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Rahman MA, Apu EH, Rakib-Uz-Zaman SM, Chakraborti S, Bhajan SK, Taleb SA, Shaikh MH, Jalouli M, Harrath AH, Kim B. Exploring Importance and Regulation of Autophagy in Cancer Stem Cells and Stem Cell-Based Therapies. Cells 2024; 13:958. [PMID: 38891090 PMCID: PMC11171866 DOI: 10.3390/cells13110958] [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: 05/04/2024] [Revised: 05/28/2024] [Accepted: 05/31/2024] [Indexed: 06/21/2024] Open
Abstract
Autophagy is a globally conserved cellular activity that plays a critical role in maintaining cellular homeostasis through the breakdown and recycling of cellular constituents. In recent years, there has been much emphasis given to its complex role in cancer stem cells (CSCs) and stem cell treatment. This study examines the molecular processes that support autophagy and how it is regulated in the context of CSCs and stem cell treatment. Although autophagy plays a dual role in the management of CSCs, affecting their removal as well as their maintenance, the intricate interaction between the several signaling channels that control cellular survival and death as part of the molecular mechanism of autophagy has not been well elucidated. Given that CSCs have a role in the development, progression, and resistance to treatment of tumors, it is imperative to comprehend their biological activities. CSCs are important for cancer biology because they also show a tissue regeneration model that helps with organoid regeneration. In other words, the manipulation of autophagy is a viable therapeutic approach in the treatment of cancer and stem cell therapy. Both synthetic and natural substances that target autophagy pathways have demonstrated promise in improving stem cell-based therapies and eliminating CSCs. Nevertheless, there are difficulties associated with the limitations of autophagy in CSC regulation, including resistance mechanisms and off-target effects. Thus, the regulation of autophagy offers a versatile strategy for focusing on CSCs and enhancing the results of stem cell therapy. Therefore, understanding the complex interactions between autophagy and CSC biology would be essential for creating therapeutic treatments that work in both regenerative medicine and cancer treatment.
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Affiliation(s)
- Md Ataur Rahman
- Department of Neurology, University of Michigan, Ann Arbor, MI 48109, USA
- Global Biotechnology and Biomedical Research Network (GBBRN), Department of Biotechnology and Genetic Engineering, Faculty of Biological Sciences, Islamic University, Kushtia 7003, Bangladesh
| | - Ehsanul Hoque Apu
- Department of Biomedical Sciences, College of Dental Medicine, Lincoln Memorial University, Knoxville, TN 37923, USA;
- DeBusk College of Osteopathic Medicine, Lincoln Memorial University, Harrogate, TN 37752, USA
- Division of Hematology and Oncology, Department of Internal Medicine, Michigan Medicine, University of Michigan, Ann Arbor, MI 48109, USA
| | - S. M Rakib-Uz-Zaman
- Department of Biological Sciences, University of Delaware, Newark, DE 19716, USA; (S.M.R.-U.-Z.); (S.C.)
- Biotechnology Program, Department of Mathematics and Natural Sciences, School of Data and Sciences, BRAC University, Dhaka 1212, Bangladesh
| | - Somdeepa Chakraborti
- Department of Biological Sciences, University of Delaware, Newark, DE 19716, USA; (S.M.R.-U.-Z.); (S.C.)
| | - Sujay Kumar Bhajan
- Department of Biotechnology and Genetic Engineering, Bangabandhu Sheikh Mujibur Rahman Science & Technology University, Gopalganj 8100, Bangladesh;
| | - Shakila Afroz Taleb
- Department of Internal Medicine, Yale School of Medicine, Yale University, New Haven, CT 06510, USA;
| | - Mushfiq H. Shaikh
- Department of Otolaryngology—Head and Neck Surgery, Western University, London, ON N6A 4V2, Canada;
| | - Maroua Jalouli
- Department of Biology, College of Science, Imam Mohammad Ibn Saud Islamic University (IMSIU), Riyadh 11623, Saudi Arabia;
| | - Abdel Halim Harrath
- Zoology Department, College of Science, King Saud University, Riyadh 11451, Saudi Arabia;
| | - Bonglee Kim
- Department of Pathology, College of Korean Medicine, Kyung Hee University, 1-5 Hoegidong, Dongdaemun-gu, Seoul 02447, Republic of Korea
- Korean Medicine-Based Drug Repositioning Cancer Research Center, College of Korean Medicine, Kyung Hee University, Seoul 02447, Republic of Korea
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Kang M, Armenteros JJA, Gulati GS, Gleyzer R, Avagyan S, Brown EL, Zhang W, Usmani A, Earland N, Wu Z, Zou J, Fields RC, Chen DY, Chaudhuri AA, Newman AM. Mapping single-cell developmental potential in health and disease with interpretable deep learning. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.03.19.585637. [PMID: 38562882 PMCID: PMC10983880 DOI: 10.1101/2024.03.19.585637] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/04/2024]
Abstract
Single-cell RNA sequencing (scRNA-seq) has transformed our understanding of cell fate in developmental systems. However, identifying the molecular hallmarks of potency - the capacity of a cell to differentiate into other cell types - has remained challenging. Here, we introduce CytoTRACE 2, an interpretable deep learning framework for characterizing potency and differentiation states on an absolute scale from scRNA-seq data. Across 31 human and mouse scRNA-seq datasets encompassing 28 tissue types, CytoTRACE 2 outperformed existing methods for recovering experimentally determined potency levels and differentiation states covering the entire range of cellular ontogeny. Moreover, it reconstructed the temporal hierarchy of mouse embryogenesis across 62 timepoints; identified pan-tissue expression programs that discriminate major potency levels; and facilitated discovery of cellular phenotypes in cancer linked to survival and immunotherapy resistance. Our results illuminate a fundamental feature of cell biology and provide a broadly applicable platform for delineating single-cell differentiation landscapes in health and disease.
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Tanaka A, Ogawa M, Zhou Y, Namba K, Hendrickson RC, Miele MM, Li Z, Klimstra DS, Buckley PG, Gulcher J, Wang JY, Roehrl MHA. Proteogenomic characterization of primary colorectal cancer and metastatic progression identifies proteome-based subtypes and signatures. Cell Rep 2024; 43:113810. [PMID: 38377004 DOI: 10.1016/j.celrep.2024.113810] [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: 11/20/2022] [Revised: 10/26/2023] [Accepted: 02/01/2024] [Indexed: 02/22/2024] Open
Abstract
Metastatic progression of colorectal adenocarcinoma (CRC) remains poorly understood and poses significant challenges for treatment. To overcome these challenges, we performed multiomics analyses of primary CRC and liver metastases. Genomic alterations, such as structural variants or copy number alterations, were enriched in oncogenes and tumor suppressor genes and increased in metastases. Unsupervised mass spectrometry-based proteomics of 135 primary and 123 metastatic CRCs uncovered distinct proteomic subtypes, three each for primary and metastatic CRCs, respectively. Integrated analyses revealed that hypoxia, stemness, and immune signatures characterize these 6 subtypes. Hypoxic CRC harbors high epithelial-to-mesenchymal transition features and metabolic adaptation. CRC with a stemness signature shows high oncogenic pathway activation and alternative telomere lengthening (ALT) phenotype, especially in metastatic lesions. Tumor microenvironment analysis shows immune evasion via modulation of major histocompatibility complex (MHC) class I/II and antigen processing pathways. This study characterizes both primary and metastatic CRCs and provides a large proteogenomics dataset of metastatic progression.
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Affiliation(s)
- Atsushi Tanaka
- Department of Pathology, Beth Israel Deaconess Medical Center, Boston, MA, USA; Harvard Medical School, Boston, MA, USA; Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Makiko Ogawa
- Department of Pathology, Beth Israel Deaconess Medical Center, Boston, MA, USA; Harvard Medical School, Boston, MA, USA; Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Yihua Zhou
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA; ICU Department, Second Affiliated Hospital of Nanchang University, Nanchang, Jiangxi, China
| | - Kei Namba
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA; Department of General Thoracic Surgery and Breast and Endocrinological Surgery, Okayama University Graduate School of Medicine, Dentistry, and Pharmaceutical Sciences, Okayama, Japan
| | - Ronald C Hendrickson
- Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Matthew M Miele
- Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Zhuoning Li
- Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - David S Klimstra
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA; Paige.AI, New York, NY, USA
| | | | | | | | - Michael H A Roehrl
- Department of Pathology, Beth Israel Deaconess Medical Center, Boston, MA, USA; Harvard Medical School, Boston, MA, USA; Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA.
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4
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Yu F, Zhang Z, Chang X, Ye X, Cheng H, Li Y, Cui H. Immunization with Embryonic Stem Cells/Induced Pluripotent Stem Cells Induces Effective Immunity against Ovarian Tumor-Initiating Cells in Mice. Stem Cells Int 2023; 2023:8188324. [PMID: 38058983 PMCID: PMC10696476 DOI: 10.1155/2023/8188324] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2022] [Revised: 09/07/2023] [Accepted: 10/10/2023] [Indexed: 12/08/2023] Open
Abstract
Cancer stem cells (CSCs) express pluripotent markers and share many features with normal pluripotent stem cells. It is possible that immunity induced by embryonic stem cells (ESCs) and induced pluripotent stem cells- (IPSCs-) based vaccines may selectively target CSCs. In our study, cells expressing the pluripotent marker CD133 in the murine ovarian cancer cell-line ID8 were isolated and identified as CSCs. We investigated the preventive efficacy of ESCs and IPSCs-based vaccines against the development of ovarian cancer in vivo and evaluated the humoral and cellular immunities targeting CSCs in vitro. Our study showed that preimmunization with both mouse-derived embryonic stem cells (mESCs) and mouse-induced pluripotent stem cells (mIPSCs) lysates, combined with an immunostimulatory adjuvant CpG, elicited strong humoral and cellular responses. These responses effectively suppressed the development of CSC-derived tumors. Immune sera collected from mESCs and mIPSCs-vaccinated mice contained antibodies that were capable of selectively targeting CSCs, resulting in the lysis of CSCs in the presence of complement. Cytotoxic T-lymphocytes generated from splenocytes of mESCs and mIPSCs-vaccinated hosts could secrete interferon- (IFN-) γ in response to CSCs and kill CSCs in vitro. These findings indicate that vaccines based on mESCs and mIPSCs can elicit effective antitumor immunities. These immunities are related to the conferring of humoral and cellular responses that directly target CSCs.
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Affiliation(s)
- Fengsheng Yu
- Center of Gynecologic Oncology, Peking University People's Hospital, Beijing 100044, China
- Department of Obstetrics and Gynecology, The Affiliated Hospital of Qingdao University, Qingdao 266000, China
| | - Zujuan Zhang
- Center of Gynecologic Oncology, Peking University People's Hospital, Beijing 100044, China
- Department of Gynecology, Women's Hospital, School of Medicine, Zhejiang University, Hangzhou 310000, China
| | - Xiaohong Chang
- Center of Gynecologic Oncology, Peking University People's Hospital, Beijing 100044, China
| | - Xue Ye
- Center of Gynecologic Oncology, Peking University People's Hospital, Beijing 100044, China
| | - Hongyan Cheng
- Center of Gynecologic Oncology, Peking University People's Hospital, Beijing 100044, China
| | - Yi Li
- Center of Gynecologic Oncology, Peking University People's Hospital, Beijing 100044, China
- Department of Obstetrics and Gynecology, Peking University People's Hospital, Beijing 100044, China
| | - Heng Cui
- Center of Gynecologic Oncology, Peking University People's Hospital, Beijing 100044, China
- Department of Obstetrics and Gynecology, Peking University People's Hospital, Beijing 100044, China
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Ruan Y, Wang J, Yu M, Wang F, Wang J, Xu Y, Liu L, Cheng Y, Yang R, Zhang C, Yang Y, Wang J, Wu W, Huang Y, Tian Y, Chen G, Zhang J, Jian R. A multi-omics integrative analysis based on CRISPR screens re-defines the pluripotency regulatory network in ESCs. Commun Biol 2023; 6:410. [PMID: 37059858 PMCID: PMC10104827 DOI: 10.1038/s42003-023-04700-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2022] [Accepted: 03/13/2023] [Indexed: 04/16/2023] Open
Abstract
A comprehensive and precise definition of the pluripotency gene regulatory network (PGRN) is crucial for clarifying the regulatory mechanisms in embryonic stem cells (ESCs). Here, after a CRISPR/Cas9-based functional genomics screen and integrative analysis with other functional genomes, transcriptomes, proteomes and epigenome data, an expanded pluripotency-associated gene set is obtained, and a new PGRN with nine sub-classes is constructed. By integrating the DNA binding, epigenetic modification, chromatin conformation, and RNA expression profiles, the PGRN is resolved to six functionally independent transcriptional modules (CORE, MYC, PAF, PRC, PCGF and TBX). Spatiotemporal transcriptomics reveal activated CORE/MYC/PAF module activity and repressed PRC/PCGF/TBX module activity in both mouse ESCs (mESCs) and pluripotent cells of early embryos. Moreover, this module activity pattern is found to be shared by human ESCs (hESCs) and cancers. Thus, our results provide novel insights into elucidating the molecular basis of ESC pluripotency.
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Affiliation(s)
- Yan Ruan
- Laboratory of Stem Cell & Developmental Biology, Department of Histology and Embryology, College of Basic Medical Sciences, Army Medical University, Chongqing, 400038, China
| | - Jiaqi Wang
- Laboratory of Stem Cell & Developmental Biology, Department of Histology and Embryology, College of Basic Medical Sciences, Army Medical University, Chongqing, 400038, China
- Department of Pathophysiology, College of High Altitude Military Medicine, Army Medical University, Chongqing, 400038, China
| | - Meng Yu
- Laboratory of Stem Cell & Developmental Biology, Department of Histology and Embryology, College of Basic Medical Sciences, Army Medical University, Chongqing, 400038, China
- Department of Joint Surgery, The First Affiliated Hospital, Army Medical University, Chongqing, 400038, China
| | - Fengsheng Wang
- Laboratory of Stem Cell & Developmental Biology, Department of Histology and Embryology, College of Basic Medical Sciences, Army Medical University, Chongqing, 400038, China
- State Key Laboratory of NBC Protection for Civilian, Beijing, 102205, China
| | - Jiangjun Wang
- Laboratory of Stem Cell & Developmental Biology, Department of Histology and Embryology, College of Basic Medical Sciences, Army Medical University, Chongqing, 400038, China
- Department of Cell Biology, College of Basic Medical Sciences, Army Medical University, Chongqing, 400038, China
| | - Yixiao Xu
- Laboratory of Stem Cell & Developmental Biology, Department of Histology and Embryology, College of Basic Medical Sciences, Army Medical University, Chongqing, 400038, China
| | - Lianlian Liu
- Laboratory of Stem Cell & Developmental Biology, Department of Histology and Embryology, College of Basic Medical Sciences, Army Medical University, Chongqing, 400038, China
| | - Yuda Cheng
- Laboratory of Stem Cell & Developmental Biology, Department of Histology and Embryology, College of Basic Medical Sciences, Army Medical University, Chongqing, 400038, China
| | - Ran Yang
- Laboratory of Stem Cell & Developmental Biology, Department of Histology and Embryology, College of Basic Medical Sciences, Army Medical University, Chongqing, 400038, China
- Department of Pathophysiology, College of High Altitude Military Medicine, Army Medical University, Chongqing, 400038, China
| | - Chen Zhang
- Laboratory of Stem Cell & Developmental Biology, Department of Histology and Embryology, College of Basic Medical Sciences, Army Medical University, Chongqing, 400038, China
| | - Yi Yang
- Experimental Center of Basic Medicine, College of Basic Medical Sciences, Army Medical University, Chongqing, 400038, China
| | - JiaLi Wang
- Laboratory of Stem Cell & Developmental Biology, Department of Histology and Embryology, College of Basic Medical Sciences, Army Medical University, Chongqing, 400038, China
| | - Wei Wu
- Thoracic Surgery Department, Southwest Hospital, The First Hospital Affiliated to Army Medical University, Chongqing, 400038, China
| | - Yi Huang
- Biomedical Analysis Center, Army Medical University, Chongqing, 400038, China
| | - Yanping Tian
- Laboratory of Stem Cell & Developmental Biology, Department of Histology and Embryology, College of Basic Medical Sciences, Army Medical University, Chongqing, 400038, China
| | - Guangxing Chen
- Department of Joint Surgery, The First Affiliated Hospital, Army Medical University, Chongqing, 400038, China.
| | - Junlei Zhang
- Laboratory of Stem Cell & Developmental Biology, Department of Histology and Embryology, College of Basic Medical Sciences, Army Medical University, Chongqing, 400038, China.
| | - Rui Jian
- Laboratory of Stem Cell & Developmental Biology, Department of Histology and Embryology, College of Basic Medical Sciences, Army Medical University, Chongqing, 400038, China.
