1
|
Sobhiafshar U, Çakici B, Yilmaz E, Yildiz Ayhan N, Hedaya L, Ayhan MC, Yerinde C, Alankuş YB, Gürkaşlar HK, Firat-Karalar EN, Emre NCT. Interferon regulatory factor 4 modulates epigenetic silencing and cancer-critical pathways in melanoma cells. Mol Oncol 2024. [PMID: 38880659 DOI: 10.1002/1878-0261.13672] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2023] [Revised: 04/14/2024] [Accepted: 05/22/2024] [Indexed: 06/18/2024] Open
Abstract
Interferon regulatory factor 4 (IRF4) was initially identified as a key controller in lymphocyte differentiation and function, and subsequently as a dependency factor and therapy target in lymphocyte-derived cancers. In melanocytes, IRF4 takes part in pigmentation. Although genetic studies have implicated IRF4 in melanoma, how IRF4 functions in melanoma cells has remained largely elusive. Here, we confirmed prevalent IRF4 expression in melanoma and showed that high expression is linked to dependency in cells and mortality in patients. Analysis of genes activated by IRF4 uncovered, as a novel target category, epigenetic silencing factors involved in DNA methylation (DNMT1, DNMT3B, UHRF1) and histone H3K27 methylation (EZH2). Consequently, we show that IRF4 controls the expression of tumour suppressor genes known to be silenced by these epigenetic modifications, for instance cyclin-dependent kinase inhibitors CDKN1A and CDKN1B, the PI3-AKT pathway regulator PTEN, and primary cilium components. Furthermore, IRF4 modulates activity of key downstream oncogenic pathways, such as WNT/β-catenin and AKT, impacting cell proliferation and survival. Accordingly, IRF4 modifies the effectiveness of pertinent epigenetic drugs on melanoma cells, a finding that encourages further studies towards therapeutic targeting of IRF4 in melanoma.
Collapse
Affiliation(s)
- Ulduz Sobhiafshar
- Department of Molecular Biology and Genetics, Boğaziçi University, Istanbul, Turkey
| | - Betül Çakici
- Department of Molecular Biology and Genetics, Boğaziçi University, Istanbul, Turkey
| | - Erdem Yilmaz
- Department of Molecular Biology and Genetics, Boğaziçi University, Istanbul, Turkey
| | - Nalan Yildiz Ayhan
- Department of Molecular Biology and Genetics, Boğaziçi University, Istanbul, Turkey
| | - Laila Hedaya
- Department of Molecular Biology and Genetics, Boğaziçi University, Istanbul, Turkey
| | - Mustafa Can Ayhan
- Department of Molecular Biology and Genetics, Boğaziçi University, Istanbul, Turkey
| | - Cansu Yerinde
- Department of Molecular Biology and Genetics, Boğaziçi University, Istanbul, Turkey
| | | | - H Kübra Gürkaşlar
- Department of Molecular Biology and Genetics, Koç University, Istanbul, Turkey
| | | | - N C Tolga Emre
- Department of Molecular Biology and Genetics, Boğaziçi University, Istanbul, Turkey
- Center for Life Sciences and Technologies, Boğaziçi University, Istanbul, Turkey
| |
Collapse
|
2
|
Takahashi M, Chong HB, Zhang S, Yang TY, Lazarov MJ, Harry S, Maynard M, Hilbert B, White RD, Murrey HE, Tsou CC, Vordermark K, Assaad J, Gohar M, Dürr BR, Richter M, Patel H, Kryukov G, Brooijmans N, Alghali ASO, Rubio K, Villanueva A, Zhang J, Ge M, Makram F, Griesshaber H, Harrison D, Koglin AS, Ojeda S, Karakyriakou B, Healy A, Popoola G, Rachmin I, Khandelwal N, Neil JR, Tien PC, Chen N, Hosp T, van den Ouweland S, Hara T, Bussema L, Dong R, Shi L, Rasmussen MQ, Domingues AC, Lawless A, Fang J, Yoda S, Nguyen LP, Reeves SM, Wakefield FN, Acker A, Clark SE, Dubash T, Kastanos J, Oh E, Fisher DE, Maheswaran S, Haber DA, Boland GM, Sade-Feldman M, Jenkins RW, Hata AN, Bardeesy NM, Suvà ML, Martin BR, Liau BB, Ott CJ, Rivera MN, Lawrence MS, Bar-Peled L. DrugMap: A quantitative pan-cancer analysis of cysteine ligandability. Cell 2024; 187:2536-2556.e30. [PMID: 38653237 PMCID: PMC11143475 DOI: 10.1016/j.cell.2024.03.027] [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: 10/01/2023] [Revised: 01/15/2024] [Accepted: 03/19/2024] [Indexed: 04/25/2024]
Abstract
Cysteine-focused chemical proteomic platforms have accelerated the clinical development of covalent inhibitors for a wide range of targets in cancer. However, how different oncogenic contexts influence cysteine targeting remains unknown. To address this question, we have developed "DrugMap," an atlas of cysteine ligandability compiled across 416 cancer cell lines. We unexpectedly find that cysteine ligandability varies across cancer cell lines, and we attribute this to differences in cellular redox states, protein conformational changes, and genetic mutations. Leveraging these findings, we identify actionable cysteines in NF-κB1 and SOX10 and develop corresponding covalent ligands that block the activity of these transcription factors. We demonstrate that the NF-κB1 probe blocks DNA binding, whereas the SOX10 ligand increases SOX10-SOX10 interactions and disrupts melanoma transcriptional signaling. Our findings reveal heterogeneity in cysteine ligandability across cancers, pinpoint cell-intrinsic features driving cysteine targeting, and illustrate the use of covalent probes to disrupt oncogenic transcription-factor activity.
