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Dyrkheeva NS, Zakharenko AL, Malakhova AA, Okorokova LS, Shtokalo DN, Medvedev SP, Tupikin AA, Kabilov MR, Lavrik OI. Transcriptomic analysis of HEK293A cells with a CRISPR/Cas9-mediated TDP1 knockout. Biochim Biophys Acta Gen Subj 2024; 1868:130616. [PMID: 38621596 DOI: 10.1016/j.bbagen.2024.130616] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2023] [Revised: 03/21/2024] [Accepted: 04/01/2024] [Indexed: 04/17/2024]
Abstract
Tyrosyl-DNA phosphodiesterase 1 (TDP1) is a human DNA repair protein. It is a member of the phospholipase D family based on structural similarity. TDP1 is a key enzyme of the repair of stalled topoisomerase 1 (TOP1)-DNA complexes. Previously, with the CRISPR/Cas9 method, we obtained HEK293A cells with a homozygous knockout of the TDP1 gene and used the TDP1 knockout cells as a cellular model for studying mechanisms of action of an anticancer therapy. In the present work, we hypothesized that the TDP1 knockout would alter the expression of DNA repair-related genes. By transcriptomic analysis, we investigated for the first time the effect of the TDP1 gene knockout on genes' expression changes in the human HEK293A cell line. We obtained original data implying a role of TDP1 in other processes besides the repair of the DNA-TOP1 complex. Differentially expressed gene analysis revealed that TDP1 may participate in cell adhesion and communication, spermatogenesis, mitochondrial function, neurodegeneration, a cytokine response, and the MAPK signaling pathway.
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Affiliation(s)
- Nadezhda S Dyrkheeva
- Institute of Chemical Biology and Fundamental Medicine (ICBFM), Siberian Branch of Russian Academy of Sciences (SB RAS), 8 Akad. Lavrentyeva Ave., Novosibirsk 630090, Russia.
| | - Alexandra L Zakharenko
- Institute of Chemical Biology and Fundamental Medicine (ICBFM), Siberian Branch of Russian Academy of Sciences (SB RAS), 8 Akad. Lavrentyeva Ave., Novosibirsk 630090, Russia.
| | - Anastasia A Malakhova
- Institute of Chemical Biology and Fundamental Medicine (ICBFM), Siberian Branch of Russian Academy of Sciences (SB RAS), 8 Akad. Lavrentyeva Ave., Novosibirsk 630090, Russia; Federal research center Institute of Cytology and Genetics, SB RAS, 10 Akad. Lavrentyeva Ave., Novosibirsk 630090, Russia.
| | | | - Dmitry N Shtokalo
- AcademGene LLC, 6 Akad. Lavrentyeva Ave., Novosibirsk 630090, Russia; A.P. Ershov Institute of Informatics Systems, SB RAS, 6 Akad. Lavrentyeva Ave., Novosibirsk 630090, Russia.
| | - Sergey P Medvedev
- Institute of Chemical Biology and Fundamental Medicine (ICBFM), Siberian Branch of Russian Academy of Sciences (SB RAS), 8 Akad. Lavrentyeva Ave., Novosibirsk 630090, Russia; Federal research center Institute of Cytology and Genetics, SB RAS, 10 Akad. Lavrentyeva Ave., Novosibirsk 630090, Russia.
| | - Alexey A Tupikin
- Institute of Chemical Biology and Fundamental Medicine (ICBFM), Siberian Branch of Russian Academy of Sciences (SB RAS), 8 Akad. Lavrentyeva Ave., Novosibirsk 630090, Russia.
| | - Marsel R Kabilov
- Institute of Chemical Biology and Fundamental Medicine (ICBFM), Siberian Branch of Russian Academy of Sciences (SB RAS), 8 Akad. Lavrentyeva Ave., Novosibirsk 630090, Russia.
| | - Olga I Lavrik
- Institute of Chemical Biology and Fundamental Medicine (ICBFM), Siberian Branch of Russian Academy of Sciences (SB RAS), 8 Akad. Lavrentyeva Ave., Novosibirsk 630090, Russia.
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Darabi S, Adeyelu T, Elliott A, Sukari A, Hodges K, Abdulla F, Zuazo CE, Wise-Draper T, Wang T, Demeure MJ. Genomic and Transcriptomic Landscape of RET Wild-Type Medullary Thyroid Cancer and Potential Use of Mitogen-Activated Protein Kinase-Targeted Therapy. J Am Coll Surg 2024; 239:50-60. [PMID: 38651727 PMCID: PMC11168784 DOI: 10.1097/xcs.0000000000001098] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2024] [Revised: 03/25/2024] [Accepted: 04/03/2024] [Indexed: 04/25/2024]
Abstract
BACKGROUND About 75% of medullary thyroid cancers (MTCs) are sporadic with 45% to 70% being driven by a RET mutation. Selpercatinib is an approved treatment for RET-mutated (mut RET ) MTC; however, treatments are needed for wild-type RET MTC (wt RET ). Genomic alterations and transcriptomic signatures of wt RET MTC may reveal new therapeutic insights. STUDY DESIGN We did a retrospective analysis of MTC samples submitted for DNA/RNA sequencing and programmed cell death ligand 1 expression using immunohistochemistry at a Clinical Laboratory Improvement Amendments/College of American Pathologists-certified laboratory. Tumor microenvironment immune cell fractions were estimated using RNA deconvolution (quanTIseq). Transcriptomic signatures of inflammation and MAP kinase pathway activation scores were calculated. Mann-Whitney U, chi-square, and Fisher's exact tests were applied (p values adjusted for multiple comparisons). RESULTS The 160-patient cohort included 108 mut RET and 52 wt RET MTC samples. wt RET tumors frequently harbored mitogen-activated protein kinase (MAPK) pathway mutations, including HRAS (42.31%), KRAS (15.7%), NF1 (6.7%), and BRAF (2%), whereas only 1 MAPK pathway mutation ( NF1 ) was identified among mut RET MTC. Recurrent mutations seen in wt RET MTC included MGA , VHL, APC , STK11 , and NFE2L2 . Increased transcriptional activation of the MAPK pathway was observed in patients with wt RET harboring mutations in MAPK genes. Although the frequency of programmed cell death ligand 1 expression was similar in wt RET and mut RET (10.2% vs 7%, p = 0.531), wt RET tumors were more often tumor mutational burden high (7.7% vs 0%, p = 0.011), and wt RET MTC exhibited higher expression of immune checkpoint genes. CONCLUSIONS We identified molecular alterations and immune-related features that distinguish wt RET from mut RET MTC. Although RET mutation drives MTC in the absence of other alterations, we showed that wt RET MTC frequently harbors MAPK pathway mutations. These findings may indicate a potential basis for MAPK-targeted therapy, possibly in combination with immuno-oncology agents for selected patients with wt RET MTC.
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Affiliation(s)
- Sourat Darabi
- From the Cancer Institute, Hoag Memorial Hospital, Newport Beach, CA (Darabi, Zuazo, Wang, Demeure)
| | - Tolulope Adeyelu
- Clinical and Translational Research, Caris Life Science, Phoenix, AZ (Adeyelu, Elliott, Hodges, Abdulla)
| | - Andrew Elliott
- Clinical and Translational Research, Caris Life Science, Phoenix, AZ (Adeyelu, Elliott, Hodges, Abdulla)
| | - Ammar Sukari
- Department of Oncology, Karmanos Cancer Institute, Detroit, MI (Sukari)
| | - Kurt Hodges
- Clinical and Translational Research, Caris Life Science, Phoenix, AZ (Adeyelu, Elliott, Hodges, Abdulla)
| | - Farah Abdulla
- Clinical and Translational Research, Caris Life Science, Phoenix, AZ (Adeyelu, Elliott, Hodges, Abdulla)
| | - Carlos E Zuazo
- From the Cancer Institute, Hoag Memorial Hospital, Newport Beach, CA (Darabi, Zuazo, Wang, Demeure)
| | - Trisha Wise-Draper
- Division of Hematology/Oncology, University of Cincinnati, Cincinnati, OH (Wise-Draper)
| | - Thomas Wang
- From the Cancer Institute, Hoag Memorial Hospital, Newport Beach, CA (Darabi, Zuazo, Wang, Demeure)
| | - Michael J Demeure
- From the Cancer Institute, Hoag Memorial Hospital, Newport Beach, CA (Darabi, Zuazo, Wang, Demeure)
- Division of Integrated Cancer Genomics, Translational Genomics Research Institute, Phoenix, AZ (Demeure)
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3
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Zuckermann M, He C, Andrews J, Bagchi A, Sloan-Henry R, Bianski B, Xie J, Wang Y, Twarog N, Onar-Thomas A, Ernst KJ, Yang L, Li Y, Zhu X, Ocasio JK, Budd KM, Dalton J, Li X, Chepyala D, Zhang J, Xu K, Hover L, Roach JT, Chan KCH, Hofmann N, McKinnon PJ, Pfister SM, Shelat AA, Rankovic Z, Freeman BB, Chiang J, Jones DTW, Tinkle CL, Baker SJ. Capmatinib is an effective treatment for MET-fusion driven pediatric high-grade glioma and synergizes with radiotherapy. Mol Cancer 2024; 23:123. [PMID: 38849845 PMCID: PMC11157767 DOI: 10.1186/s12943-024-02027-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2023] [Accepted: 05/21/2024] [Indexed: 06/09/2024] Open
Abstract
BACKGROUND Pediatric-type diffuse high-grade glioma (pHGG) is the most frequent malignant brain tumor in children and can be subclassified into multiple entities. Fusion genes activating the MET receptor tyrosine kinase often occur in infant-type hemispheric glioma (IHG) but also in other pHGG and are associated with devastating morbidity and mortality. METHODS To identify new treatment options, we established and characterized two novel orthotopic mouse models harboring distinct MET fusions. These included an immunocompetent, murine allograft model and patient-derived orthotopic xenografts (PDOX) from a MET-fusion IHG patient who failed conventional therapy and targeted therapy with cabozantinib. With these models, we analyzed the efficacy and pharmacokinetic properties of three MET inhibitors, capmatinib, crizotinib and cabozantinib, alone or combined with radiotherapy. RESULTS Capmatinib showed superior brain pharmacokinetic properties and greater in vitro and in vivo efficacy than cabozantinib or crizotinib in both models. The PDOX models recapitulated the poor efficacy of cabozantinib experienced by the patient. In contrast, capmatinib extended survival and induced long-term progression-free survival when combined with radiotherapy in two complementary mouse models. Capmatinib treatment increased radiation-induced DNA double-strand breaks and delayed their repair. CONCLUSIONS We comprehensively investigated the combination of MET inhibition and radiotherapy as a novel treatment option for MET-driven pHGG. Our seminal preclinical data package includes pharmacokinetic characterization, recapitulation of clinical outcomes, coinciding results from multiple complementing in vivo studies, and insights into molecular mechanism underlying increased efficacy. Taken together, we demonstrate the groundbreaking efficacy of capmatinib and radiation as a highly promising concept for future clinical trials.
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Affiliation(s)
- Marc Zuckermann
- Hopp Children's Cancer Center Heidelberg (KiTZ), Heidelberg, Germany.
- Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ) and German Cancer Consortium (DKTK), Im Neuenheimer Feld 280, Heidelberg, Germany.
- Division of Pediatric Glioma Research, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 280, Heidelberg, Germany.
| | - Chen He
- Department of Developmental Neurobiology, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN, 38105, USA
| | - Jared Andrews
- Department of Developmental Neurobiology, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN, 38105, USA
| | - Aditi Bagchi
- Department of Oncology, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN, 38105, USA
| | - Roketa Sloan-Henry
- Center for Pediatric Neurological Disease Research, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN, 38105, USA
| | - Brandon Bianski
- Department of Radiation Oncology, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN, 38105, USA
| | - Jia Xie
- Department of Radiation Oncology, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN, 38105, USA
| | - Yingzhe Wang
- Preclinical Pharmacokinetics Shared Resource, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN, 38105, USA
| | - Nathaniel Twarog
- Department of Chemical Biology and Therapeutics, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN, 38105, USA
| | - Arzu Onar-Thomas
- Department of Biostatistics, Departments of BiostatisticsSt. Jude Children's Research Hospital, Memphis, 262 Danny Thomas Place, TN, 38105, USA
| | - Kati J Ernst
- Hopp Children's Cancer Center Heidelberg (KiTZ), Heidelberg, Germany
- Division of Pediatric Glioma Research, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 280, Heidelberg, Germany
| | - Lei Yang
- Department of Chemical Biology and Therapeutics, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN, 38105, USA
| | - Yong Li
- Department of Chemical Biology and Therapeutics, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN, 38105, USA
| | - Xiaoyan Zhu
- Department of Developmental Neurobiology, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN, 38105, USA
| | - Jennifer K Ocasio
- Department of Developmental Neurobiology, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN, 38105, USA
| | - Kaitlin M Budd
- Department of Developmental Neurobiology, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN, 38105, USA
- St. Jude Graduate School of Biomedical Sciences, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN, 38105, USA
| | - James Dalton
- Department of Pathology, Departments of PathologySt. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN, 38105, USA
| | - Xiaoyu Li
- Department of Pathology, Departments of PathologySt. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN, 38105, USA
| | - Divyabharathi Chepyala
- Department of Chemical Biology and Therapeutics, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN, 38105, USA
| | - Junyuan Zhang
- Department of Developmental Neurobiology, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN, 38105, USA
| | - Ke Xu
- Center for Applied Bioinformatics, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN, 38105, USA
| | - Laura Hover
- Department of Developmental Neurobiology, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN, 38105, USA
| | - Jordan T Roach
- Department of Developmental Neurobiology, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN, 38105, USA
- St. Jude Graduate School of Biomedical Sciences, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN, 38105, USA
| | - Kenneth Chun-Ho Chan
- Hopp Children's Cancer Center Heidelberg (KiTZ), Heidelberg, Germany
- Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ) and German Cancer Consortium (DKTK), Im Neuenheimer Feld 280, Heidelberg, Germany
- Faculty of Biosciences, Heidelberg University, Heidelberg, Germany
| | - Nina Hofmann
- Hopp Children's Cancer Center Heidelberg (KiTZ), Heidelberg, Germany
- Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ) and German Cancer Consortium (DKTK), Im Neuenheimer Feld 280, Heidelberg, Germany
| | - Peter J McKinnon
- Center for Pediatric Neurological Disease Research, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN, 38105, USA
| | - Stefan M Pfister
- Hopp Children's Cancer Center Heidelberg (KiTZ), Heidelberg, Germany
- Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ) and German Cancer Consortium (DKTK), Im Neuenheimer Feld 280, Heidelberg, Germany
- Department of Pediatric Oncology, Hematology and Immunology, Heidelberg University Hospital, Im Neuenheimer Feld 400, 69120, Heidelberg, Germany
| | - Anang A Shelat
- Department of Chemical Biology and Therapeutics, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN, 38105, USA
| | - Zoran Rankovic
- Department of Chemical Biology and Therapeutics, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN, 38105, USA
| | - Burgess B Freeman
- Preclinical Pharmacokinetics Shared Resource, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN, 38105, USA
| | - Jason Chiang
- Department of Pathology, Departments of PathologySt. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN, 38105, USA
| | - David T W Jones
- Hopp Children's Cancer Center Heidelberg (KiTZ), Heidelberg, Germany
- Division of Pediatric Glioma Research, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 280, Heidelberg, Germany
| | - Christopher L Tinkle
- Department of Radiation Oncology, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN, 38105, USA
| | - Suzanne J Baker
- Department of Developmental Neurobiology, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN, 38105, USA.
- Center Of Excellence in Neuro-Oncology Sciences, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN, 38105, USA.
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4
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Kocher D, Cao L, Guiho R, Langhammer M, Lai YL, Becker P, Hamdi H, Friedel D, Selt F, Vonhören D, Zaman J, Valinciute G, Herter S, Picard D, Rettenmeier J, Maass KK, Pajtler KW, Remke M, von Deimling A, Pusch S, Pfister SM, Oehme I, Jones DTW, Halbach S, Brummer T, Martinez-Barbera JP, Witt O, Milde T, Sigaud R. Rebound growth of BRAF mutant pediatric glioma cells after MAPKi withdrawal is associated with MAPK reactivation and secretion of microglia-recruiting cytokines. J Neurooncol 2024; 168:317-332. [PMID: 38630384 PMCID: PMC11147834 DOI: 10.1007/s11060-024-04672-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2024] [Accepted: 03/28/2024] [Indexed: 06/04/2024]
Abstract
INTRODUCTION Patients with pediatric low-grade gliomas (pLGGs), the most common primary brain tumors in children, can often benefit from MAPK inhibitor (MAPKi) treatment. However, rapid tumor regrowth, also referred to as rebound growth, may occur once treatment is stopped, constituting a significant clinical challenge. METHODS Four patient-derived pediatric glioma models were investigated to model rebound growth in vitro based on viable cell counts in response to MAPKi treatment and withdrawal. A multi-omics dataset (RNA sequencing and LC-MS/MS based phospho-/proteomics) was generated to investigate possible rebound-driving mechanisms. Following in vitro validation, putative rebound-driving mechanisms were validated in vivo using the BT-40 orthotopic xenograft model. RESULTS Of the tested models, only a BRAFV600E-driven model (BT-40, with additional CDKN2A/Bdel) showed rebound growth upon MAPKi withdrawal. Using this model, we identified a rapid reactivation of the MAPK pathway upon MAPKi withdrawal in vitro, also confirmed in vivo. Furthermore, transient overactivation of key MAPK molecules at transcriptional (e.g. FOS) and phosphorylation (e.g. pMEK) levels, was observed in vitro. Additionally, we detected increased expression and secretion of cytokines (CCL2, CX3CL1, CXCL10 and CCL7) upon MAPKi treatment, maintained during early withdrawal. While increased cytokine expression did not have tumor cell intrinsic effects, presence of these cytokines in conditioned media led to increased attraction of microglia cells in vitro. CONCLUSION Taken together, these data indicate rapid MAPK reactivation upon MAPKi withdrawal as a tumor cell intrinsic rebound-driving mechanism. Furthermore, increased secretion of microglia-recruiting cytokines may play a role in treatment response and rebound growth upon withdrawal, warranting further evaluation.
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Affiliation(s)
- Daniela Kocher
- Hopp Children's Cancer Center Heidelberg (KiTZ), Heidelberg, Germany
- National Center for Tumor Diseases (NCT), NCT Heidelberg, a partnership between DKFZ and Heidelberg University Hospital, Heidelberg, Germany
- German Cancer Research Center (DKFZ) Heidelberg, Clinical Cooperation Unit Pediatric Oncology, Heidelberg, Germany
- Faculty of Biosciences, Heidelberg University, Heidelberg, Germany
| | - Lei Cao
- Developmental Biology and Cancer Programme, Birth Defects Research Centre, Great Ormond Street Institute of Child Health, University College London, 30 Guilford Street, WC1N 1EH, London, UK
- Department of Neurosurgery, Beijing Tiantan Hospital, Capital Medical University, Beijing, China
| | - Romain Guiho
- Developmental Biology and Cancer Programme, Birth Defects Research Centre, Great Ormond Street Institute of Child Health, University College London, 30 Guilford Street, WC1N 1EH, London, UK
- Nantes Université, Oniris, INSERM, Regenerative Medicine and Skeleton, RMeS, UMR 1229, F-44000 Nantes, France
| | - Melanie Langhammer
- Institute of Molecular Medicine and Cell Research (IMMZ), Faculty of Medicine, University of Freiburg, Freiburg, Germany
- Faculty of Biology, University of Freiburg, Freiburg, Germany
| | - Yun-Lu Lai
- Hopp Children's Cancer Center Heidelberg (KiTZ), Heidelberg, Germany
- National Center for Tumor Diseases (NCT), NCT Heidelberg, a partnership between DKFZ and Heidelberg University Hospital, Heidelberg, Germany
- German Cancer Research Center (DKFZ) Heidelberg, Clinical Cooperation Unit Pediatric Oncology, Heidelberg, Germany
| | - Pauline Becker
- Hopp Children's Cancer Center Heidelberg (KiTZ), Heidelberg, Germany
- National Center for Tumor Diseases (NCT), NCT Heidelberg, a partnership between DKFZ and Heidelberg University Hospital, Heidelberg, Germany
- German Cancer Research Center (DKFZ) Heidelberg, Clinical Cooperation Unit Pediatric Oncology, Heidelberg, Germany
- Faculty of Medicine, Heidelberg University, Heidelberg, Germany
| | - Hiba Hamdi
- Developmental Biology and Cancer Programme, Birth Defects Research Centre, Great Ormond Street Institute of Child Health, University College London, 30 Guilford Street, WC1N 1EH, London, UK
| | - Dennis Friedel
- Faculty of Biosciences, Heidelberg University, Heidelberg, Germany
- Department of Neuropathology, Heidelberg University Hospital, Heidelberg, Germany
- German Cancer Research Center (DKFZ), Clinical Cooperation Unit Neuropathology, Heidelberg, Germany
| | - Florian Selt
- Hopp Children's Cancer Center Heidelberg (KiTZ), Heidelberg, Germany
- National Center for Tumor Diseases (NCT), NCT Heidelberg, a partnership between DKFZ and Heidelberg University Hospital, Heidelberg, Germany
- German Cancer Research Center (DKFZ) Heidelberg, Clinical Cooperation Unit Pediatric Oncology, Heidelberg, Germany
- KiTZ Clinical Trial Unit (ZIPO), Department of Pediatric Hematology and Oncology, Heidelberg University Hospital, Heidelberg, Germany
| | - David Vonhören
- Faculty of Biosciences, Heidelberg University, Heidelberg, Germany
- Department of Neuropathology, Heidelberg University Hospital, Heidelberg, Germany
- German Cancer Research Center (DKFZ), Clinical Cooperation Unit Neuropathology, Heidelberg, Germany
| | - Julia Zaman
- Faculty of Biosciences, Heidelberg University, Heidelberg, Germany
- Department of Neuropathology, Heidelberg University Hospital, Heidelberg, Germany
- German Cancer Research Center (DKFZ), Clinical Cooperation Unit Neuropathology, Heidelberg, Germany
| | - Gintvile Valinciute
- Hopp Children's Cancer Center Heidelberg (KiTZ), Heidelberg, Germany
- National Center for Tumor Diseases (NCT), NCT Heidelberg, a partnership between DKFZ and Heidelberg University Hospital, Heidelberg, Germany
- German Cancer Research Center (DKFZ) Heidelberg, Clinical Cooperation Unit Pediatric Oncology, Heidelberg, Germany
| | - Sonja Herter
- Hopp Children's Cancer Center Heidelberg (KiTZ), Heidelberg, Germany
- National Center for Tumor Diseases (NCT), NCT Heidelberg, a partnership between DKFZ and Heidelberg University Hospital, Heidelberg, Germany
- German Cancer Research Center (DKFZ) Heidelberg, Clinical Cooperation Unit Pediatric Oncology, Heidelberg, Germany
- Faculty of Biosciences, Heidelberg University, Heidelberg, Germany
| | - Daniel Picard
- Department of Pediatric Oncology, Hematology, and Clinical Immunology, Medical Faculty, and University Hospital Düsseldorf, Heinrich Heine University, Düsseldorf, Germany
- German Cancer Consortium (DKTK), Partner site Essen/Düsseldorf, Düsseldorf, Germany
- Institute of Neuropathology, Medical Faculty and University Hospital Düsseldorf, Heinrich Heine University, Düsseldorf, Germany
| | - Johanna Rettenmeier
- Hopp Children's Cancer Center Heidelberg (KiTZ), Heidelberg, Germany
- National Center for Tumor Diseases (NCT), NCT Heidelberg, a partnership between DKFZ and Heidelberg University Hospital, Heidelberg, Germany
- Faculty of Medicine, Heidelberg University, Heidelberg, Germany
- German Cancer Research Center (DKFZ), Division of Pediatric Neurooncology, Heidelberg, Germany
- Department of Pediatric Oncology, Hematology, Immunology and Pulmonology, Heidelberg University Hospital, Heidelberg, Germany
| | - Kendra K Maass
- Hopp Children's Cancer Center Heidelberg (KiTZ), Heidelberg, Germany
- National Center for Tumor Diseases (NCT), NCT Heidelberg, a partnership between DKFZ and Heidelberg University Hospital, Heidelberg, Germany
- German Cancer Research Center (DKFZ), Division of Pediatric Neurooncology, Heidelberg, Germany
- Department of Pediatric Oncology, Hematology, Immunology and Pulmonology, Heidelberg University Hospital, Heidelberg, Germany
| | - Kristian W Pajtler
- Hopp Children's Cancer Center Heidelberg (KiTZ), Heidelberg, Germany
- National Center for Tumor Diseases (NCT), NCT Heidelberg, a partnership between DKFZ and Heidelberg University Hospital, Heidelberg, Germany
- KiTZ Clinical Trial Unit (ZIPO), Department of Pediatric Hematology and Oncology, Heidelberg University Hospital, Heidelberg, Germany
- German Cancer Research Center (DKFZ), Division of Pediatric Neurooncology, Heidelberg, Germany
- Department of Pediatric Oncology, Hematology, Immunology and Pulmonology, Heidelberg University Hospital, Heidelberg, Germany
| | - Marc Remke
- Pediatric Hematology and Oncology, University Children's Hospital, Saarland University, Homburg, Germany
| | - Andreas von Deimling
- Department of Neuropathology, Heidelberg University Hospital, Heidelberg, Germany
- German Cancer Research Center (DKFZ), Clinical Cooperation Unit Neuropathology, Heidelberg, Germany
| | - Stefan Pusch
- Department of Neuropathology, Heidelberg University Hospital, Heidelberg, Germany
- German Cancer Research Center (DKFZ), Clinical Cooperation Unit Neuropathology, Heidelberg, Germany
| | - Stefan M Pfister
- Hopp Children's Cancer Center Heidelberg (KiTZ), Heidelberg, Germany
- National Center for Tumor Diseases (NCT), NCT Heidelberg, a partnership between DKFZ and Heidelberg University Hospital, Heidelberg, Germany
- KiTZ Clinical Trial Unit (ZIPO), Department of Pediatric Hematology and Oncology, Heidelberg University Hospital, Heidelberg, Germany
- German Cancer Research Center (DKFZ), Division of Pediatric Neurooncology, Heidelberg, Germany
| | - Ina Oehme
- Hopp Children's Cancer Center Heidelberg (KiTZ), Heidelberg, Germany
- National Center for Tumor Diseases (NCT), NCT Heidelberg, a partnership between DKFZ and Heidelberg University Hospital, Heidelberg, Germany
- German Cancer Research Center (DKFZ) Heidelberg, Clinical Cooperation Unit Pediatric Oncology, Heidelberg, Germany
| | - David T W Jones
- Hopp Children's Cancer Center Heidelberg (KiTZ), Heidelberg, Germany
- National Center for Tumor Diseases (NCT), NCT Heidelberg, a partnership between DKFZ and Heidelberg University Hospital, Heidelberg, Germany
- German Cancer Research Center (DKFZ) Heidelberg, Division of Pediatric Glioma Research, Heidelberg, Germany
| | - Sebastian Halbach
- Institute of Molecular Medicine and Cell Research (IMMZ), Faculty of Medicine, University of Freiburg, Freiburg, Germany
- German Consortium for Translational Cancer Research (DKTK), Freiburg, Germany, German Cancer Research Center (DKFZ), Heidelberg, Germany
- German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Tilman Brummer
- Institute of Molecular Medicine and Cell Research (IMMZ), Faculty of Medicine, University of Freiburg, Freiburg, Germany
- German Consortium for Translational Cancer Research (DKTK), Freiburg, Germany, German Cancer Research Center (DKFZ), Heidelberg, Germany
- Centre for Biological Signaling Studies BIOSS, University of Freiburg, Freiburg, Germany
| | - Juan Pedro Martinez-Barbera
- Developmental Biology and Cancer Programme, Birth Defects Research Centre, Great Ormond Street Institute of Child Health, University College London, 30 Guilford Street, WC1N 1EH, London, UK
| | - Olaf Witt
- Hopp Children's Cancer Center Heidelberg (KiTZ), Heidelberg, Germany
- National Center for Tumor Diseases (NCT), NCT Heidelberg, a partnership between DKFZ and Heidelberg University Hospital, Heidelberg, Germany
- German Cancer Research Center (DKFZ) Heidelberg, Clinical Cooperation Unit Pediatric Oncology, Heidelberg, Germany
- KiTZ Clinical Trial Unit (ZIPO), Department of Pediatric Hematology and Oncology, Heidelberg University Hospital, Heidelberg, Germany
| | - Till Milde
- Hopp Children's Cancer Center Heidelberg (KiTZ), Heidelberg, Germany.
