1
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He JY, Kim YJ, Mennillo E, Rusu I, Bain J, Rao AA, Andersen C, Law K, Yang H, Tsui J, Shen A, Davidson B, Kushnoor D, Shi Y, Fan F, Cheung A, Zhang L, Fong L, Combes AJ, Pisco AO, Kattah MG, Oh DY. Dysregulation of CD4 + and CD8 + resident memory T, myeloid, and stromal cells in steroid-experienced, checkpoint inhibitor colitis. J Immunother Cancer 2024; 12:e008628. [PMID: 38642938 PMCID: PMC11033653 DOI: 10.1136/jitc-2023-008628] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/20/2024] [Indexed: 04/22/2024] Open
Abstract
BACKGROUND Colitis caused by checkpoint inhibitors (CPI) is frequent and is treated with empiric steroids, but CPI colitis mechanisms in steroid-experienced or refractory disease are unclear. METHODS Using colon biopsies and blood from predominantly steroid-experienced CPI colitis patients, we performed multiplexed single-cell transcriptomics and proteomics to nominate contributing populations. RESULTS CPI colitis biopsies showed enrichment of CD4+resident memory (RM) T cells in addition to CD8+ RM and cytotoxic CD8+ T cells. Matching T cell receptor (TCR) clonotypes suggested that both RMs are progenitors that yield cytotoxic effectors. Activated, CD38+ HLA-DR+ CD4+ RM and cytotoxic CD8+ T cells were enriched in steroid-experienced and a validation data set of steroid-naïve CPI colitis, underscoring their pathogenic potential across steroid exposure. Distinct from ulcerative colitis, CPI colitis exhibited perturbed stromal metabolism (NAD+, tryptophan) impacting epithelial survival and inflammation. Endothelial cells in CPI colitis after anti-TNF and anti-cytotoxic T-lymphocyte-associated antigen 4 (anti-CTLA-4) upregulated the integrin α4β7 ligand molecular vascular addressin cell adhesion molecule 1 (MAdCAM-1), which may preferentially respond to vedolizumab (anti-α4β7). CONCLUSIONS These findings nominate CD4+ RM and MAdCAM-1+ endothelial cells for targeting in specific subsets of CPI colitis patients.
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Affiliation(s)
- Jun Yan He
- Division of Hematology/Oncology, Department of Medicine, University of California, San Francisco, San Francisco, California, USA
| | - Yang-Joon Kim
- Chan Zuckerberg Biohub, San Francisco, California, USA
| | - Elvira Mennillo
- Division of Gastroenterology, Department of Medicine, University of California, San Francisco, San Francisco, CA, USA
| | - Iulia Rusu
- Division of Gastroenterology, Department of Medicine, University of California, San Francisco, San Francisco, CA, USA
| | - Jared Bain
- Division of Gastroenterology, Department of Medicine, University of California, San Francisco, San Francisco, CA, USA
| | - Arjun A Rao
- CoLabs, University of California, San Francisco, San Francisco, California, USA
| | | | - Karen Law
- Division of Hematology/Oncology, Department of Medicine, University of California, San Francisco, San Francisco, California, USA
| | - Hai Yang
- Division of Hematology/Oncology, Department of Medicine, University of California, San Francisco, San Francisco, California, USA
| | - Jessica Tsui
- CoLabs, University of California, San Francisco, San Francisco, California, USA
| | - Alan Shen
- CoLabs, University of California, San Francisco, San Francisco, California, USA
| | - Brittany Davidson
- CoLabs, University of California, San Francisco, San Francisco, California, USA
| | - Divyashree Kushnoor
- CoLabs, University of California, San Francisco, San Francisco, California, USA
| | - Yimin Shi
- Division of Hematology/Oncology, Department of Medicine, University of California, San Francisco, San Francisco, California, USA
| | - Frances Fan
- Division of Hematology/Oncology, Department of Medicine, University of California, San Francisco, San Francisco, California, USA
| | - Alexander Cheung
- Division of Hematology/Oncology, Department of Medicine, University of California, San Francisco, San Francisco, California, USA
| | - Li Zhang
- Division of Hematology/Oncology, Department of Medicine, University of California, San Francisco, San Francisco, California, USA
| | - Lawrence Fong
- Division of Hematology/Oncology, Department of Medicine, University of California, San Francisco, San Francisco, California, USA
| | - Alexis J Combes
- Division of Gastroenterology, Department of Medicine, University of California, San Francisco, San Francisco, CA, USA
- CoLabs, University of California, San Francisco, San Francisco, California, USA
- Department of Pathology, University of California, San Francisco, San Francisco, California, USA
- ImmunoX Initiative, University of California, San Francisco, San Francisco, California, USA
| | | | - Michael G Kattah
- Division of Gastroenterology, Department of Medicine, University of California, San Francisco, San Francisco, CA, USA
| | - David Y Oh
- Division of Hematology/Oncology, Department of Medicine, University of California, San Francisco, San Francisco, California, USA
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2
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Michino M, Khan TA, Miller MW, Fukase Y, Vendome J, Adura C, Glickman JF, Liu Y, Wan L, Allis CD, Stamford AW, Meinke PT, Renzetti LM, Kargman S, Liverton NJ, Huggins DJ. Lead Optimization of Small Molecule ENL YEATS Inhibitors to Enable In Vivo Studies: Discovery of TDI-11055. ACS Med Chem Lett 2024; 15:524-532. [PMID: 38628784 PMCID: PMC11017412 DOI: 10.1021/acsmedchemlett.4c00016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2024] [Revised: 03/04/2024] [Accepted: 03/07/2024] [Indexed: 04/19/2024] Open
Abstract
Eleven-nineteen leukemia (ENL) is an epigenetic reader protein that drives oncogenic transcriptional programs in acute myeloid leukemia (AML). AML is one of the deadliest hematopoietic malignancies, with an overall 5-year survival rate of 27%. The epigenetic reader activity of ENL is mediated by its YEATS domain that binds to acetyl and crotonyl marks on histone tails and colocalizes with promoters of actively transcribed genes that are essential for leukemia. Prior to the discovery of TDI-11055, existing inhibitors of ENL YEATS showed in vitro potency, but had not shown efficacy in in vivo animal models. During the course of the medicinal chemistry campaign described here, we identified ENL YEATS inhibitor TDI-11055 that has an improved pharmacokinetic profile and is appropriate for in vivo evaluation of the ENL YEATS inhibition mechanism in AML.
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Affiliation(s)
- Mayako Michino
- Sanders
Tri-Institutional Therapeutics Discovery Institute, 1230 York Ave, Box 122, New York, New York 10065, United States
| | - Tanweer A. Khan
- Sanders
Tri-Institutional Therapeutics Discovery Institute, 1230 York Ave, Box 122, New York, New York 10065, United States
| | - Michael W. Miller
- Sanders
Tri-Institutional Therapeutics Discovery Institute, 1230 York Ave, Box 122, New York, New York 10065, United States
| | - Yoshiyuki Fukase
- Sanders
Tri-Institutional Therapeutics Discovery Institute, 1230 York Ave, Box 122, New York, New York 10065, United States
| | - Jeremie Vendome
- Schrödinger,
Inc., 1540 Broadway,
24th Floor, New York, New
York 10036, United States
| | - Carolina Adura
- Fisher
Drug Discovery Resource Center, The Rockefeller
University, New York, New York 10065, United States
| | - J. Fraser Glickman
- Fisher
Drug Discovery Resource Center, The Rockefeller
University, New York, New York 10065, United States
| | - Yiman Liu
- Department
of Cancer Biology and Abramson Family Cancer Research Institute, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania 19104, United States
| | - Liling Wan
- Department
of Cancer Biology and Abramson Family Cancer Research Institute, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania 19104, United States
| | - C. David Allis
- Laboratory
of Chromatin Biology and Epigenetics, The
Rockefeller University, New York, New York 10065, United States
| | - Andrew W. Stamford
- Sanders
Tri-Institutional Therapeutics Discovery Institute, 1230 York Ave, Box 122, New York, New York 10065, United States
| | - Peter T. Meinke
- Sanders
Tri-Institutional Therapeutics Discovery Institute, 1230 York Ave, Box 122, New York, New York 10065, United States
- Department
of Pharmacology, Weill Cornell Medicine, New York, New York 10021, United States
| | - Louis M. Renzetti
- Bridge
Medicines, The Rockefeller University, 1230 York Avenue, Smith Hall Annex,
C-Floor, New York, New York 10065, United States
| | - Stacia Kargman
- Sanders
Tri-Institutional Therapeutics Discovery Institute, 1230 York Ave, Box 122, New York, New York 10065, United States
- Bridge
Medicines, The Rockefeller University, 1230 York Avenue, Smith Hall Annex,
C-Floor, New York, New York 10065, United States
| | - Nigel J. Liverton
- Sanders
Tri-Institutional Therapeutics Discovery Institute, 1230 York Ave, Box 122, New York, New York 10065, United States
| | - David J. Huggins
- Sanders
Tri-Institutional Therapeutics Discovery Institute, 1230 York Ave, Box 122, New York, New York 10065, United States
- Department
of Physiology and Biophysics, Weill Cornell
Medicine, New York, New York 10021, United States
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3
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Wang J, Sadeghi CA, Frock RL. DNA-PKcs suppresses illegitimate chromosome rearrangements. Nucleic Acids Res 2024:gkae140. [PMID: 38412274 DOI: 10.1093/nar/gkae140] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2023] [Revised: 02/09/2024] [Accepted: 02/14/2024] [Indexed: 02/29/2024] Open
Abstract
Two DNA repair pathways, non-homologous end joining (NHEJ) and alternative end joining (A-EJ), are involved in V(D)J recombination and chromosome translocation. Previous studies reported distinct repair mechanisms for chromosome translocation, with NHEJ involved in humans and A-EJ in mice predominantly. NHEJ depends on DNA-PKcs, a critical partner in synapsis formation and downstream component activation. While DNA-PKcs inhibition promotes chromosome translocations harboring microhomologies in mice, its synonymous effect in humans is not known. We find partial DNA-PKcs inhibition in human cells leads to increased translocations and the continued involvement of a dampened NHEJ. In contrast, complete DNA-PKcs inhibition substantially increased microhomology-mediated end joining (MMEJ), thus bridging the two different translocation mechanisms between human and mice. Similar to a previous study on Ku70 deletion, DNA-PKcs deletion in G1/G0-phase mouse progenitor B cell lines, significantly impairs V(D)J recombination and generated higher rates of translocations as a consequence of dysregulated coding and signal end joining. Genetic DNA-PKcs inhibition suppresses NHEJ entirely, with repair phenotypically resembling Ku70-deficient A-EJ. In contrast, we find DNA-PKcs necessary in generating the near-exclusive MMEJ associated with Lig4 deficiency. Our study underscores DNA-PKcs in suppressing illegitimate chromosome rearrangement while also contributing to MMEJ in both species.
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Affiliation(s)
- Jinglong Wang
- Division of Radiation and Cancer Biology, Department of Radiation Oncology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Cheyenne A Sadeghi
- Division of Radiation and Cancer Biology, Department of Radiation Oncology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Richard L Frock
- Division of Radiation and Cancer Biology, Department of Radiation Oncology, Stanford University School of Medicine, Stanford, CA 94305, USA
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4
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Trivedi V, Yang C, Klippel K, Yegorov O, von Roemeling C, Hoang-Minh L, Fenton G, Ogando-Rivas E, Castillo P, Moore G, Long-James K, Dyson K, Doonan B, Flores C, Mitchell DA. mRNA-based precision targeting of neoantigens and tumor-associated antigens in malignant brain tumors. Genome Med 2024; 16:17. [PMID: 38268001 PMCID: PMC10809449 DOI: 10.1186/s13073-024-01281-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2023] [Accepted: 01/02/2024] [Indexed: 01/26/2024] Open
Abstract
BACKGROUND Despite advancements in the successful use of immunotherapy in treating a variety of solid tumors, applications in treating brain tumors have lagged considerably. This is due, at least in part, to the lack of well-characterized antigens expressed within brain tumors that can mediate tumor rejection; the low mutational burden of these tumors that limits the abundance of targetable neoantigens; and the immunologically "cold" tumor microenvironment that hampers the generation of sustained and productive immunologic responses. The field of mRNA-based therapeutics has experienced a boon following the universal approval of COVID-19 mRNA vaccines. mRNA-based immunotherapeutics have also garnered widespread interest for their potential to revolutionize cancer treatment. In this study, we developed a novel and scalable approach for the production of personalized mRNA-based therapeutics that target multiple tumor rejection antigens in a single therapy for the treatment of refractory brain tumors. METHODS Tumor-specific neoantigens and aberrantly overexpressed tumor-associated antigens were identified for glioblastoma and medulloblastoma tumors using our cancer immunogenomics pipeline called Open Reading Frame Antigen Network (O.R.A.N). Personalized tumor antigen-specific mRNA vaccine was developed for each individual tumor model using selective gene capture and enrichment strategy. The immunogenicity and efficacy of the personalized mRNA vaccines was evaluated in combination with anti-PD-1 immune checkpoint blockade therapy or adoptive cellular therapy with ex vivo expanded tumor antigen-specific lymphocytes in highly aggressive murine GBM models. RESULTS Our results demonstrate the effectiveness of the antigen-specific mRNA vaccines in eliciting robust anti-tumor immune responses in GBM hosts. Our findings substantiate an increase in tumor-infiltrating lymphocytes characterized by enhanced effector function, both intratumorally and systemically, after antigen-specific mRNA-directed immunotherapy, resulting in a favorable shift in the tumor microenvironment from immunologically cold to hot. Capacity to generate personalized mRNA vaccines targeting human GBM antigens was also demonstrated. CONCLUSIONS We have established a personalized and customizable mRNA-therapeutic approach that effectively targets a plurality of tumor antigens and demonstrated potent anti-tumor response in preclinical brain tumor models. This platform mRNA technology uniquely addresses the challenge of tumor heterogeneity and low antigen burden, two key deficiencies in targeting the classically immunotherapy-resistant CNS malignancies, and possibly other cold tumor types.
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Affiliation(s)
- Vrunda Trivedi
- University of Florida, 1333 Center Drive, BSB B1-118, Gainesville, FL, 32610, USA
| | - Changlin Yang
- University of Florida, 1333 Center Drive, BSB B1-118, Gainesville, FL, 32610, USA
| | - Kelena Klippel
- University of Florida, 1333 Center Drive, BSB B1-118, Gainesville, FL, 32610, USA
| | - Oleg Yegorov
- University of Florida, 1333 Center Drive, BSB B1-118, Gainesville, FL, 32610, USA
| | | | - Lan Hoang-Minh
- University of Florida, 1333 Center Drive, BSB B1-118, Gainesville, FL, 32610, USA
| | - Graeme Fenton
- University of Florida, 1333 Center Drive, BSB B1-118, Gainesville, FL, 32610, USA
| | | | - Paul Castillo
- University of Florida, 1333 Center Drive, BSB B1-118, Gainesville, FL, 32610, USA
| | - Ginger Moore
- University of Florida, 1333 Center Drive, BSB B1-118, Gainesville, FL, 32610, USA
| | - Kaytora Long-James
- University of Florida, 1333 Center Drive, BSB B1-118, Gainesville, FL, 32610, USA
| | - Kyle Dyson
- University of Florida, 1333 Center Drive, BSB B1-118, Gainesville, FL, 32610, USA
| | - Bently Doonan
- University of Florida, 1333 Center Drive, BSB B1-118, Gainesville, FL, 32610, USA
| | - Catherine Flores
- University of Florida, 1333 Center Drive, BSB B1-118, Gainesville, FL, 32610, USA
| | - Duane A Mitchell
- University of Florida, 1333 Center Drive, BSB B1-118, Gainesville, FL, 32610, USA.
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5
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Chaib M, Holt JR, Fisher EL, Sipe LM, Bohm MS, Joseph SC, Simmons BW, Eugin Simon S, Yarbro JR, Tanveer U, Halle JL, Carson JA, Hollingsworth T, Wei Q, Rathmell JC, Thomas PG, Hayes DN, Makowski L. Protein kinase C delta regulates mononuclear phagocytes and hinders response to immunotherapy in cancer. Sci Adv 2023; 9:eadd3231. [PMID: 38134280 PMCID: PMC10745701 DOI: 10.1126/sciadv.add3231] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/03/2022] [Accepted: 11/21/2023] [Indexed: 12/24/2023]
Abstract
Mononuclear phagocytes (MPs) play a crucial role in tissue homeostasis; however, MPs also contribute to tumor progression and resistance to immune checkpoint blockade (ICB). Targeting MPs could be an effective strategy to enhance ICB efficacy. We report that protein kinase C delta (PKCδ), a serine/threonine kinase, is abundantly expressed by MPs in human and mouse tumors. PKCδ-/- mice displayed reduced tumor progression compared to wild types, with increased response to anti-PD-1. Tumors from PKCδ-/- mice demonstrated TH1-skewed immune response including increased antigen presentation and T cell activation. Depletion of MPs in vivo altered tumor growth in control but not PKCδ-/- mice. Coinjection of PKCδ-/- M2-like macrophages with cancer cells into wild-type mice markedly delayed tumor growth and significantly increased intratumoral T cell activation compared to PKCδ+/+ controls. PKCδ deficiency reprogrammed MPs by activating type I and type II interferon signaling. Thus, PKCδ might be targeted to reprogram MPs to augment ICB efficacy.
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Affiliation(s)
- Mehdi Chaib
- Department of Pharmaceutical Sciences, College of Pharmacy, The University of Tennessee Health Science Center, Memphis, TN 38163, USA
| | - Jeremiah R. Holt
- Department of Medicine, Division of Hematology and Oncology, College of Medicine, The University of Tennessee Health Science Center, Memphis, TN 38163, USA
| | - Emilie L. Fisher
- Vanderbilt Center for Immunobiology and Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, TN 37235, USA
| | - Laura M. Sipe
- Department of Medicine, Division of Hematology and Oncology, College of Medicine, The University of Tennessee Health Science Center, Memphis, TN 38163, USA
| | - Margaret S. Bohm
- Department of Microbiology, Immunology, and Biochemistry, College of Medicine, The University of Tennessee Health Science Center, Memphis, TN 38163, USA
| | - Sydney C. Joseph
- Department of Medicine, Division of Hematology and Oncology, College of Medicine, The University of Tennessee Health Science Center, Memphis, TN 38163, USA
| | - Boston W. Simmons
- Department of Medicine, Division of Hematology and Oncology, College of Medicine, The University of Tennessee Health Science Center, Memphis, TN 38163, USA
| | - Samson Eugin Simon
- Department of Medicine, Division of Hematology and Oncology, College of Medicine, The University of Tennessee Health Science Center, Memphis, TN 38163, USA
| | - Johnathan R. Yarbro
- Department of Medicine, Division of Hematology and Oncology, College of Medicine, The University of Tennessee Health Science Center, Memphis, TN 38163, USA
| | - Ubaid Tanveer
- Department of Medicine, Division of Hematology and Oncology, College of Medicine, The University of Tennessee Health Science Center, Memphis, TN 38163, USA
| | - Jessica L. Halle
- Department of Physical Therapy, College of Health Professions, The University of Tennessee Health Science Center, Memphis, TN 38163, USA
| | - James A. Carson
- Department of Physical Therapy, College of Health Professions, The University of Tennessee Health Science Center, Memphis, TN 38163, USA
| | - T.J. Hollingsworth
- Department of Microbiology, Immunology, and Biochemistry, College of Medicine, The University of Tennessee Health Science Center, Memphis, TN 38163, USA
- Department of Ophthalmology, Hamilton Eye Institute, College of Medicine, The University of Tennessee Health Science Center, Memphis, TN 38163, USA
- Department of Anatomy and Neurobiology, College of Medicine, The University of Tennessee Health Science Center, Memphis, TN 38163, USA
| | - QingQing Wei
- Department of Cellular Biology and Anatomy, Augusta University, Augusta, GA 30912, USA
| | - Jeffrey C. Rathmell
- Vanderbilt Center for Immunobiology and Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, TN 37235, USA
| | - Paul G. Thomas
- Department of Microbiology, Immunology, and Biochemistry, College of Medicine, The University of Tennessee Health Science Center, Memphis, TN 38163, USA
- Department of Immunology, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA
| | - D. Neil Hayes
- Department of Medicine, Division of Hematology and Oncology, College of Medicine, The University of Tennessee Health Science Center, Memphis, TN 38163, USA
- UTHSC Center for Cancer Research, College of Medicine, The University of Tennessee Health Science Center, Memphis, TN 38163, USA
| | - Liza Makowski
- Department of Pharmaceutical Sciences, College of Pharmacy, The University of Tennessee Health Science Center, Memphis, TN 38163, USA
- Department of Medicine, Division of Hematology and Oncology, College of Medicine, The University of Tennessee Health Science Center, Memphis, TN 38163, USA
- Department of Microbiology, Immunology, and Biochemistry, College of Medicine, The University of Tennessee Health Science Center, Memphis, TN 38163, USA
- UTHSC Center for Cancer Research, College of Medicine, The University of Tennessee Health Science Center, Memphis, TN 38163, USA
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6
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Fu R, Walters K, Kaufman ML, Koc K, Baldwin A, Clay MR, Basham KJ, Kiseljak-Vassiliades K, Fishbein L, Mukherjee N. In Situ Spatial Reconstruction of Distinct Normal and Pathological Cell Populations Within the Human Adrenal Gland. J Endocr Soc 2023; 7:bvad131. [PMID: 37953901 PMCID: PMC10638100 DOI: 10.1210/jendso/bvad131] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/13/2023] [Indexed: 11/14/2023] Open
Abstract
The human adrenal gland consists of concentrically organized, functionally distinct regions responsible for hormone production. Dysregulation of adrenocortical cell differentiation alters the proportion and organization of the functional zones of the adrenal cortex leading to disease. Current models of adrenocortical cell differentiation are based on mouse studies, but there are known organizational and functional differences between human and mouse adrenal glands. This study aimed to investigate the centripetal differentiation model in the human adrenal cortex and characterize aldosterone-producing micronodules (APMs) to better understand adrenal diseases such as primary aldosteronism. We applied spatially resolved in situ transcriptomics to human adrenal tissue sections from 2 individuals and identified distinct cell populations and their positional relationships. The results supported the centripetal differentiation model in humans, with cells progressing from the outer capsule to the zona glomerulosa, zona fasciculata, and zona reticularis. Additionally, we characterized 2 APMs in a 72-year-old woman. Comparison with earlier APM transcriptomes indicated a subset of core genes, but also heterogeneity between APMs. The findings contribute to our understanding of normal and pathological cellular differentiation in the human adrenal cortex.
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Affiliation(s)
- Rui Fu
- RNA Biosciences Initiative and Department of Biochemistry and Molecular Genetics, University of Colorado School of Medicine at Colorado Anschutz Medical Campus Aurora, Aurora, CO 80045, USA
- Computational Biology, New York Genome Center, New York, NY 10013, USA
| | - Kathryn Walters
- RNA Biosciences Initiative and Department of Biochemistry and Molecular Genetics, University of Colorado School of Medicine at Colorado Anschutz Medical Campus Aurora, Aurora, CO 80045, USA
| | - Michael L Kaufman
- RNA Biosciences Initiative and Department of Biochemistry and Molecular Genetics, University of Colorado School of Medicine at Colorado Anschutz Medical Campus Aurora, Aurora, CO 80045, USA
| | - Katrina Koc
- Division of Endocrinology, Metabolism and Diabetes, Department of Medicine, University of Colorado School of Medicine at Colorado Anschutz Medical Campus Aurora, Aurora, CO 80045, USA
| | - Amber Baldwin
- RNA Biosciences Initiative and Department of Biochemistry and Molecular Genetics, University of Colorado School of Medicine at Colorado Anschutz Medical Campus Aurora, Aurora, CO 80045, USA
| | - Michael R Clay
- Department of Pathology, University of Colorado School of Medicine at Colorado Anschutz Medical Campus Aurora, Aurora, CO 80045, USA
| | - Kaitlin J Basham
- Department of Oncological Sciences, Huntsman Cancer Institute, University of Utah, Salt Lake City, UT 84112, USA
| | - Katja Kiseljak-Vassiliades
- Division of Endocrinology, Metabolism and Diabetes, Department of Medicine, University of Colorado School of Medicine at Colorado Anschutz Medical Campus Aurora, Aurora, CO 80045, USA
- Research Service Veterans Affairs Medical Center, Aurora, CO 80045, USA
| | - Lauren Fishbein
- Division of Endocrinology, Metabolism and Diabetes, Department of Medicine, University of Colorado School of Medicine at Colorado Anschutz Medical Campus Aurora, Aurora, CO 80045, USA
| | - Neelanjan Mukherjee
- RNA Biosciences Initiative and Department of Biochemistry and Molecular Genetics, University of Colorado School of Medicine at Colorado Anschutz Medical Campus Aurora, Aurora, CO 80045, USA
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7
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Semenkovich NP, Szymanski JJ, Earland N, Chauhan PS, Pellini B, Chaudhuri AA. Genomic approaches to cancer and minimal residual disease detection using circulating tumor DNA. J Immunother Cancer 2023; 11:e006284. [PMID: 37349125 PMCID: PMC10314661 DOI: 10.1136/jitc-2022-006284] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/26/2023] [Indexed: 06/24/2023] Open
Abstract
Liquid biopsies using cell-free circulating tumor DNA (ctDNA) are being used frequently in both research and clinical settings. ctDNA can be used to identify actionable mutations to personalize systemic therapy, detect post-treatment minimal residual disease (MRD), and predict responses to immunotherapy. ctDNA can also be isolated from a range of different biofluids, with the possibility of detecting locoregional MRD with increased sensitivity if sampling more proximally than blood plasma. However, ctDNA detection remains challenging in early-stage and post-treatment MRD settings where ctDNA levels are minuscule giving a high risk for false negative results, which is balanced with the risk of false positive results from clonal hematopoiesis. To address these challenges, researchers have developed ever-more elegant approaches to lower the limit of detection (LOD) of ctDNA assays toward the part-per-million range and boost assay sensitivity and specificity by reducing sources of low-level technical and biological noise, and by harnessing specific genomic and epigenomic features of ctDNA. In this review, we highlight a range of modern assays for ctDNA analysis, including advancements made to improve the signal-to-noise ratio. We further highlight the challenge of detecting ultra-rare tumor-associated variants, overcoming which will improve the sensitivity of post-treatment MRD detection and open a new frontier of personalized adjuvant treatment decision-making.
