51
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Song Q, Hawkins GA, Wudel L, Chou PC, Forbes E, Pullikuth AK, Liu L, Jin G, Craddock L, Topaloglu U, Kucera G, O'Neill S, Levine EA, Sun P, Watabe K, Lu Y, Alexander-Miller MA, Pasche B, Miller LD, Zhang W. Dissecting intratumoral myeloid cell plasticity by single cell RNA-seq. Cancer Med 2019; 8:3072-3085. [PMID: 31033233 PMCID: PMC6558497 DOI: 10.1002/cam4.2113] [Citation(s) in RCA: 89] [Impact Index Per Article: 17.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2019] [Revised: 03/07/2019] [Accepted: 03/08/2019] [Indexed: 12/18/2022] Open
Abstract
Tumor‐infiltrating myeloid cells are the most abundant leukocyte population within tumors. Molecular cues from the tumor microenvironment promote the differentiation of immature myeloid cells toward an immunosuppressive phenotype. However, the in situ dynamics of the transcriptional reprogramming underlying this process are poorly understood. Therefore, we applied single cell RNA‐seq (scRNA‐seq) to computationally investigate the cellular composition and transcriptional dynamics of tumor and adjacent normal tissues from 4 early‐stage non‐small cell lung cancer (NSCLC) patients. Our scRNA‐seq analyses identified 11 485 cells that varied in identity and gene expression traits between normal and tumor tissues. Among these, myeloid cell populations exhibited the most diverse changes between tumor and normal tissues, consistent with tumor‐mediated reprogramming. Through trajectory analysis, we identified a differentiation path from CD14+ monocytes to M2 macrophages (monocyte‐to‐M2). This differentiation path was reproducible across patients, accompanied by increased expression of genes (eg, MRC1/CD206, MSR1/CD204, PPARG, TREM2) with significantly enriched functions (Oxidative phosphorylation and P53 pathway) and decreased expression of genes (eg, CXCL2, IL1B) with significantly enriched functions (TNF‐α signaling via NF‐κB and inflammatory response). Our analysis further identified a co‐regulatory network implicating upstream transcription factors (JUN, NFKBIA) in monocyte‐to‐M2 differentiation, and activated ligand‐receptor interactions (eg, SFTPA1‐TLR2, ICAM1‐ITGAM) suggesting intratumoral mechanisms whereby epithelial cells stimulate monocyte‐to‐M2 differentiation. Overall, our study identified the prevalent monocyte‐to‐M2 differentiation in NSCLC, accompanied by an intricate transcriptional reprogramming mediated by specific transcriptional activators and intercellular crosstalk involving ligand‐receptor interactions.
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Affiliation(s)
- Qianqian Song
- Center for Cancer Genomics and Precision Oncology, Wake Forest Baptist Comprehensive Cancer Center, Wake Forest Baptist Medical Center, Winston Salem, North Carolina.,Department of Cancer Biology, Wake Forest School of Medicine, Winston Salem, North Carolina
| | - Gregory A Hawkins
- Center for Cancer Genomics and Precision Oncology, Wake Forest Baptist Comprehensive Cancer Center, Wake Forest Baptist Medical Center, Winston Salem, North Carolina.,Department of Biochemistry, Wake Forest School of Medicine, Winston Salem, North Carolina
| | - Leonard Wudel
- Department of Surgery, Wake Forest School of Medicine, Winston Salem, North Carolina
| | - Ping-Chieh Chou
- Center for Cancer Genomics and Precision Oncology, Wake Forest Baptist Comprehensive Cancer Center, Wake Forest Baptist Medical Center, Winston Salem, North Carolina.,Department of Cancer Biology, Wake Forest School of Medicine, Winston Salem, North Carolina
| | - Elizabeth Forbes
- Center for Cancer Genomics and Precision Oncology, Wake Forest Baptist Comprehensive Cancer Center, Wake Forest Baptist Medical Center, Winston Salem, North Carolina.,Department of Cancer Biology, Wake Forest School of Medicine, Winston Salem, North Carolina
| | - Ashok K Pullikuth
- Center for Cancer Genomics and Precision Oncology, Wake Forest Baptist Comprehensive Cancer Center, Wake Forest Baptist Medical Center, Winston Salem, North Carolina.,Department of Cancer Biology, Wake Forest School of Medicine, Winston Salem, North Carolina
| | - Liang Liu
- Center for Cancer Genomics and Precision Oncology, Wake Forest Baptist Comprehensive Cancer Center, Wake Forest Baptist Medical Center, Winston Salem, North Carolina.,Department of Cancer Biology, Wake Forest School of Medicine, Winston Salem, North Carolina
| | - Guangxu Jin