Collapse
Affiliation(s)
- Mariko Takahashi
- Krantz Family Center for Cancer Research, Massachusetts General Hospital Cancer Center, Charlestown, MA 02129, USA.
| | - Harrison B Chong
- Krantz Family Center for Cancer Research, Massachusetts General Hospital Cancer Center, Charlestown, MA 02129, USA
| | - Siwen Zhang
- Krantz Family Center for Cancer Research, Massachusetts General Hospital Cancer Center, Charlestown, MA 02129, USA
| | - Tzu-Yi Yang
- Krantz Family Center for Cancer Research, Massachusetts General Hospital Cancer Center, Charlestown, MA 02129, USA
| | - Matthew J Lazarov
- Krantz Family Center for Cancer Research, Massachusetts General Hospital Cancer Center, Charlestown, MA 02129, USA
| | - Stefan Harry
- Krantz Family Center for Cancer Research, Massachusetts General Hospital Cancer Center, Charlestown, MA 02129, USA; Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA 02138, USA
| | | | | | | | | | | | - Kira Vordermark
- Krantz Family Center for Cancer Research, Massachusetts General Hospital Cancer Center, Charlestown, MA 02129, USA
| | - Jonathan Assaad
- Krantz Family Center for Cancer Research, Massachusetts General Hospital Cancer Center, Charlestown, MA 02129, USA
| | - Magdy Gohar
- Krantz Family Center for Cancer Research, Massachusetts General Hospital Cancer Center, Charlestown, MA 02129, USA
| | - Benedikt R Dürr
- Krantz Family Center for Cancer Research, Massachusetts General Hospital Cancer Center, Charlestown, MA 02129, USA
| | - Marianne Richter
- Krantz Family Center for Cancer Research, Massachusetts General Hospital Cancer Center, Charlestown, MA 02129, USA
| | - Himani Patel
- Krantz Family Center for Cancer Research, Massachusetts General Hospital Cancer Center, Charlestown, MA 02129, USA
| | | | | | | | - Karla Rubio
- Department of Pathology, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Antonio Villanueva
- Department of Pathology, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Junbing Zhang
- Krantz Family Center for Cancer Research, Massachusetts General Hospital Cancer Center, Charlestown, MA 02129, USA
| | - Maolin Ge
- Krantz Family Center for Cancer Research, Massachusetts General Hospital Cancer Center, Charlestown, MA 02129, USA
| | - Farah Makram
- Krantz Family Center for Cancer Research, Massachusetts General Hospital Cancer Center, Charlestown, MA 02129, USA
| | - Hanna Griesshaber
- Krantz Family Center for Cancer Research, Massachusetts General Hospital Cancer Center, Charlestown, MA 02129, USA
| | - Drew Harrison
- Krantz Family Center for Cancer Research, Massachusetts General Hospital Cancer Center, Charlestown, MA 02129, USA
| | - Ann-Sophie Koglin
- Krantz Family Center for Cancer Research, Massachusetts General Hospital Cancer Center, Charlestown, MA 02129, USA
| | - Samuel Ojeda
- Krantz Family Center for Cancer Research, Massachusetts General Hospital Cancer Center, Charlestown, MA 02129, USA
| | - Barbara Karakyriakou
- Krantz Family Center for Cancer Research, Massachusetts General Hospital Cancer Center, Charlestown, MA 02129, USA
| | - Alexander Healy
- Krantz Family Center for Cancer Research, Massachusetts General Hospital Cancer Center, Charlestown, MA 02129, USA
| | - George Popoola
- Krantz Family Center for Cancer Research, Massachusetts General Hospital Cancer Center, Charlestown, MA 02129, USA
| | - Inbal Rachmin
- Cutaneous Biology Research Center, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Neha Khandelwal
- Krantz Family Center for Cancer Research, Massachusetts General Hospital Cancer Center, Charlestown, MA 02129, USA
| | | | - Pei-Chieh Tien
- Krantz Family Center for Cancer Research, Massachusetts General Hospital Cancer Center, Charlestown, MA 02129, USA
| | - Nicholas Chen
- Krantz Family Center for Cancer Research, Massachusetts General Hospital Cancer Center, Charlestown, MA 02129, USA; Department of Pathology, Harvard Medical School, Boston, MA 02114, USA
| | - Tobias Hosp
- Krantz Family Center for Cancer Research, Massachusetts General Hospital Cancer Center, Charlestown, MA 02129, USA
| | - Sanne van den Ouweland
- Krantz Family Center for Cancer Research, Massachusetts General Hospital Cancer Center, Charlestown, MA 02129, USA
| | - Toshiro Hara
- Department of Pathology, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Lillian Bussema
- Department of Pathology, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Rui Dong
- Department of Pathology, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Lei Shi
- Krantz Family Center for Cancer Research, Massachusetts General Hospital Cancer Center, Charlestown, MA 02129, USA
| | - Martin Q Rasmussen
- Krantz Family Center for Cancer Research, Massachusetts General Hospital Cancer Center, Charlestown, MA 02129, USA
| | - Ana Carolina Domingues