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Affiliation(s)
- Nicholas P Semenkovich
- Division of Endocrinology, Metabolism, and Lipid Research, Department of Medicine, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Jeffrey J Szymanski
- Division of Cancer Biology, Department of Radiation Oncology, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Noah Earland
- Division of Biology and Biomedical Sciences, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Pradeep S Chauhan
- Division of Cancer Biology, Department of Radiation Oncology, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Bruna Pellini
- Department of Thoracic Oncology, Moffitt Cancer Center and Research Institute, Tampa, Florida, USA
- Department of Oncologic Sciences, Morsani College of Medicine, University of South Florida, Tampa, Florida, USA
| | - Aadel A Chaudhuri
- Division of Cancer Biology, Department of Radiation Oncology, Washington University School of Medicine, St. Louis, Missouri, USA
- Division of Biology and Biomedical Sciences, Washington University School of Medicine, St. Louis, Missouri, USA
- Siteman Cancer Center, Washington University School of Medicine, St. Louis, Missouri, USA
- Department of Genetics, Washington University School of Medicine, St. Louis, Missouri, USA
- Department of Biomedical Engineering, Washington University School of Medicine, St. Louis, Missouri, USA
- Department of Computer Science and Engineering, Washington University in St. Louis, St. Louis, Missouri, USA
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8
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Savoy L, Long N, Lee H, Chen R, Allen B, Lin HY, Tognon C, Malhotra S, Tyner JW, Zhang H. CDK12/13 dual inhibitors are potential therapeutics for acute myeloid leukemia. Br J Haematol 2023. [PMID: 37182843 DOI: 10.1111/bjh.18843] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2023] [Revised: 04/17/2023] [Accepted: 04/23/2023] [Indexed: 05/16/2023]
Affiliation(s)
- Lindsey Savoy
- Division of Oncological Sciences, Oregon Health & Science University, Knight Cancer Institute, Portland, Oregon, USA
| | - Nicola Long
- Division of Hematology and Medical Oncology, Oregon Health & Science University, Knight Cancer Institute, Portland, Oregon, USA
| | - Hyunjung Lee
- Department of Cell, Developmental & Cancer Biology, Oregon Health & Science University, Knight Cancer Institute, Portland, Oregon, USA
| | - Reid Chen
- Division of Oncological Sciences, Oregon Health & Science University, Knight Cancer Institute, Portland, Oregon, USA
| | - Basil Allen
- Division of Oncological Sciences, Oregon Health & Science University, Knight Cancer Institute, Portland, Oregon, USA
| | - Hsin-Yun Lin
- Department of Cell, Developmental & Cancer Biology, Oregon Health & Science University, Knight Cancer Institute, Portland, Oregon, USA
| | - Cristina Tognon
- Division of Hematology and Medical Oncology, Oregon Health & Science University, Knight Cancer Institute, Portland, Oregon, USA
| | - Sanjay Malhotra
- Center for Experimental Therapeutics, Department of Cell, Developmental & Cancer Biology, Oregon Health & Science University, Knight Cancer Institute, Portland, Oregon, USA
| | - Jeffrey W Tyner
- Department of Cell, Developmental & Cancer Biology, Oregon Health & Science University, Knight Cancer Institute, Portland, Oregon, USA
| | - Haijiao Zhang
- Division of Oncological Sciences, Oregon Health & Science University, Knight Cancer Institute, Portland, Oregon, USA
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9
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Alzobi M, Hurtz C, Mehta H, Thomas S, Corey SJ. B-cell lymphoblastic leukemia in an adolescent with Dravet syndrome. Pediatr Blood Cancer 2023:e30340. [PMID: 37073671 DOI: 10.1002/pbc.30340] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Grants] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/03/2023] [Revised: 03/07/2023] [Accepted: 03/13/2023] [Indexed: 04/20/2023]
Affiliation(s)
- Mohamed Alzobi
- Department of Pediatric Hematology/Oncology & Stem Cell Transplantation, Cleveland Clinic, Cleveland, Ohio, USA
- Jordan University of Science and Technology, College of Medicine, Irbid, Jordan
| | - Christian Hurtz
- Fels Cancer Institute for Personalized Medicine, Temple University, Philadelphia, Pennsylvania, USA
| | - Hrishikesh Mehta
- Department of Cancer Biology, Lerner Research Institute, Cleveland Clinic, Cleveland, Ohio, USA
| | - Stefanie Thomas
- Department of Pediatric Hematology/Oncology & Stem Cell Transplantation, Cleveland Clinic, Cleveland, Ohio, USA
| | - Seth J Corey
- Department of Pediatric Hematology/Oncology & Stem Cell Transplantation, Cleveland Clinic, Cleveland, Ohio, USA
- Department of Cancer Biology, Lerner Research Institute, Cleveland Clinic, Cleveland, Ohio, USA
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10
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Sayar E, Patel RA, Coleman IM, Roudier MP, Zhang A, Mustafi P, Low JY, Hanratty B, Ang LS, Bhatia V, Adil M, Bakbak H, Quigley DA, Schweizer MT, Hawley JE, Kollath L, True LD, Feng FY, Bander NH, Corey E, Lee JK, Morrissey C, Gulati R, Nelson PS, Haffner MC. Reversible epigenetic alterations mediate PSMA expression heterogeneity in advanced metastatic prostate cancer. JCI Insight 2023; 8:e162907. [PMID: 36821396 PMCID: PMC10132157 DOI: 10.1172/jci.insight.162907] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2022] [Accepted: 02/21/2023] [Indexed: 02/24/2023] Open
Abstract
Prostate-specific membrane antigen (PSMA) is an important cell surface target in prostate cancer. There are limited data on the heterogeneity of PSMA tissue expression in metastatic castration-resistant prostate cancer (mCRPC). Furthermore, the mechanisms regulating PSMA expression (encoded by the FOLH1 gene) are not well understood. Here, we demonstrate that PSMA expression is heterogeneous across different metastatic sites and molecular subtypes of mCRPC. In a rapid autopsy cohort in which multiple metastatic sites per patient were sampled, we found that 13 of 52 (25%) cases had no detectable PSMA and 23 of 52 (44%) cases showed heterogeneous PSMA expression across individual metastases, with 33 (63%) cases harboring at least 1 PSMA-negative site. PSMA-negative tumors displayed distinct transcriptional profiles with expression of druggable targets such as MUC1. Loss of PSMA was associated with epigenetic changes of the FOLH1 locus, including gain of CpG methylation and loss of histone 3 lysine 27 (H3K27) acetylation. Treatment with histone deacetylase (HDAC) inhibitors reversed this epigenetic repression and restored PSMA expression in vitro and in vivo. Collectively, these data provide insights into the expression patterns and regulation of PSMA in mCRPC and suggest that epigenetic therapies - in particular, HDAC inhibitors - can be used to augment PSMA levels.
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Affiliation(s)
- Erolcan Sayar
- Division of Human Biology, Fred Hutchinson Cancer Center, Seattle, Washington, USA
| | - Radhika A. Patel
- Division of Human Biology, Fred Hutchinson Cancer Center, Seattle, Washington, USA
| | - Ilsa M. Coleman
- Division of Human Biology, Fred Hutchinson Cancer Center, Seattle, Washington, USA
| | - Martine P. Roudier
- Department of Urology, University of Washington (UW), Seattle, Washington, USA
| | - Ailin Zhang
- Division of Human Biology, Fred Hutchinson Cancer Center, Seattle, Washington, USA
| | - Pallabi Mustafi
- Division of Human Biology, Fred Hutchinson Cancer Center, Seattle, Washington, USA
| | - Jin-Yih Low
- Division of Human Biology, Fred Hutchinson Cancer Center, Seattle, Washington, USA
| | - Brian Hanratty
- Division of Human Biology, Fred Hutchinson Cancer Center, Seattle, Washington, USA
| | - Lisa S. Ang
- Division of Human Biology, Fred Hutchinson Cancer Center, Seattle, Washington, USA
| | - Vipul Bhatia
- Division of Human Biology, Fred Hutchinson Cancer Center, Seattle, Washington, USA
| | - Mohamed Adil
- Division of Human Biology, Fred Hutchinson Cancer Center, Seattle, Washington, USA
| | - Hasim Bakbak
- Division of Human Biology, Fred Hutchinson Cancer Center, Seattle, Washington, USA
| | - David A. Quigley
- UCSF Helen Diller Family Comprehensive Cancer Center, San Francisco, California, USA
| | - Michael T. Schweizer
- Division of Medical Oncology, Department of Medicine, UW, Seattle, Washington, USA
- Division of Clinical Research, Fred Hutchinson Cancer Center, Seattle, Washington, USA
| | - Jessica E. Hawley
- Division of Medical Oncology, Department of Medicine, UW, Seattle, Washington, USA
- Division of Clinical Research, Fred Hutchinson Cancer Center, Seattle, Washington, USA
| | - Lori Kollath
- Department of Urology, University of Washington (UW), Seattle, Washington, USA
| | - Lawrence D. True
- Department of Laboratory Medicine and Pathology, UW, Seattle, Washington, USA
| | - Felix Y. Feng
- UCSF Helen Diller Family Comprehensive Cancer Center, San Francisco, California, USA
| | - Neil H. Bander
- Department of Urology, Weill Cornell Medicine, New York, New York, USA
| | - Eva Corey
- Department of Urology, University of Washington (UW), Seattle, Washington, USA
| | - John K. Lee
- Division of Human Biology, Fred Hutchinson Cancer Center, Seattle, Washington, USA
- Department of Urology, Weill Cornell Medicine, New York, New York, USA
| | - Colm Morrissey
- Department of Urology, University of Washington (UW), Seattle, Washington, USA
| | - Roman Gulati
- Division of Public Health Sciences, Fred Hutchinson Cancer Center, Seattle, Washington, USA
| | - Peter S. Nelson
- Division of Human Biology, Fred Hutchinson Cancer Center, Seattle, Washington, USA
- Department of Urology, University of Washington (UW), Seattle, Washington, USA
- Division of Medical Oncology, Department of Medicine, UW, Seattle, Washington, USA
- Division of Clinical Research, Fred Hutchinson Cancer Center, Seattle, Washington, USA
- Department of Laboratory Medicine and Pathology, UW, Seattle, Washington, USA
| | - Michael C. Haffner
- Division of Human Biology, Fred Hutchinson Cancer Center, Seattle, Washington, USA
- Division of Clinical Research, Fred Hutchinson Cancer Center, Seattle, Washington, USA
- Department of Laboratory Medicine and Pathology, UW, Seattle, Washington, USA
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11
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Chen J, Luo T, Jiang M, Liu J, Gupta GP, Li Y. Cell composition inference and identification of layer-specific spatial transcriptional profiles with POLARIS. Sci Adv 2023; 9:eadd9818. [PMID: 36857450 PMCID: PMC9977174 DOI: 10.1126/sciadv.add9818] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/17/2022] [Accepted: 01/31/2023] [Indexed: 06/18/2023]
Abstract
Spatial transcriptomics (ST) technology, providing spatially resolved transcriptional profiles, facilitates advanced understanding of key biological processes related to health and disease. Sequencing-based ST technologies provide whole-transcriptome profiles but are limited by the non-single cell-level resolution. Lack of knowledge in the number of cells or cell type composition at each spot can lead to invalid downstream analysis, which is a critical issue recognized in ST data analysis. Methods developed, however, tend to underuse histological images, which conceptually provide important and complementary information including anatomical structure and distribution of cells. To fill in the gaps, we present POLARIS, a versatile ST analysis method that can perform cell type deconvolution, identify anatomical or functional layer-wise differentially expressed (LDE) genes, and enable cell composition inference from histology images. Applied to four tissues, POLARIS demonstrates high deconvolution accuracy, accurately predicts cell composition solely from images, and identifies LDE genes that are biologically relevant and meaningful.
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Affiliation(s)
- Jiawen Chen
- Department of Biostatistics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Tianyou Luo
- Department of Biostatistics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Minzhi Jiang
- Department of Applied Physical Sciences, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Jiandong Liu
- Department of Pathology and Laboratory Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Gaorav P. Gupta
- Department of Radiation Oncology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Yun Li
- Department of Biostatistics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- Department of Computer Science, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
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12
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Siddiqui BA, Chapin BF, Jindal S, Duan F, Basu S, Yadav SS, Gu AD, Espejo AB, Kinder M, Pettaway CA, Ward JF, Tidwell RSS, Troncoso P, Corn PG, Logothetis CJ, Knoblauch R, Hutnick N, Gottardis M, Drake CG, Sharma P, Subudhi SK. Immune and pathologic responses in patients with localized prostate cancer who received daratumumab (anti-CD38) or edicotinib (CSF-1R inhibitor). J Immunother Cancer 2023; 11:e006262. [PMID: 36948506 PMCID: PMC10040066 DOI: 10.1136/jitc-2022-006262] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/08/2023] [Indexed: 03/24/2023] Open
Abstract
BACKGROUND The prostate tumor microenvironment (TME) is immunosuppressive, with few effector T cells and enrichment of inhibitory immune populations, leading to limited responses to treatments such as immune checkpoint therapies (ICTs). The immune composition of the prostate TME differs across soft tissue and bone, the most common site of treatment-refractory metastasis. Understanding immunosuppressive mechanisms specific to prostate TMEs will enable rational immunotherapy strategies to generate effective antitumor immune responses. Daratumumab (anti-CD38 antibody) and edicotinib (colony-stimulating factor-1 receptor (CSF-1R) inhibitor) may alter the balance within the prostate TME to promote antitumor immune responses. HYPOTHESIS Daratumumab or edicotinib will be safe and will alter the immune TME, leading to antitumor responses in localized prostate cancer. PATIENTS AND METHODS In this presurgical study, patients with localized prostate cancer received 4 weekly doses of daratumumab or 4 weeks of daily edicotinib prior to radical prostatectomy (RP). Treated and untreated control (Gleason score ≥8 in prostate biopsy) prostatectomy specimens and patient-matched pre- and post-treatment peripheral blood mononuclear cells (PBMCs) and bone marrow samples were evaluated. The primary endpoint was incidence of adverse events (AEs). The secondary endpoint was pathologic complete remission (pCR) rate. RESULTS Twenty-five patients were treated (daratumumab, n=15; edicotinib, n=10). All patients underwent RP without delays. Grade 3 treatment-related AEs with daratumumab occurred in 3 patients (12%), and no ≥grade 3 treatment-related AEs occurred with edicotinib. No changes in serum prostate-specific antigen (PSA) levels or pCRs were observed. Daratumumab led to a decreased frequency of CD38+ T cells, natural killer cells, and myeloid cells in prostate tumors, bone marrow, and PBMCs. There were no consistent changes in CSF-1R+ immune cells in prostate, bone marrow, or PBMCs with edicotinib. Neither treatment induced T cell infiltration into the prostate TME. CONCLUSIONS Daratumumab and edicotinib treatment was safe and well-tolerated in patients with localized prostate cancer but did not induce pCRs. Decreases in CD38+ immune cells were observed in prostate tumors, bone marrow, and PBMCs with daratumumab, but changes in CSF-1R+ immune cells were not consistently observed with edicotinib. Neither myeloid-targeted agent alone was sufficient to generate antitumor responses in prostate cancer; thus, combinations with agents to induce T cell infiltration (eg, ICTs) will be needed to overcome the immunosuppressive prostate TME.
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Affiliation(s)
- Bilal A Siddiqui
- Department of Genitourinary Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Brian F Chapin
- Department of Urology, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Sonali Jindal
- The Immunotherapy Platform, University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Fei Duan
- The Immunotherapy Platform, University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Sreyashi Basu
- The Immunotherapy Platform, University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Shalini S Yadav
- The Immunotherapy Platform, University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Ai-Di Gu
- The Immunotherapy Platform, University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Alexsandra B Espejo
- The Immunotherapy Platform, University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Michelle Kinder
- Janssen Research & Development, Spring House, Pennsylvania, USA
| | - Curtis A Pettaway
- Department of Urology, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - John F Ward
- Department of Urology, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Rebecca S S Tidwell
- Department of Biostatistics, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Patricia Troncoso
- Department of Pathology, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Paul G Corn
- Department of Genitourinary Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Christopher J Logothetis
- Department of Genitourinary Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | | | - Natalie Hutnick
- Janssen Research & Development, Spring House, Pennsylvania, USA
| | - Marco Gottardis
- Janssen Research & Development, Spring House, Pennsylvania, USA
| | - Charles G Drake
- Janssen Research & Development, Spring House, Pennsylvania, USA
- Department of Medicine, Columbia University Medical Center, New York, New York, USA
- Department of Urology, Columbia University Medical Center, New York, New York, USA
| | - Padmanee Sharma
- Department of Genitourinary Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
- The Immunotherapy Platform, University of Texas MD Anderson Cancer Center, Houston, Texas, USA
- Department of Immunology, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Sumit K Subudhi
- Department of Genitourinary Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
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13
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Gonzalez-Callejo P, Guo Z, Ziglari T, Claudio NM, Nguyen KH, Oshimori N, Seras-Franzoso J, Pucci F. Cancer stem cell-derived extracellular vesicles preferentially target MHC-II-macrophages and PD1+ T cells in the tumor microenvironment. PLoS One 2023; 18:e0279400. [PMID: 36735677 PMCID: PMC9897575 DOI: 10.1371/journal.pone.0279400] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2022] [Accepted: 12/06/2022] [Indexed: 02/04/2023] Open
Abstract
Immunotherapy is an approved treatment option for head and neck squamous cell carcinoma (HNSCC). However, the response rate to immune checkpoint blockade is only 13% for recurrent HNSCC, highlighting the urgent need to better understand tumor-immune interplay, with the ultimate goal of improving patient outcomes. HNSCC present high local recurrence rates and therapy resistance that can be attributed to the presence of cancer stem cells (CSC) within tumors. CSC exhibit singular properties that enable them to avoid immune detection and eradication. How CSC communicate with immune cells and which immune cell types are preferentially found within the CSC niche are still open questions. Here, we used genetic approaches to specifically label CSC-derived extracellular vesicles (EVs) and to perform Sortase-mediated in vivo proximity labeling of CSC niche cells. We identified specific immune cell subsets that were selectively targeted by EVCSC and that were found in the CSC niche. Native EVCSC preferentially targeted MHC-II-macrophages and PD1+ T cells in the tumor microenvironment, which were the same immune cell subsets enriched within the CSC niche. These observations indicate that the use of genetic technologies able to track EVs without in vitro isolation are a valuable tool to unveil the biology of native EVCSC.
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Affiliation(s)
- Patricia Gonzalez-Callejo
- Department of Cell, Developmental & Cancer Biology, Oregon Health and Science University, Portland, Oregon, United States of America
- Bionanoplasmonics Group, CIC biomaGUNE, Donostia-San Sebastián, Spain
| | - Zihan Guo
- Department of Cell, Developmental & Cancer Biology, Oregon Health and Science University, Portland, Oregon, United States of America
- Program in Biomedical Sciences, Oregon Health and Science University, Portland, Oregon, United States of America
| | - Tahereh Ziglari
- Department of Cell, Developmental & Cancer Biology, Oregon Health and Science University, Portland, Oregon, United States of America
| | - Natalie Marcia Claudio
- Department of Cell, Developmental & Cancer Biology, Oregon Health and Science University, Portland, Oregon, United States of America
- Department of Otolaryngology-Head and Neck Surgery, Oregon Health and Science University, Portland, Oregon, United States of America
| | - Kayla Hoang Nguyen
- Department of Cell, Developmental & Cancer Biology, Oregon Health and Science University, Portland, Oregon, United States of America
- Program in Biomedical Sciences, Oregon Health and Science University, Portland, Oregon, United States of America
| | - Naoki Oshimori
- Department of Cell, Developmental & Cancer Biology, Oregon Health and Science University, Portland, Oregon, United States of America
- Program in Biomedical Sciences, Oregon Health and Science University, Portland, Oregon, United States of America
- Department of Otolaryngology-Head and Neck Surgery, Oregon Health and Science University, Portland, Oregon, United States of America
- Department of Dermatology, Oregon Health and Science University, Portland, Oregon, United States of America
| | - Joaquim Seras-Franzoso
- Drug Delivery and Targeting Group, Vall d’Hebron Research Institute (VHIR), Barcelona, Spain
| | - Ferdinando Pucci
- Department of Cell, Developmental & Cancer Biology, Oregon Health and Science University, Portland, Oregon, United States of America
- Program in Biomedical Sciences, Oregon Health and Science University, Portland, Oregon, United States of America
- Department of Otolaryngology-Head and Neck Surgery, Oregon Health and Science University, Portland, Oregon, United States of America
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14
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Orr S, Huang L, Moser J, Stroopinsky D, Gandarilla O, DeCicco C, Liegel J, Tacettin C, Ephraim A, Cheloni G, Torres D, Kufe D, Rosenblatt J, Hidalgo M, Muthuswamy SK, Avigan D. Personalized tumor vaccine for pancreatic cancer. Cancer Immunol Immunother 2023; 72:301-313. [PMID: 35834008 DOI: 10.1007/s00262-022-03237-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2022] [Accepted: 06/04/2022] [Indexed: 02/07/2023]
Abstract
BACKGROUND Pancreatic cancer is a highly lethal malignancy often presenting with advanced disease and characterized by resistance to standard chemotherapy. Immune-based therapies such checkpoint inhibition have been largely ineffective such that pancreatic cancer is categorized as an immunologically "cold tumor". In the present study, we examine the therapeutic efficacy of a personalized cancer vaccine in which tumor cells are fused with dendritic cells (DC) resulting in the broad induction of antitumor immunity. RESULTS In the KPC spontaneous pancreatic cancer murine model, we demonstrated that vaccination with DC/KPC fusions led to expansion of pancreatic cancer specific lymphocytes with an activated phenotype. Remarkably, vaccination led to a reduction in tumor bulk and near doubling of median survival in this highly aggressive model. In a second murine pancreatic model (Panc02), vaccination with DC/tumor fusions similarly led to expansion of tumor antigen specific lymphocytes and their infiltration to the tumor site. Having shown efficacy in immunocompetent murine models, we subsequently demonstrated that DC/tumor fusions generated from primary human pancreatic cancer and autologous DCs potently stimulate tumor specific cytotoxic lymphocyte responses. CONCLUSIONS DC/tumor fusions induce the activation and expansion of tumor reactive lymphocytes with the capacity to infiltrate into the pancreatic cancer tumor bed.
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Affiliation(s)
- Shira Orr
- Beth Israel Deaconess Medical Center, Harvard Medical School, 330 Brookline Ave, Boston, MA, 02215, USA
| | - Ling Huang
- Beth Israel Deaconess Medical Center, Harvard Medical School, 330 Brookline Ave, Boston, MA, 02215, USA
| | - James Moser
- Beth Israel Deaconess Medical Center, Harvard Medical School, 330 Brookline Ave, Boston, MA, 02215, USA
| | - Dina Stroopinsky
- Beth Israel Deaconess Medical Center, Harvard Medical School, 330 Brookline Ave, Boston, MA, 02215, USA
| | - Omar Gandarilla
- Beth Israel Deaconess Medical Center, Harvard Medical School, 330 Brookline Ave, Boston, MA, 02215, USA
| | - Cori DeCicco
- Beth Israel Deaconess Medical Center, Harvard Medical School, 330 Brookline Ave, Boston, MA, 02215, USA
| | - Jessica Liegel
- Beth Israel Deaconess Medical Center, Harvard Medical School, 330 Brookline Ave, Boston, MA, 02215, USA
| | - Cansu Tacettin
- Beth Israel Deaconess Medical Center, Harvard Medical School, 330 Brookline Ave, Boston, MA, 02215, USA
| | - Adam Ephraim
- Beth Israel Deaconess Medical Center, Harvard Medical School, 330 Brookline Ave, Boston, MA, 02215, USA
| | - Giulia Cheloni
- Beth Israel Deaconess Medical Center, Harvard Medical School, 330 Brookline Ave, Boston, MA, 02215, USA
| | - Daniela Torres
- Beth Israel Deaconess Medical Center, Harvard Medical School, 330 Brookline Ave, Boston, MA, 02215, USA
| | - Donald Kufe
- Department of Medical Oncology, Dana Farber Cancer Institute, Harvard Medical School, Boston, USA
| | - Jacalyn Rosenblatt
- Beth Israel Deaconess Medical Center, Harvard Medical School, 330 Brookline Ave, Boston, MA, 02215, USA
| | - Manuel Hidalgo
- Beth Israel Deaconess Medical Center, Harvard Medical School, 330 Brookline Ave, Boston, MA, 02215, USA
| | - Senthil K Muthuswamy
- Beth Israel Deaconess Medical Center, Harvard Medical School, 330 Brookline Ave, Boston, MA, 02215, USA
| | - David Avigan
- Beth Israel Deaconess Medical Center, Harvard Medical School, 330 Brookline Ave, Boston, MA, 02215, USA.
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15
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Rupani DN, Thege FI, Chandra V, Rajaei H, Cowan RW, Wörmann SM, Le Roux O, Malaney P, Manning SL, Hashem J, Bailey-Lundberg J, Rhim AD, McAllister F. Adar1 deletion causes degeneration of the exocrine pancreas via Mavs-dependent interferon signaling. Development 2023; 150:dev201097. [PMID: 36458554 PMCID: PMC10110501 DOI: 10.1242/dev.201097] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2022] [Accepted: 11/21/2022] [Indexed: 12/03/2022]
Abstract
Adenosine deaminase acting on RNA 1 (ADAR1) is an RNA-binding protein that deaminates adenosine (A) to inosine (I). A-to-I editing alters post-transcriptional RNA processing, making ADAR1 a crucial regulator of gene expression. Consequently, Adar1 has been implicated in organogenesis. To determine the role of Adar1 in pancreatic development and homeostasis, we conditionally deleted Adar1 from the murine pancreas (Ptf1aCre/+; Adar1Fl/Fl). The resulting mice had stunted growth, likely due to malabsorption associated with exocrine pancreatic insufficiency. Analyses of pancreata revealed ductal cell expansion, heightened interferon-stimulated gene expression and an increased influx of immune cells. Concurrent deletion of Adar1 and Mavs, a signaling protein implicated in the innate immune pathway, rescued the degenerative phenotype and resulted in normal pancreatic development. Taken together, our work suggests that the primary function of Adar1 in the pancreas is to prevent aberrant activation of the Mavs-mediated innate immune pathway, thereby maintaining pancreatic homeostasis.