- National Center for Tumor Diseases (NCT), NCT Heidelberg, a partnership between DKFZ and Heidelberg University Hospital, Heidelberg, Germany.
- German Cancer Research Center (DKFZ) Heidelberg, Clinical Cooperation Unit Pediatric Oncology, Heidelberg, Germany.
- KiTZ Clinical Trial Unit (ZIPO), Department of Pediatric Hematology and Oncology, Heidelberg University Hospital, Heidelberg, Germany.
| | - Romain Sigaud
- Hopp Children's Cancer Center Heidelberg (KiTZ), Heidelberg, Germany.
- National Center for Tumor Diseases (NCT), NCT Heidelberg, a partnership between DKFZ and Heidelberg University Hospital, Heidelberg, Germany.
- German Cancer Research Center (DKFZ) Heidelberg, Clinical Cooperation Unit Pediatric Oncology, Heidelberg, Germany.
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5
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Chénard-Poirier M, Hansen AR, Gutierrez ME, Rasco D, Xing Y, Chen LC, Zhou H, Webber AL, Freshwater T, Sharma MR. A phase 1 trial of the MEK inhibitor selumetinib in combination with pembrolizumab for advanced or metastatic solid tumors. Invest New Drugs 2024; 42:241-251. [PMID: 38483782 PMCID: PMC11164811 DOI: 10.1007/s10637-024-01428-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2023] [Accepted: 02/01/2024] [Indexed: 06/11/2024]
Abstract
MEK inhibitors have immunomodulatory activity and potential for synergistic activity when combined with PD-1 inhibitors. We evaluated selumetinib (inhibitor of MEK1/2) plus pembrolizumab (anti‒PD-1 antibody) in patients with advanced/metastatic solid tumors. In this phase 1b study, adults with previously treated advanced/metastatic solid tumors received pembrolizumab 200 mg intravenously every 3 weeks plus selumetinib on days 1‒14 per 3-week cycle (2 weeks on/1 week off); selumetinib dosing began at 50 mg orally twice daily with escalation in 25 mg increments for ≤ 35 cycles. Primary endpoints were dose-limiting toxicities (DLTs), adverse events (AEs), and treatment discontinuations due to AEs. Thirty-two patients were enrolled. Dose escalation was completed up to selumetinib 125 mg twice daily. The target DLT rate of 30% was not reached at any dose level. In the selumetinib 100 mg group, 2/11 patients (18.2%) experienced DLTs (n = 1 grade 3 diarrhea, n = 1 grade 3 fatigue). In the selumetinib 125 mg group, 3/14 (21.4%) experienced DLTs (n = 1 grade 2 retinal detachment, n = 1 grade 3 retinopathy, n = 1 grade 3 stomatitis). Dose-related changes in pharmacokinetic exposures were observed for selumetinib and N-desmethyl selumetinib up to 100 mg (saturation at 125 mg). Two patients achieved partial responses (1 each with selumetinib 75 mg and 125 mg) for an objective response rate of 6%. The study was stopped early because of insufficient efficacy. Although the target DLT rate was not reached at any dose level and no new safety signals were identified, selumetinib plus pembrolizumab had limited antitumor activity in this population. Trial registration: ClinicalTrials.gov , NCT03833427.
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MESH Headings
- Humans
- Benzimidazoles/administration & dosage
- Benzimidazoles/pharmacokinetics
- Benzimidazoles/therapeutic use
- Benzimidazoles/adverse effects
- Female
- Male
- Antibodies, Monoclonal, Humanized/administration & dosage
- Antibodies, Monoclonal, Humanized/adverse effects
- Antibodies, Monoclonal, Humanized/pharmacokinetics
- Antibodies, Monoclonal, Humanized/therapeutic use
- Middle Aged
- Aged
- Neoplasms/drug therapy
- Neoplasms/pathology
- Antineoplastic Combined Chemotherapy Protocols/adverse effects
- Antineoplastic Combined Chemotherapy Protocols/therapeutic use
- Antineoplastic Combined Chemotherapy Protocols/pharmacokinetics
- Antineoplastic Combined Chemotherapy Protocols/administration & dosage
- Adult
- Protein Kinase Inhibitors/administration & dosage
- Protein Kinase Inhibitors/adverse effects
- Protein Kinase Inhibitors/pharmacokinetics
- Protein Kinase Inhibitors/therapeutic use
- Maximum Tolerated Dose
- Dose-Response Relationship, Drug
- Aged, 80 and over
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Affiliation(s)
- Maxime Chénard-Poirier
- Centre intégré de cancérologie du CHU de Québec - Université Laval, 2250 Blvd Henri-Bourassa, Quebec, QC, G1J 5B3, Canada.
| | | | - Martin E Gutierrez
- John Theurer Cancer Center at Hackensack University Medical Center, Hackensack, NJ, USA
| | - Drew Rasco
- South Texas Accelerated Research Therapeutics, LLC (START), San Antonio, TX, USA
| | - Yan Xing
- City of Hope National Medical Center, Duarte, CA, USA
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6
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Desai A, Xiao AH, Choi D, Toruner MD, Walden D, Halfdanarson TR, Alberts S, McWilliams RR, Mahipal A, Ahn D, Babiker H, Stybayeva G, Revzin A, Kizilbash S, Adjei A, Bekaii-Saab T, Mansfield AS, Carr RM, Ma WW. Molecular Characterization and Therapeutic Opportunities in KRAS Wildtype Pancreatic Ductal Adenocarcinoma. Cancers (Basel) 2024; 16:1861. [PMID: 38791940 PMCID: PMC11119482 DOI: 10.3390/cancers16101861] [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: 03/30/2024] [Revised: 05/01/2024] [Accepted: 05/03/2024] [Indexed: 05/26/2024] Open
Abstract
PURPOSE To investigate the molecular characteristics of and potential for precision medicine in KRAS wildtype pancreatic ductal adenocarcinoma (PDAC). PATIENTS AND METHODS We investigated 27 patients with KRASWT PDAC at our institution. Clinical data were obtained via chart review. Tumor specimens for each subject were interrogated for somatic single nucleotide variants, insertion and deletions, and copy number variants by DNA sequencing. Gene fusions were detected from RNA-seq. A patient-derived organoid (PDO) was developed from a patient with a MET translocation and expanded ex vivo to predict therapeutic sensitivity prior to enrollment in a phase 2 clinical trial. RESULTS Transcriptomic analysis showed our cohort may be stratified by the relative gene expression of the KRAS signaling cascade. The PDO derived from our patient harboring a TFG-MET rearrangement was found to have in vitro sensitivity to the multi-tyrosine kinase inhibitor crizotinib. The patient was enrolled in the phase 2 SPARTA clinical trial and received monotherapy with vebrelitinib, a c-MET inhibitor, and achieved a partial and durable response. CONCLUSIONS KRASWT PDAC is molecularly distinct from KRASMUT and enriched with potentially actionable genetic variants. In our study, transcriptomic profiling revealed that the KRAS signaling cascade may play a key role in KRASWT PDAC. Our report of a KRASWT PDAC patient with TFG-MET rearrangement who responded to a cMET inhibitor further supports the pursuit of precision oncology in this sub-population. Identification of targetable mutations, perhaps through approaches like RNA-seq, can help enable precision-driven approaches to select optimal treatment based on tumor characteristics.
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Affiliation(s)
- Aakash Desai
- Department of Oncology, Mayo Clinic, Rochester, MN 55902, USA; (A.D.); (M.D.T.); (T.R.H.); (S.A.); (R.R.M.); (S.K.)
| | | | - Daheui Choi
- Department of Physiology and Biomedical Engineering, Mayo Clinic, Rochester, MN 55902, USA; (D.C.); (G.S.); (A.R.)
| | - Merih D. Toruner
- Department of Oncology, Mayo Clinic, Rochester, MN 55902, USA; (A.D.); (M.D.T.); (T.R.H.); (S.A.); (R.R.M.); (S.K.)
| | - Daniel Walden
- Division of Hematology and Oncology, Mayo Clinic, Phoenix, AZ 85054, USA; (D.W.); (D.A.); (T.B.-S.)
| | - Thorvardur R. Halfdanarson
- Department of Oncology, Mayo Clinic, Rochester, MN 55902, USA; (A.D.); (M.D.T.); (T.R.H.); (S.A.); (R.R.M.); (S.K.)
| | - Steven Alberts
- Department of Oncology, Mayo Clinic, Rochester, MN 55902, USA; (A.D.); (M.D.T.); (T.R.H.); (S.A.); (R.R.M.); (S.K.)
| | - Robert R. McWilliams
- Department of Oncology, Mayo Clinic, Rochester, MN 55902, USA; (A.D.); (M.D.T.); (T.R.H.); (S.A.); (R.R.M.); (S.K.)
| | - Amit Mahipal
- Department of Oncology, University Hospitals Seidman Cancer Center, Cleveland, OH 44106, USA;
| | - Daniel Ahn
- Division of Hematology and Oncology, Mayo Clinic, Phoenix, AZ 85054, USA; (D.W.); (D.A.); (T.B.-S.)
| | - Hani Babiker
- Division of Hematology and Oncology, Mayo Clinic, Jacksonville, FL 32224, USA;
| | - Gulnaz Stybayeva
- Department of Physiology and Biomedical Engineering, Mayo Clinic, Rochester, MN 55902, USA; (D.C.); (G.S.); (A.R.)
| | - Alexander Revzin
- Department of Physiology and Biomedical Engineering, Mayo Clinic, Rochester, MN 55902, USA; (D.C.); (G.S.); (A.R.)
| | - Sani Kizilbash
- Department of Oncology, Mayo Clinic, Rochester, MN 55902, USA; (A.D.); (M.D.T.); (T.R.H.); (S.A.); (R.R.M.); (S.K.)
| | - Alex Adjei
- Taussig Cancer Institute, Cleveland Clinic, Cleveland, OH 44195, USA;
| | - Tanios Bekaii-Saab
- Division of Hematology and Oncology, Mayo Clinic, Phoenix, AZ 85054, USA; (D.W.); (D.A.); (T.B.-S.)
| | - Aaron S. Mansfield
- Department of Oncology, Mayo Clinic, Rochester, MN 55902, USA; (A.D.); (M.D.T.); (T.R.H.); (S.A.); (R.R.M.); (S.K.)
| | - Ryan M. Carr
- Department of Oncology, Mayo Clinic, Rochester, MN 55902, USA; (A.D.); (M.D.T.); (T.R.H.); (S.A.); (R.R.M.); (S.K.)
| | - Wen Wee Ma
- Taussig Cancer Institute, Cleveland Clinic, Cleveland, OH 44195, USA;
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7
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Babu S, Chen J, Robitschek E, Baron CS, McConnell A, Wu C, Dedeilia A, Sade-Feldman M, Modhurima R, Manos MP, Chen KY, Cox AM, Ludwig CG, Yang J, Kellis M, Buchbinder EI, Hacohen N, Boland GM, Abraham BJ, Liu D, Zon LI, Insco ML. Specific oncogene activation of the cell of origin in mucosal melanoma. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.04.22.590595. [PMID: 38712250 PMCID: PMC11071392 DOI: 10.1101/2024.04.22.590595] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2024]
Abstract
Mucosal melanoma (MM) is a deadly cancer derived from mucosal melanocytes. To test the consequences of MM genetics, we developed a zebrafish model in which all melanocytes experienced CCND1 expression and loss of PTEN and TP53. Surprisingly, melanoma only developed from melanocytes lining internal organs, analogous to the location of patient MM. We found that zebrafish MMs had a unique chromatin landscape from cutaneous melanoma. Internal melanocytes could be labeled using a MM-specific transcriptional enhancer. Normal zebrafish internal melanocytes shared a gene expression signature with MMs. Patient and zebrafish MMs have increased migratory neural crest gene and decreased antigen presentation gene expression, consistent with the increased metastatic behavior and decreased immunotherapy sensitivity of MM. Our work suggests the cell state of the originating melanocyte influences the behavior of derived melanomas. Our animal model phenotypically and transcriptionally mimics patient tumors, allowing this model to be used for MM therapeutic discovery.
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8
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Chapeau EA, Sansregret L, Galli GG, Chène P, Wartmann M, Mourikis TP, Jaaks P, Baltschukat S, Barbosa IAM, Bauer D, Brachmann SM, Delaunay C, Estadieu C, Faris JE, Furet P, Harlfinger S, Hueber A, Jiménez Núñez E, Kodack DP, Mandon E, Martin T, Mesrouze Y, Romanet V, Scheufler C, Sellner H, Stamm C, Sterker D, Tordella L, Hofmann F, Soldermann N, Schmelzle T. Direct and selective pharmacological disruption of the YAP-TEAD interface by IAG933 inhibits Hippo-dependent and RAS-MAPK-altered cancers. NATURE CANCER 2024:10.1038/s43018-024-00754-9. [PMID: 38565920 DOI: 10.1038/s43018-024-00754-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/22/2023] [Accepted: 03/01/2024] [Indexed: 04/04/2024]
Abstract
The YAP-TEAD protein-protein interaction mediates YAP oncogenic functions downstream of the Hippo pathway. To date, available YAP-TEAD pharmacologic agents bind into the lipid pocket of TEAD, targeting the interaction indirectly via allosteric changes. However, the consequences of a direct pharmacological disruption of the interface between YAP and TEADs remain largely unexplored. Here, we present IAG933 and its analogs as potent first-in-class and selective disruptors of the YAP-TEAD protein-protein interaction with suitable properties to enter clinical trials. Pharmacologic abrogation of the interaction with all four TEAD paralogs resulted in YAP eviction from chromatin and reduced Hippo-mediated transcription and induction of cell death. In vivo, deep tumor regression was observed in Hippo-driven mesothelioma xenografts at tolerated doses in animal models as well as in Hippo-altered cancer models outside mesothelioma. Importantly this also extended to larger tumor indications, such as lung, pancreatic and colorectal cancer, in combination with RTK, KRAS-mutant selective and MAPK inhibitors, leading to more efficacious and durable responses. Clinical evaluation of IAG933 is underway.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | - Daniel Bauer
- Novartis BioMedical Research, Basel, Switzerland
| | | | | | | | | | - Pascal Furet
- Novartis BioMedical Research, Basel, Switzerland
| | - Stefanie Harlfinger
- Novartis BioMedical Research, Basel, Switzerland
- AstraZeneca, Oncology R&D, Cambridge, UK
| | | | | | | | | | | | | | | | | | | | | | | | | | - Francesco Hofmann
- Novartis BioMedical Research, Basel, Switzerland
- Pierre Fabre Group, R&D Medical Care, Toulouse, France
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9
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Arai H, Yang Y, Baca Y, Millstein J, Denda T, Ou FS, Innocenti F, Takeda H, Kubota Y, Doi A, Horie Y, Umemoto K, Izawa N, Wang J, Battaglin F, Jayachandran P, Algaze S, Soni S, Zhang W, Goldberg RM, Hall MJ, Scott AJ, Hwang JJ, Lou E, Weinberg BA, Marshall J, Goel S, Xiu J, Michael Korn W, Venook AP, Sunakawa Y, Lenz HJ. Predictive value of CDC37 gene expression for targeted therapy in metastatic colorectal cancer. Eur J Cancer 2024; 201:113914. [PMID: 38359495 DOI: 10.1016/j.ejca.2024.113914] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2023] [Revised: 01/25/2024] [Accepted: 02/04/2024] [Indexed: 02/17/2024]
Abstract
BACKGROUND CDC37 is a key determinant of client kinase recruitment to the HSP90 chaperoning system. We hypothesized that kinase-specific dependency on CDC37 alters the efficacy of targeted therapies for metastatic colorectal cancer (mCRC). MATERIAL AND METHODS Two independent mCRC cohorts were analyzed to compare the survival outcomes between CDC37-high and CDC37-low patients (stratified by the median cutoff values): the CALGB/SWOG 80405 trial (226 and 207 patients receiving first-line bevacizumab- and cetuximab-containing chemotherapies, respectively) and Japanese retrospective (50 refractory patients receiving regorafenib) cohorts. A dataset of specimens submitted to a commercial CLIA-certified laboratory was utilized to characterize molecular profiles of CDC37-high (top quartile, N = 5055) and CDC37-low (bottom quartile, N = 5055) CRCs. RESULTS In the bevacizumab-treated group, CDC37-high patients showed significantly better progression-free survival (PFS) (median 13.3 vs 9.6 months, hazard ratio [HR] 0.59, 95% confidence interval [CI] 0.44-0.79, p < 0.01) than CDC37-low patients. In the cetuximab-treated group, CDC37-high and CDC37-low patients had similar outcomes. In the regorafenib-treated group, CDC37-high patients showed significantly better overall survival (median 11.3 vs 6.0 months, HR 0.24, 95% CI 0.11-0.54, p < 0.01) and PFS (median 3.5 vs 1.9 months, HR 0.51, 95% CI 0.28-0.94, p = 0.03). Comprehensive molecular profiling revealed that CDC37-high CRCs were associated with higher VEGFA, FLT1, and KDR expressions and activated hypoxia signature. CONCLUSIONS CDC37-high mCRC patients derived more benefit from anti-VEGF therapies, including bevacizumab and regorafenib, but not from cetuximab. Molecular profiles suggested that such tumors were dependent on angiogenesis-relating pathways.
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Affiliation(s)
- Hiroyuki Arai
- Division of Medical Oncology, Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA; Department of Clinical Oncology, St. Marianna University School of Medicine, Kawasaki, Japan
| | - Yan Yang
- Department of Population and Public Health Sciences, Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Yasmine Baca
- Clinical & Translational Research, Medical Affairs, Caris Life Sciences, Phoenix, AZ, USA
| | - Joshua Millstein
- Department of Population and Public Health Sciences, Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Tadamichi Denda
- Department of Gastroenterology, Chiba Cancer Center, Chiba, Japan
| | - Fang-Shu Ou
- Alliance Statistics and Data Management Center, Mayo Clinic, Rochester, MN, USA
| | - Federico Innocenti
- UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Hiroyuki Takeda
- Department of Clinical Oncology, St. Marianna University School of Medicine, Kawasaki, Japan
| | - Yohei Kubota
- Department of Clinical Oncology, St. Marianna University School of Medicine, Kawasaki, Japan
| | - Ayako Doi
- Department of Clinical Oncology, St. Marianna University School of Medicine, Kawasaki, Japan
| | - Yoshiki Horie
- Department of Clinical Oncology, St. Marianna University School of Medicine, Kawasaki, Japan
| | - Kumiko Umemoto
- Department of Clinical Oncology, St. Marianna University School of Medicine, Kawasaki, Japan
| | - Naoki Izawa
- Department of Clinical Oncology, St. Marianna University School of Medicine, Kawasaki, Japan
| | - Jingyuan Wang
- Division of Medical Oncology, Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Francesca Battaglin
- Division of Medical Oncology, Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Priya Jayachandran
- Division of Medical Oncology, Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Sandra Algaze
- Division of Medical Oncology, Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Shivani Soni
- Division of Medical Oncology, Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Wu Zhang
- Division of Medical Oncology, Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | | | - Michael J Hall
- Department of Clinical Genetics, Fox Chase Cancer Center, Philadelphia, PA, USA
| | - Aaron James Scott
- Department of Medicine, University of Arizona Cancer Center, Tucson, AZ, USA
| | - Jimmy J Hwang
- Department of Solid Tumor Oncology, GI Medical Oncology, Levine Cancer Institute, Charlotte, NC, USA
| | - Emil Lou
- Division of Hematology, Oncology and Transplantation, University of Minnesota, Minneapolis, MN, USA
| | - Benjamin A Weinberg
- Ruesch Center for the Cure of Gastrointestinal Cancers, Lombardi Comprehensive Cancer Center, Georgetown University, Washington, DC, USA
| | - John Marshall
- Ruesch Center for the Cure of Gastrointestinal Cancers, Lombardi Comprehensive Cancer Center, Georgetown University, Washington, DC, USA
| | - Sanjay Goel
- Rutgers Cancer Institute of New Jersey, New Brunswick, NJ, USA
| | - Joanne Xiu
- Clinical & Translational Research, Medical Affairs, Caris Life Sciences, Phoenix, AZ, USA
| | - W Michael Korn
- Clinical & Translational Research, Medical Affairs, Caris Life Sciences, Phoenix, AZ, USA
| | - Alan P Venook
- University of California, San Francisco, San Francisco, CA, USA
| | - Yu Sunakawa
- Department of Clinical Oncology, St. Marianna University School of Medicine, Kawasaki, Japan
| | - Heinz-Josef Lenz
- Division of Medical Oncology, Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA.
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10
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Boretto M, Geurts MH, Gandhi S, Ma Z, Staliarova N, Celotti M, Lim S, He GW, Millen R, Driehuis E, Begthel H, Smabers L, Roodhart J, van Es J, Wu W, Clevers H. Epidermal growth factor receptor (EGFR) is a target of the tumor-suppressor E3 ligase FBXW7. Proc Natl Acad Sci U S A 2024; 121:e2309902121. [PMID: 38483988 PMCID: PMC10962967 DOI: 10.1073/pnas.2309902121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2023] [Accepted: 01/08/2024] [Indexed: 03/19/2024] Open
Abstract
FBXW7 is an E3 ubiquitin ligase that targets proteins for proteasome-mediated degradation and is mutated in various cancer types. Here, we use CRISPR base editors to introduce different FBXW7 hotspot mutations in human colon organoids. Functionally, FBXW7 mutation reduces EGF dependency of organoid growth by ~10,000-fold. Combined transcriptomic and proteomic analyses revealed increased EGFR protein stability in FBXW7 mutants. Two distinct phosphodegron motifs reside in the cytoplasmic tail of EGFR. Mutations in these phosphodegron motifs occur in human cancer. CRISPR-mediated disruption of the phosphodegron motif at T693 reduced EGFR degradation and EGF growth factor dependency. FBXW7 mutant organoids showed reduced sensitivity to EGFR-MAPK inhibitors. These observations were further strengthened in CRC-derived organoid lines and validated in a cohort of patients treated with panitumumab. Our data imply that FBXW7 mutations reduce EGF dependency by disabling EGFR turnover.
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Affiliation(s)
- Matteo Boretto
- Organoid group, Oncode Institute, Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences and University Medical Center, 3584CTUtrecht, the Netherlands
| | - Maarten H. Geurts
- Organoid group, Oncode Institute, Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences and University Medical Center, 3584CTUtrecht, the Netherlands
| | - Shashank Gandhi
- Organoid group, Oncode Institute, Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences and University Medical Center, 3584CTUtrecht, the Netherlands
- Department of Molecular and Cellular Biology, Miller Institute for Basic Research in Science, University of California, Berkeley, CA94720
| | - Ziliang Ma
- Singapore Immunology Network, Agency for Science, Technology and Research, Singapore138648, Singapore
- Department of Pharmacy, National University of Singapore, Singapore117543, Singapore
- Department of Biomolecular Mass Spectrometry and Proteomics, Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, 3584 CHUtrecht, the Netherlands
| | - Nadzeya Staliarova
- Department of Biomolecular Mass Spectrometry and Proteomics, Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, 3584 CHUtrecht, the Netherlands
| | - Martina Celotti
- Organoid group, Oncode Institute, Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences and University Medical Center, 3584CTUtrecht, the Netherlands
| | - Sangho Lim
- Organoid group, Oncode Institute, Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences and University Medical Center, 3584CTUtrecht, the Netherlands
| | - Gui-Wei He
- Organoid group, Oncode Institute, Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences and University Medical Center, 3584CTUtrecht, the Netherlands
| | - Rosemary Millen
- Organoid group, Oncode Institute, Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences and University Medical Center, 3584CTUtrecht, the Netherlands
| | - Else Driehuis
- Organoid group, Oncode Institute, Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences and University Medical Center, 3584CTUtrecht, the Netherlands
| | - Harry Begthel
- Organoid group, Oncode Institute, Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences and University Medical Center, 3584CTUtrecht, the Netherlands
| | - Lidwien Smabers
- Department of Medical Oncology, University Medical Center Utrecht, 3584 CXUtrecht, the Netherlands
| | - Jeanine Roodhart
- Department of Medical Oncology, University Medical Center Utrecht, 3584 CXUtrecht, the Netherlands
| | - Johan van Es
- Organoid group, Oncode Institute, Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences and University Medical Center, 3584CTUtrecht, the Netherlands
| | - Wei Wu
- Singapore Immunology Network, Agency for Science, Technology and Research, Singapore138648, Singapore
- Department of Pharmacy, National University of Singapore, Singapore117543, Singapore
- Department of Biomolecular Mass Spectrometry and Proteomics, Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, 3584 CHUtrecht, the Netherlands
| | - Hans Clevers
- Organoid group, Oncode Institute, Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences and University Medical Center, 3584CTUtrecht, the Netherlands
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11
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Pehkonen H, Filippou A, Väänänen J, Lindfors I, Vänttinen M, Ianevski P, Mäkelä A, Munne P, Klefström J, Toppila‐Salmi S, Grénman R, Hagström J, Mäkitie AA, Karhemo P, Monni O. Liprin-α1 contributes to oncogenic MAPK signaling by counteracting ERK activity. Mol Oncol 2024; 18:662-676. [PMID: 38264964 PMCID: PMC10920090 DOI: 10.1002/1878-0261.13593] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2023] [Revised: 12/15/2023] [Accepted: 01/15/2024] [Indexed: 01/25/2024] Open
Abstract
PTPRF interacting protein alpha 1 (PPFIA1) encodes for liprin-α1, a member of the leukocyte common antigen-related protein tyrosine phosphatase (LAR-RPTPs)-interacting protein family. Liprin-α1 localizes to adhesive and invasive structures in the periphery of cancer cells, where it modulates migration and invasion in head and neck squamous cell carcinoma (HNSCC) and breast cancer. To study the possible role of liprin-α1 in anticancer drug responses, we screened a library of oncology compounds in cell lines with high endogenous PPFIA1 expression. The compounds with the highest differential responses between high PPFIA1-expressing and silenced cells across cell lines were inhibitors targeting mitogen-activated protein kinase kinase (MEK)/extracellular signal-regulated kinases (ERK) signaling. KRAS proto-oncogene, GTPase (KRAS)-mutated MDA-MB-231 cells were more resistant to trametinib upon PPFIA1 knockdown compared with control cells. In contrast, liprin-α1-depleted HNSCC cells with low RAS activity showed a context-dependent response to MEK/ERK inhibitors. Importantly, we showed that liprin-α1 depletion leads to increased p-ERK1/2 levels in all our studied cell lines independent of KRAS mutational status, suggesting a role of liprin-α1 in the regulation of MAPK oncogenic signaling. Furthermore, liprin-α1 depletion led to more pronounced redistribution of RAS proteins to the cell membrane. Our data suggest that liprin-α1 is an important contributor to oncogenic RAS/MAPK signaling, and the status of liprin-α1 may assist in predicting drug responses in cancer cells in a context-dependent manner.
