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Su X, Li J, Xu X, Ye Y, Wang C, Pang G, Liu W, Liu A, Zhao C, Hao X. Strategies to enhance the therapeutic efficacy of anti-PD-1 antibody, anti-PD-L1 antibody and anti-CTLA-4 antibody in cancer therapy. J Transl Med 2024; 22:751. [PMID: 39123227 PMCID: PMC11316358 DOI: 10.1186/s12967-024-05552-6] [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: 05/10/2024] [Accepted: 07/29/2024] [Indexed: 08/12/2024] Open
Abstract
Although immune checkpoint inhibitors (anti-PD-1 antibody, anti-PD-L1 antibody, and anti-CTLA-4 antibody) have displayed considerable success in the treatment of malignant tumors, the therapeutic effect is still unsatisfactory for a portion of patients. Therefore, it is imperative to develop strategies to enhance the effect of these ICIs. Increasing evidence strongly suggests that the key to this issue is to transform the tumor immune microenvironment from a state of no or low immune infiltration to a state of high immune infiltration and enhance the tumor cell-killing effect of T cells. Therefore, some combination strategies have been proposed and this review appraise a summary of 39 strategies aiming at enhancing the effectiveness of ICIs, which comprise combining 10 clinical approaches and 29 foundational research strategies. Moreover, this review improves the comprehensive understanding of combination therapy with ICIs and inspires novel ideas for tumor immunotherapy.
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Affiliation(s)
- Xin Su
- The First Clinical Medical College of Gansu University of Chinese Medicine (Gansu Provincial Hospital), Lanzhou, 730000, China
- Department of General Surgery, Gansu Provincial Hospital, No. 204 Donggang West Road, Chengguan District, Lanzhou, 730000, China
| | - Jian Li
- The First Clinical Medical College of Gansu University of Chinese Medicine (Gansu Provincial Hospital), Lanzhou, 730000, China
- Department of General Surgery, Gansu Provincial Hospital, No. 204 Donggang West Road, Chengguan District, Lanzhou, 730000, China
| | - Xiao Xu
- The First Clinical Medical College of Gansu University of Chinese Medicine (Gansu Provincial Hospital), Lanzhou, 730000, China
- Department of General Surgery, Gansu Provincial Hospital, No. 204 Donggang West Road, Chengguan District, Lanzhou, 730000, China
| | - Youbao Ye
- The First Clinical Medical College of Gansu University of Chinese Medicine (Gansu Provincial Hospital), Lanzhou, 730000, China
- Department of General Surgery, Gansu Provincial Hospital, No. 204 Donggang West Road, Chengguan District, Lanzhou, 730000, China
| | - Cailiu Wang
- The First Clinical Medical College of Gansu University of Chinese Medicine (Gansu Provincial Hospital), Lanzhou, 730000, China
- Department of General Surgery, Gansu Provincial Hospital, No. 204 Donggang West Road, Chengguan District, Lanzhou, 730000, China
| | - Guanglong Pang
- The First Clinical Medical College of Gansu University of Chinese Medicine (Gansu Provincial Hospital), Lanzhou, 730000, China
- Department of General Surgery, Gansu Provincial Hospital, No. 204 Donggang West Road, Chengguan District, Lanzhou, 730000, China
| | - Wenxiu Liu
- The First Clinical Medical College of Gansu University of Chinese Medicine (Gansu Provincial Hospital), Lanzhou, 730000, China
- Department of General Surgery, Gansu Provincial Hospital, No. 204 Donggang West Road, Chengguan District, Lanzhou, 730000, China
| | - Ang Liu
- The First Clinical Medical College of Gansu University of Chinese Medicine (Gansu Provincial Hospital), Lanzhou, 730000, China
- Department of General Surgery, Gansu Provincial Hospital, No. 204 Donggang West Road, Chengguan District, Lanzhou, 730000, China
| | - Changchun Zhao
- The First Clinical Medical College of Gansu University of Chinese Medicine (Gansu Provincial Hospital), Lanzhou, 730000, China
- Department of General Surgery, Gansu Provincial Hospital, No. 204 Donggang West Road, Chengguan District, Lanzhou, 730000, China
| | - Xiangyong Hao
- Department of General Surgery, Gansu Provincial Hospital, No. 204 Donggang West Road, Chengguan District, Lanzhou, 730000, China.
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Alhaddad H, Ospina OE, Khaled ML, Ren Y, Vallebuona E, Boozo MB, Forsyth PA, Pina Y, Macaulay R, Law V, Tsai KY, Cress WD, Fridley B, Smalley I. Spatial transcriptomics analysis identifies a tumor-promoting function of the meningeal stroma in melanoma leptomeningeal disease. Cell Rep Med 2024; 5:101606. [PMID: 38866016 PMCID: PMC11228800 DOI: 10.1016/j.xcrm.2024.101606] [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: 12/20/2023] [Revised: 03/08/2024] [Accepted: 05/16/2024] [Indexed: 06/14/2024]
Abstract
Leptomeningeal disease (LMD) remains a rapidly lethal complication for late-stage melanoma patients. Here, we characterize the tumor microenvironment of LMD and patient-matched extra-cranial metastases using spatial transcriptomics in a small number of clinical specimens (nine tissues from two patients) with extensive in vitro and in vivo validation. The spatial landscape of melanoma LMD is characterized by a lack of immune infiltration and instead exhibits a higher level of stromal involvement. The tumor-stroma interactions at the leptomeninges activate tumor-promoting signaling, mediated through upregulation of SERPINA3. The meningeal stroma is required for melanoma cells to survive in the cerebrospinal fluid (CSF) and promotes MAPK inhibitor resistance. Knocking down SERPINA3 or inhibiting the downstream IGR1R/PI3K/AKT axis results in tumor cell death and re-sensitization to MAPK-targeting therapy. Our data provide a spatial atlas of melanoma LMD, identify the tumor-promoting role of meningeal stroma, and demonstrate a mechanism for overcoming microenvironment-mediated drug resistance in LMD.