- Center for Cancer Genomics and Precision Oncology, Wake Forest Baptist Comprehensive Cancer Center, Wake Forest Baptist Medical Center, Winston Salem, North Carolina.,Department of Cancer Biology, Wake Forest School of Medicine, Winston Salem, North Carolina
| | - Lou Craddock
- Center for Cancer Genomics and Precision Oncology, Wake Forest Baptist Comprehensive Cancer Center, Wake Forest Baptist Medical Center, Winston Salem, North Carolina.,Department of Cancer Biology, Wake Forest School of Medicine, Winston Salem, North Carolina
| | - Umit Topaloglu
- Center for Cancer Genomics and Precision Oncology, Wake Forest Baptist Comprehensive Cancer Center, Wake Forest Baptist Medical Center, Winston Salem, North Carolina.,Department of Cancer Biology, Wake Forest School of Medicine, Winston Salem, North Carolina
| | - Gregory Kucera
- Center for Cancer Genomics and Precision Oncology, Wake Forest Baptist Comprehensive Cancer Center, Wake Forest Baptist Medical Center, Winston Salem, North Carolina.,Department of Cancer Biology, Wake Forest School of Medicine, Winston Salem, North Carolina
| | - Stacey O'Neill
- Center for Cancer Genomics and Precision Oncology, Wake Forest Baptist Comprehensive Cancer Center, Wake Forest Baptist Medical Center, Winston Salem, North Carolina.,Department of Pathology, Wake Forest School of Medicine, Winston Salem, North Carolina
| | - Edward A Levine
- Center for Cancer Genomics and Precision Oncology, Wake Forest Baptist Comprehensive Cancer Center, Wake Forest Baptist Medical Center, Winston Salem, North Carolina.,Department of Surgery, Wake Forest School of Medicine, Winston Salem, North Carolina
| | - Peiqing Sun
- Department of Cancer Biology, Wake Forest School of Medicine, Winston Salem, North Carolina
| | - Kounosuke Watabe
- Department of Cancer Biology, Wake Forest School of Medicine, Winston Salem, North Carolina
| | - Yong Lu
- Department of Immunology and Microbiology, Wake Forest School of Medicine, Winston Salem, North Carolina
| | - Martha A Alexander-Miller
- Department of Immunology and Microbiology, Wake Forest School of Medicine, Winston Salem, North Carolina
| | - Boris Pasche
- Center for Cancer Genomics and Precision Oncology, Wake Forest Baptist Comprehensive Cancer Center, Wake Forest Baptist Medical Center, Winston Salem, North Carolina.,Department of Cancer Biology, Wake Forest School of Medicine, Winston Salem, North Carolina
| | - Lance D Miller
- Center for Cancer Genomics and Precision Oncology, Wake Forest Baptist Comprehensive Cancer Center, Wake Forest Baptist Medical Center, Winston Salem, North Carolina.,Department of Cancer Biology, Wake Forest School of Medicine, Winston Salem, North Carolina
| | - Wei Zhang
- Center for Cancer Genomics and Precision Oncology, Wake Forest Baptist Comprehensive Cancer Center, Wake Forest Baptist Medical Center, Winston Salem, North Carolina.,Department of Cancer Biology, Wake Forest School of Medicine, Winston Salem, North Carolina
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52
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Upadhyay G. Emerging Role of Lymphocyte Antigen-6 Family of Genes in Cancer and Immune Cells. Front Immunol 2019; 10:819. [PMID: 31068932 PMCID: PMC6491625 DOI: 10.3389/fimmu.2019.00819] [Citation(s) in RCA: 65] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2018] [Accepted: 03/27/2019] [Indexed: 12/14/2022] Open
Abstract
Stem Cell Antigen-1 (Sca-1/Ly6A) was the first identified member of the Lymphocyte antigen-6 (Ly6) gene family. Sca-1 serves as a marker of cancer stem cells and tissue resident stem cells in mice. The Sca-1 gene is located on mouse chromosome 15. While a direct homolog of Sca-1 in humans is missing, human chromosome 8—the syntenic region to mouse chromosome 15—harbors several genes containing the characteristic domain known as LU domain. The function of the LU domain in human LY6 gene family is not yet defined. The LY6 gene family proteins are present on human chromosome 6, 8, 11, and 19. The most interesting of these genes are located on chromosome 8q24.3, a frequently amplified locus in human cancer. Human LY6 genes represent novel biomarkers for poor cancer prognosis and are required for cancer progression in addition to playing an important role in immune escape. Although the mechanism associated with these phenotype is not yet clear, it is timely to review the current literature in order to address the critical need for future advancements in this field. This review will summarize recent findings which describe the role of human LY6 genes—LY6D, LY6E, LY6H, LY6K, PSCA, LYPD2, SLURP1, GML, GPIHBP1, and LYNX1; and their orthologs in mice at chromosome 15.
