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Martins F, Machado AL, Ribeiro A, Oliveira SM, Carvalho J, Matthiesen R, Backman V, Velho S. KRAS silencing alters chromatin physical organization and transcriptional activity in colorectal cancer cells. RESEARCH SQUARE 2024:rs.3.rs-3752760. [PMID: 38410476 PMCID: PMC10896403 DOI: 10.21203/rs.3.rs-3752760/v2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/28/2024]
Abstract
Clinical data revealed that KRAS mutant tumors, while initially sensitive to treatment, rapidly bypass KRAS dependence to acquire a drug-tolerant phenotype. However, the mechanisms underlying the transition from a drug-sensitive to a drug-tolerant state still elude us. Here, we show that global chromatin reorganization is a recurrent and specific feature of KRAS-dependent cells that tolerated KRAS silencing. We show that KRAS-dependent cells undergo G0/G1 cell cycle arrest after KRAS silencing, presenting a transcriptomic signature of quiescence. Proteomic analysis showed upregulated chromatin-associated proteins and transcription-associated biological processes. Accordingly, these cells shifted euchromatin/heterochromatin states, gained topologically associating domains, and altered the nanoscale physical organization of chromatin, more precisely by downregulating chromatin packing domains, a feature associated with the induction of quiescence. In addition, they also accumulated transcriptional alterations over time leading to a diversification of biological processes, linking chromatin alterations to transcriptional performance. Overall, our observations pinpoint a novel molecular mechanism of tolerance to KRAS oncogenic loss driven not by specific gene alterations but by global reorganization of genomic information, in which cells transition chromatin domain structure towards a more quiescent state and gain transcriptional reprogramming capacity.
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Affiliation(s)
| | | | | | | | | | | | | | - Sérgia Velho
- i3S - Institute for Research and Innovation in Health
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Rahman M, Nguyen TM, Lee GJ, Kim B, Park MK, Lee CH. Unraveling the Role of Ras Homolog Enriched in Brain (Rheb1 and Rheb2): Bridging Neuronal Dynamics and Cancer Pathogenesis through Mechanistic Target of Rapamycin Signaling. Int J Mol Sci 2024; 25:1489. [PMID: 38338768 PMCID: PMC10855792 DOI: 10.3390/ijms25031489] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2023] [Revised: 01/14/2024] [Accepted: 01/17/2024] [Indexed: 02/12/2024] Open
Abstract
Ras homolog enriched in brain (Rheb1 and Rheb2), small GTPases, play a crucial role in regulating neuronal activity and have gained attention for their implications in cancer development, particularly in breast cancer. This study delves into the intricate connection between the multifaceted functions of Rheb1 in neurons and cancer, with a specific focus on the mTOR pathway. It aims to elucidate Rheb1's involvement in pivotal cellular processes such as proliferation, apoptosis resistance, migration, invasion, metastasis, and inflammatory responses while acknowledging that Rheb2 has not been extensively studied. Despite the recognized associations, a comprehensive understanding of the intricate interplay between Rheb1 and Rheb2 and their roles in both nerve and cancer remains elusive. This review consolidates current knowledge regarding the impact of Rheb1 on cancer hallmarks and explores the potential of Rheb1 as a therapeutic target in cancer treatment. It emphasizes the necessity for a deeper comprehension of the molecular mechanisms underlying Rheb1-mediated oncogenic processes, underscoring the existing gaps in our understanding. Additionally, the review highlights the exploration of Rheb1 inhibitors as a promising avenue for cancer therapy. By shedding light on the complicated roles between Rheb1/Rheb2 and cancer, this study provides valuable insights to the scientific community. These insights are instrumental in guiding the identification of novel targets and advancing the development of effective therapeutic strategies for treating cancer.