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Affiliation(s)
- Henna Pehkonen
- Applied Tumor Genomics Research Program, Faculty of MedicineUniversity of HelsinkiFinland
| | - Artemis Filippou
- Applied Tumor Genomics Research Program, Faculty of MedicineUniversity of HelsinkiFinland
| | - Juho Väänänen
- Applied Tumor Genomics Research Program, Faculty of MedicineUniversity of HelsinkiFinland
| | - Iida Lindfors
- Applied Tumor Genomics Research Program, Faculty of MedicineUniversity of HelsinkiFinland
| | - Mira Vänttinen
- Applied Tumor Genomics Research Program, Faculty of MedicineUniversity of HelsinkiFinland
| | - Philipp Ianevski
- Institute for Molecular Medicine Finland (FIMM)University of HelsinkiFinland
| | - Anne Mäkelä
- Applied Tumor Genomics Research Program, Faculty of MedicineUniversity of HelsinkiFinland
| | - Pauliina Munne
- Finnish Cancer Institute, FICAN South Helsinki University Hospital & Translational Cancer Medicine, Medical FacultyUniversity of HelsinkiFinland
| | - Juha Klefström
- Finnish Cancer Institute, FICAN South Helsinki University Hospital & Translational Cancer Medicine, Medical FacultyUniversity of HelsinkiFinland
- iCAN Digital Precision Cancer Medicine FlagshipHelsinkiFinland
| | - Sanna Toppila‐Salmi
- Skin and Allergy HospitalHelsinki University Hospital and University of HelsinkiFinland
- Department of Otorhinolaryngology, Kuopio University Hospital and School of Medicine, Institute of Clinical MedicineUniversity of Eastern FinlandKuopioFinland
| | - Reidar Grénman
- Department of Otorhinolaryngology‐Head and Neck SurgeryUniversity of Turku and Turku University HospitalFinland
| | - Jaana Hagström
- Department of PathologyUniversity of Helsinki and Helsinki University HospitalFinland
- Institute of DentistryUniversity of TurkuFinland
| | - Antti A. Mäkitie
- iCAN Digital Precision Cancer Medicine FlagshipHelsinkiFinland
- Department of Otorhinolaryngology‐Head and Neck Surgery, Research Program in Systems OncologyUniversity of Helsinki and Helsinki University HospitalFinland
| | - Piia‐Riitta Karhemo
- Applied Tumor Genomics Research Program, Faculty of MedicineUniversity of HelsinkiFinland
- iCAN Digital Precision Cancer Medicine FlagshipHelsinkiFinland
| | - Outi Monni
- Applied Tumor Genomics Research Program, Faculty of MedicineUniversity of HelsinkiFinland
- iCAN Digital Precision Cancer Medicine FlagshipHelsinkiFinland
- Department of Oncology, Faculty of MedicineUniversity of HelsinkiFinland
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12
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Schmid P, Turner NC, Barrios CH, Isakoff SJ, Kim SB, Sablin MP, Saji S, Savas P, Vidal GA, Oliveira M, O'Shaughnessy J, Italiano A, Espinosa E, Boni V, White S, Rojas B, Freitas-Junior R, Chae Y, Bondarenko I, Lee J, Torres Mattos C, Martinez Rodriguez JL, Lam LH, Jones S, Reilly SJ, Huang X, Shah K, Dent R. First-Line Ipatasertib, Atezolizumab, and Taxane Triplet for Metastatic Triple-Negative Breast Cancer: Clinical and Biomarker Results. Clin Cancer Res 2024; 30:767-778. [PMID: 38060199 PMCID: PMC10870115 DOI: 10.1158/1078-0432.ccr-23-2084] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2023] [Revised: 10/18/2023] [Accepted: 12/05/2023] [Indexed: 12/08/2023]
Abstract
PURPOSE To evaluate a triplet regimen combining immune checkpoint blockade, AKT pathway inhibition, and (nab-) paclitaxel as first-line therapy for locally advanced/metastatic triple-negative breast cancer (mTNBC). PATIENTS AND METHODS The single-arm CO40151 phase Ib study (NCT03800836), the single-arm signal-seeking cohort of IPATunity130 (NCT03337724), and the randomized phase III IPATunity170 trial (NCT04177108) enrolled patients with previously untreated mTNBC. Triplet therapy comprised intravenous atezolizumab 840 mg (days 1 and 15), oral ipatasertib 400 mg/day (days 1-21), and intravenous paclitaxel 80 mg/m2 (or nab-paclitaxel 100 mg/m2; days 1, 8, and 15) every 28 days. Exploratory translational research aimed to elucidate mechanisms and molecular markers of sensitivity and resistance. RESULTS Among 317 patients treated with the triplet, efficacy ranged across studies as follows: median progression-free survival (PFS) 5.4 to 7.4 months, objective response rate 44% to 63%, median duration of response 5.6 to 11.1 months, and median overall survival 15.7 to 28.3 months. The safety profile was consistent with the known toxicities of each agent. Grade ≥3 adverse events were more frequent with the triplet than with doublets or single-agent paclitaxel. Patients with PFS >10 months were characterized by NF1, CCND3, and PIK3CA alterations and increased immune pathway activity. PFS <5 months was associated with CDKN2A/CDKN2B/MTAP alterations and lower predicted phosphorylated AKT-S473 levels. CONCLUSIONS In patients with mTNBC receiving an ipatasertib/atezolizumab/taxane triplet regimen, molecular characteristics may identify those with particularly favorable or unfavorable outcomes, potentially guiding future research efforts.
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Affiliation(s)
- Peter Schmid
- Barts Cancer Institute, Queen Mary University of London, London, United Kingdom
| | - Nicholas C. Turner
- The Royal Marsden NHS Foundation Trust, London, United Kingdom
- Breast Cancer Now Research Centre, London, United Kingdom
| | - Carlos H. Barrios
- Centro de Pesquisa em Oncologia, Hospital São Lucas, PUCRS, Latin American Cooperative Oncology Group (LACOG), Brazil
| | | | - Sung-Bae Kim
- Asan Medical Center, University of Ulsan College of Medicine, Seoul, Republic of Korea
| | - Marie-Paule Sablin
- Department of Drug Development and Innovation (D3i), Institut Curie, Paris, France
| | - Shigehira Saji
- Department of Medical Oncology, Fukushima Medical University, Fukushima, Japan
| | - Peter Savas
- Peter MacCallum Cancer Centre and Sir Peter MacCallum Department of Oncology, The University of Melbourne, Melbourne, Australia
| | - Gregory A. Vidal
- West Cancer Center and Research Institute, Germantown, Tennessee
| | - Mafalda Oliveira
- Medical Oncology Department, Vall d'Hebron University Hospital and Breast Cancer Group, Vall d'Hebron Institute of Oncology, Barcelona, Spain
| | - Joyce O'Shaughnessy
- Baylor University Medical Center, Texas Oncology, US Oncology, Dallas, Texas
| | | | | | - Valentina Boni
- Oncology Service, Hospital Universitario La Paz, Madrid – Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Madrid, Spain
| | | | - Beatriz Rojas
- Oncology Service, Centro Integral Oncologico Clara Campal, Madrid, Spain
| | - Ruffo Freitas-Junior
- Gynaecology and Breast Department, Hospital Araujo Jorge, Goias Anticancer Association, Goiânia, Brazil
| | - Yeesoo Chae
- Kyungpook National University Chilgok Hospital, Daegu, Republic of Korea
| | | | - Jieun Lee
- Seoul St Mary's Hospital, The Catholic University of Korea, Seoul, Republic of Korea
| | - Cesar Torres Mattos
- Clínica San Gabriel, Unidad de Investigación Oncológica de la Clínica San Gabriel, Lima, Perú
| | | | - Lisa H. Lam
- Product Development Oncology, Genentech, Inc., South San Francisco, California
| | - Surai Jones
- Data Sciences, Safety and Medical (DSSM), IQVIA Inc., Durham, North Carolina
| | | | - Xiayu Huang
- gRED Computational Science, Roche (China) Holding Ltd, Pudong, Shanghai, China
| | - Kalpit Shah
- Oncology Biomarker Development, Genentech, Inc., South San Francisco, California
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13
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Gardner EE, Earlie EM, Li K, Thomas J, Hubisz MJ, Stein BD, Zhang C, Cantley LC, Laughney AM, Varmus H. Lineage-specific intolerance to oncogenic drivers restricts histological transformation. Science 2024; 383:eadj1415. [PMID: 38330136 PMCID: PMC11155264 DOI: 10.1126/science.adj1415] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2023] [Accepted: 12/08/2023] [Indexed: 02/10/2024]
Abstract
Lung adenocarcinoma (LUAD) and small cell lung cancer (SCLC) are thought to originate from different epithelial cell types in the lung. Intriguingly, LUAD can histologically transform into SCLC after treatment with targeted therapies. In this study, we designed models to follow the conversion of LUAD to SCLC and found that the barrier to histological transformation converges on tolerance to Myc, which we implicate as a lineage-specific driver of the pulmonary neuroendocrine cell. Histological transformations are frequently accompanied by activation of the Akt pathway. Manipulating this pathway permitted tolerance to Myc as an oncogenic driver, producing rare, stem-like cells that transcriptionally resemble the pulmonary basal lineage. These findings suggest that histological transformation may require the plasticity inherent to the basal stem cell, enabling tolerance to previously incompatible oncogenic driver programs.
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Affiliation(s)
| | - Ethan M. Earlie
- Meyer Cancer Center, Weill Cornell Medicine, New York, NY
- Department of Physiology, Biophysics, and Systems Biology, Weill Cornell Medicine, New York, NY
- Institute for Computational Biomedicine, Weill Cornell Medicine, New York, NY
| | - Kate Li
- Meyer Cancer Center, Weill Cornell Medicine, New York, NY
| | - Jerin Thomas
- Meyer Cancer Center, Weill Cornell Medicine, New York, NY
| | - Melissa J. Hubisz
- Meyer Cancer Center, Weill Cornell Medicine, New York, NY
- Department of Physiology, Biophysics, and Systems Biology, Weill Cornell Medicine, New York, NY
- Institute for Computational Biomedicine, Weill Cornell Medicine, New York, NY
- Bioinformatics Facility, Institute of Biotechnology, Cornell University, Ithaca, NY
| | - Benjamin D. Stein
- Meyer Cancer Center, Weill Cornell Medicine, New York, NY
- Department of Medicine, Weill Cornell Medicine
| | - Chen Zhang
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY
| | - Lewis C. Cantley
- Meyer Cancer Center, Weill Cornell Medicine, New York, NY
- Department of Medicine, Weill Cornell Medicine
| | - Ashley M. Laughney
- Meyer Cancer Center, Weill Cornell Medicine, New York, NY
- Department of Physiology, Biophysics, and Systems Biology, Weill Cornell Medicine, New York, NY
- Institute for Computational Biomedicine, Weill Cornell Medicine, New York, NY
| | - Harold Varmus
- Meyer Cancer Center, Weill Cornell Medicine, New York, NY
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14
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Herrington CS, Oswald AJ, Stillie LJ, Croy I, Churchman M, Hollis RL. Compartment-specific multiomic profiling identifies SRC and GNAS as candidate drivers of epithelial-to-mesenchymal transition in ovarian carcinosarcoma. Br J Cancer 2024; 130:327-335. [PMID: 38097740 PMCID: PMC10803731 DOI: 10.1038/s41416-023-02508-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2023] [Revised: 11/05/2023] [Accepted: 11/14/2023] [Indexed: 01/24/2024] Open
Abstract
BACKGROUND Ovarian carcinosarcoma (OCS) is an exceptionally aggressive and understudied ovarian cancer type harbouring distinct carcinomatous and sarcomatous compartments. Here, we seek to identify shared and compartment-specific events that may represent potential therapeutic targets and candidate drivers of sarcomatous compartment formation through epithelial-to-mesenchymal transition (EMT). METHODS We performed multiomic profiling (exome sequencing, RNA-sequencing, microRNA profiling) of paired carcinomatous and sarcomatous components in 12 OCS cases. RESULTS While paired sarcomatous and carcinomatous compartments demonstrate substantial genomic similarities, multiple loci are recurrently copy number-altered between components; regions containing GNAS and SRC are recurrently gained within the sarcomatous compartment. CCNE1 gain is a common event in OCS, occurring more frequently than in high grade serous ovarian carcinoma (HGSOC). Transcriptomic analysis suggests increased MAPK activity and subtype switching toward poor prognosis HGSOC-derived transcriptomic subtypes within the sarcomatous component. The two compartments show global differences in microRNA profiles, with differentially expressed microRNAs targeting EMT-related genes (SIRT1, ZEB2) and regulators of pro-tumourigenic pathways (TGFβ, NOTCH); chrX is a highly enriched target of these microRNAs and is also frequently deleted across samples. The sarcomatous component harbours significantly fewer CD8-positive cells, suggesting poorer immune engagement. CONCLUSION CCNE1 gain and chrX loss are frequent in OCS. SRC gain, increased GNAS expression and microRNA dysregulation represent potential mechanisms driving sarcomatous compartment formation.
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Affiliation(s)
- C Simon Herrington
- The Nicola Murray Centre for Ovarian Cancer Research, Cancer Research UK Scotland Centre, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, UK
| | - Ailsa J Oswald
- The Nicola Murray Centre for Ovarian Cancer Research, Cancer Research UK Scotland Centre, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, UK
| | - Lorna J Stillie
- The Nicola Murray Centre for Ovarian Cancer Research, Cancer Research UK Scotland Centre, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, UK
- Cancer Research UK Scotland Centre and Cancer Research UK Beatson Institute, Institute of Cancer Sciences, University of Glasgow, Glasgow, UK
| | - Ian Croy
- The Nicola Murray Centre for Ovarian Cancer Research, Cancer Research UK Scotland Centre, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, UK
| | - Michael Churchman
- The Nicola Murray Centre for Ovarian Cancer Research, Cancer Research UK Scotland Centre, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, UK
| | - Robert L Hollis
- The Nicola Murray Centre for Ovarian Cancer Research, Cancer Research UK Scotland Centre, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, UK.
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15
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Malla M, Kumar Deshkmukh S, Wu S, Samec T, Olevian D, Naili R, Bassel ER, Xiu J, Farrell A, Lenz HJ, Lou E, Goel S, Spetzler D, Goldberg RM, Hazlehurst L. Mesothelin expression correlates with elevated inhibitory immune activity in patients with colorectal cancer. RESEARCH SQUARE 2023:rs.3.rs-3787873. [PMID: 38234761 PMCID: PMC10793489 DOI: 10.21203/rs.3.rs-3787873/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/19/2024]
Abstract
The expression of the protein Mesothelin (MSLN) is highly variable in several malignancies including colorectal cancer (CRC) and high levels are associated with aggressive clinicopathological features and worse patient survival. CRC is both a common and deadly cancer; being the third most common in incidence and second most common cause of cancer related death. While systemic therapy remains the primary therapeutic option for most patients with stage IV (metastatic; m) CRC, their disease eventually becomes treatment refractory, and 85% succumb within 5 years. Microsatellite-stable (MSS) CRC tumors, which affect more than 90% of patients with mCRC, are generally refractory to immunotherapeutic interventions. In our current work, we characterize MSLN levels in CRC, specifically correlating expression with clinical outcomes in relevant CRC subtypes and explore how MSLN expression impacts the status of immune activation and suppression in the peritumoral microenvironment. High MSLN expression is highly prevalent in CMS1 and CMS4 CRC subtypes as well as in mCRC tissue and correlates with higher gene mutation rates across the patient cohorts. Further, MSLN-high patients exhibit increased M1/M2 macrophage infiltration, PD-L1 staining, immune-inhibitory gene expression, enrichment in inflammatory, TGF-β, IL6/JAK/STAT3, IL2/STAT5 signaling pathways and mutation in KRAS and FBXW7. Together, these results suggest MSLN protein is a potential target for antigen-specific therapy and supports investigation into its tumorigenic effects to identify possible therapeutic interventions for patients with high MSLN expressing MSS CRC.
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16
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Daley BR, Sealover NE, Sheffels E, Hughes JM, Gerlach D, Hofmann MH, Kostyrko K, Mair B, Linke A, Beckley Z, Frank A, Dalgard C, Kortum RL. SOS1 inhibition enhances the efficacy of and delays resistance to G12C inhibitors in lung adenocarcinoma. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.12.07.570642. [PMID: 38106234 PMCID: PMC10723384 DOI: 10.1101/2023.12.07.570642] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/19/2023]
Abstract
Clinical effectiveness of KRAS G12C inhibitors (G12Cis) is limited both by intrinsic and acquired resistance, necessitating the development of combination approaches. We found that targeting proximal receptor tyrosine kinase (RTK) signaling using the SOS1 inhibitor (SOS1i) BI-3406 both enhanced the potency of and delayed resistance to G12Ci treatment, but the extent of SOS1i effectiveness was modulated by both SOS2 expression and the specific mutational landscape. SOS1i enhanced the efficacy of G12Ci and limited rebound RTK/ERK signaling to overcome intrinsic/adaptive resistance, but this effect was modulated by SOS2 protein levels. Survival of drug-tolerant persister (DTP) cells within the heterogeneous tumor population and/or acquired mutations that reactivate RTK/RAS signaling can lead to outgrowth of tumor initiating cells (TICs) that drive therapeutic resistance. G12Ci drug tolerant persister cells showed a 2-3-fold enrichment of TICs, suggesting that these could be a sanctuary population of G12Ci resistant cells. SOS1i re-sensitized DTPs to G12Ci and inhibited G12C-induced TIC enrichment. Co-mutation of the tumor suppressor KEAP1 limits the clinical effectiveness of G12Cis, and KEAP1 and STK11 deletion increased TIC frequency and accelerated the development of acquired resistance to G12Ci in situ. SOS1i both delayed acquired G12Ci resistance and limited the total number of resistant colonies regardless of KEAP1 and STK11 mutational status. These data suggest that SOS1i could be an effective strategy to both enhance G12Ci efficacy and prevent G12Ci resistance regardless of co-mutations.
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Affiliation(s)
- Brianna R Daley
- Department of Pharmacology and Molecular Therapeutics, Uniformed Services University of the Health Sciences, Bethesda, MD 20814
| | - Nancy E Sealover
- Department of Pharmacology and Molecular Therapeutics, Uniformed Services University of the Health Sciences, Bethesda, MD 20814
| | - Erin Sheffels
- Department of Pharmacology and Molecular Therapeutics, Uniformed Services University of the Health Sciences, Bethesda, MD 20814
| | - Jacob M. Hughes
- Department of Pharmacology and Molecular Therapeutics, Uniformed Services University of the Health Sciences, Bethesda, MD 20814
| | | | | | - Kaja Kostyrko
- Boehringer Ingelheim RCV GmbH & Co KG, Vienna, Austria
| | - Barbara Mair
- Boehringer Ingelheim RCV GmbH & Co KG, Vienna, Austria
| | - Amanda Linke
- Department of Pharmacology and Molecular Therapeutics, Uniformed Services University of the Health Sciences, Bethesda, MD 20814
| | - Zaria Beckley
- Department of Pharmacology and Molecular Therapeutics, Uniformed Services University of the Health Sciences, Bethesda, MD 20814
| | - Andrew Frank
- Henry M. Jackson Foundation for the Advancement of Military Medicine; Bethesda, MD, USA
- Student Bioinformatics Initiative, Center for Military Precision Health, Uniformed Services University of the Health Sciences; Bethesda, MD, USA
| | - Clifton Dalgard
- The American Genome Center, Department of Anatomy, Cell Biology, and Genetics, Uniformed Services University of the Health Sciences, Bethesda, MD 20814
| | - Robert L Kortum
- Department of Pharmacology and Molecular Therapeutics, Uniformed Services University of the Health Sciences, Bethesda, MD 20814
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17
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Verschoor N, Smid M, Jager A, Sleijfer S, Wilting SM, Martens JWM. Integrative whole-genome and transcriptome analysis of HER2-amplified metastatic breast cancer. Breast Cancer Res 2023; 25:145. [PMID: 37968696 PMCID: PMC10648326 DOI: 10.1186/s13058-023-01743-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2023] [Accepted: 11/06/2023] [Indexed: 11/17/2023] Open
Abstract
BACKGROUND In breast cancer, the advent of anti-HER2 therapies has made HER2+ tumors a highly relevant subgroup. However, the exact characteristics which prohibit clinical response to anti-HER2 therapies and drive disease progression are not yet fully known. Integrative whole-genome and transcriptomic sequencing data from both primary and metastatic HER2-positive breast cancer will enhance our understanding of underlying biological processes. METHODS Here, we used WGS and RNA sequencing data of 700 metastatic breast tumors, of which 68 being HER2+, to search for specific genomic features of HER2+ disease and therapy resistance. Furthermore, we integrated results with transcriptomic data to associate tumors exhibiting a HER2+-specific gene expression profile with ERBB2 mutation status, prior therapy and relevant gene expression signatures. RESULTS Overall genomic profiles of primary and metastatic HER2+ breast cancers were similar, and no specific acquired genomics traits connected to prior anti-HER2 treatment were observed. However, specific genomic features were predictive of progression-free survival on post-biopsy anti-HER2 treatment. Furthermore, a HER2-driven expression profile grouped HER2-amplified tumors with ERBB2-mutated cases and cases without HER2 alterations. The latter were reported as ER positive in primary disease, but the metastatic biopsy showed low ESR1 expression and upregulation of the MAPK pathway, suggesting transformation to ER independence. CONCLUSIONS In summary, although the quantity of variants increased throughout HER2-positive breast cancer progression, the genomic composition remained largely consistent, thus yielding no new major processes beside those already operational in primary disease. Our results suggest that integrated genomic and transcriptomic analyses may be key in establishing therapeutic options.
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Affiliation(s)
- Noortje Verschoor
- Department of Medical Oncology, Erasmus MC Cancer Institute, University Medical Center Rotterdam, Dr. Molewaterplein 40, 3015 GD, Rotterdam, The Netherlands.
| | - Marcel Smid
- Department of Medical Oncology, Erasmus MC Cancer Institute, University Medical Center Rotterdam, Dr. Molewaterplein 40, 3015 GD, Rotterdam, The Netherlands
| | - Agnes Jager
- Department of Medical Oncology, Erasmus MC Cancer Institute, University Medical Center Rotterdam, Dr. Molewaterplein 40, 3015 GD, Rotterdam, The Netherlands
| | - Stefan Sleijfer
- Department of Medical Oncology, Erasmus MC Cancer Institute, University Medical Center Rotterdam, Dr. Molewaterplein 40, 3015 GD, Rotterdam, The Netherlands
| | - Saskia M Wilting
- Department of Medical Oncology, Erasmus MC Cancer Institute, University Medical Center Rotterdam, Dr. Molewaterplein 40, 3015 GD, Rotterdam, The Netherlands
| | - John W M Martens
- Department of Medical Oncology, Erasmus MC Cancer Institute, University Medical Center Rotterdam, Dr. Molewaterplein 40, 3015 GD, Rotterdam, The Netherlands
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18
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Goto H, Ohtsu T, Ito M, Sagisaka M, Naruto T, Nagai JI, Kitagawa N, Tanaka M, Yanagimachi M, Hiroshima Y, Miyagi Y. A short-term three dimensional culture-based drug sensitivity test is feasible for malignant bone tumors. Hum Cell 2023; 36:2152-2161. [PMID: 37707773 DOI: 10.1007/s13577-023-00982-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2023] [Accepted: 08/31/2023] [Indexed: 09/15/2023]
Abstract
The feasibility of a short-term, three-dimensional (3D) culture-based drug sensitivity test (DST) for surgically resected malignant bone tumors, including osteosarcoma (OS), was evaluated utilizing two OS cell line (KCS8 or KCS9)-derived xenograft (CDX) models. Twenty-three (KCS8) or 39 (KCS9) of 60 tested drugs were likely effective in OS cells derived from a cell line before xenografting. Fewer drugs (19: KCS8, 26: KCS9) were selected as effective drugs in cells derived from a CDX tumor, although the drug sensitivities of 60 drugs significantly correlated between both types of samples. The drug sensitivity of a CDX tumor was not significantly altered after the depletion of non-tumorous components in the sample. In a surgically resected metastatic tumor obtained from a patient with OS, for whom a cancer genome profiling test detected a pathogenic PIK3CA mutation, DST identified mTOR and AKT inhibitors as effective drugs. Of two CDX and six clinical samples of OS and Ewing's sarcoma, DST identified proteasome inhibitors (bortezomib, carfilzomib) and CEP-701 as potentially effective drugs in common. This unique method of in vitro drug testing using 3D-cell cultures is feasible in surgically resected tissues of metastatic malignant bone tumors.
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Affiliation(s)
- Hiroaki Goto
- Division of Hematology/Oncology, Kanagawa Children's Medical Center, 2-138-4 Mutsukawa Minami-Ku, Yokohama, 232-8555, Japan.