- Krantz Family Center for Cancer Research, Massachusetts General Hospital Cancer Center, Charlestown, MA 02129, USA
| | - Aleigha Lawless
- Department of Surgery, Massachusetts General Hospital, Boston, MA 02114, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Jacy Fang
- Krantz Family Center for Cancer Research, Massachusetts General Hospital Cancer Center, Charlestown, MA 02129, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Satoshi Yoda
- Krantz Family Center for Cancer Research, Massachusetts General Hospital Cancer Center, Charlestown, MA 02129, USA
| | - Linh Phuong Nguyen
- Krantz Family Center for Cancer Research, Massachusetts General Hospital Cancer Center, Charlestown, MA 02129, USA
| | - Sarah Marie Reeves
- Krantz Family Center for Cancer Research, Massachusetts General Hospital Cancer Center, Charlestown, MA 02129, USA
| | - Farrah Nicole Wakefield
- Krantz Family Center for Cancer Research, Massachusetts General Hospital Cancer Center, Charlestown, MA 02129, USA
| | - Adam Acker
- Krantz Family Center for Cancer Research, Massachusetts General Hospital Cancer Center, Charlestown, MA 02129, USA
| | - Sarah Elizabeth Clark
- Krantz Family Center for Cancer Research, Massachusetts General Hospital Cancer Center, Charlestown, MA 02129, USA
| | - Taronish Dubash
- Krantz Family Center for Cancer Research, Massachusetts General Hospital Cancer Center, Charlestown, MA 02129, USA
| | - John Kastanos
- Krantz Family Center for Cancer Research, Massachusetts General Hospital Cancer Center, Charlestown, MA 02129, USA
| | - Eugene Oh
- Krantz Family Center for Cancer Research, Massachusetts General Hospital Cancer Center, Charlestown, MA 02129, USA; Department of Medicine, Harvard Medical School, Boston, MA 02114, USA
| | - David E Fisher
- Cutaneous Biology Research Center, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Shyamala Maheswaran
- Krantz Family Center for Cancer Research, Massachusetts General Hospital Cancer Center, Charlestown, MA 02129, USA; Department of Medicine, Harvard Medical School, Boston, MA 02114, USA
| | - Daniel A Haber
- Krantz Family Center for Cancer Research, Massachusetts General Hospital Cancer Center, Charlestown, MA 02129, USA; Department of Medicine, Harvard Medical School, Boston, MA 02114, USA; Howard Hughes Medical Institute, Chevy Chase, MD 20815, USA
| | - Genevieve M Boland
- Krantz Family Center for Cancer Research, Massachusetts General Hospital Cancer Center, Charlestown, MA 02129, USA; Department of Surgery, Massachusetts General Hospital, Boston, MA 02114, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Department of Surgery, Harvard Medical School, Boston, MA 02114, USA
| | - Moshe Sade-Feldman
- Krantz Family Center for Cancer Research, Massachusetts General Hospital Cancer Center, Charlestown, MA 02129, USA; Department of Medicine, Harvard Medical School, Boston, MA 02114, USA
| | - Russell W Jenkins
- Krantz Family Center for Cancer Research, Massachusetts General Hospital Cancer Center, Charlestown, MA 02129, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Department of Medicine, Harvard Medical School, Boston, MA 02114, USA
| | - Aaron N Hata
- Krantz Family Center for Cancer Research, Massachusetts General Hospital Cancer Center, Charlestown, MA 02129, USA; Department of Medicine, Harvard Medical School, Boston, MA 02114, USA
| | - Nabeel M Bardeesy
- Krantz Family Center for Cancer Research, Massachusetts General Hospital Cancer Center, Charlestown, MA 02129, USA; Department of Medicine, Harvard Medical School, Boston, MA 02114, USA
| | - Mario L Suvà
- Krantz Family Center for Cancer Research, Massachusetts General Hospital Cancer Center, Charlestown, MA 02129, USA; Department of Pathology, Massachusetts General Hospital, Boston, MA 02114, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Department of Pathology, Harvard Medical School, Boston, MA 02114, USA
| | | | - Brian B Liau
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA 02138, USA
| | - Christopher J Ott
- Krantz Family Center for Cancer Research, Massachusetts General Hospital Cancer Center, Charlestown, MA 02129, USA; Department of Medicine, Harvard Medical School, Boston, MA 02114, USA
| | - Miguel N Rivera
- Krantz Family Center for Cancer Research, Massachusetts General Hospital Cancer Center, Charlestown, MA 02129, USA; Department of Pathology, Massachusetts General Hospital, Boston, MA 02114, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Department of Pathology, Harvard Medical School, Boston, MA 02114, USA
| | - Michael S Lawrence
- Krantz Family Center for Cancer Research, Massachusetts General Hospital Cancer Center, Charlestown, MA 02129, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Department of Pathology, Harvard Medical School, Boston, MA 02114, USA.
