1
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Hosohama L, Tifrea DF, Nee K, Park SY, Wu J, Habowski AN, Van C, Seldin MM, Edwards RA, Waterman ML. Colorectal Cancer Stem Cell Subtypes Orchestrate Distinct Tumor Microenvironments. bioRxiv 2024:2024.04.25.591144. [PMID: 38712298 PMCID: PMC11071458 DOI: 10.1101/2024.04.25.591144] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2024]
Abstract
Several classification systems have been developed to define tumor subtypes in colorectal cancer (CRC). One system proposes that tumor heterogeneity derives in part from distinct cancer stem cell populations that co-exist as admixtures of varying proportions. However, the lack of single cell resolution has prohibited a definitive identification of these types of stem cells and therefore any understanding of how each influence tumor phenotypes. Here were report the isolation and characterization of two cancer stem cell subtypes from the SW480 CRC cell line. We find these cancer stem cells are oncogenic versions of the normal Crypt Base Columnar (CBC) and Regenerative Stem Cell (RSC) populations from intestinal crypts and that their gene signatures are consistent with the "Admixture" and other CRC classification systems. Using publicly available single cell RNA sequencing (scRNAseq) data from CRC patients, we determine that RSC and CBC cancer stem cells are commonly co-present in human CRC. To characterize influences on the tumor microenvironment, we develop subtype-specific xenograft models and we define their tumor microenvironments at high resolution via scRNAseq. RSCs create differentiated, inflammatory, slow growing tumors. CBCs create proliferative, undifferentiated, invasive tumors. With this enhanced resolution, we unify current CRC patient classification schema with TME phenotypes and organization.
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2
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Homer JA, Koelln RA, Barrow AS, Gialelis TL, Boiarska Z, Steinohrt NS, Lee EF, Yang WH, Johnson RM, Chung T, Habowski AN, Vishwakarma DS, Bhunia D, Avanzi C, Moorhouse AD, Jackson M, Tuveson DA, Lyons SK, Lukey MJ, Fairlie WD, Haider SM, Steinmetz MO, Prota AE, Moses JE. Modular synthesis of functional libraries by accelerated SuFEx click chemistry. Chem Sci 2024; 15:3879-3892. [PMID: 38487227 PMCID: PMC10935723 DOI: 10.1039/d3sc05729a] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2023] [Accepted: 02/09/2024] [Indexed: 03/17/2024] Open
Abstract
Accelerated SuFEx Click Chemistry (ASCC) is a powerful method for coupling aryl and alkyl alcohols with SuFEx-compatible functional groups. With its hallmark favorable kinetics and exceptional product yields, ASCC streamlines the synthetic workflow, simplifies the purification process, and is ideally suited for discovering functional molecules. We showcase the versatility and practicality of the ASCC reaction as a tool for the late-stage derivatization of bioactive molecules and in the array synthesis of sulfonate-linked, high-potency, microtubule targeting agents (MTAs) that exhibit nanomolar anticancer activity against multidrug-resistant cancer cell lines. These findings underscore ASCC's promise as a robust platform for drug discovery.
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Affiliation(s)
- Joshua A Homer
- Cancer Center, Cold Spring Harbor Laboratory 1 Bungtown Rd Cold Spring Harbor NY 11724 USA
| | - Rebecca A Koelln
- Cancer Center, Cold Spring Harbor Laboratory 1 Bungtown Rd Cold Spring Harbor NY 11724 USA
| | - Andrew S Barrow
- La Trobe Institute for Molecular Science, La Trobe University Melbourne VIC 3086 Australia
| | - Timothy L Gialelis
- La Trobe Institute for Molecular Science, La Trobe University Melbourne VIC 3086 Australia
| | - Zlata Boiarska
- Laboratory of Biomolecular Research, Division of Biology and Chemistry, Paul Scherrer Institut Villigen PSI 5232 Switzerland
- Department of Chemistry, Università degli Studi di Milano Via Golgi 19 20133 Milan Italy
| | - Nikita S Steinohrt
- Olivia Newton-John Cancer Research Institute Heidelberg Victoria 3084 Australia
- School of Cancer Medicine, La Trobe University Melbourne Victoria 3086 Australia
| | - Erinna F Lee
- Olivia Newton-John Cancer Research Institute Heidelberg Victoria 3084 Australia
- School of Cancer Medicine, La Trobe University Melbourne Victoria 3086 Australia
- Department of Biochemistry and Chemistry, La Trobe Institute for Molecular Science, La Trobe University Melbourne Victoria 3086 Australia
| | - Wen-Hsuan Yang
- Cancer Center, Cold Spring Harbor Laboratory 1 Bungtown Rd Cold Spring Harbor NY 11724 USA
| | - Robert M Johnson
- Cancer Center, Cold Spring Harbor Laboratory 1 Bungtown Rd Cold Spring Harbor NY 11724 USA
| | - Taemoon Chung
- Cancer Center, Cold Spring Harbor Laboratory 1 Bungtown Rd Cold Spring Harbor NY 11724 USA
| | - Amber N Habowski
- Cancer Center, Cold Spring Harbor Laboratory 1 Bungtown Rd Cold Spring Harbor NY 11724 USA
| | | | - Debmalya Bhunia
- Cancer Center, Cold Spring Harbor Laboratory 1 Bungtown Rd Cold Spring Harbor NY 11724 USA
| | - Charlotte Avanzi
- Mycobacteria Research Laboratories, Department of Microbiology, Immunology and Pathology, Colorado State University Fort Collins CO 80523 USA
| | - Adam D Moorhouse
- Cancer Center, Cold Spring Harbor Laboratory 1 Bungtown Rd Cold Spring Harbor NY 11724 USA
| | - Mary Jackson
- Mycobacteria Research Laboratories, Department of Microbiology, Immunology and Pathology, Colorado State University Fort Collins CO 80523 USA
| | - David A Tuveson
- Cancer Center, Cold Spring Harbor Laboratory 1 Bungtown Rd Cold Spring Harbor NY 11724 USA