- Clinical Research Institute, Kanagawa Children's Medical Center, Yokohama, Japan.
| | - Takashi Ohtsu
- Division of Advanced Cancer Therapeutics, Kanagawa Cancer Center Research Institute, Yokohama, Japan
- Center for Cancer Genome Medicine, Kanagawa Cancer Center, Yokohama, Japan
| | - Mieko Ito
- Clinical Research Institute, Kanagawa Children's Medical Center, Yokohama, Japan
| | - Maiko Sagisaka
- Clinical Research Institute, Kanagawa Children's Medical Center, Yokohama, Japan
| | - Takuya Naruto
- Clinical Research Institute, Kanagawa Children's Medical Center, Yokohama, Japan
| | - Jun-Ichi Nagai
- Department of Pathology, Kanagawa Children's Medical Center, Yokohama, Japan
| | - Norihiko Kitagawa
- Department of Surgery, Kanagawa Children's Medical Center, Yokohama, Japan
| | - Mio Tanaka
- Department of Pathology, Kanagawa Children's Medical Center, Yokohama, Japan
| | - Masakatsu Yanagimachi
- Division of Hematology/Oncology, Kanagawa Children's Medical Center, 2-138-4 Mutsukawa Minami-Ku, Yokohama, 232-8555, Japan
- Clinical Research Institute, Kanagawa Children's Medical Center, Yokohama, Japan
| | - Yukihiko Hiroshima
- Division of Advanced Cancer Therapeutics, Kanagawa Cancer Center Research Institute, Yokohama, Japan
- Center for Cancer Genome Medicine, Kanagawa Cancer Center, Yokohama, Japan
| | - Yohei Miyagi
- Molecular Pathology and Genetics Division, Kanagawa Cancer Center Research Institute, Yokohama, Japan
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19
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Cotton JL, Estrada Diez J, Sagar V, Chen J, Piquet M, Alford J, Song Y, Li X, Riester M, DiMare MT, Schumacher K, Boulay G, Sprouffske K, Fan L, Burks T, Mansur L, Wagner J, Bhang HEC, Iartchouk O, Reece-Hoyes J, Morris EJ, Hammerman PS, Ruddy DA, Korn JM, Engelman JA, Niederst MJ. Expressed Barcoding Enables High-Resolution Tracking of the Evolution of Drug Tolerance. Cancer Res 2023; 83:3611-3623. [PMID: 37603596 DOI: 10.1158/0008-5472.can-23-0144] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2023] [Revised: 05/11/2023] [Accepted: 08/15/2023] [Indexed: 08/23/2023]
Abstract
For a majority of patients with non-small cell lung cancer with EGFR mutations, treatment with EGFR inhibitors (EGFRi) induces a clinical response. Despite this initial reduction in tumor size, residual disease persists that leads to disease relapse. Elucidating the preexisting biological differences between sensitive cells and surviving drug-tolerant persister cells and deciphering how drug-tolerant cells evolve in response to treatment could help identify strategies to improve the efficacy of EGFRi. In this study, we tracked the origins and clonal evolution of drug-tolerant cells at a high resolution by using an expressed barcoding system coupled with single-cell RNA sequencing. This platform enabled longitudinal profiling of gene expression and drug sensitivity in response to EGFRi across a large number of clones. Drug-tolerant cells had higher expression of key survival pathways such as YAP and EMT at baseline and could also differentially adapt their gene expression following EGFRi treatment compared with sensitive cells. In addition, drug combinations targeting common downstream components (MAPK) or orthogonal factors (chemotherapy) showed greater efficacy than EGFRi alone, which is attributable to broader targeting of the heterogeneous EGFRi-tolerance mechanisms present in tumors. Overall, this approach facilitates thorough examination of clonal evolution in response to therapy that could inform the development of improved diagnostic approaches and treatment strategies for targeting drug-tolerant cells. SIGNIFICANCE The evolution and heterogeneity of EGFR inhibitor tolerance are identified in a large number of clones at enhanced cellular and temporal resolution using an expressed barcode technology coupled with single-cell RNA sequencing.
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Affiliation(s)
- Jennifer L Cotton
- Oncology Disease Area, Novartis Institutes for BioMedical Research, Cambridge, Massachusetts
| | - Javier Estrada Diez
- Oncology Disease Area, Novartis Institutes for BioMedical Research, Cambridge, Massachusetts
| | - Vivek Sagar
- Oncology Disease Area, Novartis Institutes for BioMedical Research, Cambridge, Massachusetts
| | - Julie Chen
- Oncology Disease Area, Novartis Institutes for BioMedical Research, Cambridge, Massachusetts
| | - Michelle Piquet
- Oncology Disease Area, Novartis Institutes for BioMedical Research, Cambridge, Massachusetts
| | - John Alford
- Chemical Biology & Therapeutics, Novartis Institutes for BioMedical Research, Cambridge, Massachusetts
| | - Youngchul Song
- Oncology Disease Area, Novartis Institutes for BioMedical Research, Cambridge, Massachusetts
| | - Xiaoyan Li
- Oncology Disease Area, Novartis Institutes for BioMedical Research, Cambridge, Massachusetts
| | - Markus Riester
- Oncology Disease Area, Novartis Institutes for BioMedical Research, Cambridge, Massachusetts
| | - Matthew T DiMare
- Oncology Disease Area, Novartis Institutes for BioMedical Research, Cambridge, Massachusetts
| | - Katja Schumacher
- Oncology Disease Area, Novartis Institutes for BioMedical Research, Cambridge, Massachusetts
| | - Gaylor Boulay
- Oncology Disease Area, Novartis Institutes for BioMedical Research, Cambridge, Massachusetts
| | - Kathleen Sprouffske
- Oncology Disease Area, Novartis Institutes for BioMedical Research, Basel, Switzerland
| | - Lin Fan
- Chemical Biology & Therapeutics, Novartis Institutes for BioMedical Research, Cambridge, Massachusetts
| | - Tyler Burks
- Chemical Biology & Therapeutics, Novartis Institutes for BioMedical Research, Cambridge, Massachusetts
| | - Leandra Mansur
- Chemical Biology & Therapeutics, Novartis Institutes for BioMedical Research, Cambridge, Massachusetts
| | - Joel Wagner
- Oncology Disease Area, Novartis Institutes for BioMedical Research, Cambridge, Massachusetts
| | - Hyo-Eun C Bhang
- Oncology Disease Area, Novartis Institutes for BioMedical Research, Cambridge, Massachusetts
| | - Oleg Iartchouk
- Chemical Biology & Therapeutics, Novartis Institutes for BioMedical Research, Cambridge, Massachusetts
| | - John Reece-Hoyes
- Chemical Biology & Therapeutics, Novartis Institutes for BioMedical Research, Cambridge, Massachusetts
| | - Erick J Morris
- Oncology Disease Area, Novartis Institutes for BioMedical Research, Cambridge, Massachusetts
| | - Peter S Hammerman
- Oncology Disease Area, Novartis Institutes for BioMedical Research, Cambridge, Massachusetts
| | - David A Ruddy
- Oncology Disease Area, Novartis Institutes for BioMedical Research, Cambridge, Massachusetts
| | - Joshua M Korn
- Oncology Disease Area, Novartis Institutes for BioMedical Research, Cambridge, Massachusetts
| | - Jeffrey A Engelman
- Oncology Disease Area, Novartis Institutes for BioMedical Research, Cambridge, Massachusetts
| | - Matthew J Niederst
- Oncology Disease Area, Novartis Institutes for BioMedical Research, Cambridge, Massachusetts
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20
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Florou V, Elliott A, Bailey MH, Stone D, Affolter K, Soares HP, Nevala-Plagemann C, Scaife C, Walker P, Korn WM, Lou E, Shroff RT, Hosein PJ, Garrido-Laguna I. Comparative Genomic Analysis of Pancreatic Acinar Cell Carcinoma (PACC) and Pancreatic Ductal Adenocarcinoma (PDAC) Unveils New Actionable Genomic Aberrations in PACC. Clin Cancer Res 2023; 29:3408-3417. [PMID: 37266563 PMCID: PMC10526978 DOI: 10.1158/1078-0432.ccr-22-3724] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2022] [Revised: 02/24/2023] [Accepted: 05/30/2023] [Indexed: 06/03/2023]
Abstract
PURPOSE Pure pancreatic acinar cell carcinomas (PACC) are rare malignancies with no established treatment. PACC demonstrates significant genetic intertumoral heterogeneity with multiple pathways involved, suggesting using targeted cancer therapeutics to treat this disease. We aggregated one of the largest datasets of pure PACC to examine the genomic variability and explore patient-specific therapeutic targets. EXPERIMENTAL DESIGN PACC specimens (n = 51) underwent next-generation sequencing of DNA (n = 29) or whole exome (n = 22) and RNA (whole transcriptome, n = 29) at a commercial laboratory. We performed comparative analyses of a genomic cohort of pancreatic ductal adenocarcinomas (PDAC; n = 4,205). In parallel, we conducted a retrospective review of patients with PACC treated at Huntsman Cancer Institute (HCI). RESULTS The real-world dataset included samples from 51 patients with PACC. We found key molecular differences between pure PACC and PDAC, highlighting the unique characteristics of pure PACC. Major differences in PACC include lower MAPK signaling and less stromal cell abundance compared with PDAC. Pure PACC showed genomic loss-of-heterozygosity to largely coincide with mutations in BRCA1, BRCA2, and PALB2. Of the 7 patients treated at HCI, one had a tumor that harbored a BRAF-V600E mutation. Leveraging precision oncology, this patient is being treated with encorafenib plus binimetinib, achieving an exceptionally durable and ongoing complete response of more than 3 years. CONCLUSIONS There are major differences between PACC and PDAC, including downregulation of the MAPK signaling pathway, and less stromal cell abundance. In addition, genomic characterization of pure PACC revealed frequent targetable alterations, which can guide patient treatment.
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Affiliation(s)
- Vaia Florou
- Department of Internal Medicine, Division of Oncology, Huntsman Cancer Institute, University of Utah School of Medicine, 2000 Circle of Hope, 84112, Salt Lake City, UT, USA
| | | | - Matthew H Bailey
- Department of Biology at Brigham Young University, Salt Lake City, UT, USA
| | - David Stone
- Department of Biology at Brigham Young University, Salt Lake City, UT, USA
| | - Kajsa Affolter
- Department of Pathology, Huntsman Cancer Institute, University of Utah School of Medicine, Salt Lake City, UT, USA
| | - Heloisa P. Soares
- Department of Internal Medicine, Division of Oncology, Huntsman Cancer Institute, University of Utah School of Medicine, 2000 Circle of Hope, 84112, Salt Lake City, UT, USA
| | - Chris Nevala-Plagemann
- Department of Internal Medicine, Division of Oncology, Huntsman Cancer Institute, University of Utah School of Medicine, 2000 Circle of Hope, 84112, Salt Lake City, UT, USA
| | - Courtney Scaife
- Department of Surgery, Huntsman Cancer Institute, University of Utah School of Medicine, Salt Lake City, UT, USA
| | | | | | - Emil Lou
- Masonic Cancer Center, University of Minnesota, Minneapolis, Minnesota, USA
| | - Rachna T Shroff
- Division of Hematology and Oncology, Department of Medicine, University of Arizona Cancer Center, Tucson, AZ, USA
| | - Peter J Hosein
- Department of Medicine, Sylvester Comprehensive Cancer Center, University of Miami Miller School of Medicine, Miami, Florida, USA
| | - Ignacio Garrido-Laguna
- Department of Internal Medicine, Division of Oncology, Huntsman Cancer Institute, University of Utah School of Medicine, 2000 Circle of Hope, 84112, Salt Lake City, UT, USA
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21
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Flint AC, Mitchell DK, Angus SP, Smith AE, Bessler W, Jiang L, Mang H, Li X, Lu Q, Rodriguez B, Sandusky GE, Masters AR, Zhang C, Dang P, Koenig J, Johnson GL, Shen W, Liu J, Aggarwal A, Donoho GP, Willard MD, Bhagwat SV, Wade Clapp D, Rhodes SD. Combined CDK4/6 and ERK1/2 Inhibition Enhances Antitumor Activity in NF1-Associated Plexiform Neurofibroma. Clin Cancer Res 2023; 29:3438-3456. [PMID: 37406085 PMCID: PMC11060649 DOI: 10.1158/1078-0432.ccr-22-2854] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2022] [Revised: 04/06/2023] [Accepted: 06/29/2023] [Indexed: 07/07/2023]
Abstract
PURPOSE Plexiform neurofibromas (PNF) are peripheral nerve sheath tumors that cause significant morbidity in persons with neurofibromatosis type 1 (NF1), yet treatment options remain limited. To identify novel therapeutic targets for PNF, we applied an integrated multi-omic approach to quantitatively profile kinome enrichment in a mouse model that has predicted therapeutic responses in clinical trials for NF1-associated PNF with high fidelity. EXPERIMENTAL DESIGN Utilizing RNA sequencing combined with chemical proteomic profiling of the functionally enriched kinome using multiplexed inhibitor beads coupled with mass spectrometry, we identified molecular signatures predictive of response to CDK4/6 and RAS/MAPK pathway inhibition in PNF. Informed by these results, we evaluated the efficacy of the CDK4/6 inhibitor, abemaciclib, and the ERK1/2 inhibitor, LY3214996, alone and in combination in reducing PNF tumor burden in Nf1flox/flox;PostnCre mice. RESULTS Converging signatures of CDK4/6 and RAS/MAPK pathway activation were identified within the transcriptome and kinome that were conserved in both murine and human PNF. We observed robust additivity of the CDK4/6 inhibitor, abemaciclib, in combination with the ERK1/2 inhibitor, LY3214996, in murine and human NF1(Nf1) mutant Schwann cells. Consistent with these findings, the combination of abemaciclib (CDK4/6i) and LY3214996 (ERK1/2i) synergized to suppress molecular signatures of MAPK activation and exhibited enhanced antitumor activity in Nf1flox/flox;PostnCre mice in vivo. CONCLUSIONS These findings provide rationale for the clinical translation of CDK4/6 inhibitors alone and in combination with therapies targeting the RAS/MAPK pathway for the treatment of PNF and other peripheral nerve sheath tumors in persons with NF1.
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Affiliation(s)
- Alyssa C. Flint
- Department of Pediatrics, Herman B Wells Center for Pediatric Research, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Dana K. Mitchell
- Department of Pediatrics, Herman B Wells Center for Pediatric Research, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Steven P. Angus
- Department of Pediatrics, Herman B Wells Center for Pediatric Research, Indiana University School of Medicine, Indianapolis, IN, USA
- Department of Pharmacology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
- Indiana University Melvin and Bren Simon Comprehensive Cancer Center
| | - Abbi E. Smith
- Department of Pediatrics, Herman B Wells Center for Pediatric Research, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Waylan Bessler
- Department of Pediatrics, Herman B Wells Center for Pediatric Research, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Li Jiang
- Department of Pediatrics, Herman B Wells Center for Pediatric Research, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Henry Mang
- Department of Pediatrics, Herman B Wells Center for Pediatric Research, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Xiaohong Li
- Department of Pediatrics, Herman B Wells Center for Pediatric Research, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Qingbo Lu
- Department of Pediatrics, Herman B Wells Center for Pediatric Research, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Brooke Rodriguez
- Department of Pediatrics, Herman B Wells Center for Pediatric Research, Indiana University School of Medicine, Indianapolis, IN, USA
| | - George E. Sandusky
- Department of Pathology, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Andi R. Masters
- Clinical Pharmacology Analytical Core, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Chi Zhang
- Center for Computational Biology and Bioinformatics and Department of Medical and Molecular Genetics, Indiana University School of Medicine
| | - Pengtao Dang
- Center for Computational Biology and Bioinformatics and Department of Medical and Molecular Genetics, Indiana University School of Medicine
| | - Jenna Koenig
- Medical Scientist Training Program, Indiana University School of Medicine, Indianapolis, IN USA
| | - Gary L. Johnson
- Department of Pharmacology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
- UNC Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Weihua Shen
- Lilly Research Laboratories, Eli Lilly and Company, Indianapolis, IN, USA
| | - Jiangang Liu
- Lilly Research Laboratories, Eli Lilly and Company, Indianapolis, IN, USA
| | - Amit Aggarwal
- Lilly Research Laboratories, Eli Lilly and Company, Indianapolis, IN, USA
| | - Gregory P. Donoho
- Lilly Research Laboratories, Eli Lilly and Company, Indianapolis, IN, USA
| | - Melinda D. Willard
- Lilly Research Laboratories, Eli Lilly and Company, Indianapolis, IN, USA
| | - Shripad V. Bhagwat
- Lilly Research Laboratories, Eli Lilly and Company, Indianapolis, IN, USA
| | - D. Wade Clapp
- Department of Pediatrics, Herman B Wells Center for Pediatric Research, Indiana University School of Medicine, Indianapolis, IN, USA
- Indiana University Melvin and Bren Simon Comprehensive Cancer Center
| | - Steven D. Rhodes
- Department of Pediatrics, Herman B Wells Center for Pediatric Research, Indiana University School of Medicine, Indianapolis, IN, USA
- Indiana University Melvin and Bren Simon Comprehensive Cancer Center
- Division of Pediatric Hematology-Oncology, Indiana University School of Medicine, Indianapolis, IN, USA
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22
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Tabrizian N, Nouruzi S, Cui CJ, Kobelev M, Namekawa T, Lodhia I, Talal A, Sivak O, Ganguli D, Zoubeidi A. ASCL1 is activated downstream of the ROR2/CREB signaling pathway to support lineage plasticity in prostate cancer. Cell Rep 2023; 42:112937. [PMID: 37552603 DOI: 10.1016/j.celrep.2023.112937] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2023] [Revised: 07/16/2023] [Accepted: 07/20/2023] [Indexed: 08/10/2023] Open
Abstract
Lineage plasticity is a form of therapy-induced drug resistance. In prostate cancer, androgen receptor (AR) pathway inhibitors potentially lead to the accretion of tumor relapse with loss of AR signaling and a shift from a luminal state to an alternate program. However, the molecular and signaling mechanisms orchestrating the development of lineage plasticity under the pressure of AR-targeted therapies are not fully understood. Here, a survey of receptor tyrosine kinases (RTKs) identifies ROR2 as the top upregulated RTK following AR pathway inhibition, which feeds into lineage plasticity by promoting stem-cell-like and neuronal networks. Mechanistically, ROR2 activates the ERK/CREB signaling pathway to modulate the expression of the lineage commitment transcription factor ASCL1. Collectively, our findings nominate ROR2 as a potential therapeutic target to reverse the ENZ-induced plastic phenotype and potentially re-sensitize tumors to AR pathway inhibitors.
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Affiliation(s)
- Nakisa Tabrizian
- Department of Urologic Sciences, The University of British Columbia, Vancouver, BC V5Z 1M9, Canada; Vancouver Prostate Centre, Vancouver, BC V6H 3Z6, Canada
| | - Shaghayegh Nouruzi
- Department of Urologic Sciences, The University of British Columbia, Vancouver, BC V5Z 1M9, Canada; Vancouver Prostate Centre, Vancouver, BC V6H 3Z6, Canada
| | - Cassandra Jingjing Cui
- Department of Urologic Sciences, The University of British Columbia, Vancouver, BC V5Z 1M9, Canada; Vancouver Prostate Centre, Vancouver, BC V6H 3Z6, Canada
| | - Maxim Kobelev
- Department of Urologic Sciences, The University of British Columbia, Vancouver, BC V5Z 1M9, Canada; Vancouver Prostate Centre, Vancouver, BC V6H 3Z6, Canada
| | - Takeshi Namekawa
- Department of Urologic Sciences, The University of British Columbia, Vancouver, BC V5Z 1M9, Canada; Vancouver Prostate Centre, Vancouver, BC V6H 3Z6, Canada
| | - Ishana Lodhia
- Vancouver Prostate Centre, Vancouver, BC V6H 3Z6, Canada
| | - Amina Talal
- Vancouver Prostate Centre, Vancouver, BC V6H 3Z6, Canada
| | - Olena Sivak
- Vancouver Prostate Centre, Vancouver, BC V6H 3Z6, Canada
| | | | - Amina Zoubeidi
- Department of Urologic Sciences, The University of British Columbia, Vancouver, BC V5Z 1M9, Canada; Vancouver Prostate Centre, Vancouver, BC V6H 3Z6, Canada.
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23
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Zhang P, Tao C, Shimura T, Huang AC, Kong N, Dai Y, Yao S, Xi Y, Wang X, Fang J, Moses MA, Guo P. ICAM1 antibody drug conjugates exert potent antitumor activity in papillary and anaplastic thyroid carcinoma. iScience 2023; 26:107272. [PMID: 37520726 PMCID: PMC10371847 DOI: 10.1016/j.isci.2023.107272] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2023] [Revised: 04/27/2023] [Accepted: 06/28/2023] [Indexed: 08/01/2023] Open
Abstract
Treatment options for anaplastic thyroid cancer (ATC) and refractory papillary thyroid carcinoma (PTC) are limited and outcomes remain poor. In this study, we determined via bioinformatic expression analyses and immunohistochemistry staining that intercellular adhesion molecule-1(ICAM1) is an attractive target for ATC and PTC. We designed and engineered two ICAM1-directed antibody-drug conjugate (I1-MMAE and I1-DXd), both of which potently and selectively ablate multiple human ATC and PTC cell lines without affecting non-plastic cells in vitro. Furthermore, I1-MMAE and I1-DXd mediated a potent tumor regression in ATC and PTC xenograft models. To develop a precision medicine, we also explored magnetic resonance imaging (MRI) as a non-invasive biomarker detection method to quantitatively map ICAM1 antigen expression in heterogeneous thyroid tumors. Taken together, this study provides a strong rationale for the further development of I1-MMAE and I1-DXd as promising therapeutic candidates to treat advanced PTC and ATC.
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Affiliation(s)
- Peng Zhang
- Department of Medical Oncology, The Cancer Hospital of the University of Chinese Academy of Sciences, Zhejiang Cancer Hospital, Hangzhou, Zhejiang 310022, China
- Key Laboratory of Head and Neck Cancer Translational Research of Zhejiang Province, Zhejiang Cancer Hospital, Hangzhou, Zhejiang 310022, China
- Institute of Basic Medicine and Cancer (IBMC), Chinese Academy of Sciences, Hangzhou, Zhejiang 310022, China
| | - Changjuan Tao
- Key Laboratory of Head and Neck Cancer Translational Research of Zhejiang Province, Zhejiang Cancer Hospital, Hangzhou, Zhejiang 310022, China
- Institute of Basic Medicine and Cancer (IBMC), Chinese Academy of Sciences, Hangzhou, Zhejiang 310022, China
- Department of Radiation Oncology, The Cancer Hospital of the University of Chinese Academy of Sciences, Zhejiang Cancer Hospital, Hangzhou, Zhejiang 310022, China
| | - Takaya Shimura
- Department of Gastroenterology and Metabolism, Nagoya City University Graduate School of Medical Sciences, Nagoya 467-8601, Japan
| | | | - Nana Kong
- MabPlex International, Yantai, Shandong 264006, China
| | - Yujie Dai
- MabPlex International, Yantai, Shandong 264006, China
| | - Shili Yao
- School of Materials Science and Engineering, Tianjin University, Tianjin 300072, China
| | - Yun Xi
- Department of Pathology, The Cancer Hospital of the University of Chinese Academy of Sciences, Zhejiang Cancer Hospital, Hangzhou, Zhejiang 310022, China
| | - Xing Wang
- Department of Head and Neck Surgery, The Cancer Hospital of the University of Chinese Academy of Sciences, Zhejiang Cancer Hospital, Hangzhou, Zhejiang 310022, China
| | - Jianmin Fang
- School of Life Science and Technology, Tongji University, Shanghai 200092, China
| | - Marsha A. Moses
- Vascular Biology Program, Boston Children’s Hospital, Boston, MA 02115, USA
- Department of Surgery, Boston Children’s Hospital and Harvard Medical School, Boston, MA 02115, USA
| | - Peng Guo
- Institute of Basic Medicine and Cancer (IBMC), Chinese Academy of Sciences, Hangzhou, Zhejiang 310022, China
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24
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Das S, Idate R, Lana SE, Regan DP, Duval DL. Integrated analysis of canine soft tissue sarcomas identifies recurrent mutations in TP53, KMT genes and PDGFB fusions. Sci Rep 2023; 13:10422. [PMID: 37369741 DOI: 10.1038/s41598-023-37266-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2023] [Accepted: 06/19/2023] [Indexed: 06/29/2023] Open
Abstract
Soft tissue sarcomas (STS) are a heterogenous group of mesenchymal tumors representing over 50 distinct types with overlapping histological features and non-specific anatomical locations. Currently, localized sarcomas are treated with surgery + / - radiation in both humans and dogs with few molecularly targeted therapeutic options. However, to improve precision-based cancer therapy through trials in pet dogs with naturally occurring STS tumors, knowledge of genomic profiling and molecular drivers in both species is essential. To this purpose, we sought to characterize the transcriptomic and genomic mutation profiles of canine STS subtypes (fibrosarcoma, undifferentiated pleomorphic sarcoma, and peripheral nerve sheath tumors), by leveraging RNAseq, whole exome sequencing, immunohistochemistry, and drug assays. The most common driver mutations were in cell cycle/DNA repair (31%, TP53-21%) and chromatin organization/binding (41%, KMT2D-21%) genes. Similar to a subset of human sarcomas, we identified fusion transcripts of platelet derived growth factor B and collagen genes that predict sensitivity to PDGFR inhibitors. Transcriptomic profiling grouped these canine STS tumors into 4 clusters, one PNST group (H1), and 3 FSA groups selectively enriched for extracellular matrix interactions and PDFGB fusions (H2), homeobox transcription factors (H3), and elevated T-cell infiltration (H4). This multi-omics approach provides insights into canine STS sub-types at a molecular level for comparison to their human counterparts, to improve diagnosis, and may provide additional targets for chemo- and immuno-therapy.
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Affiliation(s)
- Sunetra Das
- Department of Clinical Sciences, College of Veterinary Medicine and Biomedical Sciences, Colorado State University, Fort Collins, CO, 80523, USA
- Flint Animal Cancer Center, Colorado State University, Fort Collins, CO, 80523, USA
| | - Rupa Idate
- Department of Clinical Sciences, College of Veterinary Medicine and Biomedical Sciences, Colorado State University, Fort Collins, CO, 80523, USA
- Flint Animal Cancer Center, Colorado State University, Fort Collins, CO, 80523, USA
| | - Susan E Lana
- Department of Clinical Sciences, College of Veterinary Medicine and Biomedical Sciences, Colorado State University, Fort Collins, CO, 80523, USA
- Flint Animal Cancer Center, Colorado State University, Fort Collins, CO, 80523, USA
| | - Daniel P Regan
- Flint Animal Cancer Center, Colorado State University, Fort Collins, CO, 80523, USA
- Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, CO, 80523, USA
| | - Dawn L Duval
- Department of Clinical Sciences, College of Veterinary Medicine and Biomedical Sciences, Colorado State University, Fort Collins, CO, 80523, USA.
- Flint Animal Cancer Center, Colorado State University, Fort Collins, CO, 80523, USA.
- University of Colorado Cancer Center, Anschutz Medical Campus, Aurora, CO, 80045, USA.