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Affiliation(s)
- Mostafizur Rahman
- College of Pharmacy, Dongguk University, Seoul 04620, Republic of Korea; (M.R.); (G.J.L.)
| | - Tuan Minh Nguyen
- College of Pharmacy, Dongguk University, Seoul 04620, Republic of Korea; (M.R.); (G.J.L.)
| | - Gi Jeong Lee
- College of Pharmacy, Dongguk University, Seoul 04620, Republic of Korea; (M.R.); (G.J.L.)
| | - Boram Kim
- College of Pharmacy, Dongguk University, Seoul 04620, Republic of Korea; (M.R.); (G.J.L.)
| | - Mi Kyung Park
- Department of BioHealthcare, Hwasung Medi-Science University, Hwaseong-si 18274, Republic of Korea
| | - Chang Hoon Lee
- College of Pharmacy, Dongguk University, Seoul 04620, Republic of Korea; (M.R.); (G.J.L.)
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Escher TE, Satchell KJF. RAS degraders: The new frontier for RAS-driven cancers. Mol Ther 2023; 31:1904-1919. [PMID: 36945775 PMCID: PMC10362401 DOI: 10.1016/j.ymthe.2023.03.017] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2022] [Revised: 01/20/2023] [Accepted: 03/16/2023] [Indexed: 03/23/2023] Open
Abstract
The function and significance of RAS proteins in cancer have been widely studied for decades. In 2013, the National Cancer Institute established the RAS Initiative to explore innovative approaches for attacking the proteins encoded by mutant forms of RAS genes and to create effective therapies for RAS-driven cancers. This initiative spurred researchers to develop novel approaches and to discover small molecules targeting this protein that was at one time termed "undruggable." More recently, advanced efforts in RAS degraders including PROTACs, linker-based degraders, and direct proteolysis degraders have been explored as novel strategies to target RAS for cancer treatment. These RAS degraders present new opportunities for RAS therapies and may prove fruitful in understanding basic cell biology. Novel delivery strategies will further enhance the efficacy of these therapeutics. In this review, we summarize recent efforts to develop RAS degraders, including PROTACs and E3 adaptor and ligase fusions as cancer therapies. This review also details the direct RAS protease degrader, RAS/RAP1-specific endopeptidase that directly and specifically cleaves RAS.
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Affiliation(s)
- Taylor E Escher
- Department of Microbiology-Immunology, Northwestern University, Feinberg School of Medicine, Chicago, IL 60611, USA; Robert H. Lurie Comprehensive Cancer Research Center, Northwestern University, Feinberg School of Medicine, Chicago, IL 60611, USA
| | - Karla J F Satchell
- Department of Microbiology-Immunology, Northwestern University, Feinberg School of Medicine, Chicago, IL 60611, USA; Robert H. Lurie Comprehensive Cancer Research Center, Northwestern University, Feinberg School of Medicine, Chicago, IL 60611, USA.
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Vidimar V, Park M, Stubbs CK, Ingram NK, Qiang W, Zhang S, Gursel D, Melnyk RA, Satchell KJF. Proteolytic pan-RAS Cleavage Leads to Tumor Regression in Patient-derived Pancreatic Cancer Xenografts. Mol Cancer Ther 2022; 21:810-820. [PMID: 35247912 PMCID: PMC9933180 DOI: 10.1158/1535-7163.mct-21-0550] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2021] [Revised: 10/12/2021] [Accepted: 02/22/2022] [Indexed: 11/16/2022]
Abstract
The lack of effective RAS inhibition represents a major unmet medical need in the treatment of pancreatic ductal adenocarcinoma (PDAC). Here, we investigate the anticancer activity of RRSP-DTB, an engineered biologic that cleaves the Switch I of all RAS isoforms, in KRAS-mutant PDAC cell lines and patient-derived xenografts (PDX). We first demonstrate that RRSP-DTB effectively engages RAS and impacts downstream ERK signaling in multiple KRAS-mutant PDAC cell lines inhibiting cell proliferation at picomolar concentrations. We next tested RRSP-DTB in immunodeficient mice bearing KRAS-mutant PDAC PDXs. Treatment with RRSP-DTB led to ≥95% tumor regression after 29 days. Residual tumors exhibited disrupted tissue architecture, increased fibrosis and fewer proliferating cells compared with controls. Intratumoral levels of phospho-ERK were also significantly lower, indicating in vivo target engagement. Importantly, tumors that started to regrow without RRSP-DTB shrank when treatment resumed, demonstrating resistance to RRSP-DTB had not developed. Tracking persistence of the toxin activity following intraperitoneal injection showed that RRSP-DTB is active in sera from immunocompetent mice for at least 1 hour, but absent after 16 hours, justifying use of daily dosing. Overall, we report that RRSP-DTB strongly regresses hard-to-treat KRAS-mutant PDX models of pancreatic cancer, warranting further development of this pan-RAS biologic for the management of RAS-addicted tumors.