| | - Liron Bar-Peled
- Krantz Family Center for Cancer Research, Massachusetts General Hospital Cancer Center, Charlestown, MA 02129, USA; Department of Medicine, Harvard Medical School, Boston, MA 02114, USA.
| |
Collapse
|
3
|
Rahnea-Nita RA, Rebegea LF, Toma RV, Mocanu H, Soare I, Mihailov R, Nechifor A, Guliciuc M, Constantin GB, Rahnea-Nita G. Immunotherapy Combined with Radiation in Malignant Melanoma without BRAF Mutations Brain Metastases-Favorable Response after Immunotherapy Continued beyond Progression. J Pers Med 2024; 14:86. [PMID: 38248787 PMCID: PMC10817469 DOI: 10.3390/jpm14010086] [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: 11/27/2023] [Accepted: 01/10/2024] [Indexed: 01/23/2024] Open
Abstract
We present the case of a patient who was diagnosed in 2018 with nodular Malignant Melanoma (MM) without BRAF V 600 mutations stage 3 C (pT4b pN1a M0), and who underwent adjuvant citokines treatment with Interferon alpha 2b-48 weeks. Immunotherapy was initiated in January 2021 for lung and lymph node metastases. In June 2021, there was a partial response of the lung and lymph node metastases, but there was also progression to brain metastases. Immunotherapy was continued and Whole Brain Radiotherapy (WBRT) was performed. In September 2023, the imaging investigations revealed a favorable response, with no lesions suggestive of secondary determinations. The combination of Radiotherapy (RT) and Immunotherapy (IT) with Immune Checkpoint Inhibitors (ICI) has an abscopal effect. There is a coordinated action in the combination of RT and IT in order to obtain a common result, with the antitumor effect being greater than if RT or IT acted separately.
Collapse
Affiliation(s)
- Roxana-Andreea Rahnea-Nita
- The Clinical Department, The Faculty of Medicine, The University of Medicine and Pharmacy “Carol Davila”, 050474 Bucharest, Romania; (R.-A.R.-N.); (R.-V.T.)
- The Oncology-Palliative Care Department, “Sf. Luca” Chronic Disease Hospital, 041915 Bucharest, Romania;
| | - Laura-Florentina Rebegea
- The Clinical Department, The Faculty of Medicine and Pharmacy, “Dunarea de Jos” University in Galati, 800008 Galati, Romania; (L.-F.R.); (R.M.); (A.N.); (M.G.)
- The Radiotherapy Department, “Sf. Ap. Andrei” County Emergency Clinical Hospital, 800579 Galati, Romania
- The Research Center in the Field of Medical and Pharmaceutical Sciences, ReFORM-UDJ, 800010 Galati, Romania
| | - Radu-Valeriu Toma
- The Clinical Department, The Faculty of Medicine, The University of Medicine and Pharmacy “Carol Davila”, 050474 Bucharest, Romania; (R.-A.R.-N.); (R.-V.T.)
- The Radiotherapy Department, The Oncological Institute, 022328 Bucharest, Romania
| | - Horia Mocanu
- The Clinical Department, The Faculty of Medicine, “Titu Maiorescu” University, 040051 Bucharest, Romania; (H.M.); (I.S.)
- The E.N.T Department, Gaesti City Hospital, 135200 Gaesti, Romania
| | - Ioana Soare
- The Clinical Department, The Faculty of Medicine, “Titu Maiorescu” University, 040051 Bucharest, Romania; (H.M.); (I.S.)
| | - Raul Mihailov
- The Clinical Department, The Faculty of Medicine and Pharmacy, “Dunarea de Jos” University in Galati, 800008 Galati, Romania; (L.-F.R.); (R.M.); (A.N.); (M.G.)
| | - Alexandru Nechifor
- The Clinical Department, The Faculty of Medicine and Pharmacy, “Dunarea de Jos” University in Galati, 800008 Galati, Romania; (L.-F.R.); (R.M.); (A.N.); (M.G.)
| | - Mădălin Guliciuc
- The Clinical Department, The Faculty of Medicine and Pharmacy, “Dunarea de Jos” University in Galati, 800008 Galati, Romania; (L.-F.R.); (R.M.); (A.N.); (M.G.)
