José Vázquez-Prado
- Department of Pharmacology, Cinvestav-IPN, Av. Instituto Politécnico Nacional 2508, Col. San Pedro Zacatenco, Mexico City 07360, Mexico
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30
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Kong Y, Liu Y, Li X, Rao M, Li D, Ruan X, Li S, Jiang Z, Zhang Q. Palmitoylation landscapes across human cancers reveal a role of palmitoylation in tumorigenesis. J Transl Med 2023; 21:826. [PMID: 37978524 PMCID: PMC10655258 DOI: 10.1186/s12967-023-04611-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2023] [Accepted: 10/10/2023] [Indexed: 11/19/2023] Open
Abstract
BACKGROUND Protein palmitoylation, which is catalyzed by palmitoyl-transferase and de-palmitoyl-transferase, plays a crucial role in various biological processes. However, the landscape and dynamics of protein palmitoylation in human cancers are not well understood. METHODS We utilized 23 palmitoyl-acyltransferases and seven de-palmitoyl-acyltransferases as palmitoylation-related genes for protein palmitoylation analysis. Multiple publicly available datasets were employed to conduct pan-cancer analysis, examining the transcriptome, genomic alterations, clinical outcomes, and correlation with c-Myc (Myc) for palmitoylation-related genes. Real-time quantitative PCR and immunoblotting were performed to assess the expression of palmitoylation-related genes and global protein palmitoylation levels in cancer cells treated with Myc depletion or small molecule inhibitors. Protein docking and drug sensitivity analyses were employed to predict small molecules that target palmitoylation-related genes. RESULTS We identified associations between palmitoylation and cancer subtype, stage, and patient survival. We discovered that abnormal DNA methylation and oncogenic Myc-driven transcriptional regulation synergistically contribute to the dysregulation of palmitoylation-related genes. This dysregulation of palmitoylation was closely correlated with immune infiltration in the tumor microenvironment and the response to immunotherapy. Importantly, dysregulated palmitoylation was found to modulate canonical cancer-related pathways, thus influencing tumorigenesis. To support our findings, we performed a proof-of-concept experiment showing that depletion of Myc led to reduced expression of most palmitoylation-related genes, resulting in decreased global protein palmitoylation levels. Through mass spectrometry and enrichment analyses, we also identified palmitoyl-acyltransferases ZDHHC7 and ZDHHC23 as significant contributors to mTOR signaling, DNA repair, and immune pathways, highlighting their potential roles in tumorigenesis. Additionally, our study explored the potential of three small molecular (BI-2531, etoposide, and piperlongumine) to modulate palmitoylation by targeting the expression or activity of palmitoylation-related genes or enzymes. CONCLUSIONS Overall, our findings underscore the critical role of dysregulated palmitoylation in tumorigenesis and the response to immunotherapy, mediated through classical cancer-related pathways and immune cell infiltration. Additionally, we propose that the aforementioned three small molecule hold promise as potential therapeutics for modulating palmitoylation, thereby offering novel avenues for cancer therapy.
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Affiliation(s)
- Yue Kong
- Department of Microbiology and Immunology, Basic Medicine College, Jinan University, No.601, West Huangpu Avenue, Guangzhou, 510632, Guangdong, China
- Key Laboratory of Ministry of Education for Viral Pathogenesis and Infection Prevention and Control, Jinan University, Guangzhou, 510632, China
| | - Yugeng Liu
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518124, China
| | - Xianzhe Li
- Division of Clinical Epidemiology and Aging Research, German Cancer Research Center (DKFZ), 69120, Heidelberg, Germany
| | - Menglan Rao
- Guangdong Provincial Key Laboratory of Virology, Institute of Medical Microbiology, Jinan University, Guangzhou, 510632, China
| | - Dawei Li
- Zhumadian Central Hospital, Huanghuai University, Zhumadian, 463000, China
| | - Xiaolan Ruan
- Guangdong Provincial Key Laboratory of Virology, Institute of Medical Microbiology, Jinan University, Guangzhou, 510632, China
| | - Shanglin Li
- Department of Microbiology and Immunology, Basic Medicine College, Jinan University, No.601, West Huangpu Avenue, Guangzhou, 510632, Guangdong, China
- Key Laboratory of Ministry of Education for Viral Pathogenesis and Infection Prevention and Control, Jinan University, Guangzhou, 510632, China
| | - Zhenyou Jiang
- Department of Microbiology and Immunology, Basic Medicine College, Jinan University, No.601, West Huangpu Avenue, Guangzhou, 510632, Guangdong, China.
- Key Laboratory of Ministry of Education for Viral Pathogenesis and Infection Prevention and Control, Jinan University, Guangzhou, 510632, China.
| | - Qiang Zhang
- Molecular Cancer Research Center, School of Medicine, Shenzhen Campus of Sun Yat-sen University, Sun Yat-sen University, No.66, Gongchang Road, Guangming District, Shenzhen, 518107, Guangdong, China.
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31
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Chen C, Liu Y, Li Q, Zhang Z, Luo M, Liu Y, Han L. The Genetic, Pharmacogenomic, and Immune Landscapes Associated with Protein Expression across Human Cancers. Cancer Res 2023; 83:3673-3680. [PMID: 37548539 PMCID: PMC10843800 DOI: 10.1158/0008-5472.can-23-0758] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2023] [Revised: 06/15/2023] [Accepted: 08/03/2023] [Indexed: 08/08/2023]
Abstract
Proteomics is a powerful approach that can rapidly enhance our understanding of cancer development. Detailed characterization of the genetic, pharmacogenomic, and immune landscape in relation to protein expression in patients with cancer could provide new insights into the functional roles of proteins in cancer. By taking advantage of the genotype data from The Cancer Genome Atlas and protein expression data from The Cancer Proteome Atlas, we characterized the effects of genetic variants on protein expression across 31 cancer types and identified approximately 100,000 protein quantitative trait loci (pQTL). Among these, over 8000 pQTLs were associated with patient overall survival. Furthermore, characterization of the impact of protein expression on more than 350 imputed anticancer drug responses in patients revealed nearly 230,000 significant associations. In addition, approximately 21,000 significant associations were identified between protein expression and immune cell abundance. Finally, a user-friendly data portal, GPIP (https://hanlaboratory.com/GPIP), was developed featuring multiple modules that enable researchers to explore, visualize, and browse multidimensional data. This detailed analysis reveals the associations between the proteomic landscape and genetic variation, patient outcome, the immune microenvironment, and drug response across cancer types, providing a resource that may offer valuable clinical insights and encourage further functional investigations of proteins in cancer. SIGNIFICANCE Comprehensive characterization of the relationship between protein expression and the genetic, pharmacogenomic, and immune landscape of tumors across cancer types provides a foundation for investigating the role of protein expression in cancer development and treatment.
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Affiliation(s)
- Chengxuan Chen
- Brown Center for Immunotherapy, School of Medicine, Indiana University, Indianapolis, IN, USA
- Department of Biostatistics and Health Data Science, School of Medicine, Indiana University, Indianapolis, IN, USA
- Center for Epigenetics and Disease Prevention, Institute of Biosciences and Technology, Texas A&M University, Houston, TX, USA
| | - Yuan Liu
- Brown Center for Immunotherapy, School of Medicine, Indiana University, Indianapolis, IN, USA
- Department of Biostatistics and Health Data Science, School of Medicine, Indiana University, Indianapolis, IN, USA
- Center for Epigenetics and Disease Prevention, Institute of Biosciences and Technology, Texas A&M University, Houston, TX, USA
| | - Qiang Li
- Center for Epigenetics and Disease Prevention, Institute of Biosciences and Technology, Texas A&M University, Houston, TX, USA
| | - Zhao Zhang
- Department of Biochemistry and Molecular Biology, The University of Texas Health Science Center at Houston McGovern Medical School, Houston, TX, USA
| | - Mei Luo
- Brown Center for Immunotherapy, School of Medicine, Indiana University, Indianapolis, IN, USA
- Department of Biostatistics and Health Data Science, School of Medicine, Indiana University, Indianapolis, IN, USA
| | - Yaoming Liu
- Department of Biochemistry and Molecular Biology, The University of Texas Health Science Center at Houston McGovern Medical School, Houston, TX, USA
| | - Leng Han
- Brown Center for Immunotherapy, School of Medicine, Indiana University, Indianapolis, IN, USA
- Department of Biostatistics and Health Data Science, School of Medicine, Indiana University, Indianapolis, IN, USA
- Center for Epigenetics and Disease Prevention, Institute of Biosciences and Technology, Texas A&M University, Houston, TX, USA
- Department of Biochemistry and Molecular Biology, The University of Texas Health Science Center at Houston McGovern Medical School, Houston, TX, USA
- Department of Translational Medical Sciences, College of Medicine, Texas A&M University, Houston, TX, USA
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Sun S, Wang W, Li G, Xiao M, Peng M, Cai J, Wang Z, Yang Q, He X. Rational therapeutic targets with biomolecular liquid-liquid phase separation regulating synergy: A pan-cancer analysis. PLoS One 2023; 18:e0287574. [PMID: 37917664 PMCID: PMC10621828 DOI: 10.1371/journal.pone.0287574] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2023] [Accepted: 06/07/2023] [Indexed: 11/04/2023] Open
Abstract
Liquid-liquid phase separation (LLPS) is characterized as an ubiquitous framework for diverse biological processes including carcinogenesis and cancer progression. While targeting cancer from perspective of LLPS offers an opportunity to drug the conventionally undruggables with cancer-driving potential, the therapeutic value of cancer associated LLPS (CAL) proteins remains elusive. Here, we report the genomic landscape, prognostic relevance, immune-infiltration association, down-stream pathway alteration and small molecular responsiveness of CAL protein-coding gene signatures based on protein-coding associated mutations and transcriptional abundance in pan-cancer. Correlations of CAL protein-coding associated mutations and transcriptional abundances to overall survival and progression-free survival were observed in an array of cancers and further characterized by differential survival outcomes between patients with intrinsic disordered region (IDR) enriched and non-IDR enriched mutations in endometrial cancer. Altered signaling pathways and universal pattern of immune infiltrates on account of CAL protein-coding associated gene-set mutations involved key components of oncogenesis in various cancer types and well established therapeutic targets including MAPK signaling pathway and implied an inflamed tumor immunity that might be highly responsive to immunotherapy. LLPS inhibitor enhanced cytotoxicity of cisplatin/paclitaxel in selective cancer cell lines. These findings provide preliminary evidences for rational chemo-, targeted- and immuno-therapeutic innovation with LLPS regulating synergy.