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6
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Wang J, Xue Y, He Y, Quan H, Zhang J, Gao YQ. Characterization of network hierarchy reflects cell state specificity in genome organization. Genome Res 2023; 33:247-260. [PMID: 36828586 PMCID: PMC10069467 DOI: 10.1101/gr.277206.122] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2022] [Accepted: 01/31/2023] [Indexed: 02/26/2023]
Abstract
Dynamic chromatin structure acts as the regulator of transcription program in crucial processes including cancer and cell development, but a unified framework for characterizing chromatin structural evolution remains to be established. Here, we performed graph inferences on Hi-C data sets and derived the chromatin contact networks. We discovered significant decreases in information transmission efficiencies in chromatin of colorectal cancer (CRC) and T-cell acute lymphoblastic leukemia (T-ALL) compared to corresponding normal controls through graph statistics. Using network embedding in the Poincaré disk, the hierarchy depths of chromatin from CRC and T-ALL patients were found to be significantly shallower compared to their normal controls. A reverse trend of change in chromatin structure was observed during early embryo development. We found tissue-specific conservation of hierarchy order in chromatin contact networks. Our findings reveal the top-down hierarchy of chromatin organization, which is significantly attenuated in cancer.
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Affiliation(s)
- Jingyao Wang
- Beijing National Laboratory for Molecular Sciences, College of Chemistry and Molecular Engineering, Peking University, Beijing, 100871, China
| | - Yue Xue
- Beijing National Laboratory for Molecular Sciences, College of Chemistry and Molecular Engineering, Peking University, Beijing, 100871, China
| | - Yueying He
- Beijing National Laboratory for Molecular Sciences, College of Chemistry and Molecular Engineering, Peking University, Beijing, 100871, China
| | - Hui Quan
- Beijing National Laboratory for Molecular Sciences, College of Chemistry and Molecular Engineering, Peking University, Beijing, 100871, China
| | - Jun Zhang
- Changping Laboratory, Beijing, 102206, China
| | - Yi Qin Gao
- Beijing National Laboratory for Molecular Sciences, College of Chemistry and Molecular Engineering, Peking University, Beijing, 100871, China; .,Biomedical Pioneering Innovation Center (BIOPIC), Peking University, Beijing, 100871, China.,Changping Laboratory, Beijing, 102206, China
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7
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Ciafrè SA, Russo M, Michienzi A, Galardi S. Long Noncoding RNAs and Cancer Stem Cells: Dangerous Liaisons Managing Cancer. Int J Mol Sci 2023; 24:ijms24031828. [PMID: 36768150 PMCID: PMC9915130 DOI: 10.3390/ijms24031828] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2022] [Revised: 01/12/2023] [Accepted: 01/13/2023] [Indexed: 01/18/2023] Open
Abstract
Decades of research have investigated the mechanisms that lead to the origin of cancer, striving to identify tumor-initiating cells. These cells, also known as cancer stem cells, are characterized by the ability to self-renew, to give rise to differentiated tumor populations, and on a larger scale, are deemed responsible not only for tumor initiation but also for recurrent tumors, often resistant to chemotherapy and radiotherapy. Long noncoding RNAs are RNA molecules longer than 200 nt, lacking the ability to code for proteins, with recognized roles as fine regulators of gene expression. They can exert these functions through a variety of mechanisms, acting at almost all steps of gene expression, from modulation of the epigenetic state of chromatin to modulation of protein stability. In all cases, lncRNAs do not work alone, but they always interact with other RNA molecules, either coding or non-coding, or with protein factors. In this review, we summarize the latest results obtained about the involvement of lncRNAs in the initiating cells of several types of tumors, and highlight the different mechanisms through which they work, while discussing how the modulation of a lncRNA can affect several aspects of tumor onset and progression.
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Affiliation(s)
- Silvia Anna Ciafrè
- Department of Biomedicine and Prevention, University of Rome Tor Vergata, 00133 Rome, Italy
- Correspondence: (S.A.C.); (S.G.)
| | - Monia Russo
- Department of Biomedicine and Prevention, University of Rome Tor Vergata, 00133 Rome, Italy
| | - Alessandro Michienzi
- Department of Biomedicine and Prevention, University of Rome Tor Vergata, 00133 Rome, Italy
| | - Silvia Galardi
- Department of Biology, University of Rome Tor Vergata, 00133 Rome, Italy
- Correspondence: (S.A.C.); (S.G.)
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8
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Chaudhary A, Raza SS, Haque R. Transcriptional factors targeting in cancer stem cells for tumor modulation. Semin Cancer Biol 2023; 88:123-137. [PMID: 36603792 DOI: 10.1016/j.semcancer.2022.12.010] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2022] [Revised: 12/29/2022] [Accepted: 12/30/2022] [Indexed: 01/03/2023]
Abstract
Cancer Stem Cells (CSCs) are now considered the primary "seeds" for the onset, development, metastasis, and recurrence of tumors. Despite therapeutic breakthroughs, cancer remains the leading cause of death worldwide. This is because the tumor microenvironment contains a key population of cells known as CSCs, which promote tumor aggression. CSCs are self-renewing cells that aid tumor recurrence by promoting tumor growth and persisting in patients after many traditional cancer treatments. According to reports, numerous transcription factors (TF) play a key role in maintaining CSC pluripotency and its self-renewal property. The understanding of the functions, structures, and interactional dynamics of these transcription factors with DNA has modified the hypothesis, paving the way for novel transcription factor-targeted therapies. These TFs, which are crucial and are required by cancer cells, play a vital function in the etiology of human cancer. Such CSC TFs will help with gene expression profiling, which provides crucial data for predicting the prognosis of patients. To overcome anti-cancer medication resistance and completely eradicate cancer, a potent therapy combining TFs-based CSC targets with traditional chemotherapy may be developed. In order to develop therapies that could eliminate CSCs, we here concentrated on the effect of TFs and other components of signalling pathways on cancer stemness.
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Affiliation(s)
- Archana Chaudhary
- Department of Biotechnology, School of Earth Biological and Environmental Sciences, Central University of South Bihar, Gaya, Bihar, India
| | - Syed Shadab Raza
- Laboratory for Stem Cell & Restorative Neurology, Era's Lucknow Medical College and Hospital, Era University, Lucknow, India
| | - Rizwanul Haque
- Department of Biotechnology, School of Earth Biological and Environmental Sciences, Central University of South Bihar, Gaya, Bihar, India.
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The Contributions of Cancer-Testis and Developmental Genes to the Pathogenesis of Keratinocyte Carcinomas. Cancers (Basel) 2022; 14:cancers14153630. [PMID: 35892887 PMCID: PMC9367444 DOI: 10.3390/cancers14153630] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2022] [Revised: 07/21/2022] [Accepted: 07/22/2022] [Indexed: 11/17/2022] Open
Abstract
Simple Summary In addition to mutations, ectopically-expressed genes are emerging as important contributors to cancer development. Efforts to characterize the expression patterns in cancers of gamete-restricted cancer-testis antigens and developmentally-restricted genes are underway, revealing these genes to be putative biomarkers and therapeutic targets for various malignancies. Basal cell carcinoma (BCC) and cutaneous squamous cell carcinoma (cSCC) are two highly-prevalent non-melanoma skin cancers that result in considerable burden on patients and our health system. To optimize disease prognostication and treatment, it is necessary to further classify the molecular complexity of these malignancies. This review describes the expression patterns and functions of cancer-testis antigens and developmentally-restricted genes in BCC and cSCC tumors. A large number of cancer-testis antigens and developmental genes exhibit substantial expression levels in BCC and cSCC. These genes have been shown to contribute to several aspects of cancer biology, including tumorigenesis, differentiation, invasion and responses to anti-cancer therapy. Abstract Keratinocyte carcinomas are among the most prevalent malignancies worldwide. Basal cell carcinoma (BCC) and cutaneous squamous cell carcinoma (cSCC) are the two cancers recognized as keratinocyte carcinomas. The standard of care for treating these cancers includes surgery and ablative therapies. However, in recent years, targeted therapies (e.g., cetuximab for cSCC and vismodegib/sonidegib for BCC) have been used to treat advanced disease as well as immunotherapy (e.g., cemiplimab). These treatments are expensive and have significant toxicities with objective response rates approaching ~50–65%. Hence, there is a need to dissect the molecular pathogenesis of these cancers to identify novel biomarkers and therapeutic targets to improve disease management. Several cancer-testis antigens (CTA) and developmental genes (including embryonic stem cell factors and fetal genes) are ectopically expressed in BCC and cSCC. When ectopically expressed in malignant tissues, functions of these genes may be recaptured to promote tumorigenesis. CTAs and developmental genes are emerging as important players in the pathogenesis of BCC and cSCC, positioning themselves as attractive candidate biomarkers and therapeutic targets requiring rigorous testing. Herein, we review the current research and offer perspectives on the contributions of CTAs and developmental genes to the pathogenesis of keratinocyte carcinomas.
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Blood-derived lncRNAs as biomarkers for cancer diagnosis: the Good, the Bad and the Beauty. NPJ Precis Oncol 2022; 6:40. [PMID: 35729321 PMCID: PMC9213432 DOI: 10.1038/s41698-022-00283-7] [Citation(s) in RCA: 56] [Impact Index Per Article: 28.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2021] [Accepted: 05/13/2022] [Indexed: 11/24/2022] Open
Abstract
Cancer ranks as one of the deadliest diseases worldwide. The high mortality rate associated with cancer is partially due to the lack of reliable early detection methods and/or inaccurate diagnostic tools such as certain protein biomarkers. Cell-free nucleic acids (cfNA) such as circulating long noncoding RNAs (lncRNAs) have been proposed as a new class of potential biomarkers for cancer diagnosis. The reported correlation between the presence of tumors and abnormal levels of lncRNAs in the blood of cancer patients has notably triggered a worldwide interest among clinicians and oncologists who have been actively investigating their potentials as reliable cancer biomarkers. In this report, we review the progress achieved (“the Good”) and challenges encountered (“the Bad”) in the development of circulating lncRNAs as potential biomarkers for early cancer diagnosis. We report and discuss the diagnostic performance of more than 50 different circulating lncRNAs and emphasize their numerous potential clinical applications (“the Beauty”) including therapeutic targets and agents, on top of diagnostic and prognostic capabilities. This review also summarizes the best methods of investigation and provides useful guidelines for clinicians and scientists who desire conducting their own clinical studies on circulating lncRNAs in cancer patients via RT-qPCR or Next Generation Sequencing (NGS).
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Abstract
Ageing, death, and potential immortality lie at the heart of biology, but two seemingly incompatible paradigms coexist in different research communities and have done since the nineteenth century. The universal senescence paradigm sees senescence as inevitable in all cells. Damage accumulates. The potential immortality paradigm sees some cells as potentially immortal, especially unicellular organisms, germ cells and cancerous cells. Recent research with animal cells, yeasts and bacteria show that damaged cell constituents do in fact build up, but can be diluted by growth and cell division, especially by asymmetric cell division. By contrast, mammalian embryonic stem cells and many cancerous and 'immortalized' cell lines divide symmetrically, and yet replicate indefinitely. How do they acquire their potential immortality? I suggest they are rejuvenated by excreting damaged cell constituents in extracellular vesicles. If so, our understanding of cellular senescence, rejuvenation and potential immortality could be brought together in a new synthesis, which I call the cellular rejuvenation hypothesis: damaged cell constituents build up in all cells, but cells can be rejuvenated either by growth and cell division or, in 'immortal' cell lines, by excreting damaged cell constituents. In electronic supplementary material, appendix, I outline nine ways in which this hypothesis could be tested.
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Loh D, Reiter RJ. Melatonin: Regulation of Prion Protein Phase Separation in Cancer Multidrug Resistance. Molecules 2022; 27:705. [PMID: 35163973 PMCID: PMC8839844 DOI: 10.3390/molecules27030705] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2021] [Revised: 01/11/2022] [Accepted: 01/17/2022] [Indexed: 12/13/2022] Open
Abstract
The unique ability to adapt and thrive in inhospitable, stressful tumor microenvironments (TME) also renders cancer cells resistant to traditional chemotherapeutic treatments and/or novel pharmaceuticals. Cancer cells exhibit extensive metabolic alterations involving hypoxia, accelerated glycolysis, oxidative stress, and increased extracellular ATP that may activate ancient, conserved prion adaptive response strategies that exacerbate multidrug resistance (MDR) by exploiting cellular stress to increase cancer metastatic potential and stemness, balance proliferation and differentiation, and amplify resistance to apoptosis. The regulation of prions in MDR is further complicated by important, putative physiological functions of ligand-binding and signal transduction. Melatonin is capable of both enhancing physiological functions and inhibiting oncogenic properties of prion proteins. Through regulation of phase separation of the prion N-terminal domain which targets and interacts with lipid rafts, melatonin may prevent conformational changes that can result in aggregation and/or conversion to pathological, infectious isoforms. As a cancer therapy adjuvant, melatonin could modulate TME oxidative stress levels and hypoxia, reverse pH gradient changes, reduce lipid peroxidation, and protect lipid raft compositions to suppress prion-mediated, non-Mendelian, heritable, but often reversible epigenetic adaptations that facilitate cancer heterogeneity, stemness, metastasis, and drug resistance. This review examines some of the mechanisms that may balance physiological and pathological effects of prions and prion-like proteins achieved through the synergistic use of melatonin to ameliorate MDR, which remains a challenge in cancer treatment.
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Affiliation(s)
- Doris Loh
- Independent Researcher, Marble Falls, TX 78654, USA
| | - Russel J. Reiter
- Department of Cellular and Structural Biology, UT Health San Antonio, San Antonio, TX 78229, USA
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13
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Johnson A, Iffland L, Northcote-Smith J, Singh K, Ortu F, Apfel UP, Suntharalingam K. A bioinspired redox-modulating copper(II)-macrocyclic complex bearing non-steroidal anti-inflammatory drugs with anti-cancer stem cell activity. Dalton Trans 2022; 51:5904-5912. [DOI: 10.1039/d2dt00788f] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Copper(II) coordination compounds have been investigated for their anticancer properties for decades, however, none have reached advanced human clinical trials. The poor translation of copper(II) complexes from in vitro studies...
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14
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Sohn EJ, Nam YK. The Transcription Factor TFCP2L1 is Associated with Myelination via miR708-5p Regulation in the Peripheral Nerve System. Neurochem Res 2021; 47:434-445. [PMID: 34581937 DOI: 10.1007/s11064-021-03457-0] [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: 06/10/2021] [Revised: 08/25/2021] [Accepted: 09/22/2021] [Indexed: 11/25/2022]
Abstract
MicroRNAs (miRNAs) have been implicated in nerve injury and demyelination; however, their functions in peripheral nerves remain unclear. To determine the potential functions of miRNAs, an miRNA array was carried out. Here, miRNA array analysis of neuregulin-treated Schwann cells revealed 18 upregulated (> 2-fold) and 13 downregulated (> 2-fold) miRNAs. After sciatic nerve injury, miR708-5p was highly expressed in neuregulin-treated Schwann cells, whereas it was downregulated during postnatal development. A predicted functional interaction was found between miR708-5p and transcription factor CP2-like protein 1 (TFCP2L1) using a bioinformatics tool. This finding suggested that miR708-5p may regulate TFCP2L1. During sciatic nerve development, TFCP2L1 was upregulated on postnatal days 1 and 4, while it was downregulated after nerve axotomy and crush injury. Notably, TFCP2L1 was upregulated in cAMP-treated Schwann cells. We also found that activity of the myelin protein zero promoter was downregulated in TFCP2L1 siRNA-treated Schwann cells, whereas it was upregulated in TFCP2L1-overexpressing cells. Immunofluorescence analysis showed that TFCP2L1 was localized in Schwann cells. In addition, miR708-5p overexpression promoted migration of Schwann cells, while miR-708-5p inhibitor inhibited migration. miR708-5p inhibitor also blocked the migration of TFCP2L1 siRNA-treated Schwann cells. These findings indicate the functions of miR708-5p in TFCP2L1 regulation in the peripheral nervous system occur via regulation of Schwann cell migration.