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25
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Napolitano S, Woods M, Lee HM, De Falco V, Martini G, Della Corte CM, Martinelli E, Famiglietti V, Ciardiello D, Anderson A, Fowlkes NW, Villareal OE, Sorokin A, Kanikarla P, Coker O, Morris V, Altucci L, Tabernero J, Troiani T, Ciardiello F, Kopetz S. Antitumor Efficacy of Dual Blockade with Encorafenib + Cetuximab in Combination with Chemotherapy in Human BRAFV600E-Mutant Colorectal Cancer. Clin Cancer Res 2023; 29:2299-2309. [PMID: 37040395 PMCID: PMC10261917 DOI: 10.1158/1078-0432.ccr-22-3894] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2022] [Revised: 03/14/2023] [Accepted: 04/07/2023] [Indexed: 04/12/2023]
Abstract
PURPOSE Encorafenib + cetuximab (E+C) is an effective therapeutic option in chemorefractory BRAFV600E metastatic colorectal cancer (mCRC). However, there is a need to improve the efficacy of this molecular-targeted therapy and evaluate regimens suitable for untreated BRAFV600E in patients with mCRC. EXPERIMENTAL DESIGN We performed a series of in vivo studies using BRAFV600E mCRC tumor xenografts. Mice were randomized to receive 5-fluoruracil (5-FU), irinotecan, or oxaliplatin regimens (FOLFIRI or FOLFOX), (E+C) or the combination. Patients received long-term treatment until disease progression, with deescalation strategies used to mimic maintenance therapy. Transcriptomic changes after progression on cytotoxic chemotherapy or targeted therapy were assessed. RESULTS Antitumor activity of either FOLFIRI or E+C was better as first-line treatment as compared with second-line, with partial cross-resistance seen between a cytotoxic regimen and targeted therapy with an average 62% loss of efficacy for FOLFIRI after E+C and a 45% loss of efficacy of E+C after FOLFIRI (P < 0.001 for both). FOLFIRI-treated models had upregulation of epithelial-mesenchymal transition (EMT) and MAPK pathway activation, where E+C treated models had suppressed MAPK signaling. In contrast, with chemotherapy with E+C, EMT and MAPK signaling remained suppressed. FOLFOX or FOLFIRI, each in combination with E+C, were the most active first-line treatments as compared with E+C or to chemotherapy alone. Furthermore, FOLFOX in combination with E+C as first-line induction therapy, followed by E+C ± 5-FU as maintenance therapy, was the most effective strategy for long-term disease control. CONCLUSIONS These results support the combination of cytotoxic chemotherapy and molecular-targeted therapy as a promising therapeutic approach in the first-line treatment of BRAFV600E mCRC.
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Affiliation(s)
- Stefania Napolitano
- Department of Precision Medicine, Università degli Studi della Campania “Luigi Vanvitelli”, Napoli, Italy
| | - Melanie Woods
- Division of Cancer Medicine, Department of Gastrointestinal Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Hey Min Lee
- Division of Cancer Medicine, Department of Gastrointestinal Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Vincenzo De Falco
- Department of Precision Medicine, Università degli Studi della Campania “Luigi Vanvitelli”, Napoli, Italy
| | - Giulia Martini
- Department of Precision Medicine, Università degli Studi della Campania “Luigi Vanvitelli”, Napoli, Italy
| | - Carminia Maria Della Corte
- Department of Precision Medicine, Università degli Studi della Campania “Luigi Vanvitelli”, Napoli, Italy
| | - Erika Martinelli
- Department of Precision Medicine, Università degli Studi della Campania “Luigi Vanvitelli”, Napoli, Italy
| | - Vincenzo Famiglietti
- Department of Precision Medicine, Università degli Studi della Campania “Luigi Vanvitelli”, Napoli, Italy
| | - Davide Ciardiello
- Department of Precision Medicine, Università degli Studi della Campania “Luigi Vanvitelli”, Napoli, Italy
| | - Amanda Anderson
- Division of Cancer Medicine, Department of Gastrointestinal Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Natalie Wall Fowlkes
- Veterinary Medicine & Surgery Department, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Oscar Eduardo Villareal
- Division of Cancer Medicine, Department of Gastrointestinal Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Alexey Sorokin
- Division of Cancer Medicine, Department of Gastrointestinal Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Preeti Kanikarla
- Division of Cancer Medicine, Department of Gastrointestinal Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Olu Coker
- Division of Cancer Medicine, Department of Gastrointestinal Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Van Morris
- Division of Cancer Medicine, Department of Gastrointestinal Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Lucia Altucci
- Department of Precision Medicine, Università degli Studi della Campania “Luigi Vanvitelli”, Napoli, Italy
| | - Josep Tabernero
- Medical Oncology Department, Vall d' Hebron Hospital Campus, Barcelona, Spain
- Institute of Oncology, University of Vic/Central University of Catalonia, Barcelona, Spain
- Oncology Institute of Barcelona-Quironsalud, Biomedical Research Center in Cancer, Barcelona, Spain
| | - Teresa Troiani
- Department of Precision Medicine, Università degli Studi della Campania “Luigi Vanvitelli”, Napoli, Italy
| | - Fortunato Ciardiello
- Department of Precision Medicine, Università degli Studi della Campania “Luigi Vanvitelli”, Napoli, Italy
| | - Scott Kopetz
- Division of Cancer Medicine, Department of Gastrointestinal Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas
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26
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Darabi S, Xiu J, Samec T, Kesari S, Carrillo J, Aulakh S, Walsh KM, Sengupta S, Sumrall A, Spetzler D, Glantz M, Demeure MJ. Capicua (CIC) mutations in gliomas in association with MAPK activation for exposing a potential therapeutic target. Med Oncol 2023; 40:197. [PMID: 37291277 DOI: 10.1007/s12032-023-02071-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2023] [Accepted: 06/02/2023] [Indexed: 06/10/2023]
Abstract
Gliomas are the most prevalent neurological cancer in the USA and care modalities are not able to effectively combat these aggressive malignancies. Identifying new, more effective treatments require a deep understanding of the complex genetic variations and relevant pathway associations behind these cancers. Drawing connections between gene mutations with a responsive genetic target can help drive therapy selections to enhance patient survival. We have performed extensive molecular profiling of the Capicua gene (CIC), a tumor and transcriptional suppressor gene, and its mutation prevalence in reference to MAPK activation within clinical glioma tissue. CIC mutations occur far more frequently in oligodendroglioma (52.1%) than in low-grade astrocytoma or glioblastoma. CIC-associated mutations were observed across all glioma subtypes, and MAPK-associated mutations were most prevalent in CIC wild-type tissue regardless of the glioma subtype. MAPK activation, however, was enhanced in CIC-mutated oligodendroglioma. The totality of our observations reported supports the use of CIC as a relevant genetic marker for MAPK activation. Identification of CIC mutations, or lack thereof, can assist in selecting, implementing, and developing MEK/MAPK-inhibitory trials to improve patient outcomes potentially.
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Affiliation(s)
- Sourat Darabi
- Hoag Family Cancer Institute, Newport Beach, CA, USA
| | | | | | - Santosh Kesari
- Hoag Family Cancer Institute, Newport Beach, CA, USA
- Pacific Neuroscience Institute, Providence Saint John's Health Center, Santa Monica, CA, USA
| | - Jose Carrillo
- Hoag Family Cancer Institute, Newport Beach, CA, USA
- Pacific Neuroscience Institute, Providence Saint John's Health Center, Santa Monica, CA, USA
| | | | - Kyle M Walsh
- Duke University School of Medicine, Durham, NC, USA
| | - Soma Sengupta
- University of Cincinnati College of Medicine, Cincinnati, OH, USA
| | | | | | | | - Michael J Demeure
- Hoag Family Cancer Institute, Newport Beach, CA, USA
- Translational Genomics Research Institute, Phoenix, AZ, USA
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27
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Hagenbeek TJ, Zbieg JR, Hafner M, Mroue R, Lacap JA, Sodir NM, Noland CL, Afghani S, Kishore A, Bhat KP, Yao X, Schmidt S, Clausen S, Steffek M, Lee W, Beroza P, Martin S, Lin E, Fong R, Di Lello P, Kubala MH, Yang MNY, Lau JT, Chan E, Arrazate A, An L, Levy E, Lorenzo MN, Lee HJ, Pham TH, Modrusan Z, Zang R, Chen YC, Kabza M, Ahmed M, Li J, Chang MT, Maddalo D, Evangelista M, Ye X, Crawford JJ, Dey A. An allosteric pan-TEAD inhibitor blocks oncogenic YAP/TAZ signaling and overcomes KRAS G12C inhibitor resistance. NATURE CANCER 2023; 4:812-828. [PMID: 37277530 PMCID: PMC10293011 DOI: 10.1038/s43018-023-00577-0] [Citation(s) in RCA: 14] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/28/2023] [Accepted: 05/10/2023] [Indexed: 06/07/2023]
Abstract
The Hippo pathway is a key growth control pathway that is conserved across species. The downstream effectors of the Hippo pathway, YAP (Yes-associated protein) and TAZ (transcriptional coactivator with PDZ-binding motif), are frequently activated in cancers to drive proliferation and survival. Based on the premise that sustained interactions between YAP/TAZ and TEADs (transcriptional enhanced associate domain) are central to their transcriptional activities, we discovered a potent small-molecule inhibitor (SMI), GNE-7883, that allosterically blocks the interactions between YAP/TAZ and all human TEAD paralogs through binding to the TEAD lipid pocket. GNE-7883 effectively reduces chromatin accessibility specifically at TEAD motifs, suppresses cell proliferation in a variety of cell line models and achieves strong antitumor efficacy in vivo. Furthermore, we uncovered that GNE-7883 effectively overcomes both intrinsic and acquired resistance to KRAS (Kirsten rat sarcoma viral oncogene homolog) G12C inhibitors in diverse preclinical models through the inhibition of YAP/TAZ activation. Taken together, this work demonstrates the activities of TEAD SMIs in YAP/TAZ-dependent cancers and highlights their potential broad applications in precision oncology and therapy resistance.
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Affiliation(s)
| | - Jason R Zbieg
- Department of Discovery Chemistry, Genentech, California, CA, USA
| | - Marc Hafner
- Department of Oncology Bioinformatics, Genentech, California, CA, USA
| | - Rana Mroue
- Department of Discovery Oncology, Genentech, California, CA, USA
| | - Jennifer A Lacap
- Department of Translational Oncology, Genentech, California, CA, USA
| | - Nicole M Sodir
- Department of Translational Oncology, Genentech, California, CA, USA
| | - Cameron L Noland
- Department of Structural Biology, Genentech, California, CA, USA
| | - Shervin Afghani
- Department of Discovery Oncology, Genentech, California, CA, USA
| | - Ayush Kishore
- Department of Discovery Oncology, Genentech, California, CA, USA
| | - Kamakoti P Bhat
- Department of Discovery Oncology, Genentech, California, CA, USA
| | - Xiaosai Yao
- Department of Oncology Bioinformatics, Genentech, California, CA, USA
| | - Stephen Schmidt
- Department of Biochemical and Cellular Pharmacology, Genentech, California, CA, USA
| | - Saundra Clausen
- Department of Biochemical and Cellular Pharmacology, Genentech, California, CA, USA
| | - Micah Steffek
- Department of Biochemical and Cellular Pharmacology, Genentech, California, CA, USA
| | - Wendy Lee
- Department of Discovery Chemistry, Genentech, California, CA, USA
| | - Paul Beroza
- Department of Discovery Chemistry, Genentech, California, CA, USA
| | - Scott Martin
- Department of Discovery Oncology, Genentech, California, CA, USA
| | - Eva Lin
- Department of Discovery Oncology, Genentech, California, CA, USA
| | - Rina Fong
- Department of Structural Biology, Genentech, California, CA, USA
| | - Paola Di Lello
- Department of Structural Biology, Genentech, California, CA, USA
| | - Marta H Kubala
- Department of Structural Biology, Genentech, California, CA, USA
| | - Michelle N-Y Yang
- Department of Translational Oncology, Genentech, California, CA, USA
| | - Jeffrey T Lau
- Department of Translational Oncology, Genentech, California, CA, USA
| | - Emily Chan
- Department of Translational Oncology, Genentech, California, CA, USA
| | - Alfonso Arrazate
- Department of Translational Oncology, Genentech, California, CA, USA
| | - Le An
- Department of Small Molecule Pharmaceutical Sciences, Genentech, California, CA, USA
| | - Elizabeth Levy
- Department of Small Molecule Pharmaceutical Sciences, Genentech, California, CA, USA
| | - Maria N Lorenzo
- Department of Protein Chemistry, Genentech, California, CA, USA
| | - Ho-June Lee
- Department of Discovery Oncology, Genentech, California, CA, USA
| | - Trang H Pham
- Department of Discovery Oncology, Genentech, California, CA, USA
| | - Zora Modrusan
- Department of Microchemistry, Proteomics and Lipidomics, Genentech, California, CA, USA
| | - Richard Zang
- Department of Drug Metabolism and Pharmacokinetics, Genentech, California, CA, USA
| | - Yi-Chen Chen
- Department of Drug Metabolism and Pharmacokinetics, Genentech, California, CA, USA
| | | | | | - Jason Li
- Department of Oncology Bioinformatics, Genentech, California, CA, USA
| | - Matthew T Chang
- Department of Oncology Bioinformatics, Genentech, California, CA, USA
| | - Danilo Maddalo
- Department of Translational Oncology, Genentech, California, CA, USA
| | | | - Xin Ye
- Department of Discovery Oncology, Genentech, California, CA, USA.
| | - James J Crawford
- Department of Discovery Chemistry, Genentech, California, CA, USA.
| | - Anwesha Dey
- Department of Discovery Oncology, Genentech, California, CA, USA.
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28
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Wiecek AJ, Cutty SJ, Kornai D, Parreno-Centeno M, Gourmet LE, Tagliazucchi GM, Jacobson DH, Zhang P, Xiong L, Bond GL, Barr AR, Secrier M. Genomic hallmarks and therapeutic implications of G0 cell cycle arrest in cancer. Genome Biol 2023; 24:128. [PMID: 37221612 PMCID: PMC10204193 DOI: 10.1186/s13059-023-02963-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2022] [Accepted: 05/07/2023] [Indexed: 05/25/2023] Open
Abstract
BACKGROUND Therapy resistance in cancer is often driven by a subpopulation of cells that are temporarily arrested in a non-proliferative G0 state, which is difficult to capture and whose mutational drivers remain largely unknown. RESULTS We develop methodology to robustly identify this state from transcriptomic signals and characterise its prevalence and genomic constraints in solid primary tumours. We show that G0 arrest preferentially emerges in the context of more stable, less mutated genomes which maintain TP53 integrity and lack the hallmarks of DNA damage repair deficiency, while presenting increased APOBEC mutagenesis. We employ machine learning to uncover novel genomic dependencies of this process and validate the role of the centrosomal gene CEP89 as a modulator of proliferation and G0 arrest capacity. Lastly, we demonstrate that G0 arrest underlies unfavourable responses to various therapies exploiting cell cycle, kinase signalling and epigenetic mechanisms in single-cell data. CONCLUSIONS We propose a G0 arrest transcriptional signature that is linked with therapeutic resistance and can be used to further study and clinically track this state.
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Affiliation(s)
- Anna J. Wiecek
- UCL Genetics Institute, Department of Genetics, Evolution and Environment, University College London, London, UK
| | - Stephen J. Cutty
- Institute of Clinical Sciences, Faculty of Medicine, Imperial College London, London, UK
| | - Daniel Kornai
- UCL Genetics Institute, Department of Genetics, Evolution and Environment, University College London, London, UK
| | - Mario Parreno-Centeno
- UCL Genetics Institute, Department of Genetics, Evolution and Environment, University College London, London, UK
| | - Lucie E. Gourmet
- UCL Genetics Institute, Department of Genetics, Evolution and Environment, University College London, London, UK
| | | | - Daniel H. Jacobson
- UCL Genetics Institute, Department of Genetics, Evolution and Environment, University College London, London, UK
- UCL Cancer Institute, Paul O’Gorman Building, University College London, London, UK
| | - Ping Zhang
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Lingyun Xiong
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Gareth L. Bond
- Institute of Cancer and Genomic Sciences, University of Birmingham, Edgbaston, Birmingham, UK
| | - Alexis R. Barr
- Institute of Clinical Sciences, Faculty of Medicine, Imperial College London, London, UK
- Cell Cycle Control Team, MRC London Institute of Medical Sciences (LMS), London, UK
| | - Maria Secrier
- UCL Genetics Institute, Department of Genetics, Evolution and Environment, University College London, London, UK
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29
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Selt F, Sigaud R, Valinciute G, Sievers P, Zaman J, Alcon C, Schmid S, Peterziel H, Tsai JW, Guiho R, Martínez-Barbera JP, Pusch S, Deng J, Zhai Y, van Tilburg CM, Schuhman MU, El Damaty A, Bandopadhayay P, Herold-Mende C, von Deimling A, Pfister SM, Montero J, Capper D, Oehme I, Sahm F, Jones DTW, Witt O, Milde T. BH3 mimetics targeting BCL-XL impact the senescent compartment of pilocytic astrocytoma. Neuro Oncol 2023; 25:735-747. [PMID: 35977048 PMCID: PMC10076946 DOI: 10.1093/neuonc/noac199] [Citation(s) in RCA: 15] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2022] [Indexed: 01/28/2023] Open
Abstract
BACKGROUND Pilocytic astrocytoma (PA) is the most common pediatric brain tumor and a mitogen-activated protein kinase (MAPK)-driven disease. Oncogenic MAPK-signaling drives the majority of cells into oncogene-induced senescence (OIS). While OIS induces resistance to antiproliferative therapies, it represents a potential vulnerability exploitable by senolytic agents. METHODS We established new patient-derived PA cell lines that preserve molecular features of the primary tumors and can be studied in OIS and proliferation depending on expression or repression of the SV40 large T antigen. We determined expression of anti-apoptotic BCL-2 members in these models and primary PA. Dependence of senescent PA cells on anti-apoptotic BCL-2 members was investigated using a comprehensive set of BH3 mimetics. RESULTS Senescent PA cells upregulate BCL-XL upon senescence induction and show dependency on BCL-XL for survival. BH3 mimetics with high affinity for BCL-XL (BCL-XLi) reduce metabolic activity and induce mitochondrial apoptosis in senescent PA cells at nano-molar concentrations. In contrast, BH3 mimetics without BCL-XLi activity, conventional chemotherapy, and MEK inhibitors show no effect. CONCLUSIONS Our data demonstrate that BCL-XL is critical for survival of senescent PA tumor cells and provides proof-of-principle for the use of clinically available BCL-XL-dependent senolytics.
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Affiliation(s)
- Florian Selt
- Hopp Children’s Cancer Center Heidelberg (KiTZ), Heidelberg, Germany
- Clinical Cooperation Unit Pediatric Oncology, German Cancer Research Center (DKFZ) and German Consortium for Translational Cancer Research (DKTK), Heidelberg, Germany
- KiTZ Clinical Trial Unit (ZIPO), Department of Pediatric Hematology, Oncology, Immunology and Pulmonology, Heidelberg University Hospital, Heidelberg, Germany
| | - Romain Sigaud
- Hopp Children’s Cancer Center Heidelberg (KiTZ), Heidelberg, Germany
- Clinical Cooperation Unit Pediatric Oncology, German Cancer Research Center (DKFZ) and German Consortium for Translational Cancer Research (DKTK), Heidelberg, Germany
| | - Gintvile Valinciute
- Hopp Children’s Cancer Center Heidelberg (KiTZ), Heidelberg, Germany
- Clinical Cooperation Unit Pediatric Oncology, German Cancer Research Center (DKFZ) and German Consortium for Translational Cancer Research (DKTK), Heidelberg, Germany
| | - Philipp Sievers
- Department of Neuropathology, Institute of Pathology, Heidelberg University Hospital, Heidelberg, Germany
- Clinical Cooperation Unit Neuropathology, German Consortium for Translational Cancer Research (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Julia Zaman
- Department of Neuropathology, Institute of Pathology, Heidelberg University Hospital, Heidelberg, Germany
- Clinical Cooperation Unit Neuropathology, German Consortium for Translational Cancer Research (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Clara Alcon
- Institute for Bioengineering of Catalonia (IBEC), Barcelona Institute of Science and Technology (BIST), 08028, Barcelona, Spain
| | - Simone Schmid
- Charité-Universitaetsmedizin Berlin, Corporate Member of Freie Universitaet Berlin, Humboldt-Universitaet zu Berlin, and Berlin Institute of Health, Department of Neuropathology, Berlin, Germany
- German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), Partner Site Berlin, Berlin, Germany
| | - Heike Peterziel
- Hopp Children’s Cancer Center Heidelberg (KiTZ), Heidelberg, Germany
- Clinical Cooperation Unit Pediatric Oncology, German Cancer Research Center (DKFZ) and German Consortium for Translational Cancer Research (DKTK), Heidelberg, Germany
| | - Jessica W Tsai
- Dana-Farber/Boston Children’s Cancer and Blood Disorder Center, Boston, Massachusetts, USA
| | - Romain Guiho
- Developmental Biology and Cancer Research & Teaching Department, Birth Defects Research Centre, Great Ormond Street Institute of Child Health, University College London, London, UK
| | - Juan Pedro Martínez-Barbera
- Developmental Biology and Cancer Research & Teaching Department, Birth Defects Research Centre, Great Ormond Street Institute of Child Health, University College London, London, UK
| | - Stefan Pusch
- Department of Neuropathology, Institute of Pathology, Heidelberg University Hospital, Heidelberg, Germany
- Clinical Cooperation Unit Neuropathology, German Consortium for Translational Cancer Research (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Jing Deng
- Ascentage Pharma (Suzhou) Co, Ltd, Suzhou, Jiangsu Province, China
| | - Yifan Zhai
- Ascentage Pharma (Suzhou) Co, Ltd, Suzhou, Jiangsu Province, China
| | - Cornelis M van Tilburg
- Hopp Children’s Cancer Center Heidelberg (KiTZ), Heidelberg, Germany
- Clinical Cooperation Unit Pediatric Oncology, German Cancer Research Center (DKFZ) and German Consortium for Translational Cancer Research (DKTK), Heidelberg, Germany
- KiTZ Clinical Trial Unit (ZIPO), Department of Pediatric Hematology, Oncology, Immunology and Pulmonology, Heidelberg University Hospital, Heidelberg, Germany
| | - Martin U Schuhman
- Department of Neurosurgery, University Hospital Tübingen, Tübingen, Germany
| | - Ahmed El Damaty
- Pediatric Neurosurgery Division, Department of Neurosurgery, Heidelberg University Hospital, Heidelberg, Germany
| | - Pratiti Bandopadhayay
- Dana-Farber/Boston Children’s Cancer and Blood Disorder Center, Boston, Massachusetts, USA
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
- Department of Pediatrics, Harvard Medical School, Boston, Massachusetts, USA
| | | | - Andreas von Deimling
- Department of Neuropathology, Institute of Pathology, Heidelberg University Hospital, Heidelberg, Germany
- Clinical Cooperation Unit Neuropathology, German Consortium for Translational Cancer Research (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Stefan M Pfister
- Hopp Children’s Cancer Center Heidelberg (KiTZ), Heidelberg, Germany
- KiTZ Clinical Trial Unit (ZIPO), Department of Pediatric Hematology, Oncology, Immunology and Pulmonology, Heidelberg University Hospital, Heidelberg, Germany
- Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ) and German Consortium for Translational Cancer Research (DKTK), Heidelberg, Germany
| | - Joan Montero
- Institute for Bioengineering of Catalonia (IBEC), Barcelona Institute of Science and Technology (BIST), 08028, Barcelona, Spain
| | - David Capper
- Charité-Universitaetsmedizin Berlin, Corporate Member of Freie Universitaet Berlin, Humboldt-Universitaet zu Berlin, and Berlin Institute of Health, Department of Neuropathology, Berlin, Germany
- German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), Partner Site Berlin, Berlin, Germany
| | - Ina Oehme
- Hopp Children’s Cancer Center Heidelberg (KiTZ), Heidelberg, Germany
- Clinical Cooperation Unit Pediatric Oncology, German Cancer Research Center (DKFZ) and German Consortium for Translational Cancer Research (DKTK), Heidelberg, Germany
| | - Felix Sahm
- Hopp Children’s Cancer Center Heidelberg (KiTZ), Heidelberg, Germany
- Department of Neuropathology, Institute of Pathology, Heidelberg University Hospital, Heidelberg, Germany
- Clinical Cooperation Unit Neuropathology, German Consortium for Translational Cancer Research (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - David T W Jones
- Hopp Children’s Cancer Center Heidelberg (KiTZ), Heidelberg, Germany
- Division of Pediatric Glioma Research, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Olaf Witt
- Hopp Children’s Cancer Center Heidelberg (KiTZ), Heidelberg, Germany
- Clinical Cooperation Unit Pediatric Oncology, German Cancer Research Center (DKFZ) and German Consortium for Translational Cancer Research (DKTK), Heidelberg, Germany
- KiTZ Clinical Trial Unit (ZIPO), Department of Pediatric Hematology, Oncology, Immunology and Pulmonology, Heidelberg University Hospital, Heidelberg, Germany
| | - Till Milde
- Hopp Children’s Cancer Center Heidelberg (KiTZ), Heidelberg, Germany
- Clinical Cooperation Unit Pediatric Oncology, German Cancer Research Center (DKFZ) and German Consortium for Translational Cancer Research (DKTK), Heidelberg, Germany
- KiTZ Clinical Trial Unit (ZIPO), Department of Pediatric Hematology, Oncology, Immunology and Pulmonology, Heidelberg University Hospital, Heidelberg, Germany
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30
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Bruce SF, Wu S, Ribeiro JR, Farrell A, Oberley MJ, Winer I, Erickson BK, Klc T, Jones NL, Thaker PH, Powell MA. HER2+ endometrioid endometrial cancer possesses distinct molecular and immunologic features associated with a more active immune microenvironment and worse prognosis. Gynecol Oncol 2023; 172:98-105. [PMID: 37003074 DOI: 10.1016/j.ygyno.2023.03.008] [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: 01/24/2023] [Revised: 03/09/2023] [Accepted: 03/10/2023] [Indexed: 04/03/2023]
Abstract
OBJECTIVE HER2 status is not routinely evaluated in endometrioid endometrial cancer (E-EMCA), though it is frequently overexpressed or amplified in high grade E-EMCA and uterine serous carcinoma. Defining characteristics and survival outcomes of HER2+ E-EMCA could reveal subsets of patients who may benefit from targeted therapies. METHODS 2927 E-EMCA tumors from the Caris Life Sciences database were analyzed by next-generation sequencing and whole exome sequencing, whole transcriptome sequencing, and immunohistochemistry for molecular and genomic features in a CLIA/CAP-certified laboratory (Caris Life Sciences, Phoenix, AZ). HER2 status was determined by transcriptomic cutoff extrapolated from uterine serous carcinoma. The relationship between HER2 status and patient outcomes was determined by Kaplan-Meier analysis. RESULTS HER2 positivity was detected in 5.47% of E-EMCA. Differences in molecular alterations based on HER2 status were most apparent in microsatellite stable (MSS) tumors, which displayed increased TP53 mutations and loss of heterozygosity (LOH) and decreased PTEN and CTNNB1 mutations. HER2+ tumors had increased immune checkpoint gene expression and immune cell infiltration, particularly among MSS tumors. All HER2+ tumors displayed increased MAPK pathway activation scores (MPAS) and patients with HER2+ tumors experienced worse overall survival. CONCLUSIONS HER2 positivity in E-EMCA corresponds with a unique molecular landscape, particularly in MSS tumors. HER2+ tumors are also associated with increased MAPK pathway activation and exhibit features of a more active immune microenvironment. These findings suggest a potential benefit of HER2 and MAPK targeted therapies as well as immunotherapies in this patient population.