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Affiliation(s)
- Hasan Alhaddad
- Department of Metabolism and Physiology, Moffitt Cancer Center, Tampa, FL, USA
| | - Oscar E Ospina
- Department of Biostatistics and Bioinformatics at the Moffitt Cancer Center, Tampa, FL, USA
| | - Mariam Lotfy Khaled
- Department of Metabolism and Physiology, Moffitt Cancer Center, Tampa, FL, USA; Department of Biochemistry, Faculty of Pharmacy, Cairo University, Cairo, Egypt
| | - Yuan Ren
- Department of Metabolism and Physiology, Moffitt Cancer Center, Tampa, FL, USA
| | - Ethan Vallebuona
- Department of Metabolism and Physiology, Moffitt Cancer Center, Tampa, FL, USA; Cancer Biology Ph.D. Program, University of South Florida, Tampa, FL, USA
| | | | - Peter A Forsyth
- Department of Tumor Biology, Moffitt Cancer Center, Tampa, FL, USA; Department of NeuroOncology, Moffitt Cancer Center, Tampa, FL, USA
| | - Yolanda Pina
- Department of NeuroOncology, Moffitt Cancer Center, Tampa, FL, USA
| | - Robert Macaulay
- Department of Pathology, Moffitt Cancer Center, Tampa, FL, USA
| | - Vincent Law
- Department of Tumor Biology, Moffitt Cancer Center, Tampa, FL, USA; Department of NeuroOncology, Moffitt Cancer Center, Tampa, FL, USA
| | - Kenneth Y Tsai
- Department of Pathology, Moffitt Cancer Center, Tampa, FL, USA
| | - W Douglas Cress
- Department of Molecular Oncology at the Moffitt Cancer Center, Tampa, FL, USA
| | - Brooke Fridley
- Department of Biostatistics and Bioinformatics at the Moffitt Cancer Center, Tampa, FL, USA; Division of Health Services & Outcomes Research, Children's Mercy Hospital, Kansas City, MO 64108, USA.
| | - Inna Smalley
- Department of Metabolism and Physiology, Moffitt Cancer Center, Tampa, FL, USA; Department of Cutaneous Oncology at the Moffitt Cancer Center, Tampa, FL, USA.
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3
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Kraft T, Grützmann K, Meinhardt M, Meier F, Westphal D, Seifert M. Personalized identification and characterization of genome-wide gene expression differences between patient-matched intracranial and extracranial melanoma metastasis pairs. Acta Neuropathol Commun 2024; 12:67. [PMID: 38671536 PMCID: PMC11055243 DOI: 10.1186/s40478-024-01764-5] [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: 01/22/2024] [Accepted: 03/26/2024] [Indexed: 04/28/2024] Open
Abstract
Melanoma is the most serious type of skin cancer that frequently spreads to other organs of the human body. Especially melanoma metastases to the brain (intracranial metastases) are hard to treat and a major cause of death of melanoma patients. Little is known about molecular alterations and altered mechanisms that distinguish intra- from extracranial melanoma metastases. So far, almost all existing studies compared intracranial metastases from one set of patients to extracranial metastases of an another set of melanoma patients. This neglects the important facts that each melanoma is highly individual and that intra- and extracranial melanoma metastases from the same patient are more similar to each other than to melanoma metastases from other patients in the same organ. To overcome this, we compared the gene expression profiles of 16 intracranial metastases to their corresponding 21 patient-matched extracranial metastases in a personalized way using a three-state Hidden Markov Model (HMM) to identify altered genes for each individual metastasis pair. This enabled three major findings by considering the predicted gene expression alterations across all patients: (i) most frequently altered pathways include cytokine-receptor interaction, calcium signaling, ECM-receptor interaction, cAMP signaling, Jak-STAT and PI3K/Akt signaling, (ii) immune-relevant signaling pathway genes were downregulated in intracranial metastases, and (iii) intracranial metastases were associated with a brain-like phenotype gene expression program. Further, the integration of all differentially expressed genes across the patient-matched melanoma metastasis pairs led to a set of 103 genes that were consistently down- or up-regulated in at least 11 of the 16 of the patients. This set of genes contained many genes involved in the regulation of immune responses, cell growth, cellular signaling and transport processes. An analysis of these genes in the TCGA melanoma cohort showed that the expression behavior of 11 genes was significantly associated with survival. Moreover, a comparison of the 103 genes to three closely related melanoma metastasis studies revealed a core set of eight genes that were consistently down- or upregulated in intra- compared to extracranial metastases in at least two of the three related studies (down: CILP, DPT, FGF7, LAMP3, MEOX2, TMEM119; up: GLDN, PMP2) including FGF7 that was also significantly associated with survival. Our findings contribute to a better characterization of genes and pathways that distinguish intra- from extracranial melanoma metastasis and provide important hints for future experimental studies to identify potential targets for new therapeutic approaches.
