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Arend RC, Scalise CB, Gordon ER, Davis AM, Foxall ME, Johnston BE, Crossman DK, Cooper SJ. Metabolic alterations and WNT signaling impact immune response in HGSOC. Clin Cancer Res 2022; 28:1433-1445. [PMID: 35031546 DOI: 10.1158/1078-0432.ccr-21-2984] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2021] [Revised: 11/24/2021] [Accepted: 01/12/2022] [Indexed: 11/16/2022]
Abstract
PURPOSE Our study used transcriptomic and metabolomic strategies to determine the molecular profiles of HGSOC patient samples derived from primary tumor and ascites cells. These data identified clinically relevant heterogeneity among and within patients and highlighted global and patient-specific cellular responses to neoadjuvant chemotherapy (NACT). EXPERIMENTAL DESIGN Tissue from 61 treatment naïve patients with HGSOC were collected. In addition, 11 benign, 32 ascites, and 18 post-NACT samples (matched to the individual patient's pre-NACT sample) were collected. RNA-sequencing (RNA-seq) was performed on all samples collected. Two-dimensional spatial proteomic data was collected for two pairs of pre-and post-NACT. Untargeted metabolomics data using GCxGC-MS was generated for 30 treatment-naive tissues. Consensus clustering, analysis of differential expression, pathway enrichment, and survival analyses were performed. RESULTS Treatment-naïve HGSOC tissues had distinct transcriptomic and metabolomic profiles. The mesenchymal subtype harbored a metabolomic profile distinct from the other subtypes. Compared to primary tumor tissue, ascites showed significant changes in immune response and signaling pathways. NACT caused significant alterations in gene expression and WNT activity, and this corresponded to altered immune response. Overall, WNT signaling levels were inversely correlated with immune cell infiltration in HGSOC tissues and WNT signaling post-NACT was inversely correlated with progression-free survival. CONCLUSIONS Our study concluded that HGSOC is a heterogenous disease at baseline and growing molecular differences can be observed between primary tumor and ascites cells or within tumors in response to treatment. Our data reveal potential exploratory biomarkers relevant for treatment selection and predicting patient outcomes that warrant further research.
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Affiliation(s)
- Rebecca C Arend
- Obstetrics and Gynecology, University of Alabama at Birmingham
| | | | | | - Allison M Davis
- Obstetrics and Gynecology, University of Alabama at Birmingham
| | | | | | | | - Sara J Cooper
- S. Cooper Lab, HudsonAlpha Institute for Biotechnology
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Molecular characteristics and clinical outcomes of patients with Neurofibromin 1-altered metastatic colorectal cancer. Oncogene 2022; 41:260-267. [PMID: 34728807 PMCID: PMC8738154 DOI: 10.1038/s41388-021-02074-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2021] [Revised: 10/01/2021] [Accepted: 10/08/2021] [Indexed: 12/14/2022]
Abstract
Loss-of-function alterations of Neurofibromin 1 (NF1) activate RAS, a driver of colorectal cancer. However, the clinical implications of NF1 alterations are largely unknown. We performed a comprehensive molecular profiling of NF1-mutant colorectal cancer using data from 8150 patients included in a dataset of commercial CLIA-certified laboratory (Caris Life Sciences). In addition, NF1 expression levels were tested for associations with clinical outcomes using data from 431 patients in the CALGB/SWOG 80405 trial. In the Caris dataset, 2.2% of patients had pathogenic or presumed pathogenic NF1 mutations. NF1-mutant tumors more frequently harbored PIK3CA (25.0% vs. 16.7%) and PTEN mutations (24.0% vs. 4.2%) than wild type tumors. Gene set enrichment analysis revealed that MAPK and PI3K pathway signatures were enriched in NF1-mutant tumors. In the CALGB/SWOG 80405 cohort, low NF1 expression was associated with poor prognosis, and high NF1 expression was associated with better efficacy of cetuximab than bevacizumab. Together, we revealed concurrent genetic alterations in the PI3K pathways in NF1-mutant tumors, suggesting the need to simultaneously block MAPK and PI3K pathways in treatment. The potential of NF1 alteration as a novel biomarker for targeted therapy was highlighted, warranting further investigations in clinical settings.
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Chang MT, Shanahan F, Nguyen TTT, Staben ST, Gazzard L, Yamazoe S, Wertz IE, Piskol R, Yang YA, Modrusan Z, Haley B, Evangelista M, Malek S, Foster SA, Ye X. Identifying transcriptional programs underlying cancer drug response with TraCe-seq. Nat Biotechnol 2022; 40:86-93. [PMID: 34531539 DOI: 10.1038/s41587-021-01005-3] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2020] [Accepted: 07/07/2021] [Indexed: 02/07/2023]
Abstract
Genetic and non-genetic heterogeneity within cancer cell populations represent major challenges to anticancer therapies. We currently lack robust methods to determine how preexisting and adaptive features affect cellular responses to therapies. Here, by conducting clonal fitness mapping and transcriptional characterization using expressed barcodes and single-cell RNA sequencing (scRNA-seq), we have developed tracking differential clonal response by scRNA-seq (TraCe-seq). TraCe-seq is a method that captures at clonal resolution the origin, fate and differential early adaptive transcriptional programs of cells in a complex population in response to distinct treatments. We used TraCe-seq to benchmark how next-generation dual epidermal growth factor receptor (EGFR) inhibitor-degraders compare to standard EGFR kinase inhibitors in EGFR-mutant lung cancer cells. We identified a loss of antigrowth activity associated with targeted degradation of EGFR protein and an essential role of the endoplasmic reticulum (ER) protein processing pathway in anti-EGFR therapeutic efficacy. Our results suggest that targeted degradation is not always superior to enzymatic inhibition and establish TraCe-seq as an approach to study how preexisting transcriptional programs affect treatment responses.
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Affiliation(s)
- Matthew T Chang
- Department of Computational Biology and Bioinformatics, Genentech Inc., South San Francisco, CA, USA
- Department of Discovery Oncology, Genentech Inc., South San Francisco, CA, USA
| | - Frances Shanahan
- Department of Discovery Oncology, Genentech Inc., South San Francisco, CA, USA
| | - Thi Thu Thao Nguyen
- Department of Computational Biology and Bioinformatics, Genentech Inc., South San Francisco, CA, USA
| | - Steven T Staben
- Department of Discovery Chemistry, Genentech Inc., South San Francisco, CA, USA
| | - Lewis Gazzard
- Department of Discovery Chemistry, Genentech Inc., South San Francisco, CA, USA
| | - Sayumi Yamazoe
- Department of Discovery Chemistry, Genentech Inc., South San Francisco, CA, USA
- Discovery Biotherapeutics, Bristol-Myers Squibb, Redwood City, CA, USA
| | - Ingrid E Wertz
- Department of Discovery Oncology, Genentech Inc., South San Francisco, CA, USA
- Department of Early Discovery Biochemistry, Genentech Inc., South San Francisco, CA, USA
| | - Robert Piskol
- Department of Computational Biology and Bioinformatics, Genentech Inc., South San Francisco, CA, USA
| | - Yeqing Angela Yang
- Department of Microchemistry, Proteomics and Lipidomics, Genentech Inc., South San Francisco, CA, USA
| | - Zora Modrusan
- Department of Microchemistry, Proteomics and Lipidomics, Genentech Inc., South San Francisco, CA, USA
| | - Benjamin Haley
- Department of Molecular Biology, Genentech Inc., South San Francisco, CA, USA
| | - Marie Evangelista
- Department of Discovery Oncology, Genentech Inc., South San Francisco, CA, USA
| | - Shiva Malek
- Department of Discovery Oncology, Genentech Inc., South San Francisco, CA, USA
| | - Scott A Foster
- Department of Discovery Oncology, Genentech Inc., South San Francisco, CA, USA.
| | - Xin Ye
- Department of Discovery Oncology, Genentech Inc., South San Francisco, CA, USA.
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Skok K, Gradišnik L, Čelešnik H, Milojević M, Potočnik U, Jezernik G, Gorenjak M, Sobočan M, Takač I, Kavalar R, Maver U. MFUM-BrTNBC-1, a Newly Established Patient-Derived Triple-Negative Breast Cancer Cell Line: Molecular Characterisation, Genetic Stability, and Comprehensive Comparison with Commercial Breast Cancer Cell Lines. Cells 2021; 11:cells11010117. [PMID: 35011679 PMCID: PMC8749978 DOI: 10.3390/cells11010117] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2021] [Revised: 12/18/2021] [Accepted: 12/27/2021] [Indexed: 12/11/2022] Open
Abstract
Triple-negative breast cancer (TNBC) is a breast cancer (BC) subtype that accounts for approximately 15–20% of all BC cases. Cancer cell lines (CLs) provide an efficient way to model the disease. We have recently isolated a patient-derived triple-negative BC CL MFUM-BrTNBC-1 and performed a detailed morphological and molecular characterisation and a comprehensive comparison with three commercial BC CLs (MCF-7, MDA-MB-231, MDA-MB-453). Light and fluorescence microscopy were used for morphological studies; immunocytochemical staining for hormone receptor, p53 and Ki67 status; RNA sequencing, qRT-PCR and STR analysis for molecular characterisation; and biomedical image analysis for comparative phenotypical analysis. The patient tissue-derived MFUM-BrTNBC-1 maintained the primary triple-negative receptor status. STR analysis showed a stable and unique STR profile up to the 6th passage. MFUM-BrTNBC-1 expressed EMT transition markers and displayed changes in several cancer-related pathways (MAPK, Wnt and PI3K signalling; nucleotide excision repair; and SWI/SNF chromatin remodelling). Morphologically, MFUM-BrTNBC-1 differed from the commercial TNBC CL MDA-MB-231. The advantages of MFUM-BrTNBC-1 are its isolation from a primary tumour, rather than a metastatic site; good growth characteristics; phenotype identical to primary tissue; complete records of origin; a unique identifier; complete, unique STR profile; quantifiable morphological properties; and genetic stability up to (at least) the 6th passage.
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Affiliation(s)
- Kristijan Skok
- Department of Pathology, Hospital Graz II, Location West, Göstinger Straße 22, 8020 Graz, Austria
- Faculty of Medicine, University of Maribor, Taborska Ulica 8, 2000 Maribor, Slovenia; (L.G.); (H.Č.); (M.M.); (U.P.); (G.J.); (M.G.); (M.S.); (I.T.); (R.K.)
- Correspondence: (K.S.); (U.M.); Tel.: +43-316-5466-5541 (K.S.); +386-2-234-5823 (U.M.)
| | - Lidija Gradišnik
- Faculty of Medicine, University of Maribor, Taborska Ulica 8, 2000 Maribor, Slovenia; (L.G.); (H.Č.); (M.M.); (U.P.); (G.J.); (M.G.); (M.S.); (I.T.); (R.K.)
| | - Helena Čelešnik
- Faculty of Medicine, University of Maribor, Taborska Ulica 8, 2000 Maribor, Slovenia; (L.G.); (H.Č.); (M.M.); (U.P.); (G.J.); (M.G.); (M.S.); (I.T.); (R.K.)
- Faculty of Chemistry & Chemical Engineering, University of Maribor, Smetanova Ulica 17, 2000 Maribor, Slovenia
| | - Marko Milojević
- Faculty of Medicine, University of Maribor, Taborska Ulica 8, 2000 Maribor, Slovenia; (L.G.); (H.Č.); (M.M.); (U.P.); (G.J.); (M.G.); (M.S.); (I.T.); (R.K.)
| | - Uroš Potočnik
- Faculty of Medicine, University of Maribor, Taborska Ulica 8, 2000 Maribor, Slovenia; (L.G.); (H.Č.); (M.M.); (U.P.); (G.J.); (M.G.); (M.S.); (I.T.); (R.K.)
- Faculty of Chemistry & Chemical Engineering, University of Maribor, Smetanova Ulica 17, 2000 Maribor, Slovenia
| | - Gregor Jezernik
- Faculty of Medicine, University of Maribor, Taborska Ulica 8, 2000 Maribor, Slovenia; (L.G.); (H.Č.); (M.M.); (U.P.); (G.J.); (M.G.); (M.S.); (I.T.); (R.K.)
| | - Mario Gorenjak
- Faculty of Medicine, University of Maribor, Taborska Ulica 8, 2000 Maribor, Slovenia; (L.G.); (H.Č.); (M.M.); (U.P.); (G.J.); (M.G.); (M.S.); (I.T.); (R.K.)
| | - Monika Sobočan
- Faculty of Medicine, University of Maribor, Taborska Ulica 8, 2000 Maribor, Slovenia; (L.G.); (H.Č.); (M.M.); (U.P.); (G.J.); (M.G.); (M.S.); (I.T.); (R.K.)
- Division for Gynecology and Perinatology, University Medical Centre Maribor, Ljubljanska Ulica 5, 2000 Maribor, Slovenia
| | - Iztok Takač
- Faculty of Medicine, University of Maribor, Taborska Ulica 8, 2000 Maribor, Slovenia; (L.G.); (H.Č.); (M.M.); (U.P.); (G.J.); (M.G.); (M.S.); (I.T.); (R.K.)
- Division for Gynecology and Perinatology, University Medical Centre Maribor, Ljubljanska Ulica 5, 2000 Maribor, Slovenia
| | - Rajko Kavalar
- Faculty of Medicine, University of Maribor, Taborska Ulica 8, 2000 Maribor, Slovenia; (L.G.); (H.Č.); (M.M.); (U.P.); (G.J.); (M.G.); (M.S.); (I.T.); (R.K.)
- Department of Pathology, University Medical Centre Maribor, Ljubljanska Ulica 5, 2000 Maribor, Slovenia
| | - Uroš Maver
- Faculty of Medicine, University of Maribor, Taborska Ulica 8, 2000 Maribor, Slovenia; (L.G.); (H.Č.); (M.M.); (U.P.); (G.J.); (M.G.); (M.S.); (I.T.); (R.K.)
- Correspondence: (K.S.); (U.M.); Tel.: +43-316-5466-5541 (K.S.); +386-2-234-5823 (U.M.)
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Urtatiz O, Haage A, Tanentzapf G, Van Raamsdonk CD. Crosstalk with keratinocytes causes GNAQ oncogene specificity in melanoma. eLife 2021; 10:71825. [PMID: 34939927 PMCID: PMC8747508 DOI: 10.7554/elife.71825] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2021] [Accepted: 12/21/2021] [Indexed: 11/13/2022] Open
Abstract
Different melanoma subtypes exhibit specific and non-overlapping sets of oncogene and tumor suppressor mutations, despite a common cell of origin in melanocytes. For example, activation of the Gαq/11 signaling pathway is a characteristic initiating event in primary melanomas that arise in the dermis, uveal tract, or central nervous system. It is rare in melanomas arising in the epidermis. The mechanism for this specificity is unknown. Here, we present evidence that in the mouse, crosstalk with the epidermal microenvironment actively impairs the survival of melanocytes expressing the GNAQQ209L oncogene. We found that GNAQQ209L, in combination with signaling from the interfollicular epidermis (IFE), stimulates dendrite extension, leads to actin cytoskeleton disorganization, inhibits proliferation, and promotes apoptosis in melanocytes. The effect was reversible and paracrine. In contrast, the epidermal environment increased the survival of wildtype and BrafV600E expressing melanocytes. Hence, our studies reveal the flip side of Gαq/11 signaling, which was hitherto unsuspected. In the future, the identification of the epidermal signals that restrain the GNAQQ209L oncogene could suggest novel therapies for GNAQ and GNA11 mutant melanomas.
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Affiliation(s)
- Oscar Urtatiz
- Department of Medical Genetics, University of British Columbia, Vancouver, Canada
| | - Amanda Haage
- Department of Cellular and Physiological Sciences, University of British Columbia, Vancouver, Canada
| | - Guy Tanentzapf
- Department of Cellular and Physiological Sciences, University of British Columbia, Vancouver, Canada
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56
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Yamasaki J, Hirata Y, Otsuki Y, Suina K, Saito Y, Masuda K, Okazaki S, Ishimoto T, Saya H, Nagano O. MEK Inhibition Suppresses Metastatic Progression of KRAS-Mutated Gastric Cancer. Cancer Sci 2021; 113:916-925. [PMID: 34931404 PMCID: PMC8898706 DOI: 10.1111/cas.15244] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2021] [Revised: 12/13/2021] [Accepted: 12/17/2021] [Indexed: 11/27/2022] Open
Abstract
Metastatic progression of tumors is driven by genetic alterations and tumor‐stroma interaction. To elucidate the mechanism underlying the oncogene‐induced gastric tumor progression, we have developed an organoid‐based model of gastric cancer from GAstric Neoplasia (GAN) mice, which express Wnt1 and the enzymes COX2 and microsomal prostaglandin E synthase 1 in the stomach. Both p53 knockout (GAN‐p53KO) organoids and KRASG12V‐expressing GAN‐p53KO (GAN‐KP) organoids were generated by genetic manipulation of GAN mouse‐derived tumor (GAN wild‐type [WT]) organoids. In contrast with GAN‐WT and GAN‐p53KO organoids, which manifested Wnt addiction, GAN‐KP organoids showed a Wnt‐independent phenotype and the ability to proliferate without formation of a Wnt‐regulated three‐dimensional epithelial architecture. After transplantation in syngeneic mouse stomach, GAN‐p53KO cells formed only small tumors, whereas GAN‐KP cells gave rise to invasive tumors associated with the development of hypoxia as well as to liver metastasis. Spatial transcriptomics analysis suggested that hypoxia signaling contributes to the metastatic progression of GAN‐KP tumors. In particular, such analysis identified a cluster of stromal cells located at the tumor invasive front that expressed genes related to hypoxia signaling, angiogenesis, and cell migration. These cells were also positive for phosphorylated extracellular signal‐regulated kinase (ERK), suggesting that mitogen‐activated protein kinase (MAPK) signaling promotes development of both tumor and microenvironment. The MEK (MAPK kinase) inhibitor trametinib suppressed the development of GAN‐KP gastric tumors, formation of a hypoxic microenvironment, tumor angiogenesis, and liver metastasis. Our findings therefore establish a rationale for application of trametinib to suppress metastatic progression of KRAS‐mutated gastric cancer.
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Affiliation(s)
- Juntaro Yamasaki
- Division of Gene Regulation, Institute for Advanced Medical Research, School of Medicine, Keio University, Tokyo, Japan
| | - Yuki Hirata
- Department of Surgery, School of Medicine, Keio University, Tokyo, Japan
| | - Yuji Otsuki
- Division of Gene Regulation, Institute for Advanced Medical Research, School of Medicine, Keio University, Tokyo, Japan
| | - Kentaro Suina
- Division of Gene Regulation, Institute for Advanced Medical Research, School of Medicine, Keio University, Tokyo, Japan
| | - Yoshiyuki Saito
- Department of Surgery, School of Medicine, Keio University, Tokyo, Japan
| | - Kenta Masuda
- Department of Obstetrics and Gynecology, School of Medicine, Keio University, Tokyo, Japan
| | - Shogo Okazaki
- Division of Development and Aging, Research Institute for Biomedical Sciences, Tokyo University of Science, Noda, Japan
| | - Takatsugu Ishimoto
- Gastrointestinal Cancer Biology, International Research Center for Medical Sciences (IRCMS), Kumamoto University, Kumamoto, Japan
| | - Hideyuki Saya
- Division of Gene Regulation, Institute for Advanced Medical Research, School of Medicine, Keio University, Tokyo, Japan
| | - Osamu Nagano
- Division of Gene Regulation, Institute for Advanced Medical Research, School of Medicine, Keio University, Tokyo, Japan
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Clonal dynamics of BRAF-driven drug resistance in EGFR-mutant lung cancer. NPJ Precis Oncol 2021; 5:102. [PMID: 34921211 PMCID: PMC8683498 DOI: 10.1038/s41698-021-00241-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2021] [Accepted: 11/16/2021] [Indexed: 11/08/2022] Open
Abstract
Activation of MAPK signaling via BRAF mutations may limit the activity of EGFR inhibitors in EGFR-mutant lung cancer patients. However, the impact of BRAF mutations on the selection and fitness of emerging resistant clones during anti-EGFR therapy remains elusive. We tracked the evolution of subclonal mutations by whole-exome sequencing and performed clonal analyses of individual metastases during therapy. Complementary functional analyses of polyclonal EGFR-mutant cell pools showed a dose-dependent enrichment of BRAFV600E and a loss of EGFR inhibitor susceptibility. The clones remain stable and become vulnerable to combined EGFR, RAF, and MEK inhibition. Moreover, only osimertinib/trametinib combination treatment, but not monotherapy with either of these drugs, leads to robust tumor shrinkage in EGFR-driven xenograft models harboring BRAFV600E mutations. These data provide insights into the dynamics of clonal evolution of EGFR-mutant tumors and the therapeutic implications of BRAF co-mutations that may facilitate the development of treatment strategies to improve the prognosis of these patients.
