1
|
Ramisetty S, Subbalakshmi AR, Pareek S, Mirzapoiazova T, Do D, Prabhakar D, Pisick E, Shrestha S, Achuthan S, Bhattacharya S, Malhotra J, Mohanty A, Singhal SS, Salgia R, Kulkarni P. Leveraging Cancer Phenotypic Plasticity for Novel Treatment Strategies. J Clin Med 2024; 13:3337. [PMID: 38893049 PMCID: PMC11172618 DOI: 10.3390/jcm13113337] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2024] [Revised: 05/30/2024] [Accepted: 06/03/2024] [Indexed: 06/21/2024] Open
Abstract
Cancer cells, like all other organisms, are adept at switching their phenotype to adjust to the changes in their environment. Thus, phenotypic plasticity is a quantitative trait that confers a fitness advantage to the cancer cell by altering its phenotype to suit environmental circumstances. Until recently, new traits, especially in cancer, were thought to arise due to genetic factors; however, it is now amply evident that such traits could also emerge non-genetically due to phenotypic plasticity. Furthermore, phenotypic plasticity of cancer cells contributes to phenotypic heterogeneity in the population, which is a major impediment in treating the disease. Finally, plasticity also impacts the group behavior of cancer cells, since competition and cooperation among multiple clonal groups within the population and the interactions they have with the tumor microenvironment also contribute to the evolution of drug resistance. Thus, understanding the mechanisms that cancer cells exploit to tailor their phenotypes at a systems level can aid the development of novel cancer therapeutics and treatment strategies. Here, we present our perspective on a team medicine-based approach to gain a deeper understanding of the phenomenon to develop new therapeutic strategies.
Collapse
Affiliation(s)
- Sravani Ramisetty
- Department of Medical Oncology and Therapeutics Research, City of Hope National Medical Center, Duarte, CA 91010, USA; (S.R.); (A.R.S.); (S.P.); (T.M.); (D.D.); (J.M.); (A.M.); (S.S.S.)
| | - Ayalur Raghu Subbalakshmi
- Department of Medical Oncology and Therapeutics Research, City of Hope National Medical Center, Duarte, CA 91010, USA; (S.R.); (A.R.S.); (S.P.); (T.M.); (D.D.); (J.M.); (A.M.); (S.S.S.)
| | - Siddhika Pareek
- Department of Medical Oncology and Therapeutics Research, City of Hope National Medical Center, Duarte, CA 91010, USA; (S.R.); (A.R.S.); (S.P.); (T.M.); (D.D.); (J.M.); (A.M.); (S.S.S.)
| | - Tamara Mirzapoiazova
- Department of Medical Oncology and Therapeutics Research, City of Hope National Medical Center, Duarte, CA 91010, USA; (S.R.); (A.R.S.); (S.P.); (T.M.); (D.D.); (J.M.); (A.M.); (S.S.S.)
| | - Dana Do
- Department of Medical Oncology and Therapeutics Research, City of Hope National Medical Center, Duarte, CA 91010, USA; (S.R.); (A.R.S.); (S.P.); (T.M.); (D.D.); (J.M.); (A.M.); (S.S.S.)
| | - Dhivya Prabhakar
- City of Hope Atlanta, 600 Celebrate Life Parkway, Newnan, GA 30265, USA;
| | - Evan Pisick
- City of Hope Chicago, 2520 Elisha Avenue, Zion, IL 60099, USA;
| | - Sagun Shrestha
- City of Hope Phoenix, 14200 West Celebrate Life Way, Goodyear, AZ 85338, USA;
| | - Srisairam Achuthan
- Center for Informatics, City of Hope National Medical Center, Duarte, CA 91010, USA;
| | - Supriyo Bhattacharya
- Integrative Genomics Core, City of Hope National Medical Center, Duarte, CA 91010, USA;
| | - Jyoti Malhotra
- Department of Medical Oncology and Therapeutics Research, City of Hope National Medical Center, Duarte, CA 91010, USA; (S.R.); (A.R.S.); (S.P.); (T.M.); (D.D.); (J.M.); (A.M.); (S.S.S.)
| | - Atish Mohanty
- Department of Medical Oncology and Therapeutics Research, City of Hope National Medical Center, Duarte, CA 91010, USA; (S.R.); (A.R.S.); (S.P.); (T.M.); (D.D.); (J.M.); (A.M.); (S.S.S.)
| | - Sharad S. Singhal
- Department of Medical Oncology and Therapeutics Research, City of Hope National Medical Center, Duarte, CA 91010, USA; (S.R.); (A.R.S.); (S.P.); (T.M.); (D.D.); (J.M.); (A.M.); (S.S.S.)
| | - Ravi Salgia
- Department of Medical Oncology and Therapeutics Research, City of Hope National Medical Center, Duarte, CA 91010, USA; (S.R.); (A.R.S.); (S.P.); (T.M.); (D.D.); (J.M.); (A.M.); (S.S.S.)
| | - Prakash Kulkarni
- Department of Medical Oncology and Therapeutics Research, City of Hope National Medical Center, Duarte, CA 91010, USA; (S.R.); (A.R.S.); (S.P.); (T.M.); (D.D.); (J.M.); (A.M.); (S.S.S.)
- Department of Systems Biology, City of Hope National Medical Center, Duarte, CA 91010, USA
| |
Collapse
|
2
|
Sahoo S, Ramu S, Nair MG, Pillai M, San Juan BP, Milioli HZ, Mandal S, Naidu CM, Mavatkar AD, Subramaniam H, Neogi AG, Chaffer CL, Prabhu JS, Somarelli JA, Jolly MK. Multi-modal transcriptomic analysis unravels enrichment of hybrid epithelial/mesenchymal state and enhanced phenotypic heterogeneity in basal breast cancer. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.09.30.558960. [PMID: 37873432 PMCID: PMC10592858 DOI: 10.1101/2023.09.30.558960] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/25/2023]
Abstract
Intra-tumoral phenotypic heterogeneity promotes tumor relapse and therapeutic resistance and remains an unsolved clinical challenge. It manifests along multiple phenotypic axes and decoding the interconnections among these different axes is crucial to understand its molecular origins and to develop novel therapeutic strategies to control it. Here, we use multi-modal transcriptomic data analysis - bulk, single-cell and spatial transcriptomics - from breast cancer cell lines and primary tumor samples, to identify associations between epithelial-mesenchymal transition (EMT) and luminal-basal plasticity - two key processes that enable heterogeneity. We show that luminal breast cancer strongly associates with an epithelial cell state, but basal breast cancer is associated with hybrid epithelial/mesenchymal phenotype(s) and higher phenotypic heterogeneity. These patterns were inherent in methylation profiles, suggesting an epigenetic crosstalk between EMT and lineage plasticity in breast cancer. Mathematical modelling of core underlying gene regulatory networks representative of the crosstalk between the luminal-basal and epithelial-mesenchymal axes recapitulate and thus elucidate mechanistic underpinnings of the observed associations from transcriptomic data. Our systems-based approach integrating multi-modal data analysis with mechanism-based modeling offers a predictive framework to characterize intra-tumor heterogeneity and to identify possible interventions to restrict it.
Collapse
Affiliation(s)
- Sarthak Sahoo
- Department of Bioengineering, Indian Institute of Science, Bangalore, 560012, India
| | - Soundharya Ramu
- Department of Bioengineering, Indian Institute of Science, Bangalore, 560012, India
| | - Madhumathy G Nair
- Division of Molecular Medicine, St. John’s Research Institute, St. John’s Medical College, Bangalore, 560012, India
| | - Maalavika Pillai
- Department of Bioengineering, Indian Institute of Science, Bangalore, 560012, India
- Current affiliation: Feinberg School of Medicine, Northwestern University, Chicago, 60611, USA
| | - Beatriz P San Juan
- Garvan Institute of Medical Research, Darlinghurst, NSW, 2010, Australia
| | | | - Susmita Mandal
- Department of Bioengineering, Indian Institute of Science, Bangalore, 560012, India
| | - Chandrakala M Naidu
- Division of Molecular Medicine, St. John’s Research Institute, St. John’s Medical College, Bangalore, 560012, India
| | - Apoorva D Mavatkar
- Division of Molecular Medicine, St. John’s Research Institute, St. John’s Medical College, Bangalore, 560012, India
| | - Harini Subramaniam
- Department of Bioengineering, Indian Institute of Science, Bangalore, 560012, India
| | - Arpita G Neogi
- Department of Bioengineering, Indian Institute of Science, Bangalore, 560012, India
| | - Christine L Chaffer
- Garvan Institute of Medical Research, Darlinghurst, NSW, 2010, Australia
- University of New South Wales, UNSW Medicine, UNSW Sydney, NSW, 2052, Australia
| | - Jyothi S Prabhu
- Division of Molecular Medicine, St. John’s Research Institute, St. John’s Medical College, Bangalore, 560012, India
| | | | - Mohit Kumar Jolly
- Department of Bioengineering, Indian Institute of Science, Bangalore, 560012, India
| |
Collapse
|
3
|
Haerinck J, Goossens S, Berx G. The epithelial-mesenchymal plasticity landscape: principles of design and mechanisms of regulation. Nat Rev Genet 2023; 24:590-609. [PMID: 37169858 DOI: 10.1038/s41576-023-00601-0] [Citation(s) in RCA: 18] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/30/2023] [Indexed: 05/13/2023]
Abstract
Epithelial-mesenchymal plasticity (EMP) enables cells to interconvert between several states across the epithelial-mesenchymal landscape, thereby acquiring hybrid epithelial/mesenchymal phenotypic features. This plasticity is crucial for embryonic development and wound healing, but also underlies the acquisition of several malignant traits during cancer progression. Recent research using systems biology and single-cell profiling methods has provided novel insights into the main forces that shape EMP, which include the microenvironment, lineage specification and cell identity, and the genome. Additionally, key roles have emerged for hysteresis (cell memory) and cellular noise, which can drive stochastic transitions between cell states. Here, we review these forces and the distinct but interwoven layers of regulatory control that stabilize EMP states or facilitate epithelial-mesenchymal transitions (EMTs) and discuss the therapeutic potential of manipulating the EMP landscape.