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Affiliation(s)
- Si Sun
- Department of Obstetrics and Gynecology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430022, China
| | - Wenwen Wang
- Department of Obstetrics and Gynecology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430022, China
| | - Guoqing Li
- Department of Obstetrics and Gynecology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430022, China
| | - Man Xiao
- Department of Obstetrics and Gynecology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430022, China
| | - Minggang Peng
- Department of Obstetrics and Gynecology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430022, China
| | - Jing Cai
- Department of Obstetrics and Gynecology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430022, China
| | - Zehua Wang
- Department of Obstetrics and Gynecology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430022, China
| | - Qiang Yang
- Department of Obstetrics and Gynecology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430022, China
| | - Xiaoqi He
- Department of Obstetrics and Gynecology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430022, China
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Liu H, Tang T. Pan-cancer genetic analysis of disulfidptosis-related gene set. Cancer Genet 2023; 278-279:91-103. [PMID: 37879141 DOI: 10.1016/j.cancergen.2023.10.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2023] [Revised: 09/11/2023] [Accepted: 10/08/2023] [Indexed: 10/27/2023]
Abstract
BACKGROUND A recent study has identified a novel programmed cell death pathway, termed disulfidptosis, which is based on disulfide proteins. This discovery provides new insight into the mechanisms of cell death and may have implications for therapeutic strategies targeting cell death pathways. This study aimed to evaluate the pan-cancer genomics and clinical association of disulfidptosis and disulfidptosis-related cell death genes, including SLC7A11, INF2, CD2AP, PDLIM1, ACTN4, MYH9, MYH10, IQGAP1, FLNA, FLNB, TLN1, MYL6, ACTB, DSTN, and CAPZB. METHODS Using multi-omics profiling data, this study provides a comprehensive and systematic characterization of disulfidptosis genes across more than 9000 samples of over 30 types of cancer. RESULTS FLNA and FLNB were the two most frequently mutated disulfidptosis cell death genes in cancer. UCEC and SKCM were the two cancer types that have the highest mutation rates while the mutation of ACTN4 was associated with worse survival of CESC and ESCA. Breast cancer was potentially affected by disulfidptosis because its subtypes are different in disulfidptosis gene expression. Similarly, KIRC might also be associated with disulfidptosis. Additionally, the association of disulfidptosis-related cell death genes with survival was analyzed, with MESO and LGG as the top cancer types with survival associated with disulfidptosis cell death genes. The correlation between CNV and survival across multiple cancer types found that UCEC, KIRP, LGG, and KIRC were the top cancer types where the CNV level was associated with survival. There was a negative correlation between expression and methylation for most of the genes and there was only a slight correlation between methylation levels and survival of cancer in LGG. About half of the disulfidptosis-related cell death proteins were associated with the activation of EMT. Disulfidptosis genes were correlated to immune cell infiltration levels in cancers. Multiple compounds were identified as potential drugs that might be affected by disulfidptosis-related cell death for future study. CONCLUSION Disulfidptosis cell death genes are potentially involved in many cancer types and can be developed as candidates for cancer diagnosis, prognosis, and therapeutic biomarkers.
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Affiliation(s)
| | - Tao Tang
- Department of Molecular Diagnostics, Sun Yat-Sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangzhou, Guangdong, China.
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Hoff FW, Qiu Y, Brown BD, Gerbing RB, Leonti AR, Ries RE, Gamis AS, Aplenc R, Kolb EA, Alonzo TA, Meshinchi S, Jenkins GN, Horton T, Kornblau SM. Valosin-containing protein (VCP/p97) is prognostically unfavorable in pediatric AML, and negatively correlates with unfolded protein response proteins IRE1 and GRP78: A report from the Children's Oncology Group. Proteomics Clin Appl 2023; 17:e2200109. [PMID: 37287368 PMCID: PMC10700663 DOI: 10.1002/prca.202200109] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2022] [Revised: 04/25/2023] [Accepted: 05/25/2023] [Indexed: 06/09/2023]
Abstract
PURPOSE The endoplasmic reticulum (ER) is the major site of protein synthesis and folding in the cell. ER-associated degradation (ERAD) and unfolded protein response (UPR) are the main mechanisms of ER-mediated cell stress adaptation. Targeting the cell stress response is a promising therapeutic approach in acute myeloid leukemia (AML). EXPERIMENTAL DESIGN Protein expression levels of valosin-containing protein (VCP), a chief element of ERAD, were measured in peripheral blood samples from in 483 pediatric AML patients using reverse phase protein array methodology. Patients participated in the Children's Oncology Group AAML1031 phase 3 clinical trial that randomized patients to standard chemotherapy (cytarabine (Ara-C), daunorubicin, and etoposide [ADE]) versus ADE plus bortezomib (ADE+BTZ). RESULTS Low-VCP expression was significantly associated with favorable 5-year overall survival (OS) rate compared to middle-high-VCP expression (81% versus 63%, p < 0.001), independent of additional bortezomib treatment. Multivariable Cox regression analysis identified VCP as independent predictor of clinical outcome. UPR proteins IRE1 and GRP78 had significant negative correlation with VCP. Five-year OS in patients characterized by low-VCP, moderately high-IRE1 and high-GRP78 improved after treatment with ADE+BTZ versus ADE (66% versus 88%, p = 0.026). CONCLUSION AND CLINICAL RELEVANCE Our findings suggest the potential of the protein VCP as biomarker in prognostication prediction in pediatric AML.
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Affiliation(s)
- Fieke W. Hoff
- Department of Internal Medicine, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Yihua Qiu
- Department of Leukemia, The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Brandon D. Brown
- Department of Pediatrics, The University of Texas MD Anderson Cancer Center, Houston, TX
| | | | - Amanda R. Leonti
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
| | - Rhonda E. Ries
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
| | - Alan S. Gamis
- Department of Hematology-Oncology, Children’s Mercy Hospitals and Clinics, Kansas City, MO
| | - Richard Aplenc
- Division of Pediatric Oncology/Stem Cell Transplant, Children’s Hospital of Philadelphia, Philadelphia, PA
| | - E. Anders Kolb
- Nemours Center for Cancer and Blood Disorders, Alfred I. DuPont Hospital for Children, Wilmington, DE
| | - Todd A. Alonzo
- COG Statistics and Data Center, Monrovia, CA
- Keck School of Medicine, University of Southern California, CA
| | - Soheil Meshinchi
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
| | - Gaye N Jenkins
- Department of Pediatrics, Baylor College of Medicine/Dan L. Duncan Cancer Center and Texas Children’s Cancer Center, Houston, Texas
| | - Terzah Horton
- Department of Pediatrics, Baylor College of Medicine/Dan L. Duncan Cancer Center and Texas Children’s Cancer Center, Houston, Texas
| | - Steven M. Kornblau
- Department of Leukemia, The University of Texas MD Anderson Cancer Center, Houston, TX
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Guo J, Sun D, Zhang J, Guo J, Wu Z, Chen Y, Xu Y, Zhou D, Cui Y, Mo Q, Li Y, Zhao T, You Q. The E3 ubiquitin ligase RBCK1: Implications in the tumor immune microenvironment and antiangiogenic therapy of glioma. Comput Struct Biotechnol J 2023; 21:5212-5227. [PMID: 37928949 PMCID: PMC10624590 DOI: 10.1016/j.csbj.2023.10.020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2023] [Revised: 10/11/2023] [Accepted: 10/11/2023] [Indexed: 11/07/2023] Open
Abstract
E3 ubiquitin ligases (E3s) play a pivotal role in regulating the specificity of protein ubiquitination, and their significant functions as regulators of immune responses against tumors are attracting considerable interest. RBCK1-an RBR E3 ligase-is involved in immune regulation and tumor development. However, the potential effect of RBCK1 on glioma remains enigmatic. In the present study, we performed comprehensive analyses of multilevel data, which disclosed distribution characteristics of RBCK1 in pan-cancer, especially in glioma. Functional roles of RBCK1 were further confirmed using immunohistochemistry, cell biological assays, and xenograft experiments. Aberrant ascending of RBCK1 in multiple types of cancer was found to remodel the immunosuppressive microenvironment of glioma by regulating immunomodulators, cancer immunity cycles, and immune cell infiltration. Notably, the MES-like/RBCK1High cell population, a unique subset of cells in the microenvironment, suppressed T cell-mediated cell killing in glioma. Elevated expression levels of RBCK1 suggested a glioma subtype characterized by immunosuppression and hypo-responsiveness to immunotherapy but manifesting surprisingly increased responses to anti-angiogenic therapy. In conclusion, anti-RBCK1 target therapy might be beneficial for glioma treatment. Moreover, RBCK1 assisted in predicting molecular subtypes of glioma and response rates of patients to different clinical treatments, which could guide personalized therapy.
