1
|
Mistry T, Nath A, Pal R, Ghosh S, Mahata S, Kumar Sahoo P, Sarkar S, Choudhury T, Nath P, Alam N, Nasare VD. Emerging Futuristic Targeted Therapeutics: A Comprising Study Towards a New Era for the Management of TNBC. Am J Clin Oncol 2024; 47:132-148. [PMID: 38145412 DOI: 10.1097/coc.0000000000001071] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2023]
Abstract
Triple-negative breast cancer is characterized by high lethality attributed to factors such as chemoresistance, transcriptomic, and genomic heterogeneity, leading to a poor prognosis and limiting available targeted treatment options. While the identification of molecular targets remains pivotal for therapy involving chemo drugs, the current challenge lies in the poor response rates, low survival rates, and frequent relapses. Despite various clinical investigations exploring molecular targeted therapies in conjunction with conventional chemo treatment, the outcomes have been less than optimal. The critical need for more effective therapies underscores the urgency to discover potent novel treatments, including molecular and immune targets, as well as emerging strategies. This review provides a comprehensive analysis of conventional treatment approaches and explores emerging molecular and immune-targeted therapeutics, elucidating their mechanisms to address the existing obstacles for a more effective management of triple-negative breast cancer.
Collapse
Affiliation(s)
- Tanuma Mistry
- Departments of Pathology and Cancer Screening
- Department of Life Science and Biotechnology, Jadavpur University, Kolkata, West Bengal
| | - Arijit Nath
- Kalinga Institute of Industrial Technology (KIIT), Deemed to be University, School of Biotechnology, Bhubaneswar, Odisha, India
| | - Ranita Pal
- Departments of Pathology and Cancer Screening
| | | | | | | | | | | | | | - Neyaz Alam
- Surgical Oncology, Chittaranjan National Cancer Institute
| | | |
Collapse
|
2
|
Nair SJ, Suter T, Wang S, Yang L, Yang F, Rosenfeld MG. Transcriptional enhancers at 40: evolution of a viral DNA element to nuclear architectural structures. Trends Genet 2022; 38:1019-1047. [PMID: 35811173 PMCID: PMC9474616 DOI: 10.1016/j.tig.2022.05.015] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2022] [Revised: 05/05/2022] [Accepted: 05/31/2022] [Indexed: 02/08/2023]
Abstract
Gene regulation by transcriptional enhancers is the dominant mechanism driving cell type- and signal-specific transcriptional diversity in metazoans. However, over four decades since the original discovery, how enhancers operate in the nuclear space remains largely enigmatic. Recent multidisciplinary efforts combining real-time imaging, genome sequencing, and biophysical strategies provide insightful but conflicting models of enhancer-mediated gene control. Here, we review the discovery and progress in enhancer biology, emphasizing the recent findings that acutely activated enhancers assemble regulatory machinery as mesoscale architectural structures with distinct physical properties. These findings help formulate novel models that explain several mysterious features of the assembly of transcriptional enhancers and the mechanisms of spatial control of gene expression.
Collapse
Affiliation(s)
- Sreejith J Nair
- Department of Oncology, Lombardi Comprehensive Cancer Center, Georgetown University, Washington, DC 20057, USA.
| | - Tom Suter
- Howard Hughes Medical Institute, Department and School of Medicine, University of California, San Diego, La Jolla, CA 92093, USA
| | - Susan Wang
- Howard Hughes Medical Institute, Department and School of Medicine, University of California, San Diego, La Jolla, CA 92093, USA; Cellular and Molecular Medicine Graduate Program, University of California, San Diego, La Jolla, CA 92093, USA
| | - Lu Yang
- Howard Hughes Medical Institute, Department and School of Medicine, University of California, San Diego, La Jolla, CA 92093, USA
| | - Feng Yang
- Howard Hughes Medical Institute, Department and School of Medicine, University of California, San Diego, La Jolla, CA 92093, USA
| | - Michael G Rosenfeld
- Howard Hughes Medical Institute, Department and School of Medicine, University of California, San Diego, La Jolla, CA 92093, USA.
| |
Collapse
|
3
|
Jeon YH, Kim GW, Kim SY, Yi SA, Yoo J, Kim JY, Lee SW, Kwon SH. Heterochromatin Protein 1: A Multiplayer in Cancer Progression. Cancers (Basel) 2022; 14:cancers14030763. [PMID: 35159030 PMCID: PMC8833910 DOI: 10.3390/cancers14030763] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2022] [Revised: 01/28/2022] [Accepted: 01/29/2022] [Indexed: 11/16/2022] Open
Abstract
Dysregulation of epigenetic mechanisms as well as genomic mutations contribute to the initiation and progression of cancer. In addition to histone code writers, including histone lysine methyltransferase (KMT), and histone code erasers, including histone lysine demethylase (KDM), histone code reader proteins such as HP1 are associated with abnormal chromatin regulation in human diseases. Heterochromatin protein 1 (HP1) recognizes histone H3 lysine 9 methylation and broadly affects chromatin biology, such as heterochromatin formation and maintenance, transcriptional regulation, DNA repair, chromatin remodeling, and chromosomal segregation. Molecular functions of HP1 proteins have been extensively studied, although their exact roles in diseases require further study. Here, we comprehensively review the studies that have revealed the altered expression of HP1 and its functions in tumorigenesis. In particular, the distinctive effects of each HP1 subtype, namely HP1α, HP1β, and HP1γ, have been thoroughly explored in various cancer types. We also highlight how HP1 can serve as a potential biomarker for cancer prognosis and therapeutic target for cancer patients.