| | - Scott K Lyons
- Cancer Center, Cold Spring Harbor Laboratory 1 Bungtown Rd Cold Spring Harbor NY 11724 USA
| | - Michael J Lukey
- Cancer Center, Cold Spring Harbor Laboratory 1 Bungtown Rd Cold Spring Harbor NY 11724 USA
| | - W Douglas Fairlie
- Olivia Newton-John Cancer Research Institute Heidelberg Victoria 3084 Australia
- School of Cancer Medicine, La Trobe University Melbourne Victoria 3086 Australia
- Department of Biochemistry and Chemistry, La Trobe Institute for Molecular Science, La Trobe University Melbourne Victoria 3086 Australia
| | - Shozeb M Haider
- School of Pharmacy, University College London 29-39 Brunswick Square London WC1N 1AX UK
| | - Michel O Steinmetz
- Laboratory of Biomolecular Research, Division of Biology and Chemistry, Paul Scherrer Institut Villigen PSI 5232 Switzerland
- Biozentrum, University of Basel 4056 Basel Switzerland
| | - Andrea E Prota
- Laboratory of Biomolecular Research, Division of Biology and Chemistry, Paul Scherrer Institut Villigen PSI 5232 Switzerland
| | - John E Moses
- Cancer Center, Cold Spring Harbor Laboratory 1 Bungtown Rd Cold Spring Harbor NY 11724 USA
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3
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Habowski AN, Budagavi DP, Scherer SD, Aurora AB, Caligiuri G, Flynn WF, Langer EM, Brody JR, Sears RC, Foggetti G, Arnal Estape A, Nguyen DX, Politi KA, Shen X, Hsu DS, Peehl DM, Kurhanewicz J, Sriram R, Suarez M, Xiao S, Du Y, Li XN, Navone NM, Labanca E, Willey CD. Patient-Derived Models of Cancer in the NCI PDMC Consortium: Selection, Pitfalls, and Practical Recommendations. Cancers (Basel) 2024; 16:565. [PMID: 38339316 PMCID: PMC10854945 DOI: 10.3390/cancers16030565] [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: 12/19/2023] [Revised: 01/16/2024] [Accepted: 01/20/2024] [Indexed: 02/12/2024] Open
Abstract
For over a century, early researchers sought to study biological organisms in a laboratory setting, leading to the generation of both in vitro and in vivo model systems. Patient-derived models of cancer (PDMCs) have more recently come to the forefront of preclinical cancer models and are even finding their way into clinical practice as part of functional precision medicine programs. The PDMC Consortium, supported by the Division of Cancer Biology in the National Cancer Institute of the National Institutes of Health, seeks to understand the biological principles that govern the various PDMC behaviors, particularly in response to perturbagens, such as cancer therapeutics. Based on collective experience from the consortium groups, we provide insight regarding PDMCs established both in vitro and in vivo, with a focus on practical matters related to developing and maintaining key cancer models through a series of vignettes. Although every model has the potential to offer valuable insights, the choice of the right model should be guided by the research question. However, recognizing the inherent constraints in each model is crucial. Our objective here is to delineate the strengths and limitations of each model as established by individual vignettes. Further advances in PDMCs and the development of novel model systems will enable us to better understand human biology and improve the study of human pathology in the lab.
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Affiliation(s)
- Amber N. Habowski
- Cold Spring Harbor Laboratory, Long Island, NY 11724, USA; (A.N.H.); (D.P.B.); (G.C.)
| | - Deepthi P. Budagavi
- Cold Spring Harbor Laboratory, Long Island, NY 11724, USA; (A.N.H.); (D.P.B.); (G.C.)
| | - Sandra D. Scherer
- Department of Oncologic Sciences, Huntsman Cancer Institute, University of Utah, Salt Lake City, UT 84112, USA;
| | - Arin B. Aurora
- Children’s Research Institute and Department of Pediatrics, University of Texas Southwestern, Dallas, TX 75235, USA;
| | - Giuseppina Caligiuri
- Cold Spring Harbor Laboratory, Long Island, NY 11724, USA; (A.N.H.); (D.P.B.); (G.C.)
| | | | - Ellen M. Langer
- Division of Oncological Sciences, Oregon Health & Science University, Portland, OR 97239, USA;
| | - Jonathan R. Brody
- Department of Surgery, Oregon Health & Science University, Portland, OR 97239, USA;
| | - Rosalie C. Sears
- Department of Molecular and Medical Genetics, Oregon Health & Science University, Portland, OR 97239, USA;
| | | | - Anna Arnal Estape
- Department of Internal Medicine, Yale University, New Haven, CT 06520, USA;
| | - Don X. Nguyen
- Department of Pathology, Yale University, New Haven, CT 06520, USA; (D.X.N.); (K.A.P.)
| | - Katerina A. Politi
- Department of Pathology, Yale University, New Haven, CT 06520, USA; (D.X.N.); (K.A.P.)
| | - Xiling Shen
- Terasaki Institute for Biomedical Innovation, Los Angeles, CA 90024, USA;
| | - David S. Hsu
- Department of Medicine, Duke University, Durham, NC 27710, USA;
| | - Donna M. Peehl
- Department of Radiology and Biomedical Imaging, University of California, San Francisco, CA 94158, USA; (D.M.P.); (J.K.); (R.S.)
| | - John Kurhanewicz
- Department of Radiology and Biomedical Imaging, University of California, San Francisco, CA 94158, USA; (D.M.P.); (J.K.); (R.S.)
| | - Renuka Sriram
- Department of Radiology and Biomedical Imaging, University of California, San Francisco, CA 94158, USA; (D.M.P.); (J.K.); (R.S.)
| | - Milagros Suarez
- Department of Pediatrics, Lurie Children’s Hospital of Chicago Northwestern University, Chicago, IL 60611, USA; (M.S.); (S.X.); (Y.D.); (X.-N.L.)
| | - Sophie Xiao
- Department of Pediatrics, Lurie Children’s Hospital of Chicago Northwestern University, Chicago, IL 60611, USA; (M.S.); (S.X.); (Y.D.); (X.-N.L.)