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Affiliation(s)
- Jing Guo
- Affiliated Cancer Hospital & Institute, Guangzhou Medical University, 78 Hengzhigang Road, Guangzhou 510095, China
- Key Laboratory of Cell Homeostasis and Cancer Research of Guangdong Higher Education Institutes, Guangzhou Medical University, Guangzhou 510182, China
- Center for Cancer and Immunology Research, State Key Laboratory of Respiratory Disease, Guangzhou, China
| | - Donglin Sun
- Department of Urology, Shenzhen Hospital, Southern Medical University, Shenzhen 518100, China
| | - Junwei Zhang
- Affiliated Cancer Hospital & Institute, Guangzhou Medical University, 78 Hengzhigang Road, Guangzhou 510095, China
- Key Laboratory of Cell Homeostasis and Cancer Research of Guangdong Higher Education Institutes, Guangzhou Medical University, Guangzhou 510182, China
- Center for Cancer and Immunology Research, State Key Laboratory of Respiratory Disease, Guangzhou, China
| | - Jie Guo
- Affiliated Cancer Hospital & Institute, Guangzhou Medical University, 78 Hengzhigang Road, Guangzhou 510095, China
- Key Laboratory of Cell Homeostasis and Cancer Research of Guangdong Higher Education Institutes, Guangzhou Medical University, Guangzhou 510182, China
- Center for Cancer and Immunology Research, State Key Laboratory of Respiratory Disease, Guangzhou, China
| | - Zhenpeng Wu
- Affiliated Cancer Hospital & Institute, Guangzhou Medical University, 78 Hengzhigang Road, Guangzhou 510095, China
- Key Laboratory of Cell Homeostasis and Cancer Research of Guangdong Higher Education Institutes, Guangzhou Medical University, Guangzhou 510182, China
- Center for Cancer and Immunology Research, State Key Laboratory of Respiratory Disease, Guangzhou, China
| | - Yongzhen Chen
- Department of Biotherapy, Second Affiliated Hospital of Nanjing Medical University, Nanjing 210011, China
| | - Yujie Xu
- Affiliated Cancer Hospital & Institute, Guangzhou Medical University, 78 Hengzhigang Road, Guangzhou 510095, China
- Key Laboratory of Cell Homeostasis and Cancer Research of Guangdong Higher Education Institutes, Guangzhou Medical University, Guangzhou 510182, China
- Center for Cancer and Immunology Research, State Key Laboratory of Respiratory Disease, Guangzhou, China
| | - Desheng Zhou
- Affiliated Cancer Hospital & Institute, Guangzhou Medical University, 78 Hengzhigang Road, Guangzhou 510095, China
- Key Laboratory of Cell Homeostasis and Cancer Research of Guangdong Higher Education Institutes, Guangzhou Medical University, Guangzhou 510182, China
- Center for Cancer and Immunology Research, State Key Laboratory of Respiratory Disease, Guangzhou, China
| | - Yachao Cui
- Affiliated Cancer Hospital & Institute, Guangzhou Medical University, 78 Hengzhigang Road, Guangzhou 510095, China
- Key Laboratory of Cell Homeostasis and Cancer Research of Guangdong Higher Education Institutes, Guangzhou Medical University, Guangzhou 510182, China
- Center for Cancer and Immunology Research, State Key Laboratory of Respiratory Disease, Guangzhou, China
| | - Qi Mo
- Affiliated Cancer Hospital & Institute, Guangzhou Medical University, 78 Hengzhigang Road, Guangzhou 510095, China
- Key Laboratory of Cell Homeostasis and Cancer Research of Guangdong Higher Education Institutes, Guangzhou Medical University, Guangzhou 510182, China
- Center for Cancer and Immunology Research, State Key Laboratory of Respiratory Disease, Guangzhou, China
| | - Yingchang Li
- Affiliated Cancer Hospital & Institute, Guangzhou Medical University, 78 Hengzhigang Road, Guangzhou 510095, China
- Key Laboratory of Cell Homeostasis and Cancer Research of Guangdong Higher Education Institutes, Guangzhou Medical University, Guangzhou 510182, China
- Center for Cancer and Immunology Research, State Key Laboratory of Respiratory Disease, Guangzhou, China
| | - Ting Zhao
- Department of Medical Oncology, Fudan University Shanghai Cancer Center, Shanghai 200032, China
| | - Qiang You
- Affiliated Cancer Hospital & Institute, Guangzhou Medical University, 78 Hengzhigang Road, Guangzhou 510095, China
- Key Laboratory of Cell Homeostasis and Cancer Research of Guangdong Higher Education Institutes, Guangzhou Medical University, Guangzhou 510182, China
- Center for Cancer and Immunology Research, State Key Laboratory of Respiratory Disease, Guangzhou, China
- Department of Biotherapy, Second Affiliated Hospital of Nanjing Medical University, Nanjing 210011, China
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Baritaki S, Zaravinos A. Cross-Talks between RKIP and YY1 through a Multilevel Bioinformatics Pan-Cancer Analysis. Cancers (Basel) 2023; 15:4932. [PMID: 37894300 PMCID: PMC10605344 DOI: 10.3390/cancers15204932] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2023] [Revised: 09/28/2023] [Accepted: 10/06/2023] [Indexed: 10/29/2023] Open
Abstract
Recent studies suggest that PEBP1 (also known as RKIP) and YY1, despite having distinct molecular functions, may interact and mutually influence each other's activity. They exhibit reciprocal control over each other's expression through regulatory loops, prompting the hypothesis that their interplay could be pivotal in cancer advancement and resistance to drugs. To delve into this interplay's functional characteristics, we conducted a comprehensive analysis using bioinformatics tools across a range of cancers. Our results confirm the association between elevated YY1 mRNA levels and varying survival outcomes in diverse tumors. Furthermore, we observed differing degrees of inhibitory or activating effects of these two genes in apoptosis, cell cycle, DNA damage, and other cancer pathways, along with correlations between their mRNA expression and immune infiltration. Additionally, YY1/PEBP1 expression and methylation displayed connections with genomic alterations across different cancer types. Notably, we uncovered links between the two genes and different indicators of immunosuppression, such as immune checkpoint blockade response and T-cell dysfunction/exclusion levels, across different patient groups. Overall, our findings underscore the significant role of the interplay between YY1 and PEBP1 in cancer progression, influencing genomic changes, tumor immunity, or the tumor microenvironment. Additionally, these two gene products appear to impact the sensitivity of anticancer drugs, opening new avenues for cancer therapy.
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Affiliation(s)
- Stavroula Baritaki
- Laboratory of Experimental Oncology, Division of Surgery, School of Medicine, University of Crete, 71003 Heraklion, Greece;
| | - Apostolos Zaravinos
- Department of Life Sciences, School of Sciences, European University Cyprus, 2404 Nicosia, Cyprus
- Cancer Genetics, Genomics and Systems Biology Group, Basic and Translational Cancer Research Center (BTCRC), 1516 Nicosia, Cyprus
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Lei JT, Jaehnig EJ, Smith H, Holt MV, Li X, Anurag M, Ellis MJ, Mills GB, Zhang B, Labrie M. The Breast Cancer Proteome and Precision Oncology. Cold Spring Harb Perspect Med 2023; 13:a041323. [PMID: 37137501 PMCID: PMC10547392 DOI: 10.1101/cshperspect.a041323] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Abstract
The goal of precision oncology is to translate the molecular features of cancer into predictive and prognostic tests that can be used to individualize treatment leading to improved outcomes and decreased toxicity. Success for this strategy in breast cancer is exemplified by efficacy of trastuzumab in tumors overexpressing ERBB2 and endocrine therapy for tumors that are estrogen receptor positive. However, other effective treatments, including chemotherapy, immune checkpoint inhibitors, and CDK4/6 inhibitors are not associated with strong predictive biomarkers. Proteomics promises another tier of information that, when added to genomic and transcriptomic features (proteogenomics), may create new opportunities to improve both treatment precision and therapeutic hypotheses. Here, we review both mass spectrometry-based and antibody-dependent proteomics as complementary approaches. We highlight how these methods have contributed toward a more complete understanding of breast cancer and describe the potential to guide diagnosis and treatment more accurately.