Collapse
Affiliation(s)
- Jef Haerinck
- Molecular and Cellular Oncology Laboratory, Department of Biomedical Molecular Biology, Ghent University, Ghent, Belgium
- Cancer Research Institute Ghent (CRIG), Ghent, Belgium
| | - Steven Goossens
- Cancer Research Institute Ghent (CRIG), Ghent, Belgium
- Unit for Translational Research in Oncology, Department of Diagnostic Sciences, Ghent University, Ghent, Belgium
| | - Geert Berx
- Molecular and Cellular Oncology Laboratory, Department of Biomedical Molecular Biology, Ghent University, Ghent, Belgium.
- Cancer Research Institute Ghent (CRIG), Ghent, Belgium.
| |
Collapse
|
4
|
Verstappe J, Berx G. A role for partial epithelial-to-mesenchymal transition in enabling stemness in homeostasis and cancer. Semin Cancer Biol 2023; 90:15-28. [PMID: 36773819 DOI: 10.1016/j.semcancer.2023.02.001] [Citation(s) in RCA: 17] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2022] [Revised: 01/19/2023] [Accepted: 02/02/2023] [Indexed: 02/12/2023]
Abstract
Stem cells have self-renewal capacities and the ability to give rise to differentiated cells thereby sustaining tissues during homeostasis and injury. This structural hierarchy extends to tumours which harbor stem-like cells deemed cancer stem cells that propagate the tumour and drive metastasis and relapse. The process of epithelial-to-mesenchymal transition (EMT), which plays an important role in development and cancer cell migration, was shown to be correlated with stemness in both homeostasis and cancer indicating that stemness can be acquired and is not necessarily an intrinsic trait. Nowadays it is experimentally proven that the activation of an EMT program does not necessarily drive cells towards a fully mesenchymal phenotype but rather to hybrid E/M states. This review offers the latest advances in connecting the EMT status and stem-cell state of both non-transformed and cancer cells. Recent literature clearly shows that hybrid EMT states have a higher probability of acquiring stem cell traits. The position of a cell along the EMT-axis which coincides with a stem cell-like state is known as the stemness window. We show how the original EMT-state of a cell dictates the EMT/MET inducing programmes required to reach stemness. Lastly we present the mechanism of stemness regulation and the regulatory feedback loops which position cells at a certain EMT state along the EMT axis.
Collapse
Affiliation(s)
- Jeroen Verstappe
- Molecular and Cellular Oncology Laboratory, Department of Biomedical Molecular Biology, Ghent University, Ghent, Belgium; Cancer Research Institute Ghent (CRIG), Ghent, Belgium
| | - Geert Berx
- Molecular and Cellular Oncology Laboratory, Department of Biomedical Molecular Biology, Ghent University, Ghent, Belgium; Cancer Research Institute Ghent (CRIG), Ghent, Belgium.
| |
Collapse
|
5
|
Subhadarshini S, Markus J, Sahoo S, Jolly MK. Dynamics of Epithelial-Mesenchymal Plasticity: What Have Single-Cell Investigations Elucidated So Far? ACS OMEGA 2023; 8:11665-11673. [PMID: 37033874 PMCID: PMC10077445 DOI: 10.1021/acsomega.2c07989] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/15/2022] [Accepted: 03/06/2023] [Indexed: 06/19/2023]
Abstract
Epithelial-mesenchymal plasticity (EMP) is a key driver of cancer metastasis and therapeutic resistance, through which cancer cells can reversibly and dynamically alter their molecular and functional traits along the epithelial-mesenchymal spectrum. While cells in the epithelial phenotype are usually tightly adherent, less metastatic, and drug-sensitive, those in the hybrid epithelial/mesenchymal and/or mesenchymal state are more invasive, migratory, drug-resistant, and immune-evasive. Single-cell studies have emerged as a powerful tool in gaining new insights into the dynamics of EMP across various cancer types. Here, we review many recent studies that employ single-cell analysis techniques to better understand the dynamics of EMP in cancer both in vitro and in vivo. These single-cell studies have underlined the plurality of trajectories cells can traverse during EMP and the consequent heterogeneity of hybrid epithelial/mesenchymal phenotypes seen at both preclinical and clinical levels. They also demonstrate how diverse EMP trajectories may exhibit hysteretic behavior and how the rate of such cell-state transitions depends on the genetic/epigenetic background of recipient cells, as well as the dose and/or duration of EMP-inducing growth factors. Finally, we discuss the relationship between EMP and patient survival across many cancer types. We also present a next set of questions related to EMP that could benefit much from single-cell observations and pave the way to better tackle phenotypic switching and heterogeneity in clinic.
Collapse
Affiliation(s)
| | - Joel Markus
- Centre
for BioSystems Science and Engineering, Indian Institute of Science, Bangalore 560012, India
| | - Sarthak Sahoo
- Centre
for BioSystems Science and Engineering, Indian Institute of Science, Bangalore 560012, India
| | - Mohit Kumar Jolly
- Centre
for BioSystems Science and Engineering, Indian Institute of Science, Bangalore 560012, India
| |
Collapse
|
6
|
Subbalakshmi AR, Sahoo S, Manjunatha P, Goyal S, Kasiviswanathan VA, Mahesh Y, Ramu S, McMullen I, Somarelli JA, Jolly MK. The ELF3 transcription factor is associated with an epithelial phenotype and represses epithelial-mesenchymal transition. J Biol Eng 2023; 17:17. [PMID: 36864480 PMCID: PMC9983220 DOI: 10.1186/s13036-023-00333-z] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2022] [Accepted: 02/09/2023] [Indexed: 03/04/2023] Open
Abstract
BACKGROUND Epithelial-mesenchymal plasticity (EMP) involves bidirectional transitions between epithelial, mesenchymal and multiple intermediary hybrid epithelial/mesenchymal phenotypes. While the process of epithelial-mesenchymal transition (EMT) and its associated transcription factors are well-characterised, the transcription factors that promote mesenchymal-epithelial transition (MET) and stabilise hybrid E/M phenotypes are less well understood. RESULTS Here, we analyse multiple publicly-available transcriptomic datasets at bulk and single-cell level and pinpoint ELF3 as a factor that is strongly associated with an epithelial phenotype and is inhibited during EMT. Using mechanism-based mathematical modelling, we also show that ELF3 inhibits the progression of EMT. This behaviour was also observed in the presence of an EMT inducing factor WT1. Our model predicts that the MET induction capacity of ELF3 is stronger than that of KLF4, but weaker than that of GRHL2. Finally, we show that ELF3 levels correlates with worse patient survival in a subset of solid tumour types. CONCLUSION ELF3 is shown to be inhibited during EMT progression and is also found to inhibit the progression of complete EMT suggesting that ELF3 may be able to counteract EMT induction, including in the presence of EMT-inducing factors, such as WT1. The analysis of patient survival data indicates that the prognostic capacity of ELF3 is specific to cell-of-origin or lineage.