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Affiliation(s)
- Theresa Kraft
- Institute for Medical Informatics and Biometry (IMB), Carl Gustav Carus Faculty of Medicine, Technische Universität Dresden, Fetscherstr. 74, 01307, Dresden, Germany
| | - Konrad Grützmann
- Institute for Medical Informatics and Biometry (IMB), Carl Gustav Carus Faculty of Medicine, Technische Universität Dresden, Fetscherstr. 74, 01307, Dresden, Germany
| | - Matthias Meinhardt
- Department of Pathology, Carl Gustav Carus Faculty of Medicine, Technische Universität Dresden, Fetscherstr. 74, 01307, Dresden, Germany
| | - Friedegund Meier
- Department of Dermatology, Faculty of Medicine and University Hospital Carl Gustav Carus, Technische Universität Dresden, Fetscherstr. 74, 01307, Dresden, Germany
- Skin Cancer Center at the University Cancer Center (UCC) Dresden and the National Center for Tumor Diseases Dresden (NCT), Fetscherstr. 74, 01307, Dresden, Germany
| | - Dana Westphal
- Department of Dermatology, Faculty of Medicine and University Hospital Carl Gustav Carus, Technische Universität Dresden, Fetscherstr. 74, 01307, Dresden, Germany
- National Center for Tumor Diseases Dresden (NCT), Fetscherstr. 74, 01307, Dresden, Germany
| | - Michael Seifert
- Institute for Medical Informatics and Biometry (IMB), Carl Gustav Carus Faculty of Medicine, Technische Universität Dresden, Fetscherstr. 74, 01307, Dresden, Germany.
- National Center for Tumor Diseases Dresden (NCT), Fetscherstr. 74, 01307, Dresden, Germany.
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Duan XP, Qin BD, Jiao XD, Liu K, Wang Z, Zang YS. New clinical trial design in precision medicine: discovery, development and direction. Signal Transduct Target Ther 2024; 9:57. [PMID: 38438349 PMCID: PMC10912713 DOI: 10.1038/s41392-024-01760-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2023] [Revised: 01/25/2024] [Accepted: 01/29/2024] [Indexed: 03/06/2024] Open
Abstract
In the era of precision medicine, it has been increasingly recognized that individuals with a certain disease are complex and different from each other. Due to the underestimation of the significant heterogeneity across participants in traditional "one-size-fits-all" trials, patient-centered trials that could provide optimal therapy customization to individuals with specific biomarkers were developed including the basket, umbrella, and platform trial designs under the master protocol framework. In recent years, the successive FDA approval of indications based on biomarker-guided master protocol designs has demonstrated that these new clinical trials are ushering in tremendous opportunities. Despite the rapid increase in the number of basket, umbrella, and platform trials, the current clinical and research understanding of these new trial designs, as compared with traditional trial designs, remains limited. The majority of the research focuses on methodologies, and there is a lack of in-depth insight concerning the underlying biological logic of these new clinical trial designs. Therefore, we provide this comprehensive review of the discovery and development of basket, umbrella, and platform trials and their underlying logic from the perspective of precision medicine. Meanwhile, we discuss future directions on the potential development of these new clinical design in view of the "Precision Pro", "Dynamic Precision", and "Intelligent Precision". This review would assist trial-related researchers to enhance the innovation and feasibility of clinical trial designs by expounding the underlying logic, which be essential to accelerate the progression of precision medicine.
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Affiliation(s)
- Xiao-Peng Duan
- Department of Medical Oncology, Changzheng Hospital, Naval Medical University, Shanghai, China
| | - Bao-Dong Qin
- Department of Medical Oncology, Changzheng Hospital, Naval Medical University, Shanghai, China
| | - Xiao-Dong Jiao
- Department of Medical Oncology, Changzheng Hospital, Naval Medical University, Shanghai, China
| | - Ke Liu
- Department of Medical Oncology, Changzheng Hospital, Naval Medical University, Shanghai, China
| | - Zhan Wang
- Department of Medical Oncology, Changzheng Hospital, Naval Medical University, Shanghai, China
| | - Yuan-Sheng Zang
- Department of Medical Oncology, Changzheng Hospital, Naval Medical University, Shanghai, China.
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Alhaddad H, Ospina OE, Khaled ML, Ren Y, Forsyth P, Pina Y, Macaulay R, Law V, Tsai KY, Cress WD, Fridley B, Smalley I. Spatial transcriptomics analysis identifies a unique tumor-promoting function of the meningeal stroma in melanoma leptomeningeal disease. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.12.18.572266. [PMID: 38187574 PMCID: PMC10769278 DOI: 10.1101/2023.12.18.572266] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/09/2024]
Abstract
Leptomeningeal disease (LMD) remains a rapidly lethal complication for late-stage melanoma patients. The inaccessible nature of the disease site and lack of understanding of the biology of this unique metastatic site are major barriers to developing efficacious therapies for patients with melanoma LMD. Here, we characterize the tumor microenvironment of the leptomeningeal tissues and patient-matched extra-cranial metastatic sites using spatial transcriptomic analyses with in vitro and in vivo validation. We show the spatial landscape of melanoma LMD to be characterized by a lack of immune infiltration and instead exhibit a higher level of stromal involvement. We show that the tumor-stroma interactions at the leptomeninges activate pathways implicated in tumor-promoting signaling, mediated through upregulation of SERPINA3 at the tumor-stroma interface. Our functional experiments establish that the meningeal stroma is required for melanoma cells to survive in the CSF environment and that these interactions lead to a lack of MAPK inhibitor sensitivity in the tumor. We show that knocking down SERPINA3 or inhibiting the downstream IGR1R/PI3K/AKT axis results in re-sensitization of the tumor to MAPK-targeting therapy and tumor cell death in the leptomeningeal environment. Our data provides a spatial atlas of melanoma LMD, identifies the tumor-promoting role of meningeal stroma, and demonstrates a mechanism for overcoming microenvironment-mediated drug resistance unique to this metastatic site.