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Affiliation(s)
- Geeta Upadhyay
- Department of Pathology, John P. Murtha Cancer Center, F. Edward Hebert School of Medicine, Uniformed Services University of the Health Sciences, Bethesda, MD, United States
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53
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Meshcheryakova A, Svoboda M, Jaritz M, Mungenast F, Salzmann M, Pils D, Cacsire Castillo-Tong D, Hager G, Wolf A, Braicu EI, Sehouli J, Lambrechts S, Vergote I, Mahner S, Birner P, Zimmermann P, Brindley DN, Heinze G, Zeillinger R, Mechtcheriakova D. Interrelations of Sphingolipid and Lysophosphatidate Signaling with Immune System in Ovarian Cancer. Comput Struct Biotechnol J 2019; 17:537-560. [PMID: 31049165 PMCID: PMC6479272 DOI: 10.1016/j.csbj.2019.04.004] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2018] [Revised: 04/03/2019] [Accepted: 04/05/2019] [Indexed: 12/16/2022] Open
Abstract
The sphingolipid and lysophosphatidate regulatory networks impact diverse mechanisms attributed to cancer cells and the tumor immune microenvironment. Deciphering the complexity demands implementation of a holistic approach combined with higher-resolution techniques. We implemented a multi-modular integrative approach consolidating the latest accomplishments in gene expression profiling, prognostic/predictive modeling, next generation digital pathology, and systems biology for epithelial ovarian cancer. We assessed patient-specific transcriptional profiles using the sphingolipid/lysophosphatidate/immune-associated signature. This revealed novel sphingolipid/lysophosphatidate-immune gene-gene associations and distinguished tumor subtypes with immune high/low context. These were characterized by robust differences in sphingolipid-/lysophosphatidate-related checkpoints and the drug response. The analysis also nominates novel survival models for stratification of patients with CD68, LPAR3, SMPD1, PPAP2B, and SMPD2 emerging as the most prognostically important genes. Alignment of proprietary data with curated transcriptomic data from public databases across a variety of malignancies (over 600 categories; over 21,000 arrays) showed specificity for ovarian carcinoma. Our systems approach identified novel sphingolipid-lysophosphatidate-immune checkpoints and networks underlying tumor immune heterogeneity and disease outcomes. This holds great promise for delivering novel stratifying and targeting strategies.
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Affiliation(s)
- Anastasia Meshcheryakova
- Molecular Systems Biology and Pathophysiology Research Group, Department of Pathophysiology and Allergy Research, Center for Pathophysiology, Infectiology and Immunology, Medical University of Vienna, Vienna, Austria
| | - Martin Svoboda
- Molecular Systems Biology and Pathophysiology Research Group, Department of Pathophysiology and Allergy Research, Center for Pathophysiology, Infectiology and Immunology, Medical University of Vienna, Vienna, Austria
| | - Markus Jaritz
- Research Institute of Molecular Pathology, Vienna Biocenter, Vienna, Austria
| | - Felicitas Mungenast
- Molecular Systems Biology and Pathophysiology Research Group, Department of Pathophysiology and Allergy Research, Center for Pathophysiology, Infectiology and Immunology, Medical University of Vienna, Vienna, Austria
| | - Martina Salzmann
- Molecular Systems Biology and Pathophysiology Research Group, Department of Pathophysiology and Allergy Research, Center for Pathophysiology, Infectiology and Immunology, Medical University of Vienna, Vienna, Austria
| | - Dietmar Pils
- Sectionfor Clinical Biometrics, Center for Medical Statistics, Informatics, and Intelligent Systems, Medical University of Vienna, Vienna, Austria
| | - Dan Cacsire Castillo-Tong
- Translational Gynecology Group, Department of Obstetrics and Gynecology, Comprehensive Cancer Center, Medical University of Vienna, Vienna, Austria
| | - Gudrun Hager
- Molecular Oncology Group, Department of Obstetrics and Gynecology and Comprehensive Cancer Center, Gynecologic Cancer Unit, Medical University of Vienna, Vienna, Austria