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Affiliation(s)
- Dhwani N. Rupani
- Department of Clinical Cancer Prevention, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
- Sheikh Ahmed Bin Zayed Al Nahyan Center for Pancreatic Cancer Research, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Fredrik I. Thege
- Sheikh Ahmed Bin Zayed Al Nahyan Center for Pancreatic Cancer Research, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Vidhi Chandra
- Department of Clinical Cancer Prevention, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Hajar Rajaei
- Department of Clinical Cancer Prevention, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Robert W. Cowan
- Sheikh Ahmed Bin Zayed Al Nahyan Center for Pancreatic Cancer Research, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
- Department of Gastroenterology, Hepatology & Nutrition, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Sonja M. Wörmann
- Sheikh Ahmed Bin Zayed Al Nahyan Center for Pancreatic Cancer Research, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Olivereen Le Roux
- Department of Clinical Cancer Prevention, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Prerna Malaney
- Department of Leukemia, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Sara L. Manning
- Sheikh Ahmed Bin Zayed Al Nahyan Center for Pancreatic Cancer Research, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
- Department of Gastroenterology, Hepatology & Nutrition, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Jack Hashem
- Sheikh Ahmed Bin Zayed Al Nahyan Center for Pancreatic Cancer Research, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
- Department of Gastroenterology, Hepatology & Nutrition, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Jennifer Bailey-Lundberg
- Department of Anesthesiology, Center for Perioperative Medicine, McGovern Medical School, The University of Texas Health Sciences Center, Houston, TX 77030, USA
- Center for Interventional Gastroenterology at UTHealth (iGUT), McGovern Medical School, Houston, TX 77030, USA
| | - Andrew D. Rhim
- Sheikh Ahmed Bin Zayed Al Nahyan Center for Pancreatic Cancer Research, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
- Department of Gastroenterology, Hepatology & Nutrition, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Florencia McAllister
- Department of Clinical Cancer Prevention, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
- Gastrointestinal Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
- Department of Immunology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
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16
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Marquardt V, Theruvath J, Pauck D, Picard D, Qin N, Blümel L, Maue M, Bartl J, Ahmadov U, Langini M, Meyer FD, Cole A, Cruz-Cruz J, Graef CM, Wölfl M, Milde T, Witt O, Erdreich-Epstein A, Leprivier G, Kahlert U, Stefanski A, Stühler K, Keir ST, Bigner DD, Hauer J, Beez T, Knobbe-Thomsen CB, Fischer U, Felsberg J, Hansen FK, Vibhakar R, Venkatraman S, Cheshier SH, Reifenberger G, Borkhardt A, Kurz T, Remke M, Mitra S. Tacedinaline (CI-994), a class I HDAC inhibitor, targets intrinsic tumor growth and leptomeningeal dissemination in MYC-driven medulloblastoma while making them susceptible to anti-CD47-induced macrophage phagocytosis via NF-kB-TGM2 driven tumor inflammation. J Immunother Cancer 2023; 11:jitc-2022-005871. [PMID: 36639156 PMCID: PMC9843227 DOI: 10.1136/jitc-2022-005871] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/13/2022] [Indexed: 01/15/2023] Open
Abstract
BACKGROUND While major advances have been made in improving the quality of life and survival of children with most forms of medulloblastoma (MB), those with MYC-driven tumors (Grp3-MB) still suffer significant morbidity and mortality. There is an urgent need to explore multimodal therapeutic regimens which are effective and safe for children. Large-scale studies have revealed abnormal cancer epigenomes caused by mutations and structural alterations of chromatin modifiers, aberrant DNA methylation, and histone modification signatures. Therefore, targeting epigenetic modifiers for cancer treatment has gained increasing interest, and inhibitors for various epigenetic modulators have been intensively studied in clinical trials. Here, we report a cross-entity, epigenetic drug screen to evaluate therapeutic vulnerabilities in MYC amplified MB, which sensitizes them to macrophage-mediated phagocytosis by targeting the CD47-signal regulatory protein α (SIRPα) innate checkpoint pathway. METHODS We performed a primary screen including 78 epigenetic inhibitors and a secondary screen including 20 histone deacetylase inhibitors (HDACi) to compare response profiles in atypical teratoid/rhabdoid tumor (AT/RT, n=11), MB (n=14), and glioblastoma (n=14). This unbiased approach revealed the preferential activity of HDACi in MYC-driven MB. Importantly, the class I selective HDACi, CI-994, showed significant cell viability reduction mediated by induction of apoptosis in MYC-driven MB, with little-to-no activity in non-MYC-driven MB, AT/RT, and glioblastoma in vitro. We tested the combinatorial effect of targeting class I HDACs and the CD47-SIRPa phagocytosis checkpoint pathway using in vitro phagocytosis assays and in vivo orthotopic xenograft models. RESULTS CI-994 displayed antitumoral effects at the primary site and the metastatic compartment in two orthotopic mouse models of MYC-driven MB. Furthermore, RNA sequencing revealed nuclear factor-kB (NF-κB) pathway induction as a response to CI-994 treatment, followed by transglutaminase 2 (TGM2) expression, which enhanced inflammatory cytokine secretion. We further show interferon-γ release and cell surface expression of engulfment ('eat-me') signals (such as calreticulin). Finally, combining CI-994 treatment with an anti-CD47 mAb targeting the CD47-SIRPα phagocytosis checkpoint enhanced in vitro phagocytosis and survival in tumor-bearing mice. CONCLUSION Together, these findings suggest a dynamic relationship between MYC amplification and innate immune suppression in MYC amplified MB and support further investigation of phagocytosis modulation as a strategy to enhance cancer immunotherapy responses.
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Affiliation(s)
- Viktoria Marquardt
- Division of Pediatric Neuro-Oncogenomics, German Cancer Research Center (DKFZ), Heidelberg, Germany, and German Cancer Consortium (DKTK), partner site Essen/Düsseldorf, Düsseldorf, Germany
- Institute of Pharmaceutical and Medicinal Chemistry, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Johanna Theruvath
- Department of Neurosurgery, Institute for StemCell Biology and Regenerative Medicine and Division of Pediatric Neurosurgery, Lucile Packard Children's Hospital, Stanford University, Stanford, California, USA
- Stanford University School of Medicine, Stanford, California, USA
| | - David Pauck
- Division of Pediatric Neuro-Oncogenomics, German Cancer Research Center (DKFZ), Heidelberg, Germany, and German Cancer Consortium (DKTK), partner site Essen/Düsseldorf, Düsseldorf, Germany
- Department of Pediatric Oncology, Hematology, and Clinical Immunology, Medical Faculty, University Hospital Düsseldorf, Düsseldorf, Germany; and DKTK, partner site Essen/Düsseldorf, Germany, Düsseldorf, Germany
| | - Daniel Picard
- Division of Pediatric Neuro-Oncogenomics, German Cancer Research Center (DKFZ), Heidelberg, Germany, and German Cancer Consortium (DKTK), partner site Essen/Düsseldorf, Düsseldorf, Germany
- Department of Pediatric Oncology, Hematology, and Clinical Immunology, Medical Faculty, University Hospital Düsseldorf, Düsseldorf, Germany; and DKTK, partner site Essen/Düsseldorf, Germany, Düsseldorf, Germany
| | - Nan Qin
- Division of Pediatric Neuro-Oncogenomics, German Cancer Research Center (DKFZ), Heidelberg, Germany, and German Cancer Consortium (DKTK), partner site Essen/Düsseldorf, Düsseldorf, Germany
- Department of Pediatric Oncology, Hematology, and Clinical Immunology, Medical Faculty, University Hospital Düsseldorf, Düsseldorf, Germany; and DKTK, partner site Essen/Düsseldorf, Germany, Düsseldorf, Germany
| | - Lena Blümel
- Division of Pediatric Neuro-Oncogenomics, German Cancer Research Center (DKFZ), Heidelberg, Germany, and German Cancer Consortium (DKTK), partner site Essen/Düsseldorf, Düsseldorf, Germany
- Department of Pediatric Oncology, Hematology, and Clinical Immunology, Medical Faculty, University Hospital Düsseldorf, Düsseldorf, Germany; and DKTK, partner site Essen/Düsseldorf, Germany, Düsseldorf, Germany
| | - Mara Maue
- Division of Pediatric Neuro-Oncogenomics, German Cancer Research Center (DKFZ), Heidelberg, Germany, and German Cancer Consortium (DKTK), partner site Essen/Düsseldorf, Düsseldorf, Germany
- Department of Pediatric Oncology, Hematology, and Clinical Immunology, Medical Faculty, University Hospital Düsseldorf, Düsseldorf, Germany; and DKTK, partner site Essen/Düsseldorf, Germany, Düsseldorf, Germany
| | - Jasmin Bartl
- Division of Pediatric Neuro-Oncogenomics, German Cancer Research Center (DKFZ), Heidelberg, Germany, and German Cancer Consortium (DKTK), partner site Essen/Düsseldorf, Düsseldorf, Germany
- Department of Pediatric Oncology, Hematology, and Clinical Immunology, Medical Faculty, University Hospital Düsseldorf, Düsseldorf, Germany; and DKTK, partner site Essen/Düsseldorf, Germany, Düsseldorf, Germany
| | - Ulvi Ahmadov
- Division of Pediatric Neuro-Oncogenomics, German Cancer Research Center (DKFZ), Heidelberg, Germany, and German Cancer Consortium (DKTK), partner site Essen/Düsseldorf, Düsseldorf, Germany
- Institute of Neuropathology, Medical Faculty, Heinrich-Heine University Düsseldorf, Düsseldorf; and DKTK, partner site Essen/Düsseldorf, Germany, Düsseldorf, Germany
| | - Maike Langini
- Division of Pediatric Neuro-Oncogenomics, German Cancer Research Center (DKFZ), Heidelberg, Germany, and German Cancer Consortium (DKTK), partner site Essen/Düsseldorf, Düsseldorf, Germany
- Molecular Proteomics Laboratory, Biomedical Research Centre (BMFZ), Heinrich-Heine University, Düsseldorf, Germany, Düsseldorf, Germany
| | - Frauke-Dorothee Meyer
- Division of Pediatric Neuro-Oncogenomics, German Cancer Research Center (DKFZ), Heidelberg, Germany, and German Cancer Consortium (DKTK), partner site Essen/Düsseldorf, Düsseldorf, Germany
- Institute of Neuropathology, Medical Faculty, Heinrich-Heine University Düsseldorf, Düsseldorf; and DKTK, partner site Essen/Düsseldorf, Germany, Düsseldorf, Germany
| | - Allison Cole
- Pediatrics, University of Colorado Denver, Aurora, Colorado, USA
| | | | - Claus M Graef
- Department of Neurosurgery, Institute for StemCell Biology and Regenerative Medicine and Division of Pediatric Neurosurgery, Lucile Packard Children's Hospital, Stanford University, Stanford, California, USA
| | - Matthias Wölfl
- Department of Pediatric Oncology, University Children's Hospital Würzburg, Würzburg, Germany
| | - Till Milde
- Hopp Children's Cancer Center Heidelberg (KiTZ), Heidelberg, Germany
- Department of Pediatric Hematology and Oncology, Heidelberg University Hospital, 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
| | - Anat Erdreich-Epstein
- Division of Hematology-Oncology and Blood and Marrow Transplantation, Department of Pediatrics and the Department of Pathology, Children's Hospital Los Angeles, and the Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, California, USA
| | - Gabriel Leprivier
- Institute of Neuropathology, Medical Faculty, Heinrich-Heine University Düsseldorf, Düsseldorf; and DKTK, partner site Essen/Düsseldorf, Germany, Düsseldorf, Germany
| | - Ulf Kahlert
- Department of Neurosurgery, Medical Faculty, Heinrich-Heine University Düsseldorf, Düsseldorf, Germany
| | - Anja Stefanski
- Molecular Proteomics Laboratory, Biomedical Research Centre (BMFZ), Heinrich-Heine University, Düsseldorf, Germany, Düsseldorf, Germany
| | - Kai Stühler
- Molecular Proteomics Laboratory, Biomedical Research Centre (BMFZ), Heinrich-Heine University, Düsseldorf, Germany, Düsseldorf, Germany
| | - Stephen T Keir
- Department of Neurosurgery, Duke University, Durham, North Carolina, USA
- Preston Robert Tisch Brain Tumor Center, Duke University, Durham, North Carolina, USA
| | - Darell D Bigner
- Department of Neurosurgery, Duke University, Durham, North Carolina, USA
- Preston Robert Tisch Brain Tumor Center, Duke University, Durham, North Carolina, USA
| | - Julia Hauer
- Department of Pediatric Oncology, Hematology, and Clinical Immunology, Medical Faculty, University Hospital Düsseldorf, Düsseldorf, Germany; and DKTK, partner site Essen/Düsseldorf, Germany, Düsseldorf, Germany
| | - Thomas Beez
- Department of Neurosurgery, Medical Faculty, Heinrich-Heine University Düsseldorf, Düsseldorf, Germany
| | - Christiane B Knobbe-Thomsen
- Institute of Neuropathology, Medical Faculty, Heinrich-Heine University Düsseldorf, Düsseldorf; and DKTK, partner site Essen/Düsseldorf, Germany, Düsseldorf, Germany
| | - Ute Fischer
- Department of Pediatric Oncology, Hematology, and Clinical Immunology, Medical Faculty, University Hospital Düsseldorf, Düsseldorf, Germany; and DKTK, partner site Essen/Düsseldorf, Germany, Düsseldorf, Germany
| | - Jörg Felsberg
- Institute of Neuropathology, Medical Faculty, Heinrich-Heine University Düsseldorf, Düsseldorf; and DKTK, partner site Essen/Düsseldorf, Germany, Düsseldorf, Germany
| | - Finn K Hansen
- Institute of Pharmaceutical and Medicinal Chemistry, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
- Pharmaceutical/Medicinal Chemistry, Institute of Pharmacy, Leipzig University, Leipzig, Germany
| | - Rajeev Vibhakar
- Pediatrics, University of Colorado Denver, Aurora, Colorado, USA
| | | | - Samuel H Cheshier
- Department of Neurosurgery, Huntsman Cancer Institute, University of Utah, Salt Lake City, Utah, USA
| | - Guido Reifenberger
- Division of Pediatric Neuro-Oncogenomics, German Cancer Research Center (DKFZ), Heidelberg, Germany, and German Cancer Consortium (DKTK), partner site Essen/Düsseldorf, Düsseldorf, Germany
- Institute of Neuropathology, Medical Faculty, Heinrich-Heine University Düsseldorf, Düsseldorf; and DKTK, partner site Essen/Düsseldorf, Germany, Düsseldorf, Germany
| | - Arndt Borkhardt
- Division of Pediatric Neuro-Oncogenomics, German Cancer Research Center (DKFZ), Heidelberg, Germany, and German Cancer Consortium (DKTK), partner site Essen/Düsseldorf, Düsseldorf, Germany
- Department of Pediatric Oncology, Hematology and Clinical Immunology, Medical Faculty, Heinrich-Heine-University, Düsseldorf, Germany
| | - Thomas Kurz
- Institute of Pharmaceutical and Medicinal Chemistry, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Marc Remke
- Division of Pediatric Neuro-Oncogenomics, German Cancer Research Center (DKFZ), Heidelberg, Germany, and German Cancer Consortium (DKTK), partner site Essen/Düsseldorf, Düsseldorf, Germany
- Department of Pediatric Oncology, Hematology, and Clinical Immunology, Medical Faculty, University Hospital Düsseldorf, Düsseldorf, Germany; and DKTK, partner site Essen/Düsseldorf, Germany, Düsseldorf, Germany
| | - Siddhartha Mitra
- Pediatrics, University of Colorado Denver, Aurora, Colorado, USA
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Stirling ER, Terabe M, Wilson AS, Kooshki M, Yamaleyeva LM, Alexander-Miller MA, Zhang W, Miller LD, Triozzi PL, Soto-Pantoja DR. Targeting the CD47/thrombospondin-1 signaling axis regulates immune cell bioenergetics in the tumor microenvironment to potentiate antitumor immune response. J Immunother Cancer 2022; 10:e004712. [PMID: 36418073 PMCID: PMC9685258 DOI: 10.1136/jitc-2022-004712] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/12/2022] [Indexed: 11/24/2022] Open
Abstract
BACKGROUND CD47 is an integral membrane protein that alters adaptive immunosurveillance when bound to the matricellular glycoprotein thrombospondin-1 (TSP1). We examined the impact of the CD47/TSP1 signaling axis on melanoma patient response to anti-PD-1 therapy due to alterations in T cell activation, proliferation, effector function, and bioenergetics. METHODS A syngeneic B16 mouse melanoma model was performed to determine if targeting CD47 as monotherapy or in combination with anti-PD-1 impacted tumor burden. Cytotoxic (CD8+) T cells from Pmel-1 transgenic mice were used for T cell activation, cytotoxic T lymphocyte, and cellular bioenergetic assays. Single-cell RNA-sequencing, ELISA, and flow cytometry was performed on peripheral blood mononuclear cells and plasma of melanoma patients receiving anti-PD-1 therapy to examine CD47/TSP1 expression. RESULTS Human malignant melanoma tissue had increased CD47 and TSP1 expression within the tumor microenvironment compared with benign tissue. Due to the negative implications CD47/TSP1 can have on antitumor immune responses, we targeted CD47 in a melanoma model and observed a decrease in tumor burden due to increased tumor oxygen saturation and granzyme B secreting CD8+ T cells compared with wild-type tumors. Additionally, Pmel-1 CD8+ T cells exposed to TSP1 had reduced activation, proliferation, and effector function against B16 melanoma cells. Targeting CD47 allowed CD8+ T cells to overcome this TSP1 interaction to sustain these functions. TSP1 exposed CD8+ T cells have a decreased rate of glycolysis; however, targeting CD47 restored glycolysis when CD8+ T cells were exposed to TSP1, suggesting CD47 mediated metabolic reprogramming of T cells. Additionally, non-responding patients to anti-PD-1 therapy had increased T cells expressing CD47 and circulating levels of TSP1 compared with responding patients. Since CD47/TSP1 signaling axis negatively impacts CD8+ T cells and non-responding patients to anti-PD-1 therapy have increased CD47/TSP1 expression, we targeted CD47 in combination with anti-PD-1 in a melanoma model. Targeting CD47 in combination with anti-PD-1 treatment further decreased tumor burden compared with monotherapy and control. CONCLUSION CD47/TSP1 expression could serve as a marker to predict patient response to immune checkpoint blockade treatment, and targeting this pathway may preserve T cell activation, proliferation, effector function, and bioenergetics to reduce tumor burden as a monotherapy or in combination with anti-PD-1.
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Affiliation(s)
- Elizabeth R Stirling
- Department of Cancer Biology, Wake Forest Univerisity School of Medicine, Winston-Salem, North Carolina, USA
| | - Masaki Terabe
- Neuro-Oncology Branch, National Cancer Institute, Bethesda, Maryland, USA
| | - Adam S Wilson
- Department of Surgery, Wake Forest Univerisity School of Medicine, Winston-Salem, North Carolina, USA
| | - Mitra Kooshki
- Department of Hematology & Oncology, Wake Forest University School of Medicine, Winston-Salem, North Carolina, USA
- Department of Radiation Oncology, Wake Forest University School of Medicine, WInston-Salem, North Carolina, USA
| | - Liliya M Yamaleyeva
- Department of Surgery, Wake Forest Univerisity School of Medicine, Winston-Salem, North Carolina, USA
| | - Martha A Alexander-Miller
- Department of Microbiology & Immunology, Wake Forest University School of Medicine, Winston-Salem, North Carolina, USA
| | - Wei Zhang
- Department of Cancer Biology, Wake Forest Univerisity School of Medicine, Winston-Salem, North Carolina, USA
- Atrium Health Wake Forest Baptist Medical Center, Comprehensive Cancer Center, Winston-Salem, North Carolina, USA
| | - Lance D Miller
- Department of Cancer Biology, Wake Forest Univerisity School of Medicine, Winston-Salem, North Carolina, USA
- Atrium Health Wake Forest Baptist Medical Center, Comprehensive Cancer Center, Winston-Salem, North Carolina, USA
| | - Pierre L Triozzi
- Department of Cancer Biology, Wake Forest Univerisity School of Medicine, Winston-Salem, North Carolina, USA
- Department of Hematology & Oncology, Wake Forest University School of Medicine, Winston-Salem, North Carolina, USA
- Atrium Health Wake Forest Baptist Medical Center, Comprehensive Cancer Center, Winston-Salem, North Carolina, USA
| | - David R Soto-Pantoja
- Department of Cancer Biology, Wake Forest Univerisity School of Medicine, Winston-Salem, North Carolina, USA
- Department of Surgery, Wake Forest Univerisity School of Medicine, Winston-Salem, North Carolina, USA
- Department of Radiation Oncology, Wake Forest University School of Medicine, WInston-Salem, North Carolina, USA
- Atrium Health Wake Forest Baptist Medical Center, Comprehensive Cancer Center, Winston-Salem, North Carolina, USA
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18
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Kerk SA, Lin L, Myers AL, Sutton DJ, Andren A, Sajjakulnukit P, Zhang L, Zhang Y, Jiménez JA, Nelson BS, Chen B, Robinson A, Thurston G, Kemp SB, Steele NG, Hoffman MT, Wen HJ, Long D, Ackenhusen SE, Ramos J, Gao X, Nwosu ZC, Galban S, Halbrook CJ, Lombard DB, Piwnica-Worms DR, Ying H, Pasca di Magliano M, Crawford HC, Shah YM, Lyssiotis CA. Metabolic requirement for GOT2 in pancreatic cancer depends on environmental context. eLife 2022; 11:e73245. [PMID: 35815941 PMCID: PMC9328765 DOI: 10.7554/elife.73245] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2021] [Accepted: 07/09/2022] [Indexed: 12/24/2022] Open
Abstract
Mitochondrial glutamate-oxaloacetate transaminase 2 (GOT2) is part of the malate-aspartate shuttle, a mechanism by which cells transfer reducing equivalents from the cytosol to the mitochondria. GOT2 is a key component of mutant KRAS (KRAS*)-mediated rewiring of glutamine metabolism in pancreatic ductal adenocarcinoma (PDA). Here, we demonstrate that the loss of GOT2 disturbs redox homeostasis and halts proliferation of PDA cells in vitro. GOT2 knockdown (KD) in PDA cell lines in vitro induced NADH accumulation, decreased Asp and α-ketoglutarate (αKG) production, stalled glycolysis, disrupted the TCA cycle, and impaired proliferation. Oxidizing NADH through chemical or genetic means resolved the redox imbalance induced by GOT2 KD, permitting sustained proliferation. Despite a strong in vitro inhibitory phenotype, loss of GOT2 had no effect on tumor growth in xenograft PDA or autochthonous mouse models. We show that cancer-associated fibroblasts (CAFs), a major component of the pancreatic tumor microenvironment (TME), release the redox active metabolite pyruvate, and culturing GOT2 KD cells in CAF conditioned media (CM) rescued proliferation in vitro. Furthermore, blocking pyruvate import or pyruvate-to-lactate reduction prevented rescue of GOT2 KD in vitro by exogenous pyruvate or CAF CM. However, these interventions failed to sensitize xenografts to GOT2 KD in vivo, demonstrating the remarkable plasticity and differential metabolism deployed by PDA cells in vitro and in vivo. This emphasizes how the environmental context of distinct pre-clinical models impacts both cell-intrinsic metabolic rewiring and metabolic crosstalk with the TME.