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Affiliation(s)
- Jonathan T Lei
- Lester and Sue Smith Breast Center and Dan L. Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, Texas 77030, USA
| | - Eric J Jaehnig
- Lester and Sue Smith Breast Center and Dan L. Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, Texas 77030, USA
| | - Hannah Smith
- Knight Cancer Institute, Oregon Health & Science University, Portland, Oregon 97239, USA
| | - Matthew V Holt
- Lester and Sue Smith Breast Center and Dan L. Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, Texas 77030, USA
| | - Xi Li
- Knight Cancer Institute, Oregon Health & Science University, Portland, Oregon 97239, USA
| | - Meenakshi Anurag
- Lester and Sue Smith Breast Center and Dan L. Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, Texas 77030, USA
| | - Matthew J Ellis
- Lester and Sue Smith Breast Center and Dan L. Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, Texas 77030, USA
| | - Gordon B Mills
- Knight Cancer Institute, Oregon Health & Science University, Portland, Oregon 97239, USA
| | - Bing Zhang
- Lester and Sue Smith Breast Center and Dan L. Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, Texas 77030, USA
| | - Marilyne Labrie
- Knight Cancer Institute, Oregon Health & Science University, Portland, Oregon 97239, USA
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Vishnoi M, Dereli Z, Yin Z, Kong EK, Kinali M, Thapa K, Babur O, Yun K, Abdelfattah N, Li X, Bozorgui B, Rostomily RC, Korkut A. A prognostic matrix code defines functional glioblastoma phenotypes and niches. RESEARCH SQUARE 2023:rs.3.rs-3285842. [PMID: 37790408 PMCID: PMC10543369 DOI: 10.21203/rs.3.rs-3285842/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/05/2023]
Abstract
Interactions among tumor, immune and vascular niches play major roles in driving glioblastoma (GBM) malignancy and treatment responses. The composition, heterogeneity, and localization of extracellular core matrix proteins (CMPs) that mediate such interactions, however, are not well understood. Here, we characterize functional and clinical relevance of genes encoding CMPs in GBM at bulk, single cell, and spatial anatomical resolution. We identify a "matrix code" for genes encoding CMPs whose expression levels categorize GBM tumors into matrisome-high and matrisome-low groups that correlate with worse and better patient survival, respectively. The matrisome enrichment is associated with specific driver oncogenic alterations, mesenchymal state, infiltration of pro-tumor immune cells and immune checkpoint gene expression. Anatomical and single cell transcriptome analyses indicate that matrisome gene expression is enriched in vascular and leading edge/infiltrative anatomic structures that are known to harbor glioma stem cells driving GBM progression. Finally, we identified a 17-gene matrisome signature that retains and further refines the prognostic value of genes encoding CMPs and, importantly, potentially predicts responses to PD1 blockade in clinical trials for GBM. The matrisome gene expression profiles provide potential biomarkers of functionally relevant GBM niches that contribute to mesenchymal-immune cross talk and patient stratification which could be applied to optimize treatment responses.
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Affiliation(s)
- Monika Vishnoi
- Department of Neurosurgery, Houston Methodist Research Institute, Houston, TX, 77030 USA
- Department of Neurosurgery, University of Washington School of Medicine, Seattle WA, 98195
| | - Zeynep Dereli
- Department of Bioinformatics and Computational Biology, MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Zheng Yin
- Department of Systems Medicine and Bioengineering, Houston Methodist Neal Cancer Center, Houston, TX, 77030 USA
| | - Elisabeth K. Kong
- Department of Bioinformatics and Computational Biology, MD Anderson Cancer Center, Houston, TX 77030, USA
- Department of Statistics, Rice University, Houston, TX, 77030, USA
| | - Meric Kinali
- Computer Science, College of Science and Mathematics, University of Massachusetts Boston, Boston, MA, 02125
| | - Kisan Thapa
- Computer Science, College of Science and Mathematics, University of Massachusetts Boston, Boston, MA, 02125
| | - Ozgun Babur
- Computer Science, College of Science and Mathematics, University of Massachusetts Boston, Boston, MA, 02125
| | - Kyuson Yun
- Department of Neurology, Houston Methodist Research Institute, Houston, TX, 77030 USA
- Department of Neurology, Weill Cornell Medical School, New York NY, 10065
| | - Nourhan Abdelfattah
- Department of Neurology, Houston Methodist Research Institute, Houston, TX, 77030 USA
- Department of Neurology, Weill Cornell Medical School, New York NY, 10065
| | - Xubin Li
- Department of Bioinformatics and Computational Biology, MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Behnaz Bozorgui
- Department of Bioinformatics and Computational Biology, MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Robert C. Rostomily
- Department of Neurosurgery, Houston Methodist Research Institute, Houston, TX, 77030 USA
- Department of Neurosurgery, University of Washington School of Medicine, Seattle WA, 98195
- Department of Neurosurgery, Weill Cornell Medical School, New York NY, 10065
| | - Anil Korkut
- Department of Bioinformatics and Computational Biology, MD Anderson Cancer Center, Houston, TX 77030, USA
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Pasquereau-Kotula E, Nigro G, Dingli F, Loew D, Poullet P, Xu Y, Kopetz S, Davis J, Peduto L, Robbe-Masselot C, Sansonetti P, Trieu-Cuot P, Dramsi S. Global proteomic identifies multiple cancer-related signaling pathways altered by a gut pathobiont associated with colorectal cancer. Sci Rep 2023; 13:14960. [PMID: 37696912 PMCID: PMC10495336 DOI: 10.1038/s41598-023-41951-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2023] [Accepted: 09/04/2023] [Indexed: 09/13/2023] Open
Abstract
In this work, we investigated the oncogenic role of Streptococcus gallolyticus subsp. gallolyticus (SGG), a gut bacterium associated with colorectal cancer (CRC). We showed that SGG UCN34 accelerates colon tumor development in a chemically induced CRC murine model. Full proteome and phosphoproteome analysis of murine colons chronically colonized by SGG UCN34 revealed that 164 proteins and 725 phosphorylation sites were differentially regulated. Ingenuity Pathway Analysis (IPA) indicates a pro-tumoral shift specifically induced by SGG UCN34, as ~ 90% of proteins and phosphoproteins identified were associated with digestive cancer. Comprehensive analysis of the altered phosphoproteins using ROMA software revealed up-regulation of several cancer hallmark pathways such as MAPK, mTOR and integrin/ILK/actin, affecting epithelial and stromal colonic cells. Importantly, an independent analysis of protein arrays of human colon tumors colonized with SGG showed up-regulation of PI3K/Akt/mTOR and MAPK pathways, providing clinical relevance to our findings. To test SGG's capacity to induce pre-cancerous transformation of the murine colonic epithelium, we grew ex vivo organoids which revealed unusual structures with compact morphology. Taken together, our results demonstrate the oncogenic role of SGG UCN34 in a murine model of CRC associated with activation of multiple cancer-related signaling pathways.
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Affiliation(s)
- Ewa Pasquereau-Kotula
- Biology of Gram-Positive Pathogens Unit, Institut Pasteur, Université Paris Cité, CNRS UMR6047, 75015, Paris, France.
| | - Giulia Nigro
- Stroma, Inflammation and Tissue Repair Unit, Institut Pasteur, Université Paris Cité, INSERM U1224, 75015, Paris, France
- Microenvironment and Immunity Unit, Institut Pasteur, Université Paris Cité, INSERM U1224, 75015, Paris, France
| | - Florent Dingli
- Institut Curie, PSL Research University, CurieCoreTech Spectrométrie de Masse Protéomique, 75005, Paris, France
| | - Damarys Loew
- Institut Curie, PSL Research University, CurieCoreTech Spectrométrie de Masse Protéomique, 75005, Paris, France
| | - Patrick Poullet
- Institut Curie, Bioinformatics Core Facility (CUBIC), INSERM U900, PSL Research University, Mines Paris Tech, 75005, Paris, France
| | - Yi Xu
- Center for Infectious and Inflammatory Diseases, Institute of Biosciences and Technology, Texas A&M Health Science Center, Houston, TX, USA
- Department of Microbial Pathogenesis and Immunology, School of Medicine, Bryan, TX, USA
- Department of Microbiology and Molecular Genetics, University of Texas Health Science Center, Houston, TX, USA
| | - Scott Kopetz
- Department of Gastrointestinal Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Jennifer Davis
- Department of Gastrointestinal Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
- University of Kansas, Kansas City, KS, USA
| | - Lucie Peduto
- Stroma, Inflammation and Tissue Repair Unit, Institut Pasteur, Université Paris Cité, INSERM U1224, 75015, Paris, France
| | - Catherine Robbe-Masselot
- Université de Lille, CNRS, UMR8576-UGSF-Unité de Glycobiologie Structurale et Fonctionnelle, 59000, Lille, France
| | - Philippe Sansonetti
- Institut Pasteur, Unité de Pathogénie Microbienne Moléculaire, INSERM U1202, and College de France, 75005, Paris, France
| | - Patrick Trieu-Cuot
- Biology of Gram-Positive Pathogens Unit, Institut Pasteur, Université Paris Cité, CNRS UMR6047, 75015, Paris, France
| | - Shaynoor Dramsi
- Biology of Gram-Positive Pathogens Unit, Institut Pasteur, Université Paris Cité, CNRS UMR6047, 75015, Paris, France.