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Affiliation(s)
- Hasan Alhaddad
- Department of Metabolism and Physiology at the Moffitt Cancer Center, Tampa, Florida, USA
| | - Oscar E. Ospina
- Department of Biostatistics and Bioinformatics at the Moffitt Cancer Center, Tampa, Florida, USA
| | - Mariam Lotfy Khaled
- Department of Metabolism and Physiology at the Moffitt Cancer Center, Tampa, Florida, USA
- Department of Biochemistry, Faculty of Pharmacy, Cairo University, Egypt
| | - Yuan Ren
- Department of Metabolism and Physiology at the Moffitt Cancer Center, Tampa, Florida, USA
| | - Peter Forsyth
- Department of Tumor Biology at the Moffitt Cancer Center, Tampa, Florida, USA
- Department of NeuroOncology at the Moffitt Cancer Center, Tampa, Florida, USA
| | - Yolanda Pina
- Department of NeuroOncology at the Moffitt Cancer Center, Tampa, Florida, USA
| | - Robert Macaulay
- Department of Pathology at the Moffitt Cancer Center, Tampa, Florida, USA
| | - Vincent Law
- Department of Tumor Biology at the Moffitt Cancer Center, Tampa, Florida, USA
- Department of NeuroOncology at the Moffitt Cancer Center, Tampa, Florida, USA
| | - Kenneth Y. Tsai
- Department of Pathology at the Moffitt Cancer Center, Tampa, Florida, USA
| | - W Douglas Cress
- Department of Molecular Oncology at the Moffitt Cancer Center, Tampa, Florida, USA
| | - Brooke Fridley
- Department of Biostatistics and Bioinformatics at the Moffitt Cancer Center, Tampa, Florida, USA
- Division of Health Services & Outcomes Research, Children’s Mercy Hospital, Kansas City, MO 64108
| | - Inna Smalley
- Department of Metabolism and Physiology at the Moffitt Cancer Center, Tampa, Florida, USA
- Department of Cutaneous Oncology at the Moffitt Cancer Center, Tampa, Florida, USA
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6
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Phadke MS, Li J, Chen Z, Rodriguez PC, Mandula JK, Karapetyan L, Forsyth PA, Chen YA, Smalley KSM. Differential requirements for CD4+ T cells in the efficacy of the anti-PD-1+LAG-3 and anti-PD-1+CTLA-4 combinations in melanoma flank and brain metastasis models. J Immunother Cancer 2023; 11:e007239. [PMID: 38056899 PMCID: PMC10711842 DOI: 10.1136/jitc-2023-007239] [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] [Accepted: 10/31/2023] [Indexed: 12/08/2023] Open
Abstract
BACKGROUND Although the anti-PD-1+LAG-3 and the anti-PD-1+CTLA-4 combinations are effective in advanced melanoma, it remains unclear whether their mechanisms of action overlap. METHODS We used single cell (sc) RNA-seq, flow cytometry and IHC analysis of responding SM1, D4M-UV2 and B16 melanoma flank tumors and SM1 brain metastases to explore the mechanism of action of the anti-PD-1+LAG-3 and the anti-PD-1+CTLA-4 combination. CD4+ and CD8+ T cell depletion, tetramer binding assays and ELISPOT assays were used to demonstrate the unique role of CD4+T cell help in the antitumor effects of the anti-PD-1+LAG-3 combination. RESULTS The anti-PD-1+CTLA-4 combination was associated with the infiltration of FOXP3+regulatory CD4+ cells (Tregs), fewer activated CD4+T cells and the accumulation of a subset of IFNγ secreting cytotoxic CD8+T cells, whereas the anti-PD-1+LAG-3 combination led to the accumulation of CD4+T helper cells that expressed CXCR4, TNFSF8, IL21R and a subset of CD8+T cells with reduced expression of cytotoxic markers. T cell depletion studies showed a requirement for CD4+T cells for the anti-PD-1+LAG-3 combination, but not the PD-1-CTLA-4 combination at both flank and brain tumor sites. In anti-PD-1+LAG-3 treated tumors, CD4+T cell depletion was associated with fewer activated (CD69+) CD8+T cells and impaired IFNγ release but, conversely, increased numbers of activated CD8+T cells and IFNγ release in anti-PD-1+CTLA-4 treated tumors. CONCLUSIONS Together these studies suggest that these two clinically relevant immune checkpoint inhibitor (ICI) combinations have differential effects on CD4+T cell polarization, which in turn, impacted cytotoxic CD8+T cell function. Further insights into the mechanisms of action/resistance of these clinically-relevant ICI combinations will allow therapy to be further personalized.