Collapse
Affiliation(s)
- Ayalur Raghu Subbalakshmi
- grid.34980.360000 0001 0482 5067Centre for BioSystems Science and Engineering, Indian Institute of Science, 560012 Bangalore, India
| | - Sarthak Sahoo
- grid.34980.360000 0001 0482 5067Centre for BioSystems Science and Engineering, Indian Institute of Science, 560012 Bangalore, India
| | - Prakruthi Manjunatha
- grid.444321.40000 0004 0501 2828Department of Medical Electronics, M S Ramaiah Institute of Technology, 560054 Bangalore, India
| | - Shaurya Goyal
- grid.429017.90000 0001 0153 2859Department of Humanities and Social Sciences, Indian Institute of Technology, 721302 Kharagpur, India
| | - Vignesh A Kasiviswanathan
- grid.512757.30000 0004 1761 9897Department of Biotechnology, JSS Science and Technology University, 570006 Mysore, India
| | - Yeshwanth Mahesh
- grid.34980.360000 0001 0482 5067Centre for BioSystems Science and Engineering, Indian Institute of Science, 560012 Bangalore, India
| | - Soundharya Ramu
- grid.419655.a0000 0001 0008 3668Department of Biotechnology, National Institute of Technology Warangal, 506004 Warangal, India
| | - Isabelle McMullen
- grid.26009.3d0000 0004 1936 7961Department of Medicine, Duke University, NC 27708 Durham, USA
| | - Jason A. Somarelli
- grid.26009.3d0000 0004 1936 7961Department of Medicine, Duke University, NC 27708 Durham, USA ,grid.26009.3d0000 0004 1936 7961Duke Cancer Institute, Duke University, NC 27708 Durham, USA
| | - Mohit Kumar Jolly
- Centre for BioSystems Science and Engineering, Indian Institute of Science, 560012, Bangalore, India.
| |
Collapse
|
7
|
Jindal R, Nanda A, Pillai M, Ware KE, Singh D, Sehgal M, Armstrong AJ, Somarelli JA, Jolly MK. Emergent dynamics of underlying regulatory network links EMT and androgen receptor-dependent resistance in prostate cancer. Comput Struct Biotechnol J 2023; 21:1498-1509. [PMID: 36851919 PMCID: PMC9957767 DOI: 10.1016/j.csbj.2023.01.031] [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: 12/05/2022] [Revised: 01/23/2023] [Accepted: 01/23/2023] [Indexed: 02/10/2023] Open
Abstract
Advanced prostate cancer patients initially respond to hormone therapy, be it in the form of androgen deprivation therapy or second-generation hormone therapies, such as abiraterone acetate or enzalutamide. However, most men with prostate cancer eventually develop hormone therapy resistance. This resistance can arise through multiple mechanisms, such as through genetic mutations, epigenetic mechanisms, or through non-genetic pathways, such as lineage plasticity along epithelial-mesenchymal or neuroendocrine-like axes. These mechanisms of hormone therapy resistance often co-exist within a single patient's tumor and can overlap within a single cell. There exists a growing need to better understand how phenotypic heterogeneity and plasticity results from emergent dynamics of the regulatory networks governing androgen independence. Here, we investigated the dynamics of a regulatory network connecting the drivers of androgen receptor (AR) splice variant-mediated androgen independence and those of epithelial-mesenchymal transition. Model simulations for this network revealed four possible phenotypes: epithelial-sensitive (ES), epithelial-resistant (ER), mesenchymal-resistant (MR) and mesenchymal-sensitive (MS), with the latter phenotype occurring rarely. We observed that well-coordinated "teams" of regulators working antagonistically within the network enable these phenotypes. These model predictions are supported by multiple transcriptomic datasets both at single-cell and bulk levels, including in vitro EMT induction models and clinical samples. Further, our simulations reveal spontaneous stochastic switching between the ES and MR states. Addition of the immune checkpoint molecule, PD-L1, to the network was able to capture the interactions between AR, PD-L1, and the mesenchymal marker SNAIL, which was also confirmed through quantitative experiments. This systems-level understanding of the driver of androgen independence and EMT could aid in understanding non-genetic transitions and progression of such cancers and help in identifying novel therapeutic strategies or targets.
Collapse
Affiliation(s)
- Rashi Jindal
- Center for BioSystems Science and Engineering, Indian Institute of Science, Bangalore 560012, India.,Undergraduate Programme, Indian Institute of Science, Bangalore 560012, India
| | - Abheepsa Nanda
- Center for BioSystems Science and Engineering, Indian Institute of Science, Bangalore 560012, India.,Undergraduate Programme, Indian Institute of Science, Bangalore 560012, India
| | - Maalavika Pillai
- Center for BioSystems Science and Engineering, Indian Institute of Science, Bangalore 560012, India.,Undergraduate Programme, Indian Institute of Science, Bangalore 560012, India
| | - Kathryn E Ware
- Department of Medicine, Duke Cancer Institute Center for Prostate and Urologic Cancers, Duke University, Durham, NC 27710, USA
| | - Divyoj Singh
- Center for BioSystems Science and Engineering, Indian Institute of Science, Bangalore 560012, India.,Undergraduate Programme, Indian Institute of Science, Bangalore 560012, India
| | - Manas Sehgal
- Center for BioSystems Science and Engineering, Indian Institute of Science, Bangalore 560012, India
| | - Andrew J Armstrong
- Department of Medicine, Duke Cancer Institute Center for Prostate and Urologic Cancers, Duke University, Durham, NC 27710, USA.,Department of Surgery, Duke University, Durham, NC 27710, USA.,Department of Pharmacology and Cancer Biology, Duke University, Durham, NC 27710, USA
| | - Jason A Somarelli
- Department of Medicine, Duke Cancer Institute Center for Prostate and Urologic Cancers, Duke University, Durham, NC 27710, USA
| | - Mohit Kumar Jolly
- Center for BioSystems Science and Engineering, Indian Institute of Science, Bangalore 560012, India
| |
Collapse
|
8
|
Network topology metrics explaining enrichment of hybrid epithelial mesenchymal phenotypes in metastasis. PLoS Comput Biol 2022; 18:e1010687. [DOI: 10.1371/journal.pcbi.1010687] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2022] [Revised: 11/18/2022] [Accepted: 10/26/2022] [Indexed: 11/10/2022] Open
Abstract
Epithelial to Mesenchymal Transition (EMT) and its reverse—Mesenchymal to Epithelial Transition (MET) are hallmarks of metastasis. Cancer cells use this reversible cellular programming to switch among Epithelial (E), Mesenchymal (M), and hybrid Epithelial/Mesenchymal (hybrid E/M) state(s) and seed tumors at distant sites. Hybrid E/M cells are often more aggressive and metastatic than the “pure” E and M cells. Thus, identifying mechanisms to inhibit hybrid E/M cells can be promising in curtailing metastasis. While multiple gene regulatory networks (GRNs) based mathematical models for EMT/MET have been developed recently, identifying topological signatures enriching hybrid E/M phenotypes remains to be done. Here, we investigate the dynamics of 13 different GRNs and report an interesting association between “hybridness” and the number of negative/positive feedback loops across the networks. While networks having more negative feedback loops favor hybrid phenotype(s), networks having more positive feedback loops (PFLs) or many HiLoops–specific combinations of PFLs, support terminal (E and M) phenotypes. We also establish a connection between “hybridness” and network-frustration by showing that hybrid phenotypes likely result from non-reinforcing interactions among network nodes (genes) and therefore tend to be more frustrated (less stable). Our analysis, thus, identifies network topology-based signatures that can give rise to, as well as prevent, the emergence of hybrid E/M phenotype in GRNs underlying EMP. Our results can have implications in terms of targeting specific interactions in GRNs as a potent way to restrict switching to the hybrid E/M phenotype(s) to curtail metastasis.
Collapse
|
9
|
Aggarwal V, Sahoo S, Donnenberg VS, Chakraborty P, Jolly MK, Sant S. P4HA2: A link between tumor-intrinsic hypoxia, partial EMT and collective migration. ADVANCES IN CANCER BIOLOGY - METASTASIS 2022; 5:100057. [PMID: 36187341 PMCID: PMC9517480 DOI: 10.1016/j.adcanc.2022.100057] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/29/2023]
Abstract
Epithelial-to-mesenchymal transition (EMT), a well-established phenomenon studied across pan-cancer types, has long been known to be a major player in driving tumor invasion and metastasis. Recent studies have highlighted the importance of partial EMT phenotypes in metastasis. Initially thought as a transitional state between epithelial and mesenchymal phenotypic states, partial EMT state is now widely recognized as a key driver of intra-tumoral heterogeneity and phenotypic plasticity, further accelerating tumor metastasis and therapeutic resistance. However, how tumor microenvironment regulates partial EMT phenotypes remains unclear. We have developed unique size-controlled three-dimensional microtumor models that recapitulate tumor-intrinsic hypoxia and the emergence of collectively migrating cells. In this study, we further interrogate these microtumor models to understand how tumor-intrinsic hypoxia regulates partial EMT and collective migration in hypoxic large microtumors fabricated from T47D breast cancer cells. We compared global gene expression profiles of hypoxic, migratory microtumors to that of non-hypoxic, non-migratory microtumors at early and late time-points. Using our microtumor models, we identified unique gene signatures for tumor-intrinsic hypoxia (early versus late), partial EMT and migration (pre-migratory versus migratory phenotype). Through differential gene expression analysis between the microtumor models with an overlap of hypoxia, partial EMT and migration signatures, we identified prolyl 4-hydroxylase subunit 2 (P4HA2), a hypoxia responsive gene, as a central regulator common to hypoxia, partial EMT and collective migration. Further, the inhibition of P4HA2 significantly blocked collective migration in hypoxic microtumors. Thus, using the integrated computational-experimental analysis, we identify the key role of P4HA2 in tumor-intrinsic hypoxia-driven partial EMT and collective migration.