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Affiliation(s)
- Shaina F Bruce
- Washington University School of Medicine, St. Louis, MO, USA.
| | - Sharon Wu
- Caris Life Sciences, Phoenix, AZ, USA
| | | | | | | | - Ira Winer
- Karmanos Cancer Institute and Wayne State University, Detroit, MI, USA
| | - Britt K Erickson
- University of Minnesota, Division of Gynecologic Oncology, Minneapolis, MN, USA
| | - Tenley Klc
- University of Minnesota, Division of Gynecologic Oncology, Minneapolis, MN, USA
| | - Nathaniel L Jones
- Mitchell Cancer Institute, University of South Alabama, Mobile, AL, USA
| | - Premal H Thaker
- Washington University School of Medicine, St. Louis, MO, USA
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31
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Chen Y, Liu S, Papageorgiou LG, Theofilatos K, Tsoka S. Optimisation Models for Pathway Activity Inference in Cancer. Cancers (Basel) 2023; 15:1787. [PMID: 36980673 PMCID: PMC10046797 DOI: 10.3390/cancers15061787] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2023] [Revised: 02/24/2023] [Accepted: 03/08/2023] [Indexed: 03/18/2023] Open
Abstract
BACKGROUND With advances in high-throughput technologies, there has been an enormous increase in data related to profiling the activity of molecules in disease. While such data provide more comprehensive information on cellular actions, their large volume and complexity pose difficulty in accurate classification of disease phenotypes. Therefore, novel modelling methods that can improve accuracy while offering interpretable means of analysis are required. Biological pathways can be used to incorporate a priori knowledge of biological interactions to decrease data dimensionality and increase the biological interpretability of machine learning models. METHODOLOGY A mathematical optimisation model is proposed for pathway activity inference towards precise disease phenotype prediction and is applied to RNA-Seq datasets. The model is based on mixed-integer linear programming (MILP) mathematical optimisation principles and infers pathway activity as the linear combination of pathway member gene expression, multiplying expression values with model-determined gene weights that are optimised to maximise discrimination of phenotype classes and minimise incorrect sample allocation. RESULTS The model is evaluated on the transcriptome of breast and colorectal cancer, and exhibits solution results of good optimality as well as good prediction performance on related cancer subtypes. Two baseline pathway activity inference methods and three advanced methods are used for comparison. Sample prediction accuracy, robustness against noise expression data, and survival analysis suggest competitive prediction performance of our model while providing interpretability and insight on key pathways and genes. Overall, our work demonstrates that the flexible nature of mathematical programming lends itself well to developing efficient computational strategies for pathway activity inference and disease subtype prediction.
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Affiliation(s)
- Yongnan Chen
- Department of Informatics, Faculty of Natural, Mathematical and Engineering Sciences, King's College London, Bush House, London WC2B 4BG, UK
| | - Songsong Liu
- School of Management, Harbin Institute of Technology, Harbin 150001, China
| | - Lazaros G Papageorgiou
- The Sargent Centre for Process Systems Engineering, Department of Chemical Engineering, University College London, Torrington Place, London WC1E 7JE, UK
| | - Konstantinos Theofilatos
- King's College London British Heart Foundation Centre, School of Cardiovascular and Metabolic Medicine and Sciences, London SE1 7EH, UK
| | - Sophia Tsoka
- Department of Informatics, Faculty of Natural, Mathematical and Engineering Sciences, King's College London, Bush House, London WC2B 4BG, UK
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32
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Varnier R, Puszkiel A, Tod M, Calattini S, Payen L, Lopez J, Guitton J, Schwiertz V, Fontaine J, Peron J, Maillet D, Tartas S, Bonnin N, Colomban O, Augu-Denechere D, Freyer G, You B. Clinical results of the EVESOR trial, a multiparameter phase I trial of everolimus and sorafenib combination in solid tumors. Cancer Chemother Pharmacol 2023; 91:361-373. [PMID: 36840749 DOI: 10.1007/s00280-023-04508-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2022] [Accepted: 01/27/2023] [Indexed: 02/26/2023]
Abstract
PURPOSE Everolimus (EVE) and sorafenib (SOR) combination was associated with synergistic activity in preclinical models. However, previous clinical studies were hampered by cumulative toxicities when both were given continuously. The academic EVESOR trial (NCT01932177) was designed to assess alternative doses and intermittent dosing schedules of EVE and SOR combination therapy to improve the benefit-risk ratio for patients with solid tumors. METHODS EVESOR is a multiparameter dose-escalation phase I trial investigating different doses and dosing schedules, with the final objective of generating data for modeling and simulation. Patients were allocated into continuous (A and B) or intermittent (C and D) schedules to determine the recommended phase II dose (RP2D). The clinical outcomes are presented here. RESULTS Forty-three patients were included from 2013 to 2019. Most of them had gynecological (25.6%), cholangiocarcinomas (23.2%), colorectal (14.0%), and breast cancers (11.6%). Dose-escalation up to EVE 10 mg QD and SOR 400 mg BID was possible on intermittent schedules. Five dose-limiting toxicities were observed, and dose reductions were required in 39.5% patients, stabilizing at EVE 5 mg and SOR 200 mg BID for 58.1% of them. The overall response rate was 6.3%, and disease control rate was 75.0%. The median progression-free survival (PFS) was 3.6 months. The longest median PFS were observed in cholangiocarcinomas (9.9 months), and gynecological adenocarcinomas (9.2 months). CONCLUSION Intermittent arms were associated with improved efficacy/toxicity profiles; and EVE 5 mg QD and SOR 200 mg BID was defined a clinically feasible dose. Strong signs of efficacy were found in cholangiocarcinomas and gynecologic carcinomas. TRIAL REGISTRATION ClinicalTrials.gov Identifier: NCT01932177.
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Affiliation(s)
- Romain Varnier
- Medical Oncology, Institut de Cancérologie des Hospices Civils de Lyon (IC-HCL), CITOHL, Centre Hospitalier Lyon-Sud, 165 Chemin du Grand Revoyet, Pierre-Benite, 69495, Lyon, France
| | - Alicja Puszkiel
- Faculté de Médecine Lyon Sud, EA 3738 CICLY, Université Claude Bernard Lyon 1, Lyon, France
| | - Michel Tod
- Faculté de Médecine Lyon Sud, EA 3738 CICLY, Université Claude Bernard Lyon 1, Lyon, France.,Pharmacy, Hôpital de La Croix-Rousse, Hospices Civils de Lyon, Lyon, France
| | - Sara Calattini
- Clinical Research, Institut de Cancérologie des Hospices Civils de Lyon (IC-HCL), CITOHL, Centre Hospitalier Lyon-Sud, Lyon, France
| | - Lea Payen
- Biochemistry and Molecular Biology, Centre Hospitalier Lyon-Sud, Hospices Civils de Lyon, Lyon, France
| | - Jonathan Lopez
- Biochemistry and Molecular Biology, Centre Hospitalier Lyon-Sud, Hospices Civils de Lyon, Lyon, France
| | - Jérome Guitton
- Pharmacology, Pharmacogenetic, Toxicology Laboratory, Centre Hospitalier Lyon-Sud, Hospices Civils de Lyon, Lyon, France.,Faculté de Pharmacie, Université Claude Bernard Lyon 1, Lyon, France
| | - Vérane Schwiertz
- Clinical Oncology Pharmacy, Centre Hospitalier Lyon-Sud, Lyon, France
| | - Juliette Fontaine
- Pathology, Centre Hospitalier Lyon-Sud, Hospices Civils de Lyon, Lyon, France
| | - Julien Peron
- Medical Oncology, Institut de Cancérologie des Hospices Civils de Lyon (IC-HCL), CITOHL, Centre Hospitalier Lyon-Sud, 165 Chemin du Grand Revoyet, Pierre-Benite, 69495, Lyon, France.,UMR UCBL/CNRS 5538 « Biometry and Evolutionary Biology Laboratory, Health and Biostatistics Team », Faculté de Médecine Lyon-Sud, Université Claude Bernard Lyon 1, Lyon, France
| | - Denis Maillet
- Medical Oncology, Institut de Cancérologie des Hospices Civils de Lyon (IC-HCL), CITOHL, Centre Hospitalier Lyon-Sud, 165 Chemin du Grand Revoyet, Pierre-Benite, 69495, Lyon, France.,Faculté de Médecine Lyon Sud, EA 3738 CICLY, Université Claude Bernard Lyon 1, Lyon, France
| | - Sophie Tartas
- Medical Oncology, Institut de Cancérologie des Hospices Civils de Lyon (IC-HCL), CITOHL, Centre Hospitalier Lyon-Sud, 165 Chemin du Grand Revoyet, Pierre-Benite, 69495, Lyon, France
| | - Nathalie Bonnin
- Medical Oncology, Institut de Cancérologie des Hospices Civils de Lyon (IC-HCL), CITOHL, Centre Hospitalier Lyon-Sud, 165 Chemin du Grand Revoyet, Pierre-Benite, 69495, Lyon, France
| | - Olivier Colomban
- Faculté de Médecine Lyon Sud, EA 3738 CICLY, Université Claude Bernard Lyon 1, Lyon, France
| | - Diane Augu-Denechere
- Clinical Research, Institut de Cancérologie des Hospices Civils de Lyon (IC-HCL), CITOHL, Centre Hospitalier Lyon-Sud, Lyon, France
| | - Gilles Freyer
- Medical Oncology, Institut de Cancérologie des Hospices Civils de Lyon (IC-HCL), CITOHL, Centre Hospitalier Lyon-Sud, 165 Chemin du Grand Revoyet, Pierre-Benite, 69495, Lyon, France.,Faculté de Médecine Lyon Sud, EA 3738 CICLY, Université Claude Bernard Lyon 1, Lyon, France
| | - Benoit You
- Medical Oncology, Institut de Cancérologie des Hospices Civils de Lyon (IC-HCL), CITOHL, Centre Hospitalier Lyon-Sud, 165 Chemin du Grand Revoyet, Pierre-Benite, 69495, Lyon, France. .,Faculté de Médecine Lyon Sud, EA 3738 CICLY, Université Claude Bernard Lyon 1, Lyon, France.
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33
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Thatikonda V, Lu H, Jurado S, Kostyrko K, Bristow CA, Bosch K, Feng N, Gao S, Gerlach D, Gmachl M, Lieb S, Jeschko A, Machado AA, Marszalek ED, Mahendra M, Jaeger PA, Sorokin A, Strauss S, Trapani F, Kopetz S, Vellano CP, Petronczki M, Kraut N, Heffernan TP, Marszalek JR, Pearson M, Waizenegger I, Hofmann MH. Combined KRAS G12C and SOS1 inhibition enhances and extends the anti-tumor response in KRAS G12C-driven cancers by addressing intrinsic and acquired resistance. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.01.23.525210. [PMID: 36747713 PMCID: PMC9900819 DOI: 10.1101/2023.01.23.525210] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
Efforts to improve the anti-tumor response to KRASG12C targeted therapy have benefited from leveraging combination approaches. Here, we compare the anti-tumor response induced by the SOS1-KRAS interaction inhibitor, BI-3406, combined with a KRASG12C inhibitor (KRASG12Ci) to those induced by KRASG12Ci alone or combined with SHP2 or EGFR inhibitors. In lung cancer and colorectal cancer (CRC) models, BI-3406 plus KRASG12Ci induces an anti-tumor response stronger than that observed with KRASG12Ci alone and comparable to those by the other combinations. This enhanced anti-tumor response is associated with a stronger and extended suppression of RAS-MAPK signaling. Importantly, BI-3406 plus KRASG12Ci treatment delays the emergence of acquired adagrasib resistance in both CRC and lung cancer models and is associated with re-establishment of anti-proliferative activity in KRASG12Ci-resistant CRC models. Our findings position KRASG12C plus SOS1 inhibition therapy as a promising strategy for treating both KRASG12C-mutated tumors as well as for addressing acquired resistance to KRASG12Ci.
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Affiliation(s)
| | - Hengyu Lu
- Translational Research to Advance Therapeutics and Innovation in Oncology (TRACTION) Platform, Therapeutics Discovery Division, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Sabine Jurado
- Boehringer Ingelheim RCV GmbH & Co KG, Vienna, Austria
| | - Kaja Kostyrko
- Boehringer Ingelheim RCV GmbH & Co KG, Vienna, Austria
| | - Christopher A. Bristow
- Translational Research to Advance Therapeutics and Innovation in Oncology (TRACTION) Platform, Therapeutics Discovery Division, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Karin Bosch
- Boehringer Ingelheim RCV GmbH & Co KG, Vienna, Austria
| | - Ningping Feng
- Translational Research to Advance Therapeutics and Innovation in Oncology (TRACTION) Platform, Therapeutics Discovery Division, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Sisi Gao
- Translational Research to Advance Therapeutics and Innovation in Oncology (TRACTION) Platform, Therapeutics Discovery Division, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | | | | | - Simone Lieb
- Boehringer Ingelheim RCV GmbH & Co KG, Vienna, Austria
| | | | - Annette A. Machado
- Translational Research to Advance Therapeutics and Innovation in Oncology (TRACTION) Platform, Therapeutics Discovery Division, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Ethan D. Marszalek
- Translational Research to Advance Therapeutics and Innovation in Oncology (TRACTION) Platform, Therapeutics Discovery Division, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Mikhila Mahendra
- Translational Research to Advance Therapeutics and Innovation in Oncology (TRACTION) Platform, Therapeutics Discovery Division, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | | | - Alexey Sorokin
- Department of Gastrointestinal Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | | | | | - Scott Kopetz
- Department of Gastrointestinal Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Christopher P. Vellano
- Translational Research to Advance Therapeutics and Innovation in Oncology (TRACTION) Platform, Therapeutics Discovery Division, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | | | - Norbert Kraut
- Boehringer Ingelheim RCV GmbH & Co KG, Vienna, Austria
| | - Timothy P. Heffernan
- Translational Research to Advance Therapeutics and Innovation in Oncology (TRACTION) Platform, Therapeutics Discovery Division, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Joseph R. Marszalek
- Translational Research to Advance Therapeutics and Innovation in Oncology (TRACTION) Platform, Therapeutics Discovery Division, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Mark Pearson
- Boehringer Ingelheim RCV GmbH & Co KG, Vienna, Austria
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34
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Integrated analysis of canine soft tissue sarcomas identifies recurrent mutations in TP53, KMT genes and PDGFB fusions. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.01.06.522911. [PMID: 36711648 PMCID: PMC9882013 DOI: 10.1101/2023.01.06.522911] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
Canine soft tissue sarcomas (STS) are a heterogenous group of malignant tumors arising from mesenchymal cells of soft tissues. This simplified collective of tumors most commonly arise from subcutaneous tissues, are treated similar clinically, and conventionally exclude other sarcomas with more definitive anatomical, histological, or biological features. Histologically, canine STS sub-types are difficult to discern at the light microscopic level due to their overlapping features. Thus, genomic, and transcriptomic profiling of canine STS may prove valuable in differentiating the diverse sub-types of mesenchymal neoplasms within this group. To this purpose we sought to characterize the transcript expression and genomic mutation profiles of canine STS. To delineate transcriptomic sub-types, hierarchical clustering was used to identify 4 groups with district expression profiles. Using the RNAseq data, we identified three samples carrying driver fusions of platelet derived growth factor B ( PDGFB ) and collagen genes. Sensitivity to imatinib was evaluated in a canine STS cell line also bearing a PDGFB fusion. Using whole exome sequencing, recurrent driver variants were identified in the cancer genes KMT2D (21% of the samples) and TP53 (21%) along with copy number losses of RB1 and CDKN2A. Gene amplifications and resulting transcript increases were identified in genes on chromosomes 13, 14, and 36. A subset of STS was identified with high T-cell infiltration. This multi-omics approach has defined canine STS sub-types at a molecular level for comparison to their human counterparts, to improve diagnosis, and may provide additional targets for therapy.
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35
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High-plex imaging of RNA and proteins at subcellular resolution in fixed tissue by spatial molecular imaging. Nat Biotechnol 2022; 40:1794-1806. [PMID: 36203011 DOI: 10.1038/s41587-022-01483-z] [Citation(s) in RCA: 130] [Impact Index Per Article: 65.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2021] [Accepted: 08/19/2022] [Indexed: 02/07/2023]
Abstract
Resolving the spatial distribution of RNA and protein in tissues at subcellular resolution is a challenge in the field of spatial biology. We describe spatial molecular imaging, a system that measures RNAs and proteins in intact biological samples at subcellular resolution by performing multiple cycles of nucleic acid hybridization of fluorescent molecular barcodes. We demonstrate that spatial molecular imaging has high sensitivity (one or two copies per cell) and very low error rate (0.0092 false calls per cell) and background (~0.04 counts per cell). The imaging system generates three-dimensional, super-resolution localization of analytes at ~2 million cells per sample. Cell segmentation is morphology based using antibodies, compatible with formalin-fixed, paraffin-embedded samples. We measured multiomic data (980 RNAs and 108 proteins) at subcellular resolution in formalin-fixed, paraffin-embedded tissues (nonsmall cell lung and breast cancer) and identified >18 distinct cell types, ten unique tumor microenvironments and 100 pairwise ligand-receptor interactions. Data on >800,000 single cells and ~260 million transcripts can be accessed at http://nanostring.com/CosMx-dataset .
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36
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Frank KJ, Mulero-Sánchez A, Berninger A, Ruiz-Cañas L, Bosma A, Görgülü K, Wu N, Diakopoulos KN, Kaya-Aksoy E, Ruess DA, Kabacaoğlu D, Schmidt F, Kohlmann L, van Tellingen O, Thijssen B, van de Ven M, Proost N, Kossatz S, Weber WA, Sainz B, Bernards R, Algül H, Lesina M, Mainardi S. Extensive preclinical validation of combined RMC-4550 and LY3214996 supports clinical investigation for KRAS mutant pancreatic cancer. Cell Rep Med 2022; 3:100815. [PMID: 36384095 PMCID: PMC9729824 DOI: 10.1016/j.xcrm.2022.100815] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2022] [Revised: 08/05/2022] [Accepted: 10/14/2022] [Indexed: 11/17/2022]
Abstract
Over 90% of pancreatic cancers present mutations in KRAS, one of the most common oncogenic drivers overall. Currently, most KRAS mutant isoforms cannot be targeted directly. Moreover, targeting single RAS downstream effectors induces adaptive resistance mechanisms. We report here on the combined inhibition of SHP2, upstream of KRAS, using the allosteric inhibitor RMC-4550 and of ERK, downstream of KRAS, using LY3214996. This combination shows synergistic anti-cancer activity in vitro, superior disruption of the MAPK pathway, and increased apoptosis induction compared with single-agent treatments. In vivo, we demonstrate good tolerability and efficacy of the combination, with significant tumor regression in multiple pancreatic ductal adenocarcinoma (PDAC) mouse models. Finally, we show evidence that 18F-fluorodeoxyglucose (FDG) positron emission tomography (PET) can be used to assess early drug responses in animal models. Based on these results, we will investigate this drug combination in the SHP2 and ERK inhibition in pancreatic cancer (SHERPA; ClinicalTrials.gov: NCT04916236) clinical trial, enrolling patients with KRAS-mutant PDAC.
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Affiliation(s)
- Katrin J Frank
- Comprehensive Cancer Center Munich at Klinikum rechts der Isar, Technische Universität München, 81675 Munich, Germany
| | - Antonio Mulero-Sánchez
- Division of Molecular Carcinogenesis, Oncode Institute, The Netherlands Cancer Institute, Plesmanlaan 121, 1066CX Amsterdam, the Netherlands
| | - Alexandra Berninger
- Comprehensive Cancer Center Munich at Klinikum rechts der Isar, Technische Universität München, 81675 Munich, Germany
| | - Laura Ruiz-Cañas
- Department of Biochemistry, Universidad Autónoma de Madrid (UAM) and Instituto de Investigaciones Biomédicas "Alberto Sols" (IIBM), CSIC-UAM, 28029 Madrid, Spain; Chronic Diseases and Cancer, Area 3, Instituto Ramón y Cajal de Investigación Sanitaria (IRYCIS), 28034 Madrid, Spain
| | - Astrid Bosma
- Division of Molecular Carcinogenesis, Oncode Institute, The Netherlands Cancer Institute, Plesmanlaan 121, 1066CX Amsterdam, the Netherlands
| | - Kıvanç Görgülü
- Comprehensive Cancer Center Munich at Klinikum rechts der Isar, Technische Universität München, 81675 Munich, Germany
| | - Nan Wu
- Comprehensive Cancer Center Munich at Klinikum rechts der Isar, Technische Universität München, 81675 Munich, Germany
| | - Kalliope N Diakopoulos
- Comprehensive Cancer Center Munich at Klinikum rechts der Isar, Technische Universität München, 81675 Munich, Germany
| | - Ezgi Kaya-Aksoy
- Comprehensive Cancer Center Munich at Klinikum rechts der Isar, Technische Universität München, 81675 Munich, Germany
| | - Dietrich A Ruess
- Department of General and Visceral Surgery, Center of Surgery, Medical Center-University of Freiburg, 79106 Freiburg, Germany
| | - Derya Kabacaoğlu
- Comprehensive Cancer Center Munich at Klinikum rechts der Isar, Technische Universität München, 81675 Munich, Germany
| | - Fränze Schmidt
- Comprehensive Cancer Center Munich at Klinikum rechts der Isar, Technische Universität München, 81675 Munich, Germany
| | - Larissa Kohlmann
- Comprehensive Cancer Center Munich at Klinikum rechts der Isar, Technische Universität München, 81675 Munich, Germany
| | - Olaf van Tellingen
- Division of Pharmacology, The Netherlands Cancer Institute, 1066CX Amsterdam, the Netherlands
| | - Bram Thijssen
- Division of Molecular Carcinogenesis, Oncode Institute, The Netherlands Cancer Institute, Plesmanlaan 121, 1066CX Amsterdam, the Netherlands
| | - Marieke van de Ven
- Mouse Clinic for Cancer and Aging Research, Preclinical Intervention Unit, The Netherlands Cancer Institute, 1066CX Amsterdam, the Netherlands
| | - Natalie Proost
- Mouse Clinic for Cancer and Aging Research, Preclinical Intervention Unit, The Netherlands Cancer Institute, 1066CX Amsterdam, the Netherlands
| | - Susanne Kossatz
- Department of Nuclear Medicine at Klinikum Rechts der Isar and Central Institute for Translational Cancer Research (TranslaTUM), Technische Universität München, 81675 Munich, Germany; Department of Chemistry, Technische Universität München, 85748 Munich, Germany
| | - Wolfgang A Weber
- Department of Nuclear Medicine at Klinikum Rechts der Isar and Central Institute for Translational Cancer Research (TranslaTUM), Technische Universität München, 81675 Munich, Germany
| | - Bruno Sainz
- Department of Biochemistry, Universidad Autónoma de Madrid (UAM) and Instituto de Investigaciones Biomédicas "Alberto Sols" (IIBM), CSIC-UAM, 28029 Madrid, Spain; Chronic Diseases and Cancer, Area 3, Instituto Ramón y Cajal de Investigación Sanitaria (IRYCIS), 28034 Madrid, Spain
| | - Rene Bernards
- Division of Molecular Carcinogenesis, Oncode Institute, The Netherlands Cancer Institute, Plesmanlaan 121, 1066CX Amsterdam, the Netherlands
| | - Hana Algül
- Comprehensive Cancer Center Munich at Klinikum rechts der Isar, Technische Universität München, 81675 Munich, Germany
| | - Marina Lesina
- Comprehensive Cancer Center Munich at Klinikum rechts der Isar, Technische Universität München, 81675 Munich, Germany
| | - Sara Mainardi
- Division of Molecular Carcinogenesis, Oncode Institute, The Netherlands Cancer Institute, Plesmanlaan 121, 1066CX Amsterdam, the Netherlands.
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37
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Jin Y, Qiu X, He Z, Wang J, Sa R, Chen L. ERBB2 as a prognostic biomarker correlates with immune infiltrates in papillary thyroid cancer. Front Genet 2022; 13:966365. [PMID: 36437939 PMCID: PMC9682178 DOI: 10.3389/fgene.2022.966365] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2022] [Accepted: 10/28/2022] [Indexed: 11/11/2022] Open
Abstract
Epidermal growth factor receptor 2 (ERBB2) is commonly over-expressed in advanced or metastatic tissues of papillary thyroid cancer (PTC) with poor prognosis, while it remains unknown whether ERBB2 plays a role in the progression of PTC. Thus, we analyzed the data derived from online repositories, including TCGA, KEGG, GO, GeneMANIA, and STRING, to explore the relationship between ERBB2 expression and prognosis, tumor phenotypes of interest, and immune infiltrates in PTC. Compared to normal thyroid tissue, ERBB2 was up-regulated in PTC samples (p < 0.001); In comparison with the group with low expression of ERBB2, the group with high expression of ERBB2 had poorer progression-free interval in stage III/IV patients (p = 0.008) and patients aged >45 years (p = 0.019). The up-regulated ERBB2 was associated with iodine metabolism dysfunction, proliferation, metastasis, angiogenesis, and drug resistance. The expression of ERBB2 negatively correlated with enrichment scores of B cells (r = −0.176, p < 0.001), CD8+ T cells (r = −0.160, p < 0.001), cytotoxic cells (r = −0.219, p < 0.001), NK CD56dim cells (r = −0.218, p < 0.001), plasmacytoid dendritic cells (r = −0.267, p < 0.001), T cells (r = −0.164, p < 0.001), T follicular helper cells (r = −0.111, p = 0.012), gamma delta T cells (r = −0.105, p = 0.017), and regulatory T cells (r = −0.125, p = 0.005). In conclusion, ERBB2 may serve as a prognostic biomarker and an immunotherapeutic target in PTC, deserving further exploration.
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38
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Chesnokov MS, Yadav A, Chefetz I. Optimized Transcriptional Signature for Evaluation of MEK/ERK Pathway Baseline Activity and Long-Term Modulations in Ovarian Cancer. Int J Mol Sci 2022; 23:13365. [PMID: 36362153 PMCID: PMC9654336 DOI: 10.3390/ijms232113365] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2022] [Revised: 10/25/2022] [Accepted: 10/29/2022] [Indexed: 11/06/2022] Open
Abstract
Ovarian cancer is the most aggressive and lethal of all gynecologic malignancies. The high activity of the MEK/ERK signaling pathway is tightly associated with tumor growth, high recurrence rate, and treatment resistance. Several transcriptional signatures were proposed recently for evaluation of MEK/ERK activity in tumor tissue. In the present study, we validated the performance of a robust multi-cancer MPAS 10-gene signature in various experimental models and publicly available sets of ovarian cancer samples. Expression of four MPAS genes (PHLDA1, DUSP4, EPHA2, and SPRY4) displayed reproducible responses to MEK/ERK activity modulations across several experimental models in vitro and in vivo. Levels of PHLDA1, DUSP4, and EPHA2 expression were also significantly associated with baseline levels of MEK/ERK pathway activity in multiple human ovarian cancer cell lines and ovarian cancer patient samples available from the TCGA database. Initial platinum therapy resistance and advanced age at diagnosis were independently associated with poor overall patient survival. Taken together, our results demonstrate that the performance of transcriptional signatures is significantly affected by tissue specificity and aspects of particular experimental models. We therefore propose that gene expression signatures derived from comprehensive multi-cancer studies should be always validated for each cancer type.