Collapse
Affiliation(s)
- Yu Hyun Jeon
- College of Pharmacy, Yonsei Institute of Pharmaceutical Sciences, Yonsei University, Incheon 21983, Korea; (Y.H.J.); (G.W.K.); (S.Y.K.); (J.Y.); (J.Y.K.); (S.W.L.)
| | - Go Woon Kim
- College of Pharmacy, Yonsei Institute of Pharmaceutical Sciences, Yonsei University, Incheon 21983, Korea; (Y.H.J.); (G.W.K.); (S.Y.K.); (J.Y.); (J.Y.K.); (S.W.L.)
| | - So Yeon Kim
- College of Pharmacy, Yonsei Institute of Pharmaceutical Sciences, Yonsei University, Incheon 21983, Korea; (Y.H.J.); (G.W.K.); (S.Y.K.); (J.Y.); (J.Y.K.); (S.W.L.)
| | - Sang Ah Yi
- School of Pharmacy, Sungkyunkwan University, Suwon 16419, Korea;
| | - Jung Yoo
- College of Pharmacy, Yonsei Institute of Pharmaceutical Sciences, Yonsei University, Incheon 21983, Korea; (Y.H.J.); (G.W.K.); (S.Y.K.); (J.Y.); (J.Y.K.); (S.W.L.)
| | - Ji Yoon Kim
- College of Pharmacy, Yonsei Institute of Pharmaceutical Sciences, Yonsei University, Incheon 21983, Korea; (Y.H.J.); (G.W.K.); (S.Y.K.); (J.Y.); (J.Y.K.); (S.W.L.)
| | - Sang Wu Lee
- College of Pharmacy, Yonsei Institute of Pharmaceutical Sciences, Yonsei University, Incheon 21983, Korea; (Y.H.J.); (G.W.K.); (S.Y.K.); (J.Y.); (J.Y.K.); (S.W.L.)
| | - So Hee Kwon
- College of Pharmacy, Yonsei Institute of Pharmaceutical Sciences, Yonsei University, Incheon 21983, Korea; (Y.H.J.); (G.W.K.); (S.Y.K.); (J.Y.); (J.Y.K.); (S.W.L.)
- Correspondence: ; Tel.: +82-32-749-4513
| |
Collapse
|
4
|
Xia L, Wang Z, Wu X, Zeng T, Luo W, Hu X, Ni Y, Che G, Liu L, Zhang W, Xie D, Li W. Multiplatform discovery and regulatory function analysis of structural variations in non-small cell lung carcinoma. Cell Rep 2021; 36:109660. [PMID: 34496260 DOI: 10.1016/j.celrep.2021.109660] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2020] [Revised: 06/06/2021] [Accepted: 08/11/2021] [Indexed: 02/08/2023] Open
Abstract
Non-small cell lung carcinoma (NSCLC), the most common form of lung cancer, is the leading cause of cancer-related death worldwide. We perform whole-genome sequencing (WGS) on samples from 43 primary patients with NSCLC and matched normal samples and analyze their matched open chromatin data and transcriptome data. Our results indicate that next-generation sequencing (NGS) and the Bionano Genomics (BNG) platform should be viewed as complementary technologies in terms of structural variations detection. By creating a framework integrating these two platforms, we detect high-technical-confidence somatic structural variations (SVs) in NSCLC cases, which could aid in the efficient investigation of new candidate oncogenes, such as TRIO and SESTD1. Our findings highlight the impact of somatic SVs on NSCLC oncogenesis and lay a foundation for exploring associations among somatic SVs, gene expression, and regulatory networks in patients with NSCLC.