| | - Yuchen Du
- Department of Pediatrics, Lurie Children’s Hospital of Chicago Northwestern University, Chicago, IL 60611, USA; (M.S.); (S.X.); (Y.D.); (X.-N.L.)
| | - Xiao-Nan Li
- Department of Pediatrics, Lurie Children’s Hospital of Chicago Northwestern University, Chicago, IL 60611, USA; (M.S.); (S.X.); (Y.D.); (X.-N.L.)
| | - Nora M. Navone
- Department of Genitourinary Medical Oncology, David H. Koch Center for Applied Research of Genitourinary Cancers, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA; (N.M.N.)
| | - Estefania Labanca
- Department of Genitourinary Medical Oncology, David H. Koch Center for Applied Research of Genitourinary Cancers, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA; (N.M.N.)
| | - Christopher D. Willey
- Department of Radiation Oncology, University of Alabama at Birmingham, Birmingham, AL 35233, USA
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4
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Yao M, Preall J, Yeh JTH, Pappin D, Cifani P, Zhao Y, Shen S, Moresco P, He B, Patel H, Habowski AN, King DA, Raphael K, Rishi A, Sejpal D, Weiss MJ, Tuveson D, Fearon DT. Plasma cells in human pancreatic ductal adenocarcinoma secrete antibodies against self-antigens. JCI Insight 2023; 8:e172449. [PMID: 37751306 PMCID: PMC10721257 DOI: 10.1172/jci.insight.172449] [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: 05/22/2023] [Accepted: 09/14/2023] [Indexed: 09/27/2023] Open
Abstract
Intratumoral B cell responses are associated with more favorable clinical outcomes in human pancreatic ductal adenocarcinoma (PDAC). However, the antigens driving these B cell responses are largely unknown. We sought to discover these antigens by using single-cell RNA sequencing (scRNA-Seq) and immunoglobulin (Ig) sequencing of tumor-infiltrating immune cells from 7 primary PDAC samples. We identified activated T and B cell responses and evidence of germinal center reactions. Ig sequencing identified plasma cell (PC) clones expressing isotype-switched and hypermutated Igs, suggesting the occurrence of T cell-dependent B cell responses. We assessed the reactivity of 41 recombinant antibodies that represented the products of 235 PCs and 12 B cells toward multiple cell lines and PDAC tissues and observed frequent staining of intracellular self-antigens. Three of these antigens were identified: the filamentous actin (F-actin), the nucleic protein RuvB like AAA ATPase 2 (RUVBL2), and the mitochondrial protein heat shock protein family D (Hsp60) member 1 (HSPD1). Antibody titers against F-actin and HSPD1 were substantially elevated in the plasma of patients with PDAC compared with healthy donors. Thus, PCs in PDAC produce autoantibodies reacting with intracellular self-antigens, which may result from promotion of preexisting, autoreactive B cell responses. These observations indicate the chronic inflammatory microenvironment of PDAC can support the adaptive immune response.
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Affiliation(s)
- Min Yao
- Cold Spring Harbor Laboratory and
| | | | | | | | | | | | - Sophia Shen
- Cold Spring Harbor High School, Cold Spring Harbor, New York, USA
| | - Philip Moresco
- Cold Spring Harbor Laboratory and
- Graduate Program in Genetics, Stony Brook University, Stony Brook, New York, USA
- Medical Scientist Training Program, Stony Brook University Renaissance School of Medicine, Stony Brook University, Stony Brook, New York, USA
| | - Brian He
- Cold Spring Harbor Laboratory and
| | | | | | - Daniel A. King
- North Shore University Hospital, Manhasset, New York, USA
| | - Kara Raphael
- North Shore University Hospital, Manhasset, New York, USA
| | - Arvind Rishi
- North Shore University Hospital, Manhasset, New York, USA
| | - Divyesh Sejpal
- North Shore University Hospital, Manhasset, New York, USA
| | | | | | - Douglas T. Fearon
- Cold Spring Harbor Laboratory and
- Weill Cornell Medicine, New York, New York, USA
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5
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Demyan L, Habowski AN, Plenker D, King DA, Standring OJ, Tsang C, St Surin L, Rishi A, Crawford JM, Boyd J, Pasha SA, Patel H, Galluzzo Z, Metz C, Gregersen PK, Fox S, Valente C, Abadali S, Matadial-Ragoo S, DePeralta DK, Deutsch GB, Herman JM, Talamini MA, Tuveson DA, Weiss MJ. Pancreatic Cancer Patient-derived Organoids Can Predict Response to Neoadjuvant Chemotherapy. Ann Surg 2022; 276:450-462. [PMID: 35972511 PMCID: PMC10202108 DOI: 10.1097/sla.0000000000005558] [Citation(s) in RCA: 22] [Impact Index Per Article: 11.0] [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] [Indexed: 11/26/2022]
Abstract
OBJECTIVE To evaluate if patient-derived organoids (PDOs) may predict response to neoadjuvant (NAT) chemotherapy in patients with pancreatic adenocarcinoma. BACKGROUND PDOs have been explored as a biomarker of therapy response and for personalized therapeutics in patients with pancreatic cancer. METHODS During 2017-2021, patients were enrolled into an IRB-approved protocol and PDO cultures were established. PDOs of interest were analyzed through a translational pipeline incorporating molecular profiling and drug sensitivity testing. RESULTS One hundred thirty-six samples, including both surgical resections and fine needle aspiration/biopsy from 117 patients with pancreatic cancer were collected. This biobank included diversity in stage, sex, age, and race, with minority populations representing 1/3 of collected cases (16% Black, 9% Asian, 7% Hispanic/Latino). Among surgical specimens, PDO generation was successful in 71% (15 of 21) of patients who had received NAT prior to sample collection and in 76% (39 of 51) of patients who were untreated with chemotherapy or radiation at the time of collection. Pathological response to NAT correlated with PDO chemotherapy response, particularly oxaliplatin. We demonstrated the feasibility of a rapid PDO drug screen and generated data within 7 days of tissue resection. CONCLUSION Herein we report a large single-institution organoid biobank, including ethnic minority samples. The ability to establish PDOs from chemotherapy-naive and post-NAT tissue enables longitudinal PDO generation to assess dynamic chemotherapy sensitivity profiling. PDOs can be rapidly screened and further development of rapid screening may aid in the initial stratification of patients to the most active NAT regimen.