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58
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Yokosuka T, Ito M, Yoshino Y, Hirose A, Nakamura W, Sakurai Y, Hayashi A, Fujita S, Miyagawa N, Keino D, Iwasaki F, Hamanoue S, Yanagimachi M, Goto S, Nagai JI, Ueno H, Takita J, Tanaka Y, Taga T, Goto H. Using the in vitro drug sensitivity test to identify candidate treatments for transient abnormal myelopoiesis. Br J Haematol 2021; 196:764-768. [PMID: 34816427 DOI: 10.1111/bjh.17970] [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: 06/27/2021] [Accepted: 11/10/2021] [Indexed: 11/26/2022]
Abstract
Approximately 20% of patients with transient abnormal myelopoiesis (TAM) die due to hepatic or multiorgan failure. To identify potential new treatments for TAM, we performed in vitro drug sensitivity testing (DST) using the peripheral blood samples of eight patients with TAM. DST screened 41 agents for cytotoxic properties against TAM blasts. Compared with the reference samples of healthy subjects, TAM blasts were more sensitive to glucocorticoids, the mitogen-activated protein kinase kinase (MAP2K) inhibitor trametinib, and cytarabine. Our present results support the therapeutic potential of glucocorticoids and the role of the RAS/MAP2K signalling pathway in TAM pathogenesis.
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Affiliation(s)
- Tomoko Yokosuka
- Division of Hematology/Oncology, Kanagawa Children's Medical Center, Yokohama, Japan
| | - Mieko Ito
- Division of Hematology/Oncology, Kanagawa Children's Medical Center, Yokohama, Japan
| | - Yuki Yoshino
- Division of Hematology/Oncology, Kanagawa Children's Medical Center, Yokohama, Japan
| | - Ayana Hirose
- Division of Hematology/Oncology, Kanagawa Children's Medical Center, Yokohama, Japan
| | - Wataru Nakamura
- Division of Hematology/Oncology, Kanagawa Children's Medical Center, Yokohama, Japan
| | - Yukari Sakurai
- Division of Hematology/Oncology, Kanagawa Children's Medical Center, Yokohama, Japan
| | - Akiko Hayashi
- Division of Hematology/Oncology, Kanagawa Children's Medical Center, Yokohama, Japan
| | - Sachio Fujita
- Division of Hematology/Oncology, Kanagawa Children's Medical Center, Yokohama, Japan
| | - Naoyuki Miyagawa
- Division of Hematology/Oncology, Kanagawa Children's Medical Center, Yokohama, Japan
| | - Dai Keino
- Division of Hematology/Oncology, Kanagawa Children's Medical Center, Yokohama, Japan
| | - Fuminori Iwasaki
- Division of Hematology/Oncology, Kanagawa Children's Medical Center, Yokohama, Japan
| | - Satoshi Hamanoue
- Division of Hematology/Oncology, Kanagawa Children's Medical Center, Yokohama, Japan
| | - Masakatsu Yanagimachi
- Division of Hematology/Oncology, Kanagawa Children's Medical Center, Yokohama, Japan
| | - Shoko Goto
- Division of Hematology/Oncology, Kanagawa Children's Medical Center, Yokohama, Japan
| | - Jun-Ichi Nagai
- Department of Laboratory Medicine, Kanagawa Children's Medical Center, Yokohama, Japan
| | - Hiroo Ueno
- Department of Pediatrics, Kyoto University Hospital, Kyoto, Japan
| | - Junko Takita
- Department of Pediatrics, Kyoto University Hospital, Kyoto, Japan
| | - Yukichi Tanaka
- Department of Pathology, Kanagawa Children's Medical Center, Yokohama, Japan
| | - Takashi Taga
- Department of Pediatrics, Shiga University of Medical Science, Otsu, Japan
| | - Hiroaki Goto
- Division of Hematology/Oncology, Kanagawa Children's Medical Center, Yokohama, Japan
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Caeser R, Hulton C, Costa E, Durani V, Little M, Chen X, Tischfield SE, Asher M, Kombak FE, Chavan SS, Shah NS, Ciampricotti M, de Stanchina E, Poirier JT, Rudin CM, Sen T. MAPK pathway activation selectively inhibits ASCL1-driven small cell lung cancer. iScience 2021; 24:103224. [PMID: 34712921 PMCID: PMC8528729 DOI: 10.1016/j.isci.2021.103224] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2021] [Revised: 08/02/2021] [Accepted: 09/30/2021] [Indexed: 12/19/2022] Open
Abstract
Activation of mitogenic signaling pathways is a common oncogenic driver of many solid tumors including lung cancer. Although activating mutations in the mitogen-activated protein kinase (MAPK) pathway are prevalent in non-small cell lung cancers, MAPK pathway activity, counterintuitively, is relatively suppressed in the more aggressively proliferative small cell lung cancer (SCLC). Here, we elucidate the role of the MAPK pathway and how it interacts with other signaling pathways in SCLC. We find that the most common SCLC subtype, SCLC-A associated with high expression of ASCL1, is selectively sensitive to MAPK activation in vitro and in vivo through induction of cell-cycle arrest and senescence. We show strong upregulation of ERK negative feedback regulators and STAT signaling upon MAPK activation in SCLC-A lines. These findings provide insight into the complexity of signaling networks in SCLC and suggest subtype-specific mitogenic vulnerabilities. MAPK activation causes cell-cycle arrest and senescence selectively in SCLC-A subtype MAPK-induced growth inhibition is independent of NOTCH signaling MAPK activation increases ERK negative feedback and activates STAT3 signaling
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Affiliation(s)
- Rebecca Caeser
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Christopher Hulton
- Louis V. Gerstner Jr. Graduate School of Biomedical Sciences, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Emily Costa
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA.,Weill Cornell Graduate School of Medical Sciences, Weill Cornell Medicine, New York, NY, USA
| | - Vidushi Durani
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA.,Weill Cornell Graduate School of Medical Sciences, Weill Cornell Medicine, New York, NY, USA
| | - Megan Little
- Molecular Pharmacology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Xiaoping Chen
- Antitumor Assessment Core Facility, Memorial Sloan Kettering Cancer Center, New York, NY 11065, USA
| | - Sam E Tischfield
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Marina Asher
- Precision Pathology Center, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Faruk Erdem Kombak
- Precision Pathology Center, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Shweta S Chavan
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Nisargbhai S Shah
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Metamia Ciampricotti
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA.,Molecular Pharmacology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Elisa de Stanchina
- Antitumor Assessment Core Facility, Memorial Sloan Kettering Cancer Center, New York, NY 11065, USA
| | - John T Poirier
- Perlmutter Cancer Center, New York University Langone Health, New York, NY, USA
| | - Charles M Rudin
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA.,Molecular Pharmacology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Triparna Sen
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA.,Molecular Pharmacology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
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Strash N, DeLuca S, Janer Carattini GL, Heo SC, Gorsuch R, Bursac N. Human Erbb2-induced Erk activity robustly stimulates cycling and functional remodeling of rat and human cardiomyocytes. eLife 2021; 10:65512. [PMID: 34665129 PMCID: PMC8589446 DOI: 10.7554/elife.65512] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2020] [Accepted: 10/19/2021] [Indexed: 12/17/2022] Open
Abstract
Multiple mitogenic pathways capable of promoting mammalian cardiomyocyte (CM) proliferation have been identified as potential candidates for functional heart repair following myocardial infarction. However, it is unclear whether the effects of these mitogens are species-specific and how they directly compare in the same cardiac setting. Here, we examined how CM-specific lentiviral expression of various candidate mitogens affects human induced pluripotent stem cell-derived CMs (hiPSC-CMs) and neonatal rat ventricular myocytes (NRVMs) in vitro. In 2D-cultured CMs from both species, and in highly mature 3D-engineered cardiac tissues generated from NRVMs, a constitutively active mutant form of the human gene Erbb2 (cahErbb2) was the most potent tested mitogen. Persistent expression of cahErbb2 induced CM proliferation, sarcomere loss, and remodeling of tissue structure and function, which were attenuated by small molecule inhibitors of Erk signaling. These results suggest transient activation of Erbb2/Erk axis in CMs as a potential strategy for regenerative heart repair.
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Affiliation(s)
- Nicholas Strash
- Department of Cell Biology, Duke University, Durham, United States
| | - Sophia DeLuca
- Department of Cell Biology, Duke University, Durham, United States
| | | | - Soon Chul Heo
- Department of Biomedical Engineering, Duke University, Durham, United States
| | - Ryne Gorsuch
- Department of Biomedical Engineering, Duke University, Durham, United States
| | - Nenad Bursac
- Department of Cell Biology, Duke University, Durham, United States.,Department of Biomedical Engineering, Duke University, Durham, United States
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Brägelmann J, Lorenz C, Borchmann S, Nishii K, Wegner J, Meder L, Ostendorp J, Ast DF, Heimsoeth A, Nakasuka T, Hirabae A, Okawa S, Dammert MA, Plenker D, Klein S, Lohneis P, Gu J, Godfrey LK, Forster J, Trajkovic-Arsic M, Zillinger T, Haarmann M, Quaas A, Lennartz S, Schmiel M, D'Rozario J, Thomas ES, Li H, Schmitt CA, George J, Thomas RK, von Karstedt S, Hartmann G, Büttner R, Ullrich RT, Siveke JT, Ohashi K, Schlee M, Sos ML. MAPK-pathway inhibition mediates inflammatory reprogramming and sensitizes tumors to targeted activation of innate immunity sensor RIG-I. Nat Commun 2021; 12:5505. [PMID: 34535668 PMCID: PMC8448826 DOI: 10.1038/s41467-021-25728-8] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2020] [Accepted: 08/23/2021] [Indexed: 12/29/2022] Open
Abstract
Kinase inhibitors suppress the growth of oncogene driven cancer but also enforce the selection of treatment resistant cells that are thought to promote tumor relapse in patients. Here, we report transcriptomic and functional genomics analyses of cells and tumors within their microenvironment across different genotypes that persist during kinase inhibitor treatment. We uncover a conserved, MAPK/IRF1-mediated inflammatory response in tumors that undergo stemness- and senescence-associated reprogramming. In these tumor cells, activation of the innate immunity sensor RIG-I via its agonist IVT4, triggers an interferon and a pro-apoptotic response that synergize with concomitant kinase inhibition. In humanized lung cancer xenografts and a syngeneic Egfr-driven lung cancer model these effects translate into reduction of exhausted CD8+ T cells and robust tumor shrinkage. Overall, the mechanistic understanding of MAPK/IRF1-mediated intratumoral reprogramming may ultimately prolong the efficacy of targeted drugs in genetically defined cancer patients.
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Affiliation(s)
- Johannes Brägelmann
- Molecular Pathology, Institute of Pathology, Faculty of Medicine and University Hospital Cologne, University of Cologne, 50931, Cologne, Germany.
- Department of Translational Genomics, Faculty of Medicine and University Hospital Cologne, University of Cologne, 50931, Cologne, Germany.
- Center for Molecular Medicine Cologne, Faculty of Medicine and University Hospital Cologne, University of Cologne, 50931, Cologne, Germany.
- Mildred Scheel School of Oncology Cologne, Faculty of Medicine and University Hospital Cologne, University of Cologne, 50931, Cologne, Germany.
| | - Carina Lorenz
- Molecular Pathology, Institute of Pathology, Faculty of Medicine and University Hospital Cologne, University of Cologne, 50931, Cologne, Germany
- Department of Translational Genomics, Faculty of Medicine and University Hospital Cologne, University of Cologne, 50931, Cologne, Germany
- Center for Molecular Medicine Cologne, Faculty of Medicine and University Hospital Cologne, University of Cologne, 50931, Cologne, Germany
| | - Sven Borchmann
- Center for Molecular Medicine Cologne, Faculty of Medicine and University Hospital Cologne, University of Cologne, 50931, Cologne, Germany
- Department I of Internal Medicine, Center for Integrated Oncology Aachen Bonn Cologne Duesseldorf, Faculty of Medicine and University Hospital Cologne, University of Cologne, 50931, Cologne, Germany
- Else-Kröner-Forschungskolleg Clonal Evolution in Cancer, Faculty of Medicine and University Hospital Cologne, University of Cologne, 50931, Cologne, Germany
| | - Kazuya Nishii
- Department of Hematology, Oncology and Respiratory Medicine, Okayama University Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama, Japan
| | - Julia Wegner
- Institute of Clinical Chemistry and Clinical Pharmacology, University Hospital Bonn, Bonn, Germany
| | - Lydia Meder
- Center for Molecular Medicine Cologne, Faculty of Medicine and University Hospital Cologne, University of Cologne, 50931, Cologne, Germany
- Mildred Scheel School of Oncology Cologne, Faculty of Medicine and University Hospital Cologne, University of Cologne, 50931, Cologne, Germany
- Department I of Internal Medicine, Center for Integrated Oncology Aachen Bonn Cologne Duesseldorf, Faculty of Medicine and University Hospital Cologne, University of Cologne, 50931, Cologne, Germany
| | - Jenny Ostendorp
- Molecular Pathology, Institute of Pathology, Faculty of Medicine and University Hospital Cologne, University of Cologne, 50931, Cologne, Germany
- Department of Translational Genomics, Faculty of Medicine and University Hospital Cologne, University of Cologne, 50931, Cologne, Germany
- Center for Molecular Medicine Cologne, Faculty of Medicine and University Hospital Cologne, University of Cologne, 50931, Cologne, Germany
| | - David F Ast
- Molecular Pathology, Institute of Pathology, Faculty of Medicine and University Hospital Cologne, University of Cologne, 50931, Cologne, Germany
- Department of Translational Genomics, Faculty of Medicine and University Hospital Cologne, University of Cologne, 50931, Cologne, Germany
- Center for Molecular Medicine Cologne, Faculty of Medicine and University Hospital Cologne, University of Cologne, 50931, Cologne, Germany
- Mildred Scheel School of Oncology Cologne, Faculty of Medicine and University Hospital Cologne, University of Cologne, 50931, Cologne, Germany
| | - Alena Heimsoeth
- Molecular Pathology, Institute of Pathology, Faculty of Medicine and University Hospital Cologne, University of Cologne, 50931, Cologne, Germany
- Department of Translational Genomics, Faculty of Medicine and University Hospital Cologne, University of Cologne, 50931, Cologne, Germany
- Center for Molecular Medicine Cologne, Faculty of Medicine and University Hospital Cologne, University of Cologne, 50931, Cologne, Germany
| | - Takamasa Nakasuka
- Department of Hematology, Oncology and Respiratory Medicine, Okayama University Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama, Japan
| | - Atsuko Hirabae
- Department of Hematology, Oncology and Respiratory Medicine, Okayama University Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama, Japan
| | - Sachi Okawa
- Department of Hematology, Oncology and Respiratory Medicine, Okayama University Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama, Japan
| | - Marcel A Dammert
- Molecular Pathology, Institute of Pathology, Faculty of Medicine and University Hospital Cologne, University of Cologne, 50931, Cologne, Germany
- Department of Translational Genomics, Faculty of Medicine and University Hospital Cologne, University of Cologne, 50931, Cologne, Germany
- Center for Molecular Medicine Cologne, Faculty of Medicine and University Hospital Cologne, University of Cologne, 50931, Cologne, Germany
| | - Dennis Plenker
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, 11724, USA
- Lustgarten Foundation Pancreatic Cancer Research Laboratory, Cold Spring Harbor, NY, 11724, USA
| | - Sebastian Klein
- Else-Kröner-Forschungskolleg Clonal Evolution in Cancer, Faculty of Medicine and University Hospital Cologne, University of Cologne, 50931, Cologne, Germany
- Institute of Pathology, Faculty of Medicine and University Hospital Cologne, University of Cologne, 50931, Cologne, Germany
| | - Philipp Lohneis
- Institute of Pathology, Faculty of Medicine and University Hospital Cologne, University of Cologne, 50931, Cologne, Germany
| | - Jianing Gu
- Institute for Developmental Cancer Therapeutics, West German Cancer Center, University Hospital Essen, Essen, Germany
- Division of Solid Tumor Translational Oncology, German Cancer Consortium (DKTK, partner site Essen) and German Cancer Research Center, DKFZ, Heidelberg, Germany
| | - Laura K Godfrey
- Institute for Developmental Cancer Therapeutics, West German Cancer Center, University Hospital Essen, Essen, Germany
- Division of Solid Tumor Translational Oncology, German Cancer Consortium (DKTK, partner site Essen) and German Cancer Research Center, DKFZ, Heidelberg, Germany
| | - Jan Forster
- Division of Solid Tumor Translational Oncology, German Cancer Consortium (DKTK, partner site Essen) and German Cancer Research Center, DKFZ, Heidelberg, Germany
- Genome Informatics, Institute of Human Genetics, University Duisburg-Essen, Essen, Germany
| | - Marija Trajkovic-Arsic
- Institute for Developmental Cancer Therapeutics, West German Cancer Center, University Hospital Essen, Essen, Germany
- Division of Solid Tumor Translational Oncology, German Cancer Consortium (DKTK, partner site Essen) and German Cancer Research Center, DKFZ, Heidelberg, Germany
| | - Thomas Zillinger
- Institute of Clinical Chemistry and Clinical Pharmacology, University Hospital Bonn, Bonn, Germany
| | - Mareike Haarmann
- Mildred Scheel School of Oncology Cologne, Faculty of Medicine and University Hospital Cologne, University of Cologne, 50931, Cologne, Germany
| | - Alexander Quaas
- Institute of Pathology, Faculty of Medicine and University Hospital Cologne, University of Cologne, 50931, Cologne, Germany
| | - Stefanie Lennartz
- Molecular Pathology, Institute of Pathology, Faculty of Medicine and University Hospital Cologne, University of Cologne, 50931, Cologne, Germany
- Department of Translational Genomics, Faculty of Medicine and University Hospital Cologne, University of Cologne, 50931, Cologne, Germany
- Center for Molecular Medicine Cologne, Faculty of Medicine and University Hospital Cologne, University of Cologne, 50931, Cologne, Germany
| | - Marcel Schmiel
- Department of Translational Genomics, Faculty of Medicine and University Hospital Cologne, University of Cologne, 50931, Cologne, Germany
- Institute of Pathology, Faculty of Medicine and University Hospital Cologne, University of Cologne, 50931, Cologne, Germany
| | - Joshua D'Rozario
- Department of Translational Genomics, Faculty of Medicine and University Hospital Cologne, University of Cologne, 50931, Cologne, Germany
| | - Emily S Thomas
- Department of Translational Genomics, Faculty of Medicine and University Hospital Cologne, University of Cologne, 50931, Cologne, Germany
- Cologne Excellence Cluster on Cellular Stress Response in Aging-Associated Diseases (CECAD), Faculty of Medicine and University Hospital Cologne, University of Cologne, 50931, Cologne, Germany
- Imperial College London, London, UK
| | - Henry Li
- Crown Bioscience, San Diego, CA, USA
| | - Clemens A Schmitt
- Department of Hematology, Oncology and Tumor Immunology, Charité - University Medical Center, Virchow Campus, and Molekulares Krebsforschungszentrum, Berlin, Germany
- Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association, Berlin, Germany
- Department of Hematology and Oncology, Kepler University Hospital, Johannes Kepler University, Linz, Austria
| | - Julie George
- Department of Translational Genomics, Faculty of Medicine and University Hospital Cologne, University of Cologne, 50931, Cologne, Germany
- Department of Head and Neck Surgery, Faculty of Medicine and University Hospital Cologne, University of Cologne, 50931, Cologne, Germany
| | - Roman K Thomas
- Department of Translational Genomics, Faculty of Medicine and University Hospital Cologne, University of Cologne, 50931, Cologne, Germany
- Institute of Pathology, Faculty of Medicine and University Hospital Cologne, University of Cologne, 50931, Cologne, Germany
- German Cancer Research Center, German Cancer Consortium (DKTK), Heidelberg, Germany
| | - Silvia von Karstedt
- Department of Translational Genomics, Faculty of Medicine and University Hospital Cologne, University of Cologne, 50931, Cologne, Germany
- Cologne Excellence Cluster on Cellular Stress Response in Aging-Associated Diseases (CECAD), Faculty of Medicine and University Hospital Cologne, University of Cologne, 50931, Cologne, Germany
| | - Gunther Hartmann
- Institute of Clinical Chemistry and Clinical Pharmacology, University Hospital Bonn, Bonn, Germany
| | - Reinhard Büttner
- Institute of Pathology, Faculty of Medicine and University Hospital Cologne, University of Cologne, 50931, Cologne, Germany
| | - Roland T Ullrich
- Center for Molecular Medicine Cologne, Faculty of Medicine and University Hospital Cologne, University of Cologne, 50931, Cologne, Germany
- Department I of Internal Medicine, Center for Integrated Oncology Aachen Bonn Cologne Duesseldorf, Faculty of Medicine and University Hospital Cologne, University of Cologne, 50931, Cologne, Germany
| | - Jens T Siveke
- Institute for Developmental Cancer Therapeutics, West German Cancer Center, University Hospital Essen, Essen, Germany
- Division of Solid Tumor Translational Oncology, German Cancer Consortium (DKTK, partner site Essen) and German Cancer Research Center, DKFZ, Heidelberg, Germany
| | - Kadoaki Ohashi
- Department of Hematology, Oncology and Respiratory Medicine, Okayama University Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama, Japan
- Department of Respiratory Medicine, Okayama University Hospital, Japan, 2-5-1 Shikata-cho, Kitaku, Okayama, 700-8558, Japan
| | - Martin Schlee
- Institute of Clinical Chemistry and Clinical Pharmacology, University Hospital Bonn, Bonn, Germany
| | - Martin L Sos
- Molecular Pathology, Institute of Pathology, Faculty of Medicine and University Hospital Cologne, University of Cologne, 50931, Cologne, Germany.