Collapse
Affiliation(s)
- Lin Xia
- Frontier Science Center for Disease Molecular Network, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, No. 17 People's South Road, Chengdu, Sichuan 610041, China
| | - Zhoufeng Wang
- Frontier Science Center for Disease Molecular Network, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, No. 17 People's South Road, Chengdu, Sichuan 610041, China; Precision Medicine Research Center, West China Hospital, Sichuan University, No. 37 Guoxue Alley, Chengdu, Sichuan 610041, China; The Research Units of West China, Chinese Academy of Medical Sciences, West China Hospital, No. 37 Guoxue Alley, Chengdu, Sichuan 610041, China
| | - Xinyue Wu
- Frontier Science Center for Disease Molecular Network, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, No. 17 People's South Road, Chengdu, Sichuan 610041, China
| | - Tianfu Zeng
- Frontier Science Center for Disease Molecular Network, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, No. 17 People's South Road, Chengdu, Sichuan 610041, China
| | - Wenxin Luo
- Department of Respiratory and Critical Care Medicine, West China Hospital, Sichuan University, No. 37 Guoxue Alley, Chengdu, Sichuan 610041, China
| | - Xinlei Hu
- Frontier Science Center for Disease Molecular Network, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, No. 17 People's South Road, Chengdu, Sichuan 610041, China
| | - Yinyun Ni
- Precision Medicine Research Center, West China Hospital, Sichuan University, No. 37 Guoxue Alley, Chengdu, Sichuan 610041, China
| | - Guowei Che
- Department of Thoracic Surgery, West China Hospital, Sichuan University, No. 37 Guoxue Alley, Chengdu, Sichuan 610041, China
| | - Lunxu Liu
- Department of Thoracic Surgery, West China Hospital, Sichuan University, No. 37 Guoxue Alley, Chengdu, Sichuan 610041, China
| | - Wei Zhang
- Department of Respiratory and Critical Care Medicine, Shanghai Changhai Hospital, the Second Military Medical University, No. 168 Changhai Road, Shanghai 200433, China
| | - Dan Xie
- Frontier Science Center for Disease Molecular Network, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, No. 17 People's South Road, Chengdu, Sichuan 610041, China; Precision Medicine Research Center, West China Hospital, Sichuan University, No. 37 Guoxue Alley, Chengdu, Sichuan 610041, China.
| | - Weimin Li
- Frontier Science Center for Disease Molecular Network, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, No. 17 People's South Road, Chengdu, Sichuan 610041, China; Precision Medicine Research Center, West China Hospital, Sichuan University, No. 37 Guoxue Alley, Chengdu, Sichuan 610041, China; Department of Respiratory and Critical Care Medicine, West China Hospital, Sichuan University, No. 37 Guoxue Alley, Chengdu, Sichuan 610041, China; The Research Units of West China, Chinese Academy of Medical Sciences, West China Hospital, No. 37 Guoxue Alley, Chengdu, Sichuan 610041, China.
| |
Collapse
|
5
|
Deepak Singh D, Han I, Choi EH, Yadav DK. CRISPR/Cas9 based genome editing for targeted transcriptional control in triple-negative breast cancer. Comput Struct Biotechnol J 2021; 19:2384-2397. [PMID: 34025931 PMCID: PMC8120801 DOI: 10.1016/j.csbj.2021.04.036] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2020] [Revised: 04/13/2021] [Accepted: 04/16/2021] [Indexed: 02/07/2023] Open
Abstract
Breast cancer (BC) is the most common type of cancer in women at the global level and the highest mortality rate has been observed with triple-negative breast cancer (TNBC). Accumulation of genetic lesions an aberrant gene expression and protein degradation are considered to underlie the onset of tumorigenesis and metastasis. Therefore, the challenge to identify the genes and molecules that could be potentially used as potent biomarkers for personalized medicine against TNBC with minimal or no associated side effects. Discovery of the clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR associated protein 9 (Cas9) arrangement and an increasing repertoire of its new variants has provided a much-needed fillip towards editing TNBC genomes. In this review, we discuss the CRISPR/Cas9 genome editing, CRISPR Technology for diagnosis of (Triple-negative breast cancer) TNBC, Drug Resistance, and potential applications of CRISPR/Cas9 and its variants in deciphering or engineering intricate molecular and epigenetic mechanisms associated with TNBC. Furthermore, we have also explored the TNBC and CRISPR/Cas9 genome editing potential for repairing, genetic modifications in TNBC.
Collapse
Affiliation(s)
- Desh Deepak Singh
- Amity Institute of Biotechnology, Amity University Rajasthan, Jaipur, India
| | - Ihn Han
- Plasma Bioscience Research Center, Applied Plasma Medicine Center, Department of Electrical & Biological Physics, Kwangwoon University, Seoul, Republic of Korea
| | - Eun-Ha Choi
- Plasma Bioscience Research Center, Applied Plasma Medicine Center, Department of Electrical & Biological Physics, Kwangwoon University, Seoul, Republic of Korea
| | - Dharmendra Kumar Yadav
- College of Pharmacy, Gachon University of Medicine and Science, Hambakmoeiro 191, Yeonsu-gu, Incheon City, Republic of Korea
| |
Collapse
|
6
|
Farcas AM, Nagarajan S, Cosulich S, Carroll JS. Genome-Wide Estrogen Receptor Activity in Breast Cancer. Endocrinology 2021; 162:bqaa224. [PMID: 33284960 PMCID: PMC7787425 DOI: 10.1210/endocr/bqaa224] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/30/2020] [Indexed: 12/13/2022]
Abstract
The largest subtype of breast cancer is characterized by the expression and activity of the estrogen receptor alpha (ERalpha/ER). Although several effective therapies have significantly improved survival, the adaptability of cancer cells means that patients frequently stop responding or develop resistance to endocrine treatment. ER does not function in isolation and multiple associating factors have been reported to play a role in regulating the estrogen-driven transcriptional program. This review focuses on the dynamic interplay between some of these factors which co-occupy ER-bound regulatory elements, their contribution to estrogen signaling, and their possible therapeutic applications. Furthermore, the review illustrates how some ER association partners can influence and reprogram the genomic distribution of the estrogen receptor. As this dynamic ER activity enables cancer cell adaptability and impacts the clinical outcome, defining how this plasticity is determined is fundamental to our understanding of the mechanisms of disease progression.