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Molstad AJ, Patra RK. Dimension reduction for integrative survival analysis. Biometrics 2023; 79:1610-1623. [PMID: 35964256 DOI: 10.1111/biom.13736] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2021] [Accepted: 06/20/2022] [Indexed: 11/26/2022]
Abstract
We propose a constrained maximum partial likelihood estimator for dimension reduction in integrative (e.g., pan-cancer) survival analysis with high-dimensional predictors. We assume that for each population in the study, the hazard function follows a distinct Cox proportional hazards model. To borrow information across populations, we assume that each of the hazard functions depend only on a small number of linear combinations of the predictors (i.e., "factors"). We estimate these linear combinations using an algorithm based on "distance-to-set" penalties. This allows us to impose both low-rankness and sparsity on the regression coefficient matrix estimator. We derive asymptotic results that reveal that our estimator is more efficient than fitting a separate proportional hazards model for each population. Numerical experiments suggest that our method outperforms competitors under various data generating models. We use our method to perform a pan-cancer survival analysis relating protein expression to survival across 18 distinct cancer types. Our approach identifies six linear combinations, depending on only 20 proteins, which explain survival across the cancer types. Finally, to validate our fitted model, we show that our estimated factors can lead to better prediction than competitors on four external datasets.
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Affiliation(s)
- Aaron J Molstad
- Department of Statistics and Genetics Institute, University of Florida, Gainesville, Florida, USA
| | - Rohit K Patra
- Department of Statistics, University of Florida, Gainesville, Florida, USA
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41
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Tan K, Song Y, Xu M, You Z. Clinical evidence for a role of E2F1-induced replication stress in modulating tumor mutational burden and immune microenvironment. DNA Repair (Amst) 2023; 129:103531. [PMID: 37453246 DOI: 10.1016/j.dnarep.2023.103531] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2022] [Revised: 06/05/2023] [Accepted: 06/28/2023] [Indexed: 07/18/2023]
Abstract
DNA replication stress (RS) is frequently induced by oncogene activation and is believed to promote tumorigenesis. However, clinical evidence for the role of oncogene-induced RS in tumorigenesis remains scarce, and the mechanisms by which RS promotes cancer development remain incompletely understood. By performing a series of bioinformatic analyses on the oncogene E2F1, other RS-inducing factors, and replication fork processing factors in TCGA cancer database using previously established tools, we show that hyperactivity of E2F1 likely promotes the expression of several of these factors in virtually all types of cancer to induce RS and cytosolic self-DNA production. In addition, the expression of these factors positively correlates with that of ATR and Chk1 that govern the cellular response to RS, the tumor mutational load, and tumor infiltration of immune-suppressive CD4+Th2 cells and myeloid-derived suppressor cells (MDSCs). Consistently, high expression of these factors is associated with poor patient survival. Our study provides new insights into the role of E2F1-induced RS in tumorigenesis and suggests therapeutic approaches for E2F1-overexpressing cancers by targeting genomic instability, cytosolic self-DNA and the tumor immune microenvironment.
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Affiliation(s)
- Ke Tan
- Department of Gastroenterology, Affiliated Hospital of Jiangsu University, Zhenjiang, Jiangsu 212013, China; Department of Cell Biology and Physiology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Yizhe Song
- McDonnell Genome Institute, Washington University in St. Louis, St. Louis, MO 63110, USA
| | - Min Xu
- Department of Gastroenterology, Affiliated Hospital of Jiangsu University, Zhenjiang, Jiangsu 212013, China
| | - Zhongsheng You
- Department of Cell Biology and Physiology, Washington University School of Medicine, St. Louis, MO 63110, USA.
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42
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Li Y, Porta-Pardo E, Tokheim C, Bailey MH, Yaron TM, Stathias V, Geffen Y, Imbach KJ, Cao S, Anand S, Akiyama Y, Liu W, Wyczalkowski MA, Song Y, Storrs EP, Wendl MC, Zhang W, Sibai M, Ruiz-Serra V, Liang WW, Terekhanova NV, Rodrigues FM, Clauser KR, Heiman DI, Zhang Q, Aguet F, Calinawan AP, Dhanasekaran SM, Birger C, Satpathy S, Zhou DC, Wang LB, Baral J, Johnson JL, Huntsman EM, Pugliese P, Colaprico A, Iavarone A, Chheda MG, Ricketts CJ, Fenyö D, Payne SH, Rodriguez H, Robles AI, Gillette MA, Kumar-Sinha C, Lazar AJ, Cantley LC, Getz G, Ding L. Pan-cancer proteogenomics connects oncogenic drivers to functional states. Cell 2023; 186:3921-3944.e25. [PMID: 37582357 DOI: 10.1016/j.cell.2023.07.014] [Citation(s) in RCA: 18] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2022] [Revised: 12/30/2022] [Accepted: 07/10/2023] [Indexed: 08/17/2023]
Abstract
Cancer driver events refer to key genetic aberrations that drive oncogenesis; however, their exact molecular mechanisms remain insufficiently understood. Here, our multi-omics pan-cancer analysis uncovers insights into the impacts of cancer drivers by identifying their significant cis-effects and distal trans-effects quantified at the RNA, protein, and phosphoprotein levels. Salient observations include the association of point mutations and copy-number alterations with the rewiring of protein interaction networks, and notably, most cancer genes converge toward similar molecular states denoted by sequence-based kinase activity profiles. A correlation between predicted neoantigen burden and measured T cell infiltration suggests potential vulnerabilities for immunotherapies. Patterns of cancer hallmarks vary by polygenic protein abundance ranging from uniform to heterogeneous. Overall, our work demonstrates the value of comprehensive proteogenomics in understanding the functional states of oncogenic drivers and their links to cancer development, surpassing the limitations of studying individual cancer types.