Collapse
Affiliation(s)
- Vaishali Aggarwal
- Department of Pharmaceutical Sciences, School of Pharmacy, University of Pittsburgh, Pittsburgh, PA, USA
| | - Sarthak Sahoo
- Centre for BioSystems Science and Engineering, Indian Institute of Science, Bangalore, India
| | - Vera S. Donnenberg
- Department of Pharmaceutical Sciences, School of Pharmacy, University of Pittsburgh, Pittsburgh, PA, USA
- Department of Cardiothoracic Surgery, School of Medicine, University of Pittsburgh, Pittsburgh, PA, USA
- McGowan Institute for Regenerative Medicine, University of Pittsburgh, Pittsburgh, PA, USA
- UPMC-Hillman Cancer Center, University of Pittsburgh, Pittsburgh, PA, USA
| | - Priyanka Chakraborty
- Centre for BioSystems Science and Engineering, Indian Institute of Science, Bangalore, India
| | - Mohit Kumar Jolly
- Centre for BioSystems Science and Engineering, Indian Institute of Science, Bangalore, India
| | - Shilpa Sant
- Department of Pharmaceutical Sciences, School of Pharmacy, University of Pittsburgh, Pittsburgh, PA, USA
- Department of Cardiothoracic Surgery, School of Medicine, University of Pittsburgh, Pittsburgh, PA, USA
- McGowan Institute for Regenerative Medicine, University of Pittsburgh, Pittsburgh, PA, USA
- UPMC-Hillman Cancer Center, University of Pittsburgh, Pittsburgh, PA, USA
- Department of Bioengineering, Swanson School of Engineering, University of Pittsburgh, Pittsburgh, PA, USA
- Corresponding author. University of Pittsburgh School of Pharmacy Department of Pharmaceutical Sciences Department of Bioengineering UPMC-Hillman Cancer Center McGowan Institute for Regenerative Medicine, 7408 Salk Hall, 3501 Terrace Street, Pittsburgh, PA, 15261, USA. (S. Sant)
| |
Collapse
|
10
|
Pillai M, Rajaram G, Thakur P, Agarwal N, Muralidharan S, Ray A, Barbhaya D, Somarelli JA, Jolly MK. Mapping phenotypic heterogeneity in melanoma onto the epithelial-hybrid-mesenchymal axis. Front Oncol 2022; 12:913803. [PMID: 36003764 PMCID: PMC9395132 DOI: 10.3389/fonc.2022.913803] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2022] [Accepted: 07/11/2022] [Indexed: 11/25/2022] Open
Abstract
Epithelial to mesenchymal transition (EMT) is a well-studied hallmark of epithelial-like cancers that is characterized by loss of epithelial markers and gain of mesenchymal markers. Melanoma, which is derived from melanocytes of the skin, also undergo phenotypic plasticity toward mesenchymal-like phenotypes under the influence of various micro-environmental cues. Our study connects EMT to the phenomenon of de-differentiation (i.e., transition from proliferative to more invasive phenotypes) observed in melanoma cells during drug treatment. By analyzing 78 publicly available transcriptomic melanoma datasets, we found that de-differentiation in melanoma is accompanied by upregulation of mesenchymal genes, but not necessarily a concomitant loss of an epithelial program, suggesting a more “one-dimensional” EMT that leads to a hybrid epithelial/mesenchymal phenotype. Samples lying in the hybrid epithelial/mesenchymal phenotype also correspond to the intermediate phenotypes in melanoma along the proliferative-invasive axis - neural crest and transitory ones. As melanoma cells progress along the invasive axis, the mesenchymal signature does not increase monotonically. Instead, we observe a peak in mesenchymal scores followed by a decline, as cells further de-differentiate. This biphasic response recapitulates the dynamics of melanocyte development, suggesting close interactions among genes controlling differentiation and mesenchymal programs in melanocytes. Similar trends were noted for metabolic changes often associated with EMT in carcinomas in which progression along mesenchymal axis correlates with the downregulation of oxidative phosphorylation, while largely maintaining glycolytic capacity. Overall, these results provide an explanation for how EMT and de-differentiation axes overlap with respect to their transcriptional and metabolic programs in melanoma.
Collapse
Affiliation(s)
- Maalavika Pillai
- Centre for BioSystems Science and Engineering, Indian Institute of Science, Bangalore, India
- Undergraduate Programme, Indian Institute of Science, Bangalore, India
| | - Gouri Rajaram
- Department of Biotechnology, Indian Institute of Technology, Kharagpur, India
| | - Pradipti Thakur
- Department of Biotechnology, Indian Institute of Technology, Kharagpur, India
| | - Nilay Agarwal
- Centre for BioSystems Science and Engineering, Indian Institute of Science, Bangalore, India
- Undergraduate Programme, Indian Institute of Science, Bangalore, India
| | - Srinath Muralidharan
- Centre for BioSystems Science and Engineering, Indian Institute of Science, Bangalore, India
| | - Ankita Ray
- Department of Biotechnology, Indian Institute of Technology, Kharagpur, India
| | - Dev Barbhaya
- Department of Biological Sciences and Bioengineering, Indian Institute of Technology, Kanpur, India
| | | | - Mohit Kumar Jolly
- Centre for BioSystems Science and Engineering, Indian Institute of Science, Bangalore, India
- *Correspondence: Mohit Kumar Jolly,
| |
Collapse
|
11
|
Mitochondrial dysfunction and epithelial to mesenchymal transition in head neck cancer cell lines. Sci Rep 2022; 12:13255. [PMID: 35918485 PMCID: PMC9345891 DOI: 10.1038/s41598-022-16829-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2022] [Accepted: 07/18/2022] [Indexed: 11/08/2022] Open
Abstract
Mitochondrial dysfunction promotes cancer aggressiveness, metastasis, and resistance to therapy. Similar traits are associated with epithelial mesenchymal transition (EMT). We questioned whether mitochondrial dysfunction induces EMT in head and neck cancer (HNC) cell lines. We induced mitochondrial dysfunction in four HNC cell lines with carbonyl cyanide-4(trifluoromethoxy)phenylhydrazone (FCCP), a mitochondrial electron transport chain uncoupling agent, and oligomycin, a mitochondrial ATP synthase inhibitor. Extracellular flux analyses and expression of the cystine/glutamate antiporter system xc (xCT) served to confirm mitochondrial dysfunction. Expression of the EMT-related transcription factor SNAI2, the mesenchymal marker vimentin and vimentin/cytokeratin double positivity served to detect EMT. In addition, holotomographic microscopy was used to search for morphological features of EMT. Extracellular flux analysis and xCT expression confirmed that FCCP/oligomycin induced mitochondrial dysfunction in all cell lines. Across the four cell lines, mitochondrial dysfunction resulted in an increase in relative SNAI2 expression from 8.5 ± 0.8 to 12.0 ± 1.1 (mean ± SEM; p = 0.007). This effect was predominantly caused by the CAL 27 cell line (increase from 2.2 ± 0.4 to 5.5 ± 1.0; p < 0.001). Similarly, only in CAL 27 cells vimentin expression increased from 2.2 ± 0.5 × 10-3 to 33.2 ± 10.2 × 10-3 (p = 0.002) and vimentin/cytokeratin double positive cells increased from 34.7 ± 5.1 to 67.5 ± 9.8% (p = 0.003), while the other 3 cell lines did not respond with EMT (all p > 0.1). Across all cell lines, FCCP/oligomycin had no effect on EMT characteristics in holotomographic microscopy. Mitochondrial dysfunction induced EMT in 1 of 4 HNC cell lines. Given the heterogeneity of HNC, mitochondrial dysfunction may be sporadically induced by EMT, but EMT does not explain the tumor promoting effects of mitochondrial dysfunction in general.
Collapse
|
12
|
Biswas K, Jolly MK, Ghosh A. Mean residence times of TF-TF and TF-miRNA toggle switches. J Biosci 2022. [DOI: 10.1007/s12038-022-00261-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
|
13
|
Hirway SU, Weinberg SH. A review of computational modeling, machine learning and image analysis in cancer metastasis dynamics. COMPUTATIONAL AND SYSTEMS ONCOLOGY 2022. [DOI: 10.1002/cso2.1044] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023] Open
Affiliation(s)
- Shreyas U. Hirway
- Department of Biomedical Engineering The Ohio State University Columbus Ohio USA
| | - Seth H. Weinberg
- Department of Biomedical Engineering The Ohio State University Columbus Ohio USA
| |
Collapse
|
14
|
Sahoo S, Ashraf B, Duddu AS, Biddle A, Jolly MK. Interconnected high-dimensional landscapes of epithelial-mesenchymal plasticity and stemness in cancer. Clin Exp Metastasis 2022; 39:279-290. [PMID: 34993766 DOI: 10.1007/s10585-021-10139-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2021] [Accepted: 11/09/2021] [Indexed: 02/06/2023]
Abstract
Establishing macrometastases at distant organs is a highly challenging process for cancer cells, with extremely high attrition rates. A very small percentage of disseminated cells have the ability to dynamically adapt to their changing micro-environments through reversibly switching to another phenotype, aiding metastasis. Such plasticity can be exhibited along one or more axes-epithelial-mesenchymal plasticity (EMP) and cancer stem cells (CSCs) being the two most studied, and often tacitly assumed to be synonymous. Here, we review the emerging concepts related to EMP and CSCs across multiple cancers. Both processes are multi-dimensional in nature; for instance, EMP can be defined on morphological, molecular and functional changes, which may or may not be synchronized. Similarly, self-renewal, multi-lineage potential, and resistance to anoikis and/or therapy may not all occur simultaneously in CSCs. Thus, understanding the complexity in defining EMP and CSCs is essential if we are to understand their contribution to cancer metastasis. This will require a more comprehensive understanding of the non-linearity of these processes. These processes are dynamic, reversible, and semi-independent in nature; cells traverse the inter-connected high-dimensional EMP and CSC landscapes in diverse paths, each of which may exhibit a distinct EMP-CSC coupling. Our proposed model offers a potential unifying framework for elucidating the coupled decision-making along these dimensions and highlights a key set of open questions to be answered.