Collapse
Affiliation(s)
- Anca M Farcas
- Bioscience, Oncology R&D, AstraZeneca, Cambridge, UK
- CRUK Cambridge Institute, University of Cambridge, Cambridge, UK
| | - Sankari Nagarajan
- CRUK Cambridge Institute, University of Cambridge, Cambridge, UK
- Division of Molecular and Cellular Function, School of Biological Sciences, Faculty of Biology, Medicine and Health, The University of Manchester, Manchester, UK
| | | | - Jason S Carroll
- CRUK Cambridge Institute, University of Cambridge, Cambridge, UK
| |
Collapse
|
7
|
Lin CL, Tan X, Chen M, Kusi M, Hung CN, Chou CW, Hsu YT, Wang CM, Kirma N, Chen CL, Lin CH, Lathrop KI, Elledge R, Kaklamani VG, Mitsuya K, Huang THM. ERα-related chromothripsis enhances concordant gene transcription on chromosome 17q11.1-q24.1 in luminal breast cancer. BMC Med Genomics 2020; 13:69. [PMID: 32408897 PMCID: PMC7222439 DOI: 10.1186/s12920-020-0729-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2019] [Accepted: 04/30/2020] [Indexed: 12/22/2022] Open
Abstract
BACKGROUND Chromothripsis is an event of genomic instability leading to complex chromosomal alterations in cancer. Frequent long-range chromatin interactions between transcription factors (TFs) and targets may promote extensive translocations and copy-number alterations in proximal contact regions through inappropriate DNA stitching. Although studies have proposed models to explain the initiation of chromothripsis, few discussed how TFs influence this process for tumor progression. METHODS This study focused on genomic alterations in amplification associated regions within chromosome 17. Inter-/intra-chromosomal rearrangements were analyzed using whole genome sequencing data of breast tumors in the Cancer Genome Atlas (TCGA) cohort. Common ERα binding sites were defined based on MCF-7, T47D, and MDA-MB-134 breast cancer cell lines using univariate K-means clustering methods. Nanopore sequencing technology was applied to validate frequent rearrangements detected between ATC loci on 17q23 and an ERα hub on 20q13. The efficacy of pharmacological inhibition of a potentially druggable target gene on 17q23 was evaluated using breast cancer cell lines and patient-derived circulating breast tumor cells. RESULTS There are five adjoining regions from 17q11.1 to 17q24.1 being hotspots of chromothripsis. Inter-/intra-chromosomal rearrangements of these regions occurred more frequently in ERα-positive tumors than in ERα-negative tumors. In addition, the locations of the rearrangements were often mapped within or close to dense ERα binding sites localized on these five 17q regions or other chromosomes. This chromothriptic event was linked to concordant upregulation of 96 loci that predominantly regulate cell-cycle machineries in advanced luminal tumors. Genome-editing analysis confirmed that an ERα hub localized on 20q13 coordinately regulates a subset of these loci localized on 17q23 through long-range chromosome interactions. One of these loci, Tousled Like Kinase 2 (TLK2) known to participate in DNA damage checkpoint control, is an actionable target using phenothiazine antipsychotics (PTZs). The antiproliferative effect of PTZs was prominent in high TLK2-expressing cells, compared to low expressing cells. CONCLUSION This study demonstrates a new approach for identifying tumorigenic drivers from genomic regions highly susceptible to ERα-related chromothripsis. We found a group of luminal breast tumors displaying 17q-related chromothripsis for which antipsychotics can be repurposed as treatment adjuncts.