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Affiliation(s)
- Lyudmyla Demyan
- Department of Surgery, Donald and Barbara Zucker School of Medicine at Hofstra/Northwell, Manhasset, NY
- Lustgarten Foundation Pancreatic Cancer Research Laboratory at Cold Spring Harbor Laboratory, Cold Spring Harbor, NY
| | - Amber N Habowski
- Lustgarten Foundation Pancreatic Cancer Research Laboratory at Cold Spring Harbor Laboratory, Cold Spring Harbor, NY
| | - Dennis Plenker
- Lustgarten Foundation Pancreatic Cancer Research Laboratory at Cold Spring Harbor Laboratory, Cold Spring Harbor, NY
- Loxo Oncology at Lilly, Discovery Technologies, New York, NY
| | - Daniel A King
- Lustgarten Foundation Pancreatic Cancer Research Laboratory at Cold Spring Harbor Laboratory, Cold Spring Harbor, NY
- Department of Medical Oncology/Hematology, Northwell Health Cancer Institute, New Hyde Park, NYY
| | - Oliver J Standring
- Department of Surgery, Donald and Barbara Zucker School of Medicine at Hofstra/Northwell, Manhasset, NY
- Lustgarten Foundation Pancreatic Cancer Research Laboratory at Cold Spring Harbor Laboratory, Cold Spring Harbor, NY
| | - Caitlin Tsang
- Lustgarten Foundation Pancreatic Cancer Research Laboratory at Cold Spring Harbor Laboratory, Cold Spring Harbor, NY
| | - Luce St Surin
- Lustgarten Foundation Pancreatic Cancer Research Laboratory at Cold Spring Harbor Laboratory, Cold Spring Harbor, NY
| | - Arvind Rishi
- Department of Pathology and Laboratory Medicine, Donald and Barbara Zucker School of Medicine at Hofstra/Northwell, Manhasset, NY
| | - James M Crawford
- Department of Pathology and Laboratory Medicine, Donald and Barbara Zucker School of Medicine at Hofstra/Northwell, Manhasset, NY
| | - Jeff Boyd
- Institute of Cancer Research, Feinstein Institutes for Medical Research, Northwell Health, Manhasset, NY
| | - Shamsher A Pasha
- Department of Surgery, Donald and Barbara Zucker School of Medicine at Hofstra/Northwell, Manhasset, NY
| | - Hardik Patel
- Lustgarten Foundation Pancreatic Cancer Research Laboratory at Cold Spring Harbor Laboratory, Cold Spring Harbor, NY
| | - Zachary Galluzzo
- Lustgarten Foundation Pancreatic Cancer Research Laboratory at Cold Spring Harbor Laboratory, Cold Spring Harbor, NY
| | - Christine Metz
- Institute of Molecular Medicine, Feinstein Institutes for Medical Research, Northwell Health, Manhasset, NY
| | - Peter K Gregersen
- Institute of Molecular Medicine, Feinstein Institutes for Medical Research, Northwell Health, Manhasset, NY
| | - Sharon Fox
- Department of Pathology and Laboratory Medicine, Donald and Barbara Zucker School of Medicine at Hofstra/Northwell, Manhasset, NY
| | - Cristina Valente
- Department of Pathology and Laboratory Medicine, Donald and Barbara Zucker School of Medicine at Hofstra/Northwell, Manhasset, NY
| | - Sonya Abadali
- Department of Pathology and Laboratory Medicine, Donald and Barbara Zucker School of Medicine at Hofstra/Northwell, Manhasset, NY
| | - Steffi Matadial-Ragoo
- Department of Pathology and Laboratory Medicine, Donald and Barbara Zucker School of Medicine at Hofstra/Northwell, Manhasset, NY
| | - Danielle K DePeralta
- Department of Surgery, Donald and Barbara Zucker School of Medicine at Hofstra/Northwell, Manhasset, NY
| | - Gary B Deutsch
- Department of Surgery, Donald and Barbara Zucker School of Medicine at Hofstra/Northwell, Manhasset, NY
| | - Joseph M Herman
- Department of Radiation Oncology, Donald and Barbara Zucker School of Medicine at Hofstra/Northwell, Manhasset, NY
| | - Mark A Talamini
- Department of Surgery, Donald and Barbara Zucker School of Medicine at Hofstra/Northwell, Manhasset, NY
| | - David A Tuveson
- Lustgarten Foundation Pancreatic Cancer Research Laboratory at Cold Spring Harbor Laboratory, Cold Spring Harbor, NY
| | - Matthew J Weiss
- Department of Surgery, Donald and Barbara Zucker School of Medicine at Hofstra/Northwell, Manhasset, NY
- Institute of Cancer Research, Feinstein Institutes for Medical Research, Northwell Health, Manhasset, NY
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6
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Chun SK, Fortin BM, Fellows RC, Habowski AN, Verlande A, Song WA, Mahieu AL, Lefebvre AEYT, Sterrenberg JN, Velez LM, Digman MA, Edwards RA, Pannunzio NR, Seldin MM, Waterman ML, Masri S. Disruption of the circadian clock drives Apc loss of heterozygosity to accelerate colorectal cancer. Sci Adv 2022; 8:eabo2389. [PMID: 35947664 PMCID: PMC9365282 DOI: 10.1126/sciadv.abo2389] [Citation(s) in RCA: 22] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/12/2023]
Abstract
An alarming rise in young onset colorectal cancer (CRC) has been reported; however, the underlying molecular mechanism remains undefined. Suspected risk factors of young onset CRC include environmental aspects, such as lifestyle and dietary factors, which are known to affect the circadian clock. We find that both genetic disruption and environmental disruption of the circadian clock accelerate Apc-driven CRC pathogenesis in vivo. Using an intestinal organoid model, we demonstrate that clock disruption promotes transformation by driving Apc loss of heterozygosity, which hyperactivates Wnt signaling. This up-regulates c-Myc, a known Wnt target, which drives heightened glycolytic metabolism. Using patient-derived organoids, we show that circadian rhythms are lost in human tumors. Last, we identify that variance between core clock and Wnt pathway genes significantly predicts the survival of patients with CRC. Overall, our findings demonstrate a previously unidentified mechanistic link between clock disruption and CRC, which has important implications for young onset cancer prevention.