| | - Andrea Wolf
- Translational Gynecology Group, Department of Obstetrics and Gynecology, Comprehensive Cancer Center, Medical University of Vienna, Vienna, Austria
| | - Elena Ioana Braicu
- Charité – Universitätsmedizin Berlin, Humboldt-Universität zu Berlin, Berlin Institute of Health, Department of Gynecology, Berlin, Germany
| | - Jalid Sehouli
- Charité – Universitätsmedizin Berlin, Humboldt-Universität zu Berlin, Berlin Institute of Health, Department of Gynecology, Berlin, Germany
| | - Sandrina Lambrechts
- Division of Gynecologic Oncology, University Hospital Leuven, Leuven Cancer Institute, KU Leuven, Leuven, Belgium
| | - Ignace Vergote
- Division of Gynecologic Oncology, University Hospital Leuven, Leuven Cancer Institute, KU Leuven, Leuven, Belgium
| | - Sven Mahner
- Department of Gynecology and Gynecologic Oncology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Peter Birner
- Department of Pathology, Medical University of Vienna, Vienna, Austria
| | | | - David N. Brindley
- Cancer Research Institute of Northern Alberta, Department of Biochemistry, University of Alberta, Edmonton, Alberta, Canada
| | - Georg Heinze
- Sectionfor Clinical Biometrics, Center for Medical Statistics, Informatics, and Intelligent Systems, Medical University of Vienna, Vienna, Austria
| | - Robert Zeillinger
- Molecular Oncology Group, Department of Obstetrics and Gynecology and Comprehensive Cancer Center, Gynecologic Cancer Unit, Medical University of Vienna, Vienna, Austria
| | - Diana Mechtcheriakova
- Molecular Systems Biology and Pathophysiology Research Group, Department of Pathophysiology and Allergy Research, Center for Pathophysiology, Infectiology and Immunology, Medical University of Vienna, Vienna, Austria
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54
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Ajina R, Zamalin D, Weiner LM. Functional genomics: paving the way for more successful cancer immunotherapy. Brief Funct Genomics 2019; 18:86-98. [PMID: 29762641 PMCID: PMC6430032 DOI: 10.1093/bfgp/ely017] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Immunotherapies have revolutionized cancer treatment. Immunotherapy is effective for the treatment of a wide range of cancer types and can mediate complete and durable tumor regression. Nonetheless, the field still faces many significant challenges, such as the need for personalized therapeutic strategies and better biomarkers, the difficulty of selecting the right combination therapy, and resistance to currently available immunotherapies. Both cancer and host immunity comprise significantly diverse and complex ecosystems, making immunogenomics an ideal field for functional genomics analysis. In this review, we describe the cancer-immunity cycle, how cancer cells manage to evade immune attack and the current hurdles in the path of cancer immunotherapy. Then, we discuss how functional genomics approaches can pave the way for more successful cancer immunotherapies.
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55
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Baker RG, Hoos AX, Adam SJ, Wholley D, Doroshow JH, Lowy DR, Tabak LA, Collins FS. The Partnership for Accelerating Cancer Therapies. Cancer J 2019; 24:111-114. [PMID: 30273184 PMCID: PMC6170010 DOI: 10.1097/ppo.0000000000000321] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
Abstract
As a part of the Cancer Moonshot, the National Cancer Institute, part of the National Institutes of Health, the Foundation for National Institutes of Health, the US Food and Drug Administration, and 12 pharmaceutical companies have formed a 5-year, $220 million precompetitive public-private research collaboration called the Partnership for Accelerating Cancer Therapies. A systematic cross-sector effort to identify and develop robust, standardized biomarkers and related clinical data, Partnership for Accelerating Cancer Therapies will support the selection and testing of promising immunotherapies for the treatment of cancer, with the goal of bringing effective therapy to more patients.