Collapse
Affiliation(s)
- Chun-Lin Lin
- Department of Molecular Medicine, University of Texas Health Science Center at San Antonio, 7703 Floyd Curl Drive, San Antonio, TX, 78229, USA
| | - Xi Tan
- Department of Molecular Medicine, University of Texas Health Science Center at San Antonio, 7703 Floyd Curl Drive, San Antonio, TX, 78229, USA
| | - Meizhen Chen
- Department of Molecular Medicine, University of Texas Health Science Center at San Antonio, 7703 Floyd Curl Drive, San Antonio, TX, 78229, USA
| | - Meena Kusi
- Department of Molecular Medicine, University of Texas Health Science Center at San Antonio, 7703 Floyd Curl Drive, San Antonio, TX, 78229, USA
| | - Chia-Nung Hung
- Department of Molecular Medicine, University of Texas Health Science Center at San Antonio, 7703 Floyd Curl Drive, San Antonio, TX, 78229, USA
| | - Chih-Wei Chou
- Department of Molecular Medicine, University of Texas Health Science Center at San Antonio, 7703 Floyd Curl Drive, San Antonio, TX, 78229, USA
| | - Ya-Ting Hsu
- Department of Molecular Medicine, University of Texas Health Science Center at San Antonio, 7703 Floyd Curl Drive, San Antonio, TX, 78229, USA
| | - Chiou-Miin Wang
- Department of Molecular Medicine, University of Texas Health Science Center at San Antonio, 7703 Floyd Curl Drive, San Antonio, TX, 78229, USA
| | - Nameer Kirma
- Department of Molecular Medicine, University of Texas Health Science Center at San Antonio, 7703 Floyd Curl Drive, San Antonio, TX, 78229, USA
| | - Chun-Liang Chen
- Department of Molecular Medicine, University of Texas Health Science Center at San Antonio, 7703 Floyd Curl Drive, San Antonio, TX, 78229, USA
| | - Ching-Hung Lin
- Department of Oncology, National Taiwan University Hospital, Taipei, Taiwan
- Department of Internal Medicine, National Taiwan University Hospital, Taipei, Taiwan
| | - Kate I Lathrop
- Department of Medicine, Mays Cancer Center, University of Texas Health Science Center at San Antonio, San Antonio, TX, USA
| | - Richard Elledge
- Department of Medicine, Mays Cancer Center, University of Texas Health Science Center at San Antonio, San Antonio, TX, USA
| | - Virginia G Kaklamani
- Department of Medicine, Mays Cancer Center, University of Texas Health Science Center at San Antonio, San Antonio, TX, USA
| | - Kohzoh Mitsuya
- Department of Molecular Medicine, University of Texas Health Science Center at San Antonio, 7703 Floyd Curl Drive, San Antonio, TX, 78229, USA.
| | - Tim H-M Huang
- Department of Molecular Medicine, University of Texas Health Science Center at San Antonio, 7703 Floyd Curl Drive, San Antonio, TX, 78229, USA.
| |
Collapse
|
8
|
Jiang C, Meng L, Yang B, Luo X. Application of CRISPR/Cas9 gene editing technique in the study of cancer treatment. Clin Genet 2019; 97:73-88. [PMID: 31231788 DOI: 10.1111/cge.13589] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2019] [Revised: 06/14/2019] [Accepted: 06/17/2019] [Indexed: 12/14/2022]
Abstract
In recent years, gene editing, especially that using clustered regularly interspaced short palindromic repeat (CRISPR)/Cas9, has made great progress in the field of gene function. Rapid development of gene editing techniques has contributed to their significance in the field of medicine. Because the CRISPR/Cas9 gene editing tool is not only powerful but also has features such as strong specificity and high efficiency, it can accurately and rapidly screen the whole genome, facilitating the administration of gene therapy for specific diseases. In the field of tumor research, CRISPR/Cas9 can be used to edit genomes to explore the mechanisms of tumor occurrence, development, and metastasis. In these years, this system has been increasingly applied in tumor treatment research. CRISPR/Cas9 can be used to treat tumors by repairing mutations or knocking out specific genes. To date, numerous preliminary studies have been conducted on tumor treatment in related fields. CRISPR/Cas9 holds great promise for gene-level tumor treatment. Personalized and targeted therapy based on CRISPR/Cas9 will possibly shape the development of tumor therapy in the future. In this study, we review the findings of CRISPR/Cas9 for tumor treatment research to provide references for related future studies on the pathogenesis and clinical treatment of tumors.