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Affiliation(s)
- Eun Jung Sohn
- Department of Convergence Medical Sciences, School of Medicine, Pusan National University, Pusan National University, Yangsan, South Korea.
| | - Yun Kyung Nam
- Department of Molecular Neuroscience, College of Medicine, Dong-A University, Busan, South Korea
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15
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Catania F, Ujvari B, Roche B, Capp JP, Thomas F. Bridging Tumorigenesis and Therapy Resistance With a Non-Darwinian and Non-Lamarckian Mechanism of Adaptive Evolution. Front Oncol 2021; 11:732081. [PMID: 34568068 PMCID: PMC8462274 DOI: 10.3389/fonc.2021.732081] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2021] [Accepted: 08/25/2021] [Indexed: 12/13/2022] Open
Abstract
Although neo-Darwinian (and less often Lamarckian) dynamics are regularly invoked to interpret cancer's multifarious molecular profiles, they shine little light on how tumorigenesis unfolds and often fail to fully capture the frequency and breadth of resistance mechanisms. This uncertainty frames one of the most problematic gaps between science and practice in modern times. Here, we offer a theory of adaptive cancer evolution, which builds on a molecular mechanism that lies outside neo-Darwinian and Lamarckian schemes. This mechanism coherently integrates non-genetic and genetic changes, ecological and evolutionary time scales, and shifts the spotlight away from positive selection towards purifying selection, genetic drift, and the creative-disruptive power of environmental change. The surprisingly simple use-it or lose-it rationale of the proposed theory can help predict molecular dynamics during tumorigenesis. It also provides simple rules of thumb that should help improve therapeutic approaches in cancer.
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Affiliation(s)
- Francesco Catania
- Institute for Evolution and Biodiversity, University of Münster, Münster, Germany
| | - Beata Ujvari
- Centre for Integrative Ecology, School of Life and Environmental Sciences, Deakin University, Deakin, VIC, Australia
| | - Benjamin Roche
- CREEC/CANECEV, MIVEGEC (CREES), Centre de Recherches Ecologiques et Evolutives sur le Cancer, University of Montpellier, CNRS, IRD, Montpellier, France
| | - Jean-Pascal Capp
- Toulouse Biotechnology Institute, University of Toulouse, INSA, CNRS, INRAE, Toulouse, France
| | - Frédéric Thomas
- CREEC/CANECEV, MIVEGEC (CREES), Centre de Recherches Ecologiques et Evolutives sur le Cancer, University of Montpellier, CNRS, IRD, Montpellier, France
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16
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Divisato G, Piscitelli S, Elia M, Cascone E, Parisi S. MicroRNAs and Stem-like Properties: The Complex Regulation Underlying Stemness Maintenance and Cancer Development. Biomolecules 2021; 11:biom11081074. [PMID: 34439740 PMCID: PMC8393604 DOI: 10.3390/biom11081074] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2021] [Revised: 07/13/2021] [Accepted: 07/19/2021] [Indexed: 12/12/2022] Open
Abstract
Embryonic stem cells (ESCs) have the extraordinary properties to indefinitely proliferate and self-renew in culture to produce different cell progeny through differentiation. This latter process recapitulates embryonic development and requires rounds of the epithelial-mesenchymal transition (EMT). EMT is characterized by the loss of the epithelial features and the acquisition of the typical phenotype of the mesenchymal cells. In pathological conditions, EMT can confer stemness or stem-like phenotypes, playing a role in the tumorigenic process. Cancer stem cells (CSCs) represent a subpopulation, found in the tumor tissues, with stem-like properties such as uncontrolled proliferation, self-renewal, and ability to differentiate into different cell types. ESCs and CSCs share numerous features (pluripotency, self-renewal, expression of stemness genes, and acquisition of epithelial-mesenchymal features), and most of them are under the control of microRNAs (miRNAs). These small molecules have relevant roles during both embryogenesis and cancer development. The aim of this review was to recapitulate molecular mechanisms shared by ESCs and CSCs, with a special focus on the recently identified classes of microRNAs (noncanonical miRNAs, mirtrons, isomiRs, and competitive endogenous miRNAs) and their complex functions during embryogenesis and cancer development.
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17
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Dvir S, Argoetti A, Lesnik C, Roytblat M, Shriki K, Amit M, Hashimshony T, Mandel-Gutfreund Y. Uncovering the RNA-binding protein landscape in the pluripotency network of human embryonic stem cells. Cell Rep 2021; 35:109198. [PMID: 34077720 DOI: 10.1016/j.celrep.2021.109198] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2020] [Revised: 03/11/2021] [Accepted: 05/11/2021] [Indexed: 12/18/2022] Open
Abstract
Embryonic stem cell (ESC) self-renewal and cell fate decisions are driven by a broad array of molecular signals. While transcriptional regulators have been extensively studied in human ESCs (hESCs), the extent to which RNA-binding proteins (RBPs) contribute to human pluripotency remains unclear. Here, we carry out a proteome-wide screen and identify 810 proteins that bind RNA in hESCs. We reveal that RBPs are preferentially expressed in hESCs and dynamically regulated during early stem cell differentiation. Notably, many RBPs are affected by knockdown of OCT4, a master regulator of pluripotency, several dozen of which are directly targeted by this factor. Using cross-linking and immunoprecipitation (CLIP-seq), we find that the pluripotency-associated STAT3 and OCT4 transcription factors interact with RNA in hESCs and confirm the binding of STAT3 to the conserved NORAD long-noncoding RNA. Our findings indicate that RBPs have a more widespread role in human pluripotency than previously appreciated.
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Affiliation(s)
- Shlomi Dvir
- Faculty of Biology, Technion - Israel Institute of Technology, Haifa 320003, Israel
| | - Amir Argoetti
- Faculty of Biology, Technion - Israel Institute of Technology, Haifa 320003, Israel
| | - Chen Lesnik
- Faculty of Biology, Technion - Israel Institute of Technology, Haifa 320003, Israel
| | | | | | - Michal Amit
- Accellta LTD, Haifa 320003, Israel; Ephraim Katzir Department of Biotechnology Engineering, ORT Braude College, Karmiel 2161002, Israel
| | - Tamar Hashimshony
- Faculty of Biology, Technion - Israel Institute of Technology, Haifa 320003, Israel
| | - Yael Mandel-Gutfreund
- Faculty of Biology, Technion - Israel Institute of Technology, Haifa 320003, Israel; Computer Science Department, Technion - Israel Institute of Technology, Haifa 320003, Israel.
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18
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Park C, Jeong K, Park JH, Jung S, Bae JM, Kim K, Ock CY, Kim M, Keam B, Kim TM, Jeon YK, Lee SH, Lee JS, Kim DW, Kang GH, Chung DH, Heo DS. Pan-cancer methylation analysis reveals an inverse correlation of tumor immunogenicity with methylation aberrancy. Cancer Immunol Immunother 2021; 70:1605-1617. [PMID: 33230567 DOI: 10.1007/s00262-020-02796-1] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2020] [Accepted: 11/07/2020] [Indexed: 12/21/2022]
Abstract
Tumor immunogenicity is driven by various genomic and transcriptomic factors but the association with the overall status of methylation aberrancy is not well established. We analyzed The Cancer Genome Atlas pan-cancer database to investigate whether the overall methylation aberrancy links to the immune evasion of tumor. We created the definitions of hypermethylation burden, hypomethylation burden and methylation burden to establish the values that represent the degree of methylation aberrancy from human methylation 450 K array data. Both hypermethylation burden and hypomethylation burden significantly correlated with global methylation level as well as methylation subtypes defined in previous literatures. Then we evaluated whether methylation burden correlates with tumor immunogenicity and found that methylation burden showed a significant negative correlation with cytolytic activity score, which represent cytotoxic T cell activity, in pan-cancer (Spearman rho = - 0.37, p < 0.001) and 30 of 33 individual cancer types. Furthermore, this correlation was independent of mutation burden and chromosomal instability in multivariate regression analysis. We validated the findings in the external cohorts and outcomes of patients who were treated with immune checkpoint inhibitors, which showed that high methylation burden group had significantly poor progression-free survival (Hazard ratio 1.74, p = 0.038). Overall, the degree of methylation aberrancy negatively correlated with tumor immunogenicity. These findings emphasize the importance of methylation aberrancy for tumors to evade immune surveillance and warrant further development of methylation biomarker.
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Affiliation(s)
- Changhee Park
- Department of Internal Medicine, Seoul National University Hospital, 101 Daehak-ro, Jongno-gu, Seoul, 03080, Republic of Korea
| | - Kyeonghun Jeong
- Division of Clinical Bioinformatics, Biomedical Research Institute, Seoul National University Hospital, 101 Daehak-ro, Jongno-gu, Seoul, 03080, Republic of Korea
| | - Joon-Hyeong Park
- Division of Clinical Bioinformatics, Biomedical Research Institute, Seoul National University Hospital, 101 Daehak-ro, Jongno-gu, Seoul, 03080, Republic of Korea
| | - Sohee Jung
- Division of Clinical Bioinformatics, Biomedical Research Institute, Seoul National University Hospital, 101 Daehak-ro, Jongno-gu, Seoul, 03080, Republic of Korea
| | - Jeong Mo Bae
- Department of Pathology, Seoul National University Hospital, Seoul, Republic of Korea
| | - Kwangsoo Kim
- Transdisciplinary Department of Medicine & Advanced Technology, Seoul National University Hospital, Seoul, Republic of Korea.
| | - Chan-Young Ock
- Department of Internal Medicine, Seoul National University Hospital, 101 Daehak-ro, Jongno-gu, Seoul, 03080, Republic of Korea.
| | - Miso Kim
- Department of Internal Medicine, Seoul National University Hospital, 101 Daehak-ro, Jongno-gu, Seoul, 03080, Republic of Korea
| | - Bhumsuk Keam
- Department of Internal Medicine, Seoul National University Hospital, 101 Daehak-ro, Jongno-gu, Seoul, 03080, Republic of Korea
- Cancer Research Institute, Seoul National University, Seoul, Republic of Korea
| | - Tae Min Kim
- Department of Internal Medicine, Seoul National University Hospital, 101 Daehak-ro, Jongno-gu, Seoul, 03080, Republic of Korea
- Cancer Research Institute, Seoul National University, Seoul, Republic of Korea
| | - Yoon Kyung Jeon
- Department of Pathology, Seoul National University Hospital, Seoul, Republic of Korea
| | - Se-Hoon Lee
- Division of Hematology/Oncology, Department of Internal Medicine, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea
| | - Ju-Seog Lee
- Department of Systems Biology, Division of Basic Sciences, MD Anderson Cancer Center, Houston, TX, USA
| | - Dong-Wan Kim
- Department of Internal Medicine, Seoul National University Hospital, 101 Daehak-ro, Jongno-gu, Seoul, 03080, Republic of Korea
- Cancer Research Institute, Seoul National University, Seoul, Republic of Korea
| | - Gyeong Hoon Kang
- Department of Pathology, Seoul National University Hospital, Seoul, Republic of Korea
| | - Doo Hyun Chung
- Department of Pathology, Seoul National University Hospital, Seoul, Republic of Korea
| | - Dae Seog Heo
- Department of Internal Medicine, Seoul National University Hospital, 101 Daehak-ro, Jongno-gu, Seoul, 03080, Republic of Korea
- Cancer Research Institute, Seoul National University, Seoul, Republic of Korea
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19
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Yang L, Zhang H, Yang X, Lu T, Ma S, Cheng H, Yen K, Cheng T. Prognostic Prediction of Cytogenetically Normal Acute Myeloid Leukemia Based on a Gene Expression Model. Front Oncol 2021; 11:659201. [PMID: 34123815 PMCID: PMC8190396 DOI: 10.3389/fonc.2021.659201] [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: 01/27/2021] [Accepted: 03/26/2021] [Indexed: 11/22/2022] Open
Abstract
Acute myeloid leukemia (AML) refers to a heterogeneous group of hematopoietic malignancies. The well-known European Leukemia Network (ELN) stratifies AML patients into three risk groups, based primarily on the detection of cytogenetic abnormalities. However, the prognosis of cytogenetically normal AML (CN-AML), which is the largest AML subset, can be hard to define. Moreover, the clinical outcomes associated with this subgroup are diverse. In this study, using transcriptome profiles collected from CN-AML patients in the BeatAML cohort, we constructed a robust prognostic Cox model named NEST (Nine-gEne SignaTure). The validity of NEST was confirmed in four external independent cohorts. Moreover, the risk score predicted by the NEST model remained an independent prognostic factor in multivariate analyses. Further analysis revealed that the NEST model was suitable for bone marrow mononuclear cell (BMMC) samples but not peripheral blood mononuclear cell (PBMC) samples, which indirectly indicated subtle differences between BMMCs and PBMCs. Our data demonstrated the robustness and accuracy of the NEST model and implied the importance of the immune dysfunction in the leukemogenesis that occurs in CN-AML, which shed new light on the further exploration of molecular mechanisms and treatment guidance for CN-AML.
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Affiliation(s)
- Liu Yang
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin, China.,Department of Stem Cell and Regenerative Medicine, Peking Union Medical College, Tianjin, China.,Center for Stem Cell Medicine, Chinese Academy of Medical Sciences, Tianjin, China
| | - Houyu Zhang
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin, China.,School of Biology and Biological Engineering, South China University of Technology, Guangzhou, China
| | - Xue Yang
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin, China.,Department of Stem Cell and Regenerative Medicine, Peking Union Medical College, Tianjin, China.,Center for Stem Cell Medicine, Chinese Academy of Medical Sciences, Tianjin, China
| | - Ting Lu
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin, China.,Department of Stem Cell and Regenerative Medicine, Peking Union Medical College, Tianjin, China.,Center for Stem Cell Medicine, Chinese Academy of Medical Sciences, Tianjin, China
| | - Shihui Ma
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin, China.,Department of Stem Cell and Regenerative Medicine, Peking Union Medical College, Tianjin, China.,Center for Stem Cell Medicine, Chinese Academy of Medical Sciences, Tianjin, China
| | - Hui Cheng
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin, China.,Department of Stem Cell and Regenerative Medicine, Peking Union Medical College, Tianjin, China.,Center for Stem Cell Medicine, Chinese Academy of Medical Sciences, Tianjin, China
| | - Kuangyu Yen
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin, China.,Department of Stem Cell and Regenerative Medicine, Peking Union Medical College, Tianjin, China.,Center for Stem Cell Medicine, Chinese Academy of Medical Sciences, Tianjin, China
| | - Tao Cheng
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin, China.,Department of Stem Cell and Regenerative Medicine, Peking Union Medical College, Tianjin, China.,Center for Stem Cell Medicine, Chinese Academy of Medical Sciences, Tianjin, China
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20
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Wang H, Chirshev E, Hojo N, Suzuki T, Bertucci A, Pierce M, Perry C, Wang R, Zink J, Glackin CA, Ioffe YJ, Unternaehrer JJ. The Epithelial-Mesenchymal Transcription Factor SNAI1 Represses Transcription of the Tumor Suppressor miRNA let-7 in Cancer. Cancers (Basel) 2021; 13:cancers13061469. [PMID: 33806868 PMCID: PMC8004805 DOI: 10.3390/cancers13061469] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2021] [Revised: 03/15/2021] [Accepted: 03/17/2021] [Indexed: 01/06/2023] Open
Abstract
Simple Summary When cells undergo epithelial–mesenchymal transition (EMT) they gain characteristics of stem cells. We investigated the mechanism by which the EMT transcription factor SNAI1 induces stem cell features. In these studies, we observed that SNAI1 represses a microRNA that maintains differentiation, let-7. This microRNA is lost in cancer, and its loss correlates with poor prognosis. In breast, pancreatic, and ovarian cancer cell lines the cell stemness in increased by SNAI1 overexpression and reduced by SNAI1 knockdown. We extended the ovarian cancer results to patient-derived cells, and to a mouse xenograft model. In mice, we used nanoparticles to deliver small RNAs (RNAi) targeting SNAI1, resulting in restoration of let-7 levels, inhibition of stemness, and reduced tumor burden. Our studies validate nanoparticle-delivered RNAi targeting SNAI1 as a clinically relevant approach. Abstract We aimed to determine the mechanism of epithelial–mesenchymal transition (EMT)-induced stemness in cancer cells. Cancer relapse and metastasis are caused by rare stem-like cells within tumors. Studies of stem cell reprogramming have linked let-7 repression and acquisition of stemness with the EMT factor, SNAI1. The mechanisms for the loss of let-7 in cancer cells are incompletely understood. In four carcinoma cell lines from breast cancer, pancreatic cancer, and ovarian cancer and in ovarian cancer patient-derived cells, we analyzed stem cell phenotype and tumor growth via mRNA, miRNA, and protein expression, spheroid formation, and growth in patient-derived xenografts. We show that treatment with EMT-promoting growth factors or SNAI1 overexpression increased stemness and reduced let-7 expression, while SNAI1 knockdown reduced stemness and restored let-7 expression. Rescue experiments demonstrate that the pro-stemness effects of SNAI1 are mediated via let-7. In vivo, nanoparticle-delivered siRNA successfully knocked down SNAI1 in orthotopic patient-derived xenografts, accompanied by reduced stemness and increased let-7 expression, and reduced tumor burden. Chromatin immunoprecipitation demonstrated that SNAI1 binds the promoters of various let-7 family members, and luciferase assays revealed that SNAI1 represses let-7 transcription. In conclusion, the SNAI1/let-7 axis is an important component of stemness pathways in cancer cells, and this study provides a rationale for future work examining this axis as a potential target for cancer stem cell-specific therapies.