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Affiliation(s)
- Sung Kook Chun
- Department of Biological Chemistry, University of California, Irvine, Irvine, CA 92697, USA
| | - Bridget M. Fortin
- Department of Biological Chemistry, University of California, Irvine, Irvine, CA 92697, USA
| | - Rachel C. Fellows
- Department of Biological Chemistry, University of California, Irvine, Irvine, CA 92697, USA
| | - Amber N. Habowski
- Department of Microbiology and Molecular Genetics, University of California, Irvine, Irvine, CA 92697, USA
| | - Amandine Verlande
- Department of Biological Chemistry, University of California, Irvine, Irvine, CA 92697, USA
| | - Wei A. Song
- Department of Biological Chemistry, University of California, Irvine, Irvine, CA 92697, USA
| | - Alisa L. Mahieu
- Department of Biological Chemistry, University of California, Irvine, Irvine, CA 92697, USA
| | | | | | - Leandro M. Velez
- Department of Biological Chemistry, University of California, Irvine, Irvine, CA 92697, USA
| | - Michelle A. Digman
- Department of Biomedical Engineering, University of California, Irvine, Irvine, CA 92697, USA
| | - Robert A. Edwards
- Department of Pathology and Laboratory Medicine, University of California, Irvine, Irvine, CA 92697, USA
| | | | - Marcus M. Seldin
- Department of Biological Chemistry, University of California, Irvine, Irvine, CA 92697, USA
| | - Marian L. Waterman
- Department of Microbiology and Molecular Genetics, University of California, Irvine, Irvine, CA 92697, USA
| | - Selma Masri
- Department of Biological Chemistry, University of California, Irvine, Irvine, CA 92697, USA
- Corresponding author.
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7
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Chen GT, Tifrea DF, Murad R, Habowski AN, Lyou Y, Duong MR, Hosohama L, Mortazavi A, Edwards RA, Waterman ML. Disruption of beta-catenin dependent Wnt signaling in colon cancer cells remodels the microenvironment to promote tumor invasion. Mol Cancer Res 2021; 20:468-484. [PMID: 34799404 DOI: 10.1158/1541-7786.mcr-21-0349] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2021] [Revised: 09/29/2021] [Accepted: 11/12/2021] [Indexed: 11/16/2022]
Abstract
The recent classification of colon cancer into molecular subtypes revealed that patients with the poorest prognosis harbor tumors with the lowest levels of Wnt signaling. This is contrary to the general understanding that overactive Wnt signaling promotes tumor progression from early initiation stages through to the later stages including invasion and metastasis. Here, we directly test this assumption by reducing the activity of ß-catenin-dependent Wnt signaling in colon cancer cell lines at either an upstream or downstream step in the pathway. We determine that Wnt-reduced cancer cells exhibit a more aggressive disease phenotype, including increased mobility in vitro and disruptive invasion into mucosa and smooth muscle in an orthotopic mouse model. RNA sequencing reveals that interference with Wnt signaling leads to an upregulation of gene programs that favor cell migration and invasion and a downregulation of inflammation signatures in the tumor microenvironment. We identify a set of upregulated genes common among the Wnt perturbations that are predictive of poor patient outcomes in early-invasive colon cancer. Our findings suggest that while targeting Wnt signaling may reduce tumor burden, an inadvertent side effect is the emergence of invasive cancer. Implications: Decreased Wnt signaling in colon tumors leads to a more aggressive disease phenotype due to an upregulation of gene programs favoring cell migration in the tumor and downregulation of inflammation programs in the tumor microenvironment; these impacts must be carefully considered in developing Wnt-targeting therapies.
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Affiliation(s)
- George T Chen
- Microbiology & Molecular Genetics, University of California, Irvine
| | | | - Rabi Murad
- Developmental and Cell Biology, University of California, Irvine
| | - Amber N Habowski
- Microbiology & Molecular Genetics, University of California, Irvine
| | - Yung Lyou
- Microbiology and Molecular Genetics, University of California, Irvine
| | | | - Linzi Hosohama
- Microbiology & Molecular Genetics, University of California, Irvine
| | - Ali Mortazavi
- Department of Developmental & Cell Biology, University of California, Irvine
| | | | - Marian L Waterman
- Microbiology and Molecular Genetics, University of California, Irvine
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8
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Martin K, Zhang T, Lin TT, Habowski AN, Zhao R, Tsai CF, Chrisler WB, Sontag RL, Orton DJ, Lu YJ, Rodland KD, Yang B, Liu T, Smith RD, Qian WJ, Waterman ML, Wiley HS, Shi T. Facile One-Pot Nanoproteomics for Label-Free Proteome Profiling of 50-1000 Mammalian Cells. J Proteome Res 2021; 20:4452-4461. [PMID: 34351778 PMCID: PMC8945255 DOI: 10.1021/acs.jproteome.1c00403] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Recent advances in sample preparation enable label-free mass spectrometry (MS)-based proteome profiling of small numbers of mammalian cells. However, specific devices are often required to downscale sample processing volume from the standard 50-200 μL to sub-μL for effective nanoproteomics, which greatly impedes the implementation of current nanoproteomics methods by the proteomics research community. Herein, we report a facile one-pot nanoproteomics method termed SOPs-MS (surfactant-assisted one-pot sample processing at the standard volume coupled with MS) for convenient robust proteome profiling of 50-1000 mammalian cells. Building upon our recent development of SOPs-MS for label-free single-cell proteomics at a low μL volume, we have systematically evaluated its processing volume at 10-200 μL using 100 human cells. The processing volume of 50 μL that is in the range of volume for standard proteomics sample preparation has been selected for easy sample handling with a benchtop micropipette. SOPs-MS allows for reliable label-free quantification of ∼1200-2700 protein groups from 50 to 1000 MCF10A cells. When applied to small subpopulations of mouse colon crypt cells, SOPs-MS has revealed protein signatures between distinct subpopulation cells with identification of ∼1500-2500 protein groups for each subpopulation. SOPs-MS may pave the way for routine deep proteome profiling of small numbers of cells and low-input samples.