- Department of Translational Genomics, Faculty of Medicine and University Hospital Cologne, University of Cologne, 50931, Cologne, Germany.
- Center for Molecular Medicine Cologne, Faculty of Medicine and University Hospital Cologne, University of Cologne, 50931, Cologne, Germany.
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Su K, Yu Q, Shen R, Sun SY, Moreno CS, Li X, Qin ZS. Pan-cancer analysis of pathway-based gene expression pattern at the individual level reveals biomarkers of clinical prognosis. CELL REPORTS METHODS 2021; 1:100050. [PMID: 34671755 PMCID: PMC8525796 DOI: 10.1016/j.crmeth.2021.100050] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/16/2020] [Revised: 05/07/2021] [Accepted: 06/16/2021] [Indexed: 02/08/2023]
Abstract
Identifying biomarkers to predict the clinical outcomes of individual patients is a fundamental problem in clinical oncology. Multiple single-gene biomarkers have already been identified and used in clinics. However, multiple oncogenes or tumor-suppressor genes are involved during the process of tumorigenesis. Additionally, the efficacy of single-gene biomarkers is limited by the extensively variable expression levels measured by high-throughput assays. In this study, we hypothesize that in individual tumor samples, the disruption of transcription homeostasis in key pathways or gene sets plays an important role in tumorigenesis and has profound implications for the patient's clinical outcome. We devised a computational method named iPath to identify, at the individual-sample level, which pathways or gene sets significantly deviate from their norms. We conducted a pan-cancer analysis and demonstrated that iPath is capable of identifying highly predictive biomarkers for clinical outcomes, including overall survival, tumor subtypes, and tumor-stage classifications.
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Affiliation(s)
- Kenong Su
- Department of Computer Science, Emory University, Atlanta, GA 30322, USA
| | - Qi Yu
- Department of Biostatistics and Bioinformatics, Emory University, Atlanta, GA 30322, USA
| | - Ronglai Shen
- Department of Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY 10017, USA
| | - Shi-Yong Sun
- Department of Hematology & Medical Oncology, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Carlos S. Moreno
- Department of Pathology and Laboratory Medicine, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Xiaoxian Li
- Department of Pathology and Laboratory Medicine, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Zhaohui S. Qin
- Department of Computer Science, Emory University, Atlanta, GA 30322, USA
- Department of Biostatistics and Bioinformatics, Emory University, Atlanta, GA 30322, USA
- Department of Biomedical Informatics, Emory University School of Medicine, Atlanta, GA 30322, USA
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63
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He C, Xu K, Zhu X, Dunphy PS, Gudenas B, Lin W, Twarog N, Hover LD, Kwon CH, Kasper LH, Zhang J, Li X, Dalton J, Jonchere B, Mercer KS, Currier DG, Caufield W, Wang Y, Xie J, Broniscer A, Wetmore C, Upadhyaya SA, Qaddoumi I, Klimo P, Boop F, Gajjar A, Zhang J, Orr BA, Robinson GW, Monje M, Freeman Iii BB, Roussel MF, Northcott PA, Chen T, Rankovic Z, Wu G, Chiang J, Tinkle CL, Shelat AA, Baker SJ. Patient-derived models recapitulate heterogeneity of molecular signatures and drug response in pediatric high-grade glioma. Nat Commun 2021; 12:4089. [PMID: 34215733 PMCID: PMC8253809 DOI: 10.1038/s41467-021-24168-8] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2020] [Accepted: 05/25/2021] [Indexed: 01/02/2023] Open
Abstract
Pediatric high-grade glioma (pHGG) is a major contributor to cancer-related death in children. In vitro and in vivo disease models reflecting the intimate connection between developmental context and pathogenesis of pHGG are essential to advance understanding and identify therapeutic vulnerabilities. Here we report establishment of 21 patient-derived pHGG orthotopic xenograft (PDOX) models and eight matched cell lines from diverse groups of pHGG. These models recapitulate histopathology, DNA methylation signatures, mutations and gene expression patterns of the patient tumors from which they were derived, and include rare subgroups not well-represented by existing models. We deploy 16 new and existing cell lines for high-throughput screening (HTS). In vitro HTS results predict variable in vivo response to PI3K/mTOR and MEK pathway inhibitors. These unique new models and an online interactive data portal for exploration of associated detailed molecular characterization and HTS chemical sensitivity data provide a rich resource for pediatric brain tumor research.
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Affiliation(s)
- Chen He
- Department of Developmental Neurobiology, Memphis, TN, USA
| | - Ke Xu
- Center for Applied Bioinformatics, Memphis, TN, USA
- Department of Computational Biology, Memphis, TN, USA
| | - Xiaoyan Zhu
- Department of Developmental Neurobiology, Memphis, TN, USA
| | - Paige S Dunphy
- Department of Developmental Neurobiology, Memphis, TN, USA
- Department of Oncology, Memphis, TN, USA
| | - Brian Gudenas
- Department of Developmental Neurobiology, Memphis, TN, USA
| | - Wenwei Lin
- Department of Chemical Biology and Therapeutics, Memphis, TN, USA
| | - Nathaniel Twarog
- Department of Chemical Biology and Therapeutics, Memphis, TN, USA
| | - Laura D Hover
- Department of Developmental Neurobiology, Memphis, TN, USA
| | | | | | - Junyuan Zhang
- Department of Developmental Neurobiology, Memphis, TN, USA
| | - Xiaoyu Li
- Department of Pathology, Memphis, TN, USA
| | | | | | | | - Duane G Currier
- Department of Chemical Biology and Therapeutics, Memphis, TN, USA
| | - William Caufield
- Preclinical Pharmacokinetics Shared Resource St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Yingzhe Wang
- Preclinical Pharmacokinetics Shared Resource St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Jia Xie
- Department of Chemical Biology and Therapeutics, Memphis, TN, USA
| | - Alberto Broniscer
- Division of Hematology-Oncology, Children's Hospital of Pittsburgh, Pittsburgh, PA, USA
| | | | | | | | - Paul Klimo
- Department of Surgery, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Frederick Boop
- Department of Surgery, St. Jude Children's Research Hospital, Memphis, TN, USA
| | | | - Jinghui Zhang
- Department of Computational Biology, Memphis, TN, USA
| | | | | | - Michelle Monje
- Department of Neurology, Stanford University, Stanford, CA, USA
| | - Burgess B Freeman Iii
- Preclinical Pharmacokinetics Shared Resource St. Jude Children's Research Hospital, Memphis, TN, USA
| | | | | | - Taosheng Chen
- Department of Chemical Biology and Therapeutics, Memphis, TN, USA
| | - Zoran Rankovic
- Department of Chemical Biology and Therapeutics, Memphis, TN, USA
| | - Gang Wu
- Center for Applied Bioinformatics, Memphis, TN, USA
- Department of Computational Biology, Memphis, TN, USA
| | | | - Christopher L Tinkle
- Department of Radiation Oncology, St. Jude Children's Research Hospital, Memphis, TN, USA.
| | - Anang A Shelat
- Department of Chemical Biology and Therapeutics, Memphis, TN, USA.
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Thornton AM, Fang L, Lo A, McSharry M, Haan D, O’Brien C, Berger AH, Giannakis M, Brooks AN. eVIP2: Expression-based variant impact phenotyping to predict the function of gene variants. PLoS Comput Biol 2021; 17:e1009132. [PMID: 34214079 PMCID: PMC8281988 DOI: 10.1371/journal.pcbi.1009132] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2020] [Revised: 07/15/2021] [Accepted: 05/30/2021] [Indexed: 11/25/2022] Open
Abstract
While advancements in genome sequencing have identified millions of somatic mutations in cancer, their functional impact is poorly understood. We previously developed the expression-based variant impact phenotyping (eVIP) method to use gene expression data to characterize the function of gene variants. The eVIP method uses a decision tree-based algorithm to predict the functional impact of somatic variants by comparing gene expression signatures induced by introduction of wild-type (WT) versus mutant cDNAs in cell lines. The method distinguishes between variants that are gain-of-function, loss-of-function, change-of-function, or neutral. We present eVIP2, software that allows for pathway analysis (eVIP Pathways) and usage with RNA-seq data. To demonstrate the eVIP2 software and approach, we characterized two recurrent frameshift variants in RNF43, a negative regulator of Wnt signaling, frequently mutated in colorectal, gastric, and endometrial cancer. RNF43 WT, RNF43 R117fs, RNF43 G659fs, or GFP control cDNA were overexpressed in HEK293T cells. Analysis with eVIP2 predicted that the frameshift at position 117 was a loss-of-function mutation, as expected. The second frameshift at position 659 has been previously described as a passenger mutation that maintains the RNF43 WT function as a negative regulator of Wnt. Surprisingly, eVIP2 predicted G659fs to be a change-of-function mutation. Additional eVIP Pathways analysis of RNF43 G659fs predicted 10 pathways to be significantly altered, including TNF-α via NFκB signaling, KRAS signaling, and hypoxia, highlighting the benefit of a more comprehensive approach when determining the impact of gene variant function. To validate these predictions, we performed reporter assays and found that each pathway activated by expression of RNF43 G659fs, but not expression of RNF43 WT, was identified as impacted by eVIP2, supporting that RNF43 G659fs is a change-of-function mutation and its effect on the identified pathways. Pathway activation was further validated by Western blot analysis. Lastly, we show primary colon adenocarcinoma patient samples with R117fs and G659fs variants have transcriptional profiles similar to BRAF missense mutations with activated RAS/MAPK signaling, consistent with KRAS signaling pathways being GOF in both variants. The eVIP2 method is an important step towards overcoming the current challenge of variant interpretation in the implementation of precision medicine. eVIP2 is available at https://github.com/BrooksLabUCSC/eVIP2.
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Affiliation(s)
- Alexis M. Thornton
- Department of Biomolecular Engineering, University of California Santa Cruz, Santa Cruz, California, United States of America
- UCSC Genomics Institute, University of California Santa Cruz, Santa Cruz, California, United States of America
| | - Lishan Fang
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts, United States of America
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, Massachusetts, United States of America
- Department of Orthopedics, The Eight Affiliated Hospital of Sun Yat-sen University, Shenzhen, China
| | - April Lo
- Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
| | - Maria McSharry
- Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
| | - David Haan
- Department of Biomolecular Engineering, University of California Santa Cruz, Santa Cruz, California, United States of America
- UCSC Genomics Institute, University of California Santa Cruz, Santa Cruz, California, United States of America
| | - Casey O’Brien
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts, United States of America
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, Massachusetts, United States of America
| | - Alice H. Berger
- Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
| | - Marios Giannakis
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts, United States of America
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, Massachusetts, United States of America
| | - Angela N. Brooks
- Department of Biomolecular Engineering, University of California Santa Cruz, Santa Cruz, California, United States of America
- UCSC Genomics Institute, University of California Santa Cruz, Santa Cruz, California, United States of America
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65
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EGFR activation limits the response of liver cancer to lenvatinib. Nature 2021; 595:730-734. [PMID: 34290403 DOI: 10.1038/s41586-021-03741-7] [Citation(s) in RCA: 176] [Impact Index Per Article: 58.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2020] [Accepted: 06/21/2021] [Indexed: 02/04/2023]
Abstract
Hepatocellular carcinoma (HCC)-the most common form of liver cancer-is an aggressive malignancy with few effective treatment options1. Lenvatinib is a small-molecule inhibitor of multiple receptor tyrosine kinases that is used for the treatment of patients with advanced HCC, but this drug has only limited clinical benefit2. Here, using a kinome-centred CRISPR-Cas9 genetic screen, we show that inhibition of epidermal growth factor receptor (EGFR) is synthetic lethal with lenvatinib in liver cancer. The combination of the EGFR inhibitor gefitinib and lenvatinib displays potent anti-proliferative effects in vitro in liver cancer cell lines that express EGFR and in vivo in xenografted liver cancer cell lines, immunocompetent mouse models and patient-derived HCC tumours in mice. Mechanistically, inhibition of fibroblast growth factor receptor (FGFR) by lenvatinib treatment leads to feedback activation of the EGFR-PAK2-ERK5 signalling axis, which is blocked by EGFR inhibition. Treatment of 12 patients with advanced HCC who were unresponsive to lenvatinib treatment with the combination of lenvatinib plus gefitinib (trial identifier NCT04642547) resulted in meaningful clinical responses. The combination therapy identified here may represent a promising strategy for the approximately 50% of patients with advanced HCC who have high levels of EGFR.
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66
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Li R, Ng TSC, Wang SJ, Prytyskach M, Rodell CB, Mikula H, Kohler RH, Garlin MA, Lauffenburger DA, Parangi S, Dinulescu DM, Bardeesy N, Weissleder R, Miller MA. Therapeutically reprogrammed nutrient signalling enhances nanoparticulate albumin bound drug uptake and efficacy in KRAS-mutant cancer. NATURE NANOTECHNOLOGY 2021; 16:830-839. [PMID: 33958764 PMCID: PMC8491539 DOI: 10.1038/s41565-021-00897-1] [Citation(s) in RCA: 55] [Impact Index Per Article: 18.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/18/2019] [Accepted: 03/11/2021] [Indexed: 05/04/2023]
Abstract
Nanoparticulate albumin bound paclitaxel (nab-paclitaxel, nab-PTX) is among the most widely prescribed nanomedicines in clinical use, yet it remains unclear how nanoformulation affects nab-PTX behaviour in the tumour microenvironment. Here, we quantified the biodistribution of the albumin carrier and its chemotherapeutic payload in optically cleared tumours of genetically engineered mouse models, and compared the behaviour of nab-PTX with other clinically relevant nanoparticles. We found that nab-PTX uptake is profoundly and distinctly affected by cancer-cell autonomous RAS signalling, and RAS/RAF/MEK/ERK inhibition blocked its selective delivery and efficacy. In contrast, a targeted screen revealed that IGF1R kinase inhibitors enhance uptake and efficacy of nab-PTX by mimicking glucose deprivation and promoting macropinocytosis via AMPK, a nutrient sensor in cells. This study thus shows how nanoparticulate albumin bound drug efficacy can be therapeutically improved by reprogramming nutrient signalling and enhancing macropinocytosis in cancer cells.
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Affiliation(s)
- Ran Li
- Center for Systems Biology, Massachusetts General Hospital Research Institute, Boston, MA, USA
- Department of Radiology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Thomas S C Ng
- Center for Systems Biology, Massachusetts General Hospital Research Institute, Boston, MA, USA
- Department of Radiology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Stephanie J Wang
- Center for Systems Biology, Massachusetts General Hospital Research Institute, Boston, MA, USA
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Mark Prytyskach
- Center for Systems Biology, Massachusetts General Hospital Research Institute, Boston, MA, USA
| | - Christopher B Rodell
- Center for Systems Biology, Massachusetts General Hospital Research Institute, Boston, MA, USA
- School of Biomedical Engineering, Science and Health Systems, Drexel University, Philadelphia, PA, USA
| | - Hannes Mikula
- Center for Systems Biology, Massachusetts General Hospital Research Institute, Boston, MA, USA
- Institute of Applied Synthetic Chemistry, Vienna University of Technology (TU Wien), Vienna, Austria
| | - Rainer H Kohler
- Center for Systems Biology, Massachusetts General Hospital Research Institute, Boston, MA, USA
| | - Michelle A Garlin
- Center for Systems Biology, Massachusetts General Hospital Research Institute, Boston, MA, USA
| | - Douglas A Lauffenburger
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Sareh Parangi
- Department of Surgery, Massachusetts General Hospital, Boston, MA, USA
| | - Daniela M Dinulescu
- Division of Women's and Perinatal Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Nabeel Bardeesy
- MGH Cancer Center, Massachusetts General Hospital Research Institute, Boston, MA, USA
| | - Ralph Weissleder
- Center for Systems Biology, Massachusetts General Hospital Research Institute, Boston, MA, USA.
- Department of Radiology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA.
- Department of Systems Biology, Harvard Medical School, Boston, MA, USA.
| | - Miles A Miller
- Center for Systems Biology, Massachusetts General Hospital Research Institute, Boston, MA, USA.
- Department of Radiology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA.