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Affiliation(s)
- Hanmin Wang
- Division of Biochemistry, Department of Basic Sciences, Loma Linda University, Loma Linda, CA 92354, USA; (H.W.); (E.C.); (N.H.); (T.S.); (A.B.); (C.P.)
| | - Evgeny Chirshev
- Division of Biochemistry, Department of Basic Sciences, Loma Linda University, Loma Linda, CA 92354, USA; (H.W.); (E.C.); (N.H.); (T.S.); (A.B.); (C.P.)
| | - Nozomi Hojo
- Division of Biochemistry, Department of Basic Sciences, Loma Linda University, Loma Linda, CA 92354, USA; (H.W.); (E.C.); (N.H.); (T.S.); (A.B.); (C.P.)
| | - Tise Suzuki
- Division of Biochemistry, Department of Basic Sciences, Loma Linda University, Loma Linda, CA 92354, USA; (H.W.); (E.C.); (N.H.); (T.S.); (A.B.); (C.P.)
| | - Antonella Bertucci
- Division of Biochemistry, Department of Basic Sciences, Loma Linda University, Loma Linda, CA 92354, USA; (H.W.); (E.C.); (N.H.); (T.S.); (A.B.); (C.P.)
| | - Michael Pierce
- Department of Biology, California State University San Bernardino, San Bernardino, CA 92407, USA;
| | - Christopher Perry
- Division of Biochemistry, Department of Basic Sciences, Loma Linda University, Loma Linda, CA 92354, USA; (H.W.); (E.C.); (N.H.); (T.S.); (A.B.); (C.P.)
| | - Ruining Wang
- Department of Chemistry and Biochemistry, University of California, Los Angeles, CA 90095, USA; (R.W.); (J.Z.)
| | - Jeffrey Zink
- Department of Chemistry and Biochemistry, University of California, Los Angeles, CA 90095, USA; (R.W.); (J.Z.)
| | | | - Yevgeniya J. Ioffe
- Division of Gynecologic Oncology, Department of Obstetrics and Gynecology, Loma Linda University Medical Center, Loma Linda, CA 92354, USA;
| | - Juli J. Unternaehrer
- Division of Biochemistry, Department of Basic Sciences, Loma Linda University, Loma Linda, CA 92354, USA; (H.W.); (E.C.); (N.H.); (T.S.); (A.B.); (C.P.)
- Center for Health Disparities and Molecular Medicine, Loma Linda University, Loma Linda, CA 92354, USA
- Correspondence: ; Tel.: +1-909-558-7691; Fax: +1-909-558-4887
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21
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Integrative pan cancer analysis reveals epigenomic variation in cancer type and cell specific chromatin domains. Nat Commun 2021; 12:1419. [PMID: 33658503 PMCID: PMC7930052 DOI: 10.1038/s41467-021-21707-1] [Citation(s) in RCA: 36] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2020] [Accepted: 02/09/2021] [Indexed: 12/15/2022] Open
Abstract
Epigenetic mechanisms contribute to the initiation and development of cancer, and epigenetic variation promotes dynamic gene expression patterns that facilitate tumor evolution and adaptation. While the NCI-60 panel represents a diverse set of human cancer cell lines that has been used to screen chemical compounds, a comprehensive epigenomic atlas of these cells has been lacking. Here, we report an integrative analysis of 60 human cancer epigenomes, representing a catalog of activating and repressive histone modifications. We identify genome-wide maps of canonical sharp and broad H3K4me3 domains at promoter regions of tumor suppressors, H3K27ac-marked conventional enhancers and super enhancers, and widespread inter-cancer and intra-cancer specific variability in H3K9me3 and H4K20me3-marked heterochromatin domains. Furthermore, we identify features of chromatin states, including chromatin state switching along chromosomes, correlation of histone modification density with genetic mutations, DNA methylation, enrichment of DNA binding motifs in regulatory regions, and gene activity and inactivity. These findings underscore the importance of integrating epigenomic maps with gene expression and genetic variation data to understand the molecular basis of human cancer. Our findings provide a resource for mining epigenomic maps of human cancer cells and for identifying epigenetic therapeutic targets.
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22
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Lu H, Xie Y, Tran L, Lan J, Yang Y, Murugan NL, Wang R, Wang YJ, Semenza GL. Chemotherapy-induced S100A10 recruits KDM6A to facilitate OCT4-mediated breast cancer stemness. J Clin Invest 2021; 130:4607-4623. [PMID: 32427586 DOI: 10.1172/jci138577] [Citation(s) in RCA: 63] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2020] [Accepted: 05/14/2020] [Indexed: 12/20/2022] Open
Abstract
Breast cancer stem cells (BCSCs) play a critical role in cancer recurrence and metastasis. Chemotherapy induces BCSC specification through increased expression of pluripotency factors, but how their expression is regulated is not fully understood. Here, we delineate a pathway controlled by hypoxia-inducible factor 1 (HIF-1) that epigenetically activates pluripotency factor gene transcription in response to chemotherapy. Paclitaxel induces HIF-1-dependent expression of S100A10, which forms a complex with ANXA2 that interacts with histone chaperone SPT6 and histone demethylase KDM6A. S100A10, ANXA2, SPT6, and KDM6A are recruited to OCT4 binding sites and KDM6A erases H3K27me3 chromatin marks, facilitating transcription of genes encoding the pluripotency factors NANOG, SOX2, and KLF4, which along with OCT4 are responsible for BCSC specification. Silencing of S100A10, ANXA2, SPT6, or KDM6A expression blocks chemotherapy-induced enrichment of BCSCs, impairs tumor initiation, and increases time to tumor recurrence after chemotherapy is discontinued. Pharmacological inhibition of KDM6A also impairs chemotherapy-induced BCSC enrichment. These results suggest that targeting HIF-1/S100A10-dependent and KDM6A-mediated epigenetic activation of pluripotency factor gene expression in combination with chemotherapy may block BCSC enrichment and improve clinical outcome.
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Affiliation(s)
- Haiquan Lu
- Vascular Program, Institute for Cell Engineering.,Sidney Kimmel Comprehensive Cancer Center
| | | | - Linh Tran
- Vascular Program, Institute for Cell Engineering
| | - Jie Lan
- Vascular Program, Institute for Cell Engineering
| | - Yongkang Yang
- Vascular Program, Institute for Cell Engineering.,Sidney Kimmel Comprehensive Cancer Center
| | | | - Ru Wang
- Vascular Program, Institute for Cell Engineering
| | | | - Gregg L Semenza
- Vascular Program, Institute for Cell Engineering.,Sidney Kimmel Comprehensive Cancer Center.,Department of Genetic Medicine.,Department of Pediatrics.,Department of Medicine.,Department of Oncology.,Department of Radiation Oncology, and.,Department of Biological Chemistry, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
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23
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Barati M, Akhondi M, Mousavi NS, Haghparast N, Ghodsi A, Baharvand H, Ebrahimi M, Hassani SN. Pluripotent Stem Cells: Cancer Study, Therapy, and Vaccination. Stem Cell Rev Rep 2021; 17:1975-1992. [PMID: 34115316 PMCID: PMC8193020 DOI: 10.1007/s12015-021-10199-7] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/02/2021] [Indexed: 02/05/2023]
Abstract
INTRODUCTION Pluripotent stem cells (PSCs) are promising tools for modern regenerative medicine applications because of their stemness properties, which include unlimited self-renewal and the ability to differentiate into all cell types in the body. Evidence suggests that a rare population of cells within a tumor, termed cancer stem cells (CSCs), exhibit stemness and phenotypic plasticity properties that are primarily responsible for resistance to chemotherapy, radiotherapy, metastasis, cancer development, and tumor relapse. Different therapeutic approaches that target CSCs have been developed for tumor eradication. RESULTS AND DISCUSSION In this review, we first provide an overview of different viewpoints about the origin of CSCs. Particular attention has been paid to views believe that CSCs are probably appeared through dysregulation of very small embryonic-like stem cells (VSELs) which reside in various tissues as the main candidate for tissue-specific stem cells. The expression of pluripotency markers in these two types of cells can strengthen the validity of this theory. In this regard, we discuss the common properties of CSCs and PSCs, and highlight the potential of PSCs in cancer studies, therapeutic applications, as well as educating the immune system against CSCs. CONCLUSION In conclusion, the resemblance of CSCs to PSCs can provide an appropriate source of CSC-specific antigens through cultivation of PSCs which brings to light promising ideas for prophylactic and therapeutic cancer vaccine development.
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Affiliation(s)
- Mojgan Barati
- Department of Developmental Biology, School of Basic Sciences and Advanced Technologies in Biology, University of Science and Culture, Tehran, Iran
- Department of Stem Cells and Developmental Biology, Cell Science Research Center, Royan Institute for Stem Cell Biology and Technology, ACECR, Tehran, Iran
| | - Maryam Akhondi
- Department of Stem Cells and Developmental Biology, Cell Science Research Center, Royan Institute for Stem Cell Biology and Technology, ACECR, Tehran, Iran
| | - Narges Sabahi Mousavi
- Department of Stem Cells and Developmental Biology, Cell Science Research Center, Royan Institute for Stem Cell Biology and Technology, ACECR, Tehran, Iran
| | - Newsha Haghparast
- Department of Stem Cells and Developmental Biology, Cell Science Research Center, Royan Institute for Stem Cell Biology and Technology, ACECR, Tehran, Iran
| | - Asma Ghodsi
- Department of Stem Cells and Developmental Biology, Cell Science Research Center, Royan Institute for Stem Cell Biology and Technology, ACECR, Tehran, Iran
| | - Hossein Baharvand
- Department of Developmental Biology, School of Basic Sciences and Advanced Technologies in Biology, University of Science and Culture, Tehran, Iran
- Department of Stem Cells and Developmental Biology, Cell Science Research Center, Royan Institute for Stem Cell Biology and Technology, ACECR, Tehran, Iran
| | - Marzieh Ebrahimi
- Department of Stem Cells and Developmental Biology, Cell Science Research Center, Royan Institute for Stem Cell Biology and Technology, ACECR, Tehran, Iran
| | - Seyedeh-Nafiseh Hassani
- Department of Stem Cells and Developmental Biology, Cell Science Research Center, Royan Institute for Stem Cell Biology and Technology, ACECR, Tehran, Iran
- Advanced Therapy Medicinal Product Technology Development Center (ATMP-TDC), Cell Science Research Center, Royan Institute for Stem Cell Biology and Technology, ACECR, Tehran, Iran
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24
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Strategies for Cancer Immunotherapy Using Induced Pluripotency Stem Cells-Based Vaccines. Cancers (Basel) 2020; 12:cancers12123581. [PMID: 33266109 PMCID: PMC7760556 DOI: 10.3390/cancers12123581] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2020] [Revised: 11/24/2020] [Accepted: 11/27/2020] [Indexed: 12/14/2022] Open
Abstract
Despite improvements in cancer therapy, metastatic solid tumors remain largely incurable. Immunotherapy has emerged as a pioneering and promising approach for cancer therapy and management, and in particular intended for advanced tumors unresponsive to current therapeutics. In cancer immunotherapy, components of the immune system are exploited to eliminate cancer cells and treat patients. The recent clinical successes of immune checkpoint blockade and chimeric antigen receptor T cell therapies represent a turning point in cancer treatment. Despite their potential success, current approaches depend on efficient tumor antigen presentation which are often inaccessible, and most tumors turn refractory to current immunotherapy. Patient-derived induced pluripotent stem cells (iPSCs) have been shown to share several characteristics with cancer (stem) cells (CSCs), eliciting a specific anti-tumoral response when injected in rodent cancer models. Indeed, artificial cellular reprogramming has been widely compared to the biogenesis of CSCs. Here, we will discuss the state-of-the-art on the potential implication of cellular reprogramming and iPSCs for the design of patient-specific immunotherapeutic strategies, debating the similarities between iPSCs and cancer cells and introducing potential strategies that could enhance the efficiency and therapeutic potential of iPSCs-based cancer vaccines.
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25
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Targeting SRC Kinase Signaling in Pancreatic Cancer Stem Cells. Int J Mol Sci 2020; 21:ijms21207437. [PMID: 33050159 PMCID: PMC7588004 DOI: 10.3390/ijms21207437] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2020] [Revised: 10/03/2020] [Accepted: 10/04/2020] [Indexed: 02/06/2023] Open
Abstract
The proto-oncogene nonreceptor tyrosine-protein kinase SRC is a member of the SRC family of tyrosine kinases (SFKs), and its activation and overexpression have been shown to play a protumorigenic role in multiple solid cancers, including pancreatic ductal adenocarcinoma (PDAC). PDAC is currently the seventh-leading cause of cancer-related death worldwide, and, by 2030, it is predicted to become the second-leading cause of cancer-related death in the United States. PDAC is characterized by its high lethality (5-year survival of rate of <10%), invasiveness, and chemoresistance, all of which have been shown to be due to the presence of pancreatic cancer stem cells (PaCSCs) within the tumor. Due to the demonstrated overexpression of SRC in PDAC, we set out to determine if SRC kinases are important for PaCSC biology using pharmacological inhibitors of SRC kinases (dasatinib or PP2). Treatment of primary PDAC cultures established from patient-derived xenografts with dasatinib or PP2 reduced the clonogenic, self-renewal, and tumor-initiating capacity of PaCSCs, which we attribute to the downregulation of key signaling factors such as p-FAK, p-ERK1-2, and p-AKT. Therefore, this study not only validates that SRC kinases are relevant and biologically important for PaCSCs but also suggests that inhibitors of SRC kinases may represent a possible future treatment option for PDAC patients, although further studies are still needed.
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Qiao Y, Agboola OS, Hu X, Wu Y, Lei L. Tumorigenic and Immunogenic Properties of Induced Pluripotent Stem Cells: a Promising Cancer Vaccine. Stem Cell Rev Rep 2020; 16:1049-1061. [PMID: 32939647 PMCID: PMC7494249 DOI: 10.1007/s12015-020-10042-5] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/09/2020] [Indexed: 02/06/2023]
Abstract
Induced pluripotent stem cells (iPSCs) are mainly characterized by their unlimited proliferation abilities and potential to develop into almost any cell type. The creation of this technology has been of great interest to many scientific fields, especially regenerative biology. However, concerns about the safety of iPSC application in transplantation have arisen due to the tumorigenic and immunogenic properties of iPSCs. This review will briefly introduce the developing history of somatic reprogramming and applications of iPSC technology in regenerative medicine. In addition, the review will highlight two challenges to the efficient usage of iPSCs and the underlying mechanisms of these challenges. Finally, the review will discuss the expanding application of iPSC technology in cancer immunotherapy as a potential cancer vaccine and its advantages in auxiliary treatment compared with oncofetal antigen-based and embryonic stem cell (ESC)-based vaccines.