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Affiliation(s)
| | | | - Stacey J Adam
- Foundation for the National Institutes of Health, North Bethesda
| | - David Wholley
- Foundation for the National Institutes of Health, North Bethesda
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56
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Franzén B, Alexeyenko A, Kamali-Moghaddam M, Hatschek T, Kanter L, Ramqvist T, Kierkegaard J, Masucci G, Auer G, Landegren U, Lewensohn R. Protein profiling of fine-needle aspirates reveals subtype-associated immune signatures and involvement of chemokines in breast cancer. Mol Oncol 2019; 13:376-391. [PMID: 30451357 PMCID: PMC6360506 DOI: 10.1002/1878-0261.12410] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2018] [Revised: 09/28/2018] [Accepted: 11/08/2018] [Indexed: 01/04/2023] Open
Abstract
There are increasing demands for informative cancer biomarkers, accessible via minimally invasive procedures, both for initial diagnostics and for follow-up of personalized cancer therapy, including immunotherapy. Fine-needle aspiration (FNA) biopsy provides ready access to relevant tissue samples; however, the minute amounts of sample require sensitive multiplex molecular analysis to be of clinical biomarker utility. We have applied proximity extension assays (PEA) to analyze 167 proteins in FNA samples from patients with breast cancer (BC; n = 25) and benign lesions (n = 32). We demonstrate that the FNA BC samples could be divided into two main clusters, characterized by differences in expression levels of the estrogen receptor (ER) and the proliferation marker Ki67. This clustering corresponded to some extent to established BC subtypes. Our analysis also revealed several proteins whose expression levels differed between BC and benign lesions (e.g., CA9, GZMB, IL-6, VEGFA, CXCL11, PDL1, and PCD1), as well as several chemokines correlating with ER and Ki67 status (e.g., CCL4, CCL8, CCL20, CXCL8, CXCL9, and CXCL17). Finally, we also identified three signatures that could predict Ki67 status, ER status, and tumor grade, respectively, based on a small subset of proteins, which was dominated by chemokines. To our knowledge, expression profiles of CCL13 in benign lesions and BC have not previously been described but were shown herein to correlate with proliferation (P = 0.00095), suggesting a role in advanced BC. Given the broad functional range of the proteins analyzed, immune-related proteins were overrepresented among the observed alterations. Our pilot study supports the emerging role of chemokines in BC progression. Due to the minimally traumatic sampling and clinically important molecular information for therapeutic decisions, this methodology is promising for future immunoscoring and monitoring of treatment efficacy in BC.
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Affiliation(s)
- Bo Franzén
- Department of Oncology and Pathology, Cancer Center Karolinska, Karolinska Institutet and University Hospital, Stockholm, Sweden
| | - Andrey Alexeyenko
- Department of Microbiology, Tumor and Cell Biology (MTC), Karolinska Institutet, Stockholm, Sweden.,National Bioinformatics Infrastructure Sweden, Science for Life Laboratory, Solna, Sweden
| | - Masood Kamali-Moghaddam
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, Sweden
| | - Thomas Hatschek
- Department of Oncology and Pathology, Cancer Center Karolinska, Karolinska Institutet and University Hospital, Stockholm, Sweden.,Theme Cancer, Patient Area Head and Neck, Lung, and Skin, Karolinska University Hospital, Stockholm, Sweden
| | - Lena Kanter
- Department of Oncology and Pathology, Cancer Center Karolinska, Karolinska Institutet and University Hospital, Stockholm, Sweden
| | - Torbjörn Ramqvist
- Department of Oncology and Pathology, Cancer Center Karolinska, Karolinska Institutet and University Hospital, Stockholm, Sweden
| | - Jonas Kierkegaard
- BröstCentrum City, Stockholm, Sweden.,Capio S:t Görans Sjukhus, Stockholm, Sweden
| | - Giuseppe Masucci
- Department of Oncology and Pathology, Cancer Center Karolinska, Karolinska Institutet and University Hospital, Stockholm, Sweden.,Theme Cancer, Patient Area Head and Neck, Lung, and Skin, Karolinska University Hospital, Stockholm, Sweden
| | - Gert Auer
- Department of Oncology and Pathology, Cancer Center Karolinska, Karolinska Institutet and University Hospital, Stockholm, Sweden
| | - Ulf Landegren
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, Sweden
| | - Rolf Lewensohn
- Department of Oncology and Pathology, Cancer Center Karolinska, Karolinska Institutet and University Hospital, Stockholm, Sweden.,Theme Cancer, Patient Area Head and Neck, Lung, and Skin, Karolinska University Hospital, Stockholm, Sweden
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57
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Sinha VC, Piwnica-Worms H. Intratumoral Heterogeneity in Ductal Carcinoma In Situ: Chaos and Consequence. J Mammary Gland Biol Neoplasia 2018; 23:191-205. [PMID: 30194658 PMCID: PMC6934090 DOI: 10.1007/s10911-018-9410-6] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/30/2018] [Accepted: 08/30/2018] [Indexed: 02/06/2023] Open
Abstract
Ductal carcinoma in situ (DCIS) is a non-invasive proliferative growth in the breast that serves as a non-obligate precursor to invasive ductal carcinoma. The widespread adoption of screening mammography has led to a steep increase in the detection of DCIS, which now comprises approximately 20% of new breast cancer diagnoses in the United States. Interestingly, the intratumoral heterogeneity (ITH) that has been observed in invasive breast cancers may have been established early in tumorigenesis, given the vast and varied ITH that has been detected in DCIS. This review will discuss the intratumoral heterogeneity of DCIS, focusing on the phenotypic and genomic heterogeneity of tumor cells, as well as the compositional heterogeneity of the tumor microenvironment. In addition, we will assess the spatial heterogeneity that is now being appreciated in these lesions, and summarize new approaches to evaluate heterogeneity of tumor and stromal cells in the context of their spatial organization. Importantly, we will discuss how a growing understanding of ITH has led to a more holistic appreciation of the complex biology of DCIS, specifically its evolution and natural history. Finally, we will consider ways in which our knowledge of DCIS ITH might be translated in the future to guide clinical care for DCIS patients.