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Sun J, Guo Y, Fan Y, Wang Q, Zhang Q, Lai D. Decreased expression of IDH1 by chronic unpredictable stress suppresses proliferation and accelerates senescence of granulosa cells through ROS activated MAPK signaling pathways. Free Radic Biol Med 2021; 169:122-136. [PMID: 33865962 DOI: 10.1016/j.freeradbiomed.2021.04.016] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/19/2021] [Revised: 04/09/2021] [Accepted: 04/10/2021] [Indexed: 12/20/2022]
Abstract
Studies suggested that psychosocial stress was associated with female fertility decline, but the underlying mechanisms remained unclear. Granulosa cells (GCs) are important somatic cells to support follicular development and oocyte maturation. Herein, by using a mouse model of chronic unpredictable stress (CUS), we found that CUS induced oxidative stress damage in mouse ovaries, also inhibited GCs proliferation and accelerated GCs senescence. Isocitrate dehydrogenase-1 (IDH1), an antioxidant related gene by generating NADPH, was shown to be downregulated in GCs of CUS mice. Consistently, IDH1 knockdown inhibited cell proliferation and accelerated cellular senescence in KGN cells in vitro. In addition, IDH1 knockdown increased ROS content, induced autophagy activation and triggered cell cycle arrest in S and G2/M phases in KGN cells, which could be rescued by N-acetyl-l-cysteine (NAC), a ROS scavenger in these cells. Besides, IDH1 knockdown activated MAPK signaling pathways, including ERK, JNK and p38 signaling pathways in KGN cells, while NAC could suppress the activation. Through using inhibitors of MAPK signaling pathways, we showed that the activation of ERK pathway participated in autophagy related cell proliferation inhibition and cellular senescence, whereas JNK and p38 MAPK signaling pathways took part in regulation cell cycle arrest associated cell proliferation inhibitory and senescence in IDH1 knockdown KGN cells. Our findings suggested that downregulated expression of IDH1 induced by CUS has a physiological function in GCs proliferation and senescence through ROS activated MAPK signaling pathways, and improvement of IDH1 activity might be a beneficial therapeutic strategy for ovarian dysfunction.
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Affiliation(s)
- Junyan Sun
- The International Peace Maternity and Child Health Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200030, China; Shanghai Key Laboratory of Embryo Original Diseases, Shanghai, 200030, China; Shanghai Municipal Key Clinical Speciality, Shanghai, 200030, China
| | - Ying Guo
- The International Peace Maternity and Child Health Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200030, China; Shanghai Key Laboratory of Embryo Original Diseases, Shanghai, 200030, China; Shanghai Municipal Key Clinical Speciality, Shanghai, 200030, China
| | - Yihui Fan
- The International Peace Maternity and Child Health Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200030, China; Shanghai Key Laboratory of Embryo Original Diseases, Shanghai, 200030, China; Shanghai Municipal Key Clinical Speciality, Shanghai, 200030, China
| | - Qian Wang
- The International Peace Maternity and Child Health Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200030, China; Shanghai Key Laboratory of Embryo Original Diseases, Shanghai, 200030, China; Shanghai Municipal Key Clinical Speciality, Shanghai, 200030, China
| | - Qiuwan Zhang
- The International Peace Maternity and Child Health Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200030, China; Shanghai Key Laboratory of Embryo Original Diseases, Shanghai, 200030, China; Shanghai Municipal Key Clinical Speciality, Shanghai, 200030, China
| | - Dongmei Lai
- The International Peace Maternity and Child Health Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200030, China; Shanghai Key Laboratory of Embryo Original Diseases, Shanghai, 200030, China; Shanghai Municipal Key Clinical Speciality, Shanghai, 200030, China.
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Baptiste M, Moinuddeen SS, Soliz CL, Ehsan H, Kaneko G. Making Sense of Genetic Information: The Promising Evolution of Clinical Stratification and Precision Oncology Using Machine Learning. Genes (Basel) 2021; 12:722. [PMID: 34065872 PMCID: PMC8151328 DOI: 10.3390/genes12050722] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2021] [Revised: 05/07/2021] [Accepted: 05/08/2021] [Indexed: 12/16/2022] Open
Abstract
Precision medicine is a medical approach to administer patients with a tailored dose of treatment by taking into consideration a person's variability in genes, environment, and lifestyles. The accumulation of omics big sequence data led to the development of various genetic databases on which clinical stratification of high-risk populations may be conducted. In addition, because cancers are generally caused by tumor-specific mutations, large-scale systematic identification of single nucleotide polymorphisms (SNPs) in various tumors has propelled significant progress of tailored treatments of tumors (i.e., precision oncology). Machine learning (ML), a subfield of artificial intelligence in which computers learn through experience, has a great potential to be used in precision oncology chiefly to help physicians make diagnostic decisions based on tumor images. A promising venue of ML in precision oncology is the integration of all available data from images to multi-omics big data for the holistic care of patients and high-risk healthy subjects. In this review, we provide a focused overview of precision oncology and ML with attention to breast cancer and glioma as well as the Bayesian networks that have the flexibility and the ability to work with incomplete information. We also introduce some state-of-the-art attempts to use and incorporate ML and genetic information in precision oncology.
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Affiliation(s)
| | | | | | | | - Gen Kaneko
- School of Arts & Sciences, University of Houston-Victoria, Victoria, TX 77901, USA; (M.B.); (S.S.M.); (C.L.S.); (H.E.)
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Zhang L, Xie D, Lei Y, Na A, Zhu L. Preclinical activity of cobimetinib alone or in combination with chemotherapy and targeted therapies in renal cell carcinoma. Future Oncol 2021; 17:3051-3060. [PMID: 33906367 DOI: 10.2217/fon-2021-0256] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Background: The poor outcome of advanced renal cell carcinoma (RCC) necessitates new treatments. Cobimetinib is a MEK inhibitor and approved for the treatment of melanoma. This work investigated the efficacy of cobimetinib alone and in combination with anti-RCC drugs. Methods: Proliferation and apoptosis assays were performed, and combination index was analyzed on RCC cell lines (CaKi-2, 786-O, A-704, ACHN and A489) and xenograft models. Immunoblotting analysis was conducted to investigate the MAPK pathway. Results: Cobimetinib was active against RCC cells, with IC50 at 0.006-0.8μM, and acted synergistically with standard-of-care therapy. Cobimetinib at nontoxic doses prevented tumor formation, inhibited tumor growth and enhanced efficacy of 5-fluorouracil, sorafenib and sunitinib via suppressing Raf/MEK/ERK, leading to MAPK pathway inhibition. Conclusion: Our findings demonstrate the potent anti-RCC activity of cobimetinib and its synergism with RCC standard-of-care drugs, and confirm the underlying mechanism of the action of cobimetinib.
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Affiliation(s)
- Lichen Zhang
- Department of Nephrology, The Second People's Hospital of Yibin, Yibin, Sichuan, 644000, PR China
| | - Deqiong Xie
- Department of Nephrology, The Second People's Hospital of Yibin, Yibin, Sichuan, 644000, PR China
| | - Yonghua Lei
- Department of Urology, Tangdu Hospital, Air Force Medical University, Xi'an, Shanxi, 710038, PR China
| | - Aoli Na
- Department of Nephrology, The Second People's Hospital of Yibin, Yibin, Sichuan, 644000, PR China
| | - Lei Zhu
- Department of Nephrology, The Second People's Hospital of Yibin, Yibin, Sichuan, 644000, PR China
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Integrated molecular and clinical analysis of low-grade gliomas in children with neurofibromatosis type 1 (NF1). Acta Neuropathol 2021; 141:605-617. [PMID: 33585982 DOI: 10.1007/s00401-021-02276-5] [Citation(s) in RCA: 35] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2020] [Revised: 01/21/2021] [Accepted: 01/22/2021] [Indexed: 02/06/2023]
Abstract
Low-grade gliomas (LGGs) are the most common childhood brain tumor in the general population and in individuals with the Neurofibromatosis type 1 (NF1) cancer predisposition syndrome. Surgical biopsy is rarely performed prior to treatment in the setting of NF1, resulting in a paucity of tumor genomic information. To define the molecular landscape of NF1-associated LGGs (NF1-LGG), we integrated clinical data, histological diagnoses, and multi-level genetic/genomic analyses on 70 individuals from 25 centers worldwide. Whereas, most tumors harbored bi-allelic NF1 inactivation as the only genetic abnormality, 11% had additional mutations. Moreover, tumors classified as non-pilocytic astrocytoma based on DNA methylation analysis were significantly more likely to harbor these additional mutations. The most common secondary alteration was FGFR1 mutation, which conferred an additional growth advantage in multiple complementary experimental murine Nf1 models. Taken together, this comprehensive characterization has important implications for the management of children with NF1-LGG, distinct from their sporadic counterparts.
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71
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Chesnokov MS, Khan I, Park Y, Ezell J, Mehta G, Yousif A, Hong LJ, Buckanovich RJ, Takahashi A, Chefetz I. The MEK1/2 Pathway as a Therapeutic Target in High-Grade Serous Ovarian Carcinoma. Cancers (Basel) 2021; 13:1369. [PMID: 33803586 PMCID: PMC8003094 DOI: 10.3390/cancers13061369] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2020] [Revised: 03/10/2021] [Accepted: 03/16/2021] [Indexed: 02/02/2023] Open
Abstract
High-grade serous ovarian carcinoma (HGSOC) is the deadliest of gynecological cancers due to its high recurrence rate and acquired chemoresistance. RAS/MEK/ERK pathway activation is linked to cell proliferation and therapeutic resistance, but the role of MEK1/2-ERK1/2 pathway in HGSOC is poorly investigated. We evaluated MEK1/2 pathway activity in clinical HGSOC samples and ovarian cancer cell lines using immunohistochemistry, immunoblotting, and RT-qPCR. HGSOC cell lines were used to assess immediate and lasting effects of MEK1/2 inhibition with trametinib in vitro. Trametinib effect on tumor growth in vivo was investigated using mouse xenografts. MEK1/2 pathway is hyperactivated in HGSOC and is further stimulated by cisplatin treatment. Trametinib treatment causes cell cycle arrest in G1/0-phase and reduces tumor growth rate in vivo but does not induce cell death or reduce fraction of CD133+ stem-like cells, while increasing expression of stemness-associated genes instead. Transient trametinib treatment causes long-term increase in a subpopulation of cells with high aldehyde dehydrogenase (ALDH)1 activity that can survive and grow in non-adherent conditions. We conclude that MEK1/2 inhibition may be a promising approach to suppress ovarian cancer growth as a maintenance therapy. Promotion of stem-like properties upon MEK1/2 inhibition suggests a possible mechanism of resistance, so a combination with CSC-targeting drugs should be considered.
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Affiliation(s)
- Mikhail S. Chesnokov
- The Hormel Institute, University of Minnesota, Austin, MN 55912, USA; (M.S.C.); (I.K.); (A.Y.); (A.T.)
| | - Imran Khan
- The Hormel Institute, University of Minnesota, Austin, MN 55912, USA; (M.S.C.); (I.K.); (A.Y.); (A.T.)
| | - Yeonjung Park
- Division of Hematology Oncology, Department of Internal Medicine, University of Michigan, Ann Arbor, MI 48109, USA; (Y.P.); (J.E.); (R.J.B.)
| | - Jessica Ezell
- Division of Hematology Oncology, Department of Internal Medicine, University of Michigan, Ann Arbor, MI 48109, USA; (Y.P.); (J.E.); (R.J.B.)
| | - Geeta Mehta
- Department of Biomedical Engineering, University of Michigan, Ann Arbor, MI 48109, USA;
| | - Abdelrahman Yousif
- The Hormel Institute, University of Minnesota, Austin, MN 55912, USA; (M.S.C.); (I.K.); (A.Y.); (A.T.)
| | - Linda J. Hong
- Division of Gynecologic Oncology, Department of Gynecology and Obstetrics, Loma Linda University School of Medicine, Loma Linda, CA 92350, USA;
| | - Ronald J. Buckanovich
- Division of Hematology Oncology, Department of Internal Medicine, University of Michigan, Ann Arbor, MI 48109, USA; (Y.P.); (J.E.); (R.J.B.)
- Division of Hematology Oncology, Department of Internal Medicine, University of Pittsburgh, Pittsburgh, PA 15213, USA
| | - Akimasa Takahashi
- The Hormel Institute, University of Minnesota, Austin, MN 55912, USA; (M.S.C.); (I.K.); (A.Y.); (A.T.)
- Department of Obstetrics and Gynecology, Shiga University of Medical Science, Otsu, Shiga 5202152, Japan
| | - Ilana Chefetz
- The Hormel Institute, University of Minnesota, Austin, MN 55912, USA; (M.S.C.); (I.K.); (A.Y.); (A.T.)
- Masonic Cancer Center, Minneapolis, MN 55455, USA
- Stem Cell Institute, Minneapolis, MN 55455, USA
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72
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Nell RJ, Menger NV, Versluis M, Luyten GPM, Verdijk RM, Madigan MC, Jager MJ, van der Velden PA. Involvement of mutant and wild-type CYSLTR2 in the development and progression of uveal nevi and melanoma. BMC Cancer 2021; 21:164. [PMID: 33588787 PMCID: PMC7885466 DOI: 10.1186/s12885-021-07865-x] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2020] [Accepted: 02/01/2021] [Indexed: 12/16/2022] Open
Abstract
Background Activating Gαq signalling mutations are considered an early event in the development of uveal melanoma. Whereas most tumours harbour a mutation in GNAQ or GNA11, CYSLTR2 (encoding G-protein coupled receptor CysLT2R) forms a rare alternative. The role of wild-type CysLT2R in uveal melanoma remains unknown. Methods We performed a digital PCR-based molecular analysis of benign choroidal nevi and primary uveal melanomas. Publicly available bulk and single cell sequencing data were mined to further study mutant and wild-type CYSLTR2 in primary and metastatic uveal melanoma. Results 1/16 nevi and 2/120 melanomas carried the CYSLTR2 mutation. The mutation was found in a subpopulation of the nevus, while being clonal in both melanomas. In the melanomas, secondary, subclonal CYSLTR2 alterations shifted the allelic balance towards the mutant. The resulting genetic heterogeneity was confirmed in distinct areas of both tumours. At the RNA level, further silencing of wild-type and preferential expression of mutant CYSLTR2 was identified, which was also observed in two CYSLTR2 mutant primary melanomas and one metastatic lesion from other cohorts. In CYSLTR2 wild-type melanomas, high expression of CYSLTR2 correlated to tumour inflammation, but expression originated from melanoma cells specifically. Conclusions Our findings suggest that CYSLTR2 is involved in both early and late development of uveal melanoma. Whereas the CYSLTR2 p.L129Q mutation is likely to be the initiating oncogenic event, various mechanisms further increase the mutant allele abundance during tumour progression. This makes mutant CysLT2R an attractive therapeutic target in uveal melanoma. Supplementary Information The online version contains supplementary material available at 10.1186/s12885-021-07865-x.
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Affiliation(s)
- Rogier J Nell
- Department of Ophthalmology, Leiden University Medical Center, Leiden, the Netherlands
| | - Nino V Menger
- Department of Ophthalmology, Leiden University Medical Center, Leiden, the Netherlands
| | - Mieke Versluis
- Department of Ophthalmology, Leiden University Medical Center, Leiden, the Netherlands
| | - Gregorius P M Luyten
- Department of Ophthalmology, Leiden University Medical Center, Leiden, the Netherlands
| | - Robert M Verdijk
- Department of Pathology, Leiden University Medical Center, Leiden, the Netherlands.,Department of Pathology, Erasmus MC University Medical Center, Rotterdam, the Netherlands
| | - Michele C Madigan
- Save Sight Institute and Department of Ophthalmology, University of Sydney, Sydney, Australia.,School of Optometry and Vision Science, University of New South Wales, Sydney, Australia
| | - Martine J Jager
- Department of Ophthalmology, Leiden University Medical Center, Leiden, the Netherlands
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73
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Overview of New Treatments with Immunotherapy for Breast Cancer and a Proposal of a Combination Therapy. Molecules 2020; 25:molecules25235686. [PMID: 33276556 DOI: 10.3390/molecules25235686] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2020] [Revised: 11/26/2020] [Accepted: 11/28/2020] [Indexed: 01/08/2023] Open
Abstract
According to data from the U.S. National Cancer Institute, cancer is one of the leading causes of death worldwide with approximately 14 million new cases and 8.2 million cancer-related deaths in 2018. More than 60% of the new annual cases in the world occur in Africa, Asia, Central America, and South America, with 70% of cancer deaths in these regions. Breast cancer is the most common cancer in women, with 266,120 new cases in American women and an estimated 40,920 deaths for 2018. Approximately one in six women diagnosed with breast cancer will die in the coming years. Recently, novel therapeutic strategies have been implemented in the fight against breast cancer, including molecules able to block signaling pathways, an inhibitor of poly [ADP-ribose] polymerase (PARP), growth receptor blocker antibodies, or those that reactivate the immune system by inhibiting the activities of inhibitory receptors like cytotoxic T-lymphocyte antigen 4 (CTLA-4) and programmed death protein 1 (PD-1). However, novel targets include reactivating the Th1 immune response, changing tumor microenvironment, and co-activation of other components of the immune response such as natural killer cells and CD8+ T cells among others. In this article, we review advances in the treatment of breast cancer focused essentially on immunomodulatory drugs in targeted cancer therapy. Based on this knowledge, we formulate a proposal for the implementation of combined therapy using an extracorporeal immune response reactivation model and cytokines plus modulating antibodies for co-activation of the Th1- and natural killer cell (NK)-dependent immune response, either in situ or through autologous cell therapy. The implementation of "combination immunotherapy" is new hope in breast cancer treatment. Therefore, we consider the coordinated activation of each cell of the immune response that would probably produce better outcomes. Although more research is required, the results recently achieved by combination therapy suggest that for most, if not all, cancer patients, this tailored therapy may become a realistic approach in the near future.
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74
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Sun Y, Meyers BA, Czako B, Leonard P, Mseeh F, Harris AL, Wu Q, Johnson S, Parker CA, Cross JB, Di Francesco ME, Bivona BJ, Bristow CA, Burke JP, Carrillo CC, Carroll CL, Chang Q, Feng N, Gao G, Gera S, Giuliani V, Huang JK, Jiang Y, Kang Z, Kovacs JJ, Liu CY, Lopez AM, Ma X, Mandal PK, McAfoos T, Miller MA, Mullinax RA, Peoples M, Ramamoorthy V, Seth S, Spencer ND, Suzuki E, Williams CC, Yu SS, Zuniga AM, Draetta GF, Marszalek JR, Heffernan TP, Kohl NE, Jones P. Allosteric SHP2 Inhibitor, IACS-13909, Overcomes EGFR-Dependent and EGFR-Independent Resistance Mechanisms toward Osimertinib. Cancer Res 2020; 80:4840-4853. [PMID: 32928921 PMCID: PMC11106563 DOI: 10.1158/0008-5472.can-20-1634] [Citation(s) in RCA: 43] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2020] [Revised: 08/04/2020] [Accepted: 09/01/2020] [Indexed: 11/16/2022]
Abstract
Src homology 2 domain-containing phosphatase (SHP2) is a phosphatase that mediates signaling downstream of multiple receptor tyrosine kinases (RTK) and is required for full activation of the MAPK pathway. SHP2 inhibition has demonstrated tumor growth inhibition in RTK-activated cancers in preclinical studies. The long-term effectiveness of tyrosine kinase inhibitors such as the EGFR inhibitor (EGFRi), osimertinib, in non-small cell lung cancer (NSCLC) is limited by acquired resistance. Multiple clinically identified mechanisms underlie resistance to osimertinib, including mutations in EGFR that preclude drug binding as well as EGFR-independent activation of the MAPK pathway through alternate RTK (RTK-bypass). It has also been noted that frequently a tumor from a single patient harbors more than one resistance mechanism, and the plasticity between multiple resistance mechanisms could restrict the effectiveness of therapies targeting a single node of the oncogenic signaling network. Here, we report the discovery of IACS-13909, a specific and potent allosteric inhibitor of SHP2, that suppresses signaling through the MAPK pathway. IACS-13909 potently impeded proliferation of tumors harboring a broad spectrum of activated RTKs as the oncogenic driver. In EGFR-mutant osimertinib-resistant NSCLC models with EGFR-dependent and EGFR-independent resistance mechanisms, IACS-13909, administered as a single agent or in combination with osimertinib, potently suppressed tumor cell proliferation in vitro and caused tumor regression in vivo. Together, our findings provide preclinical evidence for using a SHP2 inhibitor as a therapeutic strategy in acquired EGFRi-resistant NSCLC. SIGNIFICANCE: These findings highlight the discovery of IACS-13909 as a potent, selective inhibitor of SHP2 with drug-like properties, and targeting SHP2 may serve as a therapeutic strategy to overcome tumor resistance to osimertinib.