Collapse
Affiliation(s)
- Sarthak Sahoo
- Centre for BioSystems Science and Engineering (BSSE), Indian Institute of Science, Bangalore, 560012, India.,UG Programme, Indian Institute of Science, Bangalore, 560012, India
| | - Bazella Ashraf
- Department of Biotechnology, Central University of Kashmir, Ganderbal, India
| | - Atchuta Srinivas Duddu
- Centre for BioSystems Science and Engineering (BSSE), Indian Institute of Science, Bangalore, 560012, India
| | - Adrian Biddle
- Blizard Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London, UK.
| | - Mohit Kumar Jolly
- Centre for BioSystems Science and Engineering (BSSE), Indian Institute of Science, Bangalore, 560012, India.
| |
Collapse
|
15
|
Subbalakshmi AR, Ashraf B, Jolly MK. Biophysical and biochemical attributes of hybrid epithelial/mesenchymal phenotypes. Phys Biol 2022; 19. [PMID: 34986465 DOI: 10.1088/1478-3975/ac482c] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2021] [Accepted: 01/05/2022] [Indexed: 11/11/2022]
Abstract
The Epithelial-Mesenchymal Transition (EMT) is a biological phenomenon associated with explicit phenotypic and molecular changes in cellular traits. Unlike the earlier-held popular belief of it being a binary process, EMT is now thought of as a landscape including diverse hybrid E/M phenotypes manifested by varying degrees of the transition. These hybrid cells can co-express both epithelial and mesenchymal markers and/or functional traits, and can possess the property of collective cell migration, enhanced tumor-initiating ability, and immune/targeted therapy-evasive features, all of which are often associated with worse patient outcomes. These characteristics of the hybrid E/M cells have led to a surge in studies that map their biophysical and biochemical hallmarks that can be helpful in exploiting their therapeutic vulnerabilities. This review discusses recent advances made in investigating hybrid E/M phenotype(s) from diverse biophysical and biochemical aspects by integrating live cell-imaging, cellular morphology quantification and mathematical modelling, and highlights a set of questions that remain unanswered about the dynamics of hybrid E/M states.
Collapse
Affiliation(s)
- Ayalur Raghu Subbalakshmi
- Indian Institute of Science, Centre for BioSystems Science and Engineering, Bangalore, 560012, INDIA
| | - Bazella Ashraf
- Central University of Kashmir, Department of Biotechnology, Ganderbal, Jammu and Kashmir, 191201, INDIA
| | - Mohit Kumar Jolly
- Indian Institute of Science, Centre for BioSystems Science and Engineering, Bangalore, 560012, INDIA
| |
Collapse
|
16
|
Sahoo S, Nayak SP, Hari K, Purkait P, Mandal S, Kishore A, Levine H, Jolly MK. Immunosuppressive Traits of the Hybrid Epithelial/Mesenchymal Phenotype. Front Immunol 2022; 12:797261. [PMID: 34975907 PMCID: PMC8714906 DOI: 10.3389/fimmu.2021.797261] [Citation(s) in RCA: 41] [Impact Index Per Article: 20.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2021] [Accepted: 11/24/2021] [Indexed: 12/13/2022] Open
Abstract
Recent preclinical and clinical data suggests enhanced metastatic fitness of hybrid epithelial/mesenchymal (E/M) phenotypes, but mechanistic details regarding their survival strategies during metastasis remain unclear. Here, we investigate immune-evasive strategies of hybrid E/M states. We construct and simulate the dynamics of a minimalistic regulatory network encompassing the known associations among regulators of EMT (epithelial-mesenchymal transition) and PD-L1, an established immune-suppressor. Our simulations for the network consisting of SLUG, ZEB1, miR-200, CDH1 and PD-L1, integrated with single-cell and bulk RNA-seq data analysis, elucidate that hybrid E/M cells can have high levels of PD-L1, similar to those seen in cells with a full EMT phenotype, thus obviating the need for cancer cells to undergo a full EMT to be immune-evasive. Specifically, in breast cancer, we show the co-existence of hybrid E/M phenotypes, enhanced resistance to anti-estrogen therapy and increased PD-L1 levels. Our results underscore how the emergent dynamics of interconnected regulatory networks can coordinate different axes of cellular fitness during metastasis.
Collapse
Affiliation(s)
- Sarthak Sahoo
- Undergraduate Program, Indian Institute of Science, Bangalore, India.,Centre for BioSystems Science and Engineering, Indian Institute of Science, Bangalore, India
| | | | - Kishore Hari
- Centre for BioSystems Science and Engineering, Indian Institute of Science, Bangalore, India
| | - Prithu Purkait
- Undergraduate Program, Indian Institute of Science, Bangalore, India
| | - Susmita Mandal
- Centre for BioSystems Science and Engineering, Indian Institute of Science, Bangalore, India
| | - Akash Kishore
- Department of Computer Science & Engineering, Sri Sivasubramaniya Nadar (SSN) College of Engineering, Chennai, India
| | - Herbert Levine
- Center for Theoretical Biological Physics, Northeastern University, Boston, MA, United States.,Departments of Physics and Bioengineering, Northeastern University, Boston, MA, United States
| | - Mohit Kumar Jolly
- Centre for BioSystems Science and Engineering, Indian Institute of Science, Bangalore, India
| |
Collapse
|
17
|
Garg M. Emerging roles of epithelial-mesenchymal plasticity in invasion-metastasis cascade and therapy resistance. Cancer Metastasis Rev 2022; 41:131-145. [PMID: 34978017 DOI: 10.1007/s10555-021-10003-5] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Accepted: 11/19/2021] [Indexed: 12/12/2022]
Abstract
Strong association of cancer incidence and its progression with mortality highlights the need to decipher the cellular and molecular mechanisms that drive tumor cells to rapidly progress to metastatic disease and therapy resistance. Epithelial-mesenchymal plasticity (EMP) emerged as a key regulator of metastatic outgrowth. It allows neoplastic epithelial cells to delaminate from their neighbors either individually or collectively, traverse the extracellular matrix (ECM) barrier, enter into the circulation, and establish distal metastases. Plasticity between epithelial and mesenchymal states and the existence of hybrid epithelial/mesenchymal (E/M) phenotypes are increasingly being reported in different tumor contexts. Small subset of cancer cells with stemness called cancer stem cells (CSCs) exhibit plasticity, possess high tumorigenic potential, and contribute to high degree of tumoral heterogeneity. EMP characterized by the presence of dynamic intermediate states is reported to be influenced by (epi)genomic reprograming, growth factor signaling, inflammation, and low oxygen generated by tumor stromal microenvironment. EMP alters the genotypic and phenotypic characteristics of tumor cells/CSCs, disrupts tissue homeostasis, induces the reprogramming of angiogenic and immune recognition functions, and renders tumor cells to survive hostile microenvironments and resist therapy. The present review summarizes the roles of EMP in tumor invasion and metastasis and provides an update on therapeutic strategies to target the metastatic and refractory cancers.
Collapse
Affiliation(s)
- Minal Garg
- Department of Biochemistry, University of Lucknow, Lucknow, 226007, Uttar Pradesh, India.
| |
Collapse
|
18
|
Johnson KS, Hussein S, Chakraborty P, Muruganantham A, Mikhail S, Gonzalez G, Song S, Jolly MK, Toneff MJ, Benton ML, Lin YC, Taube JH. CTCF Expression and Dynamic Motif Accessibility Modulates Epithelial-Mesenchymal Gene Expression. Cancers (Basel) 2022; 14:cancers14010209. [PMID: 35008373 PMCID: PMC8750563 DOI: 10.3390/cancers14010209] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2021] [Revised: 11/22/2021] [Accepted: 11/23/2021] [Indexed: 12/14/2022] Open
Abstract
Epithelial-mesenchymal transition (EMT) and its reversal, mesenchymal-epithelial transition (MET) drive tissue reorganization critical for early development. In carcinomas, processing through EMT, MET, or partial states promotes migration, invasion, dormancy, and metastatic colonization. As a reversible process, EMT is inherently regulated at epigenetic and epigenomic levels. To understand the epigenomic nature of reversible EMT and its partial states, we characterized chromatin accessibility dynamics, transcriptomic output, protein expression, and cellular phenotypes during stepwise reversible EMT. We find that the chromatin insulating protein machinery, including CTCF, is suppressed and re-expressed, coincident with broad alterations in chromatin accessibility, during EMT/MET, and is lower in triple-negative breast cancer cell lines with EMT features. Through an analysis of chromatin accessibility using ATAC-seq, we identify that early phases of EMT are characterized by enrichment for AP-1 family member binding motifs, but also by a diminished enrichment for CTCF binding motifs. Through a loss-of-function analysis, we demonstrate that the suppression of CTCF alters cellular plasticity, strengthening the epithelial phenotype via the upregulation of epithelial markers E-cadherin/CDH1 and downregulation of N-cadherin/CDH2. Conversely, the upregulation of CTCF leads to the upregulation of EMT gene expression and an increase in mesenchymal traits. These findings are indicative of a role of CTCF in regulating epithelial-mesenchymal plasticity and gene expression.