- The Urology Department, “Sf. Ap. Andrei” County Emergency Clinical Hospital, 800579 Galati, Romania
| | - Georgiana Bianca Constantin
- The Morphological and Functional Sciences Department, The Faculty of Medicine and Pharmacy, “Dunarea de Jos” University in Galati, 800008 Galati, Romania
| | - Gabriela Rahnea-Nita
- The Oncology-Palliative Care Department, “Sf. Luca” Chronic Disease Hospital, 041915 Bucharest, Romania;
- The Clinical Department, The Faculty of Midwifery and Nursing, The University of Medicine and Pharmacy “Carol Davila”, 050474 Bucharest, Romania
| |
Collapse
|
4
|
Li Y, Guo Z, Gao X, Wang G. MMCL-CDR: enhancing cancer drug response prediction with multi-omics and morphology images contrastive representation learning. Bioinformatics 2023; 39:btad734. [PMID: 38070154 PMCID: PMC10756335 DOI: 10.1093/bioinformatics/btad734] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2023] [Revised: 11/09/2023] [Indexed: 12/30/2023] Open
Abstract
MOTIVATION Cancer is a complex disease that results in a significant number of global fatalities. Treatment strategies can vary among patients, even if they have the same type of cancer. The application of precision medicine in cancer shows promise for treating different types of cancer, reducing healthcare expenses, and improving recovery rates. To achieve personalized cancer treatment, machine learning models have been developed to predict drug responses based on tumor and drug characteristics. However, current studies either focus on constructing homogeneous networks from single data source or heterogeneous networks from multiomics data. While multiomics data have shown potential in predicting drug responses in cancer cell lines, there is still a lack of research that effectively utilizes insights from different modalities. Furthermore, effectively utilizing the multimodal knowledge of cancer cell lines poses a challenge due to the heterogeneity inherent in these modalities. RESULTS To address these challenges, we introduce MMCL-CDR (Multimodal Contrastive Learning for Cancer Drug Responses), a multimodal approach for cancer drug response prediction that integrates copy number variation, gene expression, morphology images of cell lines, and chemical structure of drugs. The objective of MMCL-CDR is to align cancer cell lines across different data modalities by learning cell line representations from omic and image data, and combined with structural drug representations to enhance the prediction of cancer drug responses (CDR). We have carried out comprehensive experiments and show that our model significantly outperforms other state-of-the-art methods in CDR prediction. The experimental results also prove that the model can learn more accurate cell line representation by integrating multiomics and morphological data from cell lines, thereby improving the accuracy of CDR prediction. In addition, the ablation study and qualitative analysis also confirm the effectiveness of each part of our proposed model. Last but not least, MMCL-CDR opens up a new dimension for cancer drug response prediction through multimodal contrastive learning, pioneering a novel approach that integrates multiomics and multimodal drug and cell line modeling. AVAILABILITY AND IMPLEMENTATION MMCL-CDR is available at https://github.com/catly/MMCL-CDR.
Collapse
Affiliation(s)
- Yang Li
- College of Computer and Control Engineering, Northeast Forestry University, Harbin 150006, China
| | - Zihou Guo
- College of Computer and Control Engineering, Northeast Forestry University, Harbin 150006, China
| | - Xin Gao
- Computational Bioscience Research Center, King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
- Computer Science Program, Computer, Electrical and Mathematical Sciences and Engineering Division, King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Guohua Wang
- College of Computer and Control Engineering, Northeast Forestry University, Harbin 150006, China
| |
Collapse
|
5
|
Takahashi M, Chong HB, Zhang S, Lazarov MJ, Harry S, Maynard M, White R, Murrey HE, Hilbert B, Neil JR, Gohar M, Ge M, Zhang J, Durr BR, Kryukov G, Tsou CC, Brooijmans N, Alghali ASO, Rubio K, Vilanueva A, Harrison D, Koglin AS, Ojeda S, Karakyriakou B, Healy A, Assaad J, Makram F, Rachman I, Khandelwal N, Tien PC, Popoola G, Chen N, Vordermark K, Richter M, Patel H, Yang TY, Griesshaber H, Hosp T, van den Ouweland S, Hara T, Bussema L, Dong R, Shi L, Rasmussen MQ, Domingues AC, Lawless A, Fang J, Yoda S, Nguyen LP, Reeves SM, Wakefield FN, Acker A, Clark SE, Dubash T, Fisher DE, Maheswaran S, Haber DA, Boland G, Sade-Feldman M, Jenkins R, Hata A, Bardeesy N, Suva ML, Martin B, Liau B, Ott C, Rivera MN, Lawrence MS, Bar-Peled L. DrugMap: A quantitative pan-cancer analysis of cysteine ligandability. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.10.20.563287. [PMID: 37961514 PMCID: PMC10634688 DOI: 10.1101/2023.10.20.563287] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/15/2023]
Abstract
Cysteine-focused chemical proteomic platforms have accelerated the clinical development of covalent inhibitors of a wide-range of targets in cancer. However, how different oncogenic contexts influence cysteine targeting remains unknown. To address this question, we have developed DrugMap , an atlas of cysteine ligandability compiled across 416 cancer cell lines. We unexpectedly find that cysteine ligandability varies across cancer cell lines, and we attribute this to differences in cellular redox states, protein conformational changes, and genetic mutations. Leveraging these findings, we identify actionable cysteines in NFκB1 and SOX10 and develop corresponding covalent ligands that block the activity of these transcription factors. We demonstrate that the NFκB1 probe blocks DNA binding, whereas the SOX10 ligand increases SOX10-SOX10 interactions and disrupts melanoma transcriptional signaling. Our findings reveal heterogeneity in cysteine ligandability across cancers, pinpoint cell-intrinsic features driving cysteine targeting, and illustrate the use of covalent probes to disrupt oncogenic transcription factor activity.