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Affiliation(s)
- Vania Vidimar
- Department of Microbiology and Immunology, Northwestern University, Feinberg School of Medicine, Chicago, Illinois
| | - Minyoung Park
- Program in Molecular Medicine, The Hospital for Sick Children, Toronto, Ontario, Canada
- Department of Biochemistry, University of Toronto, Toronto, Canada
| | - Caleb K Stubbs
- Department of Microbiology and Immunology, Northwestern University, Feinberg School of Medicine, Chicago, Illinois
| | - Nana K Ingram
- Department of Microbiology and Immunology, Northwestern University, Feinberg School of Medicine, Chicago, Illinois
| | - Wenan Qiang
- Center for Developmental Therapeutics, Chemistry of Life Processes Institute, Northwestern University, Evanston, Illinois
- Department of Obstetrics and Gynecology (Reproductive Science in Medicine), Feinberg School of Medicine, Northwestern University, Chicago, Illinois
- Pathology Core Facility, Northwestern University Feinberg School of Medicine, Chicago, Illinois
- Robert H. Lurie Comprehensive Cancer Research Center, Northwestern University, Feinberg School of Medicine, Chicago, Illinois
| | - Shanshan Zhang
- Pathology Core Facility, Northwestern University Feinberg School of Medicine, Chicago, Illinois
| | - Demirkan Gursel
- Pathology Core Facility, Northwestern University Feinberg School of Medicine, Chicago, Illinois
| | - Roman A Melnyk
- Program in Molecular Medicine, The Hospital for Sick Children, Toronto, Ontario, Canada
- Department of Biochemistry, University of Toronto, Toronto, Canada
| | - Karla J F Satchell
- Department of Microbiology and Immunology, Northwestern University, Feinberg School of Medicine, Chicago, Illinois
- Robert H. Lurie Comprehensive Cancer Research Center, Northwestern University, Feinberg School of Medicine, Chicago, Illinois
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Woida PJ, Satchell KJF. Bacterial Toxin and Effector Regulation of Intestinal Immune Signaling. Front Cell Dev Biol 2022; 10:837691. [PMID: 35252199 PMCID: PMC8888934 DOI: 10.3389/fcell.2022.837691] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2021] [Accepted: 01/24/2022] [Indexed: 11/13/2022] Open
Abstract
The host immune response is highly effective to detect and clear infecting bacterial pathogens. Given the elaborate surveillance systems of the host, it is evident that in order to productively infect a host, the bacteria often coordinate virulence factors to fine-tune the host response during infection. These coordinated events can include either suppressing or activating the signaling pathways that control the immune response and thereby promote bacterial colonization and infection. This review will cover the surveillance and signaling systems for detection of bacteria in the intestine and a sample of the toxins and effectors that have been characterized that cirumvent these signaling pathways. These factors that promote infection and disease progression have also been redirected as tools or therapeutics. Thus, these toxins are enemies deployed to enhance infection, but can also be redeployed as allies to enable research and protect against infection.
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