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Affiliation(s)
| | - Anil Yadav
- The Hormel Institute, University of Minnesota, Austin, MN 55912, USA
| | - Ilana Chefetz
- The Hormel Institute, University of Minnesota, Austin, MN 55912, USA
- Masonic Cancer Center, Minneapolis, MN 55455, USA
- Stem Cell Institute, Minneapolis, MN 55455, USA
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39
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Hyper-active RAS/MAPK introduces cancer-specific mitotic vulnerabilities. Proc Natl Acad Sci U S A 2022; 119:e2208255119. [PMID: 36191188 PMCID: PMC9565228 DOI: 10.1073/pnas.2208255119] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
Aneuploidy, the incorrect number of whole chromosomes, is a common feature of tumors that contributes to their initiation and evolution. Preventing aneuploidy requires properly functioning kinetochores, which are large protein complexes assembled on centromeric DNA that link mitotic chromosomes to dynamic spindle microtubules and facilitate chromosome segregation. The kinetochore leverages at least two mechanisms to prevent aneuploidy: error correction and the spindle assembly checkpoint (SAC). BubR1, a factor involved in both processes, was identified as a cancer dependency and therapeutic target in multiple tumor types; however, it remains unclear what specific oncogenic pressures drive this enhanced dependency on BubR1 and whether it arises from BubR1's regulation of the SAC or error-correction pathways. Here, we use a genetically controlled transformation model and glioblastoma tumor isolates to show that constitutive signaling by RAS or MAPK is necessary for cancer-specific BubR1 vulnerability. The MAPK pathway enzymatically hyperstimulates a network of kinetochore kinases that compromises chromosome segregation, rendering cells more dependent on two BubR1 activities: counteracting excessive kinetochore-microtubule turnover for error correction and maintaining the SAC. This work expands our understanding of how chromosome segregation adapts to different cellular states and reveals an oncogenic trigger of a cancer-specific defect.
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40
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Kong Y, Allison DB, Zhang Q, He D, Li Y, Mao F, Li C, Li Z, Zhang Y, Wang J, Wang C, Brainson CF, Liu X. The kinase PLK1 promotes the development of <i>Kras</i>/<i>Tp53</i>-mutant lung adenocarcinoma through transcriptional activation of the receptor RET. Sci Signal 2022; 15:eabj4009. [PMID: 36194647 PMCID: PMC9737055 DOI: 10.1126/scisignal.abj4009] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Increased abundance of polo-like kinase 1 (PLK1) is observed in various tumor types, particularly in lung adenocarcinoma (LUAD). Here, we found that PLK1 accelerated the progression of LUAD through a mechanism that was independent of its role in mediating mitotic cell division. Analysis of human tumor databases revealed that increased PLK1 abundance in LUAD correlated with mutations in KRAS and p53, with tumor stage, and with reduced survival in patients. In a mouse model of KRAS<sup>G12D</sup>-driven, p53-deficient LUAD, PLK1 overexpression increased tumor burden, decreased tumor cell differentiation, and reduced animal survival. PLK1 overexpression in cultured cells and mice indirectly increased the expression of the gene encoding the receptor tyrosine kinase RET by phosphorylating the transcription factor TTF-1. Signaling by RET and mutant KRAS in these tumors converged to activate the mitogen-activated protein kinase (MAPK) pathway. Pharmacological inhibition of the MAPK pathway kinase MEK combined with inhibition of either RET or PLK1 markedly suppressed tumor growth. Our findings show that PLK1 can amplify MAPK signaling and reveal a potential target for stemming progression in lung cancers with high PLK1 abundance.
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Affiliation(s)
- Yifan Kong
- Department of Toxicology and Cancer Biology, University of Kentucky, Lexington, Kentucky, 40536, USA,Markey Cancer Center, University of Kentucky, Lexington, Kentucky 40536, USA
| | - Derek B. Allison
- Markey Cancer Center, University of Kentucky, Lexington, Kentucky 40536, USA,Department of Pathology and Laboratory Medicine, University of Kentucky, Lexington, Kentucky 40536, USA
| | - Qiongsi Zhang
- Department of Toxicology and Cancer Biology, University of Kentucky, Lexington, Kentucky, 40536, USA,Markey Cancer Center, University of Kentucky, Lexington, Kentucky 40536, USA
| | - Daheng He
- Markey Cancer Center, University of Kentucky, Lexington, Kentucky 40536, USA
| | - Yuntong Li
- Markey Cancer Center, University of Kentucky, Lexington, Kentucky 40536, USA
| | - Fengyi Mao
- Department of Toxicology and Cancer Biology, University of Kentucky, Lexington, Kentucky, 40536, USA,Markey Cancer Center, University of Kentucky, Lexington, Kentucky 40536, USA
| | - Chaohao Li
- Department of Toxicology and Cancer Biology, University of Kentucky, Lexington, Kentucky, 40536, USA,Markey Cancer Center, University of Kentucky, Lexington, Kentucky 40536, USA
| | - Zhiguo Li
- Department of Toxicology and Cancer Biology, University of Kentucky, Lexington, Kentucky, 40536, USA,Markey Cancer Center, University of Kentucky, Lexington, Kentucky 40536, USA
| | - Yanquan Zhang
- Department of Toxicology and Cancer Biology, University of Kentucky, Lexington, Kentucky, 40536, USA,Markey Cancer Center, University of Kentucky, Lexington, Kentucky 40536, USA
| | - Jianlin Wang
- Department of Toxicology and Cancer Biology, University of Kentucky, Lexington, Kentucky, 40536, USA,Markey Cancer Center, University of Kentucky, Lexington, Kentucky 40536, USA
| | - Chi Wang
- Markey Cancer Center, University of Kentucky, Lexington, Kentucky 40536, USA
| | - Christine F. Brainson
- Department of Toxicology and Cancer Biology, University of Kentucky, Lexington, Kentucky, 40536, USA,Markey Cancer Center, University of Kentucky, Lexington, Kentucky 40536, USA
| | - Xiaoqi Liu
- Department of Toxicology and Cancer Biology, University of Kentucky, Lexington, Kentucky, 40536, USA,Markey Cancer Center, University of Kentucky, Lexington, Kentucky 40536, USA,Corresponding author.
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41
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Ye LF, Huang ZY, Chen XX, Chen ZG, Wu SX, Ren C, Hu MT, Bao H, Jin Y, Wang F, Wang FH, Du ZM, Wu X, Ju HQ, Shao Y, Li YH, Xu RH, Wang DS. Monitoring tumour resistance to the BRAF inhibitor combination regimen in colorectal cancer patients via circulating tumour DNA. Drug Resist Updat 2022; 65:100883. [DOI: 10.1016/j.drup.2022.100883] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2022] [Revised: 09/26/2022] [Accepted: 09/26/2022] [Indexed: 11/27/2022]
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42
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Seidlitz T, Schmäche T, Garcίa F, Lee JH, Qin N, Kochall S, Fohgrub J, Pauck D, Rothe A, Koo BK, Weitz J, Remke M, Muñoz J, Stange DE. Sensitivity towards HDAC inhibition is associated with RTK/MAPK pathway activation in gastric cancer. EMBO Mol Med 2022; 14:e15705. [PMID: 35993110 PMCID: PMC9549728 DOI: 10.15252/emmm.202215705] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2022] [Revised: 08/01/2022] [Accepted: 08/02/2022] [Indexed: 12/24/2022] Open
Abstract
Gastric cancer ranks the fifth most common and third leading cause of cancer-related deaths worldwide. Alterations in the RTK/MAPK, WNT, cell adhesion, TP53, TGFβ, NOTCH, and NFκB signaling pathways could be identified as main oncogenic drivers. A combination of altered pathways can be associated with molecular subtypes of gastric cancer. In order to generate model systems to study the impact of different pathway alterations in a defined genetic background, we generated three murine organoid models: a RAS-activated (KrasG12D , Tp53R172H ), a WNT-activated (Apcfl/fl , Tp53R172H ), and a diffuse (Cdh1fl/fl , Apcfl/fl ) model. These organoid models were morphologically and phenotypically diverse, differed in proteome expression signatures and possessed individual drug sensitivities. A differential vulnerability to RTK/MAPK pathway interference based on the different mitogenic drivers and according to the level of dependence on the pathway could be uncovered. Furthermore, an association between RTK/MAPK pathway activity and susceptibility to HDAC inhibition was observed. This finding was further validated in patient-derived organoids from gastric adenocarcinoma, thus identifying a novel treatment approach for RTK/MAPK pathway altered gastric cancer patients.
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Affiliation(s)
- Therese Seidlitz
- Department of Visceral, Thoracic and Vascular Surgery, Medical Faculty and University Hospital Carl Gustav Carus, Technische Universität Dresden, Dresden, Germany
| | - Tim Schmäche
- Department of Visceral, Thoracic and Vascular Surgery, Medical Faculty and University Hospital Carl Gustav Carus, Technische Universität Dresden, Dresden, Germany.,National Center for Tumor Diseases (NCT), Dresden, Germany.,German Cancer Research Center (DKFZ), Heidelberg, Germany.,Helmholtz-Zentrum Dresden - Rossendorf (HZDR), Dresden, Germany
| | - Fernando Garcίa
- Proteomics Unit, Spanish National Cancer Research Centre (CNIO), Madrid, Spain
| | - Joon Ho Lee
- Department of Visceral, Thoracic and Vascular Surgery, Medical Faculty and University Hospital Carl Gustav Carus, Technische Universität Dresden, Dresden, Germany
| | - Nan Qin
- Department of Pediatric Oncology, Hematology, and Clinical Immunology, Medical Faculty, University Hospital Düsseldorf, Düsseldorf, Germany
| | - Susan Kochall
- Department of Visceral, Thoracic and Vascular Surgery, Medical Faculty and University Hospital Carl Gustav Carus, Technische Universität Dresden, Dresden, Germany
| | - Juliane Fohgrub
- Department of Visceral, Thoracic and Vascular Surgery, Medical Faculty and University Hospital Carl Gustav Carus, Technische Universität Dresden, Dresden, Germany
| | - David Pauck
- Department of Pediatric Oncology, Hematology, and Clinical Immunology, Medical Faculty, University Hospital Düsseldorf, Düsseldorf, Germany
| | - Alexander Rothe
- Department of Visceral, Thoracic and Vascular Surgery, Medical Faculty and University Hospital Carl Gustav Carus, Technische Universität Dresden, Dresden, Germany
| | - Bon-Kyoung Koo
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna Biocenter (VBC), Vienna, Austria.,Center for Genome Engineering, Institute for Basic Science, Daejeon, Republic of Korea
| | - Jürgen Weitz
- Department of Visceral, Thoracic and Vascular Surgery, Medical Faculty and University Hospital Carl Gustav Carus, Technische Universität Dresden, Dresden, Germany.,National Center for Tumor Diseases (NCT), Dresden, Germany.,German Cancer Research Center (DKFZ), Heidelberg, Germany.,Helmholtz-Zentrum Dresden - Rossendorf (HZDR), Dresden, Germany
| | - Marc Remke
- Department of Pediatric Oncology, Hematology, and Clinical Immunology, Medical Faculty, University Hospital Düsseldorf, Düsseldorf, Germany
| | - Javier Muñoz
- Proteomics Unit, Spanish National Cancer Research Centre (CNIO), Madrid, Spain.,Biocruces Bizkaia Health Research Institute, Barakaldo, Spain.,Ikerbasque, Basque Foundation for Science, Bilbao, Spain
| | - Daniel E Stange
- Department of Visceral, Thoracic and Vascular Surgery, Medical Faculty and University Hospital Carl Gustav Carus, Technische Universität Dresden, Dresden, Germany.,National Center for Tumor Diseases (NCT), Dresden, Germany.,German Cancer Research Center (DKFZ), Heidelberg, Germany.,Helmholtz-Zentrum Dresden - Rossendorf (HZDR), Dresden, Germany
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Identification of cell type-specific correlations between ERK activity and cell viability upon treatment with ERK1/2 inhibitors. J Biol Chem 2022; 298:102226. [PMID: 35787369 PMCID: PMC9358475 DOI: 10.1016/j.jbc.2022.102226] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2022] [Revised: 06/20/2022] [Accepted: 06/22/2022] [Indexed: 12/05/2022] Open
Abstract
Increased MAPK signaling is a hallmark of various cancers and is a central regulator of cell survival. Direct ERK1/2 inhibition is considered a promising approach to avoid ERK1/2 reactivation caused by upstream kinases BRAF, MEK1/2, and KRAS, as well as by receptor tyrosine kinase inhibitors, but the dynamics and selectivity of ERK1/2 inhibitors are much less studied compared with BRAF or MEK inhibitors. Using ERK1/2 and downstream kinase ELK1 reporter cell lines of lung cancer (H1299; NRASQ61K), colon cancer (HCT-116; KRASG13D), neuroblastoma (SH-SY5Y), and leukemia (U937), we examined the relationship between ERK inhibition and drug-induced toxicity for five ERK inhibitors: SCH772984, ravoxertinib, LY3214996, ulixertinib, and VX-11e, as well as one MEK inhibitor, PD0325901. Comparing cell viability and ERK inhibition revealed different ERK dependencies for these cell lines. We identify several drugs, such as SCH772984 and VX-11e, which induce excessive toxicity not directly related to ERK1/2 inhibition in specific cell lines. We also show that PD0325901, LY3214996, and ulixertinib are prone to ERK1/2 reactivation over time. We distinguished two types of ERK1/2 reactivation: the first could be reversed by adding a fresh dose of inhibitors, while the second persists even after additional treatments. We also showed that cells that became resistant to the MEK1/2 inhibitor PD0325901 due to ERK1/2 reactivation remained sensitive to ERK1/2 inhibitor ulixertinib. Our data indicate that correlation of ERK inhibition with drug-induced toxicity in multiple cell lines may help to find more selective and effective ERK1/2 inhibitors.
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Philip PA, Azar I, Xiu J, Hall MJ, Hendifar AE, Lou E, Hwang JJ, Gong J, Feldman R, Ellis M, Stafford P, Spetzler D, Khushman MM, Sohal D, Lockhart AC, Weinberg BA, El-Deiry WS, Marshall J, Shields AF, Korn WM. Molecular Characterization of KRAS Wild-type Tumors in Patients with Pancreatic Adenocarcinoma. Clin Cancer Res 2022; 28:2704-2714. [PMID: 35302596 PMCID: PMC9541577 DOI: 10.1158/1078-0432.ccr-21-3581] [Citation(s) in RCA: 45] [Impact Index Per Article: 22.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2021] [Revised: 12/20/2021] [Accepted: 03/16/2022] [Indexed: 11/16/2022]
Abstract
PURPOSE KRAS mutation (MT) is a major oncogenic driver in pancreatic ductal adenocarcinoma (PDAC). A small subset of PDACs harbor KRAS wild-type (WT). We aim to characterize the molecular profiles of KRAS WT PDAC to uncover new pathogenic drivers and offer targeted treatments. EXPERIMENTAL DESIGN Tumor tissue obtained from surgical or biopsy material was subjected to next-generation DNA/RNA sequencing, microsatellite instability (MSI) and mismatch repair status determination. RESULTS Of the 2,483 patients (male 53.7%, median age 66 years) studied, 266 tumors (10.7%) were KRAS WT. The most frequently mutated gene in KRAS WT PDAC was TP53 (44.5%), followed by BRAF (13.0%). Multiple mutations within the DNA-damage repair (BRCA2, ATM, BAP1, RAD50, FANCE, PALB2), chromatin remodeling (ARID1A, PBRM1, ARID2, KMT2D, KMT2C, SMARCA4, SETD2), and cell-cycle control pathways (CDKN2A, CCND1, CCNE1) were detected frequently. There was no statistically significant difference in PD-L1 expression between KRAS WT (15.8%) and MT (17%) tumors. However, KRAS WT PDAC were more likely to be MSI-high (4.7% vs. 0.7%; P < 0.05), tumor mutational burden-high (4.5% vs. 1%; P < 0.05), and exhibit increased infiltration of CD8+ T cells, natural killer cells, and myeloid dendritic cells. KRAS WT PDACs exhibited gene fusions of BRAF (6.6%), FGFR2 (5.2%), ALK (2.6%), RET (1.3%), and NRG1 (1.3%), as well as amplification of FGF3 (3%), ERBB2 (2.2%), FGFR3 (1.8%), NTRK (1.8%), and MET (1.3%). Real-world evidence reveals a survival advantage of KRAS WT patients in overall cohorts as well as in patients treated with gemcitabine/nab-paclitaxel or 5-FU/oxaliplatin. CONCLUSIONS KRAS WT PDAC represents 10.7% of PDAC and is enriched with targetable alterations, including immuno-oncologic markers. Identification of KRAS WT patients in clinical practice may expand therapeutic options in a clinically meaningful manner.
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Affiliation(s)
- Philip A Philip
- Wayne State University, School of Medicine, Karmanos Cancer Center, Detroit, Michigan
| | - Ibrahim Azar
- Wayne State University, School of Medicine, Karmanos Cancer Center, Detroit, Michigan
| | | | | | | | - Emil Lou
- Masonic Cancer Center, University of Minnesota, Minneapolis, Minnesota
| | | | - Jun Gong
- Samuel Oschin Cancer Center, Cedars-Sinai Medical Center, Los Angeles, California
| | | | | | | | | | - Moh'd M Khushman
- Medical Oncology, The University of South Alabama, Mitchell Cancer Institute, Mobile, Alabama
| | | | - A Craig Lockhart
- Medical University of South Carolina, Charleston, South Carolina
| | | | - Wafik S El-Deiry
- Cancer Center at Brown University, The Warren Alpert Medical School, Brown University, Providence, Rhode Island
| | - John Marshall
- Georgetown University, Washington, District of Columbia
| | - Anthony F Shields
- Wayne State University, School of Medicine, Karmanos Cancer Center, Detroit, Michigan
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Phelps GB, Hagen HR, Amsterdam A, Lees JA. MITF deficiency accelerates GNAQ-driven uveal melanoma. Proc Natl Acad Sci U S A 2022; 119:e2107006119. [PMID: 35512098 PMCID: PMC9172632 DOI: 10.1073/pnas.2107006119] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2021] [Accepted: 02/17/2022] [Indexed: 01/02/2023] Open
Abstract
Cutaneous melanoma (CM) and uveal melanoma (UM) both originate from the melanocytic lineage but are primarily driven by distinct oncogenic drivers, BRAF/NRAS or GNAQ/GNA11, respectively. The melanocytic master transcriptional regulator, MITF, is essential for both CM development and maintenance, but its role in UM is largely unexplored. Here, we use zebrafish models to dissect the key UM oncogenic signaling events and establish the role of MITF in UM tumors. Using a melanocytic lineage expression system, we showed that patient-derived mutations of GNAQ (GNAQQ209L) or its upstream CYSLTR2 receptor (CYSLTR2L129Q) both drive UM when combined with a cooperating mutation, tp53M214K/M214K. The tumor-initiating potential of the major GNAQ/11 effector pathways, YAP, and phospholipase C-β (PLCβ)–ERK was also investigated in this system and thus showed that while activated YAP (YAPAA) induced UM with high potency, the patient-derived PLCβ4 mutation (PLCB4D630Y) very rarely yielded UM tumors in the tp53M214K/M214K context. Remarkably, mitfa deficiency was profoundly UM promoting, dramatically accelerating the onset and progression of tumors induced by Tg(mitfa:GNAQQ209L);tp53M214K/M214K or Tg(mitfa:CYSLTR2L129Q);tp53M214K/M214K. Moreover, mitfa loss was sufficient to cooperate with GNAQQ209L to drive tp53–wild type UM development and allowed Tg(mitfa:PLCB4D630Y);tp53M214K/M214K melanocyte lineage cells to readily form tumors. Notably, all of the mitfa−/− UM tumors, including those arising in Tg(mitfa:PLCB4D630Y);tp53M214K/M214K;mitfa−/− zebrafish, displayed nuclear YAP while lacking hyperactive ERK indicative of PLCβ signaling. Collectively, these data show that YAP signaling is the major mediator of UM and that MITF acts as a bona fide tumor suppressor in UM in direct opposition to its essential role in CM.
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Affiliation(s)
- Grace B. Phelps
- David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139
| | - Hannah R. Hagen
- David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139
| | - Adam Amsterdam
- David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139
| | - Jacqueline A. Lees
- David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139
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Winkler E, Wu D, Gil E, McCoy D, Narsinh K, Sun Z, Mueller K, Ross J, Kim H, Weinsheimer S, Berger M, Nowakowski T, Lim D, Abla A, Cooke D. Endoluminal Biopsy for Molecular Profiling of Human Brain Vascular Malformations. Neurology 2022; 98:e1637-e1647. [PMID: 35145012 PMCID: PMC9052570 DOI: 10.1212/wnl.0000000000200109] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2021] [Accepted: 01/11/2022] [Indexed: 02/01/2023] Open
Abstract
BACKGROUND AND OBJECTIVES Ras-mitogen-activated protein kinase (MAPK) signaling abnormalities occur in most brain arteriovenous malformations (bAVMs). No means exist to molecularly profile bAVMs without open surgery, limiting precision medicine approaches to treatment. Here, we report use of endoluminal biopsy of the vessel lumen of bAVMs to characterize gene expression and blood flow-mediated transcriptional changes in living patients. METHODS Endoluminal biopsy and computational fluid dynamic modeling (CFD) were performed in adults with unruptured AVMs with cerebral angiography. Each patient underwent surgical resection and cell sampling from a contiguous arterial segment. Fluorescence-assisted cell sorting enriched endothelial cells, which were sequenced on an Illumina HiSeq 4000 sequencer. Gene expression was quantified with RNA sequencing (RNAseq). Differential gene expression, ontology, and correlative analyses were performed. Results were validated with quantitative reverse transcription PCR (RT-qPCR). RESULTS Endoluminal biopsy was successful in 4 patients without complication. Endoluminal biopsy yielded 269.0 ± 79.9 cells per biopsy (control 309.2 ± 86.6 cells, bAVM 228.8 ± 133.4 cells). RNAseq identified 106 differentially expressed genes (DEGs) in bAVMs (false discovery rate ≤0.05). DEGs were enriched for bAVM pathogenic cascades, including Ras-MAPK signaling (p < 0.05), and confirmed with RT-qPCR and a panel predictive of MAPK/extracellular signal-regulated kinase inhibitor response. Compared to patient-matched surgically excised tissues, endoluminal biopsy detected 83.3% of genes, and genome-wide expression strongly correlated (Pearson r = 0.77). Wall shear stress measured by CFD correlated with inflammatory pathway upregulation. Comparison of pre-embolization and postembolization samples confirmed flow-mediated gene expression changes. DISCUSSION Endoluminal biopsy allows molecular profiling of bAVMs in living patients. Gene expression profiles are similar to those of tissues acquired with open surgery and identify potentially targetable Ras-MAPK signaling abnormalities in bAVMs. Integration with CFD allows determination of flow-mediated transcriptomic alterations. Endoluminal biopsy may help facilitate trials of precision medicine approaches to bAVMs in humans.