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Affiliation(s)
- Yu Qiao
- Department of Histology and Embryology, Basic Medical Science College, Harbin Medical University, 194 Xuefu Rd, Nangang District, Harbin, Heilongjiang Province, 150081, People's Republic of China
| | - Oluwafemi Solomon Agboola
- Department of Histology and Embryology, Basic Medical Science College, Harbin Medical University, 194 Xuefu Rd, Nangang District, Harbin, Heilongjiang Province, 150081, People's Republic of China
| | - Xinglin Hu
- Department of Histology and Embryology, Basic Medical Science College, Harbin Medical University, 194 Xuefu Rd, Nangang District, Harbin, Heilongjiang Province, 150081, People's Republic of China
| | - Yanshuang Wu
- Department of Histology and Embryology, Basic Medical Science College, Harbin Medical University, 194 Xuefu Rd, Nangang District, Harbin, Heilongjiang Province, 150081, People's Republic of China
| | - Lei Lei
- Department of Histology and Embryology, Basic Medical Science College, Harbin Medical University, 194 Xuefu Rd, Nangang District, Harbin, Heilongjiang Province, 150081, People's Republic of China.
- Key laboratory of Preservation of Human Genetic Resources and Disease Control in China, Harbin Medical University, Ministry of Education, Harbin, China.
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Khadirnaikar S, Chatterjee A, Kumar P, Shukla S. A Greedy Algorithm-Based Stem Cell LncRNA Signature Identifies a Novel Subgroup of Lung Adenocarcinoma Patients With Poor Prognosis. Front Oncol 2020; 10:1203. [PMID: 32850350 PMCID: PMC7431877 DOI: 10.3389/fonc.2020.01203] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2019] [Accepted: 06/12/2020] [Indexed: 12/26/2022] Open
Abstract
Cancer stem cells play an essential role in therapy response and aggressiveness of various cancers, including lung adenocarcinoma (LUAD). Interestingly it also shares many features of embryonic stem cells (ESCs). Recently, long non-coding RNAs (lncRNAs) have emerged as a critical regulator of cell physiology. Here, we used expression data of ESCs, LUAD, and normal lung to identify 198 long non-coding hESC-associated lncRNAs (hESC-lncRNAs). Intriguingly, K-means clustering of hESC-associated lncRNAs identified a subgroup of LUAD patients [undifferentiated LUAD (uLUAD)] with high stem cell-like characteristic, decreased differentiation genes expression, and poor survival. We also observed that the uLUAD patients had overexpression of proteins associated with cell proliferation. Interestingly, uLUAD patients were highly enriched with the stemness-related gene sets, and had higher mutation load. A notable result observed was high infiltration of T cells and a higher level of neopeptides in uLUAD patients, making these patients an optimal candidate for immunotherapy. Further, feature selection using greedy algorithm identified 17-hESC-lncRNAs signature, which showed significant consistency with 198 hESC-lncRNAs-based classification, and identified a group of patients with high stem cell-like characteristic in the 10 most common cancer types and CCLE cell lines. These results suggest the conventional role of hESC-lncRNAs in stem cell biology. In summary, we identified a novel subgroup of LUAD patients (uLUAD) using a set of hESC-lncRNAs. The uLUAD patients had high stem cell-like characteristic and reduced survival rate and may be referred for immunotherapy. Furthermore, our analysis also showed the importance of lncRNAs in cancer and cancer stem cells.
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Affiliation(s)
- Seema Khadirnaikar
- Department of Biosciences and Bioengineering, Indian Institute of Technology Dharwad, Dharwad, India
- Department of Electrical Engineering, Indian Institute of Technology Dharwad, Dharwad, India
| | - Annesha Chatterjee
- Department of Biosciences and Bioengineering, Indian Institute of Technology Dharwad, Dharwad, India
| | - Pranjal Kumar
- Department of Biosciences and Bioengineering, Indian Institute of Technology Dharwad, Dharwad, India
| | - Sudhanshu Shukla
- Department of Biosciences and Bioengineering, Indian Institute of Technology Dharwad, Dharwad, India
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Walcher L, Kistenmacher AK, Suo H, Kitte R, Dluczek S, Strauß A, Blaudszun AR, Yevsa T, Fricke S, Kossatz-Boehlert U. Cancer Stem Cells-Origins and Biomarkers: Perspectives for Targeted Personalized Therapies. Front Immunol 2020; 11:1280. [PMID: 32849491 PMCID: PMC7426526 DOI: 10.3389/fimmu.2020.01280] [Citation(s) in RCA: 438] [Impact Index Per Article: 109.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2020] [Accepted: 05/20/2020] [Indexed: 02/06/2023] Open
Abstract
The use of biomarkers in diagnosis, therapy and prognosis has gained increasing interest over the last decades. In particular, the analysis of biomarkers in cancer patients within the pre- and post-therapeutic period is required to identify several types of cells, which carry a risk for a disease progression and subsequent post-therapeutic relapse. Cancer stem cells (CSCs) are a subpopulation of tumor cells that can drive tumor initiation and can cause relapses. At the time point of tumor initiation, CSCs originate from either differentiated cells or adult tissue resident stem cells. Due to their importance, several biomarkers that characterize CSCs have been identified and correlated to diagnosis, therapy and prognosis. However, CSCs have been shown to display a high plasticity, which changes their phenotypic and functional appearance. Such changes are induced by chemo- and radiotherapeutics as well as senescent tumor cells, which cause alterations in the tumor microenvironment. Induction of senescence causes tumor shrinkage by modulating an anti-tumorigenic environment in which tumor cells undergo growth arrest and immune cells are attracted. Besides these positive effects after therapy, senescence can also have negative effects displayed post-therapeutically. These unfavorable effects can directly promote cancer stemness by increasing CSC plasticity phenotypes, by activating stemness pathways in non-CSCs, as well as by promoting senescence escape and subsequent activation of stemness pathways. At the end, all these effects can lead to tumor relapse and metastasis. This review provides an overview of the most frequently used CSC markers and their implementation as biomarkers by focussing on deadliest solid (lung, stomach, liver, breast and colorectal cancers) and hematological (acute myeloid leukemia, chronic myeloid leukemia) cancers. Furthermore, it gives examples on how the CSC markers might be influenced by therapeutics, such as chemo- and radiotherapy, and the tumor microenvironment. It points out, that it is crucial to identify and monitor residual CSCs, senescent tumor cells, and the pro-tumorigenic senescence-associated secretory phenotype in a therapy follow-up using specific biomarkers. As a future perspective, a targeted immune-mediated strategy using chimeric antigen receptor based approaches for the removal of remaining chemotherapy-resistant cells as well as CSCs in a personalized therapeutic approach are discussed.
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Affiliation(s)
- Lia Walcher
- Department of Immunology, Fraunhofer Institute for Cell Therapy and Immunology, Leipzig, Germany
| | - Ann-Kathrin Kistenmacher
- Department of Immunology, Fraunhofer Institute for Cell Therapy and Immunology, Leipzig, Germany
| | - Huizhen Suo
- Department of Gastroenterology, Hepatology and Endocrinology, Hannover Medical School, Hannover, Germany
| | - Reni Kitte
- Department of Immunology, Fraunhofer Institute for Cell Therapy and Immunology, Leipzig, Germany
| | - Sarah Dluczek
- Department of Immunology, Fraunhofer Institute for Cell Therapy and Immunology, Leipzig, Germany
| | - Alexander Strauß
- Department of Immunology, Fraunhofer Institute for Cell Therapy and Immunology, Leipzig, Germany
| | - André-René Blaudszun
- Department of Immunology, Fraunhofer Institute for Cell Therapy and Immunology, Leipzig, Germany
| | - Tetyana Yevsa
- Department of Gastroenterology, Hepatology and Endocrinology, Hannover Medical School, Hannover, Germany
| | - Stephan Fricke
- Department of Immunology, Fraunhofer Institute for Cell Therapy and Immunology, Leipzig, Germany
| | - Uta Kossatz-Boehlert
- Department of Immunology, Fraunhofer Institute for Cell Therapy and Immunology, Leipzig, Germany
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29
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Carvalho J. Cell Reversal From a Differentiated to a Stem-Like State at Cancer Initiation. Front Oncol 2020; 10:541. [PMID: 32351900 PMCID: PMC7174973 DOI: 10.3389/fonc.2020.00541] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2020] [Accepted: 03/25/2020] [Indexed: 12/12/2022] Open
Abstract
Even if the Somatic Mutation Theory of carcinogenesis explains many of the relevant experimental results in tumor origin and development, there are frequent events that are not justified, or are even contradictory to this widely accepted theory. A Cell Reversal Theory is presented, putting forward the hypothesis that cancer is originated by reversal of a differentiated cell into a non-differentiated stem-like state, by a change of its intrinsic epigenetic state, following a perturbation on the cell and/or its microenvironment. In the current proposal a cluster of cancer stem cells can be established, without the strict control mechanisms of a normal stem cell niche, and initiate a tumor. It is proposed that a reversal to a pluripotent state is at tumor origin and not tumor progress that prompts cell dedifferentiation. The uncontrolled proliferation of cancer stem cells causes a microenvironment disorganization, resulting in stressful conditions, like hypoxia and nutrient deprivation, which induces the genetic instability characteristic of a tumor; thus, in most cases, mutations are a consequence and not the direct cause of a tumor. It is also proposed that metastases result from dedifferentiation signaling dispersion instead of cell migration. However, conceivably, once the microenvironment is normalized, the stem cell-like state can differentiate back to a mature cell state and loose its oncogenic capacity. Therefore, this can be a reversible condition, suggesting important therapeutic opportunities.
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Affiliation(s)
- João Carvalho
- CFisUC, Department of Physics, University of Coimbra, Coimbra, Portugal
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30
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Tsuchiya Y, Umemura Y, Yagita K. Circadian clock and cancer: From a viewpoint of cellular differentiation. Int J Urol 2020; 27:518-524. [PMID: 32223039 DOI: 10.1111/iju.14231] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2019] [Accepted: 02/27/2020] [Indexed: 12/18/2022]
Abstract
The circadian clock controls and adapts diverse physiological and behavioral processes according to Earth's 24-h cycle of environmental changes. The master pacemaker of the mammalian circadian clock resides in the hypothalamic suprachiasmatic nucleus, but almost all cells throughout the body show circadian oscillations in gene expression patterns and associated functions. Recent studies have shown that the circadian clock gradually develops during embryogenesis. Embryonic stem cells and induced pluripotent stem cells do not show circadian oscillations of gene expression, but gradually develop circadian clock oscillation during differentiation; thus, the developmental program of circadian clock emergence appears closely associated with cellular differentiation. Like embryonic stem cells, certain cancer cell types also lack the circadian clock. Given this similarity between embryonic stem cells and cancer cells, interest is growing in the contributions of circadian clock dysfunction to dedifferentiation and cancer development. In this review, we summarize recent advances in our understanding of circadian clock emergence during ontogenesis, and discuss possible associations with cellular differentiation and carcinogenesis. Considering the multiple physiological functions of circadian rhythms, circadian abnormalities might contribute to a host of diseases, including cancer. Insights on circadian function could lead to the identification of biomarkers for cancer diagnosis and prognosis, as well as novel targets for treatment.
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Affiliation(s)
- Yoshiki Tsuchiya
- Department of Physiology and Systems Bioscience, Kyoto Prefectural University of Medicine, Kyoto, Japan
| | - Yasuhiro Umemura
- Department of Physiology and Systems Bioscience, Kyoto Prefectural University of Medicine, Kyoto, Japan
| | - Kazuhiro Yagita
- Department of Physiology and Systems Bioscience, Kyoto Prefectural University of Medicine, Kyoto, Japan
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31
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Identification of a stemness-related gene panel associated with BET inhibition in triple negative breast cancer. Cell Oncol (Dordr) 2020; 43:431-444. [PMID: 32166583 PMCID: PMC7214516 DOI: 10.1007/s13402-020-00497-6] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/20/2020] [Indexed: 12/11/2022] Open
Abstract
Purpose Triple negative breast cancers (TNBCs) are enriched in cells bearing stem-like features, i.e., cancer stem cells (CSCs), which underlie cancer progression. Thus, targeting stemness may be an interesting treatment approach. The epigenetic machinery is crucial for maintaining the stemness phenotype. Bromodomain and extra-terminal domain (BET) epigenetic reader family members are emerging as novel targets for cancer therapy, and have already shown preclinical effects in breast cancer. Here, we aimed to evaluate the effect of the BET inhibitor JQ1 on stemness in TNBC. Methods Transcriptomic, functional annotation and qRT-PCR studies were performed on JQ1-exposed TNBC cells in culture. The results obtained were confirmed in spheroids and spheroid-derived tumours. In addition, limiting dilution, secondary and tertiary tumour sphere formation, matrigel invasion, immunofluorescence and flow cytometry assays were performed to evaluate the effect of JQ1 on CSC features. For clinical outcome analyses, the online tool Kaplan-Meier Plotter and an integrated response database were used. Results We found that JQ1 modified the expression of stemness-related genes in two TNBC-derived cell lines, MDA-MB-231 and BT549. Among these changes, the CD44 Antigen/CD24 Antigen (CD44/CD24) ratio and Aldehyde Dehydrogenase 1 Family Member A1 (ALDH1A1) expression level, i.e., both classical stemness markers, were found to be decreased by JQ1. Using a validated spheroid model to mimic the intrinsic characteristics of CSCs, we found that JQ1 decreased surface CD44 expression, inhibited self-renewal and invasion, and induced cell cycle arrest in G0/G1, thereby altering the stemness phenotype. We also found associations between four of the identified stemness genes, Gap Junction Protein Alpha 1 (GJA1), CD24, Epithelial Adhesion Molecule (EPCAM) and SRY-related HMG-box gene 9 (SOX9), and a worse TNBC patient outcome. The expression of another two of the stemness-related genes was found to be decreased by JQ1, i.e., ATP Binding Cassette Subfamily G Member 2 (ABCG2) and RUNX2, and predicted a low response to chemotherapy in TNBC patients, which supports a role for RUNX2 as a potential predictive marker for chemotherapy response in TNBC. Conclusions We identified a stemness-related gene panel associated with JQ1 and describe how this inhibitor modifies the stemness landscape in TNBC. Therefore, we propose a novel role for JQ1 as a stemness-targeting drug. Loss of the stem cell phenotype via JQ1 treatment could lead to less aggressive and more chemo-sensitive tumours, reflecting a better patient prognosis. Thus, the identified gene panel may be of interest for the clinical management of patients with aggressive TNBC. Electronic supplementary material The online version of this article (10.1007/s13402-020-00497-6) contains supplementary material, which is available to authorized users.
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32
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Cejas P, Long HW. Principles and methods of integrative chromatin analysis in primary tissues and tumors. Biochim Biophys Acta Rev Cancer 2019; 1873:188333. [PMID: 31759992 DOI: 10.1016/j.bbcan.2019.188333] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2019] [Revised: 10/22/2019] [Accepted: 10/23/2019] [Indexed: 12/16/2022]
Abstract
Recent methodological advances have enabled the genome-wide interrogation of chromatin from primary tumor tissues. Integrative analysis of histone post-translational modifications, transcription factor (TF) binding and open chromatin sites in tumors across cancer stages can elucidate the aberrant epigenetic states accompanying tumor progression. Cancer-associated chromatin alterations can activate or inactivate enhancers at genes involved in cancer while still respecting cell-of-origin constrictions. Accordingly, enhancer analysis in cancer could have uses for biomarker discovery to further refine patient diagnosis and potentially sub-classify patients for tailored therapy. Methodologies used for chromatin analyses of primary tissues need to address issues distinct from cell line studies including the specific sources of variability coming from the heterogeneous cellular composition of tissues and from inter-individual (epi)genetic differences. This leads to requirements for careful histological analysis to select the specific samples and cells of interest. In analyzing tumors somatic changes should be taken into account to distinguish the genuine epigenetic changes across tumor specimens from any genetic alterations such as copy number variations (CNV). In this contribution we review a selection of current results from chromatin profiling, examine experimental methodologies and discuss specific analysis approaches. We also review specific considerations regarding tissue preparation for epigenetic analysis and conclude with our perspectives on emerging approaches that will impact studies of chromatin landscapes of clinical samples in the future.