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Affiliation(s)
- Samuel A Kerk
- Doctoral Program in Cancer Biology, University of Michigan-Ann ArborAnn ArborUnited States
| | - Lin Lin
- Department of Molecular and Integrative Physiology, University of Michigan-Ann ArborAnn ArborUnited States
| | - Amy L Myers
- Department of Molecular and Integrative Physiology, University of Michigan-Ann ArborAnn ArborUnited States
| | - Damien J Sutton
- Department of Molecular and Integrative Physiology, University of Michigan-Ann ArborAnn ArborUnited States
| | - Anthony Andren
- Department of Molecular and Integrative Physiology, University of Michigan-Ann ArborAnn ArborUnited States
| | - Peter Sajjakulnukit
- Doctoral Program in Cancer Biology, University of Michigan-Ann ArborAnn ArborUnited States
| | - Li Zhang
- Department of Molecular and Integrative Physiology, University of Michigan-Ann ArborAnn ArborUnited States
| | - Yaqing Zhang
- Department of Surgery, University of Michigan-Ann ArborAnn ArborUnited States
| | - Jennifer A Jiménez
- Doctoral Program in Cancer Biology, University of Michigan-Ann ArborAnn ArborUnited States
| | - Barbara S Nelson
- Doctoral Program in Cancer Biology, University of Michigan-Ann ArborAnn ArborUnited States
- Department of Molecular and Integrative Physiology, University of Michigan-Ann ArborAnn ArborUnited States
| | - Brandon Chen
- Department of Molecular and Integrative Physiology, University of Michigan-Ann ArborAnn ArborUnited States
| | - Anthony Robinson
- Department of Cell and Developmental Biology, University of Michigan-Ann ArborAnn ArborUnited States
| | - Galloway Thurston
- Department of Molecular and Integrative Physiology, University of Michigan-Ann ArborAnn ArborUnited States
| | - Samantha B Kemp
- Molecular and Cellular Pathology Graduate Program, University of Michigan-Ann ArborAnn ArborUnited States
| | - Nina G Steele
- Department of Cell and Developmental Biology, University of Michigan-Ann ArborAnn ArborUnited States
| | - Megan T Hoffman
- Department of Molecular and Integrative Physiology, University of Michigan-Ann ArborAnn ArborUnited States
| | - Hui-Ju Wen
- Department of Molecular and Integrative Physiology, University of Michigan-Ann ArborAnn ArborUnited States
| | - Daniel Long
- Department of Molecular and Integrative Physiology, University of Michigan-Ann ArborAnn ArborUnited States
| | - Sarah E Ackenhusen
- Program in Chemical Biology, University of Michigan-Ann ArborAnn ArborUnited States
| | - Johanna Ramos
- Department of Molecular and Integrative Physiology, University of Michigan-Ann ArborAnn ArborUnited States
| | - Xiaohua Gao
- Department of Molecular and Integrative Physiology, University of Michigan-Ann ArborAnn ArborUnited States
| | - Zeribe C Nwosu
- Department of Molecular and Integrative Physiology, University of Michigan-Ann ArborAnn ArborUnited States
| | - Stefanie Galban
- Department of Radiology, University of MichiganAnn ArborUnited States
- Rogel Cancer Center, University of MichiganAnn ArborUnited States
| | - Christopher J Halbrook
- Department of Molecular and Integrative Physiology, University of Michigan-Ann ArborAnn ArborUnited States
| | - David B Lombard
- Department of Pathology and Institute of Gerontology, University of MichiganAnn ArborUnited States
| | - David R Piwnica-Worms
- Department of Cancer Systems Imaging, University of Texas MD Anderson Cancer CenterHoustonUnited States
| | - Haoqiang Ying
- Department of Molecular and Cellular Oncology, University of Texas MD Anderson Cancer CenterHoustonUnited States
| | - Marina Pasca di Magliano
- Department of Surgery, University of Michigan-Ann ArborAnn ArborUnited States
- Rogel Cancer Center, University of MichiganAnn ArborUnited States
| | - Howard C Crawford
- Department of Molecular and Integrative Physiology, University of Michigan-Ann ArborAnn ArborUnited States
- Rogel Cancer Center, University of MichiganAnn ArborUnited States
| | - Yatrik M Shah
- Department of Molecular and Integrative Physiology, University of Michigan-Ann ArborAnn ArborUnited States
- Rogel Cancer Center, University of MichiganAnn ArborUnited States
- Department of Internal Medicine, Division of Gastroenterology and Hepatology, University of MichiganAnn ArborUnited States
| | - Costas A Lyssiotis
- Doctoral Program in Cancer Biology, University of Michigan-Ann ArborAnn ArborUnited States
- Department of Molecular and Integrative Physiology, University of Michigan-Ann ArborAnn ArborUnited States
- Rogel Cancer Center, University of MichiganAnn ArborUnited States
- Department of Internal Medicine, Division of Gastroenterology and Hepatology, University of MichiganAnn ArborUnited States
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19
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Labadie J, Swafford B, DePena M, Tietje K, Page R, Patterson-Kane J. Cohort profile: The Golden Retriever Lifetime Study (GRLS). PLoS One 2022; 17:e0269425. [PMID: 35679242 PMCID: PMC9182714 DOI: 10.1371/journal.pone.0269425] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2021] [Accepted: 05/20/2022] [Indexed: 11/18/2022] Open
Abstract
The aim of this article is to provide a detailed description of the Golden Retriever Lifetime Study (GRLS), a prospective cohort study investigating nutritional, environmental, lifestyle, and genetic risk factors for cancer and other common diseases in dogs. Primary outcomes of interest include hemangiosarcoma, lymphoma, osteosarcoma, and high-grade mast cell tumors. Secondary outcomes of interest include other cancers, hypothyroidism, epilepsy, atopy, otitis externa, hip dysplasia, heart failure, and renal failure. A total of 3,044 United States Golden Retrievers aged 6 months to 2 years completed baseline enrollment from June 2012 to April 2015. As of May 31, 2021, 2,251 dogs remain engaged in the study, 352 have died, and 441 are lost to follow-up. Extensive annual questionnaires completed by owners and veterinarians gather information about lifestyle, environmental exposures, physical activity, reproductive history, behavior, diet, medications, and diagnoses. Dogs also have annual veterinary examinations and biospecimen collection (blood, serum, hair, nails, feces, urine) for biobanking. Additional reporting, including histology and tumor biobanking, is conducted for any malignancies or deaths. When an animal dies, full medical records are obtained, and necropsies are requested at owner discretion. Full or partial necropsies have been performed on 218 dogs. Questionnaire data are freely available to researchers with approved credentials who agree to a data use agreement. In addition, researchers can submit proposals to utilize biospecimens or obtain additional data.
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Affiliation(s)
- Julia Labadie
- Scientific Programs Department, Morris Animal Foundation, Denver, Colorado, United States of America
- * E-mail:
| | - Brenna Swafford
- Scientific Programs Department, Morris Animal Foundation, Denver, Colorado, United States of America
| | - Mara DePena
- Scientific Programs Department, Morris Animal Foundation, Denver, Colorado, United States of America
| | - Kathy Tietje
- Scientific Programs Department, Morris Animal Foundation, Denver, Colorado, United States of America
| | - Rodney Page
- Flint Animal Cancer Center, Colorado State University, Fort Collins, Colorado, United States of America
| | - Janet Patterson-Kane
- Scientific Programs Department, Morris Animal Foundation, Denver, Colorado, United States of America
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20
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Hwang M, Canzoniero JV, Rosner S, Zhang G, White JR, Belcaid Z, Cherry C, Balan A, Pereira G, Curry A, Niknafs N, Zhang J, Smith KN, Sivapalan L, Chaft JE, Reuss JE, Marrone K, Murray JC, Li QK, Lam V, Levy BP, Hann C, Velculescu VE, Brahmer JR, Forde PM, Seiwert T, Anagnostou V. Peripheral blood immune cell dynamics reflect antitumor immune responses and predict clinical response to immunotherapy. J Immunother Cancer 2022; 10:e004688. [PMID: 35688557 PMCID: PMC9189831 DOI: 10.1136/jitc-2022-004688] [Citation(s) in RCA: 32] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/09/2022] [Indexed: 12/18/2022] Open
Abstract
BACKGROUND Despite treatment advancements with immunotherapy, our understanding of response relies on tissue-based, static tumor features such as tumor mutation burden (TMB) and programmed death-ligand 1 (PD-L1) expression. These approaches are limited in capturing the plasticity of tumor-immune system interactions under selective pressure of immune checkpoint blockade and predicting therapeutic response and long-term outcomes. Here, we investigate the relationship between serial assessment of peripheral blood cell counts and tumor burden dynamics in the context of an evolving tumor ecosystem during immune checkpoint blockade. METHODS Using machine learning, we integrated dynamics in peripheral blood immune cell subsets, including neutrophil-lymphocyte ratio (NLR), from 239 patients with metastatic non-small cell lung cancer (NSCLC) and predicted clinical outcome with immune checkpoint blockade. We then sought to interpret NLR dynamics in the context of transcriptomic and T cell repertoire trajectories for 26 patients with early stage NSCLC who received neoadjuvant immune checkpoint blockade. We further determined the relationship between NLR dynamics, pathologic response and circulating tumor DNA (ctDNA) clearance. RESULTS Integrated dynamics of peripheral blood cell counts, predominantly NLR dynamics and changes in eosinophil levels, predicted clinical outcome, outperforming both TMB and PD-L1 expression. As early changes in NLR were a key predictor of response, we linked NLR dynamics with serial RNA sequencing deconvolution and T cell receptor sequencing to investigate differential tumor microenvironment reshaping during therapy for patients with reduction in peripheral NLR. Reductions in NLR were associated with induction of interferon-γ responses driving the expression of antigen presentation and proinflammatory gene sets coupled with reshaping of the intratumoral T cell repertoire. In addition, NLR dynamics reflected tumor regression assessed by pathological responses and complemented ctDNA kinetics in predicting long-term outcome. Elevated peripheral eosinophil levels during immune checkpoint blockade were correlated with therapeutic response in both metastatic and early stage cohorts. CONCLUSIONS Our findings suggest that early dynamics in peripheral blood immune cell subsets reflect changes in the tumor microenvironment and capture antitumor immune responses, ultimately reflecting clinical outcomes with immune checkpoint blockade.
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Affiliation(s)
- Michael Hwang
- The Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Jenna Vanliere Canzoniero
- The Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Samuel Rosner
- The Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Guangfan Zhang
- The Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - James R White
- The Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Zineb Belcaid
- The Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Christopher Cherry
- The Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Archana Balan
- The Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Gavin Pereira
- The Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Alexandria Curry
- The Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Noushin Niknafs
- The Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Jiajia Zhang
- The Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- The Bloomberg-Kimmel Institute for Cancer Immunotherapy, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Kellie N Smith
- The Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- The Bloomberg-Kimmel Institute for Cancer Immunotherapy, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Lavanya Sivapalan
- The Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Jamie E Chaft
- Thoracic Oncology Service, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Joshua E Reuss
- Georgetown Lombardi Comprehensive Cancer Center, Washington, DC, USA
| | - Kristen Marrone
- The Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Joseph C Murray
- The Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Qing Kay Li
- The Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Vincent Lam
- The Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Benjamin P Levy
- The Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Christine Hann
- The Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Victor E Velculescu
- The Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Julie R Brahmer
- The Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- The Bloomberg-Kimmel Institute for Cancer Immunotherapy, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Patrick M Forde
- The Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- The Bloomberg-Kimmel Institute for Cancer Immunotherapy, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Tanguy Seiwert
- The Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- The Bloomberg-Kimmel Institute for Cancer Immunotherapy, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Valsamo Anagnostou
- The Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- The Bloomberg-Kimmel Institute for Cancer Immunotherapy, Johns Hopkins University School of Medicine, Baltimore, MD, USA
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21
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Brooks E, Islam JY, Perdue DG, Petersen E, Camacho-Rivera M, Kennedy C, Rogers CR. The Black Panther, Masculinity Barriers to Medical Care, and Colorectal Cancer Screening Intention Among Unscreened American Indian/Alaska Native, Black, and White Men. Front Public Health 2022; 10:814596. [PMID: 35462819 PMCID: PMC9019156 DOI: 10.3389/fpubh.2022.814596] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2021] [Accepted: 03/15/2022] [Indexed: 12/24/2022] Open
Abstract
Objective To determine if masculinity barriers to medical care and the death from colorectal cancer (CRC) of actor Chadwick Boseman (The Black Panther) influenced CRC early-detection screening intent among unscreened American Indian/Alaska Native (AIAN) and Non-Hispanic-Black (Black) men compared with Non-Hispanic-White (White) men. Methods Using a consumer-panel, we surveyed U.S. men aged 18-75 years (N = 895) using the 24-item Masculinity Barriers to Medical Care (MBMC) scale. We calculated the median score to create binary exposures to evaluate associations with CRC screening intent and conducted multivariable logistic regression to evaluate independent associations stratified by race/ethnicity. Results Overall, Black respondents were most likely to have a high MBMC score (55%) compared to White (44%) and AIAN (51%) men (p = 0.043). AIAN men were least likely to report CRC screening intent (51.1%) compared with Black (68%) and White men (64%) (p < 0.001). Black men who reported the recent death of Chadwick Boseman increased their awareness of CRC were more likely (78%) to report intention to screen for CRC compared to those who did not (56%) (p < 0.001). Black men who exhibited more masculinity-related barriers to care were more likely to intend to screen for CRC (OR: 1.76, 95% CI: 0.98-3.16) than their counterparts, as were Black men who reported no impact of Boseman's death on their CRC awareness (aOR: 2.96, 95% CI: 1.13-7.67). Conversely, among AIAN men, those who exhibited more masculinity-related barriers to care were less likely to have CRC screening intent (aOR: 0.47, 95% CI: 0.27-0.82) compared with their counterparts. Conclusions Masculinity barriers to medical care play a significant role in intention to screen for CRC. While Black men were most likely to state that The Black Panther's death increased their awareness of CRC, it did not appear to modify the role of masculine barriers in CRC screening intention as expected. Further research is warranted to better understand how masculine barriers combined with celebrity-driven health-promotion interventions influence the uptake of early-detection screening for CRC. Impact Our study provides formative data to develop behavioral interventions focused on improving CRC screening completion among diverse men.
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Affiliation(s)
- Ellen Brooks
- Department of Family and Preventive Medicine, University of Utah School of Medicine, Salt Lake City, UT, United States
| | - Jessica Y. Islam
- Center for Immunization and Infections in Cancer, Cancer Epidemiology Program, H. Lee Moffitt Cancer and Research Institute, Tampa, FL, United States
| | | | - Ethan Petersen
- Department of Family and Preventive Medicine, University of Utah School of Medicine, Salt Lake City, UT, United States
| | - Marlene Camacho-Rivera
- Department of Community Health Sciences, SUNY Downstate Health Sciences University, Brooklyn, NY, United States
| | - Carson Kennedy
- Department of Family and Preventive Medicine, University of Utah School of Medicine, Salt Lake City, UT, United States
| | - Charles R. Rogers
- Department of Family and Preventive Medicine, University of Utah School of Medicine, Salt Lake City, UT, United States
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22
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Perez J, Twigg CAI, Guan W, Thomas SN. Proteomic Analysis Reveals Low-Dose PARP Inhibitor-Induced Differential Protein Expression in BRCA1-Mutated High-Grade Serous Ovarian Cancer Cells. J Am Soc Mass Spectrom 2022; 33:242-250. [PMID: 34958553 PMCID: PMC8824432 DOI: 10.1021/jasms.1c00215] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/13/2021] [Revised: 10/12/2021] [Accepted: 10/12/2021] [Indexed: 06/14/2023]
Abstract
High-grade serous ovarian cancer (HGSOC) is the most common form of ovarian cancer diagnosed in patients worldwide. Patients with BRCA1/2-mutated HGSOC have benefited from targeted treatments such as poly(ADP-ribose) polymerase inhibitors (PARPi). Despite the initial success of PARPi-based ovarian cancer treatment regimens, approximately 70% of patients with ovarian cancer relapse and the 5-year survival rate remains at 30%. PARPi exhibit variable treatment efficacy and toxicity profiles. Furthermore, the off-target effects of PARP inhibition have not yet been fully elucidated, warranting further study of these classes of molecules in the context of HGSOC treatment. Highly reproducible quantitative mass spectrometry-based proteomic workflows have been developed for the analysis of tumor tissues and cell lines. To detect the off-target effects of PARP inhibition, we conducted a quantitative mass spectrometry-based proteomic analysis of a BRCA1-mutated HGSOC cell line treated with low doses of two PARPi, niraparib and rucaparib. Our goal was to identify PARPi-induced protein signaling pathway alterations toward a more comprehensive elucidation of the mechanism of action of PARPi beyond the DNA damage response pathway. A significant enrichment of nuclear and nucleoplasm proteins that are involved in protein binding was observed in the rucaparib-treated cells. Shared upregulated proteins between niraparib and rucaparib treatment demonstrated RNA II pol promoter-associated pathway enrichment in transcription regulation. Pathway enrichment analyses also revealed off-target effects in the Golgi apparatus and the ER. The results from our mass spectrometry-based proteomic analysis highlights notable off-target effects produced by low-dose treatment of BRCA1-mutated HGSOC cells treated with rucaparib or niraparib.
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Affiliation(s)
- Jesenia
M. Perez
- Microbiology,
Immunology, and Cancer Biology Graduate Program, University of Minnesota School of Medicine, Minneapolis, Minnesota 55455, United States
| | - Carly A. I. Twigg
- Department
of Laboratory Medicine and Pathology, University
of Minnesota School of Medicine, Minneapolis, Minnesota 55455, United States
| | - Weihua Guan
- Division
of Biostatistics, University of Minnesota
School of Public Health, Minneapolis, Minnesota 55455, United States
| | - Stefani N. Thomas
- Department
of Laboratory Medicine and Pathology, University
of Minnesota School of Medicine, Minneapolis, Minnesota 55455, United States
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23
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Sun X, Bieber JM, Hammerlindl H, Chalkley RJ, Li KH, Burlingame AL, Jacobson MP, Wu LF, Altschuler SJ. Modulating environmental signals to reveal mechanisms and vulnerabilities of cancer persisters. Sci Adv 2022; 8:eabi7711. [PMID: 35089788 PMCID: PMC8797778 DOI: 10.1126/sciadv.abi7711] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/30/2021] [Accepted: 12/08/2021] [Indexed: 06/14/2023]
Abstract
Cancer persister cells are able to survive otherwise lethal doses of drugs through nongenetic mechanisms, which can lead to cancer regrowth and drug resistance. The broad spectrum of molecular differences observed between persisters and their treatment-naïve counterparts makes it challenging to identify causal mechanisms underlying persistence. Here, we modulate environmental signals to identify cellular mechanisms that promote the emergence of persisters and to pinpoint actionable vulnerabilities that eliminate them. We found that interferon-γ (IFNγ) can induce a pro-persistence signal that can be specifically eliminated by inhibition of type I protein arginine methyltransferase (PRMT) (PRMTi). Mechanistic investigation revealed that signal transducer and activator of transcription 1 (STAT1) is a key component connecting IFNγ's pro-persistence and PRMTi's antipersistence effects, suggesting a previously unknown application of PRMTi to target persisters in settings with high STAT1 expression. Modulating environmental signals can accelerate the identification of mechanisms that promote and eliminate cancer persistence.
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Affiliation(s)
| | | | | | | | | | | | | | - Lani F. Wu
- Corresponding author. (S.J.A.); (L.F.W.)
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24
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Kim PK, Halbrook CJ, Kerk SA, Radyk M, Wisner S, Kremer DM, Sajjakulnukit P, Andren A, Hou SW, Trivedi A, Thurston G, Anand A, Yan L, Salamanca-Cardona L, Welling SD, Zhang L, Pratt MR, Keshari KR, Ying H, Lyssiotis CA. Hyaluronic acid fuels pancreatic cancer cell growth. eLife 2021; 10:e62645. [PMID: 34951587 PMCID: PMC8730721 DOI: 10.7554/elife.62645] [Citation(s) in RCA: 36] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2020] [Accepted: 12/21/2021] [Indexed: 11/13/2022] Open
Abstract
Rewired metabolism is a hallmark of pancreatic ductal adenocarcinomas (PDA). Previously, we demonstrated that PDA cells enhance glycosylation precursor biogenesis through the hexosamine biosynthetic pathway (HBP) via activation of the rate limiting enzyme, glutamine-fructose 6-phosphate amidotransferase 1 (GFAT1). Here, we genetically ablated GFAT1 in human PDA cell lines, which completely blocked proliferation in vitro and led to cell death. In contrast, GFAT1 knockout did not preclude the growth of human tumor xenografts in mice, suggesting that cancer cells can maintain fidelity of glycosylation precursor pools by scavenging nutrients from the tumor microenvironment. We found that hyaluronic acid (HA), an abundant carbohydrate polymer in pancreatic tumors composed of repeating N-acetyl-glucosamine (GlcNAc) and glucuronic acid sugars, can bypass GFAT1 to refuel the HBP via the GlcNAc salvage pathway. Together, these data show HA can serve as a nutrient fueling PDA metabolism beyond its previously appreciated structural and signaling roles.
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Affiliation(s)
- Peter K Kim
- Doctoral Program in Cancer Biology, University of MichiganAnn ArborUnited States
- Department of Molecular & Integrative Physiology, University of MichiganAnn ArborUnited States
| | - Christopher J Halbrook
- Department of Molecular & Integrative Physiology, University of MichiganAnn ArborUnited States
| | - Samuel A Kerk
- Doctoral Program in Cancer Biology, University of MichiganAnn ArborUnited States
- Department of Molecular & Integrative Physiology, University of MichiganAnn ArborUnited States
| | - Megan Radyk
- Department of Molecular & Integrative Physiology, University of MichiganAnn ArborUnited States
| | - Stephanie Wisner
- Department of Molecular & Integrative Physiology, University of MichiganAnn ArborUnited States
| | - Daniel M Kremer
- Department of Molecular & Integrative Physiology, University of MichiganAnn ArborUnited States
- Program in Chemical Biology, University of MichiganAnn ArborUnited States
| | - Peter Sajjakulnukit
- Doctoral Program in Cancer Biology, University of MichiganAnn ArborUnited States
- Department of Molecular & Integrative Physiology, University of MichiganAnn ArborUnited States
| | - Anthony Andren
- Department of Molecular & Integrative Physiology, University of MichiganAnn ArborUnited States
| | - Sean W Hou
- Department of Molecular & Integrative Physiology, University of MichiganAnn ArborUnited States
| | - Ayush Trivedi
- Department of Molecular & Integrative Physiology, University of MichiganAnn ArborUnited States
| | - Galloway Thurston
- Department of Molecular & Integrative Physiology, University of MichiganAnn ArborUnited States
| | - Abhinav Anand
- Department of Molecular & Integrative Physiology, University of MichiganAnn ArborUnited States
| | - Liang Yan
- Department of Molecular and Cellular Oncology, University of Texas MD Anderson Cancer CenterHoustonUnited States
| | | | - Samuel D Welling
- Department of Molecular & Integrative Physiology, University of MichiganAnn ArborUnited States
| | - Li Zhang
- Department of Molecular & Integrative Physiology, University of MichiganAnn ArborUnited States
| | - Matthew R Pratt
- Department of Chemistry, University of Southern CaliforniaLos AngelesUnited States
- Department of Biological Sciences, University of Southern CaliforniaLos AngelesUnited States
| | - Kayvan R Keshari
- Department of Radiology, Memorial Sloan Kettering Cancer CenterNew York CityUnited States
- Molecular Pharmacology Program, Memorial Sloan Kettering Cancer CenterNew York CityUnited States
| | - Haoqiang Ying
- Department of Molecular and Cellular Oncology, University of Texas MD Anderson Cancer CenterHoustonUnited States
| | - Costas A Lyssiotis
- Department of Molecular & Integrative Physiology, University of MichiganAnn ArborUnited States
- Department of Internal Medicine, Division of Gastroenterology and Hepatology, University of MichiganAnn ArborUnited States
- Rogel Cancer Center, University of MichiganAnn ArborUnited States
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25
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Rogers CR, Brooks E, Curtin K, De Vera MA, Qeadan F, Rogers TN, Petersen E, Gallagher P, Pesmen C, Johnson W, Henley C, Hickman W, Newcomb E, Korous KM, Handley MA. Protocol for #iBeatCRC: a community-based intervention to increase early-onset colorectal cancer awareness using a sequential explanatory mixed-methods approach. BMJ Open 2021; 11:e048959. [PMID: 34862279 PMCID: PMC8647393 DOI: 10.1136/bmjopen-2021-048959] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
INTRODUCTION Th last two decades have seen a twofold increase in colorectal cancer (CRC) incidence among individuals under the recommended screening age of 50 years. Although the origin of this early-onset CRC (EOCRC) spike remains unknown, prior studies have reported that EOCRC harbours a distinct molecular and clinical phenotype in younger individuals. The sharp increase in EOCRC incidence rates may be attributable to a complex interplay of factors, including race; lifestyle; and ecological, sociodemographic and geographical factors. However, more research that address psychosocial experiences and accounts for lifestyle-related behaviours before, during and after an EOCRC diagnosis are warranted. This study aims to develop and pilot test a theory-driven, community-based intervention to increase awareness of EOCRC, reduce its associated risk factors and improve early detection among adults aged 18-49 years. METHODS AND ANALYSIS Guided by the Behaviour Change Wheel, we will use a multistage mixed-methods study design. We will pilot a sequential mixed-methods intervention study as follows: (1) First, we will analyse linked quantitative data from the Utah Cancer Registry and National Cancer Institute Surveillance, Epidemiology and End Results registry, linked to state-wide demographic and vital records in the Utah Population Database to identify EOCRC hotspots in Utah by examining the EOCRC incidence and survival variance explained by personal and county-level factors. (2) Next, we will conduct one-on-one interviews with 20 EOCRC survivors residing in EOCRC hotspots to ascertain psychosocial and lifestyle challenges that accompany an EOCRC diagnosis. (3) Finally, we will consider existing evidence-based approaches, our integrated results (quantitative +qualitative) and community action board input to design a community-based intervention to increase EOCRC awareness that can feasibly be delivered by means of outdoor mass media, and via social media. We will pilot the multicomponent media campaign with a quasiexperimental design among 17 EOCRC hotspot residents and 17 EOCRC 'coldspot' residents. ETHICS AND DISSEMINATION Ethics approval was obtained from the University of Utah Institutional Review Board (IRB_00138357). Signed informed consent will be obtained from all participants prior to any data collection. Study results will be disseminated through CRC community blogs, targeted infographics, conference presentations at national and international professional conferences and publications in peer-reviewed journals. Final intervention-specific data will be available on reasonable request from the corresponding author. TRIAL REGISTRATION NUMBER NCT04715074.
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Affiliation(s)
- Charles R Rogers
- Department of Family and Preventive Medicine, University of Utah School of Medicine, Salt Lake City, Utah, USA
| | - Ellen Brooks
- Department of Family and Preventive Medicine, University of Utah School of Medicine, Salt Lake City, Utah, USA
| | - Karen Curtin
- Internal Medicine, University of Utah School of Medicine, Salt Lake City, Utah, USA
| | - Mary A De Vera
- Faculty of Pharmaceutical Sciences, University of British Columbia, Vancouver, British Columbia, Canada
| | - Fares Qeadan
- Department of Family and Preventive Medicine, University of Utah School of Medicine, Salt Lake City, Utah, USA
| | - Tiana N Rogers
- Sorenson Impact Center, University of Utah Eccles School of Business, Salt Lake City, Utah, USA
| | - Ethan Petersen
- Department of Family and Preventive Medicine, University of Utah School of Medicine, Salt Lake City, Utah, USA
| | | | - Curt Pesmen
- BoCo Media, Boulder, Colorado, USA
- Fight Colorectal Cancer, Alexandria, Virginia, USA
| | | | | | | | | | - Kevin M Korous
- Department of Family and Preventive Medicine, University of Utah School of Medicine, Salt Lake City, Utah, USA
| | - Margaret A Handley
- Epidemiology and Biostatistics, University of California San Francisco, San Francisco, California, USA
- Medicine, University of California San Francisco, San Francisco, California, USA
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26
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Jin N, Keam B, Cho J, Lee MJ, Kim HR, Torosyan H, Jura N, Ng PK, Mills GB, Li H, Zeng Y, Barbash Z, Tarcic G, Kang H, Bauman JE, Kim MO, VanLandingham NK, Swaney DL, Krogan NJ, Johnson DE, Grandis JR. Therapeutic implications of activating noncanonical PIK3CA mutations in head and neck squamous cell carcinoma. J Clin Invest 2021; 131:e150335. [PMID: 34779417 PMCID: PMC8592538 DOI: 10.1172/jci150335] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2021] [Accepted: 09/21/2021] [Indexed: 12/16/2022] Open
Abstract
Alpelisib selectively inhibits the p110α catalytic subunit of PI3Kα and is approved for treatment of breast cancers harboring canonical PIK3CA mutations. In head and neck squamous cell carcinoma (HNSCC), 63% of PIK3CA mutations occur at canonical hotspots. The oncogenic role of the remaining 37% of PIK3CA noncanonical mutations is incompletely understood. We report a patient with HNSCC with a noncanonical PIK3CA mutation (Q75E) who exhibited a durable (12 months) response to alpelisib in a phase II clinical trial. Characterization of all 32 noncanonical PIK3CA mutations found in HNSCC using several functional and phenotypic assays revealed that the majority (69%) were activating, including Q75E. The oncogenic impact of these mutations was validated in 4 cellular models, demonstrating that their activity was lineage independent. Further, alpelisib exhibited antitumor effects in a xenograft derived from a patient with HNSCC containing an activating noncanonical PIK3CA mutation. Structural analyses revealed plausible mechanisms for the functional phenotypes of the majority of the noncanonical PIK3CA mutations. Collectively, these findings highlight the importance of characterizing the function of noncanonical PIK3CA mutations and suggest that patients with HNSCC whose tumors harbor activating noncanonical PIK3CA mutations may benefit from treatment with PI3Kα inhibitors.