Collapse
|
6
|
Grafanaki K, Grammatikakis I, Ghosh A, Gopalan V, Olgun G, Liu H, Kyriakopoulos GC, Skeparnias I, Georgiou S, Stathopoulos C, Hannenhalli S, Merlino G, Marie KL, Day CP. Noncoding RNA circuitry in melanoma onset, plasticity, and therapeutic response. Pharmacol Ther 2023; 248:108466. [PMID: 37301330 PMCID: PMC10527631 DOI: 10.1016/j.pharmthera.2023.108466] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2023] [Revised: 05/24/2023] [Accepted: 05/31/2023] [Indexed: 06/12/2023]
Abstract
Melanoma, the cancer of the melanocyte, is the deadliest form of skin cancer with an aggressive nature, propensity to metastasize and tendency to resist therapeutic intervention. Studies have identified that the re-emergence of developmental pathways in melanoma contributes to melanoma onset, plasticity, and therapeutic response. Notably, it is well known that noncoding RNAs play a critical role in the development and stress response of tissues. In this review, we focus on the noncoding RNAs, including microRNAs, long non-coding RNAs, circular RNAs, and other small RNAs, for their functions in developmental mechanisms and plasticity, which drive onset, progression, therapeutic response and resistance in melanoma. Going forward, elucidation of noncoding RNA-mediated mechanisms may provide insights that accelerate development of novel melanoma therapies.
Collapse
Affiliation(s)
- Katerina Grafanaki
- Laboratory of Cancer Biology and Genetics, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA; Department of Dermatology, School of Medicine, University of Patras, 26504 Patras, Greece
| | - Ioannis Grammatikakis
- Cancer Genetics Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Arin Ghosh
- Laboratory of Cancer Biology and Genetics, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Vishaka Gopalan
- Cancer Data Science Laboratory, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Gulden Olgun
- Cancer Data Science Laboratory, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Huaitian Liu
- Laboratory of Human Carcinogenesis, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - George C Kyriakopoulos
- Department of Biochemistry, School of Medicine, University of Patras, 26504 Patras, Greece
| | - Ilias Skeparnias
- Laboratory of Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, Bethesda, MD, USA
| | - Sophia Georgiou
- Department of Dermatology, School of Medicine, University of Patras, 26504 Patras, Greece
| | | | - Sridhar Hannenhalli
- Cancer Data Science Laboratory, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Glenn Merlino
- Laboratory of Cancer Biology and Genetics, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Kerrie L Marie
- Division of Molecular and Cellular Function, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, UK.
| | - Chi-Ping Day
- Laboratory of Cancer Biology and Genetics, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA.
| |
Collapse
|
7
|
Yuan P, Teng D, de Groot E, Li M, Trousil S, Shen CH, Roszik J, Davies MA, Gopal YV, Zheng B. Loss of AMPKα2 promotes melanoma tumor growth and brain metastasis. iScience 2023; 26:106791. [PMID: 37213225 PMCID: PMC10197146 DOI: 10.1016/j.isci.2023.106791] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2023] [Revised: 04/02/2023] [Accepted: 04/26/2023] [Indexed: 05/23/2023] Open
Abstract
AMP-activated protein kinase (AMPK) is a critical cellular energy sensor at the interface of metabolism and cancer. However, the role of AMPK in carcinogenesis remains unclear. Here, through analysis of the TCGA melanoma dataset, we found that PRKAA2 gene that encodes the α2 subunit of AMPK is mutated in ∼9% of cutaneous melanomas, and these mutations tend to co-occur with NF1 mutations. Knockout of AMPKα2 promoted anchorage-independent growth of NF1-mutant melanoma cells, whereas ectopic expression of AMPKα2 inhibited their growth in soft agar assays. Moreover, loss of AMPKα2 accelerated tumor growth of NF1-mutant melanoma and enhanced their brain metastasis in immune-deficient mice. Our findings support that AMPKα2 serves as a tumor suppressor in NF1-mutant melanoma and suggest that AMPK could be a therapeutic target for treating melanoma brain metastasis.