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Affiliation(s)
- Paloma Cejas
- Department of Medical Oncology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, MA, USA; Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA, USA; Translational Oncology Laboratory, Hospital La Paz Institute for Health Research (IdiPAZ) and CIBERONC, La Paz University Hospital, Madrid, Spain
| | - Henry W Long
- Department of Medical Oncology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, MA, USA; Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA, USA.
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Abstract
Introduction: Although many current cancer therapies are effective, the mortality rate globally is unacceptably high. Cancer remains the second leading cause of death worldwide after heart disease and has caused nearly 10 million deaths in 2018. Additionally, current preventive therapies for cancer are underdeveloped, undermining the quality of life of high-risk individuals. Therefore, new treatment options for targeting cancer are urgently needed. In a recent study, researchers adopted an autologous iPSC-based vaccine to present a broad spectrum of tumor antigens to the immune system and succeeded in orchestrating a strong prophylactic immunity towards multiple types of cancer in mice. Areas covered: In this review, we provide an overview of how cancer develops, the role of immune surveillance in cancer progression, the current status and challenges of cancer immunotherapy as well as the genetic overlap between pluripotent stem cells and cancer cells. Finally, we discuss the rationale for an autologous iPSC-based vaccine and its applications in murine cancer models. Expert opinion: The autologous iPSC-based vaccine is a promising preventive and therapeutic strategy for fighting various types of cancers. Continuing efforts and clinical/translational follow-up studies may bring an autologous iPSC-based cancer vaccination approach from bench to bedside.
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Affiliation(s)
- Lin Wang
- Cardiovascular Institute, Stanford University School of Medicine , Stanford , CA , USA.,Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine , Stanford , CA , USA
| | - Mark D Pegram
- Stanford Women's Cancer Center, Stanford University School of Medicine , Stanford , CA , USA.,Department of Medicine, Stanford University , Stanford , CA , USA
| | - Joseph C Wu
- Cardiovascular Institute, Stanford University School of Medicine , Stanford , CA , USA.,Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine , Stanford , CA , USA.,Department of Medicine, Stanford University , Stanford , CA , USA.,Department of Radiology, Stanford University , Stanford , CA , USA
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34
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Hyaluronan-CD44 axis orchestrates cancer stem cell functions. Cell Signal 2019; 63:109377. [PMID: 31362044 DOI: 10.1016/j.cellsig.2019.109377] [Citation(s) in RCA: 79] [Impact Index Per Article: 15.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2019] [Revised: 07/26/2019] [Accepted: 07/26/2019] [Indexed: 02/06/2023]
Abstract
The prominent role of CD44 in tumor cell signaling together with its establishment as a cancer stem cell (CSC) marker for various tumor entities imply a key role for CD44 in CSC functional properties. Hyaluronan, the main ligand of CD44, is a major constituent of CSC niche and, therefore, the hyaluronan-CD44 signaling axis is of functional importance in this special microenvironment. This review aims to provide recent advances in the importance of hyaluronan-CD44 interactions in the acquisition and maintenance of a CSC phenotype. Hyaluronan-CD44 axis has a substantial impact on stemness properties of CSCs and drug resistance through induction of EMT program, oxidative stress resistance, secretion of extracellular vesicles/exosomes and epigenetic control. Potential therapeutic approaches targeting CSCs based on the hyaluronan-CD44 axis are also presented.
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35
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Zhang Z, Wiencke JK, Koestler DC, Salas LA, Christensen BC, Kelsey KT. Absence of an embryonic stem cell DNA methylation signature in human cancer. BMC Cancer 2019; 19:711. [PMID: 31324166 PMCID: PMC6642562 DOI: 10.1186/s12885-019-5932-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2018] [Accepted: 07/12/2019] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND Differentiated cells that arise from stem cells in early development contain DNA methylation features that provide a memory trace of their fetal cell origin (FCO). The FCO signature was developed to estimate the proportion of cells in a mixture of cell types that are of fetal origin and are reminiscent of embryonic stem cell lineage. Here we implemented the FCO signature estimation method to compare the fraction of cells with the FCO signature in tumor tissues and their corresponding nontumor normal tissues. METHODS We applied our FCO algorithm to discovery data sets obtained from The Cancer Genome Atlas (TCGA) and replication data sets obtained from the Gene Expression Omnibus (GEO) data repository. Wilcoxon rank sum tests, linear regression models with adjustments for potential confounders and non-parametric randomization-based tests were used to test the association of FCO proportion between tumor tissues and nontumor normal tissues. P-values of < 0.05 were considered statistically significant. RESULTS Across 20 different tumor types we observed a consistently lower FCO signature in tumor tissues compared with nontumor normal tissues, with 18 observed to have significantly lower FCO fractions in tumor tissue (total n = 6,795 tumor, n = 922 nontumor, P < 0.05). We replicated our findings in 15 tumor types using data from independent subjects in 15 publicly available data sets (total n = 740 tumor, n = 424 nontumor, P < 0.05). CONCLUSIONS The results suggest that cancer development itself is substantially devoid of recapitulation of normal embryologic processes. Our results emphasize the distinction between DNA methylation in normal tightly regulated stem cell driven differentiation and cancer stem cell reprogramming that involves altered methylation in the service of great cell heterogeneity and plasticity.
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Affiliation(s)
- Ze Zhang
- Department of Epidemiology, School of Public Health, Brown University, Providence, RI USA
| | - John K. Wiencke
- Department of Neurological Surgery, Institute for Human Genetics, University of California San Francisco, San Francisco, CA USA
| | - Devin C. Koestler
- Department of Biostatistics, University of Kansas Medical Center, Kansas City, KS USA
| | - Lucas A. Salas
- Department of Epidemiology, Geisel School of Medicine, Dartmouth College, Lebanon, NH USA
| | - Brock C. Christensen
- Department of Epidemiology, Geisel School of Medicine, Dartmouth College, Lebanon, NH USA
- Departments of Molecular and Systems Biology, and Community and Family Medicine, Geisel School of Medicine, Dartmouth College, Lebanon, NH USA
| | - Karl T. Kelsey
- Department of Epidemiology, School of Public Health, Brown University, Providence, RI USA
- Department of Pathology and Laboratory Medicine, Brown University, Providence, RI USA
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36
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Han X, Wei Y, Wang H, Wang F, Ju Z, Li T. Nonsense-mediated mRNA decay: a 'nonsense' pathway makes sense in stem cell biology. Nucleic Acids Res 2019; 46:1038-1051. [PMID: 29272451 PMCID: PMC5814811 DOI: 10.1093/nar/gkx1272] [Citation(s) in RCA: 38] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2017] [Accepted: 12/09/2017] [Indexed: 01/04/2023] Open
Abstract
Nonsense-mediated mRNA decay (NMD) is a highly conserved post-transcriptional regulatory mechanism of gene expression in eukaryotes. Originally, NMD was identified as an RNA surveillance machinery in degrading 'aberrant' mRNA species with premature termination codons. Recent studies indicate that NMD regulates the stability of natural gene transcripts that play significant roles in cell functions. Although components and action modes of the NMD machinery in degrading its RNA targets have been extensively studied with biochemical and structural approaches, the biological roles of NMD remain to be defined. Stem cells are rare cell populations, which play essential roles in tissue homeostasis and hold great promises in regenerative medicine. Stem cells self-renew to maintain the cellular identity and differentiate into somatic lineages with specialized functions to sustain tissue integrity. Transcriptional regulations and epigenetic modulations have been extensively implicated in stem cell biology. However, post-transcriptional regulatory mechanisms, such as NMD, in stem cell regulation are largely unknown. In this paper, we summarize the recent findings on biological roles of NMD factors in embryonic and tissue-specific stem cells. Furthermore, we discuss the possible mechanisms of NMD in regulating stem cell fates.
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Affiliation(s)
- Xin Han
- Institute of Aging Research, School of Medicine, Hangzhou Normal University, Hangzhou, Zhejiang 310036, China
| | - Yanling Wei
- Institute of Aging Research, School of Medicine, Hangzhou Normal University, Hangzhou, Zhejiang 310036, China
| | - Hua Wang
- Institute of Aging Research, School of Medicine, Hangzhou Normal University, Hangzhou, Zhejiang 310036, China
| | - Feilong Wang
- Institute of Aging Research, School of Medicine, Hangzhou Normal University, Hangzhou, Zhejiang 310036, China
| | - Zhenyu Ju
- Institute of Aging Research, School of Medicine, Hangzhou Normal University, Hangzhou, Zhejiang 310036, China
| | - Tangliang Li
- Institute of Aging Research, School of Medicine, Hangzhou Normal University, Hangzhou, Zhejiang 310036, China
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37
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Kim J, Kim HS, Shim JJ, Lee J, Kim AY, Kim J. Critical role of the fibroblast growth factor signalling pathway in Ewing's sarcoma octamer-binding transcription factor 4-mediated cell proliferation and tumorigenesis. FEBS J 2019; 286:4443-4472. [PMID: 31155838 DOI: 10.1111/febs.14946] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2018] [Revised: 02/18/2019] [Accepted: 05/31/2019] [Indexed: 12/27/2022]
Abstract
Certain bone and soft tissue (BST) tumours harbour a chromosomal translocation [t(6;22)(p21;q12)], which fuses the Ewing's sarcoma (EWS) gene at 22q12 with the octamer-binding transcription factor 4 (Oct-4) gene at 6p21, resulting in the chimeric EWS-Oct-4 protein that possesses high transactivation ability. Although abnormal activation of signalling pathways can lead to human cancer development, the pathways underlying these processes in human BST tumours remain poorly explored. Here, we investigated the functional significance of fibroblast growth factor (FGF) signalling in human BST tumours. To identify the gene(s) involved in the FGF signalling pathway and potentially regulated by EWS-Oct-4 (also called EWS-POU5F1), we performed RNA-Seq analysis, electrophoretic mobility shift assays, chromatin immunoprecipitation assays, and xenograft assays. Treating GBS6 or ZHBTc4 cells-expressing EWS-Oct-4 with the small molecule FGF receptor (FGFR) inhibitors PD173074, NVPBGJ398, ponatinib, and dovitinib suppressed cellular proliferation. Gene expression analysis revealed that, among 22 Fgf and four Fgfr family members, Fgf-4 showed the highest upregulation (by 145-fold) in ZHBTc4 cells-expressing EWS-Oct-4. Computer-assisted analysis identified a putative EWS-Oct-4-binding site at +3017/+3024, suggesting that EWS-Oct-4 regulates Fgf-4 expression in human BST tumours. Fgf-4 enhancer constructs showed that EWS-Oct-4 transactivated the Fgf-4 gene reporter in vitro, and that overexpression of EWS-Oct-4 stimulated endogenous Fgf-4 gene expression in vivo. Finally, PD173074 significantly decreased tumour volume in mice. Taken together, these data suggest that FGF-4 signalling is involved in EWS-Oct-4-mediated tumorigenesis, and that its inhibition impairs tumour growth in vivo significantly.
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Affiliation(s)
- Junghoon Kim
- Laboratory of Molecular and Cellular Biology, Department of Life Science, Sogang University, Seoul, Korea
| | - Hyo Sun Kim
- Laboratory of Molecular and Cellular Biology, Department of Life Science, Sogang University, Seoul, Korea
| | - Jung-Jae Shim
- Laboratory of Molecular and Cellular Biology, Department of Life Science, Sogang University, Seoul, Korea
| | - Jungwoon Lee
- Laboratory of Molecular and Cellular Biology, Department of Life Science, Sogang University, Seoul, Korea
| | - Ah-Young Kim
- Laboratory of Molecular and Cellular Biology, Department of Life Science, Sogang University, Seoul, Korea
| | - Jungho Kim
- Laboratory of Molecular and Cellular Biology, Department of Life Science, Sogang University, Seoul, Korea
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38
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Malta TM, Sokolov A, Gentles AJ, Burzykowski T, Poisson L, Weinstein JN, Kamińska B, Huelsken J, Omberg L, Gevaert O, Colaprico A, Czerwińska P, Mazurek S, Mishra L, Heyn H, Krasnitz A, Godwin AK, Lazar AJ, Stuart JM, Hoadley KA, Laird PW, Noushmehr H, Wiznerowicz M. Machine Learning Identifies Stemness Features Associated with Oncogenic Dedifferentiation. Cell 2019; 173:338-354.e15. [PMID: 29625051 DOI: 10.1016/j.cell.2018.03.034] [Citation(s) in RCA: 1250] [Impact Index Per Article: 250.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2017] [Revised: 01/30/2018] [Accepted: 03/14/2018] [Indexed: 12/16/2022]
Abstract
Cancer progression involves the gradual loss of a differentiated phenotype and acquisition of progenitor and stem-cell-like features. Here, we provide novel stemness indices for assessing the degree of oncogenic dedifferentiation. We used an innovative one-class logistic regression (OCLR) machine-learning algorithm to extract transcriptomic and epigenetic feature sets derived from non-transformed pluripotent stem cells and their differentiated progeny. Using OCLR, we were able to identify previously undiscovered biological mechanisms associated with the dedifferentiated oncogenic state. Analyses of the tumor microenvironment revealed unanticipated correlation of cancer stemness with immune checkpoint expression and infiltrating immune cells. We found that the dedifferentiated oncogenic phenotype was generally most prominent in metastatic tumors. Application of our stemness indices to single-cell data revealed patterns of intra-tumor molecular heterogeneity. Finally, the indices allowed for the identification of novel targets and possible targeted therapies aimed at tumor differentiation.
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Affiliation(s)
- Tathiane M Malta
- Henry Ford Health System, Detroit, MI 48202, USA; University of São Paulo, Ribeirão Preto-SP 14049, Brazil
| | | | | | | | | | - John N Weinstein
- The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Bożena Kamińska
- Nencki Institute of Experimental Biology of PAS, 02093 Warsaw, Poland
| | - Joerg Huelsken
- Swiss Federal Institute of Technology Lausanne (EPFL), CH-1015 Lausanne; Switzerland
| | | | | | - Antonio Colaprico
- Université Libre de Bruxelles, 1050 Bruxelles, Belgium; Interuniversity Institute of Bioinformatics in Brussels (IB)(2), 1050 Bruxelles; Belgium
| | | | - Sylwia Mazurek
- Poznań University of Medical Sciences, 61701 Poznań, Poland; Postgraduate School of Molecular Medicine, Medical University of Warsaw, 02109 Warsaw, Poland
| | - Lopa Mishra
- George Washington University, Washington, D.C. 20052, USA
| | - Holger Heyn
- Centre for Genomic Regulation (CNAG-CRG), 08003 Barcelona, Spain
| | - Alex Krasnitz
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA
| | - Andrew K Godwin
- University of Kansas Medical Center, Kansas City, KS 66160, USA
| | - Alexander J Lazar
- The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | | | - Joshua M Stuart
- University of California, Santa Cruz, Santa Cruz, CA 95064, USA
| | | | - Peter W Laird
- Van Andel Research Institute, Grand Rapids, MI 49503, USA
| | - Houtan Noushmehr
- Henry Ford Health System, Detroit, MI 48202, USA; University of São Paulo, Ribeirão Preto-SP 14049, Brazil.
| | - Maciej Wiznerowicz
- Poznań University of Medical Sciences, 61701 Poznań, Poland; Greater Poland Cancer Center, 61866 Poznań, Poland; International Institute for Molecular Oncology, 60203 Poznań, Poland.