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Affiliation(s)
- Manali S Phadke
- Department of Tumor Biology, Moffitt Cancer Center and Research Institute, Tampa, FL, USA
| | - Jiannong Li
- Department of Bioinformatics and Biostatistics, Moffitt Cancer Cancer Center and Research Institute, Tampa, FL, USA
| | - Zhihua Chen
- Department of Bioinformatics and Biostatistics, Moffitt Cancer Cancer Center and Research Institute, Tampa, FL, USA
| | - Paulo C Rodriguez
- Department of Immunology, Moffitt Cancer Center and Research Institute, Tampa, FL, USA
| | - Jessica K Mandula
- Department of Immunology, Moffitt Cancer Center and Research Institute, Tampa, FL, USA
| | - Lilit Karapetyan
- Department of Cutaneous Oncology, Moffitt Cancer Center and Research Institute, Tampa, FL, USA
| | - Peter A Forsyth
- Department of Neurooncology, Moffitt Cancer Center and Research Institute, Tampa, FL, USA
| | - Y Ann Chen
- Department of Bioinformatics and Biostatistics, Moffitt Cancer Cancer Center and Research Institute, Tampa, FL, USA
| | - Keiran S M Smalley
- Department of Tumor Biology, Moffitt Cancer Center and Research Institute, Tampa, FL, USA
- Department of Cutaneous Oncology, Moffitt Cancer Center and Research Institute, Tampa, FL, USA
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Kichina JV, Maslov A, Kandel ES. PAK1 and Therapy Resistance in Melanoma. Cells 2023; 12:2373. [PMID: 37830586 PMCID: PMC10572217 DOI: 10.3390/cells12192373] [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: 08/18/2023] [Revised: 09/23/2023] [Accepted: 09/27/2023] [Indexed: 10/14/2023] Open
Abstract
Malignant melanoma claims more lives than any other skin malignancy. While primary melanomas are usually cured via surgical excision, the metastatic form of the disease portents a poor prognosis. Decades of intense research has yielded an extensive armamentarium of anti-melanoma therapies, ranging from genotoxic chemo- and radiotherapies to targeted interventions in specific signaling pathways and immune functions. Unfortunately, even the most up-to-date embodiments of these therapies are not curative for the majority of metastatic melanoma patients, and the need to improve their efficacy is widely recognized. Here, we review the reports that implicate p21-regulated kinase 1 (PAK1) and PAK1-related pathways in the response of melanoma to various therapeutic modalities. Ample data suggest that PAK1 may decrease cell sensitivity to programmed cell death, provide additional stimulation to growth-promoting molecular pathways, and contribute to the creation of an immunosuppressive tumor microenvironment. Accordingly, there is mounting evidence that the concomitant inhibition of PAK1 enhances the potency of various anti-melanoma regimens. Overall, the available information suggests that a safe and effective inhibition of PAK1-dependent molecular processes would enhance the potency of the currently available anti-melanoma treatments, although considerable challenges in implementing such strategies still exist.
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Affiliation(s)
- Julia V. Kichina
- Department of Immunology, Roswell Park Comprehensive Cancer Center, Elm & Carlton St., Buffalo, NY 14263, USA
| | - Alexei Maslov
- Department of Cell Stress Biology, Roswell Park Comprehensive Cancer Center, Elm & Carlton St., Buffalo, NY 14263, USA
| | - Eugene S. Kandel
- Department of Cell Stress Biology, Roswell Park Comprehensive Cancer Center, Elm & Carlton St., Buffalo, NY 14263, USA
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8
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Phadke MS, Smalley KS. Targeting NRAS Mutations in Advanced Melanoma. J Clin Oncol 2023; 41:2661-2664. [PMID: 36947724 PMCID: PMC10414701 DOI: 10.1200/jco.23.00205] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2023] [Revised: 02/14/2023] [Accepted: 02/17/2023] [Indexed: 03/24/2023] Open
Affiliation(s)
- Manali S. Phadke
- Department of Tumor Biology, Moffitt Cancer Center & Research Institute, Tampa, FL
| | - Keiran S.M. Smalley
- Department of Tumor Biology, Moffitt Cancer Center & Research Institute, Tampa, FL
- Department of Cutaneous Oncology, Moffitt Cancer Center & Research Institute, Tampa, FL
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Hänggi K, Ruffell B. Cell death, therapeutics, and the immune response in cancer. Trends Cancer 2023; 9:381-396. [PMID: 36841748 PMCID: PMC10121860 DOI: 10.1016/j.trecan.2023.02.001] [Citation(s) in RCA: 44] [Impact Index Per Article: 44.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2022] [Revised: 01/19/2023] [Accepted: 02/03/2023] [Indexed: 02/27/2023]
Abstract
Induction of cell death is inexorably linked with cancer therapy, but this can also initiate wound-healing processes that have been linked to cancer progression and therapeutic resistance. Here we describe the contribution of apoptosis and the lytic cell death pathways in the response to therapy (including chemotherapy and immunotherapy). We also discuss how necroptosis, pyroptosis, and ferroptosis function to promote tumor immunogenicity, along with emerging findings that these same forms of death can paradoxically contribute to immune suppression and tumor progression. Understanding the duality of cell death in cancer may allow for the development of therapeutics that shift the balance towards regression.
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Affiliation(s)
- Kay Hänggi
- Department of Immunology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL, USA
| | - Brian Ruffell
- Department of Immunology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL, USA; Department of Breast Oncology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL, USA.
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10
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Patient-specific identification of genome-wide DNA-methylation differences between intracranial and extracranial melanoma metastases. Sci Rep 2023; 13:444. [PMID: 36624125 PMCID: PMC9829750 DOI: 10.1038/s41598-022-24940-w] [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: 07/14/2022] [Accepted: 11/22/2022] [Indexed: 01/11/2023] Open
Abstract
Melanomas frequently metastasize to distant organs and especially intracranial metastases still represent a major clinical challenge. Epigenetic reprogramming of intracranial metastases is thought to be involved in therapy failure, but so far only little is known about patient-specific DNA-methylation differences between intra- and extracranial melanoma metastases. Hierarchical clustering of the methylomes of 24 patient-matched intra- and extracranial melanoma metastases pairs revealed that intra- and extracranial metastases of individual patients were more similar to each other than to metastases in the same tissue from other patients. Therefore, a personalized analysis of each metastases pair was done by a Hidden Markov Model to classify methylation levels of individual CpGs as decreased, unchanged or increased in the intra- compared to the extracranial metastasis. The predicted DNA-methylation alterations were highly patient-specific differing in the number and methylation states of altered CpGs. Nevertheless, four important general observations were made: (i) intracranial metastases of most patients mainly showed a reduction of DNA-methylation, (ii) cytokine signaling was most frequently affected by differential methylation in individual metastases pairs, but also MAPK, PI3K/Akt and ECM signaling were often altered, (iii) frequently affected genes were mainly involved in signaling, growth, adhesion or apoptosis, and (iv) an enrichment of functional terms related to channel and transporter activities supports previous findings for a brain-like phenotype. In addition, the derived set of 17 signaling pathway genes that distinguished intra- from extracranial metastases in more than 50% of patients included well-known oncogenes (e.g. PRKCA, DUSP6, BMP4) and several other genes known from neuronal disorders (e.g. EIF4B, SGK1, CACNG8). Moreover, associations of gene body methylation alterations with corresponding gene expression changes revealed that especially the three signaling pathway genes JAK3, MECOM, and TNXB differ strongly in their expression between patient-matched intra- and extracranial metastases. Our analysis contributes to an in-depth characterization of DNA-methylation differences between patient-matched intra- and extracranial melanoma metastases and may provide a basis for future experimental studies to identify targets for new therapeutic approaches.