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Affiliation(s)
- Yize Li
- Department of Medicine, Washington University in St. Louis, St. Louis, MO 63110, USA; McDonnell Genome Institute, Washington University in St. Louis, St. Louis, MO 63108, USA
| | - Eduard Porta-Pardo
- Josep Carreras Leukaemia Research Institute (IJC), Badalona 08916, Spain; Barcelona Supercomputing Center (BSC), Barcelona 08034, Spain
| | - Collin Tokheim
- Department of Data Science, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA 02115, USA
| | - Matthew H Bailey
- Department of Biology and Simmons Center for Cancer Research, Brigham Young University, Provo, UT 84602, USA
| | - Tomer M Yaron
- Meyer Cancer Center, Weill Cornell Medicine, New York, NY 10021, USA; Department of Medicine, Weill Cornell Medicine, New York, NY 10021, USA; Englander Institute for Precision Medicine, Institute for Computational Biomedicine, Weill Cornell Medicine, New York, NY 10021, USA
| | - Vasileios Stathias
- Sylvester Comprehensive Cancer Center, University of Miami Miller School of Medicine, Miami, FL 33136, USA; Department of Molecular and Cellular Pharmacology, University of Miami Miller School of Medicine, Miami, FL 33136, USA
| | - Yifat Geffen
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA 02142, USA; Cancer Center and Department of Pathology, Massachusetts General Hospital, Boston, MA 02115, USA
| | - Kathleen J Imbach
- Josep Carreras Leukaemia Research Institute (IJC), Badalona 08916, Spain; Barcelona Supercomputing Center (BSC), Barcelona 08034, Spain
| | - Song Cao
- Department of Medicine, Washington University in St. Louis, St. Louis, MO 63110, USA; McDonnell Genome Institute, Washington University in St. Louis, St. Louis, MO 63108, USA
| | - Shankara Anand
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA 02142, USA
| | - Yo Akiyama
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA 02142, USA
| | - Wenke Liu
- Institute for Systems Genetics, NYU Grossman School of Medicine, New York, NY 10016, USA; Department of Biochemistry and Molecular Pharmacology, NYU Grossman School of Medicine, New York, NY 10016, USA
| | - Matthew A Wyczalkowski
- Department of Medicine, Washington University in St. Louis, St. Louis, MO 63110, USA; McDonnell Genome Institute, Washington University in St. Louis, St. Louis, MO 63108, USA
| | - Yizhe Song
- Department of Medicine, Washington University in St. Louis, St. Louis, MO 63110, USA; McDonnell Genome Institute, Washington University in St. Louis, St. Louis, MO 63108, USA
| | - Erik P Storrs
- Department of Medicine, Washington University in St. Louis, St. Louis, MO 63110, USA; McDonnell Genome Institute, Washington University in St. Louis, St. Louis, MO 63108, USA
| | - Michael C Wendl
- McDonnell Genome Institute, Washington University in St. Louis, St. Louis, MO 63108, USA; Department of Genetics, Washington University in St. Louis, St. Louis, MO 63130, USA; Department of Mathematics, Washington University in St. Louis, St. Louis, MO 63130, USA
| | - Wubing Zhang
- Department of Data Science, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Mustafa Sibai
- Josep Carreras Leukaemia Research Institute (IJC), Badalona 08916, Spain; Barcelona Supercomputing Center (BSC), Barcelona 08034, Spain
| | - Victoria Ruiz-Serra
- Josep Carreras Leukaemia Research Institute (IJC), Badalona 08916, Spain; Barcelona Supercomputing Center (BSC), Barcelona 08034, Spain
| | - Wen-Wei Liang
- Department of Medicine, Washington University in St. Louis, St. Louis, MO 63110, USA; McDonnell Genome Institute, Washington University in St. Louis, St. Louis, MO 63108, USA
| | - Nadezhda V Terekhanova
- Department of Medicine, Washington University in St. Louis, St. Louis, MO 63110, USA; McDonnell Genome Institute, Washington University in St. Louis, St. Louis, MO 63108, USA
| | - Fernanda Martins Rodrigues
- Department of Medicine, Washington University in St. Louis, St. Louis, MO 63110, USA; McDonnell Genome Institute, Washington University in St. Louis, St. Louis, MO 63108, USA
| | - Karl R Clauser
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA 02142, USA
| | - David I Heiman
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA 02142, USA
| | - Qing Zhang
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA 02142, USA
| | - Francois Aguet
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA 02142, USA
| | - Anna P Calinawan
- Department of Genetic and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Saravana M Dhanasekaran
- Michigan Center for Translational Pathology, Department of Pathology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Chet Birger
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA 02142, USA
| | - Shankha Satpathy
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA 02142, USA
| | - Daniel Cui Zhou
- Department of Medicine, Washington University in St. Louis, St. Louis, MO 63110, USA; McDonnell Genome Institute, Washington University in St. Louis, St. Louis, MO 63108, USA
| | - Liang-Bo Wang
- Department of Medicine, Washington University in St. Louis, St. Louis, MO 63110, USA; McDonnell Genome Institute, Washington University in St. Louis, St. Louis, MO 63108, USA
| | - Jessika Baral
- Department of Medicine, Washington University in St. Louis, St. Louis, MO 63110, USA; McDonnell Genome Institute, Washington University in St. Louis, St. Louis, MO 63108, USA
| | - Jared L Johnson
- Meyer Cancer Center, Weill Cornell Medicine, New York, NY 10021, USA; Department of Medicine, Weill Cornell Medicine, New York, NY 10021, USA
| | - Emily M Huntsman
- Meyer Cancer Center, Weill Cornell Medicine, New York, NY 10021, USA; Department of Medicine, Weill Cornell Medicine, New York, NY 10021, USA
| | - Pietro Pugliese
- Department of Science and Technology, University of Sannio, 82100 Benevento, Italy
| | - Antonio Colaprico
- Sylvester Comprehensive Cancer Center, University of Miami Miller School of Medicine, Miami, FL 33136, USA; Department of Public Health Sciences, University of Miami Miller School of Medicine, Miami, FL 33136, USA
| | - Antonio Iavarone
- Sylvester Comprehensive Cancer Center, University of Miami Miller School of Medicine, Miami, FL 33136, USA; Department of Neurological Surgery, Department of Biochemistry and Molecular Biology, University of Miami Miller School of Medicine, Miami, FL 33136, USA
| | - Milan G Chheda
- Department of Medicine, Washington University in St. Louis, St. Louis, MO 63110, USA; Siteman Cancer Center, Washington University in St. Louis, St. Louis, MO 63130, USA; Department of Neurology, Washington University in St. Louis, St. Louis, MO 63130, USA
| | - Christopher J Ricketts
- Urologic Oncology Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - David Fenyö
- Institute for Systems Genetics, NYU Grossman School of Medicine, New York, NY 10016, USA; Department of Biochemistry and Molecular Pharmacology, NYU Grossman School of Medicine, New York, NY 10016, USA
| | - Samuel H Payne
- Department of Biology, Brigham Young University, Provo, UT 84602, USA
| | - Henry Rodriguez
- Office of Cancer Clinical Proteomics Research, National Cancer Institute, Rockville, MD 20850, USA
| | - Ana I Robles
- Office of Cancer Clinical Proteomics Research, National Cancer Institute, Rockville, MD 20850, USA
| | - Michael A Gillette
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA 02142, USA; Harvard Medical School, Boston, MA 02115, USA
| | - Chandan Kumar-Sinha
- Michigan Center for Translational Pathology, Department of Pathology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Alexander J Lazar
- Departments of Pathology & Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Lewis C Cantley
- Meyer Cancer Center, Weill Cornell Medicine, New York, NY 10021, USA; Department of Medicine, Weill Cornell Medicine, New York, NY 10021, USA.
| | - Gad Getz
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA 02142, USA; Cancer Center and Department of Pathology, Massachusetts General Hospital, Boston, MA 02115, USA; Harvard Medical School, Boston, MA 02115, USA.
| | - Li Ding
- Department of Medicine, Washington University in St. Louis, St. Louis, MO 63110, USA; McDonnell Genome Institute, Washington University in St. Louis, St. Louis, MO 63108, USA; Department of Genetics, Washington University in St. Louis, St. Louis, MO 63130, USA; Siteman Cancer Center, Washington University in St. Louis, St. Louis, MO 63130, USA.
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43
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Orsini A, Diquigiovanni C, Bonora E. Omics Technologies Improving Breast Cancer Research and Diagnostics. Int J Mol Sci 2023; 24:12690. [PMID: 37628869 PMCID: PMC10454385 DOI: 10.3390/ijms241612690] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2023] [Revised: 08/09/2023] [Accepted: 08/10/2023] [Indexed: 08/27/2023] Open
Abstract
Breast cancer (BC) has yielded approximately 2.26 million new cases and has caused nearly 685,000 deaths worldwide in the last two years, making it the most common diagnosed cancer type in the world. BC is an intricate ecosystem formed by both the tumor microenvironment and malignant cells, and its heterogeneity impacts the response to treatment. Biomedical research has entered the era of massive omics data thanks to the high-throughput sequencing revolution, quick progress and widespread adoption. These technologies-liquid biopsy, transcriptomics, epigenomics, proteomics, metabolomics, pharmaco-omics and artificial intelligence imaging-could help researchers and clinicians to better understand the formation and evolution of BC. This review focuses on the findings of recent multi-omics-based research that has been applied to BC research, with an introduction to every omics technique and their applications for the different BC phenotypes, biomarkers, target therapies, diagnosis, treatment and prognosis, to provide a comprehensive overview of the possibilities of BC research.
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Affiliation(s)
| | - Chiara Diquigiovanni
- Department of Medical and Surgical Sciences (DIMEC), University of Bologna, 40131 Bologna, Italy; (A.O.); (E.B.)
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44
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Li X, Poire A, Jeong KJ, Zhang D, Chen G, Sun C, Mills GB. Single-cell trajectory analysis reveals a CD9 positive state to contribute to exit from stem cell-like and embryonic diapause states and transit to drug-resistant states. Cell Death Discov 2023; 9:285. [PMID: 37542044 PMCID: PMC10403509 DOI: 10.1038/s41420-023-01586-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2023] [Revised: 07/12/2023] [Accepted: 07/27/2023] [Indexed: 08/06/2023] Open
Abstract
Bromo- and extra-terminal domain (BET) inhibitors (BETi) have been shown to decrease tumor growth in preclinical models and clinical trials. However, toxicity and rapid emergence of resistance have limited their clinical implementation. To identify state changes underlying acquisition of resistance to the JQ1 BETi, we reanalyzed single-cell RNAseq data from JQ1 sensitive and resistant SUM149 and SUM159 triple-negative breast cancer cell lines. Parental and JQ1-resistant SUM149 and SUM159 exhibited a stem cell-like and embryonic diapause (SCLED) cell state as well as a transitional cell state between the SCLED state that is present in both treatment naïve and JQ1 treated cells, and a number of JQ1 resistant cell states. A transitional cell state transcriptional signature but not a SCLED state transcriptional signature predicted worsened outcomes in basal-like breast cancer patients suggesting that transit from the SCLED state to drug-resistant states contributes to patient outcomes. Entry of SUM149 and SUM159 into the transitional cell state was characterized by elevated expression of the CD9 tetraspanin. Knockdown or inhibition of CD9-sensitized cells to multiple targeted and cytotoxic drugs in vitro. Importantly, CD9 knockdown or blockade sensitized SUM149 to JQ1 in vivo by trapping cells in the SCLED state and limiting transit to resistant cell states. Thus, CD9 appears to be critical for the transition from a SCLED state into treatment-resistant cell states and warrants exploration as a therapeutic target in basal-like breast cancer.