Collapse
Affiliation(s)
- Ping Yuan
- Cutaneous Biology Research Center, Massachusetts General Hospital and Harvard Medical School, Charlestown, MA, USA
| | - Da Teng
- Cutaneous Biology Research Center, Massachusetts General Hospital and Harvard Medical School, Charlestown, MA, USA
| | - Evelyn de Groot
- Department of Melanoma Medical Oncology, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Man Li
- Cutaneous Biology Research Center, Massachusetts General Hospital and Harvard Medical School, Charlestown, MA, USA
| | - Sebastian Trousil
- Cutaneous Biology Research Center, Massachusetts General Hospital and Harvard Medical School, Charlestown, MA, USA
| | - Che-Hung Shen
- Cutaneous Biology Research Center, Massachusetts General Hospital and Harvard Medical School, Charlestown, MA, USA
| | - Jason Roszik
- Department of Melanoma Medical Oncology, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Michael A. Davies
- Department of Melanoma Medical Oncology, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Y.N. Vashisht Gopal
- Department of Melanoma Medical Oncology, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Bin Zheng
- Cutaneous Biology Research Center, Massachusetts General Hospital and Harvard Medical School, Charlestown, MA, USA
| |
Collapse
|
8
|
Kontogianni G, Voutetakis K, Piroti G, Kypreou K, Stefanaki I, Vlachavas EI, Pilalis E, Stratigos A, Chatziioannou A, Papadodima O. A Comprehensive Analysis of Cutaneous Melanoma Patients in Greece Based on Multi-Omic Data. Cancers (Basel) 2023; 15:cancers15030815. [PMID: 36765773 PMCID: PMC9913631 DOI: 10.3390/cancers15030815] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2022] [Revised: 01/20/2023] [Accepted: 01/24/2023] [Indexed: 02/01/2023] Open
Abstract
Cutaneous melanoma (CM) is the most aggressive type of skin cancer, and it is characterised by high mutational load and heterogeneity. In this study, we aimed to analyse the genomic and transcriptomic profile of primary melanomas from forty-six Formalin-Fixed, Paraffin-Embedded (FFPE) tissues from Greek patients. Molecular analysis for both germline and somatic variations was performed in genomic DNA from peripheral blood and melanoma samples, respectively, exploiting whole exome and targeted sequencing, and transcriptomic analysis. Detailed clinicopathological data were also included in our analyses and previously reported associations with specific mutations were recognised. Most analysed samples (43/46) were found to harbour at least one clinically actionable somatic variant. A subset of samples was profiled at the transcriptomic level, and it was shown that specific melanoma phenotypic states could be inferred from bulk RNA isolated from FFPE primary melanoma tissue. Integrative bioinformatics analyses, including variant prioritisation, differential gene expression analysis, and functional and gene set enrichment analysis by group and per sample, were conducted and molecular circuits that are implicated in melanoma cell programmes were highlighted. Integration of mutational and transcriptomic data in CM characterisation could shed light on genes and pathways that support the maintenance of phenotypic states encrypted into heterogeneous primary tumours.
Collapse
Affiliation(s)
- Georgia Kontogianni
- Institute of Chemical Biology, National Hellenic Research Foundation, 11635 Athens, Greece
- Centre of Systems Biology, Biomedical Research Foundation of the Academy of Athens, 11527 Athens, Greece
| | | | - Georgia Piroti
- Institute of Chemical Biology, National Hellenic Research Foundation, 11635 Athens, Greece
| | - Katerina Kypreou
- 1st Department of Dermatology, Andreas Syggros Hospital, Medical School, National and Kapodistrian University of Athens, 16121 Athens, Greece
| | - Irene Stefanaki
- 1st Department of Dermatology, Andreas Syggros Hospital, Medical School, National and Kapodistrian University of Athens, 16121 Athens, Greece
| | | | | | - Alexander Stratigos
- 1st Department of Dermatology, Andreas Syggros Hospital, Medical School, National and Kapodistrian University of Athens, 16121 Athens, Greece
| | - Aristotelis Chatziioannou
- Centre of Systems Biology, Biomedical Research Foundation of the Academy of Athens, 11527 Athens, Greece
- e-NIOS Applications Private Company, 17671 Kallithea, Greece
- Correspondence: (A.C.); (O.P.); Tel.: +30-210-727-3721 (A.C. & O.P.)
| | - Olga Papadodima
- Institute of Chemical Biology, National Hellenic Research Foundation, 11635 Athens, Greece
- Correspondence: (A.C.); (O.P.); Tel.: +30-210-727-3721 (A.C. & O.P.)