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Affiliation(s)
- Vidya C Sinha
- Department of Experimental Radiation Oncology, The University of Texas MD Anderson Cancer Center, 6565 MD Anderson Blvd, Houston, TX, 77030, USA
| | - Helen Piwnica-Worms
- Department of Experimental Radiation Oncology, The University of Texas MD Anderson Cancer Center, 6565 MD Anderson Blvd, Houston, TX, 77030, USA.
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58
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Liu K, Guo J, Liu K, Fan P, Zeng Y, Xu C, Zhong J, Li Q, Zhou Y. Integrative analysis reveals distinct subtypes with therapeutic implications in KRAS-mutant lung adenocarcinoma. EBioMedicine 2018; 36:196-208. [PMID: 30268834 PMCID: PMC6197714 DOI: 10.1016/j.ebiom.2018.09.034] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2018] [Revised: 09/11/2018] [Accepted: 09/19/2018] [Indexed: 12/20/2022] Open
Abstract
BACKGROUND KRAS-mutant lung adenocarcinomas (LUADs) are heterogeneous and frequently occur in smokers. The heterogeneity of KRAS-mutant LUAD has been an obstacle for the drug discovery. METHODS We integrated multiplatform datatypes and identified two corresponding subtypes in the patients and cell lines. We further characterized the features of these two subtypes and performed drug screening to identify subtype-specific drugs. Finally, we used the defining features of the KRAS subtypes for drug sensitivity prediction. FINDINGS Patient-Subtype 1 (PS1) was characterized by increased smoking-related mutational signature activity, a low tumor-infiltrating lymphocyte (TIL)-associating score and STK11/KEAP1 co-mutations. Patient-Subtype 2 (PS2) was characterized by an increased smoking-related methylation signature activity, a high TIL-associating score and increased KRAS dependency. The cell line subtypes faithfully recapitulated all the patients' features. Drug screening of the two cell line subtypes yielded several potential candidates, such as cytarabine and enzastaurin for Cell-line-Subtype 1 (CS1) and a BTK inhibitor QL-XII-61 for Cell-line-Subtype 2 (CS2). The defining features, such as smoking-related methylation signature, were significantly associated with the sensitivity to several drugs. INTERPRETATION The heterogeneity of KRAS-mutant LUAD is associated with smoking-related genomic and epigenomic aberration along with other features such as immunogenicity, KRAS dependency and STK11/KEAP1 co-mutations. These features might be used as biomarkers for drug sensitivity prediction. FUND: This research was funded by the Young Scientists Fund of the National Natural Science Foundation of China, the Natural Science Foundation of Fujian Province, China and the Education and Research Foundation for Young Scholars of Education Department of Fujian Province, China.