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Affiliation(s)
- Xi Li
- Division of Oncological Sciences Knight Cancer Institute, Oregon Health and Science University, Portland, OR, 97201, USA.
- Department of Obstetrics and Gynecology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, 430030, Wuhan, China.
| | - Alfonso Poire
- Division of Oncological Sciences Knight Cancer Institute, Oregon Health and Science University, Portland, OR, 97201, USA
| | - Kang Jin Jeong
- Division of Oncological Sciences Knight Cancer Institute, Oregon Health and Science University, Portland, OR, 97201, USA
| | - Dong Zhang
- Division of Oncological Sciences Knight Cancer Institute, Oregon Health and Science University, Portland, OR, 97201, USA
| | - Gang Chen
- Department of Obstetrics and Gynecology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, 430030, Wuhan, China
| | - Chaoyang Sun
- Department of Obstetrics and Gynecology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, 430030, Wuhan, China
| | - Gordon B Mills
- Division of Oncological Sciences Knight Cancer Institute, Oregon Health and Science University, Portland, OR, 97201, USA
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45
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Li Z, Vacanti NM. A Tale of Three Proteomes: Visualizing Protein and Transcript Abundance Relationships in the Breast Cancer Proteome Portal. J Proteome Res 2023; 22:2727-2733. [PMID: 37493333 DOI: 10.1021/acs.jproteome.3c00290] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/27/2023]
Abstract
Molecular characterization is transforming research on novel therapeutics in breast cancer. High-throughput methodologies are unbiased to hypotheses; thus, data produced are relevant to address unlimited questions and provide resources for the experimental design process. However, the opportunity is often overlooked because data are not readily accessed or analyzed. Herein, the Breast Cancer Proteome Portal, the only online tool for analyzing protein and transcript abundances across the three breast cancer proteomics studies, is presented. The tool is applied to demonstrate that cofunctioning protein abundances are highly correlated and, conversely, high abundance correlation may be an indicator of cofunction. Furthermore, the cofunction-correlation relationship is less resolved at the transcript level. By applying analysis and visualization tools within the Breast Cancer Proteome Portal, insights are garnered about serine synthesis and the compartmentalization of one-carbon metabolism in breast cancer, and a transcription factor tumorigenic regulatory network of glutamine deamination and oxidation is proposed, illustrating that the Breast Cancer Proteome Portal provides an interface for garnering insights from the information-rich studies of the breast cancer proteome.
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Affiliation(s)
- Zhuoheng Li
- Division of Nutritional Sciences, Cornell University, Ithaca, New York 14853-0001, United States
| | - Nathaniel M Vacanti
- Division of Nutritional Sciences, Cornell University, Ithaca, New York 14853-0001, United States
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46
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Upadhya SR, Ryan CJ. Antibody reliability influences observed mRNA-protein correlations in tumour samples. Life Sci Alliance 2023; 6:e202201885. [PMID: 37169592 PMCID: PMC10176110 DOI: 10.26508/lsa.202201885] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2022] [Revised: 05/02/2023] [Accepted: 05/02/2023] [Indexed: 05/13/2023] Open
Abstract
Reverse phase protein arrays (RPPA) have been used to quantify the abundance of hundreds of proteins across thousands of tumour samples in the Cancer Genome Atlas. By number of samples, this is the largest tumour proteomic dataset available and it provides an opportunity to systematically assess the correlation between mRNA and protein abundances. However, the RPPA approach is highly dependent on antibody reliability and approximately one-quarter of the antibodies used in the the Cancer Genome Atlas are deemed to be somewhat less reliable. Here, we assess the impact of antibody reliability on observed mRNA-protein correlations. We find that, in general, proteins measured with less reliable antibodies have lower observed mRNA-protein correlations. This is not true of the same proteins when measured using mass spectrometry. Furthermore, in cell lines, we find that when the same protein is quantified by both mass spectrometry and RPPA, the overall correlation between the two measurements is lower for proteins measured with less reliable antibodies. Overall our results reinforce the need for caution in using RPPA measurements from less reliable antibodies.
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Affiliation(s)
- Swathi Ramachandra Upadhya
- School of Computer Science, University College Dublin, Dublin, Ireland
- Conway Institute, University College Dublin, Dublin, Ireland
- Systems Biology Ireland, University College Dublin, Dublin, Ireland
| | - Colm J Ryan
- School of Computer Science, University College Dublin, Dublin, Ireland
- Conway Institute, University College Dublin, Dublin, Ireland
- Systems Biology Ireland, University College Dublin, Dublin, Ireland
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47
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Medvedev KE, Schaeffer RD, Chen KS, Grishin NV. Pan-cancer structurome reveals overrepresentation of beta sandwiches and underrepresentation of alpha helical domains. Sci Rep 2023; 13:11988. [PMID: 37491511 PMCID: PMC10368619 DOI: 10.1038/s41598-023-39273-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2023] [Accepted: 07/22/2023] [Indexed: 07/27/2023] Open
Abstract
The recent progress in the prediction of protein structures marked a historical milestone. AlphaFold predicted 200 million protein models with an accuracy comparable to experimental methods. Protein structures are widely used to understand evolution and to identify potential drug targets for the treatment of various diseases, including cancer. Thus, these recently predicted structures might convey previously unavailable information about cancer biology. Evolutionary classification of protein domains is challenging and different approaches exist. Recently our team presented a classification of domains from human protein models released by AlphaFold. Here we evaluated the pan-cancer structurome, domains from over and under expressed proteins in 21 cancer types, using the broadest levels of the ECOD classification: the architecture (A-groups) and possible homology (X-groups) levels. Our analysis reveals that AlphaFold has greatly increased the three-dimensional structural landscape for proteins that are differentially expressed in these 21 cancer types. We show that beta sandwich domains are significantly overrepresented and alpha helical domains are significantly underrepresented in the majority of cancer types. Our data suggest that the prevalence of the beta sandwiches is due to the high levels of immunoglobulins and immunoglobulin-like domains that arise during tumor development-related inflammation. On the other hand, proteins with exclusively alpha domains are important elements of homeostasis, apoptosis and transmembrane transport. Therefore cancer cells tend to reduce representation of these proteins to promote successful oncogeneses.
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Affiliation(s)
- Kirill E Medvedev
- Department of Biophysics, University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA.
| | - R Dustin Schaeffer
- Department of Biophysics, University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA
| | - Kenneth S Chen
- Department of Pediatrics, University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA
- Children's Medical Center Research Institute, University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA
| | - Nick V Grishin
- Department of Biophysics, University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA
- Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA
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48
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Álvez MB, Edfors F, von Feilitzen K, Zwahlen M, Mardinoglu A, Edqvist PH, Sjöblom T, Lundin E, Rameika N, Enblad G, Lindman H, Höglund M, Hesselager G, Stålberg K, Enblad M, Simonson OE, Häggman M, Axelsson T, Åberg M, Nordlund J, Zhong W, Karlsson M, Gyllensten U, Ponten F, Fagerberg L, Uhlén M. Next generation pan-cancer blood proteome profiling using proximity extension assay. Nat Commun 2023; 14:4308. [PMID: 37463882 DOI: 10.1038/s41467-023-39765-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2022] [Accepted: 06/27/2023] [Indexed: 07/20/2023] Open
Abstract
A comprehensive characterization of blood proteome profiles in cancer patients can contribute to a better understanding of the disease etiology, resulting in earlier diagnosis, risk stratification and better monitoring of the different cancer subtypes. Here, we describe the use of next generation protein profiling to explore the proteome signature in blood across patients representing many of the major cancer types. Plasma profiles of 1463 proteins from more than 1400 cancer patients are measured in minute amounts of blood collected at the time of diagnosis and before treatment. An open access Disease Blood Atlas resource allows the exploration of the individual protein profiles in blood collected from the individual cancer patients. We also present studies in which classification models based on machine learning have been used for the identification of a set of proteins associated with each of the analyzed cancers. The implication for cancer precision medicine of next generation plasma profiling is discussed.