Collapse
Affiliation(s)
- Kelsey S. Johnson
- Department of Biology, Baylor University, Waco, TX 76706, USA; (K.S.J.); (A.M.); (S.M.); (G.G.); (S.S.)
| | - Shaimaa Hussein
- Baylor Institute for Immunology Research, Baylor Scott & White, Dallas, TX 75246, USA; (S.H.); (Y.C.L.)
| | - Priyanka Chakraborty
- Centre for BioSystems Science and Engineering, Indian Institute of Science, Bangalore 560012, India; (P.C.); (M.K.J.)
| | - Arvind Muruganantham
- Department of Biology, Baylor University, Waco, TX 76706, USA; (K.S.J.); (A.M.); (S.M.); (G.G.); (S.S.)
| | - Sheridan Mikhail
- Department of Biology, Baylor University, Waco, TX 76706, USA; (K.S.J.); (A.M.); (S.M.); (G.G.); (S.S.)
| | - Giovanny Gonzalez
- Department of Biology, Baylor University, Waco, TX 76706, USA; (K.S.J.); (A.M.); (S.M.); (G.G.); (S.S.)
| | - Shuxuan Song
- Department of Biology, Baylor University, Waco, TX 76706, USA; (K.S.J.); (A.M.); (S.M.); (G.G.); (S.S.)
| | - Mohit Kumar Jolly
- Centre for BioSystems Science and Engineering, Indian Institute of Science, Bangalore 560012, India; (P.C.); (M.K.J.)
| | | | | | - Yin C. Lin
- Baylor Institute for Immunology Research, Baylor Scott & White, Dallas, TX 75246, USA; (S.H.); (Y.C.L.)
| | - Joseph H. Taube
- Department of Biology, Baylor University, Waco, TX 76706, USA; (K.S.J.); (A.M.); (S.M.); (G.G.); (S.S.)
- Dan L. Duncan Cancer Center, Houston, TX 76706, USA
- Correspondence:
| |
Collapse
|
19
|
Brasier AR, Qiao D, Zhao Y. The Hexosamine Biosynthetic Pathway Links Innate Inflammation With Epithelial-Mesenchymal Plasticity in Airway Remodeling. Front Pharmacol 2021; 12:808735. [PMID: 35002741 PMCID: PMC8727908 DOI: 10.3389/fphar.2021.808735] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2021] [Accepted: 12/07/2021] [Indexed: 01/15/2023] Open
Abstract
Disruption of the lower airway epithelial barrier plays a major role in the initiation and progression of chronic lung disease. Here, repetitive environmental insults produced by viral and allergens triggers metabolic adaptations, epithelial-mesenchymal plasticity (EMP) and airway remodeling. Epithelial plasticity disrupts epithelial barrier function, stimulates release of fibroblastic growth factors, and remodels the extracellular matrix (ECM). This review will focus on recent work demonstrating how the hexosamine biosynthetic pathway (HBP) links innate inflammation to airway remodeling. The HBP is a core metabolic pathway of the unfolded protein response (UPR) responsible for protein N-glycosylation, relief of proteotoxic stress and secretion of ECM modifiers. We will overview findings that the IκB kinase (IKK)-NFκB pathway directly activates expression of the SNAI-ZEB1 mesenchymal transcription factor module through regulation of the Bromodomain Containing Protein 4 (BRD4) chromatin modifier. BRD4 mediates transcriptional elongation of SNAI1-ZEB as well as enhancing chromatin accessibility and transcription of fibroblast growth factors, ECM and matrix metalloproteinases (MMPs). In addition, recent exciting findings that IKK cross-talks with the UPR by controlling phosphorylation and nuclear translocation of the autoregulatory XBP1s transcription factor are presented. HBP is required for N glycosylation and secretion of ECM components that play an important signaling role in airway remodeling. This interplay between innate inflammation, metabolic reprogramming and lower airway plasticity expands a population of subepithelial myofibroblasts by secreting fibroblastic growth factors, producing changes in ECM tensile strength, and fibroblast stimulation by MMP binding. Through these actions on myofibroblasts, EMP in lower airway cells produces expansion of the lamina reticularis and promotes airway remodeling. In this manner, metabolic reprogramming by the HBP mediates environmental insult-induced inflammation with remodeling in chronic airway diseases.
Collapse
Affiliation(s)
- Allan R. Brasier
- Department of Medicine, University of Wisconsin-Madison School of Medicine and Public Health (SMPH), Madison, WI, United States
- Institute for Clinical and Translational Research (ICTR), University of Wisconsin-Madison, Madison, WI, United States
| | - Dianhua Qiao
- Department of Medicine, University of Wisconsin-Madison School of Medicine and Public Health (SMPH), Madison, WI, United States
| | - Yingxin Zhao
- Department of Internal Medicine, University of Texas Medical Branch Galveston, Galveston, TX, United States
| |
Collapse
|
20
|
Tiwari A, Ashary N, Singh N, Sharma S, Modi D. Modulation of E-Cadherin and N-Cadherin by ovarian steroids and embryonic stimuli. Tissue Cell 2021; 73:101670. [PMID: 34710830 DOI: 10.1016/j.tice.2021.101670] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2021] [Revised: 10/01/2021] [Accepted: 10/18/2021] [Indexed: 12/26/2022]
Abstract
Endometrium is a dynamic tissue that undergoes extensive remodelling to attain a receptive state which is further modulated in presence of an embryo for successful initiation of pregnancy. Cadherins are the proteins of the junctional complex of which E-cadherin (E-Cad) is crucial for maintaining epithelial cell state and integrity of the epithelial barrier; gain of N-cadherin (N-Cad) in epithelial cells leads to epithelial to mesenchymal transition (EMT). In the present study, we investigated the expression of E-Cad and N-Cad in the mouse endometrial luminal epithelium and its modulation by estrogen, progesterone, and embryonic stimuli. We observed that E-Cad is diffusely expressed in the luminal epithelium of mouse endometrium during the estrus stage and upon estrogen treatment. It is apico-laterally and basolaterally sorted at the diestrus stage and in response to the combined treatment of estrogen and progesterone. In 3D spheroids of human endometrial epithelial cells, combined treatment with estrogen and progesterone led to lateral sorting of E-Cad without any effects on its mRNA levels. at the time of embryo implantation, there is loss of E-Cad along with the gain of N-Cad and SNAIL expression suggestive of EMT in the luminal epithelium. This EMT is possibly driven by embryonic stimuli as treatment with estrogen and progesterone did not lead to the gain of N-Cad expression in the mouse endometrium in vivo or in human endometrial epithelial cells in vitro. In conclusion, the present study demonstrates that steroid hormones directly affect E-Cad sorting in the endometrial epithelium which undergo EMT in response to embryonic stimuli.
Collapse
Affiliation(s)
- Abhishek Tiwari
- Molecular and Cellular Biology Laboratory, ICMR-National Institute for Research in Reproductive Health, Indian Council of Medical Research (ICMR), JM Street, Parel, Mumbai, 400012, India
| | - Nancy Ashary
- Molecular and Cellular Biology Laboratory, ICMR-National Institute for Research in Reproductive Health, Indian Council of Medical Research (ICMR), JM Street, Parel, Mumbai, 400012, India
| | - Neha Singh
- Molecular and Cellular Biology Laboratory, ICMR-National Institute for Research in Reproductive Health, Indian Council of Medical Research (ICMR), JM Street, Parel, Mumbai, 400012, India
| | - Shipra Sharma
- Molecular and Cellular Biology Laboratory, ICMR-National Institute for Research in Reproductive Health, Indian Council of Medical Research (ICMR), JM Street, Parel, Mumbai, 400012, India
| | - Deepak Modi
- Molecular and Cellular Biology Laboratory, ICMR-National Institute for Research in Reproductive Health, Indian Council of Medical Research (ICMR), JM Street, Parel, Mumbai, 400012, India.
| |
Collapse
|
21
|
Yang D, Ma Y, Zhao P, Ma J, He C. HMMR is a downstream target of FOXM1 in enhancing proliferation and partial epithelial-to-mesenchymal transition of bladder cancer cells. Exp Cell Res 2021; 408:112860. [PMID: 34624323 DOI: 10.1016/j.yexcr.2021.112860] [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: 07/19/2021] [Revised: 09/26/2021] [Accepted: 10/04/2021] [Indexed: 01/06/2023]
Abstract
Our previous that HMMR upregulation independently predicts poor survival in patients with papillary muscle-invasive bladder cancer (MIBC). In this study, we explored its downstream regulations and the potential transcriptional factors activating its expression. MIBC derived T24 cells, and non-MIBC (NMIBC) derived RT4 cells were used for in vitro and in vivo studies. HMMR expression enhanced cell proliferation, the expression of mesenchymal markers, and cell invasion. It induced the nuclear entry of β-catenin, increased its active form in the nuclear part, and elevated the relative TOP/FOP activity. The promoter region of HMMR has a canonical FKH motif. FOXM1 bound to this site and activated HMMR transcription. HMMR knockdown significantly weakened FOXM1 overexpression induced bladder cancer growth, invasion, partial epithelial-to-mesenchymal transition (pEMT), as well as the activation of the Wnt/β-catenin signaling pathway. In conclusion, the findings in this study expanded our understanding of the mechanisms underlying HMMR dysregulation and the functional role of the FOXM1-HMMR axis in bladder cancer.