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Affiliation(s)
- Nan Jin
- Department of Otolaryngology, Head and Neck Surgery, University of California San Francisco, San Francisco, California, USA
| | - Bhumsuk Keam
- Department of Internal Medicine, Seoul National University Hospital, Seoul, South Korea
| | - Janice Cho
- Department of Otolaryngology, Head and Neck Surgery, University of California San Francisco, San Francisco, California, USA
| | - Michelle J. Lee
- Department of Otolaryngology, Head and Neck Surgery, University of California San Francisco, San Francisco, California, USA
| | - Hye Ryun Kim
- Division of Medical Oncology, Department of Internal Medicine, Yonsei University College of Medicine, Yonsei Cancer Center, Seoul, South Korea
| | | | - Natalia Jura
- Cardiovascular Research Institute and
- Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, California, USA
| | - Patrick K.S. Ng
- Institute for Personalized Cancer Therapy, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
- The Jackson Laboratory for Genomic Medicine, Farmington, Connecticut, USA
| | - Gordon B. Mills
- Knight Cancer Institute, Oregon Health & Science University, Portland, Oregon, USA
| | - Hua Li
- Department of Otolaryngology, Head and Neck Surgery, University of California San Francisco, San Francisco, California, USA
| | - Yan Zeng
- Department of Otolaryngology, Head and Neck Surgery, University of California San Francisco, San Francisco, California, USA
| | | | | | - Hyunseok Kang
- Department of Medicine, University of California San Francisco, San Francisco, California, USA
| | - Julie E. Bauman
- Department of Medicine, University of Arizona, Tucson, Arizona, USA
| | - Mi-Ok Kim
- Department of Epidemiology and Biostatistics and
| | - Nathan K. VanLandingham
- Department of Otolaryngology, Head and Neck Surgery, University of California San Francisco, San Francisco, California, USA
| | - Danielle L. Swaney
- Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, California, USA
- Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, California, USA
- J. David Gladstone Institutes, San Francisco, California, USA
| | - Nevan J. Krogan
- Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, California, USA
- Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, California, USA
- J. David Gladstone Institutes, San Francisco, California, USA
| | - Daniel E. Johnson
- Department of Otolaryngology, Head and Neck Surgery, University of California San Francisco, San Francisco, California, USA
| | - Jennifer R. Grandis
- Department of Otolaryngology, Head and Neck Surgery, University of California San Francisco, San Francisco, California, USA
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27
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Subudhi SK, Siddiqui BA, Aparicio AM, Yadav SS, Basu S, Chen H, Jindal S, Tidwell RSS, Varma A, Logothetis CJ, Allison JP, Corn PG, Sharma P. Combined CTLA-4 and PD-L1 blockade in patients with chemotherapy-naïve metastatic castration-resistant prostate cancer is associated with increased myeloid and neutrophil immune subsets in the bone microenvironment. J Immunother Cancer 2021; 9:e002919. [PMID: 34663638 PMCID: PMC8524287 DOI: 10.1136/jitc-2021-002919] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/14/2021] [Indexed: 12/18/2022] Open
Abstract
BACKGROUND Immune checkpoint therapy (ICT) has low response rates in patients with metastatic castration-resistant prostate cancer (mCRPC), in part due to few T cells in the tumor microenvironment (TME). Anti-cytotoxic T lymphocyte-associated protein 4 (CTLA-4) promotes intratumoral T cell infiltration but induces upregulation of PD-1 and programmed death ligand-1 (PD-L1) within the prostate TME. Combined anti-CTLA-4 plus anti-PD-1 can partly overcome this adaptive resistance and was recently shown to augment responses in patients with mCRPC with measurable disease. Although bone is the most common site of metastasis in prostate cancer, patients with bone-predominant disease are frequently excluded from trials because they lack measurable disease, which limits assessment of disease progression and tissue sampling. We therefore designed this study to investigate combined ICT in mCRPC to bone. HYPOTHESIS Combined anti-CTLA-4 (tremelimumab) plus anti-PD-L1 (durvalumab) is safe and well tolerated in patients with chemotherapy-naïve mCRPC to bone. PATIENTS AND METHODS In this single-arm pilot study, men with chemotherapy-naïve mCRPC to bone received tremelimumab (75 mg intravenous) plus durvalumab (1500 mg intravenous) every 4 weeks (up to four doses), followed by durvalumab (1500 mg intravenous) maintenance every 4 weeks (up to nine doses). The primary endpoint was incidence of adverse events. Secondary endpoints included serum prostate-specific antigen (PSA), progression-free survival (PFS), radiographic PFS (rPFS), and maximal PSA decline. RESULTS Twenty-six patients were treated between August 8, 2017 and March 28, 2019. Grade ≥3 treatment-related adverse events (TRAEs) occurred in 11 patients (42%), with no grade 4 or 5 events. TRAEs leading to discontinuation occurred in three patients (12%). PSA decline ≥50% occurred in three patients (12%). Six patients (24%) achieved stable disease for >6 months. At a median follow-up of 43.6 months, median rPFS was 3.7 months (95% CI: 1.9 to 5.7), and median overall survival was 28.1 months (95% CI: 14.5 to 37.3). Post-treatment evaluation of the bone microenvironment revealed transcriptional upregulation in myeloid and neutrophil immune subset signatures and increased expression of inhibitory immune checkpoints. CONCLUSIONS Tremelimumab plus durvalumab was safe and well tolerated in patients with chemotherapy-naïve mCRPC to bone, with potential activity in a small number of patients as measured by rPFS. Combination of CTLA-4 and PD-L1 blockade with therapies targeting the myeloid compartment or other inhibitory immune receptors may be necessary to overcome mechanisms of resistance within prostate bone microenvironment. TRIAL REGISTRATION NUMBER NCT03204812.
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Affiliation(s)
- Sumit K Subudhi
- Department of Genitourinary Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Bilal A Siddiqui
- Department of Genitourinary Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Ana M Aparicio
- Department of Genitourinary Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Shalini S Yadav
- The Immunotherapy Platform, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Sreyashi Basu
- The Immunotherapy Platform, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Hong Chen
- The Immunotherapy Platform, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Sonali Jindal
- The Immunotherapy Platform, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Rebecca S S Tidwell
- Department of Biostatistics, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Ashwin Varma
- Department of Genitourinary Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Christopher J Logothetis
- Department of Genitourinary Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - James P Allison
- The Immunotherapy Platform, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
- Department of Immunology, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Paul G Corn
- Department of Genitourinary Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Padmanee Sharma
- Department of Genitourinary Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
- Department of Immunology, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
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Chauhan PS, Chen K, Babbra RK, Feng W, Pejovic N, Nallicheri A, Harris PK, Dienstbach K, Atkocius A, Maguire L, Qaium F, Szymanski JJ, Baumann BC, Ding L, Cao D, Reimers MA, Kim EH, Smith ZL, Arora VK, Chaudhuri AA. Urine tumor DNA detection of minimal residual disease in muscle-invasive bladder cancer treated with curative-intent radical cystectomy: A cohort study. PLoS Med 2021; 18:e1003732. [PMID: 34464379 PMCID: PMC8407541 DOI: 10.1371/journal.pmed.1003732] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/13/2021] [Accepted: 07/12/2021] [Indexed: 12/21/2022] Open
Abstract
BACKGROUND The standard of care treatment for muscle-invasive bladder cancer (MIBC) is radical cystectomy, which is typically preceded by neoadjuvant chemotherapy. However, the inability to assess minimal residual disease (MRD) noninvasively limits our ability to offer bladder-sparing treatment. Here, we sought to develop a liquid biopsy solution via urine tumor DNA (utDNA) analysis. METHODS AND FINDINGS We applied urine Cancer Personalized Profiling by Deep Sequencing (uCAPP-Seq), a targeted next-generation sequencing (NGS) method for detecting utDNA, to urine cell-free DNA (cfDNA) samples acquired between April 2019 and November 2020 on the day of curative-intent radical cystectomy from 42 patients with localized bladder cancer. The average age of patients was 69 years (range: 50 to 86), of whom 76% (32/42) were male, 64% (27/42) were smokers, and 76% (32/42) had a confirmed diagnosis of MIBC. Among MIBC patients, 59% (19/32) received neoadjuvant chemotherapy. utDNA variant calling was performed noninvasively without prior sequencing of tumor tissue. The overall utDNA level for each patient was represented by the non-silent mutation with the highest variant allele fraction after removing germline variants. Urine was similarly analyzed from 15 healthy adults. utDNA analysis revealed a median utDNA level of 0% in healthy adults and 2.4% in bladder cancer patients. When patients were classified as those who had residual disease detected in their surgical sample (n = 16) compared to those who achieved a pathologic complete response (pCR; n = 26), median utDNA levels were 4.3% vs. 0%, respectively (p = 0.002). Using an optimal utDNA threshold to define MRD detection, positive utDNA MRD detection was highly correlated with the absence of pCR (p < 0.001) with a sensitivity of 81% and specificity of 81%. Leave-one-out cross-validation applied to the prediction of pathologic response based on utDNA MRD detection in our cohort yielded a highly significant accuracy of 81% (p = 0.007). Moreover, utDNA MRD-positive patients exhibited significantly worse progression-free survival (PFS; HR = 7.4; 95% CI: 1.4-38.9; p = 0.02) compared to utDNA MRD-negative patients. Concordance between urine- and tumor-derived mutations, determined in 5 MIBC patients, was 85%. Tumor mutational burden (TMB) in utDNA MRD-positive patients was inferred from the number of non-silent mutations detected in urine cfDNA by applying a linear relationship derived from The Cancer Genome Atlas (TCGA) whole exome sequencing of 409 MIBC tumors. We suggest that about 58% of these patients with high inferred TMB might have been candidates for treatment with early immune checkpoint blockade. Study limitations included an analysis restricted only to single-nucleotide variants (SNVs), survival differences diminished by surgery, and a low number of DNA damage response (DRR) mutations detected after neoadjuvant chemotherapy at the MRD time point. CONCLUSIONS utDNA MRD detection prior to curative-intent radical cystectomy for bladder cancer correlated significantly with pathologic response, which may help select patients for bladder-sparing treatment. utDNA MRD detection also correlated significantly with PFS. Furthermore, utDNA can be used to noninvasively infer TMB, which could facilitate personalized immunotherapy for bladder cancer in the future.
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Affiliation(s)
- Pradeep S. Chauhan
- Division of Cancer Biology, Department of Radiation Oncology, Washington University School of Medicine, St. Louis, Missouri, United States of America
| | - Kevin Chen
- Division of Cancer Biology, Department of Radiation Oncology, Washington University School of Medicine, St. Louis, Missouri, United States of America
| | - Ramandeep K. Babbra
- Division of Cancer Biology, Department of Radiation Oncology, Washington University School of Medicine, St. Louis, Missouri, United States of America
| | - Wenjia Feng
- Division of Cancer Biology, Department of Radiation Oncology, Washington University School of Medicine, St. Louis, Missouri, United States of America
| | - Nadja Pejovic
- Division of Cancer Biology, Department of Radiation Oncology, Washington University School of Medicine, St. Louis, Missouri, United States of America
| | - Armaan Nallicheri
- Division of Cancer Biology, Department of Radiation Oncology, Washington University School of Medicine, St. Louis, Missouri, United States of America
| | - Peter K. Harris
- Division of Cancer Biology, Department of Radiation Oncology, Washington University School of Medicine, St. Louis, Missouri, United States of America
| | - Katherine Dienstbach
- Division of Medical Oncology, Department of Medicine, Washington University School of Medicine, St. Louis, Missouri, United States of America
- Siteman Cancer Center, Barnes Jewish Hospital and Washington University School of Medicine, St. Louis, Missouri, United States of America
| | - Andrew Atkocius
- Division of Medical Oncology, Department of Medicine, Washington University School of Medicine, St. Louis, Missouri, United States of America
- Siteman Cancer Center, Barnes Jewish Hospital and Washington University School of Medicine, St. Louis, Missouri, United States of America
| | - Lenon Maguire
- Division of Medical Oncology, Department of Medicine, Washington University School of Medicine, St. Louis, Missouri, United States of America
- Siteman Cancer Center, Barnes Jewish Hospital and Washington University School of Medicine, St. Louis, Missouri, United States of America
| | - Faridi Qaium
- Division of Cancer Biology, Department of Radiation Oncology, Washington University School of Medicine, St. Louis, Missouri, United States of America
| | - Jeffrey J. Szymanski
- Division of Cancer Biology, Department of Radiation Oncology, Washington University School of Medicine, St. Louis, Missouri, United States of America
| | - Brian C. Baumann
- Division of Cancer Biology, Department of Radiation Oncology, Washington University School of Medicine, St. Louis, Missouri, United States of America
- Siteman Cancer Center, Barnes Jewish Hospital and Washington University School of Medicine, St. Louis, Missouri, United States of America
| | - Li Ding
- Division of Medical Oncology, Department of Medicine, Washington University School of Medicine, St. Louis, Missouri, United States of America
- Siteman Cancer Center, Barnes Jewish Hospital and Washington University School of Medicine, St. Louis, Missouri, United States of America
- Department of Genetics, Washington University School of Medicine, St. Louis, Missouri, United States of America
- McDonnell Genome Institute, Washington University School of Medicine, St. Louis, Missouri, United States of America
- Division of Biology and Biomedical Sciences, Washington University School of Medicine, St. Louis, Missouri, United States of America
| | - Dengfeng Cao
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, Missouri, United States of America
| | - Melissa A. Reimers
- Division of Medical Oncology, Department of Medicine, Washington University School of Medicine, St. Louis, Missouri, United States of America
- Siteman Cancer Center, Barnes Jewish Hospital and Washington University School of Medicine, St. Louis, Missouri, United States of America
| | - Eric H. Kim
- Siteman Cancer Center, Barnes Jewish Hospital and Washington University School of Medicine, St. Louis, Missouri, United States of America
- Division of Urology, Department of Surgery, Washington University School of Medicine, St. Louis, Missouri, United States of America
| | - Zachary L. Smith
- Siteman Cancer Center, Barnes Jewish Hospital and Washington University School of Medicine, St. Louis, Missouri, United States of America
- Division of Urology, Department of Surgery, Washington University School of Medicine, St. Louis, Missouri, United States of America
| | - Vivek K. Arora
- Division of Medical Oncology, Department of Medicine, Washington University School of Medicine, St. Louis, Missouri, United States of America
- Siteman Cancer Center, Barnes Jewish Hospital and Washington University School of Medicine, St. Louis, Missouri, United States of America
| | - Aadel A. Chaudhuri
- Division of Cancer Biology, Department of Radiation Oncology, Washington University School of Medicine, St. Louis, Missouri, United States of America
- Siteman Cancer Center, Barnes Jewish Hospital and Washington University School of Medicine, St. Louis, Missouri, United States of America
- Department of Genetics, Washington University School of Medicine, St. Louis, Missouri, United States of America
- Division of Biology and Biomedical Sciences, Washington University School of Medicine, St. Louis, Missouri, United States of America
- Department of Biomedical Engineering, Washington University School of Medicine, St. Louis, Missouri, United States of America
- Department of Computer Science and Engineering, Washington University in St. Louis, St. Louis, Missouri, United States of America
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Szymanski JJ, Sundby RT, Jones PA, Srihari D, Earland N, Harris PK, Feng W, Qaium F, Lei H, Roberts D, Landeau M, Bell J, Huang Y, Hoffman L, Spencer M, Spraker MB, Ding L, Widemann BC, Shern JF, Hirbe AC, Chaudhuri AA. Cell-free DNA ultra-low-pass whole genome sequencing to distinguish malignant peripheral nerve sheath tumor (MPNST) from its benign precursor lesion: A cross-sectional study. PLoS Med 2021; 18:e1003734. [PMID: 34464388 PMCID: PMC8407545 DOI: 10.1371/journal.pmed.1003734] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/16/2021] [Accepted: 07/14/2021] [Indexed: 12/14/2022] Open
Abstract
BACKGROUND The leading cause of mortality for patients with the neurofibromatosis type 1 (NF1) cancer predisposition syndrome is the development of malignant peripheral nerve sheath tumor (MPNST), an aggressive soft tissue sarcoma. In the setting of NF1, this cancer type frequently arises from within its common and benign precursor, plexiform neurofibroma (PN). Transformation from PN to MPNST is challenging to diagnose due to difficulties in distinguishing cross-sectional imaging results and intralesional heterogeneity resulting in biopsy sampling errors. METHODS AND FINDINGS This multi-institutional study from the National Cancer Institute and Washington University in St. Louis used fragment size analysis and ultra-low-pass whole genome sequencing (ULP-WGS) of plasma cell-free DNA (cfDNA) to distinguish between MPNST and PN in patients with NF1. Following in silico enrichment for short cfDNA fragments and copy number analysis to estimate the fraction of plasma cfDNA originating from tumor (tumor fraction), we developed a noninvasive classifier that differentiates MPNST from PN with 86% pretreatment accuracy (91% specificity, 75% sensitivity) and 89% accuracy on serial analysis (91% specificity, 83% sensitivity). Healthy controls without NF1 (participants = 16, plasma samples = 16), PN (participants = 23, plasma samples = 23), and MPNST (participants = 14, plasma samples = 46) cohorts showed significant differences in tumor fraction in plasma (P = 0.001) as well as cfDNA fragment length (P < 0.001) with MPNST samples harboring shorter fragments and being enriched for tumor-derived cfDNA relative to PN and healthy controls. No other covariates were significant on multivariate logistic regression. Mutational analysis demonstrated focal NF1 copy number loss in PN and MPNST patient plasma but not in healthy controls. Greater genomic instability including alterations associated with malignant transformation (focal copy number gains in chromosome arms 1q, 7p, 8q, 9q, and 17q; focal copy number losses in SUZ12, SMARCA2, CDKN2A/B, and chromosome arms 6p and 9p) was more prominently observed in MPNST plasma. Furthermore, the sum of longest tumor diameters (SLD) visualized by cross-sectional imaging correlated significantly with paired tumor fractions in plasma from MPNST patients (r = 0.39, P = 0.024). On serial analysis, tumor fraction levels in plasma dynamically correlated with treatment response to therapy and minimal residual disease (MRD) detection before relapse. Study limitations include a modest MPNST sample size despite accrual from 2 major referral centers for this rare malignancy, and lack of uniform treatment and imaging protocols representing a real-world cohort. CONCLUSIONS Tumor fraction levels derived from cfDNA fragment size and copy number alteration analysis of plasma cfDNA using ULP-WGS significantly correlated with MPNST tumor burden, accurately distinguished MPNST from its benign PN precursor, and dynamically correlated with treatment response. In the future, our findings could form the basis for improved early cancer detection and monitoring in high-risk cancer-predisposed populations.
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Affiliation(s)
- Jeffrey J. Szymanski
- Division of Cancer Biology, Department of Radiation Oncology, Washington University School of Medicine, St. Louis, Missouri, United States of America
| | - R. Taylor Sundby
- Pediatric Oncology Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Paul A. Jones
- Division of Cancer Biology, Department of Radiation Oncology, Washington University School of Medicine, St. Louis, Missouri, United States of America
- Division of Biology and Biomedical Sciences, Washington University School of Medicine, St. Louis, Missouri, United States of America
| | - Divya Srihari
- Division of Oncology, Department of Medicine, Washington University School of Medicine, St. Louis, Missouri, United States of America
| | - Noah Earland
- Division of Cancer Biology, Department of Radiation Oncology, Washington University School of Medicine, St. Louis, Missouri, United States of America
- Division of Biology and Biomedical Sciences, Washington University School of Medicine, St. Louis, Missouri, United States of America
| | - Peter K. Harris
- Division of Cancer Biology, Department of Radiation Oncology, Washington University School of Medicine, St. Louis, Missouri, United States of America
| | - Wenjia Feng
- Division of Cancer Biology, Department of Radiation Oncology, Washington University School of Medicine, St. Louis, Missouri, United States of America
| | - Faridi Qaium
- Division of Cancer Biology, Department of Radiation Oncology, Washington University School of Medicine, St. Louis, Missouri, United States of America
| | - Haiyan Lei
- Pediatric Oncology Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, United States of America
| | - David Roberts
- Division of Oncology, Department of Medicine, Washington University School of Medicine, St. Louis, Missouri, United States of America
| | - Michele Landeau
- Division of Oncology, Department of Medicine, Washington University School of Medicine, St. Louis, Missouri, United States of America
| | - Jamie Bell
- Division of Oncology, Department of Medicine, Washington University School of Medicine, St. Louis, Missouri, United States of America
| | - Yi Huang
- Division of Cancer Biology, Department of Radiation Oncology, Washington University School of Medicine, St. Louis, Missouri, United States of America
| | - Leah Hoffman
- Pediatric Oncology Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Melissa Spencer
- Pediatric Oncology Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Matthew B. Spraker
- Division of Cancer Biology, Department of Radiation Oncology, Washington University School of Medicine, St. Louis, Missouri, United States of America
- Siteman Cancer Center, Barnes Jewish Hospital and Washington University School of Medicine, St. Louis, Missouri, United States of America
| | - Li Ding
- Division of Oncology, Department of Medicine, Washington University School of Medicine, St. Louis, Missouri, United States of America
- Siteman Cancer Center, Barnes Jewish Hospital and Washington University School of Medicine, St. Louis, Missouri, United States of America
- McDonnel Genome Institute, Washington University in Saint Louis, Missouri, United States of America
- Department of Genetics, Washington University School of Medicine, St. Louis, Missouri, United States of America
| | - Brigitte C. Widemann
- Pediatric Oncology Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Jack F. Shern
- Pediatric Oncology Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, United States of America
- * E-mail: (JFS); (ACH); (AAC)
| | - Angela C. Hirbe
- Division of Biology and Biomedical Sciences, Washington University School of Medicine, St. Louis, Missouri, United States of America
- Division of Oncology, Department of Medicine, Washington University School of Medicine, St. Louis, Missouri, United States of America
- Siteman Cancer Center, Barnes Jewish Hospital and Washington University School of Medicine, St. Louis, Missouri, United States of America
- Department of Pediatrics, Washington University School of Medicine, St. Louis, Missouri, United States of America
- * E-mail: (JFS); (ACH); (AAC)
| | - Aadel A. Chaudhuri
- Division of Cancer Biology, Department of Radiation Oncology, Washington University School of Medicine, St. Louis, Missouri, United States of America
- Division of Biology and Biomedical Sciences, Washington University School of Medicine, St. Louis, Missouri, United States of America
- Siteman Cancer Center, Barnes Jewish Hospital and Washington University School of Medicine, St. Louis, Missouri, United States of America
- Department of Biomedical Engineering, Washington University School of Medicine, St. Louis, Missouri, United States of America
- Department of Computer Science and Engineering, Washington University in St. Louis, St. Louis, Missouri, United States of America
- * E-mail: (JFS); (ACH); (AAC)
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Su S, Chen J, Jiang Y, Wang Y, Vital T, Zhang J, Laggner C, Nguyen KT, Zhu Z, Prevatte AW, Barker NK, Herring LE, Davis IJ, Liu P. SPOP and OTUD7A Control EWS-FLI1 Protein Stability to Govern Ewing Sarcoma Growth. Adv Sci (Weinh) 2021; 8:e2004846. [PMID: 34060252 PMCID: PMC8292909 DOI: 10.1002/advs.202004846] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/15/2020] [Revised: 03/11/2021] [Indexed: 05/08/2023]
Abstract
Chromosomal translocation results in development of an Ewing sarcoma breakpoint region 1-Friend leukemia integration 1 (EWS-FLI1) fusion oncogene in the majority of Ewing sarcoma. The persistent dependence of the tumor for this oncoprotein points to EWS-FLI1 as an ideal drug target. Although EWS-FLI1 transcriptional targets and binding partners are evaluated, the mechanisms regulating EWS-FLI1 protein stability remain elusive. Speckle-type POZ protein (SPOP) and OTU domain-containing protein 7A (OTUD7A) are identified as the bona fide E3 ligase and deubiquitinase, respectively, that control EWS-FLI1 protein turnover in Ewing sarcoma. Casein kinase 1-mediated phosphorylation of the VTSSS degron in the FLI1 domain enhances SPOP activity to degrade EWS-FLI1. Opposing this process, OTUD7A deubiquitinates and stabilizes EWS-FLI1. Depletion of OTUD7A in Ewing sarcoma cell lines reduces EWS-FLI1 protein abundance and impedes Ewing sarcoma growth in vitro and in mice. Performing an artificial-intelligence-based virtual drug screen of a 4-million small molecule library, 7Ai is identified as a potential OTUD7A catalytic inhibitor. 7Ai reduces EWS-FLI1 protein levels and decreases Ewing sarcoma growth in vitro and in a xenograft mouse model. This study supports the therapeutic targeting of OTUD7A as a novel strategy for Ewing sarcoma bearing EWS-FLI1 and related fusions, and may also be applicable to other cancers dependent on aberrant FLI1 expression.