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Thompson ZJ, Teer JK, Li J, Chen Z, Welsh EA, Zhang Y, Ayoubi N, Eroglu Z, Tan AC, Smalley KSM, Chen YA. Drepmel-A Multi-Omics Melanoma Drug Repurposing Resource for Prioritizing Drug Combinations and Understanding Tumor Microenvironment. Cells 2022; 11:cells11182894. [PMID: 36139469 PMCID: PMC9497118 DOI: 10.3390/cells11182894] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2022] [Revised: 09/08/2022] [Accepted: 09/13/2022] [Indexed: 11/22/2022] Open
Abstract
Although substantial progress has been made in treating patients with advanced melanoma with targeted and immuno-therapies, de novo and acquired resistance is commonplace. After treatment failure, therapeutic options are very limited and novel strategies are urgently needed. Combination therapies are often more effective than single agents and are now widely used in clinical practice. Thus, there is a strong need for a comprehensive computational resource to define rational combination therapies. We developed a Shiny app, DRepMel to provide rational combination treatment predictions for melanoma patients from seventy-three thousand combinations based on a multi-omics drug repurposing computational approach using whole exome sequencing and RNA-seq data in bulk samples from two independent patient cohorts. DRepMel provides robust predictions as a resource and also identifies potential treatment effects on the tumor microenvironment (TME) using single-cell RNA-seq data from melanoma patients. Availability: DRepMel is accessible online.
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Affiliation(s)
- Zachary J. Thompson
- Biostatistics and Bioinformatics Shared Resource, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL 33612, USA
| | - Jamie K. Teer
- Department of Biostatistics and Bioinformatics, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL 33612, USA
| | - Jiannong Li
- Biostatistics and Bioinformatics Shared Resource, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL 33612, USA
| | - Zhihua Chen
- Biostatistics and Bioinformatics Shared Resource, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL 33612, USA
| | - Eric A. Welsh
- Biostatistics and Bioinformatics Shared Resource, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL 33612, USA
| | - Yonghong Zhang
- Biostatistics and Bioinformatics Shared Resource, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL 33612, USA
| | - Noura Ayoubi
- Department of Dermatology and Cutaneous Surgery, University of South Florida, Tampa, FL 33612, USA
| | - Zeynep Eroglu
- Department of Cutaneous Oncology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL 33612, USA
| | - Aik Choon Tan
- Department of Biostatistics and Bioinformatics, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL 33612, USA
| | - Keiran S. M. Smalley
- Department of Tumor Biology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL 33612, USA
| | - Yian Ann Chen
- Department of Biostatistics and Bioinformatics, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL 33612, USA
- Correspondence:
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12
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Zhang Z, Richmond A, Yan C. Immunomodulatory Properties of PI3K/AKT/mTOR and MAPK/MEK/ERK Inhibition Augment Response to Immune Checkpoint Blockade in Melanoma and Triple-Negative Breast Cancer. Int J Mol Sci 2022; 23:ijms23137353. [PMID: 35806358 PMCID: PMC9266842 DOI: 10.3390/ijms23137353] [Citation(s) in RCA: 24] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2022] [Revised: 06/28/2022] [Accepted: 06/28/2022] [Indexed: 02/03/2023] Open
Abstract
Hyperactivation of PI3K/AKT/mTOR and MAPK/MEK/ERK signaling pathways is commonly observed in many cancers, including triple-negative breast cancer (TNBC) and melanoma. Moreover, the compensatory upregulation of the MAPK/MEK/ERK pathway has been associated with therapeutic resistance to targeted inhibition of the PI3K/AKT/mTOR pathway, and vice versa. The immune-modulatory effects of both PI3K and MAPK inhibition suggest that inhibition of these pathways might enhance response to immune checkpoint inhibitors (ICIs). ICIs have become the standard-of-care for metastatic melanoma and are recently an option for TNBC when combined with chemotherapy, but alternative options are needed when resistance develops. In this review, we present the current mechanistic understandings, along with preclinical and clinical evidence, that outline the efficacy and safety profile of combinatorial or sequential treatments with PI3K inhibitors, MAPK inhibitors, and ICIs for treatment of malignant melanoma and metastatic TNBC. This approach may present a potential strategy to overcome resistance in patients who are a candidate for ICI therapy with tumors harboring either or both of these pathway-associated mutations.
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Affiliation(s)
- Zhizhu Zhang
- Department of Veterans Affairs, Tennessee Valley Healthcare System, Nashville, TN 37212, USA; (Z.Z.); (A.R.)
- Department of Pharmacology, Vanderbilt University School of Medicine, Nashville, TN 37240, USA
| | - Ann Richmond
- Department of Veterans Affairs, Tennessee Valley Healthcare System, Nashville, TN 37212, USA; (Z.Z.); (A.R.)
- Department of Pharmacology, Vanderbilt University School of Medicine, Nashville, TN 37240, USA
| | - Chi Yan
- Department of Veterans Affairs, Tennessee Valley Healthcare System, Nashville, TN 37212, USA; (Z.Z.); (A.R.)