Collapse
Affiliation(s)
- Dong Yang
- Department of Urology, Affiliated Cancer Hospital of Zhengzhou University, Henan Cancer Hospital, Zhengzhou, 450008, China
| | - Yan Ma
- Department of Urology, Affiliated Cancer Hospital of Zhengzhou University, Henan Cancer Hospital, Zhengzhou, 450008, China
| | - Pengcheng Zhao
- Department of Urology, Affiliated Cancer Hospital of Zhengzhou University, Henan Cancer Hospital, Zhengzhou, 450008, China
| | - Jing Ma
- Department of Urology, Affiliated Cancer Hospital of Zhengzhou University, Henan Cancer Hospital, Zhengzhou, 450008, China
| | - Chaohong He
- Department of Urology, Affiliated Cancer Hospital of Zhengzhou University, Henan Cancer Hospital, Zhengzhou, 450008, China.
| |
Collapse
|
22
|
Lang J, Nie Q, Li C. Landscape and kinetic path quantify critical transitions in epithelial-mesenchymal transition. Biophys J 2021; 120:4484-4500. [PMID: 34480928 PMCID: PMC8553640 DOI: 10.1016/j.bpj.2021.08.043] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2021] [Revised: 08/04/2021] [Accepted: 08/30/2021] [Indexed: 01/11/2023] Open
Abstract
Epithelial-mesenchymal transition (EMT), a basic developmental process that might promote cancer metastasis, has been studied from various perspectives. Recently, the early warning theory has been used to anticipate critical transitions in EMT from mathematical modeling. However, the underlying mechanisms of EMT involving complex molecular networks remain to be clarified. Especially, how to quantify the global stability and stochastic transition dynamics of EMT and what the underlying mechanism for early warning theory in EMT is remain to be fully clarified. To address these issues, we constructed a comprehensive gene regulatory network model for EMT and quantified the corresponding potential landscape. The landscape for EMT displays multiple stable attractors, which correspond to E, M, and some other intermediate states. Based on the path-integral approach, we identified the most probable transition paths of EMT, which are supported by experimental data. Correspondingly, the results of transition actions demonstrated that intermediate states can accelerate EMT, consistent with recent studies. By integrating the landscape and path with early warning concept, we identified the potential barrier height from the landscape as a global and more accurate measure for early warning signals to predict critical transitions in EMT. The landscape results also provide an intuitive and quantitative explanation for the early warning theory. Overall, the landscape and path results advance our mechanistic understanding of dynamical transitions and roles of intermediate states in EMT, and the potential barrier height provides a new, to our knowledge, measure for critical transitions and quantitative explanations for the early warning theory.
Collapse
Affiliation(s)
- Jintong Lang
- Institute of Science and Technology for Brain-Inspired Intelligence, Shanghai, China; Shanghai Center for Mathematical Sciences, Fudan University, Shanghai, China
| | - Qing Nie
- Department of Mathematics, University of California, Irvine, Irvine, California
| | - Chunhe Li
- Institute of Science and Technology for Brain-Inspired Intelligence, Shanghai, China; Shanghai Center for Mathematical Sciences, Fudan University, Shanghai, China; School of Mathematical Sciences, Fudan University, Shanghai, China.
| |
Collapse
|
23
|
Subbalakshmi AR, Sahoo S, McMullen I, Saxena AN, Venugopal SK, Somarelli JA, Jolly MK. KLF4 Induces Mesenchymal-Epithelial Transition (MET) by Suppressing Multiple EMT-Inducing Transcription Factors. Cancers (Basel) 2021; 13:5135. [PMID: 34680284 PMCID: PMC8533753 DOI: 10.3390/cancers13205135] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2021] [Revised: 10/06/2021] [Accepted: 10/08/2021] [Indexed: 12/24/2022] Open
Abstract
Epithelial-Mesenchymal Plasticity (EMP) refers to reversible dynamic processes where cells can transition from epithelial to mesenchymal (EMT) or from mesenchymal to epithelial (MET) phenotypes. Both these processes are modulated by multiple transcription factors acting in concert. While EMT-inducing transcription factors (TFs)-TWIST1/2, ZEB1/2, SNAIL1/2/3, GSC, and FOXC2-are well-characterized, the MET-inducing TFs are relatively poorly understood (OVOL1/2 and GRHL1/2). Here, using mechanism-based mathematical modeling, we show that transcription factor KLF4 can delay the onset of EMT by suppressing multiple EMT-TFs. Our simulations suggest that KLF4 overexpression can promote a phenotypic shift toward a more epithelial state, an observation suggested by the negative correlation of KLF4 with EMT-TFs and with transcriptomic-based EMT scoring metrics in cancer cell lines. We also show that the influence of KLF4 in modulating the EMT dynamics can be strengthened by its ability to inhibit cell-state transitions at the epigenetic level. Thus, KLF4 can inhibit EMT through multiple parallel paths and can act as a putative MET-TF. KLF4 associates with the patient survival metrics across multiple cancers in a context-specific manner, highlighting the complex association of EMP with patient survival.
Collapse
Affiliation(s)
- Ayalur Raghu Subbalakshmi
- Centre for BioSystems Science and Engineering, Indian Institute of Science, Bangalore 560012, India; (A.R.S.); (S.S.); (S.K.V.)
| | - Sarthak Sahoo
- Centre for BioSystems Science and Engineering, Indian Institute of Science, Bangalore 560012, India; (A.R.S.); (S.S.); (S.K.V.)
| | | | | | - Sudhanva Kalasapura Venugopal
- Centre for BioSystems Science and Engineering, Indian Institute of Science, Bangalore 560012, India; (A.R.S.); (S.S.); (S.K.V.)
| | - Jason A. Somarelli
- Department of Medicine, Duke University, Durham, NC 27708, USA;
- Duke Cancer Institute, Duke University, Durham, NC 27708, USA
| | - Mohit Kumar Jolly
- Centre for BioSystems Science and Engineering, Indian Institute of Science, Bangalore 560012, India; (A.R.S.); (S.S.); (S.K.V.)
| |
Collapse
|
24
|
Thankamony AP, Subbalakshmi AR, Jolly MK, Nair R. Lineage Plasticity in Cancer: The Tale of a Skin-Walker. Cancers (Basel) 2021; 13:3602. [PMID: 34298815 PMCID: PMC8306016 DOI: 10.3390/cancers13143602] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2021] [Revised: 07/04/2021] [Accepted: 07/14/2021] [Indexed: 12/11/2022] Open
Abstract
Lineage plasticity, the switching of cells from one lineage to another, has been recognized as a cardinal property essential for embryonic development, tissue repair and homeostasis. However, such a highly regulated process goes awry when cancer cells exploit this inherent ability to their advantage, resulting in tumorigenesis, relapse, metastasis and therapy resistance. In this review, we summarize our current understanding on the role of lineage plasticity in tumor progression and therapeutic resistance in multiple cancers. Lineage plasticity can be triggered by treatment itself and is reported across various solid as well as liquid tumors. Here, we focus on the importance of lineage switching in tumor progression and therapeutic resistance of solid tumors such as the prostate, lung, hepatocellular and colorectal carcinoma and the myeloid and lymphoid lineage switch observed in leukemias. Besides this, we also discuss the role of epithelial-mesenchymal transition (EMT) in facilitating the lineage switch in biphasic cancers such as aggressive carcinosarcomas. We also discuss the mechanisms involved, current therapeutic approaches and challenges that lie ahead in taming the scourge of lineage plasticity in cancer.