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Affiliation(s)
- Siyuan Su
- Lineberger Comprehensive Cancer CenterThe University of North Carolina at Chapel HillChapel HillNC27599USA
- Department of Biochemistry and BiophysicsSchool of MedicineThe University of North Carolina at Chapel HillChapel HillNC27599USA
| | - Jianfeng Chen
- Lineberger Comprehensive Cancer CenterThe University of North Carolina at Chapel HillChapel HillNC27599USA
- Department of Biochemistry and BiophysicsSchool of MedicineThe University of North Carolina at Chapel HillChapel HillNC27599USA
| | - Yao Jiang
- Lineberger Comprehensive Cancer CenterThe University of North Carolina at Chapel HillChapel HillNC27599USA
- Present address:
Cancer CenterUnion HospitalTongji Medical CollegeHuazhong University of Science and TechnologyWuhan430022China
| | - Ying Wang
- Lineberger Comprehensive Cancer CenterThe University of North Carolina at Chapel HillChapel HillNC27599USA
- Department of Biochemistry and BiophysicsSchool of MedicineThe University of North Carolina at Chapel HillChapel HillNC27599USA
| | - Tamara Vital
- Lineberger Comprehensive Cancer CenterThe University of North Carolina at Chapel HillChapel HillNC27599USA
- Department of GeneticsThe University of North Carolina at Chapel HillChapel HillNC27599USA
- Department of PediatricsThe University of North Carolina at Chapel HillChapel HillNC 27599USA
| | - Jiaming Zhang
- Lineberger Comprehensive Cancer CenterThe University of North Carolina at Chapel HillChapel HillNC27599USA
- Present address:
Department of Oral Medicine, Infection, and ImmunityHarvard School of Dental MedicineBostonMA02215USA
| | | | | | - Zhichuan Zhu
- Lineberger Comprehensive Cancer CenterThe University of North Carolina at Chapel HillChapel HillNC27599USA
- Department of Biochemistry and BiophysicsSchool of MedicineThe University of North Carolina at Chapel HillChapel HillNC27599USA
| | - Alex W. Prevatte
- UNC Proteomics Core FacilityDepartment of PharmacologyThe University of North Carolina at Chapel HillChapel HillNC27599USA
| | - Natalie K. Barker
- UNC Proteomics Core FacilityDepartment of PharmacologyThe University of North Carolina at Chapel HillChapel HillNC27599USA
| | - Laura E. Herring
- UNC Proteomics Core FacilityDepartment of PharmacologyThe University of North Carolina at Chapel HillChapel HillNC27599USA
| | - Ian J. Davis
- Lineberger Comprehensive Cancer CenterThe University of North Carolina at Chapel HillChapel HillNC27599USA
- Department of GeneticsThe University of North Carolina at Chapel HillChapel HillNC27599USA
- Department of PediatricsThe University of North Carolina at Chapel HillChapel HillNC 27599USA
| | - Pengda Liu
- Lineberger Comprehensive Cancer CenterThe University of North Carolina at Chapel HillChapel HillNC27599USA
- Department of Biochemistry and BiophysicsSchool of MedicineThe University of North Carolina at Chapel HillChapel HillNC27599USA
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Kasson S, Dharmapriya N, Kim IK. Selective monitoring of the protein-free ADP-ribose released by ADP-ribosylation reversal enzymes. PLoS One 2021; 16:e0254022. [PMID: 34191856 PMCID: PMC8244878 DOI: 10.1371/journal.pone.0254022] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2020] [Accepted: 06/17/2021] [Indexed: 11/18/2022] Open
Abstract
ADP-ribosylation is a key post-translational modification that regulates a wide variety of cellular stress responses. The ADP-ribosylation cycle is maintained by writers and erasers. For example, poly(ADP-ribosyl)ation cycles consist of two predominant enzymes, poly(ADP-ribose) polymerases (PARPs) and poly(ADP-ribose) glycohydrolase (PARG). However, historically, mechanisms of erasers of ADP-ribosylations have been understudied, primarily due to the lack of quantitative tools to selectively monitor specific activities of different ADP-ribosylation reversal enzymes. Here, we developed a new NUDT5-coupled AMP-Glo (NCAG) assay to specifically monitor the protein-free ADP-ribose released by ADP-ribosylation reversal enzymes. We found that NUDT5 selectively cleaves protein-free ADP-ribose, but not protein-bound poly- and mono-ADP-ribosylations, protein-free poly(ADP-ribose) chains, or NAD+. As a proof-of-concept, we successfully measured the kinetic parameters for the exo-glycohydrolase activity of PARG, which releases monomeric ADP-ribose, and monitored activities of site-specific mono-ADP-ribosyl-acceptor hydrolases, such as ARH3 and TARG1. This NCAG assay can be used as a general platform to study the mechanisms of diverse ADP-ribosylation reversal enzymes that release protein-free ADP-ribose as a product. Furthermore, this assay provides a useful tool to identify small-molecule probes targeting ADP-ribosylation metabolism and to quantify ADP-ribose concentrations in cells.
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Affiliation(s)
- Samuel Kasson
- Department of Chemistry, University of Cincinnati, Cincinnati, OH, United States of America
| | - Nuwani Dharmapriya
- Department of Chemistry, University of Cincinnati, Cincinnati, OH, United States of America
| | - In-Kwon Kim
- Department of Chemistry, University of Cincinnati, Cincinnati, OH, United States of America
- * E-mail:
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32
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Schulz L, Torres-Diz M, Cortés-López M, Hayer KE, Asnani M, Tasian SK, Barash Y, Sotillo E, Zarnack K, König J, Thomas-Tikhonenko A. Direct long-read RNA sequencing identifies a subset of questionable exitrons likely arising from reverse transcription artifacts. Genome Biol 2021; 22:190. [PMID: 34183059 PMCID: PMC8240250 DOI: 10.1186/s13059-021-02411-1] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2021] [Accepted: 06/16/2021] [Indexed: 11/24/2022] Open
Abstract
Resistance to CD19-directed immunotherapies in lymphoblastic leukemia has been attributed, among other factors, to several aberrant CD19 pre-mRNA splicing events, including recently reported excision of a cryptic intron embedded within CD19 exon 2. While "exitrons" are known to exist in hundreds of human transcripts, we discovered, using reporter assays and direct long-read RNA sequencing (dRNA-seq), that the CD19 exitron is an artifact of reverse transcription. Extending our analysis to publicly available datasets, we identified dozens of questionable exitrons, dubbed "falsitrons," that appear only in cDNA-seq, but never in dRNA-seq. Our results highlight the importance of dRNA-seq for transcript isoform validation.
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MESH Headings
- Alternative Splicing
- Antibodies, Bispecific/pharmacology
- Antineoplastic Agents, Immunological/pharmacology
- Artifacts
- B-Lymphocytes/drug effects
- B-Lymphocytes/immunology
- B-Lymphocytes/pathology
- Base Pairing
- Base Sequence
- Cell Line, Tumor
- Datasets as Topic
- Exons
- High-Throughput Nucleotide Sequencing
- Humans
- Immunotherapy/methods
- Introns
- Models, Biological
- Nucleic Acid Conformation
- Precursor Cell Lymphoblastic Leukemia-Lymphoma/drug therapy
- Precursor Cell Lymphoblastic Leukemia-Lymphoma/genetics
- Precursor Cell Lymphoblastic Leukemia-Lymphoma/immunology
- Precursor Cell Lymphoblastic Leukemia-Lymphoma/pathology
- Protein Isoforms/chemistry
- Protein Isoforms/genetics
- Protein Isoforms/immunology
- RNA, Messenger/chemistry
- RNA, Messenger/genetics
- RNA, Messenger/immunology
- Receptors, Antigen, T-Cell/genetics
- Receptors, Antigen, T-Cell/immunology
- Reverse Transcription
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Affiliation(s)
- Laura Schulz
- Institute of Molecular Biology (IMB), Ackermannweg 4, 55128, Mainz, Germany
| | - Manuel Torres-Diz
- Division of Cancer Pathobiology, Children's Hospital of Philadelphia, Philadelphia, PA, 19104, USA
| | | | - Katharina E Hayer
- The Bioinformatics Group, Children's Hospital of Philadelphia, Philadelphia, PA, 19104, USA
| | - Mukta Asnani
- Division of Cancer Pathobiology, Children's Hospital of Philadelphia, Philadelphia, PA, 19104, USA
| | - Sarah K Tasian
- Division of Oncology, Children's Hospital of Philadelphia, Philadelphia, PA, 19104, USA
| | - Yoseph Barash
- Department of Genetics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Elena Sotillo
- Division of Cancer Pathobiology, Children's Hospital of Philadelphia, Philadelphia, PA, 19104, USA
- Present address: Stanford Cancer Institute, 265 Campus Dr., Stanford, CA, 94305, USA
| | - Kathi Zarnack
- Buchmann Institute for Molecular Life Sciences (BMLS) and Faculty of Biological Sciences, Goethe University Frankfurt, Max-von-Laue-Str. 15, 60438, Frankfurt, Germany
| | - Julian König
- Institute of Molecular Biology (IMB), Ackermannweg 4, 55128, Mainz, Germany.
| | - Andrei Thomas-Tikhonenko
- Division of Cancer Pathobiology, Children's Hospital of Philadelphia, Philadelphia, PA, 19104, USA.
- Division of Oncology, Children's Hospital of Philadelphia, Philadelphia, PA, 19104, USA.
- Department of Pathology & Laboratory Medicine, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, 19104, USA.
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Singh DK, Patel VG, Oh WK, Aguirre-Ghiso JA. Prostate Cancer Dormancy and Reactivation in Bone Marrow. J Clin Med 2021; 10:2648. [PMID: 34208521 PMCID: PMC8234151 DOI: 10.3390/jcm10122648] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2021] [Revised: 06/03/2021] [Accepted: 06/14/2021] [Indexed: 12/14/2022] Open
Abstract
Prostate cancer has a variable clinical course, ranging from curable local disease to lethal metastatic spread. Eradicating metastatic cells is a unique challenge that is rarely met with the available therapies. Thus, targeting prostate cancer cells in earlier disease states is a crucial window of opportunity. Interestingly, cancer cells migrate from their primary site during pre-cancerous and malignant phases to seed secondary organs. These cells, known as disseminated cancer cells (DCCs), may remain dormant for months or decades before activating to form metastases. Bone marrow, a dormancy-permissive site, is the major organ for housed DCCs and eventual metastases in prostate cancer. The dynamic interplay between DCCs and the primary tumor microenvironment (TME), as well as that between DCCs and the secondary organ niche, controls the conversion between states of dormancy and activation. Here, we discuss recent discoveries that have improved our understanding of dormancy signaling and the role of the TME in modulating the epigenetic reprogramming of DCCs. We offer potential strategies to target DCCs in prostate cancer.
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Affiliation(s)
- Deepak K. Singh
- Division of Hematology and Oncology, Department of Medicine, Department of Otolaryngology, Department of Oncological Sciences, Tisch Cancer Institute, Black Family Stem Cell Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA;
| | - Vaibhav G. Patel
- Division of Hematology and Oncology, Department of Medicine, Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA;
| | - William K. Oh
- Division of Hematology and Oncology, Department of Medicine, Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA;
| | - Julio A. Aguirre-Ghiso
- Division of Hematology and Oncology, Department of Medicine, Department of Otolaryngology, Department of Oncological Sciences, Tisch Cancer Institute, Black Family Stem Cell Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA;
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Smith CC, Olsen KS, Gentry KM, Sambade M, Beck W, Garness J, Entwistle S, Willis C, Vensko S, Woods A, Fini M, Carpenter B, Routh E, Kodysh J, O'Donnell T, Haber C, Heiss K, Stadler V, Garrison E, Sandor AM, Ting JPY, Weiss J, Krajewski K, Grant OC, Woods RJ, Heise M, Vincent BG, Rubinsteyn A. Landscape and selection of vaccine epitopes in SARS-CoV-2. Genome Med 2021; 13:101. [PMID: 34127050 PMCID: PMC8201469 DOI: 10.1186/s13073-021-00910-1] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2020] [Accepted: 05/14/2021] [Indexed: 12/11/2022] Open
Abstract
BACKGROUND Early in the pandemic, we designed a SARS-CoV-2 peptide vaccine containing epitope regions optimized for concurrent B cell, CD4+ T cell, and CD8+ T cell stimulation. The rationale for this design was to drive both humoral and cellular immunity with high specificity while avoiding undesired effects such as antibody-dependent enhancement (ADE). METHODS We explored the set of computationally predicted SARS-CoV-2 HLA-I and HLA-II ligands, examining protein source, concurrent human/murine coverage, and population coverage. Beyond MHC affinity, T cell vaccine candidates were further refined by predicted immunogenicity, sequence conservation, source protein abundance, and coverage of high frequency HLA alleles. B cell epitope regions were chosen from linear epitope mapping studies of convalescent patient serum, followed by filtering for surface accessibility, sequence conservation, spatial localization near functional domains of the spike glycoprotein, and avoidance of glycosylation sites. RESULTS From 58 initial candidates, three B cell epitope regions were identified. From 3730 (MHC-I) and 5045 (MHC-II) candidate ligands, 292 CD8+ and 284 CD4+ T cell epitopes were identified. By combining these B cell and T cell analyses, as well as a manufacturability heuristic, we proposed a set of 22 SARS-CoV-2 vaccine peptides for use in subsequent murine studies. We curated a dataset of ~ 1000 observed T cell epitopes from convalescent COVID-19 patients across eight studies, showing 8/15 recurrent epitope regions to overlap with at least one of our candidate peptides. Of the 22 candidate vaccine peptides, 16 (n = 10 T cell epitope optimized; n = 6 B cell epitope optimized) were manually selected to decrease their degree of sequence overlap and then synthesized. The immunogenicity of the synthesized vaccine peptides was validated using ELISpot and ELISA following murine vaccination. Strong T cell responses were observed in 7/10 T cell epitope optimized peptides following vaccination. Humoral responses were deficient, likely due to the unrestricted conformational space inhabited by linear vaccine peptides. CONCLUSIONS Overall, we find our selection process and vaccine formulation to be appropriate for identifying T cell epitopes and eliciting T cell responses against those epitopes. Further studies are needed to optimize prediction and induction of B cell responses, as well as study the protective capacity of predicted T and B cell epitopes.
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Affiliation(s)
- Christof C Smith
- Department of Microbiology and Immunology, UNC School of Medicine, Chapel Hill, NC, USA
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, CB# 7295, Chapel Hill, NC, 27599-7295, USA
| | - Kelly S Olsen
- Department of Microbiology and Immunology, UNC School of Medicine, Chapel Hill, NC, USA
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, CB# 7295, Chapel Hill, NC, 27599-7295, USA
| | - Kaylee M Gentry
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, CB# 7295, Chapel Hill, NC, 27599-7295, USA
| | - Maria Sambade
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, CB# 7295, Chapel Hill, NC, 27599-7295, USA
| | - Wolfgang Beck
- Department of Microbiology and Immunology, UNC School of Medicine, Chapel Hill, NC, USA
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, CB# 7295, Chapel Hill, NC, 27599-7295, USA
| | - Jason Garness
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, CB# 7295, Chapel Hill, NC, 27599-7295, USA
| | - Sarah Entwistle
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, CB# 7295, Chapel Hill, NC, 27599-7295, USA
| | - Caryn Willis
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, CB# 7295, Chapel Hill, NC, 27599-7295, USA
| | - Steven Vensko
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, CB# 7295, Chapel Hill, NC, 27599-7295, USA
| | - Allison Woods
- Department of Microbiology and Immunology, UNC School of Medicine, Chapel Hill, NC, USA
| | - Misha Fini
- Department of Microbiology and Immunology, UNC School of Medicine, Chapel Hill, NC, USA
| | - Brandon Carpenter
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, CB# 7295, Chapel Hill, NC, 27599-7295, USA
| | - Eric Routh
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, CB# 7295, Chapel Hill, NC, 27599-7295, USA
| | - Julia Kodysh
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Timothy O'Donnell
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | | | | | | | - Erik Garrison
- Genomics Institute, University of California, Santa Cruz, CA, USA
| | - Adam M Sandor
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, CB# 7295, Chapel Hill, NC, 27599-7295, USA
| | - Jenny P Y Ting
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, CB# 7295, Chapel Hill, NC, 27599-7295, USA
- Department of Genetics, UNC School of Medicine, Chapel Hill, NC, USA
- Institute for Inflammatory Diseases, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- Center for Translational Immunology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Jared Weiss
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, CB# 7295, Chapel Hill, NC, 27599-7295, USA
- Division of Medical Oncology, Department of Medicine, UNC School of Medicine, Chapel Hill, NC, USA
| | - Krzysztof Krajewski
- Department of Biochemistry and Biophysics, UNC School of Medicine, Chapel Hill, NC, USA
| | - Oliver C Grant
- Complex Carbohydrate Research Center, University of Georgia, Athens, GA, USA
| | - Robert J Woods
- Complex Carbohydrate Research Center, University of Georgia, Athens, GA, USA
| | - Mark Heise
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, CB# 7295, Chapel Hill, NC, 27599-7295, USA
- Department of Genetics, UNC School of Medicine, Chapel Hill, NC, USA
| | - Benjamin G Vincent
- Department of Microbiology and Immunology, UNC School of Medicine, Chapel Hill, NC, USA.
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, CB# 7295, Chapel Hill, NC, 27599-7295, USA.
- Computational Medicine Program, UNC School of Medicine, Chapel Hill, NC, USA.
- Curriculum in Bioinformatics and Computational Biology, UNC School of Medicine, Chapel Hill, NC, USA.
- Division of Hematology, Department of Medicine, UNC School of Medicine, Chapel Hill, NC, USA.
| | - Alex Rubinsteyn
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, CB# 7295, Chapel Hill, NC, 27599-7295, USA.
- Department of Genetics, UNC School of Medicine, Chapel Hill, NC, USA.
- Computational Medicine Program, UNC School of Medicine, Chapel Hill, NC, USA.
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Song N, Hsu CW, Pan H, Zheng Y, Hou L, Sim JA, Li Z, Mulder H, Easton J, Walker E, Neale G, Wilson CL, Ness KK, Krull KR, Srivastava DK, Yasui Y, Zhang J, Hudson MM, Robison LL, Huang IC, Wang Z. Persistent variations of blood DNA methylation associated with treatment exposures and risk for cardiometabolic outcomes in long-term survivors of childhood cancer in the St. Jude Lifetime Cohort. Genome Med 2021; 13:53. [PMID: 33823916 PMCID: PMC8025387 DOI: 10.1186/s13073-021-00875-1] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2020] [Accepted: 03/22/2021] [Indexed: 12/12/2022] Open
Abstract
BACKGROUND It is well-established that cancer treatment substantially increases the risk of long-term adverse health outcomes among childhood cancer survivors. However, there is limited research on the underlying mechanisms. To elucidate the pathophysiology and a possible causal pathway from treatment exposures to cardiometabolic conditions, we conducted epigenome-wide association studies (EWAS) to identify the DNA methylation (DNAm) sites associated with cancer treatment exposures and examined whether treatment-associated DNAm sites mediate associations between specific treatments and cardiometabolic conditions. METHODS We included 2052 survivors (median age 33.7 years) of European ancestry from the St. Jude Lifetime Cohort Study, a retrospective hospital-based study with prospective clinical follow-up. Cumulative doses of chemotherapy and region-specific radiation were abstracted from medical records. Seven cardiometabolic conditions were clinically assessed. DNAm profile was measured using MethylationEPIC BeadChip with blood-derived DNA. RESULTS By performing multiple treatment-specific EWAS, we identified 935 5'-cytosine-phosphate-guanine-3' (CpG) sites mapped to 538 genes/regions associated with one or more cancer treatments at the epigenome-wide significance level (p < 9 × 10-8). Among the treatment-associated CpGs, 8 were associated with obesity, 63 with hypercholesterolemia, and 17 with hypertriglyceridemia (false discovery rate-adjusted p < 0.05). We observed substantial mediation by methylation at four independent CpGs (cg06963130, cg21922478, cg22976567, cg07403981) for the association between abdominal field radiotherapy (abdominal-RT) and risk of hypercholesterolemia (70.3%) and by methylation at three CpGs (cg19634849, cg13552692, cg09853238) for the association between abdominal-RT and hypertriglyceridemia (54.6%). In addition, three CpGs (cg26572901, cg12715065, cg21163477) partially mediated the association between brain-RT and obesity with a 32.9% mediation effect, and two CpGs mediated the association between corticosteroids and obesity (cg22351187, 14.2%) and between brain-RT and hypertriglyceridemia (cg13360224, 10.5%). Notably, several mediator CpGs reside in the proximity of well-established dyslipidemia genes: cg21922478 (ITGA1) and cg22976567 (LMNA). CONCLUSIONS In childhood cancer survivors, cancer treatment exposures are associated with DNAm patterns present decades following the exposure. Treatment-associated DNAm sites may mediate the causal pathway from specific treatment exposures to certain cardiometabolic conditions, suggesting the utility of DNAm sites as risk predictors and potential mechanistic targets for future intervention studies.
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Affiliation(s)
- Nan Song
- Department of Epidemiology and Cancer Control, St. Jude Children's Research Hospital, 262 Danny Thomas Place, MS 735, Memphis, TN, 38105, USA
- Department of Pharmacy, Chungbuk National University, Cheongju, Korea
| | - Chia-Wei Hsu
- Department of Biostatistics, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Haitao Pan
- Department of Biostatistics, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Yinan Zheng
- Department of Preventive Medicine, Northwestern University, Chicago, IL, USA
| | - Lifang Hou
- Department of Preventive Medicine, Northwestern University, Chicago, IL, USA
| | - Jin-Ah Sim
- Department of Epidemiology and Cancer Control, St. Jude Children's Research Hospital, 262 Danny Thomas Place, MS 735, Memphis, TN, 38105, USA
| | - Zhenghong Li
- Department of Epidemiology and Cancer Control, St. Jude Children's Research Hospital, 262 Danny Thomas Place, MS 735, Memphis, TN, 38105, USA
| | - Heather Mulder
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - John Easton
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Emily Walker
- Hartwell Center, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Geoffrey Neale
- Hartwell Center, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Carmen L Wilson
- Department of Epidemiology and Cancer Control, St. Jude Children's Research Hospital, 262 Danny Thomas Place, MS 735, Memphis, TN, 38105, USA
| | - Kirsten K Ness
- Department of Epidemiology and Cancer Control, St. Jude Children's Research Hospital, 262 Danny Thomas Place, MS 735, Memphis, TN, 38105, USA
| | - Kevin R Krull
- Department of Epidemiology and Cancer Control, St. Jude Children's Research Hospital, 262 Danny Thomas Place, MS 735, Memphis, TN, 38105, USA
| | - Deo Kumar Srivastava
- Department of Biostatistics, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Yutaka Yasui
- Department of Epidemiology and Cancer Control, St. Jude Children's Research Hospital, 262 Danny Thomas Place, MS 735, Memphis, TN, 38105, USA
| | - Jinghui Zhang
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Melissa M Hudson
- Department of Epidemiology and Cancer Control, St. Jude Children's Research Hospital, 262 Danny Thomas Place, MS 735, Memphis, TN, 38105, USA
- Department of Oncology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Leslie L Robison
- Department of Epidemiology and Cancer Control, St. Jude Children's Research Hospital, 262 Danny Thomas Place, MS 735, Memphis, TN, 38105, USA
| | - I-Chan Huang
- Department of Epidemiology and Cancer Control, St. Jude Children's Research Hospital, 262 Danny Thomas Place, MS 735, Memphis, TN, 38105, USA
| | - Zhaoming Wang
- Department of Epidemiology and Cancer Control, St. Jude Children's Research Hospital, 262 Danny Thomas Place, MS 735, Memphis, TN, 38105, USA.
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, TN, USA.
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Zewdu R, Mehrabad EM, Ingram K, Fang P, Gillis KL, Camolotto SA, Orstad G, Jones A, Mendoza MC, Spike BT, Snyder EL. An NKX2-1/ERK/WNT feedback loop modulates gastric identity and response to targeted therapy in lung adenocarcinoma. eLife 2021; 10:e66788. [PMID: 33821796 PMCID: PMC8102067 DOI: 10.7554/elife.66788] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2021] [Accepted: 04/05/2021] [Indexed: 12/13/2022] Open
Abstract
Cancer cells undergo lineage switching during natural progression and in response to therapy. NKX2-1 loss in human and murine lung adenocarcinoma leads to invasive mucinous adenocarcinoma (IMA), a lung cancer subtype that exhibits gastric differentiation and harbors a distinct spectrum of driver oncogenes. In murine BRAFV600E-driven lung adenocarcinoma, NKX2-1 is required for early tumorigenesis, but dispensable for established tumor growth. NKX2-1-deficient, BRAFV600E-driven tumors resemble human IMA and exhibit a distinct response to BRAF/MEK inhibitors. Whereas BRAF/MEK inhibitors drive NKX2-1-positive tumor cells into quiescence, NKX2-1-negative cells fail to exit the cell cycle after the same therapy. BRAF/MEK inhibitors induce cell identity switching in NKX2-1-negative lung tumors within the gastric lineage, which is driven in part by WNT signaling and FoxA1/2. These data elucidate a complex, reciprocal relationship between lineage specifiers and oncogenic signaling pathways in the regulation of lung adenocarcinoma identity that is likely to impact lineage-specific therapeutic strategies.
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Affiliation(s)
- Rediet Zewdu
- Huntsman Cancer InstituteSalt Lake CityUnited States
- Department of Pathology, University of UtahSalt Lake CityUnited States
| | - Elnaz Mirzaei Mehrabad
- Huntsman Cancer InstituteSalt Lake CityUnited States
- School of Computing, University of UtahSalt Lake CityUnited States
| | - Kelley Ingram
- Huntsman Cancer InstituteSalt Lake CityUnited States
- Department of Oncological Sciences, University of UtahSalt Lake CityUnited States
| | - Pengshu Fang
- Huntsman Cancer InstituteSalt Lake CityUnited States
- Department of Oncological Sciences, University of UtahSalt Lake CityUnited States
| | - Katherine L Gillis
- Huntsman Cancer InstituteSalt Lake CityUnited States
- Department of Oncological Sciences, University of UtahSalt Lake CityUnited States
| | - Soledad A Camolotto
- Huntsman Cancer InstituteSalt Lake CityUnited States
- Department of Pathology, University of UtahSalt Lake CityUnited States
| | - Grace Orstad
- Huntsman Cancer InstituteSalt Lake CityUnited States
- Department of Oncological Sciences, University of UtahSalt Lake CityUnited States
| | - Alex Jones
- Huntsman Cancer InstituteSalt Lake CityUnited States
- Department of Pathology, University of UtahSalt Lake CityUnited States
| | - Michelle C Mendoza
- Huntsman Cancer InstituteSalt Lake CityUnited States
- Department of Oncological Sciences, University of UtahSalt Lake CityUnited States
| | - Benjamin T Spike
- Huntsman Cancer InstituteSalt Lake CityUnited States
- Department of Oncological Sciences, University of UtahSalt Lake CityUnited States
| | - Eric L Snyder
- Huntsman Cancer InstituteSalt Lake CityUnited States
- Department of Pathology, University of UtahSalt Lake CityUnited States
- Department of Oncological Sciences, University of UtahSalt Lake CityUnited States
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Ablain J, Liu S, Moriceau G, Lo RS, Zon LI. SPRED1 deletion confers resistance to MAPK inhibition in melanoma. J Exp Med 2021; 218:e20201097. [PMID: 33306107 PMCID: PMC7927430 DOI: 10.1084/jem.20201097] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2020] [Revised: 10/12/2020] [Accepted: 11/06/2020] [Indexed: 12/16/2022] Open
Abstract
Functional evaluation of genetic lesions can discover a role in cancer initiation and progression and help develop novel therapeutic strategies. We previously identified the negative MAPK regulator SPRED1 as a novel tumor suppressor in KIT-driven melanoma. Here, we show that SPRED1 is also frequently deleted in human melanoma driven by mutant BRAF. We found that SPRED1 inactivation in human melanoma cell lines and primary zebrafish melanoma conferred resistance to BRAFV600E inhibition in vitro and in vivo. Mechanistically, SPRED1 loss promoted melanoma cell proliferation under mutant BRAF inhibition by reactivating MAPK activity. Consistently, biallelic deletion of SPRED1 was observed in a patient whose melanoma acquired resistance to MAPK-targeted therapy. These studies combining work in human cells and in vivo modeling in zebrafish demonstrate a new mechanism of resistance to BRAFV600E inhibition in melanoma.