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Affiliation(s)
- Ethan Winkler
- From the Department of Neurological Surgery (E.W., D.W., E.G., J.R., M.B., D.L., A.A.), Department of Radiology and Biomedical Imaging (D.M., K.N., Z.S., D.C.), Center for Cerebrovascular Research (H.K., S.W.), Department of Psychiatry (T.N.), Department of Behavioral Sciences (T.N.), and Eli and Edythe Broad Center for Regeneration Medicine and Stem Cell Research (T.N., D.L.), University of California San Francisco; Siemens Medical Solutions Inc (K.M.), Malvern, PA; and Department of Anatomy (J.R., T.N.), University of California San Francisco, Chan Zuckerberg Biohub
| | - David Wu
- From the Department of Neurological Surgery (E.W., D.W., E.G., J.R., M.B., D.L., A.A.), Department of Radiology and Biomedical Imaging (D.M., K.N., Z.S., D.C.), Center for Cerebrovascular Research (H.K., S.W.), Department of Psychiatry (T.N.), Department of Behavioral Sciences (T.N.), and Eli and Edythe Broad Center for Regeneration Medicine and Stem Cell Research (T.N., D.L.), University of California San Francisco; Siemens Medical Solutions Inc (K.M.), Malvern, PA; and Department of Anatomy (J.R., T.N.), University of California San Francisco, Chan Zuckerberg Biohub
| | - Eugene Gil
- From the Department of Neurological Surgery (E.W., D.W., E.G., J.R., M.B., D.L., A.A.), Department of Radiology and Biomedical Imaging (D.M., K.N., Z.S., D.C.), Center for Cerebrovascular Research (H.K., S.W.), Department of Psychiatry (T.N.), Department of Behavioral Sciences (T.N.), and Eli and Edythe Broad Center for Regeneration Medicine and Stem Cell Research (T.N., D.L.), University of California San Francisco; Siemens Medical Solutions Inc (K.M.), Malvern, PA; and Department of Anatomy (J.R., T.N.), University of California San Francisco, Chan Zuckerberg Biohub
| | - David McCoy
- From the Department of Neurological Surgery (E.W., D.W., E.G., J.R., M.B., D.L., A.A.), Department of Radiology and Biomedical Imaging (D.M., K.N., Z.S., D.C.), Center for Cerebrovascular Research (H.K., S.W.), Department of Psychiatry (T.N.), Department of Behavioral Sciences (T.N.), and Eli and Edythe Broad Center for Regeneration Medicine and Stem Cell Research (T.N., D.L.), University of California San Francisco; Siemens Medical Solutions Inc (K.M.), Malvern, PA; and Department of Anatomy (J.R., T.N.), University of California San Francisco, Chan Zuckerberg Biohub
| | - Kazim Narsinh
- From the Department of Neurological Surgery (E.W., D.W., E.G., J.R., M.B., D.L., A.A.), Department of Radiology and Biomedical Imaging (D.M., K.N., Z.S., D.C.), Center for Cerebrovascular Research (H.K., S.W.), Department of Psychiatry (T.N.), Department of Behavioral Sciences (T.N.), and Eli and Edythe Broad Center for Regeneration Medicine and Stem Cell Research (T.N., D.L.), University of California San Francisco; Siemens Medical Solutions Inc (K.M.), Malvern, PA; and Department of Anatomy (J.R., T.N.), University of California San Francisco, Chan Zuckerberg Biohub
| | - Zhengda Sun
- From the Department of Neurological Surgery (E.W., D.W., E.G., J.R., M.B., D.L., A.A.), Department of Radiology and Biomedical Imaging (D.M., K.N., Z.S., D.C.), Center for Cerebrovascular Research (H.K., S.W.), Department of Psychiatry (T.N.), Department of Behavioral Sciences (T.N.), and Eli and Edythe Broad Center for Regeneration Medicine and Stem Cell Research (T.N., D.L.), University of California San Francisco; Siemens Medical Solutions Inc (K.M.), Malvern, PA; and Department of Anatomy (J.R., T.N.), University of California San Francisco, Chan Zuckerberg Biohub
| | - Kerstin Mueller
- From the Department of Neurological Surgery (E.W., D.W., E.G., J.R., M.B., D.L., A.A.), Department of Radiology and Biomedical Imaging (D.M., K.N., Z.S., D.C.), Center for Cerebrovascular Research (H.K., S.W.), Department of Psychiatry (T.N.), Department of Behavioral Sciences (T.N.), and Eli and Edythe Broad Center for Regeneration Medicine and Stem Cell Research (T.N., D.L.), University of California San Francisco; Siemens Medical Solutions Inc (K.M.), Malvern, PA; and Department of Anatomy (J.R., T.N.), University of California San Francisco, Chan Zuckerberg Biohub
| | - Jayden Ross
- From the Department of Neurological Surgery (E.W., D.W., E.G., J.R., M.B., D.L., A.A.), Department of Radiology and Biomedical Imaging (D.M., K.N., Z.S., D.C.), Center for Cerebrovascular Research (H.K., S.W.), Department of Psychiatry (T.N.), Department of Behavioral Sciences (T.N.), and Eli and Edythe Broad Center for Regeneration Medicine and Stem Cell Research (T.N., D.L.), University of California San Francisco; Siemens Medical Solutions Inc (K.M.), Malvern, PA; and Department of Anatomy (J.R., T.N.), University of California San Francisco, Chan Zuckerberg Biohub
| | - Helen Kim
- From the Department of Neurological Surgery (E.W., D.W., E.G., J.R., M.B., D.L., A.A.), Department of Radiology and Biomedical Imaging (D.M., K.N., Z.S., D.C.), Center for Cerebrovascular Research (H.K., S.W.), Department of Psychiatry (T.N.), Department of Behavioral Sciences (T.N.), and Eli and Edythe Broad Center for Regeneration Medicine and Stem Cell Research (T.N., D.L.), University of California San Francisco; Siemens Medical Solutions Inc (K.M.), Malvern, PA; and Department of Anatomy (J.R., T.N.), University of California San Francisco, Chan Zuckerberg Biohub
| | - Shantel Weinsheimer
- From the Department of Neurological Surgery (E.W., D.W., E.G., J.R., M.B., D.L., A.A.), Department of Radiology and Biomedical Imaging (D.M., K.N., Z.S., D.C.), Center for Cerebrovascular Research (H.K., S.W.), Department of Psychiatry (T.N.), Department of Behavioral Sciences (T.N.), and Eli and Edythe Broad Center for Regeneration Medicine and Stem Cell Research (T.N., D.L.), University of California San Francisco; Siemens Medical Solutions Inc (K.M.), Malvern, PA; and Department of Anatomy (J.R., T.N.), University of California San Francisco, Chan Zuckerberg Biohub
| | - Mitchel Berger
- From the Department of Neurological Surgery (E.W., D.W., E.G., J.R., M.B., D.L., A.A.), Department of Radiology and Biomedical Imaging (D.M., K.N., Z.S., D.C.), Center for Cerebrovascular Research (H.K., S.W.), Department of Psychiatry (T.N.), Department of Behavioral Sciences (T.N.), and Eli and Edythe Broad Center for Regeneration Medicine and Stem Cell Research (T.N., D.L.), University of California San Francisco; Siemens Medical Solutions Inc (K.M.), Malvern, PA; and Department of Anatomy (J.R., T.N.), University of California San Francisco, Chan Zuckerberg Biohub
| | - Tomasz Nowakowski
- From the Department of Neurological Surgery (E.W., D.W., E.G., J.R., M.B., D.L., A.A.), Department of Radiology and Biomedical Imaging (D.M., K.N., Z.S., D.C.), Center for Cerebrovascular Research (H.K., S.W.), Department of Psychiatry (T.N.), Department of Behavioral Sciences (T.N.), and Eli and Edythe Broad Center for Regeneration Medicine and Stem Cell Research (T.N., D.L.), University of California San Francisco; Siemens Medical Solutions Inc (K.M.), Malvern, PA; and Department of Anatomy (J.R., T.N.), University of California San Francisco, Chan Zuckerberg Biohub
| | - Daniel Lim
- From the Department of Neurological Surgery (E.W., D.W., E.G., J.R., M.B., D.L., A.A.), Department of Radiology and Biomedical Imaging (D.M., K.N., Z.S., D.C.), Center for Cerebrovascular Research (H.K., S.W.), Department of Psychiatry (T.N.), Department of Behavioral Sciences (T.N.), and Eli and Edythe Broad Center for Regeneration Medicine and Stem Cell Research (T.N., D.L.), University of California San Francisco; Siemens Medical Solutions Inc (K.M.), Malvern, PA; and Department of Anatomy (J.R., T.N.), University of California San Francisco, Chan Zuckerberg Biohub
| | - Adib Abla
- From the Department of Neurological Surgery (E.W., D.W., E.G., J.R., M.B., D.L., A.A.), Department of Radiology and Biomedical Imaging (D.M., K.N., Z.S., D.C.), Center for Cerebrovascular Research (H.K., S.W.), Department of Psychiatry (T.N.), Department of Behavioral Sciences (T.N.), and Eli and Edythe Broad Center for Regeneration Medicine and Stem Cell Research (T.N., D.L.), University of California San Francisco; Siemens Medical Solutions Inc (K.M.), Malvern, PA; and Department of Anatomy (J.R., T.N.), University of California San Francisco, Chan Zuckerberg Biohub
| | - Daniel Cooke
- From the Department of Neurological Surgery (E.W., D.W., E.G., J.R., M.B., D.L., A.A.), Department of Radiology and Biomedical Imaging (D.M., K.N., Z.S., D.C.), Center for Cerebrovascular Research (H.K., S.W.), Department of Psychiatry (T.N.), Department of Behavioral Sciences (T.N.), and Eli and Edythe Broad Center for Regeneration Medicine and Stem Cell Research (T.N., D.L.), University of California San Francisco; Siemens Medical Solutions Inc (K.M.), Malvern, PA; and Department of Anatomy (J.R., T.N.), University of California San Francisco, Chan Zuckerberg Biohub
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Darabi S, Elliott A, Braxton DR, Zeng J, Hodges K, Poorman K, Swensen J, Shanthappa BU, Hinton JP, Gibney GT, Moser J, Phung T, Atkins MB, In GK, Korn WM, Eisenberg BL, Demeure MJ. Transcriptional Profiling of Malignant Melanoma Reveals Novel and Potentially Targetable Gene Fusions. Cancers (Basel) 2022; 14:cancers14061505. [PMID: 35326655 PMCID: PMC8946593 DOI: 10.3390/cancers14061505] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2022] [Revised: 03/08/2022] [Accepted: 03/10/2022] [Indexed: 11/24/2022] Open
Abstract
Simple Summary Malignant melanoma is a complex disease that is estimated to claim over 7000 lives in the United States in 2021. Although recent advances in genomic technology have helped with the identification of driver variants, molecular studies and clinical trials have often focused on prevalent alterations, such as the BRAF-V600E mutation. With the inclusion of whole transcriptome sequencing, molecular profiling of melanomas has identified gene fusions and revealed gene expression profiles that are consistent with the activation of signaling pathways by common driver mutations. Patients harboring such fusions may benefit from currently approved targeted therapies and should be considered in the design of future clinical trials to further personalize treatments for patients with malignant melanoma. Abstract Invasive melanoma is the deadliest type of skin cancer, with 101,110 expected cases to be diagnosed in 2021. Recurrent BRAF and NRAS mutations are well documented in melanoma. Biologic implications of gene fusions and the efficacy of therapeutically targeting them remains unknown. Retrospective review of patient samples that underwent next-generation sequencing of the exons of 592 cancer-relevant genes and whole transcriptome sequencing for the detection of gene fusion events and gene expression profiling. Expression of PDL1 and ERK1/2 was assessed by immunohistochemistry (IHC). There were 33 (2.6%) cases with oncogenic fusions (14 novel), involving BRAF, RAF1, PRKCA, TERT, AXL, and FGFR3. MAPK pathway-associated genes were over-expressed in BRAF and RAF1 fusion-positive tumors in absence of other driver alterations. Increased expression in tumors with PRKCA and TERT fusions was concurrent with MAPK pathway alterations. For a subset of samples with available tissue, increased phosphorylation of ERK1/2 was observed in BRAF, RAF1, and PRKCA fusion-positive tumors. Oncogenic gene fusions are associated with transcriptional activation of the MAPK pathway, suggesting they could be therapeutic targets with available inhibitors. Additional analyses to fully characterize the oncogenic effects of these fusions may support biomarker driven clinical trials.
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Affiliation(s)
- Sourat Darabi
- Hoag Family Cancer Institute, Newport Beach, CA 92663, USA; (D.R.B.); (B.L.E.); (M.J.D.)
- Correspondence:
| | - Andrew Elliott
- Caris Life Sciences, Phoenix, AZ 85040, USA; (A.E.); (J.Z.); (K.H.); (K.P.); (J.S.); (B.U.S.); (J.P.H.); (W.M.K.)
| | - David R. Braxton
- Hoag Family Cancer Institute, Newport Beach, CA 92663, USA; (D.R.B.); (B.L.E.); (M.J.D.)
| | - Jia Zeng
- Caris Life Sciences, Phoenix, AZ 85040, USA; (A.E.); (J.Z.); (K.H.); (K.P.); (J.S.); (B.U.S.); (J.P.H.); (W.M.K.)
| | - Kurt Hodges
- Caris Life Sciences, Phoenix, AZ 85040, USA; (A.E.); (J.Z.); (K.H.); (K.P.); (J.S.); (B.U.S.); (J.P.H.); (W.M.K.)
| | - Kelsey Poorman
- Caris Life Sciences, Phoenix, AZ 85040, USA; (A.E.); (J.Z.); (K.H.); (K.P.); (J.S.); (B.U.S.); (J.P.H.); (W.M.K.)
| | - Jeff Swensen
- Caris Life Sciences, Phoenix, AZ 85040, USA; (A.E.); (J.Z.); (K.H.); (K.P.); (J.S.); (B.U.S.); (J.P.H.); (W.M.K.)
| | - Basavaraja U. Shanthappa
- Caris Life Sciences, Phoenix, AZ 85040, USA; (A.E.); (J.Z.); (K.H.); (K.P.); (J.S.); (B.U.S.); (J.P.H.); (W.M.K.)
| | - James P. Hinton
- Caris Life Sciences, Phoenix, AZ 85040, USA; (A.E.); (J.Z.); (K.H.); (K.P.); (J.S.); (B.U.S.); (J.P.H.); (W.M.K.)
| | - Geoffrey T. Gibney
- Lombardi Comprehensive Cancer Center, MedStar Georgetown University Hospital, Washington, DC 20007, USA; (G.T.G.); (M.B.A.)
| | - Justin Moser
- Honor Health Research Institute, Scottsdale, AZ 85258, USA;
| | - Thuy Phung
- Department of Pathology, University of South Alabama, Mobile, AL 36617, USA;
| | - Michael B. Atkins
- Lombardi Comprehensive Cancer Center, MedStar Georgetown University Hospital, Washington, DC 20007, USA; (G.T.G.); (M.B.A.)
| | - Gino K. In
- Division of Oncology, Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, CA 90033, USA;
| | - Wolfgang M. Korn
- Caris Life Sciences, Phoenix, AZ 85040, USA; (A.E.); (J.Z.); (K.H.); (K.P.); (J.S.); (B.U.S.); (J.P.H.); (W.M.K.)
| | - Burton L. Eisenberg
- Hoag Family Cancer Institute, Newport Beach, CA 92663, USA; (D.R.B.); (B.L.E.); (M.J.D.)
- Division of Oncology, Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, CA 90033, USA;
| | - Michael J. Demeure
- Hoag Family Cancer Institute, Newport Beach, CA 92663, USA; (D.R.B.); (B.L.E.); (M.J.D.)
- Translational Genomics Research Institution, Phoenix, AZ 85004, USA
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Cronise KE, Das S, Hernandez BG, Regan DP, Dailey DD, McGeachan RI, Lana SE, Page RL, Gustafson DL, Duval DL. Characterizing the molecular and immune landscape of canine bladder cancer. Vet Comp Oncol 2022; 20:69-81. [PMID: 34021685 PMCID: PMC8606617 DOI: 10.1111/vco.12740] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2021] [Revised: 05/17/2021] [Accepted: 05/20/2021] [Indexed: 12/24/2022]
Abstract
Transitional cell carcinoma (TCC), also known as urothelial carcinoma, is the most common bladder cancer in humans and dogs. Approximately one-quarter of human TCCs are muscle-invasive and associated with a high risk of death from metastasis. Canine TCC (cTCC) tumours are typically high-grade and muscle-invasive. Shared similarities in risk factors, histopathology, and clinical presentation suggest that cTCC may serve as a model for the assessment of novel therapeutics that may inform therapies for human muscle-invasive TCC. The goal of this study was to characterize cTCC at the molecular level to identify drivers of oncogenesis and druggable targets. We performed whole exome sequencing (WES) of 11 cTCC tumours and three matched normal samples, identifying 583 variants in protein-coding genes. The most common variant was a V-to-E missense mutation in BRAF, identified in 4 out of 11 samples (36%) via WES. Sanger sequencing identified BRAF variants in 8 out of the same 11 cTCC samples, as well as in 22 out of 32 formalin-fixed paraffin embedded (FFPE) cTCC samples, suggesting an overall prevalence of 70%. RNA-Seq was performed to compare the gene expression profiles of cTCC tumours to normal bladder tissue. cTCC tumours exhibited up-regulation of genes involved in the cell cycle, DNA repair, and antiviral immunity. We also analysed the immune landscape of cTCC using immune gene signatures and immunohistochemical analysis. A subset of tumours had characteristics of a hot tumour microenvironment and exhibited high expression of signatures associated with complete response to PD-1/PD-L1 blockade in human bladder cancer.
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Affiliation(s)
- Kathryn E. Cronise
- Flint Animal Cancer Center, Colorado State University, Fort Collins, Colorado, USA,Department of Clinical Sciences, Colorado State University, Fort Collins, Colorado, USA,Cell and Molecular Biology Graduate Program, Colorado State University, Fort Collins, Colorado, USA
| | - Sunetra Das
- Flint Animal Cancer Center, Colorado State University, Fort Collins, Colorado, USA,Department of Clinical Sciences, Colorado State University, Fort Collins, Colorado, USA
| | - Belen G. Hernandez
- Flint Animal Cancer Center, Colorado State University, Fort Collins, Colorado, USA,Department of Clinical Sciences, Colorado State University, Fort Collins, Colorado, USA
| | - Daniel P. Regan
- Flint Animal Cancer Center, Colorado State University, Fort Collins, Colorado, USA,Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, Colorado, USA,Cell and Molecular Biology Graduate Program, Colorado State University, Fort Collins, Colorado, USA,University of Colorado Comprehensive Cancer Center, Anschutz Medical Campus, Aurora, Colorado, USA
| | - Deanna D. Dailey
- Flint Animal Cancer Center, Colorado State University, Fort Collins, Colorado, USA,Department of Clinical Sciences, Colorado State University, Fort Collins, Colorado, USA
| | - Robert I. McGeachan
- Flint Animal Cancer Center, Colorado State University, Fort Collins, Colorado, USA,Royal (Dick) School of Veterinary Studies, The University of Edinburgh, Midlothian, UK
| | - Susan E. Lana
- Flint Animal Cancer Center, Colorado State University, Fort Collins, Colorado, USA,Department of Clinical Sciences, Colorado State University, Fort Collins, Colorado, USA
| | - Rodney L. Page
- Flint Animal Cancer Center, Colorado State University, Fort Collins, Colorado, USA,Department of Clinical Sciences, Colorado State University, Fort Collins, Colorado, USA,University of Colorado Comprehensive Cancer Center, Anschutz Medical Campus, Aurora, Colorado, USA
| | - Daniel L. Gustafson
- Flint Animal Cancer Center, Colorado State University, Fort Collins, Colorado, USA,Department of Clinical Sciences, Colorado State University, Fort Collins, Colorado, USA,Cell and Molecular Biology Graduate Program, Colorado State University, Fort Collins, Colorado, USA,University of Colorado Comprehensive Cancer Center, Anschutz Medical Campus, Aurora, Colorado, USA
| | - Dawn L. Duval
- Flint Animal Cancer Center, Colorado State University, Fort Collins, Colorado, USA,Department of Clinical Sciences, Colorado State University, Fort Collins, Colorado, USA,Cell and Molecular Biology Graduate Program, Colorado State University, Fort Collins, Colorado, USA,University of Colorado Comprehensive Cancer Center, Anschutz Medical Campus, Aurora, Colorado, USA
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49
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Parkes EE, Savage KI, Lioe T, Boyd C, Halliday S, Walker SM, Lowry K, Knight L, Buckley NE, Grogan A, Logan GE, Clayton A, Hurwitz J, Kirk SJ, Xu J, Sidi FA, Humphries MP, Bingham V, James JA, James CR, Paul Harkin D, Kennedy RD, McIntosh SA. Activation of a cGAS-STING-mediated immune response predicts response to neoadjuvant chemotherapy in early breast cancer. Br J Cancer 2022; 126:247-258. [PMID: 34728791 PMCID: PMC8770594 DOI: 10.1038/s41416-021-01599-0] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2021] [Revised: 09/21/2021] [Accepted: 10/11/2021] [Indexed: 12/12/2022] Open
Abstract
BACKGROUND The DNA-damage immune-response (DDIR) signature is an immune-driven gene expression signature retrospectively validated as predicting response to anthracycline-based therapy. This feasibility study prospectively evaluates the use of this assay to predict neoadjuvant chemotherapy response in early breast cancer. METHODS This feasibility study assessed the integration of a novel biomarker into clinical workflows. Tumour samples were collected from patients receiving standard of care neoadjuvant chemotherapy (FEC + /-taxane and anti-HER2 therapy as appropriate) at baseline, mid- and post-chemotherapy. Baseline DDIR signature scores were correlated with pathological treatment response. RNA sequencing was used to assess chemotherapy/response-related changes in biologically linked gene signatures. RESULTS DDIR signature reports were available within 14 days for 97.8% of 46 patients (13 TNBC, 16 HER2 + ve, 27 ER + HER2-ve). Positive scores predicted response to treatment (odds ratio 4.67 for RCB 0-1 disease (95% CI 1.13-15.09, P = 0.032)). DDIR positivity correlated with immune infiltration and upregulated immune-checkpoint gene expression. CONCLUSIONS This study validates the DDIR signature as predictive of response to neoadjuvant chemotherapy which can be integrated into clinical workflows, potentially identifying a subgroup with high sensitivity to anthracycline chemotherapy. Transcriptomic data suggest induction with anthracycline-containing regimens in immune restricted, "cold" tumours may be effective for immune priming. TRIAL REGISTRATION Not applicable (non-interventional study). CRUK Internal Database Number 14232.
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Affiliation(s)
- Eileen E Parkes
- Patrick G Johnston Centre for Cancer Research, Queen's University Belfast, 97 Lisburn Road, Belfast, BT9 7AE, UK
- Belfast Health and Social Care Trust, Belfast City Hospital, Lisburn Road, Belfast, BT9 7AB, UK
- Department of Oncology, Medical Sciences Division, University of Oxford, Oxford, UK
| | - Kienan I Savage
- Patrick G Johnston Centre for Cancer Research, Queen's University Belfast, 97 Lisburn Road, Belfast, BT9 7AE, UK
| | - Tong Lioe
- Belfast Health and Social Care Trust, Belfast City Hospital, Lisburn Road, Belfast, BT9 7AB, UK
| | - Clinton Boyd
- Belfast Health and Social Care Trust, Belfast City Hospital, Lisburn Road, Belfast, BT9 7AB, UK
| | - Sophia Halliday
- Patrick G Johnston Centre for Cancer Research, Queen's University Belfast, 97 Lisburn Road, Belfast, BT9 7AE, UK
| | - Steven M Walker
- Almac Diagnostic Services, Almac Group, 19 Seagoe Industrial Estate, Craigavon, BT63 5QD, UK
| | - Keith Lowry
- Belfast Health and Social Care Trust, Belfast City Hospital, Lisburn Road, Belfast, BT9 7AB, UK
| | - Laura Knight
- Almac Diagnostic Services, Almac Group, 19 Seagoe Industrial Estate, Craigavon, BT63 5QD, UK
| | - Niamh E Buckley
- School of Pharmacy, Queen's University Belfast, 97 Lisburn Road, Belfast, BT9 7AE, UK
| | - Andrena Grogan
- Almac Diagnostic Services, Almac Group, 19 Seagoe Industrial Estate, Craigavon, BT63 5QD, UK
| | - Gemma E Logan
- Almac Diagnostic Services, Almac Group, 19 Seagoe Industrial Estate, Craigavon, BT63 5QD, UK
| | - Alison Clayton
- Belfast Health and Social Care Trust, Belfast City Hospital, Lisburn Road, Belfast, BT9 7AB, UK
| | - Jane Hurwitz
- Belfast Health and Social Care Trust, Belfast City Hospital, Lisburn Road, Belfast, BT9 7AB, UK
| | - Stephen J Kirk
- South Eastern Health and Social Care Trust, Ulster Hospital, Upper Newtownards Road, BT 16 1RH, Dundonald, UK
| | - Jiamei Xu
- Precision Medicine Centre, Patrick G Johnston Centre for Cancer Research, Queen's University Belfast, 97 Lisburn Road, Belfast, BT9 7AE, UK
| | - Fatima Abdullahi Sidi
- Precision Medicine Centre, Patrick G Johnston Centre for Cancer Research, Queen's University Belfast, 97 Lisburn Road, Belfast, BT9 7AE, UK
| | - Matthew P Humphries
- Precision Medicine Centre, Patrick G Johnston Centre for Cancer Research, Queen's University Belfast, 97 Lisburn Road, Belfast, BT9 7AE, UK
| | - Victoria Bingham
- Precision Medicine Centre, Patrick G Johnston Centre for Cancer Research, Queen's University Belfast, 97 Lisburn Road, Belfast, BT9 7AE, UK
| | - Jaqueline A James
- Precision Medicine Centre, Patrick G Johnston Centre for Cancer Research, Queen's University Belfast, 97 Lisburn Road, Belfast, BT9 7AE, UK
| | - Colin R James
- Belfast Health and Social Care Trust, Belfast City Hospital, Lisburn Road, Belfast, BT9 7AB, UK
| | - D Paul Harkin
- Patrick G Johnston Centre for Cancer Research, Queen's University Belfast, 97 Lisburn Road, Belfast, BT9 7AE, UK
- Almac Diagnostic Services, Almac Group, 19 Seagoe Industrial Estate, Craigavon, BT63 5QD, UK
| | - Richard D Kennedy
- Patrick G Johnston Centre for Cancer Research, Queen's University Belfast, 97 Lisburn Road, Belfast, BT9 7AE, UK
- Almac Diagnostic Services, Almac Group, 19 Seagoe Industrial Estate, Craigavon, BT63 5QD, UK
| | - Stuart A McIntosh
- Patrick G Johnston Centre for Cancer Research, Queen's University Belfast, 97 Lisburn Road, Belfast, BT9 7AE, UK.
- Belfast Health and Social Care Trust, Belfast City Hospital, Lisburn Road, Belfast, BT9 7AB, UK.
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50
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Safaee MM, Wang EJ, Jain S, Chen JS, Gill S, Zheng AC, Garcia JH, Beniwal AS, Tran Y, Nguyen AT, Trieu M, Leung K, Wells J, Maclean JM, Wycoff K, Aghi MK. CD97 is associated with mitogenic pathway activation, metabolic reprogramming, and immune microenvironment changes in glioblastoma. Sci Rep 2022; 12:1464. [PMID: 35087132 PMCID: PMC8795421 DOI: 10.1038/s41598-022-05259-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2021] [Accepted: 01/03/2022] [Indexed: 12/12/2022] Open
Abstract
Glioblastoma (GBM) is the most common primary brain tumor with a median survival under two years. Using in silico and in vitro techniques, we demonstrate heterogeneous expression of CD97, a leukocyte adhesion marker, in human GBM. Beyond its previous demonstrated role in tumor invasion, we show that CD97 is also associated with upregulation of the mitogen-activated protein kinase/extracellular signal-regulated kinase (MAPK/Erk) and phosphatidylinositol 3-kinase/protein kinase B (PI3K/Akt) pathways in GBM. While CD97 knockout decreased Akt activation, CD97 targeting did not alter MAPK/Erk activation, did not slow GBM cell proliferation in culture, and increased levels of glycolytic and oxidative phosphorylation metabolites. Treatment with a soluble CD97 inhibitor did not alter activation of the MAPK/Erk and PI3K/Akt pathways. Tumors with high CD97 expression were associated with immune microenvironment changes including increased naïve macrophages, regulatory T cells, and resting natural killer (NK) cells. These data suggest that, while CD97 expression is associated with conflicting effects on tumor cell proliferative and metabolic pathways that overall do not affect tumor cell proliferation, CD97 exerts pro-tumoral effects on the tumor immune microenvironment, which along with the pro-invasive effects of CD97 we previously demonstrated, provides impetus to continue exploring CD97 as a therapeutic target in GBM.
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Affiliation(s)
- Michael M Safaee
- Department of Neurological Surgery, Brain Tumor Center, Helen Diller Comprehensive Cancer Center, University of California, San Francisco (UCSF), San Francisco, USA
| | - Elaina J Wang
- Department of Neurological Surgery, Brain Tumor Center, Helen Diller Comprehensive Cancer Center, University of California, San Francisco (UCSF), San Francisco, USA
| | - Saket Jain
- Department of Neurological Surgery, Brain Tumor Center, Helen Diller Comprehensive Cancer Center, University of California, San Francisco (UCSF), San Francisco, USA
| | - Jia-Shu Chen
- Department of Neurological Surgery, Brain Tumor Center, Helen Diller Comprehensive Cancer Center, University of California, San Francisco (UCSF), San Francisco, USA
| | - Sabraj Gill
- Department of Neurological Surgery, Brain Tumor Center, Helen Diller Comprehensive Cancer Center, University of California, San Francisco (UCSF), San Francisco, USA
| | - Allison C Zheng
- Department of Neurological Surgery, Brain Tumor Center, Helen Diller Comprehensive Cancer Center, University of California, San Francisco (UCSF), San Francisco, USA
| | - Joseph H Garcia
- Department of Neurological Surgery, Brain Tumor Center, Helen Diller Comprehensive Cancer Center, University of California, San Francisco (UCSF), San Francisco, USA
| | - Angad S Beniwal
- Department of Neurological Surgery, Brain Tumor Center, Helen Diller Comprehensive Cancer Center, University of California, San Francisco (UCSF), San Francisco, USA
| | - Y Tran
- Planet Biotechnology, Inc., Hayward, CA, USA
| | - Alan T Nguyen
- Department of Neurological Surgery, Brain Tumor Center, Helen Diller Comprehensive Cancer Center, University of California, San Francisco (UCSF), San Francisco, USA
| | - Melissa Trieu
- School of Pharmacy, University of California, San Francisco (UCSF), San Francisco, USA
| | - Kevin Leung
- School of Pharmacy, University of California, San Francisco (UCSF), San Francisco, USA
| | - Jim Wells
- School of Pharmacy, University of California, San Francisco (UCSF), San Francisco, USA
| | | | | | - Manish K Aghi
- Department of Neurological Surgery, Brain Tumor Center, Helen Diller Comprehensive Cancer Center, University of California, San Francisco (UCSF), San Francisco, USA.
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