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Turhan A, Foudi A, Hwang JW, Desterke C, Griscelli F, Bennaceur-Griscelli A. Modeling malignancies using induced pluripotent stem cells: from chronic myeloid leukemia to hereditary cancers. Exp Hematol 2019; 71:61-67. [PMID: 30659851 DOI: 10.1016/j.exphem.2019.01.003] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2018] [Revised: 01/07/2019] [Accepted: 01/11/2019] [Indexed: 11/18/2022]
Abstract
Over the last decade, the possibility of reprogramming malignant cells to a pluripotent state has been achieved in several hematological malignancies, including myeloproliferative neoplasms, myelodysplastic syndromes, and chronic myeloid leukemia (CML). It has been shown that it is readily possible to generate induced pluripotent stem cells (iPSCs) from several types of primary CML cells and to generate progenitors and differentiated cells with variable efficiency. Although these experiments have brought some new insights in the understanding of CML pathophysiology, the ultimate goal of generating induced leukemic stem cells (LSCs) with long-term multilineage potential has not yet been demonstrated. Experiments under way will determine whether additional signaling events are required to induce the emergence of bona fide LSCs. However, iPSC modeling offers the unique possibility to generate pluripotent cells harboring cancer-predisposing mutations using patient-derived noncancerous cells, as has been shown in Li-Fraumeni syndrome, BRCA-1 associated breast carcinomas, or RET-mutated medullary thyroid carcinomas. In these conditions, mutated iPSCs can then be used to study the mutational history that precedes the appearance of the malignant transformation and to develop novel drug-screening strategies. The ability to induce a successful differentiation program toward the tissue in which a given cancer develops or to generate tissue-specific cancer organoids in which the full oncogenic potential can be revealed remains a major challenge in the field. Similarly, in hematological malignancies, a significant hurdle remains due to the lack of adequate technology to induce the emergence of leukemic cells that resemble LSCs, which hinders our ability to study the mechanisms of therapy resistance.
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MESH Headings
- Animals
- Biomarkers
- Cell Differentiation
- Cell Transformation, Neoplastic/genetics
- Cell Transformation, Neoplastic/metabolism
- Disease Susceptibility
- Humans
- Induced Pluripotent Stem Cells/cytology
- Induced Pluripotent Stem Cells/metabolism
- Leukemia, Myelogenous, Chronic, BCR-ABL Positive/etiology
- Leukemia, Myelogenous, Chronic, BCR-ABL Positive/metabolism
- Leukemia, Myelogenous, Chronic, BCR-ABL Positive/pathology
- Models, Biological
- Neoplastic Syndromes, Hereditary/etiology
- Neoplastic Syndromes, Hereditary/metabolism
- Neoplastic Syndromes, Hereditary/pathology
- Tumor Microenvironment
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Affiliation(s)
- Ali Turhan
- INSERM UMR-S 935 and ESTeam Paris Sud, Université Paris Sud, Villejuif, France; INGESTEM National iPSC Infrastructure, Villejuif, France.
| | - Adlen Foudi
- ATIP-Avenir INSERM UMR-S 935, Université Paris Sud, Villejuif, France
| | - Jin Wook Hwang
- INSERM UMR-S 935 and ESTeam Paris Sud, Université Paris Sud, Villejuif, France
| | - Christophe Desterke
- INSERM UMR-S 935 and ESTeam Paris Sud, Université Paris Sud, Villejuif, France
| | - Frank Griscelli
- INSERM UMR-S 935 and ESTeam Paris Sud, Université Paris Sud, Villejuif, France; INGESTEM National iPSC Infrastructure, Villejuif, France; Université Paris Descartes, Faculté Sorbonne Paris Cité, Faculté des Sciences Pharmaceutiques et Biologiques, Paris, France
| | - Annelise Bennaceur-Griscelli
- INSERM UMR-S 935 and ESTeam Paris Sud, Université Paris Sud, Villejuif, France; INGESTEM National iPSC Infrastructure, Villejuif, France
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40
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Abstract
Life starts with a zygote, which is formed by the fusion of a haploid sperm and egg. The formation of a blastomere by cleavage division (nuclear division without an increase in cell size) is the first step in embryogenesis, after the formation of the zygote. Blastomeres are responsible for reprogramming the parental genome as a new embryonic genome for generation of the pluripotent stem cells which then differentiate by Waddington's epigenetic landscape to create a new life. Multiple authors over the past 150 years have proposed that tumors arises from development gone awry at a point within Waddington's landscape. Recent discoveries showing that differentiated somatic cells can be reprogrammed into induced pluripotent stem cells, and that somatic cell nuclear transfer can be used to successfully clone animals, have fundamentally reshaped our understanding of tumor development and origin. Differentiated somatic cells are plastic and can be induced to dedifferentiate into pluripotent stem cells. Here, I review the evidence that suggests somatic cells may have a previously overlooked endogenous embryonic program that can be activated to dedifferentiate somatic cells into stem cells of various potencies for tumor initiation. Polyploid giant cancer cells (PGCCs) have long been observed in cancer and were thought originally to be nondividing. Contrary to this belief, recent findings show that stress-induced PGCCs divide by endoreplication, which may recapitulate the pattern of cleavage-like division in blastomeres and lead to dedifferentiation of somatic cells by a programmed process known as "the giant cell cycle", which comprise four distinct but overlapping phases: initiation, self-renewal, termination and stability. Depending on the intensity and type of stress, different levels of dedifferentiation result in the formation of tumors of different grades of malignancy. Based on these results, I propose a unified dualistic model to demonstrate the origin of human tumors. The tenet of this model includes four points, as follows. 1. Tumors originate from a stem cell at a specific developmental hierarchy, which can be achieved by dualistic origin: dedifferentiation of the zygote formed by two haploid gametes (sexual reproduction) via the blastomere during normal development, or transformation from damaged or aged mature somatic cells via a blastomere-like embryonic program (asexual reproduction). 2. Initiation of the tumor begins with a stem cell that has uncoupled the differentiation from the proliferation program which results in stem cell maturation arrest. 3. The developmental hierarchy at which stem cells arrest determines the degree of malignancy: the more primitive the level at which stem cells arrest, the greater the likelihood of the tumor being malignant. 4. Environmental factors and intrinsic genetic or epigenetic alterations represent the risk factors or stressors that facilitate stem cell arrest and somatic cell dedifferentiation. However, they, per se, are not the driving force of tumorigenesis. Thus, the birth of a tumor can be viewed as a triad that originates from a stem cell via dedifferentiation through a blastomere or blastomere-like program, which then differentiates along Waddington's landscape, and arrests at a developmental hierarchy. Blocking the PGCC-mediated dedifferentiation process and inducing their differentiation may represent a novel alternative approach to eliminate the tumor occurrence and therapeutic resistance.
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Affiliation(s)
- Jinsong Liu
- Department of Pathology, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Boulevard, Houston, TX 77030-4095, United States.
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Olney KC, Nyer DB, Vargas DA, Wilson Sayres MA, Haynes KA. The synthetic histone-binding regulator protein PcTF activates interferon genes in breast cancer cells. BMC SYSTEMS BIOLOGY 2018; 12:83. [PMID: 30253781 PMCID: PMC6156859 DOI: 10.1186/s12918-018-0608-4] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/06/2018] [Accepted: 09/12/2018] [Indexed: 02/06/2023]
Abstract
Background Mounting evidence from genome-wide studies of cancer shows that chromatin-mediated epigenetic silencing at large cohorts of genes is strongly linked to a poor prognosis. This mechanism is thought to prevent cell differentiation and enable evasion of the immune system. Drugging the cancer epigenome with small molecule inhibitors to release silenced genes from the repressed state has emerged as a powerful approach for cancer research and drug development. Targets of these inhibitors include chromatin-modifying enzymes that can acquire drug-resistant mutations. In order to directly target a generally conserved feature, elevated trimethyl-lysine 27 on histone H3 (H3K27me3), we developed the Polycomb-based Transcription Factor (PcTF), a fusion activator that targets methyl-histone marks via its N-terminal H3K27me3-binding motif, and co-regulates sets of silenced genes. Results Here, we report transcriptome profiling analyses of PcTF-treated breast cancer model cell lines. We identified a set of 19 PcTF-upregulated genes, or PUGs, that were consistent across three distinct breast cancer cell lines. These genes are associated with the interferon response pathway. Conclusions Our results demonstrate for the first time a chromatin-mediated interferon-related transcriptional response driven by an engineered fusion protein that physically links repressive histone marks with active transcription. Electronic supplementary material The online version of this article (10.1186/s12918-018-0608-4) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Kimberly C Olney
- School of Life Sciences, Arizona State University, 427 E Tyler Mall, Tempe, 85287-4501, AZ, USA
| | - David B Nyer
- School of Biological and Health Systems Engineering, Arizona State University, 501 E Tyler Mall, Tempe, AZ, 85287-9709, USA
| | - Daniel A Vargas
- School of Biological and Health Systems Engineering, Arizona State University, 501 E Tyler Mall, Tempe, AZ, 85287-9709, USA
| | - Melissa A Wilson Sayres
- School of Life Sciences, Arizona State University, 427 E Tyler Mall, Tempe, 85287-4501, AZ, USA.,Center for Evolution and Medicine, Arizona State University, 427 E Tyler Mall, Tempe, 85287-1701, AZ, USA
| | - Karmella A Haynes
- School of Biological and Health Systems Engineering, Arizona State University, 501 E Tyler Mall, Tempe, AZ, 85287-9709, USA.
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42
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Dedifferentiation process driven by TGF-beta signaling enhances stem cell properties in human colorectal cancer. Oncogene 2018; 38:780-793. [PMID: 30181548 DOI: 10.1038/s41388-018-0480-0] [Citation(s) in RCA: 55] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2017] [Revised: 08/06/2018] [Accepted: 08/10/2018] [Indexed: 02/07/2023]
Abstract
Cancer stem cells (CSCs) possess the capacity for self-renewal and the potential to differentiate into non-CSCs. The recent discoveries of dynamic equilibrium between CSCs and non-CSCs revealed the significance of acquiring CSC-like properties in non-CSCs as an important process in progression of cancer. The mechanism underlying acquisition of CSC-like properties has mainly been investigated in the context of epithelial-mesenchymal transition. Here, we demonstrate the dedifferentiation process may be an alternative mechanism in acquisition of CSC-like properties in human colorectal cancer cells. By exploring the single-cell gene expression analysis of organoids developed from CD44+ CSCs, we identified TWIST1 as a key molecule for maintaining the undifferentiated state of cancer cells. Consistent with the finding, we found that TGF-beta signaling pathway, a regulator of TWIST1, was specifically activated in the undifferentiated CD44+ CSCs in human colorectal cancer using microarray-based gene expression analysis and quantitative pathology imaging system. Furthermore, we showed that external stimulation with TGF-beta and the induction of TWIST1 converted CD44- non-CSCs into the undifferentiated CD44+ CSCs, leading to the significant increment of CSCs in xenograft models. This study strongly suggests dedifferentiation driven by TGF-beta signaling enhances stem cell properties in human colorectal cancer.
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Shah SR, David JM, Tippens ND, Mohyeldin A, Martinez-Gutierrez JC, Ganaha S, Schiapparelli P, Hamilton DH, Palena C, Levchenko A, Quiñones-Hinojosa A. Brachyury-YAP Regulatory Axis Drives Stemness and Growth in Cancer. Cell Rep 2018; 21:495-507. [PMID: 29020634 DOI: 10.1016/j.celrep.2017.09.057] [Citation(s) in RCA: 47] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2017] [Revised: 07/19/2017] [Accepted: 09/15/2017] [Indexed: 12/16/2022] Open
Abstract
Molecular factors that define stem cell identity have recently emerged as oncogenic drivers. For instance, brachyury, a key developmental transcriptional factor, is also implicated in carcinogenesis, most notably of chordoma, through mechanisms that remain elusive. Here, we show that brachyury is a crucial regulator of stemness in chordoma and in more common aggressive cancers. Furthermore, this effect of brachyury is mediated by control of synthesis and stability of Yes-associated protein (YAP), a key regulator of tissue growth and homeostasis, providing an unexpected mechanism of control of YAP expression. We further demonstrate that the brachyury-YAP regulatory pathway is associated with tumor aggressiveness. These results elucidate a mechanism of controlling both tumor stemness and aggressiveness through regulatory coupling of two developmental factors.
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Affiliation(s)
- Sagar R Shah
- Department of Neurologic Surgery, The Mayo Clinic, Jacksonville, FL, USA; Department of Biomedical Engineering, The Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Justin M David
- Laboratory of Tumor Immunology and Biology, Center for Cancer Research, National Cancer Institute, Bethesda, MD, USA
| | - Nathaniel D Tippens
- Department of Biological Statistics and Computational Biology, Cornell University, Ithaca, NY, USA
| | - Ahmed Mohyeldin
- Department of Neurological Surgery, The Ohio State University Wexner Medical Center, Columbus, OH, USA
| | | | - Sara Ganaha
- Department of Neurologic Surgery, The Mayo Clinic, Jacksonville, FL, USA
| | | | - Duane H Hamilton
- Laboratory of Tumor Immunology and Biology, Center for Cancer Research, National Cancer Institute, Bethesda, MD, USA
| | - Claudia Palena
- Laboratory of Tumor Immunology and Biology, Center for Cancer Research, National Cancer Institute, Bethesda, MD, USA
| | - Andre Levchenko
- Department of Biomedical Engineering and Systems Biology Institute, Yale University, New Haven, CT, USA.
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McCulloh CJ, Olson JK, Wang Y, Zhou Y, Tengberg NH, Deshpande S, Besner GE. Treatment of experimental necrotizing enterocolitis with stem cell-derived exosomes. J Pediatr Surg 2018; 53:1215-1220. [PMID: 29661576 PMCID: PMC5994352 DOI: 10.1016/j.jpedsurg.2018.02.086] [Citation(s) in RCA: 62] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/22/2018] [Accepted: 02/27/2018] [Indexed: 12/28/2022]
Abstract
PURPOSE Necrotizing enterocolitis (NEC) remains a devastating disease in premature infants. We previously showed that four stem cell (SC) types equivalently improve experimental NEC. Exosomes are intercellular nanovesicles containing RNA, miRNA, DNA, and protein. Because SC therapy faces challenges, our aim was to determine if the beneficial effects of SC are achievable with cell-free exosomes. METHODS Exosomes from four SC types were compared: (1) amniotic fluid-derived mesenchymal SC (AF-MSC); (2) bone marrow-derived MSC (BM-MSC); (3) amniotic fluid-derived neural SC (AF-NSC); and (4) neonatal enteric NSC (E-NSC). Rat pups exposed to NEC received a varying concentration of a single type of exosome with control pups receiving PBS only. Intestinal damage was graded histologically. RESULTS The incidence of NEC was 0% in unstressed pups and 60.7% in control pups subjected to NEC. Exosomes (4.0×108) reduced NEC incidence to: AF-MSC 25.0%; BM-MSC 23.1%; AF-NSC 11.1%; E-NSC 27.3%. When administered at a concentration of at least 4.0×108, all groups demonstrated a significant reduction in NEC compared to untreated pups. At this minimum concentration, there was no difference in treatment efficacy between exosomes and the SC from which they were derived. CONCLUSION Stem cell-derived exosomes reduce the incidence and severity of experimental NEC as effectively as the stem cells from which they are derived, supporting the potential for novel cell-free exosome therapy for NEC. TYPE OF STUDY Basic science.
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MESH Headings
- Amniotic Fluid/cytology
- Animals
- Animals, Newborn
- Bone Marrow Cells/cytology
- Disease Models, Animal
- Enterocolitis, Necrotizing/pathology
- Enterocolitis, Necrotizing/therapy
- Exosomes
- Humans
- Infant
- Infant, Newborn
- Infant, Premature
- Infant, Premature, Diseases/pathology
- Infant, Premature, Diseases/therapy
- Intestines/pathology
- Mesenchymal Stem Cells/cytology
- Neural Stem Cells/cytology
- Rats, Sprague-Dawley
- Stem Cell Transplantation
- Treatment Outcome
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Affiliation(s)
- Christopher J McCulloh
- Department of Pediatric Surgery, Center for Perinatal Research, The Research Institute at Nationwide Children's Hospital, Columbus, OH
| | - Jacob K Olson
- Department of Pediatric Surgery, Center for Perinatal Research, The Research Institute at Nationwide Children's Hospital, Columbus, OH
| | - Yijie Wang
- Department of Pediatric Surgery, Center for Perinatal Research, The Research Institute at Nationwide Children's Hospital, Columbus, OH
| | - Yu Zhou
- Department of Pediatric Surgery, Center for Perinatal Research, The Research Institute at Nationwide Children's Hospital, Columbus, OH
| | - Natalie Huibregtse Tengberg
- Department of Pediatric Surgery, Center for Perinatal Research, The Research Institute at Nationwide Children's Hospital, Columbus, OH
| | - Shivani Deshpande
- Department of Pediatric Surgery, Center for Perinatal Research, The Research Institute at Nationwide Children's Hospital, Columbus, OH
| | - Gail E Besner
- Department of Pediatric Surgery, Center for Perinatal Research, The Research Institute at Nationwide Children's Hospital, Columbus, OH.