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Affiliation(s)
- Julien Ablain
- Stem Cell Program and Division of Hematology/Oncology, Boston Children’s Hospital and Dana Farber Cancer Institute, Boston, MA
| | - Sixue Liu
- Division of Dermatology, Department of Medicine, University of California, Los Angeles, Los Angeles, CA
- David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA
| | - Gatien Moriceau
- Division of Dermatology, Department of Medicine, University of California, Los Angeles, Los Angeles, CA
- David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA
- Jonsson Comprehensive Cancer Center, University of California, Los Angeles, Los Angeles, CA
| | - Roger S. Lo
- Division of Dermatology, Department of Medicine, University of California, Los Angeles, Los Angeles, CA
- Department of Molecular and Medical Pharmacology, University of California, Los Angeles, Los Angeles, CA
- David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA
- Jonsson Comprehensive Cancer Center, University of California, Los Angeles, Los Angeles, CA
| | - Leonard I. Zon
- Stem Cell Program and Division of Hematology/Oncology, Boston Children’s Hospital and Dana Farber Cancer Institute, Boston, MA
- Harvard Stem Cell Institute, Harvard University, Cambridge, MA
- Howard Hughes Medical Institute, Boston, MA
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Khella CA, Mehta GA, Mehta RN, Gatza ML. Recent Advances in Integrative Multi-Omics Research in Breast and Ovarian Cancer. J Pers Med 2021; 11:149. [PMID: 33669749 PMCID: PMC7922242 DOI: 10.3390/jpm11020149] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2021] [Revised: 02/13/2021] [Accepted: 02/14/2021] [Indexed: 02/07/2023] Open
Abstract
The underlying molecular heterogeneity of cancer is responsible for the dynamic clinical landscape of this disease. The combination of genomic and proteomic alterations, including both inherited and acquired mutations, promotes tumor diversity and accounts for variable disease progression, therapeutic response, and clinical outcome. Recent advances in high-throughput proteogenomic profiling of tumor samples have resulted in the identification of novel oncogenic drivers, tumor suppressors, and signaling networks; biomarkers for the prediction of drug sensitivity and disease progression; and have contributed to the development of novel and more effective treatment strategies. In this review, we will focus on the impact of historical and recent advances in single platform and integrative proteogenomic studies in breast and ovarian cancer, which constitute two of the most lethal forms of cancer for women, and discuss the molecular similarities of these diseases, the impact of these findings on our understanding of tumor biology as well as the clinical applicability of these discoveries.
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Affiliation(s)
- Christen A Khella
- Rutgers Cancer Institute of New Jersey, New Brunswick, NJ 08903, USA
| | - Gaurav A Mehta
- Rutgers Cancer Institute of New Jersey, New Brunswick, NJ 08903, USA
| | - Rushabh N Mehta
- Rutgers Cancer Institute of New Jersey, New Brunswick, NJ 08903, USA
| | - Michael L Gatza
- Rutgers Cancer Institute of New Jersey, New Brunswick, NJ 08903, USA
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Wrenn ED, Moore BM, Greenwood E, McBirney M, Cheung KJ. Optimal, Large-Scale Propagation of Mouse Mammary Tumor Organoids. J Mammary Gland Biol Neoplasia 2020; 25:337-350. [PMID: 33106923 PMCID: PMC7587543 DOI: 10.1007/s10911-020-09464-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/03/2020] [Accepted: 10/09/2020] [Indexed: 12/12/2022] Open
Abstract
Tumor organoids mimic the architecture and heterogeneity of in vivo tumors and enable studies of collective interactions between tumor cells as well as with their surrounding microenvironment. Although tumor organoids hold significant promise as cancer models, they are also more costly and labor-intensive to cultivate than traditional 2D cell culture. We sought to identify critical factors regulating organoid growth ex vivo, and to use these observations to develop a more efficient organoid expansion method. Using time-lapse imaging of mouse mammary tumor organoids in 3D culture, we observed that outgrowth potential varies non-linearly with initial organoid size. Maximal outgrowth occurred in organoids with a starting size between ~10 to 1000 cells. Based on these observations, we developed a suspension culture method that maintains organoids in the ideal size range, enabling expansion from 1 million to over 100 million cells in less than 2 weeks and less than 3 hours of hands-on time. Our method facilitates the rapid, cost-effective expansion of organoids for CRISPR based studies and other assays requiring a large amount of organoid starting material.
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Affiliation(s)
- Emma D Wrenn
- Translational Research Program, Public Health Sciences and Human Biology Divisions, Fred Hutchinson Cancer Research Center, Seattle, WA, 98109, USA
- Molecular and Cellular Biology Graduate Program, University of Washington, Seattle, WA, 98195, USA
| | - Breanna M Moore
- Translational Research Program, Public Health Sciences and Human Biology Divisions, Fred Hutchinson Cancer Research Center, Seattle, WA, 98109, USA
| | - Erin Greenwood
- Translational Research Program, Public Health Sciences and Human Biology Divisions, Fred Hutchinson Cancer Research Center, Seattle, WA, 98109, USA
| | - Margaux McBirney
- Translational Research Program, Public Health Sciences and Human Biology Divisions, Fred Hutchinson Cancer Research Center, Seattle, WA, 98109, USA
| | - Kevin J Cheung
- Translational Research Program, Public Health Sciences and Human Biology Divisions, Fred Hutchinson Cancer Research Center, Seattle, WA, 98109, USA.
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40
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Dai Z, Zhang XN, Nasertorabi F, Cheng Q, Li J, Katz BB, Smbatyan G, Pei H, Louie SG, Lenz HJ, Stevens RC, Zhang Y. Synthesis of site-specific antibody-drug conjugates by ADP-ribosyl cyclases. Sci Adv 2020; 6:eaba6752. [PMID: 32537509 PMCID: PMC7269645 DOI: 10.1126/sciadv.aba6752] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/27/2019] [Accepted: 04/02/2020] [Indexed: 05/02/2023]
Abstract
Most of the current antibody-drug conjugates (ADCs) in clinic are heterogeneous mixtures. To produce homogeneous ADCs, established procedures often require multiple steps or long reaction times. The introduced mutations or foreign sequences may cause high immunogenicity. Here, we explore a new concept of transforming CD38 enzymatic activity into a facile approach for generating site-specific ADCs. This was achieved through coupling bifunctional antibody-CD38 fusion proteins with designer dinucleotide-based covalent inhibitors with stably attached payloads. The resulting adenosine diphosphate-ribosyl cyclase-enabled ADC (ARC-ADC) with a drug-to-antibody ratio of 2 could be rapidly generated through single-step conjugation. The generated ARC-ADC targeting human epidermal growth factor receptor 2 (HER2) displays excellent stability and potency against HER2-positive breast cancer both in vitro and in vivo. This proof-of-concept study demonstrates a new strategy for production of site-specific ADCs. It may provide a general approach for the development of a novel class of ADCs with potentially enhanced properties.
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Affiliation(s)
- Zhefu Dai
- Department of Pharmacology and Pharmaceutical Sciences, School of Pharmacy, University of Southern California, Los Angeles, CA 90089, USA
| | - Xiao-Nan Zhang
- Department of Pharmacology and Pharmaceutical Sciences, School of Pharmacy, University of Southern California, Los Angeles, CA 90089, USA
| | - Fariborz Nasertorabi
- Departments of Biological Sciences and Chemistry, Bridge Institute, Michelson Center for Convergent Bioscience, University of Southern California, Los Angeles, CA 90089, USA
| | - Qinqin Cheng
- Department of Pharmacology and Pharmaceutical Sciences, School of Pharmacy, University of Southern California, Los Angeles, CA 90089, USA
| | - Jiawei Li
- Department of Pharmacology and Pharmaceutical Sciences, School of Pharmacy, University of Southern California, Los Angeles, CA 90089, USA
| | - Benjamin B. Katz
- Department of Chemistry, University of California, Irvine, Irvine, CA 92697, USA
| | - Goar Smbatyan
- Division of Medical Oncology, Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, CA 90089, USA
| | - Hua Pei
- Titus Family Department of Clinical Pharmacy, School of Pharmacy, University of Southern California, Los Angeles, CA 90089, USA
| | - Stan G. Louie
- Titus Family Department of Clinical Pharmacy, School of Pharmacy, University of Southern California, Los Angeles, CA 90089, USA
| | - Heinz-Josef Lenz
- Division of Medical Oncology, Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, CA 90089, USA
| | - Raymond C. Stevens
- Departments of Biological Sciences and Chemistry, Bridge Institute, Michelson Center for Convergent Bioscience, University of Southern California, Los Angeles, CA 90089, USA
| | - Yong Zhang
- Department of Pharmacology and Pharmaceutical Sciences, School of Pharmacy, University of Southern California, Los Angeles, CA 90089, USA
- Department of Chemistry, Dornsife College of Letters, Arts and Sciences, University of Southern California, Los Angeles, CA 90089, USA
- Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, CA 90089, USA
- Research Center for Liver Diseases, University of Southern California, Los Angeles, CA 90089, USA
- Corresponding author.
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41
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Waagmeester A, Stupp G, Burgstaller-Muehlbacher S, Good BM, Griffith M, Griffith OL, Hanspers K, Hermjakob H, Hudson TS, Hybiske K, Keating SM, Manske M, Mayers M, Mietchen D, Mitraka E, Pico AR, Putman T, Riutta A, Queralt-Rosinach N, Schriml LM, Shafee T, Slenter D, Stephan R, Thornton K, Tsueng G, Tu R, Ul-Hasan S, Willighagen E, Wu C, Su AI. Wikidata as a knowledge graph for the life sciences. eLife 2020; 9:e52614. [PMID: 32180547 PMCID: PMC7077981 DOI: 10.7554/elife.52614] [Citation(s) in RCA: 43] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2019] [Accepted: 02/28/2020] [Indexed: 12/22/2022] Open
Abstract
Wikidata is a community-maintained knowledge base that has been assembled from repositories in the fields of genomics, proteomics, genetic variants, pathways, chemical compounds, and diseases, and that adheres to the FAIR principles of findability, accessibility, interoperability and reusability. Here we describe the breadth and depth of the biomedical knowledge contained within Wikidata, and discuss the open-source tools we have built to add information to Wikidata and to synchronize it with source databases. We also demonstrate several use cases for Wikidata, including the crowdsourced curation of biomedical ontologies, phenotype-based diagnosis of disease, and drug repurposing.
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Affiliation(s)
| | - Gregory Stupp
- Department of Integrative Structural and Computational Biology, The Scripps Research InstituteLa JollaUnited States
| | - Sebastian Burgstaller-Muehlbacher
- Center for Integrative Bioinformatics Vienna, Max Perutz Laboratories, University of Vienna and Medical University of ViennaViennaAustria
| | - Benjamin M Good
- Department of Integrative Structural and Computational Biology, The Scripps Research InstituteLa JollaUnited States
| | - Malachi Griffith
- McDonnell Genome Institute, Washington University School of MedicineSt. LouisUnited States
| | - Obi L Griffith
- McDonnell Genome Institute, Washington University School of MedicineSt. LouisUnited States
| | - Kristina Hanspers
- Institute of Data Science and Biotechnology, Gladstone InstitutesSan FranciscoUnited States
| | | | - Toby S Hudson
- School of Chemistry, The University of SydneySydneyAustralia
| | - Kevin Hybiske
- Division of Allergy and Infectious Diseases, Department of Medicine, University of WashingtonSeattleUnited States
| | - Sarah M Keating
- European Bioinformatics Institute (EMBL-EBI)HinxtonUnited Kingdom
| | - Magnus Manske
- Wellcome Trust Sanger InstituteCambridgeUnited Kingdom
| | - Michael Mayers
- Department of Integrative Structural and Computational Biology, The Scripps Research InstituteLa JollaUnited States
| | - Daniel Mietchen
- School of Data Science, University of VirginiaCharlottesvilleUnited States
| | - Elvira Mitraka
- University of Maryland School of MedicineBaltimoreUnited States
| | - Alexander R Pico
- Institute of Data Science and Biotechnology, Gladstone InstitutesSan FranciscoUnited States
| | - Timothy Putman
- Department of Integrative Structural and Computational Biology, The Scripps Research InstituteLa JollaUnited States
| | - Anders Riutta
- Institute of Data Science and Biotechnology, Gladstone InstitutesSan FranciscoUnited States
| | - Nuria Queralt-Rosinach
- Department of Integrative Structural and Computational Biology, The Scripps Research InstituteLa JollaUnited States
| | - Lynn M Schriml
- University of Maryland School of MedicineBaltimoreUnited States
| | - Thomas Shafee
- Department of Animal Plant and Soil Sciences, La Trobe UniversityMelbourneAustralia
| | - Denise Slenter
- Department of Bioinformatics-BiGCaT, NUTRIM, Maastricht UniversityMaastrichtNetherlands
| | | | | | - Ginger Tsueng
- Department of Integrative Structural and Computational Biology, The Scripps Research InstituteLa JollaUnited States
| | - Roger Tu
- Department of Integrative Structural and Computational Biology, The Scripps Research InstituteLa JollaUnited States
| | - Sabah Ul-Hasan
- Department of Integrative Structural and Computational Biology, The Scripps Research InstituteLa JollaUnited States
| | - Egon Willighagen
- Department of Bioinformatics-BiGCaT, NUTRIM, Maastricht UniversityMaastrichtNetherlands
| | - Chunlei Wu
- Department of Integrative Structural and Computational Biology, The Scripps Research InstituteLa JollaUnited States
| | - Andrew I Su
- Department of Integrative Structural and Computational Biology, The Scripps Research InstituteLa JollaUnited States
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Comandante-Lou N, Khaliq M, Venkat D, Manikkam M, Fallahi-Sichani M. Phenotype-based probabilistic analysis of heterogeneous responses to cancer drugs and their combination efficacy. PLoS Comput Biol 2020; 16:e1007688. [PMID: 32084135 PMCID: PMC7055924 DOI: 10.1371/journal.pcbi.1007688] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2019] [Revised: 03/04/2020] [Accepted: 01/27/2020] [Indexed: 12/12/2022] Open
Abstract
Cell-to-cell variability generates subpopulations of drug-tolerant cells that diminish the efficacy of cancer drugs. Efficacious combination therapies are thus needed to block drug-tolerant cells via minimizing the impact of heterogeneity. Probabilistic models such as Bliss independence have been developed to evaluate drug interactions and their combination efficacy based on probabilities of specific actions mediated by drugs individually and in combination. In practice, however, these models are often applied to conventional dose-response curves in which a normalized parameter with a value between zero and one, generally referred to as fraction of cells affected (fa), is used to evaluate the efficacy of drugs and their combined interactions. We use basic probability theory, computer simulations, time-lapse live cell microscopy, and single-cell analysis to show that fa metrics may bias our assessment of drug efficacy and combination effectiveness. This bias may be corrected when dynamic probabilities of drug-induced phenotypic events, i.e. induction of cell death and inhibition of division, at a single-cell level are used as metrics to assess drug efficacy. Probabilistic phenotype metrics offer the following three benefits. First, in contrast to the commonly used fa metrics, they directly represent probabilities of drug action in a cell population. Therefore, they deconvolve differential degrees of drug effect on tumor cell killing versus inhibition of cell division, which may not be correlated for many drugs. Second, they increase the sensitivity of short-term drug response assays to cell-to-cell heterogeneities and the presence of drug-tolerant subpopulations. Third, their probabilistic nature allows them to be used directly in unbiased evaluation of synergistic efficacy in drug combinations using probabilistic models such as Bliss independence. Altogether, we envision that probabilistic analysis of single-cell phenotypes complements currently available assays via improving our understanding of heterogeneity in drug response, thereby facilitating the discovery of more efficacious combination therapies to block drug-tolerant cells.
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Affiliation(s)
- Natacha Comandante-Lou
- Department of Biomedical Engineering, University of Michigan Medical School, Ann Arbor, Michigan, United States of America
| | - Mehwish Khaliq
- Department of Biomedical Engineering, University of Michigan Medical School, Ann Arbor, Michigan, United States of America
- Program in Cancer Biology, University of Michigan Medical School, Ann Arbor, Michigan, United States of America
| | - Divya Venkat
- Department of Biochemistry, University of Michigan Medical School, Ann Arbor, Michigan, United States of America
| | - Mohan Manikkam
- Department of Biomedical Engineering, University of Michigan Medical School, Ann Arbor, Michigan, United States of America
| | - Mohammad Fallahi-Sichani
- Department of Biomedical Engineering, University of Michigan Medical School, Ann Arbor, Michigan, United States of America
- Program in Cancer Biology, University of Michigan Medical School, Ann Arbor, Michigan, United States of America
- Department of Dermatology, University of Michigan, Ann Arbor, Michigan, United States of America
- * E-mail:
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43
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Huot JR, Novinger LJ, Pin F, Bonetto A. HCT116 colorectal liver metastases exacerbate muscle wasting in a mouse model for the study of colorectal cancer cachexia. Dis Model Mech 2020; 13:dmm043166. [PMID: 31915140 PMCID: PMC6994937 DOI: 10.1242/dmm.043166] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2019] [Accepted: 12/16/2019] [Indexed: 12/24/2022] Open
Abstract
Colorectal cancer (CRC) is often accompanied by formation of liver metastases (LM) and skeletal muscle wasting, i.e. cachexia. Despite affecting the majority of CRC patients, cachexia remains underserved, understudied and uncured. Animal models for the study of CRC-induced cachexia, in particular models containing LM, are sparse; therefore, we aimed to characterize two new models of CRC cachexia. Male NSG mice were injected subcutaneously (HCT116) or intrasplenically (mHCT116) with human HCT116 CRC tumor cells to disseminate LM, whereas experimental controls received saline (n=5-8/group). Tumor growth was accompanied by loss of skeletal muscle mass (HCT116: -20%; mHCT116: -31%; quadriceps muscle) and strength (HCT116: -20%; mHCT116: -27%), with worsened loss of skeletal muscle mass in mHCT116 compared with HCT116 (gastrocnemius: -19%; tibialis anterior: -22%; quadriceps: -21%). Molecular analyses revealed elevated protein ubiquitination in HCT116, whereas mHCT116 also displayed elevated Murf1 and atrogin-1 expression, along with reduced mitochondrial proteins PGC1α, OPA1, mitofusin 2 and cytochrome C. Further, elevated IL6 levels were found in the blood of mHCT116 hosts, which was associated with higher phosphorylation of STAT3 in skeletal muscle. To clarify whether STAT3 was a main player in muscle wasting in this model, HCT116 cells were co-cultured with C2C12 myotubes. Marked myotube atrophy (-53%) was observed, along with elevated phospho-STAT3 levels (+149%). Conversely, inhibition of STAT3 signaling by means of a JAK/STAT3 inhibitor was sufficient to rescue myotube atrophy induced by HCT116 cells (+55%). Overall, our results indicate that the formation of LM exacerbates cachectic phenotype and associated skeletal muscle molecular alterations in HCT116 tumor hosts.
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Affiliation(s)
- Joshua R Huot
- Department of Surgery, Indiana University School of Medicine, Indianapolis, IN 46202, USA
| | - Leah J Novinger
- Department of Otolaryngology - Head & Neck Surgery, Indiana University School of Medicine, Indianapolis, IN 46202, USA
| | - Fabrizio Pin
- Department of Anatomy, Cell Biology and Physiology, Indiana University School of Medicine, Indianapolis, IN 46202, USA
| | - Andrea Bonetto
- Department of Surgery, Indiana University School of Medicine, Indianapolis, IN 46202, USA
- Department of Otolaryngology - Head & Neck Surgery, Indiana University School of Medicine, Indianapolis, IN 46202, USA
- Department of Anatomy, Cell Biology and Physiology, Indiana University School of Medicine, Indianapolis, IN 46202, USA
- Indiana Center for Musculoskeletal Health, Indiana University School of Medicine, Indianapolis, IN 46202, USA
- IUPUI Center for Cachexia Research Innovation and Therapy, Indiana University School of Medicine, Indianapolis, IN 46202, USA
- Simon Cancer Center, Indiana University School of Medicine, Indianapolis, IN 46202, USA
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44
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Nelson BS, Lin L, Kremer DM, Sousa CM, Cotta-Ramusino C, Myers A, Ramos J, Gao T, Kovalenko I, Wilder-Romans K, Dresser J, Davis M, Lee HJ, Nwosu ZC, Campit S, Mashadova O, Nicolay BN, Tolstyka ZP, Halbrook CJ, Chandrasekaran S, Asara JM, Crawford HC, Cantley LC, Kimmelman AC, Wahl DR, Lyssiotis CA. Tissue of origin dictates GOT1 dependence and confers synthetic lethality to radiotherapy. Cancer Metab 2020; 8:1. [PMID: 31908776 PMCID: PMC6941320 DOI: 10.1186/s40170-019-0202-2] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2019] [Accepted: 11/20/2019] [Indexed: 12/20/2022] Open
Abstract
BACKGROUND Metabolic programs in cancer cells are influenced by genotype and the tissue of origin. We have previously shown that central carbon metabolism is rewired in pancreatic ductal adenocarcinoma (PDA) to support proliferation through a glutamate oxaloacetate transaminase 1 (GOT1)-dependent pathway. METHODS We utilized a doxycycline-inducible shRNA-mediated strategy to knockdown GOT1 in PDA and colorectal cancer (CRC) cell lines and tumor models of similar genotype. These cells were analyzed for the ability to form colonies and tumors to test if tissue type impacted GOT1 dependence. Additionally, the ability of GOT1 to impact the response to chemo- and radiotherapy was assessed. Mechanistically, the associated specimens were examined using a combination of steady-state and stable isotope tracing metabolomics strategies and computational modeling. Statistics were calculated using GraphPad Prism 7. One-way ANOVA was performed for experiments comparing multiple groups with one changing variable. Student's t test (unpaired, two-tailed) was performed when comparing two groups to each other. Metabolomics data comparing three PDA and three CRC cell lines were analyzed by performing Student's t test (unpaired, two-tailed) between all PDA metabolites and CRC metabolites. RESULTS While PDA exhibits profound growth inhibition upon GOT1 knockdown, we found CRC to be insensitive. In PDA, but not CRC, GOT1 inhibition disrupted glycolysis, nucleotide metabolism, and redox homeostasis. These insights were leveraged in PDA, where we demonstrate that radiotherapy potently enhanced the effect of GOT1 inhibition on tumor growth. CONCLUSIONS Taken together, these results illustrate the role of tissue type in dictating metabolic dependencies and provide new insights for targeting metabolism to treat PDA.