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Affiliation(s)
- Ke Liu
- Department of Translational Medicine, Medical College of Xiamen University, Xiamen 361102, China; Center for Biomedical Big Data Research, Medical College of Xiamen University, Xiamen 361102, China
| | - Jintao Guo
- Department of Translational Medicine, Medical College of Xiamen University, Xiamen 361102, China; Center for Biomedical Big Data Research, Medical College of Xiamen University, Xiamen 361102, China
| | - Kuai Liu
- Department of Translational Medicine, Medical College of Xiamen University, Xiamen 361102, China; Center for Biomedical Big Data Research, Medical College of Xiamen University, Xiamen 361102, China
| | - Peiyang Fan
- Department of Translational Medicine, Medical College of Xiamen University, Xiamen 361102, China; Center for Biomedical Big Data Research, Medical College of Xiamen University, Xiamen 361102, China
| | - Yuanyuan Zeng
- BGI-Shenzhen, Bei Shan Industrial Zone, Yantian District, Shenzhen, Guangdong Province 518083, China
| | - Chaoqun Xu
- Department of Translational Medicine, Medical College of Xiamen University, Xiamen 361102, China; Center for Biomedical Big Data Research, Medical College of Xiamen University, Xiamen 361102, China
| | - Jiaxin Zhong
- Department of Translational Medicine, Medical College of Xiamen University, Xiamen 361102, China; Center for Biomedical Big Data Research, Medical College of Xiamen University, Xiamen 361102, China
| | - Qiyuan Li
- Department of Translational Medicine, Medical College of Xiamen University, Xiamen 361102, China; Center for Biomedical Big Data Research, Medical College of Xiamen University, Xiamen 361102, China.
| | - Ying Zhou
- Department of Translational Medicine, Medical College of Xiamen University, Xiamen 361102, China; Center for Biomedical Big Data Research, Medical College of Xiamen University, Xiamen 361102, China.
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59
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Duszka K, Ellero-Simatos S, Ow GS, Defernez M, Paramalingam E, Tett A, Ying S, König J, Narbad A, Kuznetsov VA, Guillou H, Wahli W. Complementary intestinal mucosa and microbiota responses to caloric restriction. Sci Rep 2018; 8:11338. [PMID: 30054525 PMCID: PMC6063912 DOI: 10.1038/s41598-018-29815-7] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2018] [Accepted: 07/18/2018] [Indexed: 12/21/2022] Open
Abstract
The intestine is key for nutrient absorption and for interactions between the microbiota and its host. Therefore, the intestinal response to caloric restriction (CR) is thought to be more complex than that of any other organ. Submitting mice to 25% CR during 14 days induced a polarization of duodenum mucosa cell gene expression characterised by upregulation, and downregulation of the metabolic and immune/inflammatory pathways, respectively. The HNF, PPAR, STAT, and IRF families of transcription factors, particularly the Pparα and Isgf3 genes, were identified as potentially critical players in these processes. The impact of CR on metabolic genes in intestinal mucosa was mimicked by inhibition of the mTOR pathway. Furthermore, multiple duodenum and faecal metabolites were altered in CR mice. These changes were dependent on microbiota and their magnitude corresponded to microbial density. Further experiments using mice with depleted gut bacteria and CR-specific microbiota transfer showed that the gene expression polarization observed in the mucosa of CR mice is independent of the microbiota and its metabolites. The holistic interdisciplinary approach that we applied allowed us to characterize various regulatory aspects of the host and microbiota response to CR.
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Affiliation(s)
- Kalina Duszka
- Lee Kong Chian School of Medicine, Nanyang Technological University Singapore, Singapore, 308232, Singapore.
- Center for Integrative Genomics, University of Lausanne, Lausanne, 1015, Switzerland.
- Department of Nutritional Sciences, University of Vienna, Vienna, 1090, Austria.
| | - Sandrine Ellero-Simatos
- Toxalim (Research Centre in Food Toxicology), Université de Toulouse, INRA, ENVT, INP-Purpan, UPS, Toulouse, 31300, France
| | - Ghim Siong Ow
- Bioinformatics Institute, A*STAR Biomedical Sciences Institutes, Singapore, 13867, Singapore
| | - Marianne Defernez
- Quadram Institute Bioscience, , Norwich Science Park, Norwich, Norfolk, NR7UA, UK
| | - Eeswari Paramalingam
- Lee Kong Chian School of Medicine, Nanyang Technological University Singapore, Singapore, 308232, Singapore
| | - Adrian Tett
- Quadram Institute Bioscience, , Norwich Science Park, Norwich, Norfolk, NR7UA, UK
| | - Shi Ying
- Quadram Institute Bioscience, , Norwich Science Park, Norwich, Norfolk, NR7UA, UK
| | - Jürgen König
- Department of Nutritional Sciences, University of Vienna, Vienna, 1090, Austria
- Vienna Metabolomics Center (VIME), University of Vienna, Vienna, 1090, Austria
| | - Arjan Narbad
- Quadram Institute Bioscience, , Norwich Science Park, Norwich, Norfolk, NR7UA, UK
| | - Vladimir A Kuznetsov
- Bioinformatics Institute, A*STAR Biomedical Sciences Institutes, Singapore, 13867, Singapore
- SUNY Upstate Medical University Syracuse, Syracuse, NY, 13210, USA
| | - Hervé Guillou
- Toxalim (Research Centre in Food Toxicology), Université de Toulouse, INRA, ENVT, INP-Purpan, UPS, Toulouse, 31300, France
| | - Walter Wahli
- Lee Kong Chian School of Medicine, Nanyang Technological University Singapore, Singapore, 308232, Singapore.