- Department of Pharmacology, Vanderbilt University School of Medicine, Nashville, TN 37240, USA
- Correspondence:
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13
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Alvarez-Breckenridge C, Remon J, Piña Y, Nieblas-Bedolla E, Forsyth P, Hendriks L, Brastianos PK. Emerging Systemic Treatment Perspectives on Brain Metastases: Moving Toward a Better Outlook for Patients. Am Soc Clin Oncol Educ Book 2022; 42:1-19. [PMID: 35522917 DOI: 10.1200/edbk_352320] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
The diagnosis of brain metastases has historically been a dreaded, end-stage complication of systemic disease. Additionally, with the increasing effectiveness of systemic therapies that prolong life expectancy and improved imaging tools, the incidence of intracranial progression is becoming more common. Within this context, there has been increasing attention directed at understanding the molecular underpinnings of intracranial progression. Exploring the unique features of brain metastases compared with their extracranial counterparts to identify aberrant signaling pathways, which can be targeted pharmacologically, may help lead to new treatments for this patient population. Additionally, critical discoveries outside the sphere of the central nervous system are increasingly being applied to brain metastases with the emergence of immune checkpoint inhibition, becoming a prevalent treatment option for patients with brain metastases across multiple histologies. As novel treatment strategies are considered, they require thoughtful incorporation of agents that can cross the blood-brain barrier and can synergize with pre-existing agents through rational combinations. Lastly, as clinicians and scientists continue to understand key molecular features of these tumors, they will continue to influence the treatment algorithms that are developing for the management of these patients. Due to the complexity of treatment decisions for patients with brain metastases, an emerging tool is the utilization of multidisciplinary brain metastasis tumor boards to ensure optimal treatment decisions are made and that patients are provided access to applicable clinical trials. Looking to the future, the collective effort to understand the various tumor-intrinsic and tumor-extrinsic factors that promote central nervous system seeding and propagation will have the potential to change the clinical trajectory for these patients.
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Affiliation(s)
| | - Jordi Remon
- Department of Medical Oncology, HM CIOCC Barcelona (Centro Integral Oncológico Clara Campal), Hospital HM Delfos, HM Hospitales, Barcelona, Spain
| | - Yolanda Piña
- Department of Neuro-Oncology, H. Lee Moffitt Cancer Center and Research Institute, University of South Florida, Tampa, FL
| | | | - Peter Forsyth
- Department of Neuro-Oncology, H. Lee Moffitt Cancer Center and Research Institute, University of South Florida, Tampa, FL
| | - Lizza Hendriks
- Department of Pulmonary Diseases - GROW School for Oncology and Reproduction, Maastricht University Medical Center, Maastricht, Netherlands
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14
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Barreno A, Orgaz JL. Cytoskeletal Remodelling as an Achilles’ Heel for Therapy Resistance in Melanoma. Cells 2022; 11:cells11030518. [PMID: 35159327 PMCID: PMC8834185 DOI: 10.3390/cells11030518] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2021] [Revised: 01/28/2022] [Accepted: 01/30/2022] [Indexed: 12/10/2022] Open
Abstract
Melanoma is an aggressive skin cancer with a poor prognosis when diagnosed late. MAPK-targeted therapies and immune checkpoint blockers benefit a subset of melanoma patients; however, acquired therapy resistance inevitably arises within a year. In addition, some patients display intrinsic (primary) resistance and never respond to therapy. There is mounting evidence that resistant cells adapt to therapy through the rewiring of cytoskeleton regulators, leading to a profound remodelling of the actomyosin cytoskeleton. Importantly, this renders therapy-resistant cells highly dependent on cytoskeletal signalling pathways for sustaining their survival under drug pressure, which becomes a vulnerability that can be exploited therapeutically. Here, we discuss the current knowledge on cytoskeletal pathways involved in mainly targeted therapy resistance and future avenues, as well as potential clinical interventions.
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15
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Roma S, Carpen L, Raveane A, Bertolini F. The Dual Role of Innate Lymphoid and Natural Killer Cells in Cancer. from Phenotype to Single-Cell Transcriptomics, Functions and Clinical Uses. Cancers (Basel) 2021; 13:cancers13205042. [PMID: 34680190 PMCID: PMC8533946 DOI: 10.3390/cancers13205042] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2021] [Revised: 10/05/2021] [Accepted: 10/06/2021] [Indexed: 02/07/2023] Open
Abstract
Simple Summary Innate lymphoid cells (ILCs), a family of innate immune cells including natural killers (NKs), play a multitude of roles in first-line cancer control, in escape from immunity and in cancer progression. In this review, we summarize preclinical and clinical data on ILCs and NK cells concerning their phenotype, function and clinical applications in cellular therapy trials. We also describe how single-cell transcriptome sequencing has been used and forecast how it will be used to better understand ILC and NK involvement in cancer control and progression as well as their therapeutic potential. Abstract The role of innate lymphoid cells (ILCs), including natural killer (NK) cells, is pivotal in inflammatory modulation and cancer. Natural killer cell activity and count have been demonstrated to be regulated by the expression of activating and inhibitory receptors together with and as a consequence of different stimuli. The great majority of NK cell populations have an anti-tumor activity due to their cytotoxicity, and for this reason have been used for cellular therapies in cancer patients. On the other hand, the recently classified helper ILCs are fundamentally involved in inflammation and they can be either helpful or harmful in cancer development and progression. Tissue niche seems to play an important role in modulating ILC function and conversion, as observed at the transcriptional level. In the past, these cell populations have been classified by the presence of specific cellular receptor markers; more recently, due to the advent of single-cell RNA sequencing (scRNA-seq), it has been possible to also explore them at the transcriptomic level. In this article we review studies on ILC (and NK cell) classification, function and their involvement in cancer. We also summarize the potential application of NK cells in cancer therapy and give an overview of the most recent studies involving ILCs and NKs at scRNA-seq, focusing on cancer. Finally, we provide a resource for those who wish to start single-cell transcriptomic analysis on the context of these innate lymphoid cell populations.