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Affiliation(s)
- Yuting Sun
- TRACTION - Translational Research to AdvanCe Therapeutics and Innovation in ONcology, The University of Texas MD Anderson Cancer Center, Houston, Texas.
| | - Brooke A Meyers
- TRACTION - Translational Research to AdvanCe Therapeutics and Innovation in ONcology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Barbara Czako
- Institute for Applied Cancer Science (IACS), The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Paul Leonard
- Institute for Applied Cancer Science (IACS), The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Faika Mseeh
- Institute for Applied Cancer Science (IACS), The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Angela L Harris
- TRACTION - Translational Research to AdvanCe Therapeutics and Innovation in ONcology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Qi Wu
- Institute for Applied Cancer Science (IACS), The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Sarah Johnson
- TRACTION - Translational Research to AdvanCe Therapeutics and Innovation in ONcology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Connor A Parker
- Institute for Applied Cancer Science (IACS), The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Jason B Cross
- Institute for Applied Cancer Science (IACS), The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Maria Emilia Di Francesco
- Institute for Applied Cancer Science (IACS), The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Benjamin J Bivona
- TRACTION - Translational Research to AdvanCe Therapeutics and Innovation in ONcology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Christopher A Bristow
- TRACTION - Translational Research to AdvanCe Therapeutics and Innovation in ONcology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Jason P Burke
- Institute for Applied Cancer Science (IACS), The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Caroline C Carrillo
- TRACTION - Translational Research to AdvanCe Therapeutics and Innovation in ONcology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Christopher L Carroll
- Institute for Applied Cancer Science (IACS), The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Qing Chang
- TRACTION - Translational Research to AdvanCe Therapeutics and Innovation in ONcology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Ningping Feng
- TRACTION - Translational Research to AdvanCe Therapeutics and Innovation in ONcology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Guang Gao
- TRACTION - Translational Research to AdvanCe Therapeutics and Innovation in ONcology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Sonal Gera
- TRACTION - Translational Research to AdvanCe Therapeutics and Innovation in ONcology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Virginia Giuliani
- TRACTION - Translational Research to AdvanCe Therapeutics and Innovation in ONcology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Justin K Huang
- TRACTION - Translational Research to AdvanCe Therapeutics and Innovation in ONcology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Yongying Jiang
- Institute for Applied Cancer Science (IACS), The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Zhijun Kang
- Institute for Applied Cancer Science (IACS), The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Jeffrey J Kovacs
- TRACTION - Translational Research to AdvanCe Therapeutics and Innovation in ONcology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Chiu-Yi Liu
- TRACTION - Translational Research to AdvanCe Therapeutics and Innovation in ONcology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Anastasia M Lopez
- TRACTION - Translational Research to AdvanCe Therapeutics and Innovation in ONcology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Xiaoyan Ma
- TRACTION - Translational Research to AdvanCe Therapeutics and Innovation in ONcology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Pijus K Mandal
- Institute for Applied Cancer Science (IACS), The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Timothy McAfoos
- Institute for Applied Cancer Science (IACS), The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Meredith A Miller
- TRACTION - Translational Research to AdvanCe Therapeutics and Innovation in ONcology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Robert A Mullinax
- TRACTION - Translational Research to AdvanCe Therapeutics and Innovation in ONcology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Michael Peoples
- TRACTION - Translational Research to AdvanCe Therapeutics and Innovation in ONcology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Vandhana Ramamoorthy
- TRACTION - Translational Research to AdvanCe Therapeutics and Innovation in ONcology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Sahil Seth
- TRACTION - Translational Research to AdvanCe Therapeutics and Innovation in ONcology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Nakia D Spencer
- TRACTION - Translational Research to AdvanCe Therapeutics and Innovation in ONcology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Erika Suzuki
- TRACTION - Translational Research to AdvanCe Therapeutics and Innovation in ONcology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Christopher C Williams
- Institute for Applied Cancer Science (IACS), The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Simon S Yu
- Institute for Applied Cancer Science (IACS), The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Andy M Zuniga
- TRACTION - Translational Research to AdvanCe Therapeutics and Innovation in ONcology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Giulio F Draetta
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Joseph R Marszalek
- TRACTION - Translational Research to AdvanCe Therapeutics and Innovation in ONcology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Timothy P Heffernan
- TRACTION - Translational Research to AdvanCe Therapeutics and Innovation in ONcology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | | | - Philip Jones
- Institute for Applied Cancer Science (IACS), The University of Texas MD Anderson Cancer Center, Houston, Texas
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Fang J, Pian C, Xu M, Kong L, Li Z, Ji J, Zhang L, Chen Y. Revealing Prognosis-Related Pathways at the Individual Level by a Comprehensive Analysis of Different Cancer Transcription Data. Genes (Basel) 2020; 11:genes11111281. [PMID: 33138076 PMCID: PMC7692404 DOI: 10.3390/genes11111281] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2020] [Revised: 10/26/2020] [Accepted: 10/26/2020] [Indexed: 02/07/2023] Open
Abstract
Identifying perturbed pathways at an individual level is important to discover the causes of cancer and develop individualized custom therapeutic strategies. Though prognostic gene lists have had success in prognosis prediction, using single genes that are related to the relevant system or specific network cannot fully reveal the process of tumorigenesis. We hypothesize that in individual samples, the disruption of transcription homeostasis can influence the occurrence, development, and metastasis of tumors and has implications for patient survival outcomes. Here, we introduced the individual-level pathway score, which can measure the correlation perturbation of the pathways in a single sample well. We applied this method to the expression data of 16 different cancer types from The Cancer Genome Atlas (TCGA) database. Our results indicate that different cancer types as well as their tumor-adjacent tissues can be clearly distinguished by the individual-level pathway score. Additionally, we found that there was strong heterogeneity among different cancer types and the percentage of perturbed pathways as well as the perturbation proportions of tumor samples in each pathway were significantly different. Finally, the prognosis-related pathways of different cancer types were obtained by survival analysis. We demonstrated that the individual-level pathway score (iPS) is capable of classifying cancer types and identifying some key prognosis-related pathways.
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Affiliation(s)
- Jingya Fang
- College of Agriculture, Nanjing Agricultural University, Nanjing 210095, China; (J.F.); (M.X.); (L.K.); (Z.L.); (J.J.)
| | - Cong Pian
- Department of Mathematics, College of Science, Nanjing Agricultural University, Nanjing 210095, China;
| | - Mingmin Xu
- College of Agriculture, Nanjing Agricultural University, Nanjing 210095, China; (J.F.); (M.X.); (L.K.); (Z.L.); (J.J.)
| | - Lingpeng Kong
- College of Agriculture, Nanjing Agricultural University, Nanjing 210095, China; (J.F.); (M.X.); (L.K.); (Z.L.); (J.J.)
| | - Zutan Li
- College of Agriculture, Nanjing Agricultural University, Nanjing 210095, China; (J.F.); (M.X.); (L.K.); (Z.L.); (J.J.)
| | - Jinwen Ji
- College of Agriculture, Nanjing Agricultural University, Nanjing 210095, China; (J.F.); (M.X.); (L.K.); (Z.L.); (J.J.)
| | - Liangyun Zhang
- College of Agriculture, Nanjing Agricultural University, Nanjing 210095, China; (J.F.); (M.X.); (L.K.); (Z.L.); (J.J.)
- Correspondence: (L.Z.); (Y.C.)
| | - Yuanyuan Chen
- Department of Mathematics, College of Science, Nanjing Agricultural University, Nanjing 210095, China;
- Correspondence: (L.Z.); (Y.C.)
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76
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Zoetemelk M, Ramzy GM, Rausch M, Koessler T, van Beijnum JR, Weiss A, Mieville V, Piersma SR, de Haas RR, Delucinge-Vivier C, Andres A, Toso C, Henneman AA, Ragusa S, Petrova TV, Docquier M, McKee TA, Jimenez CR, Daali Y, Griffioen AW, Rubbia-Brandt L, Dietrich PY, Nowak-Sliwinska P. Optimized low-dose combinatorial drug treatment boosts selectivity and efficacy of colorectal carcinoma treatment. Mol Oncol 2020; 14:2894-2919. [PMID: 33021054 PMCID: PMC7607171 DOI: 10.1002/1878-0261.12797] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2020] [Revised: 07/24/2020] [Accepted: 08/11/2020] [Indexed: 12/19/2022] Open
Abstract
The current standard of care for colorectal cancer (CRC) is a combination of chemotherapeutics, often supplemented with targeted biological drugs. An urgent need exists for improved drug efficacy and minimized side effects, especially at late‐stage disease. We employed the phenotypically driven therapeutically guided multidrug optimization (TGMO) technology to identify optimized drug combinations (ODCs) in CRC. We identified low‐dose synergistic and selective ODCs for a panel of six human CRC cell lines also active in heterotypic 3D co‐culture models. Transcriptome sequencing and phosphoproteome analyses showed that the mechanisms of action of these ODCs converged toward MAP kinase signaling and cell cycle inhibition. Two cell‐specific ODCs were translated to in vivo mouse models. The ODCs reduced tumor growth by ~80%, outperforming standard chemotherapy (FOLFOX). No toxicity was observed for the ODCs, while significant side effects were induced in the group treated with FOLFOX therapy. Identified ODCs demonstrated significantly enhanced bioavailability of the individual components. Finally, ODCs were also active in primary cells from CRC patient tumor tissues. Taken together, we show that the TGMO technology efficiently identifies selective and potent low‐dose drug combinations, optimized regardless of tumor mutation status, outperforming conventional chemotherapy.
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Affiliation(s)
- Marloes Zoetemelk
- Molecular Pharmacology Group, School of Pharmaceutical Sciences, University of Geneva, Switzerland.,Institute of Pharmaceutical Sciences of Western Switzerland, University of Geneva, Switzerland.,Translational Research Center in Oncohaematology, Geneva, Switzerland
| | - George M Ramzy
- Molecular Pharmacology Group, School of Pharmaceutical Sciences, University of Geneva, Switzerland.,Institute of Pharmaceutical Sciences of Western Switzerland, University of Geneva, Switzerland.,Translational Research Center in Oncohaematology, Geneva, Switzerland
| | - Magdalena Rausch
- Molecular Pharmacology Group, School of Pharmaceutical Sciences, University of Geneva, Switzerland.,Institute of Pharmaceutical Sciences of Western Switzerland, University of Geneva, Switzerland.,Translational Research Center in Oncohaematology, Geneva, Switzerland
| | - Thibaud Koessler
- Department of Oncology, Geneva University Hospitals and Faculty of Medicine, Switzerland
| | - Judy R van Beijnum
- Angiogenesis Laboratory, Department of Medical Oncology, Cancer Center Amsterdam, Amsterdam UMC-location VUmc, VU University Amsterdam, The Netherlands
| | - Andrea Weiss
- Molecular Pharmacology Group, School of Pharmaceutical Sciences, University of Geneva, Switzerland.,Institute of Pharmaceutical Sciences of Western Switzerland, University of Geneva, Switzerland
| | - Valentin Mieville
- Molecular Pharmacology Group, School of Pharmaceutical Sciences, University of Geneva, Switzerland.,Institute of Pharmaceutical Sciences of Western Switzerland, University of Geneva, Switzerland
| | - Sander R Piersma
- Department of Medical Oncology, Cancer Center Amsterdam, Amsterdam UMC, Vrije Universiteit Amsterdam, The Netherlands.,OncoProteomics Laboratory, Cancer Center Amsterdam, Amsterdam UMC, Vrije Universiteit Amsterdam, The Netherlands
| | - Richard R de Haas
- Department of Medical Oncology, Cancer Center Amsterdam, Amsterdam UMC, Vrije Universiteit Amsterdam, The Netherlands.,OncoProteomics Laboratory, Cancer Center Amsterdam, Amsterdam UMC, Vrije Universiteit Amsterdam, The Netherlands
| | | | - Axel Andres
- Translational Department of Digestive and Transplant Surgery, Geneva University Hospitals and Faculty of Medicine, Switzerland.,Hepato-Pancreato-Biliary Centre, Geneva University Hospitals and Faculty of Medicine, Switzerland
| | - Christian Toso
- Translational Department of Digestive and Transplant Surgery, Geneva University Hospitals and Faculty of Medicine, Switzerland.,Hepato-Pancreato-Biliary Centre, Geneva University Hospitals and Faculty of Medicine, Switzerland
| | - Alexander A Henneman
- Department of Medical Oncology, Cancer Center Amsterdam, Amsterdam UMC, Vrije Universiteit Amsterdam, The Netherlands.,OncoProteomics Laboratory, Cancer Center Amsterdam, Amsterdam UMC, Vrije Universiteit Amsterdam, The Netherlands
| | - Simone Ragusa
- Department of Oncology, University of Lausanne, Switzerland.,Ludwig Institute for Cancer Research Lausanne, Switzerland
| | - Tatiana V Petrova
- Department of Oncology, University of Lausanne, Switzerland.,Ludwig Institute for Cancer Research Lausanne, Switzerland
| | - Mylène Docquier
- iGE3 Genomics Platform, University of Geneva, Switzerland.,Department of Genetics & Evolution, University of Geneva, Switzerland
| | - Thomas A McKee
- Division of Clinical Pathology, Diagnostic Department, University Hospitals of Geneva (HUG), Switzerland
| | - Connie R Jimenez
- Department of Medical Oncology, Cancer Center Amsterdam, Amsterdam UMC, Vrije Universiteit Amsterdam, The Netherlands.,OncoProteomics Laboratory, Cancer Center Amsterdam, Amsterdam UMC, Vrije Universiteit Amsterdam, The Netherlands
| | - Youssef Daali
- Division of Clinical Pharmacology and Toxicology, Department of Anaesthesiology, Intensive Care and Emergency Medicine, Geneva University Hospitals, Pharmacology, Switzerland
| | - Arjan W Griffioen
- Angiogenesis Laboratory, Department of Medical Oncology, Cancer Center Amsterdam, Amsterdam UMC-location VUmc, VU University Amsterdam, The Netherlands
| | - Laura Rubbia-Brandt
- Division of Clinical Pathology, Diagnostic Department, University Hospitals of Geneva (HUG), Switzerland
| | - Pierre-Yves Dietrich
- Translational Research Center in Oncohaematology, Geneva, Switzerland.,Department of Oncology, Geneva University Hospitals and Faculty of Medicine, Switzerland
| | - Patrycja Nowak-Sliwinska
- Molecular Pharmacology Group, School of Pharmaceutical Sciences, University of Geneva, Switzerland.,Institute of Pharmaceutical Sciences of Western Switzerland, University of Geneva, Switzerland.,Translational Research Center in Oncohaematology, Geneva, Switzerland
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77
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Combined PD-1, BRAF and MEK inhibition in advanced BRAF-mutant melanoma: safety run-in and biomarker cohorts of COMBI-i. Nat Med 2020; 26:1557-1563. [PMID: 33020648 DOI: 10.1038/s41591-020-1082-2] [Citation(s) in RCA: 74] [Impact Index Per Article: 18.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2020] [Accepted: 08/26/2020] [Indexed: 12/12/2022]
Abstract
Immune and targeted therapies achieve long-term survival in metastatic melanoma; however, new treatment strategies are needed to improve patients' outcomes1,2. We report on the efficacy, safety and biomarker analysis from the single-arm safety run-in (part 1; n = 9) and biomarker (part 2; n = 27) cohorts of the randomized, placebo-controlled, phase 3 COMBI-i trial (NCT02967692) of the anti-PD-1 antibody spartalizumab, in combination with the BRAF inhibitor dabrafenib and MEK inhibitor trametinib. Patients (n = 36) had previously untreated BRAF V600-mutant unresectable or metastatic melanoma. In part 1, the recommended phase 3 regimen was identified based on the incidence of dose-limiting toxicities (DLTs; primary endpoint): 400 mg of spartalizumab every 4 weeks plus 150 mg of dabrafenib twice daily plus 2 mg of trametinib once daily. Part 2 characterized changes in PD-L1 levels and CD8+ cells following treatment (primary endpoint), and analyzed additional biomarkers. Assessments of efficacy and safety were key secondary endpoints (median follow-up, 24.3 months). Spartalizumab plus dabrafenib and trametinib led to an objective response rate (ORR) of 78%, including 44% complete responses (CRs). Grade ≥3 treatment-related adverse events (TRAEs) were experienced by 72% of patients. All patients had temporary dose modifications, and 17% permanently discontinued all three study drugs due to TRAEs. Early progression-free survival (PFS) events were associated with low tumor mutational burden/T cell-inflamed gene expression signature (GES) or high immunosuppressive tumor microenvironment (TME) GES levels at baseline; an immunosuppressive TME may also preclude CR. Overall, the efficacy, safety and on-treatment biomarker modulations associated with spartalizumab plus dabrafenib and trametinib are promising, and biomarkers that may predict long-term benefit were identified.
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78
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Proietti I, Skroza N, Bernardini N, Tolino E, Balduzzi V, Marchesiello A, Michelini S, Volpe S, Mambrin A, Mangino G, Romeo G, Maddalena P, Rees C, Potenza C. Mechanisms of Acquired BRAF Inhibitor Resistance in Melanoma: A Systematic Review. Cancers (Basel) 2020; 12:E2801. [PMID: 33003483 PMCID: PMC7600801 DOI: 10.3390/cancers12102801] [Citation(s) in RCA: 65] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2020] [Revised: 09/21/2020] [Accepted: 09/25/2020] [Indexed: 12/18/2022] Open
Abstract
This systematic review investigated the literature on acquired v-raf murine sarcoma viral oncogene homolog B1 (BRAF) inhibitor resistance in patients with melanoma. We searched MEDLINE for articles on BRAF inhibitor resistance in patients with melanoma published since January 2010 in the following areas: (1) genetic basis of resistance; (2) epigenetic and transcriptomic mechanisms; (3) influence of the immune system on resistance development; and (4) combination therapy to overcome resistance. Common resistance mutations in melanoma are BRAF splice variants, BRAF amplification, neuroblastoma RAS viral oncogene homolog (NRAS) mutations and mitogen-activated protein kinase kinase 1/2 (MEK1/2) mutations. Genetic and epigenetic changes reactivate previously blocked mitogen-activated protein kinase (MAPK) pathways, activate alternative signaling pathways, and cause epithelial-to-mesenchymal transition. Once BRAF inhibitor resistance develops, the tumor microenvironment reverts to a low immunogenic state secondary to the induction of programmed cell death ligand-1. Combining a BRAF inhibitor with a MEK inhibitor delays resistance development and increases duration of response. Multiple other combinations based on known mechanisms of resistance are being investigated. BRAF inhibitor-resistant cells develop a range of 'escape routes', so multiple different treatment targets will probably be required to overcome resistance. In the future, it may be possible to personalize combination therapy towards the specific resistance pathway in individual patients.