- Center for Integrative Genomics, University of Lausanne, Lausanne, 1015, Switzerland.
- Toxalim (Research Centre in Food Toxicology), Université de Toulouse, INRA, ENVT, INP-Purpan, UPS, Toulouse, 31300, France.
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Okla K, Wertel I, Wawruszak A, Bobiński M, Kotarski J. Blood-based analyses of cancer: Circulating myeloid-derived suppressor cells - is a new era coming? Crit Rev Clin Lab Sci 2018; 55:376-407. [PMID: 29927668 DOI: 10.1080/10408363.2018.1477729] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Progress in cancer treatment made by the beginning of the 21st century has shifted the paradigm from one-size-fits-all to tailor-made treatment. The popular vision, to study solid tumors through the relatively noninvasive sampling of blood, is one of the most thrilling and rapidly advancing fields in global cancer diagnostics. From this perspective, immune-cell analysis in cancer could play a pivotal role in oncology practice. This approach is driven both by rapid technological developments, including the analysis of circulating myeloid-derived suppressor cells (cMDSCs), and by the increasing application of (immune) therapies, the success or failure of which may depend on effective and timely measurements of relevant biomarkers. Although the implementation of these powerful noninvasive diagnostic capabilities in guiding precision cancer treatment is poised to change the ways in which we select and monitor cancer therapy, challenges remain. Here, we discuss the challenges associated with the analysis and clinical aspects of cMDSCs and assess whether the problems in implementing tumor-evolution monitoring as a global tool in personalized oncology can be overcome.
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Affiliation(s)
- Karolina Okla
- a 1st Chair and Department of Oncological Gynaecology and Gynaecology, Tumor Immunology Laboratory , Medical University of Lublin , Lublin , Poland
| | - Iwona Wertel
- a 1st Chair and Department of Oncological Gynaecology and Gynaecology, Tumor Immunology Laboratory , Medical University of Lublin , Lublin , Poland
| | - Anna Wawruszak
- b Department of Biochemistry and Molecular Biology , Medical University of Lublin , Lublin , Poland
| | - Marcin Bobiński
- a 1st Chair and Department of Oncological Gynaecology and Gynaecology, Tumor Immunology Laboratory , Medical University of Lublin , Lublin , Poland
| | - Jan Kotarski
- a 1st Chair and Department of Oncological Gynaecology and Gynaecology, Tumor Immunology Laboratory , Medical University of Lublin , Lublin , Poland
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Bode AM, Dong Z. Recent advances in precision oncology research. NPJ Precis Oncol 2018; 2:11. [PMID: 30202789 PMCID: PMC5988666 DOI: 10.1038/s41698-018-0055-0] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2018] [Revised: 03/26/2018] [Accepted: 03/28/2018] [Indexed: 12/25/2022] Open
Affiliation(s)
- Ann M Bode
- The Hormel Institute, University of Minnesota, 801 16th Ave NE, Austin, MN 55912 USA
| | - Zigang Dong
- The Hormel Institute, University of Minnesota, 801 16th Ave NE, Austin, MN 55912 USA
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Addressing the challenges of applying precision oncology. NPJ Precis Oncol 2017; 1:28. [PMID: 29872710 PMCID: PMC5871855 DOI: 10.1038/s41698-017-0032-z] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2017] [Revised: 07/25/2017] [Accepted: 07/26/2017] [Indexed: 02/07/2023] Open
Abstract
Precision oncology is described as the matching of the most accurate and effective treatments with the individual cancer patient. Identification of important gene mutations, such as BRCA1/2 that drive carcinogenesis, helped pave the way for precision diagnosis in cancer. Oncoproteins and their signaling pathways have been extensively studied, leading to the development of target-based precision therapies against several types of cancers. Although many challenges exist that could hinder the success of precision oncology, cutting-edge tools for precision diagnosis and precision therapy will assist in overcoming many of these difficulties. Based on the continued rapid progression of genomic analysis, drug development, and clinical trial design, precision oncology will ultimately become the standard of care in cancer therapeutics.
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