Collapse
Affiliation(s)
- Chunyang Jiang
- Department of Thoracic Surgery, Tianjin Union Medical Center, Tianjin, People's Republic of China
| | - Lingxiang Meng
- Department of Anorectal Surgery, Anorectal Surgery Center, Tianjin Union Medical Center, Tianjin, People's Republic of China
| | - Bingjun Yang
- Department of Thoracic Surgery, Tianjin Union Medical Center, Tianjin, People's Republic of China
| | - Xin Luo
- Department of Radiotherapy, The Second Hospital of PingLiang City, Second Affiliated Hospital of Gansu Medical College, PingLiang, People's Republic of China
| |
Collapse
|
9
|
Wang Z, Tu K, Xia L, Luo K, Luo W, Tang J, Lu K, Hu X, He Y, Qiao W, Zhou Y, Zhang J, Cao F, Dai S, Tian P, Wang Y, Liu L, Che G, Zhou Q, Xie D, Li W. The Open Chromatin Landscape of Non-Small Cell Lung Carcinoma. Cancer Res 2019; 79:4840-4854. [PMID: 31209061 DOI: 10.1158/0008-5472.can-18-3663] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2018] [Revised: 04/12/2019] [Accepted: 06/10/2019] [Indexed: 02/05/2023]
Abstract
Non-small cell lung carcinoma (NSCLC) is a major cancer type whose epigenetic alteration remains unclear. We analyzed open chromatin data with matched whole-genome sequencing and RNA-seq data of 50 primary NSCLC cases. We observed high interpatient heterogeneity of open chromatin profiles and the degree of heterogeneity correlated to several clinical parameters. Lung adenocarcinoma and lung squamous cell carcinoma (LUSC) exhibited distinct open chromatin patterns. Beyond this, we uncovered that the broadest open chromatin peaks indicated key NSCLC genes and led to less stable expression. Furthermore, we found that the open chromatin peaks were gained or lost together with somatic copy number alterations and affected the expression of important NSCLC genes. In addition, we identified 21 joint-quantitative trait loci (joint-QTL) that correlated to both assay for transposase accessible chromatin sequencing peak intensity and gene expression levels. Finally, we identified 87 regulatory risk loci associated with lung cancer-related phenotypes by intersecting the QTLs with genome-wide association study significant loci. In summary, this compendium of multiomics data provides valuable insights and a resource to understand the landscape of open chromatin features and regulatory networks in NSCLC. SIGNIFICANCE: This study utilizes state of the art genomic methods to differentiate lung cancer subtypes.See related commentary by Bowcock, p. 4808.
Collapse
Affiliation(s)
- Zhoufeng Wang
- Department of Respiratory and Critical Care Medicine, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Kailing Tu
- National Frontier Center of Disease Molecular Network, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Lin Xia
- National Frontier Center of Disease Molecular Network, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Kai Luo
- National Frontier Center of Disease Molecular Network, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Wenxin Luo
- Department of Respiratory and Critical Care Medicine, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Jie Tang
- National Frontier Center of Disease Molecular Network, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Keying Lu
- National Frontier Center of Disease Molecular Network, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Xinlei Hu
- National Frontier Center of Disease Molecular Network, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Yijing He
- National Frontier Center of Disease Molecular Network, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Wenliang Qiao
- Lung Cancer Center, West China Hospital Sichuan University, Chengdu, Sichuan, China
| | - Yongzhao Zhou
- Department of Respiratory and Critical Care Medicine, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Jun Zhang
- National Frontier Center of Disease Molecular Network, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Feng Cao
- National Frontier Center of Disease Molecular Network, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Shuiping Dai
- Department of Respiratory and Critical Care Medicine, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Panwen Tian
- Department of Respiratory and Critical Care Medicine, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Ye Wang
- Department of Respiratory and Critical Care Medicine, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Lunxu Liu
- Department of Thoracic Surgery, West China Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Guowei Che
- Department of Thoracic Surgery, West China Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Qinghua Zhou
- Lung Cancer Center, West China Hospital Sichuan University, Chengdu, Sichuan, China
| | - Dan Xie
- National Frontier Center of Disease Molecular Network, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, Sichuan, China.
| | - Weimin Li
- Department of Respiratory and Critical Care Medicine, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, Sichuan, China.
| |
Collapse
|
10
|
Zhou Y, Gerrard DL, Wang J, Li T, Yang Y, Fritz AJ, Rajendran M, Fu X, Stein G, Schiff R, Lin S, Frietze S, Jin VX. Temporal dynamic reorganization of 3D chromatin architecture in hormone-induced breast cancer and endocrine resistance. Nat Commun 2019; 10:1522. [PMID: 30944316 PMCID: PMC6447566 DOI: 10.1038/s41467-019-09320-9] [Citation(s) in RCA: 43] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2017] [Accepted: 02/27/2019] [Indexed: 01/01/2023] Open
Abstract
Recent studies have demonstrated that chromatin architecture is linked to the progression of cancers. However, the roles of 3D structure and its dynamics in hormone-dependent breast cancer and endocrine resistance are largely unknown. Here we report the dynamics of 3D chromatin structure across a time course of estradiol (E2) stimulation in human estrogen receptor α (ERα)-positive breast cancer cells. We identified subsets of temporally highly dynamic compartments predominantly associated with active open chromatin and found that these highly dynamic compartments showed higher alteration in tamoxifen-resistant breast cancer cells. Remarkably, these compartments are characterized by active chromatin states, and enhanced ERα binding but decreased transcription factor CCCTC-binding factor (CTCF) binding. We finally identified a set of ERα-bound promoter-enhancer looping genes enclosed within altered domains that are enriched with cancer invasion, aggressiveness or metabolism signaling pathways. This large-scale analysis expands our understanding of high-order temporal chromatin reorganization underlying hormone-dependent breast cancer.