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Affiliation(s)
- Ilaria Proietti
- Dermatology Unit “Daniele Innocenzi”, Department of Medical-Surgical Sciences and Bio-Technologies, Sapienza University of Rome, Fiorini Hospital, Polo Pontino, 04019 Terracina, Italy; (N.S.); (N.B.); (E.T.); (V.B.); (A.M.); (S.M.); (S.V.); (A.M.); (P.M.); (C.P.)
| | - Nevena Skroza
- Dermatology Unit “Daniele Innocenzi”, Department of Medical-Surgical Sciences and Bio-Technologies, Sapienza University of Rome, Fiorini Hospital, Polo Pontino, 04019 Terracina, Italy; (N.S.); (N.B.); (E.T.); (V.B.); (A.M.); (S.M.); (S.V.); (A.M.); (P.M.); (C.P.)
| | - Nicoletta Bernardini
- Dermatology Unit “Daniele Innocenzi”, Department of Medical-Surgical Sciences and Bio-Technologies, Sapienza University of Rome, Fiorini Hospital, Polo Pontino, 04019 Terracina, Italy; (N.S.); (N.B.); (E.T.); (V.B.); (A.M.); (S.M.); (S.V.); (A.M.); (P.M.); (C.P.)
| | - Ersilia Tolino
- Dermatology Unit “Daniele Innocenzi”, Department of Medical-Surgical Sciences and Bio-Technologies, Sapienza University of Rome, Fiorini Hospital, Polo Pontino, 04019 Terracina, Italy; (N.S.); (N.B.); (E.T.); (V.B.); (A.M.); (S.M.); (S.V.); (A.M.); (P.M.); (C.P.)
| | - Veronica Balduzzi
- Dermatology Unit “Daniele Innocenzi”, Department of Medical-Surgical Sciences and Bio-Technologies, Sapienza University of Rome, Fiorini Hospital, Polo Pontino, 04019 Terracina, Italy; (N.S.); (N.B.); (E.T.); (V.B.); (A.M.); (S.M.); (S.V.); (A.M.); (P.M.); (C.P.)
| | - Anna Marchesiello
- Dermatology Unit “Daniele Innocenzi”, Department of Medical-Surgical Sciences and Bio-Technologies, Sapienza University of Rome, Fiorini Hospital, Polo Pontino, 04019 Terracina, Italy; (N.S.); (N.B.); (E.T.); (V.B.); (A.M.); (S.M.); (S.V.); (A.M.); (P.M.); (C.P.)
| | - Simone Michelini
- Dermatology Unit “Daniele Innocenzi”, Department of Medical-Surgical Sciences and Bio-Technologies, Sapienza University of Rome, Fiorini Hospital, Polo Pontino, 04019 Terracina, Italy; (N.S.); (N.B.); (E.T.); (V.B.); (A.M.); (S.M.); (S.V.); (A.M.); (P.M.); (C.P.)
| | - Salvatore Volpe
- Dermatology Unit “Daniele Innocenzi”, Department of Medical-Surgical Sciences and Bio-Technologies, Sapienza University of Rome, Fiorini Hospital, Polo Pontino, 04019 Terracina, Italy; (N.S.); (N.B.); (E.T.); (V.B.); (A.M.); (S.M.); (S.V.); (A.M.); (P.M.); (C.P.)
| | - Alessandra Mambrin
- Dermatology Unit “Daniele Innocenzi”, Department of Medical-Surgical Sciences and Bio-Technologies, Sapienza University of Rome, Fiorini Hospital, Polo Pontino, 04019 Terracina, Italy; (N.S.); (N.B.); (E.T.); (V.B.); (A.M.); (S.M.); (S.V.); (A.M.); (P.M.); (C.P.)
| | - Giorgio Mangino
- Department of Medico-Surgical Sciences and Biotechnologies, Sapienza University of Rome, 00185 Rome, Italy; (G.M.); (G.R.)
| | - Giovanna Romeo
- Department of Medico-Surgical Sciences and Biotechnologies, Sapienza University of Rome, 00185 Rome, Italy; (G.M.); (G.R.)
- Department of Infectious, Parasitic and Immune-Mediated Diseases, Istituto Superiore di Sanità, 00185 Rome, Italy
- Institute of Molecular Biology and Pathology, Consiglio Nazionale delle Ricerche, 00185 Rome, Italy
| | - Patrizia Maddalena
- Dermatology Unit “Daniele Innocenzi”, Department of Medical-Surgical Sciences and Bio-Technologies, Sapienza University of Rome, Fiorini Hospital, Polo Pontino, 04019 Terracina, Italy; (N.S.); (N.B.); (E.T.); (V.B.); (A.M.); (S.M.); (S.V.); (A.M.); (P.M.); (C.P.)
| | | | - Concetta Potenza
- Dermatology Unit “Daniele Innocenzi”, Department of Medical-Surgical Sciences and Bio-Technologies, Sapienza University of Rome, Fiorini Hospital, Polo Pontino, 04019 Terracina, Italy; (N.S.); (N.B.); (E.T.); (V.B.); (A.M.); (S.M.); (S.V.); (A.M.); (P.M.); (C.P.)
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79
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Mechanisms of resistance and predictive biomarkers of response to targeted therapies and immunotherapies in metastatic melanoma. Curr Opin Oncol 2020; 32:91-97. [PMID: 31833956 DOI: 10.1097/cco.0000000000000603] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
PURPOSE OF REVIEW Thanks to mitogen-activated protein kinase inhibitors (MAPKi) and immune checkpoint inhibitors (ICI), major progress has been made in the field of melanoma treatment. However, long-term success is still scarce because of the development of resistance. Understanding these mechanisms of resistance and identifying predictive genomic biomarkers are now key points in the therapeutic management of melanoma patients. RECENT FINDINGS Multiple and complex mechanisms of resistance to MAPKi or ICI have been uncovered in the past few years. The lack of response can be driven by mutations and nonmutational events in tumor cells, as well as by changes in the tumor microenvironment. Melanoma cells are also capable of rapidly switching their molecular and cellular phenotype, leading to an initial drug-tolerant favorizing melanoma resistance. Tumor molecular profiling and circulating tumor cell analyses are of high interest as predictive biomarkers as well as studying immunogenic changes and microbiome in ICI-treated patients. SUMMARY Resistance to MAPKi and ICI is a key point in therapeutic management of metastatic melanoma patients. Validated biomarkers predicting response to therapy are urgently needed to move toward personalized medicine. Combinatory treatments guided by the understanding of resistance mechanisms will be of major importance in the future of melanoma therapy.
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80
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Hofmann MH, Gmachl M, Ramharter J, Savarese F, Gerlach D, Marszalek JR, Sanderson MP, Kessler D, Trapani F, Arnhof H, Rumpel K, Botesteanu DA, Ettmayer P, Gerstberger T, Kofink C, Wunberg T, Zoephel A, Fu SC, Teh JL, Böttcher J, Pototschnig N, Schachinger F, Schipany K, Lieb S, Vellano CP, O'Connell JC, Mendes RL, Moll J, Petronczki M, Heffernan TP, Pearson M, McConnell DB, Kraut N. BI-3406, a Potent and Selective SOS1-KRAS Interaction Inhibitor, Is Effective in KRAS-Driven Cancers through Combined MEK Inhibition. Cancer Discov 2020; 11:142-157. [PMID: 32816843 DOI: 10.1158/2159-8290.cd-20-0142] [Citation(s) in RCA: 221] [Impact Index Per Article: 55.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2020] [Revised: 07/14/2020] [Accepted: 08/14/2020] [Indexed: 12/13/2022]
Abstract
KRAS is the most frequently mutated driver of pancreatic, colorectal, and non-small cell lung cancers. Direct KRAS blockade has proved challenging, and inhibition of a key downstream effector pathway, the RAF-MEK-ERK cascade, has shown limited success because of activation of feedback networks that keep the pathway in check. We hypothesized that inhibiting SOS1, a KRAS activator and important feedback node, represents an effective approach to treat KRAS-driven cancers. We report the discovery of a highly potent, selective, and orally bioavailable small-molecule SOS1 inhibitor, BI-3406, that binds to the catalytic domain of SOS1, thereby preventing the interaction with KRAS. BI-3406 reduces formation of GTP-loaded RAS and limits cellular proliferation of a broad range of KRAS-driven cancers. Importantly, BI-3406 attenuates feedback reactivation induced by MEK inhibitors and thereby enhances sensitivity of KRAS-dependent cancers to MEK inhibition. Combined SOS1 and MEK inhibition represents a novel and effective therapeutic concept to address KRAS-driven tumors. SIGNIFICANCE: To date, there are no effective targeted pan-KRAS therapies. In-depth characterization of BI-3406 activity and identification of MEK inhibitors as effective combination partners provide an attractive therapeutic concept for the majority of KRAS-mutant cancers, including those fueled by the most prevalent mutant KRAS oncoproteins, G12D, G12V, G12C, and G13D.See related commentary by Zhao et al., p. 17.This article is highlighted in the In This Issue feature, p. 1.
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Affiliation(s)
| | | | | | | | | | - Joseph R Marszalek
- TRACTION Platform, Division of Therapeutics Discovery, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | | | - Dirk Kessler
- Boehringer Ingelheim RCV GmbH & Co KG, Vienna, Austria
| | | | | | - Klaus Rumpel
- Boehringer Ingelheim RCV GmbH & Co KG, Vienna, Austria
| | | | | | | | | | | | | | - Szu-Chin Fu
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Jessica L Teh
- TRACTION Platform, Division of Therapeutics Discovery, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Jark Böttcher
- Boehringer Ingelheim RCV GmbH & Co KG, Vienna, Austria
| | | | | | | | - Simone Lieb
- Boehringer Ingelheim RCV GmbH & Co KG, Vienna, Austria
| | - Christopher P Vellano
- TRACTION Platform, Division of Therapeutics Discovery, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | | | | | - Jurgen Moll
- Boehringer Ingelheim RCV GmbH & Co KG, Vienna, Austria
| | | | - Timothy P Heffernan
- TRACTION Platform, Division of Therapeutics Discovery, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Mark Pearson
- Boehringer Ingelheim RCV GmbH & Co KG, Vienna, Austria
| | | | - Norbert Kraut
- Boehringer Ingelheim RCV GmbH & Co KG, Vienna, Austria.
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81
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Subbiah V, Lassen U, Élez E, Italiano A, Curigliano G, Javle M, de Braud F, Prager GW, Greil R, Stein A, Fasolo A, Schellens JHM, Wen PY, Viele K, Boran AD, Gasal E, Burgess P, Ilankumaran P, Wainberg ZA. Dabrafenib plus trametinib in patients with BRAF V600E-mutated biliary tract cancer (ROAR): a phase 2, open-label, single-arm, multicentre basket trial. Lancet Oncol 2020; 21:1234-1243. [PMID: 32818466 DOI: 10.1016/s1470-2045(20)30321-1] [Citation(s) in RCA: 261] [Impact Index Per Article: 65.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2020] [Revised: 03/20/2020] [Accepted: 05/28/2020] [Indexed: 01/08/2023]
Abstract
BACKGROUND Effective treatments for patients with cholangiocarcinoma after progression on gemcitabine-based chemotherapy are urgently needed. Mutations in the BRAF gene have been found in 5% of biliary tract tumours. The combination of dabrafenib and trametinib has shown activity in several BRAFV600E-mutated cancers. We aimed to assess the activity and safety of dabrafenib and trametinib combination therapy in patients with BRAFV600E-mutated biliary tract cancer. METHODS This study is part of an ongoing, phase 2, open-label, single-arm, multicentre, Rare Oncology Agnostic Research (ROAR) basket trial in patients with BRAFV600E-mutated rare cancers. Patients were eligible for the biliary tract cancer cohort if they were aged 18 years or older, had BRAFV600E-mutated, unresectable, metastatic, locally advanced, or recurrent biliary tract cancer, an Eastern Cooperative Oncology Group performance status of 0-2, and had received previous systemic treatment. All patients were treated with oral dabrafenib 150 mg twice daily and oral trametinib 2 mg once daily until disease progression or intolerance of treatment. The primary endpoint was the overall response rate, which was determined by Response Evaluation Criteria in Solid Tumors version 1.1 in the intention-to-treat evaluable population, which comprised all enrolled patients regardless of receiving treatment who were evaluable (ie, had progression, began a new anticancer treatment, withdrew consent, died, had stable disease for 6 weeks or longer, or had two or more post-baseline assessments). The ROAR trial is registered with ClinicalTrials.gov, NCT02034110. These results are based on an interim analysis; the study is active but not recruiting. FINDINGS Between March 12, 2014, and July 18, 2018, 43 patients with BRAFV600E-mutated biliary tract cancer were enrolled to the study and were evaluable. Median follow-up was 10 months (IQR 6-15). An investigator-assessed overall response was achieved by 22 (51%, 95% CI 36-67) of 43 patients. An independent reviewer-assessed overall response was achieved by 20 (47%, 95% CI 31-62) of 43 patients. The most common grade 3 or worse adverse event was increased γ-glutamyltransferase in five (12%) patients. 17 (40%) patients had serious adverse events and nine (21%) had treatment-related serious adverse events, the most frequent of which was pyrexia (eight [19%]). No treatment-related deaths were reported. INTERPRETATION Dabrafenib plus trametinib combination treatment showed promising activity in patients with BRAFV600E-mutated biliary tract cancer, with a manageable safety profile. Routine testing for BRAFV600E mutations should be considered in patients with biliary tract cancer. FUNDING GlaxoSmithKline and Novartis.
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Affiliation(s)
- Vivek Subbiah
- Department of Investigational Cancer Therapeutics, Division of Cancer Medicine, University of Texas MD Anderson Cancer Center, Houston, TX, USA.
| | - Ulrik Lassen
- Department of Oncology, Rigshospitalet, University of Copenhagen, Copenhagen, Denmark
| | - Elena Élez
- Medical Oncology Department, Vall d'Hebron Institute of Oncology, Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Antoine Italiano
- Early Phase Trials and Sarcoma Units, Institut Bergonié, Bordeaux, France
| | - Giuseppe Curigliano
- Division of Early Drug Development, Istituto Europeo di Oncologia, IRCCS, and University of Milano, Milan, Italy
| | - Milind Javle
- Department of Gastrointestinal Medical Oncology, Division of Cancer Medicine, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Filippo de Braud
- Dipartimento di Oncologia, Istituto Nazionale dei Tumori, Milan, Italy
| | - Gerald W Prager
- Department of Medicine I, Comprehensive Cancer Center Vienna, Medical University Vienna, Vienna, Austria
| | - Richard Greil
- Third Medical Department, Paracelsus Medical University Salzburg, Salzburg Cancer Research Institute, CCS Salzburg, Salzburg, Austria
| | - Alexander Stein
- Department of Internal Medicine II (Oncology Center), University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Angelica Fasolo
- Department of Medical Oncology, IRCCS Ospedale San Raffaele, Milan, Italy
| | - Jan H M Schellens
- Department of Clinical Pharmacology, Netherlands Cancer Institute, Antoni van Leeuwenhoek, Amsterdam, Netherlands
| | - Patrick Y Wen
- Center for Neuro-Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Kert Viele
- Berry Consultants, Austin, TX, USA; Department of Biostatistics, University of Kentucky, Lexington, KY, USA
| | - Aislyn D Boran
- Precision Medicine, Novartis Pharmaceuticals, East Hanover, NJ, USA
| | - Eduard Gasal
- Global Drug Development, Novartis Pharmaceuticals, East Hanover, NJ, USA
| | - Paul Burgess
- Global Drug Development, Novartis Pharma, Basel, Switzerland
| | | | - Zev A Wainberg
- Department of Medicine, David Geffen School of Medicine at the University of California Los Angeles, Los Angeles, CA, USA
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82
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Middleton G, Yang Y, Campbell CD, André T, Atreya CE, Schellens JHM, Yoshino T, Bendell JC, Hollebecque A, McRee AJ, Siena S, Gordon MS, Tabernero J, Yaeger R, O'Dwyer PJ, De Vos F, Van Cutsem E, Millholland JM, Brase JC, Rangwala F, Gasal E, Corcoran RB. BRAF-Mutant Transcriptional Subtypes Predict Outcome of Combined BRAF, MEK, and EGFR Blockade with Dabrafenib, Trametinib, and Panitumumab in Patients with Colorectal Cancer. Clin Cancer Res 2020; 26:2466-2476. [PMID: 32047001 PMCID: PMC8194012 DOI: 10.1158/1078-0432.ccr-19-3579] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2019] [Revised: 12/20/2019] [Accepted: 02/07/2020] [Indexed: 12/22/2022]
Abstract
PURPOSE The influence of the transcriptional and immunologic context of mutations on therapeutic outcomes with targeted therapy in cancer has not been well defined. BRAF V600E-mutant (BM) colorectal cancer comprises two main transcriptional subtypes, BM1 and BM2. We sought to determine the impact of BM subtype, as well as distinct biological features of those subtypes, on response to BRAF/MEK/EGFR inhibition in patients with colorectal cancer. PATIENTS AND METHODS Paired fresh tumor biopsies were acquired at baseline and on day 15 of treatment from all consenting patients with BM colorectal cancer enrolled in a phase II clinical trial of dabrafenib, trametinib, and panitumumab. For each sample, BM subtype, cell cycle, and immune gene signature expression were determined using RNA-sequencing (RNA-seq), and a Cox proportional hazards model was applied to determine association with progression-free survival (PFS). RESULTS Confirmed response rates, median PFS, and median overall survival (OS) were higher in BM1 subtype patients compared with BM2 subtype patients. Evaluation of immune contexture identified greater immune reactivity in BM1, whereas cell-cycle signatures were more highly expressed in BM2. A multivariate model of PFS incorporating BM subtype plus immune and cell-cycle signatures revealed that BM subtype encompasses the majority of the effect. CONCLUSIONS BM subtype is significantly associated with the outcome of combination dabrafenib, trametinib, and panitumumab therapy and may serve as a standalone predictive biomarker beyond mutational status. Our findings support a more nuanced approach to targeted therapeutic decisions that incorporates assessment of transcriptional context.
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Affiliation(s)
- Gary Middleton
- Institute of Immunology and Immunotherapy, University of Birmingham, Birmingham, United Kingdom.
| | - Yiqun Yang
- Novartis Institutes for BioMedical Research, Cambridge, Massachusetts
| | | | - Thierry André
- Hôpital Saint-Antoine and Sorbonne Universités, UPMC Paris 06, Paris, France
| | - Chloe E Atreya
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, California
| | | | | | - Johanna C Bendell
- Sarah Cannon Research Institute/Tennessee Oncology, Nashville, Tennessee
| | | | - Autumn J McRee
- University of North Carolina, Chapel Hill, North Carolina
| | - Salvatore Siena
- Department of Oncology and Hemato-Oncology, Università degli Studi di Milano, Milan, Italy
- Niguarda Cancer Center, Grande Ospedale Metropolitano Niguarda, Milan, Italy
| | | | | | - Rona Yaeger
- Memorial Sloan Kettering Cancer Center, New York, New York
| | - Peter J O'Dwyer
- Abramson Cancer Center, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Filip De Vos
- Department of Medical Oncology, University Medical Center Utrecht, Utrecht University, Utrecht, the Netherlands
| | | | | | | | - Fatima Rangwala
- Novartis Pharmaceuticals Corporation, East Hanover, New Jersey
| | - Eduard Gasal
- Novartis Pharmaceuticals Corporation, East Hanover, New Jersey
| | - Ryan B Corcoran
- Massachusetts General Hospital Cancer Center and Department of Medicine, Harvard Medical School, Boston, Massachusetts
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83
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Connectivity map-based drug repositioning of bortezomib to reverse the metastatic effect of GALNT14 in lung cancer. Oncogene 2020; 39:4567-4580. [PMID: 32388539 DOI: 10.1038/s41388-020-1316-2] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2019] [Revised: 04/11/2020] [Accepted: 04/24/2020] [Indexed: 12/11/2022]
Abstract
Despite the continual discovery of promising new cancer targets, drug discovery is often hampered by the poor druggability of these targets. As such, repurposing FDA-approved drugs based on cancer signatures is a useful alternative to cancer precision medicine. Here, we adopted an in silico approach based on large-scale gene expression signatures to identify drug candidates for lung cancer metastasis. Our clinicogenomic analysis identified GALNT14 as a putative driver of lung cancer metastasis, leading to poor survival. To overcome the poor druggability of GALNT14 in the control of metastasis, we utilized the Connectivity Map and identified bortezomib (BTZ) as a potent metastatic inhibitor, bypassing the direct inhibition of the enzymatic activity of GALNT14. The antimetastatic effect of BTZ was verified both in vitro and in vivo. Notably, both BTZ treatment and GALNT14 knockdown attenuated TGFβ-mediated gene expression and suppressed TGFβ-dependent metastatic genes. These results demonstrate that our in silico approach is a viable strategy for the use of undruggable targets in cancer therapies and for revealing the underlying mechanisms of these targets.