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Czerwińska P, Mazurek S, Wiznerowicz M. Application of induced pluripotency in cancer studies. Rep Pract Oncol Radiother 2018; 23:207-214. [PMID: 29760595 DOI: 10.1016/j.rpor.2018.04.005] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2017] [Revised: 02/20/2018] [Accepted: 04/08/2018] [Indexed: 12/13/2022] Open
Abstract
As soon as induced pluripotent stem cells (iPSCs) reprogramming of somatic cells were developed, the discovery attracted the attention of scientists, offering new perspectives for personalized medicine and providing a powerful platform for drug testing. The technology was almost immediately applied to cancer studies. As presented in this review, direct reprogramming of cancer cells with enforced expression of pluripotency factors have several basic purposes, all of which aim to explain the complex nature of cancer development and progression, therapy-resistance and relapse, and ultimately lead to the development of novel anti-cancer therapies. Here, we briefly present recent advances in reprogramming methodologies as well as commonalities between cell reprogramming and carcinogenesis and discuss recent outcomes from the implementation of induced pluripotency into cancer research.
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Affiliation(s)
- Patrycja Czerwińska
- Laboratory of Gene Therapy, Department of Diagnostics and Cancer Immunology, Greater Poland Cancer Centre, Poznan, Poland
- Department of Cancer Immunology, Chair of Medical Biotechnology, Poznan University of Medical Sciences, Poznan, Poland
| | - Sylwia Mazurek
- Laboratory of Gene Therapy, Department of Diagnostics and Cancer Immunology, Greater Poland Cancer Centre, Poznan, Poland
- Department of Cancer Immunology, Chair of Medical Biotechnology, Poznan University of Medical Sciences, Poznan, Poland
- Postgraduate School of Molecular Medicine, Medical University of Warsaw, Warsaw, Poland
| | - Maciej Wiznerowicz
- Laboratory of Gene Therapy, Department of Diagnostics and Cancer Immunology, Greater Poland Cancer Centre, Poznan, Poland
- Department of Cancer Immunology, Chair of Medical Biotechnology, Poznan University of Medical Sciences, Poznan, Poland
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Abstract
Most human cancers harbor mutations in the gene encoding p53. As a result, research on p53 in the past few decades has focused primarily on its role as a tumor suppressor. One consequence of this focus is that the functions of p53 in development have largely been ignored. However, recent advances, such as the genomic profiling of embryonic stem cells, have uncovered the significance and mechanisms of p53 functions in mammalian cell differentiation and development. As we review here, these recent findings reveal roles that complement the well-established roles for p53 in tumor suppression.
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Affiliation(s)
- Abhinav K Jain
- Department of Epigenetics and Molecular Carcinogenesis, Center for Stem Cell and Development Biology, Center for Cancer Epigenetics, The University of Texas MD Anderson UT Health Graduate School of Biomedical Sciences, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Michelle Craig Barton
- Department of Epigenetics and Molecular Carcinogenesis, Center for Stem Cell and Development Biology, Center for Cancer Epigenetics, The University of Texas MD Anderson UT Health Graduate School of Biomedical Sciences, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
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Tarasewicz E, Oakes RS, Aviles MO, Straehla J, Chilton KM, Decker JT, Wu J, Shea LD, Jeruss JS. Embryonic stem cell secreted factors decrease invasiveness of triple-negative breast cancer cells through regulome modulation. Cancer Biol Ther 2018; 19:271-281. [PMID: 29053396 DOI: 10.1080/15384047.2017.1385681] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Stem cell microenvironments decrease the invasiveness of cancer cells, and elucidating the mechanisms associated with disease regression could further the development of targeted therapies for aggressive cancer subtypes. To this end, we applied an emerging technology, TRanscriptional Activity CEll aRray (TRACER), to investigate the reprogramming of triple-negative breast cancer (TNBC) cells in conditions that promoted a less aggressive phenotype. The repressive environment was established through exposure to mouse embryonic stem cell conditioned media (mESC CM). Assessment of carcinogenic phenotypes indicated that mESC CM exposure decreased proliferation, invasion, migration, and stemness in TNBC cells. Protein expression analysis revealed that mESC CM exposure increased expression of the epithelial protein E-cadherin and decreased the mesenchymal protein MMP9. Gene expression analysis showed that mESC CM decreased epithelial to mesenchymal transition (EMT) markers fibronectin, vimentin, and Snail. Over a period of 6 d, TRACER quantified changes in activity of 11 transcription factors (TFs) associated with oncogenic progression. The EMT profile was decreased in association with the activity of 7 TFs (Smad3, NF-κΒ, MEF2, GATA, Hif1, Sp1, and RXR). Further examination of Smad3 and GATA expression and phosphorylation revealed that mESC CM exposure decreased noncanonical Smad3 phosphorylation and Smad3-mediated gene expression, increased GATA3 expression and phosphorylation, and resulted in a synergistic decrease in migration of GATA3 overexpressing MDA-MB-231 cells. Collectively, the application of TRACER to examine TF activity associated with the transition of cancer cells to a less aggressive phenotype, as directed by mESC CM, identified novel mechanistic events linking the embryonic microenvironment to both favorable changes and cellular plasticity in TNBC cell phenotypes.
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Affiliation(s)
- Elizabeth Tarasewicz
- a Department of Surgery , Northwestern University Feinberg School of Medicine , Chicago , IL , USA
| | - Robert S Oakes
- b Department of Biomedical Engineering , University of Michigan , Ann Arbor , MI , USA
| | - Misael O Aviles
- c Department of Chemical and Biological Engineering , Northwestern University , Evanston , IL , USA
| | - Joelle Straehla
- a Department of Surgery , Northwestern University Feinberg School of Medicine , Chicago , IL , USA
| | - Kathryn M Chilton
- a Department of Surgery , Northwestern University Feinberg School of Medicine , Chicago , IL , USA
| | - Joseph T Decker
- b Department of Biomedical Engineering , University of Michigan , Ann Arbor , MI , USA
| | - Jia Wu
- c Department of Chemical and Biological Engineering , Northwestern University , Evanston , IL , USA
| | - Lonnie D Shea
- b Department of Biomedical Engineering , University of Michigan , Ann Arbor , MI , USA.,c Department of Chemical and Biological Engineering , Northwestern University , Evanston , IL , USA
| | - Jacqueline S Jeruss
- b Department of Biomedical Engineering , University of Michigan , Ann Arbor , MI , USA.,d Department of Surgery , University of Michigan , Ann Arbor , MI , USA
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48
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Kotarba G, Krzywinska E, Grabowska AI, Taracha A, Wilanowski T. TFCP2/TFCP2L1/UBP1 transcription factors in cancer. Cancer Lett 2018; 420:72-79. [PMID: 29410248 DOI: 10.1016/j.canlet.2018.01.078] [Citation(s) in RCA: 58] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2017] [Revised: 01/30/2018] [Accepted: 01/30/2018] [Indexed: 12/20/2022]
Abstract
The TFCP2/Grainyhead family of transcription factors is divided into two distinct subfamilies, one of which includes the Grainyhead-like 1-3 (GRHL1-3) proteins and the other consists of TFCP2 (synonyms: CP2, LSF, LBP-1c), TFCP2L1 (synonyms: CRTR-1, LBP-9) and UBP1 (synonyms: LBP-1a, NF2d9). Transcription factors from the TFCP2/TFCP2L1/UBP1 subfamily are involved in various aspects of cancer development. TFCP2 is a pro-oncogenic factor in hepatocellular carcinoma, pancreatic cancer and breast cancer, may be important in cervical carcinogenesis and in colorectal cancer. TFCP2 can also act as a tumor suppressor, for example, it inhibits melanoma growth. Furthermore, TFCP2 is involved in epithelial-mesenchymal transition and enhances angiogenesis. TFCP2L1 maintains pluripotency and self-renewal of embryonic stem cells and was implicated in a wide variety of cancers, including clear cell renal cell carcinoma, breast cancer and thyroid cancer. Here we present a systematic review of current knowledge of this protein subfamily in the context of cancer. We also discuss potential challenges in investigating this family of transcription factors. These challenges include redundancies between these factors as well as their interactions with each other and their ability to modulate each other's activity.
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Affiliation(s)
- Grzegorz Kotarba
- Laboratory of Signal Transduction, Department of Cell Biology, Nencki Institute of Experimental Biology of Polish Academy of Sciences, 3 Pasteur St., 02-093 Warsaw, Poland.
| | - Ewa Krzywinska
- Laboratory of Signal Transduction, Department of Cell Biology, Nencki Institute of Experimental Biology of Polish Academy of Sciences, 3 Pasteur St., 02-093 Warsaw, Poland.
| | - Anna I Grabowska
- Laboratory of Neuroplasticity, Department of Molecular and Cellular Neurobiology, Nencki Institute of Experimental Biology of Polish Academy of Sciences, 3 Pasteur St., 02-093 Warsaw, Poland.
| | - Agnieszka Taracha
- Laboratory of Signal Transduction, Department of Cell Biology, Nencki Institute of Experimental Biology of Polish Academy of Sciences, 3 Pasteur St., 02-093 Warsaw, Poland.
| | - Tomasz Wilanowski
- Laboratory of Signal Transduction, Department of Cell Biology, Nencki Institute of Experimental Biology of Polish Academy of Sciences, 3 Pasteur St., 02-093 Warsaw, Poland.
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Flavahan WA, Gaskell E, Bernstein BE. Epigenetic plasticity and the hallmarks of cancer. Science 2018; 357:357/6348/eaal2380. [PMID: 28729483 DOI: 10.1126/science.aal2380] [Citation(s) in RCA: 799] [Impact Index Per Article: 133.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Chromatin and associated epigenetic mechanisms stabilize gene expression and cellular states while also facilitating appropriate responses to developmental or environmental cues. Genetic, environmental, or metabolic insults can induce overly restrictive or overly permissive epigenetic landscapes that contribute to pathogenesis of cancer and other diseases. Restrictive chromatin states may prevent appropriate induction of tumor suppressor programs or block differentiation. By contrast, permissive or "plastic" states may allow stochastic oncogene activation or nonphysiologic cell fate transitions. Whereas many stochastic events will be inconsequential "passengers," some will confer a fitness advantage to a cell and be selected as "drivers." We review the broad roles played by epigenetic aberrations in tumor initiation and evolution and their potential to give rise to all classic hallmarks of cancer.
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Affiliation(s)
- William A Flavahan
- Department of Pathology and Center for Cancer Research, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA, and Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA
| | - Elizabeth Gaskell
- Department of Pathology and Center for Cancer Research, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA, and Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA
| | - Bradley E Bernstein
- Department of Pathology and Center for Cancer Research, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA, and Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA.
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50
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Xu Q, Junttila S, Scherer A, Giri KR, Kivelä O, Skovorodkin I, Röning J, Quaggin SE, Marti HP, Shan J, Samoylenko A, Vainio SJ. Renal carcinoma/kidney progenitor cell chimera organoid as a novel tumorigenesis gene discovery model. Dis Model Mech 2017; 10:1503-1515. [PMID: 29084770 PMCID: PMC5769601 DOI: 10.1242/dmm.028332] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2016] [Accepted: 10/16/2017] [Indexed: 12/13/2022] Open
Abstract
Three-dimensional (3D) organoids provide a new way to model various diseases, including cancer. We made use of recently developed kidney-organ-primordia tissue-engineering technologies to create novel renal organoids for cancer gene discovery. We then tested whether our novel assays can be used to examine kidney cancer development. First, we identified the transcriptomic profiles of quiescent embryonic mouse metanephric mesenchyme (MM) and of MM in which the nephrogenesis program had been induced ex vivo. The transcriptome profiles were then compared to the profiles of tumor biopsies from renal cell carcinoma (RCC) patients, and control samples from the same kidneys. Certain signature genes were identified that correlated in the developmentally induced MM and RCC, including components of the caveolar-mediated endocytosis signaling pathway. An efficient siRNA-mediated knockdown (KD) of Bnip3, Gsn, Lgals3, Pax8, Cav1, Egfr or Itgb2 gene expression was achieved in mouse RCC (Renca) cells. The live-cell imaging analysis revealed inhibition of cell migration and cell viability in the gene-KD Renca cells in comparison to Renca controls. Upon siRNA treatment, the transwell invasion capacity of Renca cells was also inhibited. Finally, we mixed E11.5 MM with yellow fluorescent protein (YFP)-expressing Renca cells to establish chimera organoids. Strikingly, we found that the Bnip3-, Cav1- and Gsn-KD Renca-YFP+ cells as a chimera with the MM in 3D organoid rescued, in part, the RCC-mediated inhibition of the nephrogenesis program during epithelial tubules formation. Altogether, our research indicates that comparing renal ontogenesis control genes to the genes involved in kidney cancer may provide new growth-associated gene screens and that 3D RCC-MM chimera organoids can serve as a novel model with which to investigate the behavioral roles of cancer cells within the context of emergent complex tissue structures. Editor’s Choice: Chimeras between embryonic kidney cells and renal carcinoma cells serve as a novel model to assay the roles of co-regulated genes in kidney development and renal carcinogenesis.
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Affiliation(s)
- Qi Xu
- Biocenter Oulu, Laboratory of Developmental Biology, InfoTech Oulu, Center for Cell Matrix Research, Faculty of Biochemistry and Molecular Medicine, Oulu University, FI-90014 Oulu, Finland
| | - Sanna Junttila
- Biocenter Oulu, Laboratory of Developmental Biology, InfoTech Oulu, Center for Cell Matrix Research, Faculty of Biochemistry and Molecular Medicine, Oulu University, FI-90014 Oulu, Finland
| | | | - Khem Raj Giri
- Biocenter Oulu, Laboratory of Developmental Biology, InfoTech Oulu, Center for Cell Matrix Research, Faculty of Biochemistry and Molecular Medicine, Oulu University, FI-90014 Oulu, Finland
| | - Oona Kivelä
- Biocenter Oulu, Laboratory of Developmental Biology, InfoTech Oulu, Center for Cell Matrix Research, Faculty of Biochemistry and Molecular Medicine, Oulu University, FI-90014 Oulu, Finland.,ValiFinn, FI-90220 Oulu, Finland
| | - Ilya Skovorodkin
- Biocenter Oulu, Laboratory of Developmental Biology, InfoTech Oulu, Center for Cell Matrix Research, Faculty of Biochemistry and Molecular Medicine, Oulu University, FI-90014 Oulu, Finland
| | - Juha Röning
- Department of Computer Science and Engineering, University of Oulu, FI-90014 Oulu, Finland
| | - Susan E Quaggin
- Biocenter Oulu, Laboratory of Developmental Biology, InfoTech Oulu, Center for Cell Matrix Research, Faculty of Biochemistry and Molecular Medicine, Oulu University, FI-90014 Oulu, Finland.,Feinberg Cardiovascular Research Institute, Division of Medicine-Nephrology, Northwestern University, Feinberg School of Medicine, Chicago, IL 60611, USA
| | - Hans-Peter Marti
- Department of Clinical Medicine, University of Bergen, N-5020 Bergen, Norway
| | - Jingdong Shan
- Biocenter Oulu, Laboratory of Developmental Biology, InfoTech Oulu, Center for Cell Matrix Research, Faculty of Biochemistry and Molecular Medicine, Oulu University, FI-90014 Oulu, Finland
| | - Anatoly Samoylenko
- Biocenter Oulu, Laboratory of Developmental Biology, InfoTech Oulu, Center for Cell Matrix Research, Faculty of Biochemistry and Molecular Medicine, Oulu University, FI-90014 Oulu, Finland
| | - Seppo J Vainio
- Biocenter Oulu, Laboratory of Developmental Biology, InfoTech Oulu, Center for Cell Matrix Research, Faculty of Biochemistry and Molecular Medicine, Oulu University, FI-90014 Oulu, Finland
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