Collapse
Affiliation(s)
- Yufan Zhou
- Department of Molecular Medicine, University of Texas Health San Antonio, San Antonio, TX, 78229, USA
| | - Diana L Gerrard
- MLRS Department, University of Vermont, Burlington, VT, 05405, USA
| | - Junbai Wang
- Department of Pathology, Oslo University Hospital-Norwegian Radium Hospital, 0310, Montebello, Oslo, Norway
| | - Tian Li
- Department of Molecular Medicine, University of Texas Health San Antonio, San Antonio, TX, 78229, USA
| | - Yini Yang
- Department of Molecular Medicine, University of Texas Health San Antonio, San Antonio, TX, 78229, USA
| | - Andrew J Fritz
- Department of Biochemistry, University of Vermont, Burlington, VT, 05405, USA
| | - Mahitha Rajendran
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX, 77030, USA.,Department of Medicine, Baylor College of Medicine, Houston, TX, 77030, USA.,Lester and Sue Smith Breast Center, Baylor College of Medicine, Houston, TX, 77030, USA.,Dan L. Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Xiaoyong Fu
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX, 77030, USA.,Department of Medicine, Baylor College of Medicine, Houston, TX, 77030, USA.,Lester and Sue Smith Breast Center, Baylor College of Medicine, Houston, TX, 77030, USA.,Dan L. Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Gary Stein
- Department of Surgery, University of Vermont Larner College of Medicine, 89 Beaumont Avenue, Given C401, Burlington, Vermont, 05405, USA
| | - Rachel Schiff
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX, 77030, USA.,Department of Medicine, Baylor College of Medicine, Houston, TX, 77030, USA.,Lester and Sue Smith Breast Center, Baylor College of Medicine, Houston, TX, 77030, USA.,Dan L. Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Shili Lin
- Department of Statistics, The Ohio State University, Columbus, OH, 43210, USA
| | - Seth Frietze
- MLRS Department, University of Vermont, Burlington, VT, 05405, USA.
| | - Victor X Jin
- Department of Molecular Medicine, University of Texas Health San Antonio, San Antonio, TX, 78229, USA.
| |
Collapse
|
11
|
Liu S, Yin P, Kujawa SA, Coon JS, Okeigwe I, Bulun SE. Progesterone receptor integrates the effects of mutated MED12 and altered DNA methylation to stimulate RANKL expression and stem cell proliferation in uterine leiomyoma. Oncogene 2019; 38:2722-2735. [PMID: 30538295 PMCID: PMC6461478 DOI: 10.1038/s41388-018-0612-6] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2018] [Revised: 10/31/2018] [Accepted: 11/17/2018] [Indexed: 01/22/2023]
Abstract
Progesterone and its receptor, PR, are essential for uterine leiomyoma (LM, a.k.a., fibroid) tumorigenesis, but the underlying cellular and molecular mechanisms remain unclear. The receptor activator of NF-κB (RANKL) was recently identified as a novel progesterone/PR-responsive gene that plays an important role in promoting LM growth. Here, we used RANKL as a representative gene to investigate how steroid hormone, genetic, and epigenetic signals are integrated to regulate LM stem cell (LSC) function. We demonstrated that RANKL specifically upregulates LSC proliferation through activation of Cyclin D1. RANKL gene transcription was robustly induced by the progesterone agonist R5020, leading to a dramatically higher RANKL expression in LM compared to adjacent myometrial (MM) tissue. MethylCap-Seq revealed a differentially methylated region (DMR) adjacent to the distal PR-binding site (PRBS) 87 kb upstream of the RANKL transcription start site. Hypermethylation of the DMR inhibited recruitment of PR to the adjacent PRBS. Luciferase assays indicated that the DMR and distal PRBS constitute a novel RANKL distal regulatory element that actively regulates RANKL expression. Furthermore, MED12 physically interacts with PR in LM tissue. The interaction between MED12 and PR, binding of PR and MED12 to PRBS, and RANKL gene expression are significantly higher in LM containing a distinct MED12 mutation (G44D) than in LM with wild-type MED12. In summary, our findings suggest that DNA methylation and MED12 mutation together constitute a complex regulatory network that affects progesterone/PR-mediated RANKL gene expression, with an important role in activating stem cell proliferation and fibroid tumor development.