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84
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Louveau B, Jouenne F, Kaguelidou F, Landras A, Goldwirt L, Mourah S. The key role of oncopharmacology in therapeutic management, from common to rare cancers: A literature review. Therapie 2020; 75:183-193. [DOI: 10.1016/j.therap.2020.02.010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2019] [Accepted: 11/15/2019] [Indexed: 01/18/2023]
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85
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Reger de Moura C, Vercellino L, Jouenne F, Baroudjian B, Sadoux A, Louveau B, Delyon J, Serror K, Goldwirt L, Merlet P, Bouquet F, Battistella M, Lebbé C, Mourah S. Intermittent Versus Continuous Dosing of MAPK Inhibitors in the Treatment of BRAF-Mutated Melanoma. Transl Oncol 2020; 13:275-286. [PMID: 31874374 PMCID: PMC6931208 DOI: 10.1016/j.tranon.2019.10.003] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2019] [Accepted: 10/08/2019] [Indexed: 02/02/2023] Open
Abstract
The development of BRAF and MEK inhibitors (BRAFi/MEKi) has led to major advances in melanoma treatment. However, the emergence of resistance mechanisms limits the benefit duration and a complete response occurs in less than 20% of patients receiving BRAFi ± MEKi. In this study, we evaluated the impact of an intermittent versus continuous dosing schedule of BRAF/MEK inhibition in a melanoma model mildly sensitive to a BRAF inhibitor. The combination of a BRAFi with three different MEKi was studied with a continuous or intermittent dosing schedule in vivo, in a xenografted melanoma model and ex vivo using histoculture drug response assays (HDRAs) of patient-derived xenografts (PDX). To further understand the underlying molecular mechanisms of therapeutic efficacy, a biomarker pharmacodynamic readout was evaluated. An equal impact on tumor growth was observed in monotherapy or bitherapy regimens whether we used continuous and intermittent dosing schedules, with no significant differences in biomarkers expression between the treatments. The antitumoral effect was mostly due to modulations of expression of cell cycle and apoptotic mediators. Moreover, ex vivo studies did not show significant differences between the dosing schedules. In this context, our preclinical and pharmacodynamic results converged to show the similarity between intermittent and continuous treatments with either BRAFi or MEKi alone or with the combination of both.
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Affiliation(s)
- Coralie Reger de Moura
- Université de Paris, Inserm, UMR_S976, Paris, France; Department of Pharmacogenomics, Hôpital Saint-Louis, AP-HP, Paris, France
| | | | - Fanélie Jouenne
- Université de Paris, Inserm, UMR_S976, Paris, France; Department of Pharmacogenomics, Hôpital Saint-Louis, AP-HP, Paris, France
| | | | - Aurélie Sadoux
- Université de Paris, Inserm, UMR_S976, Paris, France; Department of Pharmacogenomics, Hôpital Saint-Louis, AP-HP, Paris, France
| | - Baptiste Louveau
- Université de Paris, Inserm, UMR_S976, Paris, France; Department of Pharmacogenomics, Hôpital Saint-Louis, AP-HP, Paris, France
| | - Julie Delyon
- Department of Dermatology, Hôpital Saint-Louis, AP-HP, Paris, France
| | - Kevin Serror
- Department of Plastic, Reconstructive and Aesthetic Surgery, Hôpital Saint-Louis, AP-HP, Paris, France
| | - Lauriane Goldwirt
- Université de Paris, Inserm, UMR_S976, Paris, France; Department of Pharmacogenomics, Hôpital Saint-Louis, AP-HP, Paris, France
| | - Pascal Merlet
- Department of Nuclear Medicine, Hôpital Saint-Louis, AP-HP, Paris, France
| | | | - Maxime Battistella
- Department of Pathology, Hôpital Saint-Louis, AP-HP, Paris, France; Université de Paris, Inserm, UMR_S1165, Paris, France
| | - Céleste Lebbé
- Université de Paris, Inserm, UMR_S976, Paris, France; Department of Dermatology, Hôpital Saint-Louis, AP-HP, Paris, France
| | - Samia Mourah
- Université de Paris, Inserm, UMR_S976, Paris, France; Department of Pharmacogenomics, Hôpital Saint-Louis, AP-HP, Paris, France.
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86
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Varga A, Soria JC, Hollebecque A, LoRusso P, Bendell J, Huang SMA, Wagle MC, Okrah K, Liu L, Murray E, Sanabria-Bohorquez SM, Tagen M, Dokainish H, Mueller L, Burris H. A First-in-Human Phase I Study to Evaluate the ERK1/2 Inhibitor GDC-0994 in Patients with Advanced Solid Tumors. Clin Cancer Res 2019; 26:1229-1236. [PMID: 31848189 DOI: 10.1158/1078-0432.ccr-19-2574] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2019] [Revised: 11/27/2019] [Accepted: 12/13/2019] [Indexed: 11/16/2022]
Abstract
PURPOSE ERK1/2 signaling can be dysregulated in cancer. GDC-0994 is an oral inhibitor of ERK1/2. A first-in-human, phase I dose escalation study of GDC-0994 was conducted in patients with locally advanced or metastatic solid tumors. PATIENTS AND METHODS GDC-0994 was administered once daily on a 21-day on/7-day off schedule to evaluate safety, pharmacokinetics, and preliminary signs of efficacy. Patients with pancreatic adenocarcinoma and BRAF-mutant colorectal cancer were enrolled in the expansion stage. RESULTS Forty-seven patients were enrolled in six successive cohorts (50-800 mg). A single DLT of grade 3 rash occurred at 600 mg. The most common drug-related adverse events (AE) were diarrhea, rash, nausea, fatigue, and vomiting. Pharmacokinetic data showed dose-proportional increases in exposure, with a mean half-life of 23 hours, supportive of once daily dosing. In evaluable paired biopsies, MAPK pathway inhibition ranged from 19% to 51%. Partial metabolic responses by FDG-PET were observed in 11 of 20 patients across dose levels in multiple tumor types. Overall, 15 of 45 (33%) patients had a best overall response of stable disease and 2 patients with BRAF-mutant colorectal cancer had a confirmed partial response. CONCLUSIONS GDC-0994 had an acceptable safety profile and pharmacodynamic effects were observed by FDG-PET and in serial tumor biopsies. Single-agent activity was observed in 2 patients with BRAF-mutant colorectal cancer.
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Affiliation(s)
- Andrea Varga
- Gustave Roussy Cancer Center, Villejuif, France.
| | - Jean-Charles Soria
- Gustave Roussy Cancer Center, Villejuif, France.,Universite Paris Sud, Orsay, France
| | | | | | - Johanna Bendell
- Sarah Cannon Research Institute/Tennessee Oncology, Nashville, Tennessee
| | | | | | - Kwame Okrah
- Genentech, Inc., South San Francisco, California
| | - Lichuan Liu
- Genentech, Inc., South San Francisco, California
| | | | | | | | | | - Lars Mueller
- Genentech, Inc., South San Francisco, California
| | - Howard Burris
- Sarah Cannon Research Institute/Tennessee Oncology, Nashville, Tennessee
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87
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Carroll MJ, Parent CR, Page D, Kreeger PK. Tumor cell sensitivity to vemurafenib can be predicted from protein expression in a BRAF-V600E basket trial setting. BMC Cancer 2019; 19:1025. [PMID: 31672130 PMCID: PMC6822426 DOI: 10.1186/s12885-019-6175-2] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2019] [Accepted: 09/20/2019] [Indexed: 01/25/2023] Open
Abstract
BACKGROUND Genetics-based basket trials have emerged to test targeted therapeutics across multiple cancer types. However, while vemurafenib is FDA-approved for BRAF-V600E melanomas, the non-melanoma basket trial was unsuccessful, suggesting mutation status is insufficient to predict response. We hypothesized that proteomic data would complement mutation status to identify vemurafenib-sensitive tumors and effective co-treatments for BRAF-V600E tumors with inherent resistance. METHODS Reverse Phase Proteomic Array (RPPA, MD Anderson Cell Lines Project), RNAseq (Cancer Cell Line Encyclopedia) and vemurafenib sensitivity (Cancer Therapeutic Response Portal) data for BRAF-V600E cancer cell lines were curated. Linear and nonlinear regression models using RPPA protein or RNAseq were evaluated and compared based on their ability to predict BRAF-V600E cell line sensitivity (area under the dose response curve). Accuracies of all models were evaluated using hold-out testing. CausalPath software was used to identify protein-protein interaction networks that could explain differential protein expression in resistant cells. Human examination of features employed by the model, the identified protein interaction networks, and model simulation suggested anti-ErbB co-therapy would counter intrinsic resistance to vemurafenib. To validate this potential co-therapy, cell lines were treated with vemurafenib and dacomitinib (a pan-ErbB inhibitor) and the number of viable cells was measured. RESULTS Orthogonal partial least squares (O-PLS) predicted vemurafenib sensitivity with greater accuracy in both melanoma and non-melanoma BRAF-V600E cell lines than other leading machine learning methods, specifically Random Forests, Support Vector Regression (linear and quadratic kernels) and LASSO-penalized regression. Additionally, use of transcriptomic in place of proteomic data weakened model performance. Model analysis revealed that resistant lines had elevated expression and activation of ErbB receptors, suggesting ErbB inhibition could improve vemurafenib response. As predicted, experimental evaluation of vemurafenib plus dacomitinb demonstrated improved efficacy relative to monotherapies. CONCLUSIONS Combined, our results support that inclusion of proteomics can predict drug response and identify co-therapies in a basket setting.
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Affiliation(s)
- Molly J Carroll
- Department of Biomedical Engineering, University of Wisconsin-Madison 1111 Highland Ave, WIMR 4553, Madison, WI, 53705, USA
| | - Carl R Parent
- Department of Biomedical Engineering, University of Wisconsin-Madison 1111 Highland Ave, WIMR 4553, Madison, WI, 53705, USA
| | - David Page
- Department of Biostatistics and Bioinformatics, Duke University, Box 2721, Durham, NC, 27710, USA.
- University of Wisconsin Carbone Cancer Center, University of Wisconsin School of Medicine and Public Health, Madison, WI, USA.
| | - Pamela K Kreeger
- Department of Biomedical Engineering, University of Wisconsin-Madison 1111 Highland Ave, WIMR 4553, Madison, WI, 53705, USA.
- Department of Obstetrics and Gynecology, University of Wisconsin School of Medicine and Public Health, Madison, WI, USA.
- Department of Cell and Regenerative Biology, University of Wisconsin School of Medicine and Public Health, Madison, WI, USA.
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88
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Flavahan WA, Drier Y, Johnstone SE, Hemming ML, Tarjan DR, Hegazi E, Shareef SJ, Javed NM, Raut CP, Eschle BK, Gokhale PC, Hornick JL, Sicinska ET, Demetri GD, Bernstein BE. Altered chromosomal topology drives oncogenic programs in SDH-deficient GISTs. Nature 2019; 575:229-233. [PMID: 31666694 PMCID: PMC6913936 DOI: 10.1038/s41586-019-1668-3] [Citation(s) in RCA: 139] [Impact Index Per Article: 27.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2017] [Accepted: 09/10/2019] [Indexed: 12/22/2022]
Abstract
Epigenetic aberrations are widespread in cancer, yet the underlying
mechanisms and causality remain poorly understood1-3.
A subset of gastrointestinal stromal tumors (GISTs) lack canonical kinase
mutations but instead have succinate dehydrogenase (SDH)-deficiency and global
DNA hyper-methylation4,5. Here we associate this hyper-methylation
with changes in genome topology that activate oncogenic programs. To investigate
epigenetic alterations systematically, we mapped DNA methylation, CTCF
insulators, enhancers, and chromosome topology in KIT-mutant,
PDGFRA-mutant, and SDH-deficient GISTs. Although these
respective subtypes shared similar enhancer landscapes, we identified hundreds
of putative insulators where DNA methylation replaced CTCF binding in
SDH-deficient GISTs. We focused on a disrupted insulator that normally
partitions a core GIST super-enhancer from the FGF4 oncogene.
Recurrent loss of this insulator alters locus topology in SDH-deficient GISTs,
allowing aberrant physical interaction between enhancer and oncogene.
CRISPR-mediated excision of the corresponding CTCF motifs in an SDH-intact GIST
model disrupted the boundary and strongly up-regulated FGF4
expression. We also identified a second recurrent insulator loss event near the
KIT oncogene, which is also highly expressed across
SDH-deficient GISTs. Finally, we established a patient-derived xenograft (PDX)
from an SDH-deficient GIST that faithfully maintains the epigenetics of the
parental tumor, including hyper-methylation and insulator defects. This PDX
model is highly sensitive to FGF receptor (FGFR) inhibitor, and more so to
combined FGFR and KIT inhibition, validating the functional significance of the
underlying epigenetic lesions. Our study reveals how epigenetic alterations can
drive oncogenic programs in the absence of canonical kinase mutations, with
implications for mechanistic targeting of aberrant pathways in cancers.
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Affiliation(s)
- William A Flavahan
- Department of Pathology and Center for Cancer Research, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA.,Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Yotam Drier
- Department of Pathology and Center for Cancer Research, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA. .,Broad Institute of MIT and Harvard, Cambridge, MA, USA. .,The Lautenberg Center for Immunology and Cancer Research, IMRIC, Faculty of Medicine, The Hebrew University, Jerusalem, Israel.
| | - Sarah E Johnstone
- Department of Pathology and Center for Cancer Research, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA.,Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Matthew L Hemming
- Center for Sarcoma and Bone Oncology, Dana-Farber Cancer Institute, Boston, MA, USA.,Department of Medical Oncology, Dana-Farber Cancer Institute and Harvard Medical School Boston, Boston, MA, USA
| | - Daniel R Tarjan
- Department of Pathology and Center for Cancer Research, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA.,Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Esmat Hegazi
- Department of Pathology and Center for Cancer Research, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA.,Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Sarah J Shareef
- Department of Pathology and Center for Cancer Research, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA.,Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Nauman M Javed
- Department of Pathology and Center for Cancer Research, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA.,Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Chandrajit P Raut
- Department of Surgery, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Benjamin K Eschle
- Experimental Therapeutics Core, Belfer Center for Applied Cancer Science, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Prafulla C Gokhale
- Experimental Therapeutics Core, Belfer Center for Applied Cancer Science, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Jason L Hornick
- Department of Pathology, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Ewa T Sicinska
- Department of Oncologic Pathology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, MA, USA
| | - George D Demetri
- Center for Sarcoma and Bone Oncology, Dana-Farber Cancer Institute, Boston, MA, USA. .,Department of Medical Oncology, Dana-Farber Cancer Institute and Harvard Medical School Boston, Boston, MA, USA. .,Ludwig Center at Harvard, Harvard Medical School, Boston, MA, USA.
| | - Bradley E Bernstein
- Department of Pathology and Center for Cancer Research, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA. .,Broad Institute of MIT and Harvard, Cambridge, MA, USA. .,Ludwig Center at Harvard, Harvard Medical School, Boston, MA, USA.
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89
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Feng T, Golji J, Li A, Zhang X, Ruddy DA, Rakiec DP, Geyer FC, Gu J, Gao H, Williams JA, Stuart DD, Meyer MJ. Distinct Transcriptional Programming Drive Response to MAPK Inhibition in BRAF V600-Mutant Melanoma Patient-Derived Xenografts. Mol Cancer Ther 2019; 18:2421-2432. [PMID: 31527224 DOI: 10.1158/1535-7163.mct-19-0028] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2019] [Revised: 06/26/2019] [Accepted: 09/10/2019] [Indexed: 11/16/2022]
Abstract
Inhibitors targeting BRAF and its downstream kinase MEK produce robust response in patients with advanced BRAF V600-mutant melanoma. However, the duration and depth of response vary significantly between patients; therefore, predicting response a priori remains a significant challenge. Here, we utilized the Novartis collection of patient-derived xenografts to characterize transcriptional alterations elicited by BRAF and MEK inhibitors in vivo, in an effort to identify mechanisms governing differential response to MAPK inhibition. We show that the expression of an MITF-high, "epithelial-like" transcriptional program is associated with reduced sensitivity and adaptive response to BRAF and MEK inhibitor treatment. On the other hand, xenograft models that express an MAPK-driven "mesenchymal-like" transcriptional program are preferentially sensitive to MAPK inhibition. These gene-expression programs are somewhat similar to the MITF-high and -low phenotypes described in cancer cell lines, but demonstrate an inverse relationship with drug response. This suggests a discrepancy between in vitro and in vivo experimental systems that warrants future investigations. Finally, BRAF V600-mutant melanoma relies on either MAPK or alternative pathways for survival under BRAF and MEK inhibition in vivo, which in turn predicts their response to further pathway suppression using a combination of BRAF, MEK, and ERK inhibitors. Our findings highlight the intertumor heterogeneity in BRAF V600-mutant melanoma, and the need for precision medicine strategies to target this aggressive cancer.
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Affiliation(s)
- Tianshu Feng
- Oncology Drug Discovery, Novartis Institutes for BioMedical Research (NIBR), Cambridge, Massachusetts
| | - Javad Golji
- Oncology Drug Discovery, Novartis Institutes for BioMedical Research (NIBR), Cambridge, Massachusetts
| | - Ailing Li
- Oncology Drug Discovery, Novartis Institutes for BioMedical Research (NIBR), Cambridge, Massachusetts
| | - Xiamei Zhang
- Oncology Drug Discovery, Novartis Institutes for BioMedical Research (NIBR), Cambridge, Massachusetts
| | - David A Ruddy
- Oncology Drug Discovery, Novartis Institutes for BioMedical Research (NIBR), Cambridge, Massachusetts
| | - Daniel P Rakiec
- Oncology Drug Discovery, Novartis Institutes for BioMedical Research (NIBR), Cambridge, Massachusetts
| | - Felipe C Geyer
- Oncology Drug Discovery, Novartis Institutes for BioMedical Research (NIBR), Cambridge, Massachusetts
| | - Jane Gu
- Oncology Drug Discovery, Novartis Institutes for BioMedical Research (NIBR), Cambridge, Massachusetts
| | - Hui Gao
- Oncology Drug Discovery, Novartis Institutes for BioMedical Research (NIBR), Cambridge, Massachusetts
| | - Juliet A Williams
- Oncology Drug Discovery, Novartis Institutes for BioMedical Research (NIBR), Cambridge, Massachusetts
| | - Darrin D Stuart
- Oncology Drug Discovery, Novartis Institutes for BioMedical Research (NIBR), Cambridge, Massachusetts.
| | - Matthew J Meyer
- Oncology Drug Discovery, Novartis Institutes for BioMedical Research (NIBR), Cambridge, Massachusetts.