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Affiliation(s)
| | | | - Tai-Tu Lin
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99354, United States
| | - Amber N. Habowski
- Department of Microbiology and Molecular Genetics, University of California Irvine, Irvine, California 92697, United States
| | - Rui Zhao
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, Washington 99354, United States
| | - Chia-Feng Tsai
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99354, United States
| | - William B. Chrisler
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99354, United States
| | - Ryan L. Sontag
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99354, United States
| | - Daniel J. Orton
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99354, United States
| | - Yong-Jie Lu
- Centre for Cancer Biomarker and Biotherapeutics, Barts Cancer Institute, Queen Mary University of London, London EC1M 6BQ, United Kingdom
| | - Karin D. Rodland
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99354, United States
| | - Bin Yang
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99354, United States; Bioproducts, Sciences & Engineering Laboratory, Department of Biological Systems Engineering, Washington State University, Richland, Washington 99354, United States
| | - Tao Liu
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99354, United States
| | - Richard D. Smith
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99354, United States
| | - Wei-Jun Qian
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99354, United States
| | - Marian L. Waterman
- Department of Microbiology and Molecular Genetics, University of California Irvine, Irvine, California 92697, United States
| | - H. Steven Wiley
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, Washington 99354, United States
| | - Tujin Shi
- Corresponding Author Tujin Shi – Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99354, United States; Phone: (509) 371-6579;
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9
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Habowski AN, Habowski TJ, Waterman ML. GECO: gene expression clustering optimization app for non-linear data visualization of patterns. BMC Bioinformatics 2021; 22:29. [PMID: 33494695 PMCID: PMC7831185 DOI: 10.1186/s12859-020-03951-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2020] [Accepted: 12/28/2020] [Indexed: 01/23/2023] Open
Abstract
Background Due to continued advances in sequencing technology, the limitation in understanding biological systems through an “-omics” lens is no longer the generation of data, but the ability to analyze it. Importantly, much of this rich -omics data is publicly available waiting to be further investigated. Although many code-based pipelines exist, there is a lack of user-friendly and accessible applications that enable rapid analysis or visualization of data.
Results GECO (Gene Expression Clustering Optimization; http://www.theGECOapp.com) is a minimalistic GUI app that utilizes non-linear reduction techniques to rapidly visualize expression trends in many types of biological data matrices (such as bulk RNA-seq or proteomics). The required input is a data matrix with samples and any type of expression level of genes/protein/other with a unique ID. The output is an interactive t-SNE or UMAP analysis that clusters genes (or proteins/other unique IDs) based on their expression patterns across the multiple samples enabling visualization of expression trends. Customizable settings for dimensionality reduction, data normalization, along with visualization parameters including coloring and filters, ensure adaptability to a variety of user uploaded data. Conclusion This local and cloud-hosted web browser app enables investigation of any -omic data matrix in a rapid and code-independent manner. With the continued growth of available -omic data, the ability to quickly evaluate a dataset, including specific genes of interest, is more important than ever. GECO is intended to supplement traditional statistical analysis methods and is particularly useful when visualizing clusters of genes with similar trajectories across many samples (ex: multiple cell types, time course, dose response). Users will be empowered to investigate -omic data with a new lens of visualization and analysis that has the potential to uncover genes of interest, cohorts of co-regulated genes programs, and previously undetected patterns of expression.
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Affiliation(s)
- A N Habowski
- Department of Microbiology and Molecular Genetics, University of California Irvine, Irvine, CA, 92697, USA.
| | - T J Habowski
- Department of Microbiology and Molecular Genetics, University of California Irvine, Irvine, CA, 92697, USA
| | - M L Waterman
- Department of Microbiology and Molecular Genetics, University of California Irvine, Irvine, CA, 92697, USA
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Habowski AN, Flesher JL, Bates JM, Tsai CF, Martin K, Zhao R, Ganesan AK, Edwards RA, Shi T, Wiley HS, Shi Y, Hertel KJ, Waterman ML. Publisher Correction: Transcriptomic and proteomic signatures of stemness and differentiation in the colon crypt. Commun Biol 2020; 3:495. [PMID: 32884070 PMCID: PMC7471919 DOI: 10.1038/s42003-020-01237-0] [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] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Abstract
An amendment to this paper has been published and can be accessed via a link at the top of the paper.
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Affiliation(s)
- Amber N Habowski
- Department of Microbiology and Molecular Genetics, University of California Irvine, Irvine, CA, 92697, USA
| | - Jessica L Flesher
- Department of Biological Chemistry, University of California Irvine, Irvine, CA, 92697, USA
| | - Jennifer M Bates
- Institute for Immunology, University of California Irvine, Irvine, CA, 92697, USA
| | - Chia-Feng Tsai
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, 99354, USA
| | - Kendall Martin
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, 99354, USA
| | - Rui Zhao
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, WA, 99354, USA
| | - Anand K Ganesan
- Department of Biological Chemistry, University of California Irvine, Irvine, CA, 92697, USA
- Department of Dermatology, University of California Irvine, Irvine, CA, 92697, USA
| | - Robert A Edwards
- Department of Pathology and Laboratory Medicine, University of California Irvine, Irvine, CA, 92697, USA
| | - Tujin Shi
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, 99354, USA
| | - H Steven Wiley
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, WA, 99354, USA
| | - Yongsheng Shi
- Department of Microbiology and Molecular Genetics, University of California Irvine, Irvine, CA, 92697, USA
| | - Klemens J Hertel
- Department of Microbiology and Molecular Genetics, University of California Irvine, Irvine, CA, 92697, USA
| | - Marian L Waterman
- Department of Microbiology and Molecular Genetics, University of California Irvine, Irvine, CA, 92697, USA.