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Affiliation(s)
- Barbara S. Nelson
- Department of Molecular and Integrative Physiology, University of Michigan Medical School, Ann Arbor, MI 48109 USA
- Division of Genomic Stability and DNA Repair, Department of Radiation Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02215 USA
- Experimental Therapeutics Core and Belfer Center for Applied Cancer Science, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02215 USA
- Department of Radiation Oncology, University of Michigan Medical School, Ann Arbor, MI 48109 USA
- Department of Biomedical Engineering, University of Michigan Medical School, Ann Arbor, MI 48109 USA
- Meyer Cancer Center, Weill Cornell Medicine, New York City, NY 10065 USA
- Agios Pharmaceuticals, Inc., Cambridge, MA 02139 USA
- Beth Israel Deaconess Medical Center and Harvard Medical School, Boston, MA 02115 USA
- Center for Computational Medicine and Bioinformatics, University of Michigan Medical School, Ann Arbor, MI 48109 USA
- Rogel Cancer Center, University of Michigan Medical School, Ann Arbor, MI 48109 USA
- Department of Internal Medicine, Division of Gastroenterology and Hepatology, University of Michigan Medical School, Ann Arbor, MI 48109 USA
- Department of Radiation Oncology, Perlmutter Cancer Center, NYU Langone Medical Center, New York, NY 10016 USA
| | - Lin Lin
- Department of Molecular and Integrative Physiology, University of Michigan Medical School, Ann Arbor, MI 48109 USA
- Division of Genomic Stability and DNA Repair, Department of Radiation Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02215 USA
- Experimental Therapeutics Core and Belfer Center for Applied Cancer Science, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02215 USA
- Department of Radiation Oncology, University of Michigan Medical School, Ann Arbor, MI 48109 USA
- Department of Biomedical Engineering, University of Michigan Medical School, Ann Arbor, MI 48109 USA
- Meyer Cancer Center, Weill Cornell Medicine, New York City, NY 10065 USA
- Agios Pharmaceuticals, Inc., Cambridge, MA 02139 USA
- Beth Israel Deaconess Medical Center and Harvard Medical School, Boston, MA 02115 USA
- Center for Computational Medicine and Bioinformatics, University of Michigan Medical School, Ann Arbor, MI 48109 USA
- Rogel Cancer Center, University of Michigan Medical School, Ann Arbor, MI 48109 USA
- Department of Internal Medicine, Division of Gastroenterology and Hepatology, University of Michigan Medical School, Ann Arbor, MI 48109 USA
- Department of Radiation Oncology, Perlmutter Cancer Center, NYU Langone Medical Center, New York, NY 10016 USA
| | - Daniel M. Kremer
- Department of Molecular and Integrative Physiology, University of Michigan Medical School, Ann Arbor, MI 48109 USA
| | - Cristovão M. Sousa
- Division of Genomic Stability and DNA Repair, Department of Radiation Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02215 USA
- Agios Pharmaceuticals, Inc., Cambridge, MA 02139 USA
| | - Cecilia Cotta-Ramusino
- Experimental Therapeutics Core and Belfer Center for Applied Cancer Science, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02215 USA
| | - Amy Myers
- Department of Molecular and Integrative Physiology, University of Michigan Medical School, Ann Arbor, MI 48109 USA
| | - Johanna Ramos
- Department of Molecular and Integrative Physiology, University of Michigan Medical School, Ann Arbor, MI 48109 USA
| | - Tina Gao
- Department of Molecular and Integrative Physiology, University of Michigan Medical School, Ann Arbor, MI 48109 USA
| | - Ilya Kovalenko
- Department of Molecular and Integrative Physiology, University of Michigan Medical School, Ann Arbor, MI 48109 USA
| | - Kari Wilder-Romans
- Department of Radiation Oncology, University of Michigan Medical School, Ann Arbor, MI 48109 USA
| | - Joseph Dresser
- Department of Radiation Oncology, University of Michigan Medical School, Ann Arbor, MI 48109 USA
| | - Mary Davis
- Department of Radiation Oncology, University of Michigan Medical School, Ann Arbor, MI 48109 USA
| | - Ho-Joon Lee
- Department of Molecular and Integrative Physiology, University of Michigan Medical School, Ann Arbor, MI 48109 USA
| | - Zeribe C. Nwosu
- Department of Molecular and Integrative Physiology, University of Michigan Medical School, Ann Arbor, MI 48109 USA
| | - Scott Campit
- Department of Biomedical Engineering, University of Michigan Medical School, Ann Arbor, MI 48109 USA
| | - Oksana Mashadova
- Meyer Cancer Center, Weill Cornell Medicine, New York City, NY 10065 USA
| | | | - Zachary P. Tolstyka
- Department of Molecular and Integrative Physiology, University of Michigan Medical School, Ann Arbor, MI 48109 USA
| | - Christopher J. Halbrook
- Department of Molecular and Integrative Physiology, University of Michigan Medical School, Ann Arbor, MI 48109 USA
| | - Sriram Chandrasekaran
- Department of Biomedical Engineering, University of Michigan Medical School, Ann Arbor, MI 48109 USA
- Center for Computational Medicine and Bioinformatics, University of Michigan Medical School, Ann Arbor, MI 48109 USA
- Rogel Cancer Center, University of Michigan Medical School, Ann Arbor, MI 48109 USA
| | - John M. Asara
- Beth Israel Deaconess Medical Center and Harvard Medical School, Boston, MA 02115 USA
| | - Howard C. Crawford
- Department of Molecular and Integrative Physiology, University of Michigan Medical School, Ann Arbor, MI 48109 USA
- Rogel Cancer Center, University of Michigan Medical School, Ann Arbor, MI 48109 USA
- Department of Internal Medicine, Division of Gastroenterology and Hepatology, University of Michigan Medical School, Ann Arbor, MI 48109 USA
| | - Lewis C. Cantley
- Meyer Cancer Center, Weill Cornell Medicine, New York City, NY 10065 USA
| | - Alec C. Kimmelman
- Division of Genomic Stability and DNA Repair, Department of Radiation Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02215 USA
- Department of Radiation Oncology, Perlmutter Cancer Center, NYU Langone Medical Center, New York, NY 10016 USA
| | - Daniel R. Wahl
- Department of Radiation Oncology, University of Michigan Medical School, Ann Arbor, MI 48109 USA
- Rogel Cancer Center, University of Michigan Medical School, Ann Arbor, MI 48109 USA
| | - Costas A. Lyssiotis
- Department of Molecular and Integrative Physiology, University of Michigan Medical School, Ann Arbor, MI 48109 USA
- Rogel Cancer Center, University of Michigan Medical School, Ann Arbor, MI 48109 USA
- Department of Internal Medicine, Division of Gastroenterology and Hepatology, University of Michigan Medical School, Ann Arbor, MI 48109 USA
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45
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Flores C, Wildes T, Dean BD, Moore G, Drake J, Abraham R, Gil J, Yegorov O, Yang C, Dean J, Moneypenny C, Shin D, Pham C, Krauser J, King J, Grant G, Driscoll T, Kurtzberg J, McLendon R, Gururangan S, Mitchell D. Massive clonal expansion of medulloblastoma-specific T cells during adoptive cellular therapy. Sci Adv 2019; 5:eaav9879. [PMID: 31807694 PMCID: PMC6881165 DOI: 10.1126/sciadv.aav9879] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/07/2018] [Accepted: 09/17/2019] [Indexed: 05/04/2023]
Abstract
In both human and murine systems, we have developed an adoptive cellular therapy platform against medulloblastoma and glioblastoma that uses dendritic cells pulsed with a tumor RNA transcriptome to expand polyclonal tumor-reactive T cells against a plurality of antigens within heterogeneous brain tumors. We demonstrate that peripheral TCR Vβ repertoire analysis after adoptive cellular therapy reveals that effective response to adoptive cellular therapy is concordant with massive in vivo expansion and persistence of tumor-specific T cell clones within the peripheral blood. In preclinical models of medulloblastoma and glioblastoma, and in a patient with relapsed medulloblastoma receiving adoptive cellular therapy, an early and massive expansion of tumor-reactive lymphocytes, coupled with prolonged persistence in the peripheral blood, is observed during effective therapeutic response to immunotherapy treatment.
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Affiliation(s)
- C. Flores
- University of Florida Brain Tumor Immunotherapy Program, Preston A. Wells, Jr. Center for Brain Tumor Therapy, Lillian S. Wells Department of Neurosurgery, McKnight Brain Institute, University of Florida, Gainesville, FL, USA
| | - T. Wildes
- University of Florida Brain Tumor Immunotherapy Program, Preston A. Wells, Jr. Center for Brain Tumor Therapy, Lillian S. Wells Department of Neurosurgery, McKnight Brain Institute, University of Florida, Gainesville, FL, USA
| | - B. DiVita Dean
- University of Florida Brain Tumor Immunotherapy Program, Preston A. Wells, Jr. Center for Brain Tumor Therapy, Lillian S. Wells Department of Neurosurgery, McKnight Brain Institute, University of Florida, Gainesville, FL, USA
| | - G. Moore
- University of Florida Brain Tumor Immunotherapy Program, Preston A. Wells, Jr. Center for Brain Tumor Therapy, Lillian S. Wells Department of Neurosurgery, McKnight Brain Institute, University of Florida, Gainesville, FL, USA
| | - J. Drake
- University of Florida Brain Tumor Immunotherapy Program, Preston A. Wells, Jr. Center for Brain Tumor Therapy, Lillian S. Wells Department of Neurosurgery, McKnight Brain Institute, University of Florida, Gainesville, FL, USA
| | - R. Abraham
- University of Florida Brain Tumor Immunotherapy Program, Preston A. Wells, Jr. Center for Brain Tumor Therapy, Lillian S. Wells Department of Neurosurgery, McKnight Brain Institute, University of Florida, Gainesville, FL, USA
| | - J. Gil
- University of Florida Brain Tumor Immunotherapy Program, Preston A. Wells, Jr. Center for Brain Tumor Therapy, Lillian S. Wells Department of Neurosurgery, McKnight Brain Institute, University of Florida, Gainesville, FL, USA
| | - O. Yegorov
- University of Florida Brain Tumor Immunotherapy Program, Preston A. Wells, Jr. Center for Brain Tumor Therapy, Lillian S. Wells Department of Neurosurgery, McKnight Brain Institute, University of Florida, Gainesville, FL, USA
| | - C. Yang
- University of Florida Brain Tumor Immunotherapy Program, Preston A. Wells, Jr. Center for Brain Tumor Therapy, Lillian S. Wells Department of Neurosurgery, McKnight Brain Institute, University of Florida, Gainesville, FL, USA
| | - J. Dean
- University of Florida Brain Tumor Immunotherapy Program, Preston A. Wells, Jr. Center for Brain Tumor Therapy, Lillian S. Wells Department of Neurosurgery, McKnight Brain Institute, University of Florida, Gainesville, FL, USA
| | - C. Moneypenny
- University of Florida Brain Tumor Immunotherapy Program, Preston A. Wells, Jr. Center for Brain Tumor Therapy, Lillian S. Wells Department of Neurosurgery, McKnight Brain Institute, University of Florida, Gainesville, FL, USA
| | - D. Shin
- University of Florida Brain Tumor Immunotherapy Program, Preston A. Wells, Jr. Center for Brain Tumor Therapy, Lillian S. Wells Department of Neurosurgery, McKnight Brain Institute, University of Florida, Gainesville, FL, USA
- U.S. Army, 1600 Spearhead Division Ave., Fort Knox, KY, USA
| | - C. Pham
- University of Florida Brain Tumor Immunotherapy Program, Preston A. Wells, Jr. Center for Brain Tumor Therapy, Lillian S. Wells Department of Neurosurgery, McKnight Brain Institute, University of Florida, Gainesville, FL, USA
| | - J. Krauser
- University of Florida Brain Tumor Immunotherapy Program, Preston A. Wells, Jr. Center for Brain Tumor Therapy, Lillian S. Wells Department of Neurosurgery, McKnight Brain Institute, University of Florida, Gainesville, FL, USA
| | - J. King
- University of Florida Brain Tumor Immunotherapy Program, Preston A. Wells, Jr. Center for Brain Tumor Therapy, Lillian S. Wells Department of Neurosurgery, McKnight Brain Institute, University of Florida, Gainesville, FL, USA
| | - G. Grant
- Department of Neurosurgery, Stanford University Medical Center, Palo Alto, CA, USA
| | - T. Driscoll
- Department of Pediatrics, Duke University Medical Center, Durham, NC, USA
| | - J. Kurtzberg
- Department of Pediatrics, Duke University Medical Center, Durham, NC, USA
| | - R. McLendon
- Department of Pathology, Duke University Medical Center, Durham, NC, USA
| | - S. Gururangan
- University of Florida Brain Tumor Immunotherapy Program, Preston A. Wells, Jr. Center for Brain Tumor Therapy, Lillian S. Wells Department of Neurosurgery, McKnight Brain Institute, University of Florida, Gainesville, FL, USA
- Department of Pediatrics, University of Florida, Gainesville, FL, USA
| | - D. Mitchell
- University of Florida Brain Tumor Immunotherapy Program, Preston A. Wells, Jr. Center for Brain Tumor Therapy, Lillian S. Wells Department of Neurosurgery, McKnight Brain Institute, University of Florida, Gainesville, FL, USA
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Richters MM, Xia H, Campbell KM, Gillanders WE, Griffith OL, Griffith M. Best practices for bioinformatic characterization of neoantigens for clinical utility. Genome Med 2019; 11:56. [PMID: 31462330 PMCID: PMC6714459 DOI: 10.1186/s13073-019-0666-2] [Citation(s) in RCA: 113] [Impact Index Per Article: 22.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2019] [Accepted: 08/16/2019] [Indexed: 12/13/2022] Open
Abstract
Neoantigens are newly formed peptides created from somatic mutations that are capable of inducing tumor-specific T cell recognition. Recently, researchers and clinicians have leveraged next generation sequencing technologies to identify neoantigens and to create personalized immunotherapies for cancer treatment. To create a personalized cancer vaccine, neoantigens must be computationally predicted from matched tumor-normal sequencing data, and then ranked according to their predicted capability in stimulating a T cell response. This candidate neoantigen prediction process involves multiple steps, including somatic mutation identification, HLA typing, peptide processing, and peptide-MHC binding prediction. The general workflow has been utilized for many preclinical and clinical trials, but there is no current consensus approach and few established best practices. In this article, we review recent discoveries, summarize the available computational tools, and provide analysis considerations for each step, including neoantigen prediction, prioritization, delivery, and validation methods. In addition to reviewing the current state of neoantigen analysis, we provide practical guidance, specific recommendations, and extensive discussion of critical concepts and points of confusion in the practice of neoantigen characterization for clinical use. Finally, we outline necessary areas of development, including the need to improve HLA class II typing accuracy, to expand software support for diverse neoantigen sources, and to incorporate clinical response data to improve neoantigen prediction algorithms. The ultimate goal of neoantigen characterization workflows is to create personalized vaccines that improve patient outcomes in diverse cancer types.
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Affiliation(s)
- Megan M Richters
- Division of Oncology, Department of Internal Medicine, Washington University School of Medicine, St. Louis, MO, 63110, USA
- McDonnell Genome Institute, Forest Park Avenue, Washington University School of Medicine, St. Louis, MO, 63108, USA
| | - Huiming Xia
- Division of Oncology, Department of Internal Medicine, Washington University School of Medicine, St. Louis, MO, 63110, USA
- McDonnell Genome Institute, Forest Park Avenue, Washington University School of Medicine, St. Louis, MO, 63108, USA
| | - Katie M Campbell
- Division of Hematology and Oncology, Medical Plaza Driveway, Department of Medicine, University of California, Los Angeles, Los Angeles, CA, 90024, USA
| | - William E Gillanders
- Department of Surgery, South Euclid Avenue, Washington University School of Medicine, St. Louis, MO, 63110, USA
- Siteman Cancer Center, Parkview Place, Washington University School of Medicine, St. Louis, MO, 63110, USA
| | - Obi L Griffith
- Division of Oncology, Department of Internal Medicine, Washington University School of Medicine, St. Louis, MO, 63110, USA.
- McDonnell Genome Institute, Forest Park Avenue, Washington University School of Medicine, St. Louis, MO, 63108, USA.
- Siteman Cancer Center, Parkview Place, Washington University School of Medicine, St. Louis, MO, 63110, USA.
- Department of Genetics, South Euclid Avenue, Washington University School of Medicine, St. Louis, MO, 63110, USA.
| | - Malachi Griffith
- Division of Oncology, Department of Internal Medicine, Washington University School of Medicine, St. Louis, MO, 63110, USA.
- McDonnell Genome Institute, Forest Park Avenue, Washington University School of Medicine, St. Louis, MO, 63108, USA.
- Siteman Cancer Center, Parkview Place, Washington University School of Medicine, St. Louis, MO, 63110, USA.
- Department of Genetics, South Euclid Avenue, Washington University School of Medicine, St. Louis, MO, 63110, USA.
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Lee HJ, Kremer DM, Sajjakulnukit P, Zhang L, Lyssiotis CA. A large-scale analysis of targeted metabolomics data from heterogeneous biological samples provides insights into metabolite dynamics. Metabolomics 2019; 15:103. [PMID: 31289941 PMCID: PMC6616221 DOI: 10.1007/s11306-019-1564-8] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/25/2019] [Accepted: 06/20/2019] [Indexed: 12/31/2022]
Abstract
INTRODUCTION We previously developed a tandem mass spectrometry-based label-free targeted metabolomics analysis framework coupled to two distinct chromatographic methods, reversed-phase liquid chromatography (RPLC) and hydrophilic interaction liquid chromatography (HILIC), with dynamic multiple reaction monitoring (dMRM) for simultaneous detection of over 200 metabolites to study core metabolic pathways. OBJECTIVES We aim to analyze a large-scale heterogeneous data compendium generated from our LC-MS/MS platform with both RPLC and HILIC methods to systematically assess measurement quality in biological replicate groups and to investigate metabolite abundance changes and patterns across different biological conditions. METHODS Our metabolomics framework was applied in a wide range of experimental systems including cancer cell lines, tumors, extracellular media, primary cells, immune cells, organoids, organs (e.g. pancreata), tissues, and sera from human and mice. We also developed computational and statistical analysis pipelines, which include hierarchical clustering, replicate-group CV analysis, correlation analysis, and case-control paired analysis. RESULTS We generated a compendium of 42 heterogeneous deidentified datasets with 635 samples using both RPLC and HILIC methods. There exist metabolite signatures that correspond to various phenotypes of the heterogeneous datasets, involved in several metabolic pathways. The RPLC method shows overall better reproducibility than the HILIC method for most metabolites including polar amino acids. Correlation analysis reveals high confidence metabolites irrespective of experimental systems such as methionine, phenylalanine, and taurine. We also identify homocystine, reduced glutathione, and phosphoenolpyruvic acid as highly dynamic metabolites across all case-control paired samples. CONCLUSIONS Our study is expected to serve as a resource and a reference point for a systematic analysis of label-free LC-MS/MS targeted metabolomics data in both RPLC and HILIC methods with dMRM.
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Affiliation(s)
- Ho-Joon Lee
- Department of Molecular and Integrative Physiology, University of Michigan Medical School, Ann Arbor, MI, 48109, USA.
- Center for Computational Medicine and Bioinformatics, University of Michigan Medical School, Ann Arbor, MI, 48109, USA.
- Michigan Institute for Data Science, University of Michigan, Ann Arbor, MI, 48109, USA.
- Rogel Cancer Center, University of Michigan, Ann Arbor, MI, 48109, USA.
| | - Daniel M Kremer
- Department of Molecular and Integrative Physiology, University of Michigan Medical School, Ann Arbor, MI, 48109, USA
| | - Peter Sajjakulnukit
- Department of Molecular and Integrative Physiology, University of Michigan Medical School, Ann Arbor, MI, 48109, USA
| | - Li Zhang
- Department of Molecular and Integrative Physiology, University of Michigan Medical School, Ann Arbor, MI, 48109, USA
- Michigan Regional Comprehensive Metabolomics Resource Core, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Costas A Lyssiotis
- Department of Molecular and Integrative Physiology, University of Michigan Medical School, Ann Arbor, MI, 48109, USA.
- Rogel Cancer Center, University of Michigan, Ann Arbor, MI, 48109, USA.
- Department of Internal Medicine, Division of Gastroenterology and Hepatology, University of Michigan Medical School, Ann Arbor, MI, 48109, USA.
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Su Y, Bintz M, Yang Y, Robert L, Ng AHC, Liu V, Ribas A, Heath JR, Wei W. Phenotypic heterogeneity and evolution of melanoma cells associated with targeted therapy resistance. PLoS Comput Biol 2019; 15:e1007034. [PMID: 31166947 PMCID: PMC6576794 DOI: 10.1371/journal.pcbi.1007034] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2018] [Revised: 06/17/2019] [Accepted: 04/15/2019] [Indexed: 01/26/2023] Open
Abstract
Phenotypic plasticity is associated with non-genetic drug tolerance in several cancers. Such plasticity can arise from chromatin remodeling, transcriptomic reprogramming, and/or protein signaling rewiring, and is characterized as a cell state transition in response to molecular or physical perturbations. This, in turn, can confound interpretations of drug responses and resistance development. Using BRAF-mutant melanoma cell lines as the prototype, we report on a joint theoretical and experimental investigation of the cell-state transition dynamics associated with BRAF inhibitor drug tolerance. Thermodynamically motivated surprisal analysis of transcriptome data was used to treat the cell population as an entropy maximizing system under the influence of time-dependent constraints. This permits the extraction of an epigenetic potential landscape for drug-induced phenotypic evolution. Single-cell flow cytometry data of the same system were modeled with a modified Fokker-Planck-type kinetic model. The two approaches yield a consistent picture that accounts for the phenotypic heterogeneity observed over the course of drug tolerance development. The results reveal that, in certain plastic cancers, the population heterogeneity and evolution of cell phenotypes may be understood by accounting for the competing interactions of the epigenetic potential landscape and state-dependent cell proliferation. Accounting for such competition permits accurate, experimentally verifiable predictions that can potentially guide the design of effective treatment strategies. Cancer cells exhibit varied degrees of phenotypic heterogeneity. These phenotypes, each of them with unique molecular and functional profiles, display dynamic interconversion in response to drug perturbations, and can evolve to form new drug-tolerant phenotypes. Such phenotypic plasticity, in turn, renders tumor cells extremely difficult to treat. To get a quantitative biophysical understanding of the origins of the phenotypic equilibrium and evolution associated with drug tolerance development in highly plastic patient-derived melanoma cells, we employed joint experimental and computational approaches, using either bulk or single cell measurements as input, to interrogate the epigenetic landscape of the phenotypic evolution. We found that the observed phenotypic equilibria were established via competition between state-dependent net proliferation rates and landscape potential. The results reveal how the tumor cells maintain a phenotypic heterogeneity that facilitates appropriate responses to external cues. They implicate that, in certain phenotypically plastic tumor cells, drug targeting the driver oncogenes may not have sustained efficacy unless the phenotypic plasticity of the tumor is co-targeted.
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Affiliation(s)
- Yapeng Su
- Institute for Systems Biology, Seattle, Washington, United State of America
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California, United State of America
| | - Marcus Bintz
- Department of Molecular and Medical Pharmacology, University of California – Los Angeles, Los Angeles, California, United State of America
| | - Yezi Yang
- Department of Molecular and Medical Pharmacology, University of California – Los Angeles, Los Angeles, California, United State of America
| | - Lidia Robert
- Department of Medicine, University of California – Los Angeles, Los Angeles, California, United State of America
| | - Alphonsus H. C. Ng
- Institute for Systems Biology, Seattle, Washington, United State of America
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California, United State of America
| | - Victoria Liu
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California, United State of America
| | - Antoni Ribas
- Department of Molecular and Medical Pharmacology, University of California – Los Angeles, Los Angeles, California, United State of America
- Department of Medicine, University of California – Los Angeles, Los Angeles, California, United State of America
- Department of Surgery, Division of Surgical-Oncology, University of California – Los Angeles, Los Angeles, California, United State of America
- Jonsson Comprehensive Cancer Center, University of California – Los Angeles, Los Angeles, California, United State of America
| | - James R. Heath
- Institute for Systems Biology, Seattle, Washington, United State of America
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California, United State of America
- Jonsson Comprehensive Cancer Center, University of California – Los Angeles, Los Angeles, California, United State of America
- * E-mail: (J.R.H.); (W.W.)
| | - Wei Wei
- Institute for Systems Biology, Seattle, Washington, United State of America
- Department of Molecular and Medical Pharmacology, University of California – Los Angeles, Los Angeles, California, United State of America
- Jonsson Comprehensive Cancer Center, University of California – Los Angeles, Los Angeles, California, United State of America
- * E-mail: (J.R.H.); (W.W.)
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Wong KY, Fan C, Tanioka M, Parker JS, Nobel AB, Zeng D, Lin DY, Perou CM. I-Boost: an integrative boosting approach for predicting survival time with multiple genomics platforms. Genome Biol 2019; 20:52. [PMID: 30845957 PMCID: PMC6404283 DOI: 10.1186/s13059-019-1640-4] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2018] [Accepted: 01/23/2019] [Indexed: 11/30/2022] Open
Abstract
We propose a statistical boosting method, termed I-Boost, to integrate multiple types of high-dimensional genomics data with clinical data for predicting survival time. I-Boost provides substantially higher prediction accuracy than existing methods. By applying I-Boost to The Cancer Genome Atlas, we show that the integration of multiple genomics platforms with clinical variables improves the prediction of survival time over the use of clinical variables alone; gene expression values are typically more prognostic of survival time than other genomics data types; and gene modules/signatures are at least as prognostic as the collection of individual gene expression data.
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Affiliation(s)
- Kin Yau Wong
- Department of Applied Mathematics, The Hong Kong Polytechnic University, Hung Hom, Hong Kong
| | - Cheng Fan
- Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, 27599 NC USA
| | - Maki Tanioka
- Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, 27599 NC USA
- Department of Genetics, University of North Carolina, Chapel Hill, 27599 NC USA
| | - Joel S. Parker
- Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, 27599 NC USA
- Department of Genetics, University of North Carolina, Chapel Hill, 27599 NC USA
| | - Andrew B. Nobel
- Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, 27599 NC USA
- Department of Statistics and Operations Research, University of North Carolina, Chapel Hill, 27599 NC USA
- Department of Biostatistics, University of North Carolina, Chapel Hill, 27599 NC USA
| | - Donglin Zeng
- Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, 27599 NC USA
- Department of Biostatistics, University of North Carolina, Chapel Hill, 27599 NC USA
| | - Dan-Yu Lin
- Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, 27599 NC USA
- Department of Biostatistics, University of North Carolina, Chapel Hill, 27599 NC USA
| | - Charles M. Perou
- Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, 27599 NC USA
- Department of Genetics, University of North Carolina, Chapel Hill, 27599 NC USA
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Bhoyar S, Godet I, DiGiacomo JW, Gilkes DM. A software tool for the quantification of metastatic colony growth dynamics and size distributions in vitro and in vivo. PLoS One 2018; 13:e0209591. [PMID: 30589908 PMCID: PMC6307751 DOI: 10.1371/journal.pone.0209591] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2018] [Accepted: 12/07/2018] [Indexed: 02/07/2023] Open
Abstract
The majority of cancer-related deaths are due to metastasis, hence improved methods to biologically and computationally model metastasis are required. Computational models rely on robust data that is machine-readable. The current methods used to model metastasis in mice involve generating primary tumors by injecting human cells into immune-compromised mice, or by examining genetically engineered mice that are pre-disposed to tumor development and that eventually metastasize. The degree of metastasis can be measured using flow cytometry, bioluminescence imaging, quantitative PCR, and/or by manually counting individual lesions from metastatic tissue sections. The aforementioned methods are time-consuming and do not provide information on size distribution or spatial localization of individual metastatic lesions. In this work, we describe and provide a MATLAB script for an image-processing based method designed to obtain quantitative data from tissue sections comprised of multiple subpopulations of disseminated cells localized at metastatic sites in vivo. We further show that this method can be easily adapted for high throughput imaging of live or fixed cells in vitro under a multitude of conditions in order to assess clonal fitness and evolution. The inherent variation in mouse studies, increasing complexity in experimental design which incorporate fate-mapping of individual cells, result in the need for a large cohort of mice to generate a robust dataset. High-throughput imaging techniques such as the one that we describe will enhance the data that can be used as input for the development of computational models aimed at modeling the metastatic process.
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Affiliation(s)
- Soumitra Bhoyar
- Department of Chemical and Biomolecular Engineering, The Johns Hopkins University, Baltimore, Maryland, United States of America
- Department of Oncology, The Sidney Kimmel Comprehensive Cancer Center, The Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America
| | - Inês Godet
- Department of Chemical and Biomolecular Engineering, The Johns Hopkins University, Baltimore, Maryland, United States of America
- Department of Oncology, The Sidney Kimmel Comprehensive Cancer Center, The Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America
| | - Josh W. DiGiacomo
- Department of Chemical and Biomolecular Engineering, The Johns Hopkins University, Baltimore, Maryland, United States of America
- Department of Oncology, The Sidney Kimmel Comprehensive Cancer Center, The Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America
| | - Daniele M. Gilkes
- Department of Chemical and Biomolecular Engineering, The Johns Hopkins University, Baltimore, Maryland, United States of America
- Department of Oncology, The Sidney Kimmel Comprehensive Cancer Center, The Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America
- * E-mail:
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