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90
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Hao HX, Wang H, Liu C, Kovats S, Velazquez R, Lu H, Pant B, Shirley M, Meyer MJ, Pu M, Lim J, Fleming M, Alexander L, Farsidjani A, LaMarche MJ, Moody S, Silver SJ, Caponigro G, Stuart DD, Abrams TJ, Hammerman PS, Williams J, Engelman JA, Goldoni S, Mohseni M. Tumor Intrinsic Efficacy by SHP2 and RTK Inhibitors in KRAS-Mutant Cancers. Mol Cancer Ther 2019; 18:2368-2380. [DOI: 10.1158/1535-7163.mct-19-0170] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2019] [Revised: 07/10/2019] [Accepted: 08/16/2019] [Indexed: 11/16/2022]
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91
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Louveau B, Jouenne F, Reger de Moura C, Sadoux A, Baroudjian B, Delyon J, Herms F, De Masson A, Da Meda L, Battistella M, Dumaz N, Lebbe C, Mourah S. Baseline Genomic Features in BRAFV600-Mutated Metastatic Melanoma Patients Treated with BRAF Inhibitor + MEK Inhibitor in Routine Care. Cancers (Basel) 2019; 11:E1203. [PMID: 31426590 PMCID: PMC6721518 DOI: 10.3390/cancers11081203] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2019] [Revised: 08/08/2019] [Accepted: 08/09/2019] [Indexed: 12/26/2022] Open
Abstract
In BRAFV600mut metastatic melanoma, the combination of BRAF and MEK inhibitors (BRAFi, MEKi) has undergone multiple resistance mechanisms, limiting its clinical benefit and resulting in the need for response predicting biomarkers. Based on phase III clinical trial data, several studies have previously explored baseline genomic features associated with response to BRAFi + MEKi. Using a targeted approach that combines the examination of mRNA expression and DNA alterations in a subset of genes, we performed an analysis of baseline genomic alterations involved in MAPK inhibitors' resistance in a real-life cohort of BRAFV600mut metastatic melanoma patients. Twenty-seven patients were included in this retrospective study, and tumor samples were analyzed when the BRAFi + MEKi therapy was initiated. The clinical characteristics of our cohort were consistent with previously published studies. The BRAFi + MEKi treatment was initiated in seven patients as a following-line treatment, and had a specific transcriptomic profile exhibiting 14 genes with lower mRNA expression. However, DNA alterations in CCND1, RB1, and MET were only observed in patients who received BRAFi + MEKi as the first-line treatment. Furthermore, KIT mRNA expression was significantly higher in patients showing clinical benefit from the combined therapy, emphasizing the tumor-suppressor role of KIT already described within the context of BRAF-mutant melanoma.
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Affiliation(s)
- Baptiste Louveau
- Pharmacogenomics Department, Assistance Publique-Hôpitaux de Paris (APHP), Saint Louis Hospital, 75010 Paris, France
- Université de Paris, INSERM UMRS 976, 75010 Paris, France
| | - Fanelie Jouenne
- Pharmacogenomics Department, Assistance Publique-Hôpitaux de Paris (APHP), Saint Louis Hospital, 75010 Paris, France
- Université de Paris, INSERM UMRS 976, 75010 Paris, France
| | - Coralie Reger de Moura
- Pharmacogenomics Department, Assistance Publique-Hôpitaux de Paris (APHP), Saint Louis Hospital, 75010 Paris, France
| | - Aurelie Sadoux
- Pharmacogenomics Department, Assistance Publique-Hôpitaux de Paris (APHP), Saint Louis Hospital, 75010 Paris, France
| | - Barouyr Baroudjian
- Université de Paris, INSERM UMRS 976, 75010 Paris, France
- Dermatology Department and Centre d'investigation clinique (CIC), Assistance Publique-Hôpitaux de Paris (APHP), Saint Louis Hospital, 75010 Paris, France
| | - Julie Delyon
- Université de Paris, INSERM UMRS 976, 75010 Paris, France
- Dermatology Department and Centre d'investigation clinique (CIC), Assistance Publique-Hôpitaux de Paris (APHP), Saint Louis Hospital, 75010 Paris, France
| | - Florian Herms
- Dermatology Department and Centre d'investigation clinique (CIC), Assistance Publique-Hôpitaux de Paris (APHP), Saint Louis Hospital, 75010 Paris, France
| | - Adele De Masson
- Dermatology Department and Centre d'investigation clinique (CIC), Assistance Publique-Hôpitaux de Paris (APHP), Saint Louis Hospital, 75010 Paris, France
| | - Laetitia Da Meda
- Dermatology Department and Centre d'investigation clinique (CIC), Assistance Publique-Hôpitaux de Paris (APHP), Saint Louis Hospital, 75010 Paris, France
| | - Maxime Battistella
- Pathology Department, Assistance Publique-Hôpitaux de Paris (APHP), Saint Louis Hospital, 75010 Paris, France
- Université de Paris, INSERM UMRS 1165, 75010 Paris, France
| | - Nicolas Dumaz
- Université de Paris, INSERM UMRS 976, 75010 Paris, France
| | - Celeste Lebbe
- Université de Paris, INSERM UMRS 976, 75010 Paris, France
- Dermatology Department and Centre d'investigation clinique (CIC), Assistance Publique-Hôpitaux de Paris (APHP), Saint Louis Hospital, 75010 Paris, France
| | - Samia Mourah
- Pharmacogenomics Department, Assistance Publique-Hôpitaux de Paris (APHP), Saint Louis Hospital, 75010 Paris, France.
- Université de Paris, INSERM UMRS 976, 75010 Paris, France.
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92
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Zulauf N, Brüggmann D, Groneberg D, Oremek GM. Expressiveness of Bone Markers in Breast Cancer with Bone Metastases. Oncology 2019; 97:236-244. [PMID: 31412345 DOI: 10.1159/000500675] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2019] [Accepted: 04/28/2019] [Indexed: 11/19/2022]
Abstract
INTRODUCTION On a global scale, the malignant growth of mammary gland is the most common type of cancer in women. In the progress of mammary carcinoma, osseous metastatic invasion has a pivotal significance because it is a frequent complication occurring at an early stage of the disease. BACKGROUND Bone metastases in breast cancer patients lead to increased mortality and decreased health-related quality of life. Therefore, early diagnostic assessment and treatment is requested. Meanwhile the progress of the disease should be monitored closely. Regarding health-related quality of life and lifetime prolongation, osseous metastases should be early diagnosed, therapied, and monitored. Up to date the gold standard is the whole-body scintigraphy. This kind of bone imaging features has high sensitivity but shows loss of specificity. AIM This study aims to investigate the diagnostic versatility of bone markers in its resorption and formation function to detect bone metastases in patients with breast cancer. PATIENTS, MATERIALS, AND METHODS For this purpose, the concentration of competing bone processing tumor markers in serums of 78 patients was detected and analyzed. Two groups of women with mammary carcinoma with and without osseous metastases were built to examine the presence (or absence) of statistically significant disparity of tumor marker concentration. The tumor markers employed in this study were the carboxyterminal collagen type I telopeptid (CTX), known as beta-crosslaps (β-CTx), the alkaline phosphatase (AP), and its isoenzymes (especially the bone-specific AP [B-AP]). Additionally, the tumor markers for breast cancer (CA 15-3 and CEA) were analyzed in both groups. RESULTS Our results provide evidence that in both groups, tumor markers such as β-CTx and B-AP were a promising tool for the detection and exclusion of bone metastases in breast cancer. This comprehensive investigation shows both β-CTx and B-AP are able to fulfill the conditions of a competent appliance to detect osseous metastases of patients with mammary carcinoma. CONCLUSION Concerning the urgency of early and frequent detection, staging, and disease monitoring of mammary carcinoma with osseous metastases, this study renewed and underlined the importance of biochemical tumor markers - especially β-CTx and B-AP - and laid a clinical-based cornerstone to build up on a prospective research.
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Affiliation(s)
- Nicole Zulauf
- Division of Laboratory Diagnostics, Institute of Occupational, Social and Environmental Medicine, Goethe University Frankfurt, Frankfurt, Germany,
| | - Dörthe Brüggmann
- Department of Gynaecology, Obstetrics and Perinatal Medicine, Goethe University Frankfurt, Frankfurt, Germany
| | - David Groneberg
- Division of Epidemiology, Institute of Occupational, Social and Environmental Medicine, Goethe University Frankfurt, Frankfurt, Germany
| | - Gerhard Maximilian Oremek
- Division of Laboratory Diagnostics, Institute of Occupational, Social and Environmental Medicine, Goethe University Frankfurt, Frankfurt, Germany
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93
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Zamanian Azodi M, Rezaei Tavirani M, Rezaei Tavirani M. Identification of the Key Genes of Autism Spectrum Disorder Through Protein-Protein Interaction Network. Galen Med J 2019; 8:e1367. [PMID: 34466502 PMCID: PMC8343959 DOI: 10.31661/gmj.v0i0.1367] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2018] [Revised: 10/09/2018] [Accepted: 11/17/2018] [Indexed: 12/01/2022] Open
Abstract
Background: Currently, the prevalence of autism spectrum disorder (ASD) is increasing, which widely spurs the interest in the molecular investigation. Thereby, a better understanding of the given disorder mechanisms is likely to be achieved. Bioinformatics suiting protein-protein interactions analysis via the application of high-throughput studies, such as protein array, is one of these achievements. Materials and Methods: The gene expression data from Gene Expression Omnibus (GEO) database were downloaded, and the expression profile of patients with developmental delay and autistic features were analyzed via Cytoscape and its relevant plug-ins. Results: Our findings indicated that EGFR, ACTB, RHOA, CALM1, MAPK1, and JUN genes as the hub-bottlenecks and their related terms could be important in ASD risk. In other words, any expression modification in these genes could trigger dysfunctions in the corresponding biological processes. Conclusion: We suggest that differentially expressed genes could be used as suitable targets for ASD after being validated.
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Affiliation(s)
- Mona Zamanian Azodi
- Proteomics Research Center, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Mostafa Rezaei Tavirani
- Proteomics Research Center, Faculty of Paramedical Sciences, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Majid Rezaei Tavirani
- Faculty of Medicine, Iran University of Medical Sciences, Tehran, Iran
- Correspondence to: Majid Rezaei Tavirani, Faculty of Medicine, Iran University of Medical Sciences, Tehran, Iran Telephon Number: 09183420279 Email Address:
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94
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Cronise KE, Hernandez BG, Gustafson DL, Duval DL. Identifying the ErbB/MAPK Signaling Cascade as a Therapeutic Target in Canine Bladder Cancer. Mol Pharmacol 2019; 96:36-46. [PMID: 31048548 DOI: 10.1124/mol.119.115808] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2019] [Accepted: 04/27/2019] [Indexed: 12/19/2022] Open
Abstract
Transitional cell carcinoma (TCC) of the bladder comprises 2% of diagnosed canine cancers. TCC tumors are generally inoperable and unresponsive to traditional chemotherapy, indicating a need for more effective therapies. BRAF, a kinase in the mitogen-activated protein kinase (MAPK) pathway, is mutated in 70% of canine TCCs. In this study, we use BRAF mutant and wild-type TCC cell lines to characterize the role of BRAF mutations in TCC pathogenesis and assess the efficacy of inhibition of the MAPK pathway alone and in combination with other gene targets as a treatment for canine TCC. Analysis of MAPK target gene expression and assessment of extracellular signal-regulated kinase (ERK) 1/2 phosphorylation following serum starvation indicated constitutive MAPK activity in all TCC cell lines. BRAF mutant TCC cell lines were insensitive to the BRAF inhibitor vemurafenib, with IC50 values greater than 5 μM, but exhibited greater sensitivity to a paradox-breaking BRAF inhibitor (IC50: 0.2-1 μM). All TCC cell lines had IC50 values less than 7 nM to the mitogen-activated protein kinase kinase (MEK) 1/2 inhibitor trametinib independent of their BRAF mutation status. ERK1/2 phosphorylation decreased after 6-hour treatments with MAPK inhibitors, but rebounded by 24 hours, suggesting the presence of resistance mechanisms. Microarray analysis identified elevated expression of the ErbB family of receptors and ligands in TCC cell lines. The pan-ErbB inhibitor sapitinib synergized with BRAF inhibition in BRAF mutant Bliley TCC cells and synergized with MEK1/2 inhibition in Bliley and BRAF wild-type Kinsey cells. These findings suggest the potential for combined MAPK and ErbB receptor inhibition as a therapy for canine TCC. SIGNIFICANCE STATEMENT: The results of this study (1) identify a novel combination strategy for canine bladder cancer treatment: targeting the ErbB/MAPK signaling cascade and (2) establish the utility of canine bladder cancer as a naturally-occurring model for human MAPK-driven cancers.
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Affiliation(s)
- Kathryn E Cronise
- Flint Animal Cancer Center, Department of Clinical Sciences (K.E.C., B.G.H., D.L.G., D.L.D.), and Cell and Molecular Biology Graduate Program (K.E.C., D.L.G., D.L.D.), Colorado State University, Fort Collins, Colorado; and University of Colorado Cancer Center, Aurora, Colorado (D.L.G., D.L.D.)
| | - Belen G Hernandez
- Flint Animal Cancer Center, Department of Clinical Sciences (K.E.C., B.G.H., D.L.G., D.L.D.), and Cell and Molecular Biology Graduate Program (K.E.C., D.L.G., D.L.D.), Colorado State University, Fort Collins, Colorado; and University of Colorado Cancer Center, Aurora, Colorado (D.L.G., D.L.D.)
| | - Daniel L Gustafson
- Flint Animal Cancer Center, Department of Clinical Sciences (K.E.C., B.G.H., D.L.G., D.L.D.), and Cell and Molecular Biology Graduate Program (K.E.C., D.L.G., D.L.D.), Colorado State University, Fort Collins, Colorado; and University of Colorado Cancer Center, Aurora, Colorado (D.L.G., D.L.D.)
| | - Dawn L Duval
- Flint Animal Cancer Center, Department of Clinical Sciences (K.E.C., B.G.H., D.L.G., D.L.D.), and Cell and Molecular Biology Graduate Program (K.E.C., D.L.G., D.L.D.), Colorado State University, Fort Collins, Colorado; and University of Colorado Cancer Center, Aurora, Colorado (D.L.G., D.L.D.)
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95
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Louveau B, Delyon J, De Moura CR, Battistella M, Jouenne F, Golmard L, Sadoux A, Podgorniak MP, Chami I, Marco O, Caramel J, Dalle S, Feugeas JP, Dumaz N, Lebbe C, Mourah S. A targeted genomic alteration analysis predicts survival of melanoma patients under BRAF inhibitors. Oncotarget 2019; 10:1669-1687. [PMID: 30899440 PMCID: PMC6422198 DOI: 10.18632/oncotarget.26707] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2018] [Accepted: 01/31/2019] [Indexed: 11/25/2022] Open
Abstract
Several mechanisms have been described to elucidate the emergence of resistance to MAPK inhibitors in melanoma and there is a crucial need for biomarkers to identify patients who are likely to achieve a better and long-lasting response to BRAF inhibitors therapy. In this study, we developed a targeted approach combining both mRNA and DNA alterations analysis focusing on relevant gene alterations involved in acquired BRAF inhibitor resistance. We collected baseline tumor samples from 64 melanoma patients at BRAF inhibitor treatment initiation and showed that the presence, prior to treatment, of mRNA over-expression of genes' subset was significantly associated with improved progression free survival and overall survival. The presence of DNA alterations was in favor of better overall survival. The genomic analysis of relapsed-matched tumor samples from 20 patients allowed us to uncover the largest landscape of resistance mechanisms reported to date as at least one resistance mechanism was identified for each patient studied. Alterations in RB1 have been most frequent and hence represent an important additional acquired resistance mechanism. Our targeted genomic analysis emerges as a relevant tool in clinical practice to identify those patients who are more likely to achieve durable response to targeted therapies and to exhaustively describe the spectrum of resistance mechanisms. Our approach can be adapted to new targeted therapies by including newly identified genetic alterations.
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Affiliation(s)
- Baptiste Louveau
- Paris-Diderot University, Sorbonne Paris Cité, Paris, France.,Paris-Diderot University, Inserm, UMR_S976, Paris, France.,Department of Pharmacogenomics, Saint-Louis Hospital, AP-HP, Paris, France
| | - Julie Delyon
- Paris-Diderot University, Sorbonne Paris Cité, Paris, France.,Paris-Diderot University, Inserm, UMR_S976, Paris, France.,Department of Dermatology, Saint-Louis Hospital, AP-HP, Paris, France
| | - Coralie Reger De Moura
- Paris-Diderot University, Inserm, UMR_S976, Paris, France.,Department of Pharmacogenomics, Saint-Louis Hospital, AP-HP, Paris, France
| | - Maxime Battistella
- Paris-Diderot University, Sorbonne Paris Cité, Paris, France.,Department of Pathology, Saint-Louis Hospital, AP-HP, Paris, France.,Paris Diderot University, Inserm, UMR_S1165, Paris, France
| | - Fanelie Jouenne
- Paris-Diderot University, Sorbonne Paris Cité, Paris, France.,Paris-Diderot University, Inserm, UMR_S976, Paris, France.,Department of Pharmacogenomics, Saint-Louis Hospital, AP-HP, Paris, France
| | - Lisa Golmard
- Department of Genetics, Pôle de Médecine Diagnostique et Théranostique, Institut Curie, Paris, France
| | - Aurelie Sadoux
- Paris-Diderot University, Sorbonne Paris Cité, Paris, France.,Paris-Diderot University, Inserm, UMR_S976, Paris, France.,Department of Pharmacogenomics, Saint-Louis Hospital, AP-HP, Paris, France
| | - Marie-Pierre Podgorniak
- Paris-Diderot University, Sorbonne Paris Cité, Paris, France.,Paris-Diderot University, Inserm, UMR_S976, Paris, France.,Department of Pharmacogenomics, Saint-Louis Hospital, AP-HP, Paris, France
| | - Ichrak Chami
- Department of Dermatology, Saint-Louis Hospital, AP-HP, Paris, France
| | - Oren Marco
- Department of Plastic, Reconstructive and Esthetic Surgery, Saint-Louis Hospital, AP-HP, Paris, France
| | - Julie Caramel
- Université de Lyon, Université Claude Bernard Lyon 1, INSERM 1052, CNRS 5286, Centre Léon Bérard, Cancer Research Center of Lyon, Equipe Labellisée Ligue contre le Cancer, Lyon, France
| | - Stephane Dalle
- Université de Lyon, Université Claude Bernard Lyon 1, INSERM 1052, CNRS 5286, Centre Léon Bérard, Cancer Research Center of Lyon, Equipe Labellisée Ligue contre le Cancer, Lyon, France.,Centre Hospitalier Lyon Sud, Hospices Civils de Lyon, Pierre Bénite, France
| | | | - Nicolas Dumaz
- Paris-Diderot University, Sorbonne Paris Cité, Paris, France.,Paris-Diderot University, Inserm, UMR_S976, Paris, France
| | - Celeste Lebbe
- Paris-Diderot University, Sorbonne Paris Cité, Paris, France.,Paris-Diderot University, Inserm, UMR_S976, Paris, France.,Department of Dermatology, Saint-Louis Hospital, AP-HP, Paris, France
| | - Samia Mourah
- Paris-Diderot University, Sorbonne Paris Cité, Paris, France.,Paris-Diderot University, Inserm, UMR_S976, Paris, France.,Department of Pharmacogenomics, Saint-Louis Hospital, AP-HP, Paris, France
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