Collapse
Affiliation(s)
- Archana P. Thankamony
- Cancer Research Program, Rajiv Gandhi Centre for Biotechnology, Kerala 695014, India;
- Manipal Academy of Higher Education (MAHE), Manipal 576104, India
| | - Ayalur Raghu Subbalakshmi
- Centre for BioSystems Science and Engineering, Indian Institute of Science, Bangalore 560012, India;
| | - Mohit Kumar Jolly
- Centre for BioSystems Science and Engineering, Indian Institute of Science, Bangalore 560012, India;
| | - Radhika Nair
- Cancer Research Program, Rajiv Gandhi Centre for Biotechnology, Kerala 695014, India;
| |
Collapse
|
25
|
Gilbert RJ, Sheng G, Viebahn C, Liebau S, Marra KG, De Bartolo L. Inaugural Young Investigator Issue for Cells Tissues Organs. Cells Tissues Organs 2021; 211:638-640. [PMID: 34348277 DOI: 10.1159/000518410] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2021] [Accepted: 07/10/2021] [Indexed: 01/07/2023] Open
Affiliation(s)
- Ryan J Gilbert
- Center for Biotechnology and Interdisciplinary Studies, Department of Biomedical Engineering, Rensselaer Polytechnic Institute, Troy, New York, USA
| | - Guojun Sheng
- International Research Center for Medical Sciences, Kumamoto University, Kumamoto, Japan
| | - Christoph Viebahn
- Institute of Anatomy and Embryology, University Medical Center Gottingen, Gottingen, Germany
| | - Stefan Liebau
- Institute of Neuroanatomy and Developmental Biology, University of Tübingen, Tübingen, Germany
| | - Kacey G Marra
- Departments of Plastic Surgery and Bioengineering, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Loredana De Bartolo
- Institute of Membrane Technology, National Research Council of Italy, Rome, Italy
| |
Collapse
|
26
|
Sahoo S, Mishra A, Kaur H, Hari K, Muralidharan S, Mandal S, Jolly MK. A mechanistic model captures the emergence and implications of non-genetic heterogeneity and reversible drug resistance in ER+ breast cancer cells. NAR Cancer 2021; 3:zcab027. [PMID: 34316714 PMCID: PMC8271219 DOI: 10.1093/narcan/zcab027] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2021] [Revised: 06/02/2021] [Accepted: 06/18/2021] [Indexed: 02/07/2023] Open
Abstract
Resistance to anti-estrogen therapy is an unsolved clinical challenge in successfully treating ER+ breast cancer patients. Recent studies have demonstrated the role of non-genetic (i.e. phenotypic) adaptations in tolerating drug treatments; however, the mechanisms and dynamics of such non-genetic adaptation remain elusive. Here, we investigate coupled dynamics of epithelial–mesenchymal transition (EMT) in breast cancer cells and emergence of reversible drug resistance. Our mechanism-based model for underlying regulatory network reveals that these two axes can drive one another, thus enabling non-genetic heterogeneity in a cell population by allowing for six co-existing phenotypes: epithelial-sensitive, mesenchymal-resistant, hybrid E/M-sensitive, hybrid E/M-resistant, mesenchymal-sensitive and epithelial-resistant, with the first two ones being most dominant. Next, in a population dynamics framework, we exemplify the implications of phenotypic plasticity (both drug-induced and intrinsic stochastic switching) and/or non-genetic heterogeneity in promoting population survival in a mixture of sensitive and resistant cells, even in the absence of any cell–cell cooperation. Finally, we propose the potential therapeutic use of mesenchymal–epithelial transition inducers besides canonical anti-estrogen therapy to limit the emergence of reversible drug resistance. Our results offer mechanistic insights into empirical observations on EMT and drug resistance and illustrate how such dynamical insights can be exploited for better therapeutic designs.
Collapse
Affiliation(s)
- Sarthak Sahoo
- Centre for BioSystems Science and Engineering, Indian Institute of Science, Bangalore 560012, India
| | - Ashutosh Mishra
- Centre for BioSystems Science and Engineering, Indian Institute of Science, Bangalore 560012, India
| | - Harsimran Kaur
- Centre for BioSystems Science and Engineering, Indian Institute of Science, Bangalore 560012, India
| | - Kishore Hari
- Centre for BioSystems Science and Engineering, Indian Institute of Science, Bangalore 560012, India
| | - Srinath Muralidharan
- Department of Biotechnology, Indian Institute of Technology Madras, Chennai 600036, India
| | - Susmita Mandal
- Centre for BioSystems Science and Engineering, Indian Institute of Science, Bangalore 560012, India
| | - Mohit Kumar Jolly
- Centre for BioSystems Science and Engineering, Indian Institute of Science, Bangalore 560012, India
| |
Collapse
|
27
|
Chakraborty P, Chen EL, McMullen I, Armstrong AJ, Kumar Jolly M, Somarelli JA. Analysis of immune subtypes across the epithelial-mesenchymal plasticity spectrum. Comput Struct Biotechnol J 2021; 19:3842-3851. [PMID: 34306571 PMCID: PMC8283019 DOI: 10.1016/j.csbj.2021.06.023] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2021] [Revised: 06/14/2021] [Accepted: 06/15/2021] [Indexed: 12/13/2022] Open
Abstract
Epithelial-mesenchymal plasticity plays a critical role in many solid tumor types as a mediator of metastatic dissemination and treatment resistance. In addition, there is also a growing appreciation that the epithelial/mesenchymal status of a tumor plays a role in immune evasion and immune suppression. A deeper understanding of the immunological features of different tumor types has been facilitated by the availability of large gene expression datasets and the development of methods to deconvolute bulk RNA-Seq data. These resources have generated powerful new ways of characterizing tumors, including classification of immune subtypes based on differential expression of immunological genes. In the present work, we combine scoring algorithms to quantify epithelial-mesenchymal plasticity with immune subtype analysis to understand the relationship between epithelial plasticity and immune subtype across cancers. We find heterogeneity of epithelial-mesenchymal transition (EMT) status both within and between cancer types, with greater heterogeneity in the expression of EMT-related factors than of MET-related factors. We also find that specific immune subtypes have associated EMT scores and differential expression of immune checkpoint markers.
Collapse
Affiliation(s)
- Priyanka Chakraborty
- Centre for BioSystems Science and Engineering, Indian Institute of Science, Bangalore 560012, India
| | | | | | - Andrew J. Armstrong
- Department of Medicine, Durham, NC, United Kingdom
- Duke Cancer Institute Center for Prostate and Urologic Cancers, Durham, NC, United Kingdom
- Department of Pharmacology and Cancer Biology, Duke University, Durham, NC, United Kingdom
| | - Mohit Kumar Jolly
- Centre for BioSystems Science and Engineering, Indian Institute of Science, Bangalore 560012, India
| | - Jason A. Somarelli
- Department of Medicine, Durham, NC, United Kingdom
- Duke Cancer Institute Center for Prostate and Urologic Cancers, Durham, NC, United Kingdom
| |
Collapse
|
28
|
Kvokačková B, Remšík J, Jolly MK, Souček K. Phenotypic Heterogeneity of Triple-Negative Breast Cancer Mediated by Epithelial-Mesenchymal Plasticity. Cancers (Basel) 2021; 13:2188. [PMID: 34063254 PMCID: PMC8125677 DOI: 10.3390/cancers13092188] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2021] [Accepted: 04/29/2021] [Indexed: 12/27/2022] Open
Abstract
Triple-negative breast cancer (TNBC) is a subtype of breast carcinoma known for its unusually aggressive behavior and poor clinical outcome. Besides the lack of molecular targets for therapy and profound intratumoral heterogeneity, the relatively quick overt metastatic spread remains a major obstacle in effective clinical management. The metastatic colonization of distant sites by primary tumor cells is affected by the microenvironment, epigenetic state of particular subclones, and numerous other factors. One of the most prominent processes contributing to the intratumoral heterogeneity is an epithelial-mesenchymal transition (EMT), an evolutionarily conserved developmental program frequently hijacked by tumor cells, strengthening their motile and invasive features. In response to various intrinsic and extrinsic stimuli, malignant cells can revert the EMT state through the mesenchymal-epithelial transition (MET), a process that is believed to be critical for the establishment of macrometastasis at secondary sites. Notably, cancer cells rarely undergo complete EMT and rather exist in a continuum of E/M intermediate states, preserving high levels of plasticity, as demonstrated in primary tumors and, ultimately, in circulating tumor cells, representing a simplified element of the metastatic cascade. In this review, we focus on cellular drivers underlying EMT/MET phenotypic plasticity and its detrimental consequences in the context of TNBC cancer.
Collapse
Affiliation(s)
- Barbora Kvokačková
- Department of Cytokinetics, Institute of Biophysics of the Czech Academy of Sciences, 612 65 Brno, Czech Republic;
- International Clinical Research Center, St. Anne’s University Hospital, 656 91 Brno, Czech Republic
- Department of Experimental Biology, Faculty of Science, Masaryk University, 625 00 Brno, Czech Republic
| | - Ján Remšík
- Human Oncology & Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA;
| | - Mohit Kumar Jolly
- Centre for BioSystems Science and Engineering, Indian Institute of Science, Bangalore 560012, India;
| | - Karel Souček
- Department of Cytokinetics, Institute of Biophysics of the Czech Academy of Sciences, 612 65 Brno, Czech Republic;
- International Clinical Research Center, St. Anne’s University Hospital, 656 91 Brno, Czech Republic
- Department of Experimental Biology, Faculty of Science, Masaryk University, 625 00 Brno, Czech Republic
| |
Collapse
|
29
|
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.
Collapse
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
| |
Collapse
|