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11
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Habowski AN, Flesher JL, Bates JM, Tsai CF, Martin K, Zhao R, Ganesan AK, Edwards RA, Shi T, Wiley HS, Shi Y, Hertel KJ, Waterman ML. Transcriptomic and proteomic signatures of stemness and differentiation in the colon crypt. Commun Biol 2020; 3:453. [PMID: 32814826 PMCID: PMC7438495 DOI: 10.1038/s42003-020-01181-z] [Citation(s) in RCA: 20] [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] [Received: 05/27/2020] [Accepted: 07/16/2020] [Indexed: 02/07/2023] Open
Abstract
Intestinal stem cells are non-quiescent, dividing epithelial cells that rapidly differentiate into progenitor cells of the absorptive and secretory cell lineages. The kinetics of this process is rapid such that the epithelium is replaced weekly. To determine how the transcriptome and proteome keep pace with rapid differentiation, we developed a new cell sorting method to purify mouse colon epithelial cells. Here we show that alternative mRNA splicing and polyadenylation dominate changes in the transcriptome as stem cells differentiate into progenitors. In contrast, as progenitors differentiate into mature cell types, changes in mRNA levels dominate the transcriptome. RNA processing targets regulators of cell cycle, RNA, cell adhesion, SUMOylation, and Wnt and Notch signaling. Additionally, global proteome profiling detected >2,800 proteins and revealed RNA:protein patterns of abundance and correlation. Paired together, these data highlight new potentials for autocrine and feedback regulation and provide new insights into cell state transitions in the crypt.
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Affiliation(s)
- Amber N Habowski
- Department of Microbiology and Molecular Genetics, University of California Irvine, Irvine, CA, 92697, USA
| | - Jessica L Flesher
- Department of Biological Chemistry, University of California Irvine, Irvine, CA, 92697, USA
| | - Jennifer M Bates
- Institute for Immunology, University of California Irvine, Irvine, CA, 92697, USA
| | - Chia-Feng Tsai
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, 99354, USA
| | - Kendall Martin
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, 99354, USA
| | - Rui Zhao
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, WA, 99354, USA
| | - Anand K Ganesan
- Department of Biological Chemistry, University of California Irvine, Irvine, CA, 92697, USA
- Department of Dermatology, University of California Irvine, Irvine, CA, 92697, USA
| | - Robert A Edwards
- Department of Pathology and Laboratory Medicine, University of California Irvine, Irvine, CA, 92697, USA
| | - Tujin Shi
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, 99354, USA
| | - H Steven Wiley
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, WA, 99354, USA
| | - Yongsheng Shi
- Department of Microbiology and Molecular Genetics, University of California Irvine, Irvine, CA, 92697, USA
| | - Klemens J Hertel
- Department of Microbiology and Molecular Genetics, University of California Irvine, Irvine, CA, 92697, USA
| | - Marian L Waterman
- Department of Microbiology and Molecular Genetics, University of California Irvine, Irvine, CA, 92697, USA.
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Tran TQ, Hanse EA, Habowski AN, Li H, Ishak Gabra MB, Yang Y, Lowman XH, Ooi AM, Liao SY, Edwards RA, Waterman ML, Kong M. α-Ketoglutarate attenuates Wnt signaling and drives differentiation in colorectal cancer. Nat Cancer 2020; 1:345-358. [PMID: 32832918 PMCID: PMC7442208 DOI: 10.1038/s43018-020-0035-5] [Citation(s) in RCA: 71] [Impact Index Per Article: 17.8] [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: 04/30/2019] [Accepted: 01/27/2020] [Indexed: 02/07/2023]
Abstract
Genetic-driven deregulation of the Wnt pathway is crucial but not sufficient for colorectal cancer (CRC) tumourigenesis. Here, we show that environmental glutamine restriction further augments Wnt signaling in APC mutant intestinal organoids to promote stemness and leads to adenocarcinoma formation in vivo via decreasing intracellular alpha-ketoglutarate (aKG) levels. aKG supplementation is sufficient to rescue low-glutamine induced stemness and Wnt hyperactivation. Mechanistically, we found that aKG promotes hypomethylation of DNA and histone H3K4me3, leading to an upregulation of differentiation-associated genes and downregulation of Wnt target genes, respectively. Using CRC patient-derived organoids and several in vivo CRC tumour models, we show that aKG supplementation suppresses Wnt signaling and promotes cellular differentiation, thereby significantly restricting tumour growth and extending survival. Together, our results reveal how metabolic microenvironment impacts Wnt signaling and identify aKG as a potent antineoplastic metabolite for potential differentiation therapy for CRC patients.
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Affiliation(s)
- Thai Q Tran
- Department of Molecular Biology and Biochemistry, University of California, Irvine, Irvine, CA, USA
| | - Eric A Hanse
- Department of Molecular Biology and Biochemistry, University of California, Irvine, Irvine, CA, USA
| | - Amber N Habowski
- Department of Microbiology and Molecular Genetics, University of California, Irvine, Irvine, CA, USA
| | - Haiqing Li
- Division of Informatics, Department of Computational and Quantitative Medicine, Center of Informatics, Beckman Research Institute of City of Hope Cancer Center, Duarte, CA, USA
| | - Mari B Ishak Gabra
- Department of Molecular Biology and Biochemistry, University of California, Irvine, Irvine, CA, USA
| | - Ying Yang
- Department of Molecular Biology and Biochemistry, University of California, Irvine, Irvine, CA, USA
| | - Xazmin H Lowman
- Department of Molecular Biology and Biochemistry, University of California, Irvine, Irvine, CA, USA
| | - Amelia M Ooi
- Department of Molecular Biology and Biochemistry, University of California, Irvine, Irvine, CA, USA
| | - Shu Y Liao
- Department of Pathology and Laboratory Medicine, University of California, Irvine, Irvine, CA, USA
| | - Robert A Edwards
- Department of Pathology and Laboratory Medicine, University of California, Irvine, Irvine, CA, USA
| | - Marian L Waterman
- Department of Microbiology and Molecular Genetics, University of California, Irvine, Irvine, CA, USA
| | - Mei Kong
- Department of Molecular Biology and Biochemistry, University of California, Irvine, Irvine, CA, USA.