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Affiliation(s)
- María Bueno Álvez
- Science for Life Laboratory, Department of Protein Science, KTH Royal Institute of Technology, Stockholm, Sweden
| | - Fredrik Edfors
- Science for Life Laboratory, Department of Protein Science, KTH Royal Institute of Technology, Stockholm, Sweden
| | - Kalle von Feilitzen
- Science for Life Laboratory, Department of Protein Science, KTH Royal Institute of Technology, Stockholm, Sweden
| | - Martin Zwahlen
- Science for Life Laboratory, Department of Protein Science, KTH Royal Institute of Technology, Stockholm, Sweden
| | - Adil Mardinoglu
- Science for Life Laboratory, Department of Protein Science, KTH Royal Institute of Technology, Stockholm, Sweden
- Centre for Host-Microbiome Interactions, Faculty of Dentistry, Oral & Craniofacial Sciences, King's College London, London, SE1 9RT, UK
| | - Per-Henrik Edqvist
- Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala, Sweden
| | - Tobias Sjöblom
- Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala, Sweden
| | - Emma Lundin
- Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala, Sweden
| | - Natallia Rameika
- Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala, Sweden
| | - Gunilla Enblad
- Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala, Sweden
| | - Henrik Lindman
- Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala, Sweden
| | - Martin Höglund
- Department of Medical Sciences, Uppsala University, Uppsala, Sweden
| | - Göran Hesselager
- Department of Medical Sciences, Uppsala University, Uppsala, Sweden
| | - Karin Stålberg
- Department of Women's and Children's Health, Uppsala University, Uppsala, Sweden
| | - Malin Enblad
- Department of Surgical Sciences, Uppsala University, Uppsala, Sweden
| | - Oscar E Simonson
- Department of Surgical Sciences, Uppsala University, Uppsala, Sweden
| | - Michael Häggman
- Department of Surgical Sciences, Uppsala University, Uppsala, Sweden
| | - Tomas Axelsson
- Department of Medical Sciences, Uppsala University, Uppsala, Sweden
| | - Mikael Åberg
- Department of Medical Sciences, Clinical Chemistry and SciLifeLab Affinity Proteomics, Uppsala University, Uppsala, Sweden
| | - Jessica Nordlund
- Department of Medical Sciences, Uppsala University, Uppsala, Sweden
| | - Wen Zhong
- Science for Life Laboratory, Department of Biomedical and Clinical Sciences (BKV), Linköping University, Linköping, Sweden
| | - Max Karlsson
- Science for Life Laboratory, Department of Protein Science, KTH Royal Institute of Technology, Stockholm, Sweden
| | - Ulf Gyllensten
- Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala, Sweden
| | - Fredrik Ponten
- Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala, Sweden
| | - Linn Fagerberg
- Science for Life Laboratory, Department of Protein Science, KTH Royal Institute of Technology, Stockholm, Sweden
| | - Mathias Uhlén
- Science for Life Laboratory, Department of Protein Science, KTH Royal Institute of Technology, Stockholm, Sweden.
- Department of Neuroscience, Karolinska Institutet, Stockholm, Sweden.
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49
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Shao Y, Fan X, Yang X, Li S, Huang L, Zhou X, Zhang S, Zheng M, Sun J. Impact of Cuproptosis-related markers on clinical status, tumor immune microenvironment and immunotherapy in colorectal cancer: A multi-omic analysis. Comput Struct Biotechnol J 2023; 21:3383-3403. [PMID: 37389187 PMCID: PMC10300104 DOI: 10.1016/j.csbj.2023.06.011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2023] [Revised: 06/07/2023] [Accepted: 06/10/2023] [Indexed: 07/01/2023] Open
Abstract
Background Cuproptosis, a novel identified cell death form induced by copper, is characterized by aggregation of lipoylated mitochondrial enzymes and the destabilization of Fe-S cluster proteins. However, the function and potential clinical value of cuproptosis and cuproptosis-related biomarkers in colorectal cancer (CRC) remain largely unknown. Methods A comprehensive multi-omics (transcriptomics, genomics, and single-cell transcriptome) analysis was performed for identifying the influence of 16 cuproptosis-related markers on clinical status, molecular functions and tumor microenvironment (TME) in CRC. A novel cuproptosis-related scoring system (CuproScore) based on cuproptosis-related markers was also constructed to predict the prognosis of CRC individuals, TME and the response to immunotherapy. In addition, our transcriptome cohort of 15 paired CRC tissue, tissue-array, and various assays in 4 kinds of CRC cell lines in vitro were applied for verification. Results Cuproptosis-related markers were closely associated with both clinical prognosis and molecular functions. And the cuproptosis-related molecular phenotypes and scoring system (CuproScore) could distinguish and predict the prognosis of CRC patients, TME, and the response to immunotherapy in both public and our transcriptome cohorts. Besides, the expression, function and clinical significance of these markers were also checked and analyzed in CRC cell lines and CRC tissues in our own cohorts. Conclusions In conclusion, we indicated that cuproptosis and CPRMs played a significant role in CRC progression and in modeling the TME. Inducing cuproptosis may be a useful tool for tumor therapy in the future.
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Affiliation(s)
- Yanfei Shao
- Department of General Surgery, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Shanghai Minimally Invasive Surgery Center, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Shanghai Institute of Digestive Surgery, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Xiaodong Fan
- Department of General Surgery, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Shanghai Minimally Invasive Surgery Center, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Shanghai Institute of Digestive Surgery, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Xiao Yang
- Department of General Surgery, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Shanghai Minimally Invasive Surgery Center, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Shuchun Li
- Department of General Surgery, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Shanghai Minimally Invasive Surgery Center, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Ling Huang
- Department of General Surgery, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Shanghai Minimally Invasive Surgery Center, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Shanghai Institute of Digestive Surgery, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Xueliang Zhou
- Department of General Surgery, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Shanghai Minimally Invasive Surgery Center, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Shanghai Institute of Digestive Surgery, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Sen Zhang
- Department of General Surgery, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Shanghai Minimally Invasive Surgery Center, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Minhua Zheng
- Department of General Surgery, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Shanghai Minimally Invasive Surgery Center, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Jing Sun
- Department of General Surgery, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Shanghai Minimally Invasive Surgery Center, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
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50
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Vishnoi M, Dereli Z, Yin Z, Kong EK, Kinali M, Thapa K, Babur O, Yun K, Abdelfattah N, Li X, Bozorgui B, Rostomily RC, Korkut A. A prognostic matrix code defines functional glioblastoma phenotypes and niches. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.06.06.543903. [PMID: 37333072 PMCID: PMC10274725 DOI: 10.1101/2023.06.06.543903] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/20/2023]
Abstract
Interactions among tumor, immune and vascular niches play major roles in driving glioblastoma (GBM) malignancy and treatment responses. The composition, heterogeneity, and localization of extracellular core matrix proteins (CMPs) that mediate such interactions, however, are not well understood. Here, we characterize functional and clinical relevance of genes encoding CMPs in GBM at bulk, single cell, and spatial anatomical resolution. We identify a "matrix code" for genes encoding CMPs whose expression levels categorize GBM tumors into matrisome-high and matrisome-low groups that correlate with worse and better survival, respectively, of patients. The matrisome enrichment is associated with specific driver oncogenic alterations, mesenchymal state, infiltration of pro-tumor immune cells and immune checkpoint gene expression. Anatomical and single cell transcriptome analyses indicate that matrisome gene expression is enriched in vascular and leading edge/infiltrative anatomic structures that are known to harbor glioma stem cells driving GBM progression. Finally, we identified a 17-gene matrisome signature that retains and further refines the prognostic value of genes encoding CMPs and, importantly, potentially predicts responses to PD1 blockade in clinical trials for GBM. The matrisome gene expression profiles may provide biomarkers of functionally relevant GBM niches that contribute to mesenchymal-immune cross talk and patient stratification to optimize treatment responses.
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Affiliation(s)
- Monika Vishnoi
- Department of Neurosurgery, Houston Methodist Research Institute, Houston, TX, 77030 USA
- Department of Neurosurgery, University of Washington School of Medicine, Seattle WA, 98195
| | - Zeynep Dereli
- Department of Bioinformatics and Computational Biology, MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Zheng Yin
- Department of Systems Medicine and Bioengineering, Houston Methodist Neal Cancer Center, Houston, TX, 77030 USA
| | - Elisabeth K. Kong
- Department of Bioinformatics and Computational Biology, MD Anderson Cancer Center, Houston, TX 77030, USA
- Department of Statistics, Rice University, Houston, TX, 77030, USA
| | - Meric Kinali
- Computer Science, College of Science and Mathematics, University of Massachusetts Boston, Boston, MA, 02125
| | - Kisan Thapa
- Computer Science, College of Science and Mathematics, University of Massachusetts Boston, Boston, MA, 02125
| | - Ozgun Babur
- Computer Science, College of Science and Mathematics, University of Massachusetts Boston, Boston, MA, 02125
| | - Kyuson Yun
- Department of Neurology, Houston Methodist Research Institute, Houston, TX, 77030 USA
- Department of Neurology, Weill Cornell Medical School, New York NY, 10065
| | - Nourhan Abdelfattah
- Department of Neurology, Houston Methodist Research Institute, Houston, TX, 77030 USA
- Department of Neurology, Weill Cornell Medical School, New York NY, 10065
| | - Xubin Li
- Department of Bioinformatics and Computational Biology, MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Behnaz Bozorgui
- Department of Bioinformatics and Computational Biology, MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Robert C. Rostomily
- Department of Neurosurgery, Houston Methodist Research Institute, Houston, TX, 77030 USA
- Department of Neurosurgery, University of Washington School of Medicine, Seattle WA, 98195
- Department of Neurosurgery, Weill Cornell Medical School, New York NY, 10065
| | - Anil Korkut
- Department of Bioinformatics and Computational Biology, MD Anderson Cancer Center, Houston, TX 77030, USA
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