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16
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Smalley I, Chen Z, Phadke M, Li J, Yu X, Wyatt C, Evernden B, Messina JL, Sarnaik A, Sondak VK, Zhang C, Law V, Tran N, Etame A, Macaulay RJB, Eroglu Z, Forsyth PA, Rodriguez PC, Chen YA, Smalley KSM. Single-Cell Characterization of the Immune Microenvironment of Melanoma Brain and Leptomeningeal Metastases. Clin Cancer Res 2021; 27:4109-4125. [PMID: 34035069 DOI: 10.1158/1078-0432.ccr-21-1694] [Citation(s) in RCA: 62] [Impact Index Per Article: 20.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2021] [Revised: 05/13/2021] [Accepted: 05/19/2021] [Indexed: 12/14/2022]
Abstract
PURPOSE Melanoma brain metastases (MBM) and leptomeningeal melanoma metastases (LMM) are two different manifestations of melanoma CNS metastasis. Here, we used single-cell RNA sequencing (scRNA-seq) to define the immune landscape of MBM, LMM, and melanoma skin metastases. EXPERIMENTAL DESIGN scRNA-seq was undertaken on 43 patient specimens, including 8 skin metastases, 14 MBM, and 19 serial LMM specimens. Detailed cell type curation was performed, the immune landscapes were mapped, and key results were validated by IHC and flow cytometry. Association analyses were undertaken to identify immune cell subsets correlated with overall survival. RESULTS The LMM microenvironment was characterized by an immune-suppressed T-cell landscape distinct from that of brain and skin metastases. An LMM patient with long-term survival demonstrated an immune repertoire distinct from that of poor survivors and more similar to normal cerebrospinal fluid (CSF). Upon response to PD-1 therapy, this extreme responder showed increased levels of T cells and dendritic cells in their CSF, whereas poor survivors showed little improvement in their T-cell responses. In MBM patients, therapy led to increased immune infiltrate, with similar T-cell transcriptional diversity noted between skin metastases and MBM. A correlation analysis across the entire immune landscape identified the presence of a rare population of dendritic cells (DC3) that was associated with increased overall survival and positively regulated the immune environment through modulation of activated T cells and MHC expression. CONCLUSIONS Our study provides the first atlas of two distinct sites of melanoma CNS metastases and defines the immune cell landscape that underlies the biology of this devastating disease.
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Affiliation(s)
- Inna Smalley
- The Department of Tumor Biology, The Moffitt Cancer Center and Research Institute, Tampa, Florida.
| | - Zhihua Chen
- Department of Bioinformatics and Biostatistics, The Moffitt Cancer Center and Research Institute, Tampa, Florida
| | - Manali Phadke
- The Department of Tumor Biology, The Moffitt Cancer Center and Research Institute, Tampa, Florida
| | - Jiannong Li
- Department of Bioinformatics and Biostatistics, The Moffitt Cancer Center and Research Institute, Tampa, Florida
| | - Xiaoqing Yu
- Department of Bioinformatics and Biostatistics, The Moffitt Cancer Center and Research Institute, Tampa, Florida
| | - Clayton Wyatt
- The Department of Tumor Biology, The Moffitt Cancer Center and Research Institute, Tampa, Florida
| | - Brittany Evernden
- Department of Neurooncology, The Moffitt Cancer Center and Research Institute, Tampa, Florida
| | - Jane L Messina
- Department of Cutaneous Oncology, The Moffitt Cancer Center and Research Institute, Tampa, Florida.,Department of Pathology, The Moffitt Cancer Center and Research Institute, Tampa, Florida
| | - Amod Sarnaik
- Department of Cutaneous Oncology, The Moffitt Cancer Center and Research Institute, Tampa, Florida
| | - Vernon K Sondak
- Department of Cutaneous Oncology, The Moffitt Cancer Center and Research Institute, Tampa, Florida
| | - Chaomei Zhang
- Molecular Genomics Core, The Moffitt Cancer Center and Research Institute, Tampa, Florida
| | - Vincent Law
- Department of Neurooncology, The Moffitt Cancer Center and Research Institute, Tampa, Florida
| | - Nam Tran
- Department of Neurooncology, The Moffitt Cancer Center and Research Institute, Tampa, Florida
| | - Arnold Etame
- Department of Neurooncology, The Moffitt Cancer Center and Research Institute, Tampa, Florida
| | - Robert J B Macaulay
- Department of Neurooncology, The Moffitt Cancer Center and Research Institute, Tampa, Florida.,Department of Pathology, The Moffitt Cancer Center and Research Institute, Tampa, Florida
| | - Zeynep Eroglu
- Department of Cutaneous Oncology, The Moffitt Cancer Center and Research Institute, Tampa, Florida
| | - Peter A Forsyth
- Department of Neurooncology, The Moffitt Cancer Center and Research Institute, Tampa, Florida
| | - Paulo C Rodriguez
- Department of Immunology, The Moffitt Cancer Center and Research Institute, Tampa, Florida
| | - Y Ann Chen
- Department of Bioinformatics and Biostatistics, The Moffitt Cancer Center and Research Institute, Tampa, Florida.
| | - Keiran S M Smalley
- The Department of Tumor Biology, The Moffitt Cancer Center and Research Institute, Tampa, Florida. .,Department of Cutaneous Oncology, The Moffitt Cancer Center and Research Institute, Tampa, Florida
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