Collapse
Affiliation(s)
- Shimeng Liu
- Division of Reproductive Science in Medicine, Department of Obstetrics and Gynecology, Feinberg School of Medicine, Northwestern University, Chicago, IL, 60611, USA
| | - Ping Yin
- Division of Reproductive Science in Medicine, Department of Obstetrics and Gynecology, Feinberg School of Medicine, Northwestern University, Chicago, IL, 60611, USA
| | - Stacy A Kujawa
- Division of Reproductive Science in Medicine, Department of Obstetrics and Gynecology, Feinberg School of Medicine, Northwestern University, Chicago, IL, 60611, USA
| | - John S Coon
- Division of Reproductive Science in Medicine, Department of Obstetrics and Gynecology, Feinberg School of Medicine, Northwestern University, Chicago, IL, 60611, USA
| | - Ijeoma Okeigwe
- Division of Reproductive Science in Medicine, Department of Obstetrics and Gynecology, Feinberg School of Medicine, Northwestern University, Chicago, IL, 60611, USA
| | - Serdar E Bulun
- Division of Reproductive Science in Medicine, Department of Obstetrics and Gynecology, Feinberg School of Medicine, Northwestern University, Chicago, IL, 60611, USA.
| |
Collapse
|
12
|
Yang H, Jaeger M, Walker A, Wei D, Leiker K, Weitao T. Break Breast Cancer Addiction by CRISPR/Cas9 Genome Editing. J Cancer 2018; 9:219-231. [PMID: 29344267 PMCID: PMC5771328 DOI: 10.7150/jca.22554] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2017] [Accepted: 09/25/2017] [Indexed: 12/14/2022] Open
Abstract
Breast cancer is the leading diagnosed cancer for women globally. Evolution of breast cancer in tumorigenesis, metastasis and treatment resistance appears to be driven by the aberrant gene expression and protein degradation encoded by the cancer genomes. The uncontrolled cancer growth relies on these cellular events, thus constituting the cancerous programs and rendering the addiction towards them. These programs are likely the potential anticancer biomarkers for Personalized Medicine of breast cancer. This review intends to delineate the impact of the CRSPR/Cas-mediated genome editing in identification and validation of these anticancer biomarkers. It reviews the progress in three aspects of CRISPR/Cas9-mediated editing of the breast cancer genomes: Somatic genome editing, transcription and protein degradation addictions.
Collapse
Affiliation(s)
- Haitao Yang
- Laboratory for Cancer Genome Editing, Zhuhai Lifecode Medical Technologies. Inc. Department of Prenatal Diagnosis, Huizhou 2nd Hospital for Children and Women, #101 University Road, Tangjiawan, Zhuhai, 518900, Guangdong, China
| | - MariaLynn Jaeger
- College of Science and Mathematics, Southwest Baptist University, 1600 University Avenue, Bolivar, Missouri 65613, USA
| | - Averi Walker
- College of Science and Mathematics, Southwest Baptist University, 1600 University Avenue, Bolivar, Missouri 65613, USA
| | - Daniel Wei
- University of Texas at Dallas, 800 W Campbell Rd, Richardson, TX 75080, USA
| | - Katie Leiker
- College of Science and Mathematics, Southwest Baptist University, 1600 University Avenue, Bolivar, Missouri 65613, USA
| | - Tao Weitao
- College of Science and Mathematics, Southwest Baptist University, 1600 University Avenue, Bolivar, Missouri 65613, USA
| |
Collapse
|
13
|
Capurso D, Bengtsson H, Segal MR. Discovering hotspots in functional genomic data superposed on 3D chromatin configuration reconstructions. Nucleic Acids Res 2016; 44:2028-35. [PMID: 26869583 PMCID: PMC4797302 DOI: 10.1093/nar/gkw070] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2015] [Accepted: 01/25/2016] [Indexed: 11/14/2022] Open
Abstract
The spatial organization of the genome influences cellular function, notably gene regulation. Recent studies have assessed the three-dimensional (3D) co-localization of functional annotations (e.g. centromeres, long terminal repeats) using 3D genome reconstructions from Hi-C (genome-wide chromosome conformation capture) data; however, corresponding assessments for continuous functional genomic data (e.g. chromatin immunoprecipitation-sequencing (ChIP-seq) peak height) are lacking. Here, we demonstrate that applying bump hunting via the patient rule induction method (PRIM) to ChIP-seq data superposed on a Saccharomyces cerevisiae 3D genome reconstruction can discover ‘functional 3D hotspots’, regions in 3-space for which the mean ChIP-seq peak height is significantly elevated. For the transcription factor Swi6, the top hotspot by P-value contains MSB2 and ERG11 – known Swi6 target genes on different chromosomes. We verify this finding in a number of ways. First, this top hotspot is relatively stable under PRIM across parameter settings. Second, this hotspot is among the top hotspots by mean outcome identified by an alternative algorithm, k-Nearest Neighbor (k-NN) regression. Third, the distance between MSB2 and ERG11 is smaller than expected (by resampling) in two other 3D reconstructions generated via different normalization and reconstruction algorithms. This analytic approach can discover functional 3D hotspots and potentially reveal novel regulatory interactions.
Collapse
Affiliation(s)
- Daniel Capurso
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, CA 94158, USA
| | - Henrik Bengtsson
- Department of Epidemiology and Biostatistics, University of California, San Francisco, CA 94158, USA
| | - Mark R Segal
- Department of Epidemiology and Biostatistics, University of California, San Francisco, CA 94158, USA
| |
Collapse
|