| |
Collapse
|
9
|
Zhou W, Xu X, Cen Y, Chen J. The role of lncRNAs in the tumor microenvironment and immunotherapy of melanoma. Front Immunol 2022; 13:1085766. [PMID: 36601121 PMCID: PMC9806239 DOI: 10.3389/fimmu.2022.1085766] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2022] [Accepted: 12/05/2022] [Indexed: 12/23/2022] Open
Abstract
Melanoma is one of the most lethal tumors with highly aggressive and metastatic properties. Although immunotherapy and targeted therapy have certain therapeutic effects in melanoma, a significant proportion of patients still have drug resistance after treatment. Recent studies have shown that long noncoding RNAs (lncRNAs) are widely recognized as regulatory factors in cancer. They can regulate numerous cellular processes, including cell proliferation, metastasis, epithelial-mesenchymal transition (EMT) progression and the immune microenvironment. The role of lncRNAs in malignant tumors has received much attention, whereas the relationship between lncRNAs and melanoma requires further investigation. Our review summarizes tumor suppressive and oncogenic lncRNAs closely related to the occurrence and development of melanoma. We summarize the role of lncRNAs in the immune microenvironment, immunotherapy and targeted therapy to provide new targets and therapeutic methods for clinical treatment.
Collapse
|
10
|
Ulisse S, Baldini E, Pironi D, Gagliardi F, Tripodi D, Lauro A, Carbotta S, Tarroni D, D’Armiento M, Morrone A, Forte F, Frattaroli F, Persechino S, Odorisio T, D’Andrea V, Lori E, Sorrenti S. Is Melanoma Progression Affected by Thyroid Diseases? Int J Mol Sci 2022; 23:ijms231710036. [PMID: 36077430 PMCID: PMC9456309 DOI: 10.3390/ijms231710036] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2022] [Revised: 08/25/2022] [Accepted: 08/31/2022] [Indexed: 11/16/2022] Open
Abstract
Clinical and epidemiological evidence indicate a relationship between thyroid diseases and melanoma. In particular, the hypothyroidism condition appears to promote melanoma spread, which suggests a protective role of thyroid hormones against disease progression. In addition, experimental data suggest that, in addition to thyroid hormones, other hormonal players of the hypothalamic–pituitary–thyroid (HPT) axis, namely the thyrotropin releasing hormone and the thyrotropin, are likely to affect melanoma cells behavior. This information warrants further clinical and experimental studies in order to build a precise pattern of action of the HPT hormones on melanoma cells. An improved knowledge of the involved molecular mechanism(s) could lead to a better and possibly personalized clinical management of these patients.
Collapse
Affiliation(s)
- Salvatore Ulisse
- Department of Surgical Sciences, “Sapienza” University of Rome, 00161 Rome, Italy
- Correspondence:
| | - Enke Baldini
- Department of Surgical Sciences, “Sapienza” University of Rome, 00161 Rome, Italy
| | - Daniele Pironi
- Department of Surgical Sciences, “Sapienza” University of Rome, 00161 Rome, Italy
| | - Federica Gagliardi
- Department of Surgical Sciences, “Sapienza” University of Rome, 00161 Rome, Italy
| | - Domenico Tripodi
- Department of Surgical Sciences, “Sapienza” University of Rome, 00161 Rome, Italy
| | - Augusto Lauro
- Department of Surgical Sciences, “Sapienza” University of Rome, 00161 Rome, Italy
| | - Sabino Carbotta
- Department of Surgical Sciences, “Sapienza” University of Rome, 00161 Rome, Italy
| | - Danilo Tarroni
- Department of Surgical Sciences, “Sapienza” University of Rome, 00161 Rome, Italy
| | - Matteo D’Armiento
- Scientific Direction, IRCCS San Gallicano Dermatological Institute, 00144 Rome, Italy
| | - Aldo Morrone
- Scientific Direction, IRCCS San Gallicano Dermatological Institute, 00144 Rome, Italy
| | - Flavio Forte
- Urology Department, M.G. Vannini Hospital, 00177 Rome, Italy
| | - Flaminia Frattaroli
- Department of Surgical Sciences, “Sapienza” University of Rome, 00161 Rome, Italy
| | - Severino Persechino
- Department of Neurosciences, Mental Health and Sensory Organs, “Sapienza” University of Rome, 00161 Rome, Italy
| | - Teresa Odorisio
- Laboratory of Molecular and Cell Biology, Istituto Dermopatico dell’Immacolata, IDI-IRCCS, 00167 Rome, Italy
| | - Vito D’Andrea
- Department of Surgical Sciences, “Sapienza” University of Rome, 00161 Rome, Italy
| | - Eleonora Lori
- Department of Surgical Sciences, “Sapienza” University of Rome, 00161 Rome, Italy
| | - Salvatore Sorrenti
- Department of Surgical Sciences, “Sapienza” University of Rome, 00161 Rome, Italy
| |
Collapse
|