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Lyou Y, Habowski AN, Chen GT, Waterman ML. Inhibition of nuclear Wnt signalling: challenges of an elusive target for cancer therapy. Br J Pharmacol 2017; 174:4589-4599. [PMID: 28752891 PMCID: PMC5727325 DOI: 10.1111/bph.13963] [Citation(s) in RCA: 38] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2017] [Revised: 07/12/2017] [Accepted: 07/17/2017] [Indexed: 12/21/2022] Open
Abstract
The highly conserved Wnt signalling pathway plays an important role in embryonic development and disease pathogenesis, most notably cancer. The 'canonical' or β-catenin-dependent Wnt signal initiates at the cell plasma membrane with the binding of Wnt proteins to Frizzled:LRP5/LRP6 receptor complexes and is mediated by the translocation of the transcription co-activator protein, β-catenin, into the nucleus. β-Catenin then forms a complex with T-cell factor (TCF)/lymphoid enhancer binding factor (LEF) transcription factors to regulate multiple gene programmes. These programmes play roles in cell proliferation, migration, vasculogenesis, survival and metabolism. Mutations in Wnt signalling pathway components lead to constitutively active Wnt signalling that drives aberrant expression of these programmes and development of cancer. It has been a longstanding and challenging goal to develop therapies that can interfere with the TCF/LEF-β-catenin transcriptional complex. This review will focus on the (i) structural considerations for targeting the TCF/LEF-β-catenin and co-regulatory complexes in the nucleus, (ii) current molecules that directly target TCF/LEF-β-catenin activity and (iii) ideas for targeting newly discovered components of the TCF/LEF-β-catenin complex and/or downstream gene programmes regulated by these complexes. LINKED ARTICLES This article is part of a themed section on WNT Signalling: Mechanisms and Therapeutic Opportunities. To view the other articles in this section visit http://onlinelibrary.wiley.com/doi/10.1111/bph.v174.24/issuetoc.
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Affiliation(s)
- Yung Lyou
- Department of Medicine, Division of Hematology OncologyUniversity of California Irvine Medical CenterOrangeCAUSA
| | - Amber N Habowski
- Department of Microbiology and Molecular GeneticsUniversity of California IrvineIrvineCAUSA
| | - George T Chen
- Department of Microbiology and Molecular GeneticsUniversity of California IrvineIrvineCAUSA
| | - Marian L Waterman
- Department of Microbiology and Molecular GeneticsUniversity of California IrvineIrvineCAUSA
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Sprowl-Tanio S, Habowski AN, Pate KT, McQuade MM, Wang K, Edwards RA, Grun F, Lyou Y, Waterman ML. Lactate/pyruvate transporter MCT-1 is a direct Wnt target that confers sensitivity to 3-bromopyruvate in colon cancer. Cancer Metab 2016; 4:20. [PMID: 27729975 PMCID: PMC5046889 DOI: 10.1186/s40170-016-0159-3] [Citation(s) in RCA: 49] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2016] [Accepted: 09/12/2016] [Indexed: 12/21/2022] Open
Abstract
Background There is increasing evidence that oncogenic Wnt signaling directs metabolic reprogramming of cancer cells to favor aerobic glycolysis or Warburg metabolism. In colon cancer, this reprogramming is due to direct regulation of pyruvate dehydrogenase kinase 1 (PDK1) gene transcription. Additional metabolism genes are sensitive to Wnt signaling and exhibit correlative expression with PDK1. Whether these genes are also regulated at the transcriptional level, and therefore a part of a core metabolic gene program targeted by oncogenic WNT signaling, is not known. Results Here, we identify monocarboxylate transporter 1 (MCT-1; encoded by SLC16A1) as a direct target gene supporting Wnt-driven Warburg metabolism. We identify and validate Wnt response elements (WREs) in the proximal SLC16A1 promoter and show that they mediate sensitivity to Wnt inhibition via dominant-negative LEF-1 (dnLEF-1) expression and the small molecule Wnt inhibitor XAV939. We also show that WREs function in an independent and additive manner with c-Myc, the only other known oncogenic regulator of SLC16A1 transcription. MCT-1 can export lactate, the byproduct of Warburg metabolism, and it is the essential transporter of pyruvate as well as a glycolysis-targeting cancer drug, 3-bromopyruvate (3-BP). Using sulforhodamine B (SRB) assays to follow cell proliferation, we tested a panel of colon cancer cell lines for sensitivity to 3-BP. We observe that all cell lines are highly sensitive and that reduction of Wnt signaling by XAV939 treatment does not synergize with 3-BP, but instead is protective and promotes rapid recovery. Conclusions We conclude that MCT-1 is part of a core Wnt signaling gene program for glycolysis in colon cancer and that modulation of this program could play an important role in shaping sensitivity to drugs that target cancer metabolism. Electronic supplementary material The online version of this article (doi:10.1186/s40170-016-0159-3) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Stephanie Sprowl-Tanio
- Department of Microbiology and Molecular Genetics, University of California, Irvine, Irvine, CA USA
| | - Amber N Habowski
- Department of Microbiology and Molecular Genetics, University of California, Irvine, Irvine, CA USA
| | - Kira T Pate
- Department of Microbiology and Molecular Genetics, University of California, Irvine, Irvine, CA USA
| | - Miriam M McQuade
- Department of Microbiology and Molecular Genetics, University of California, Irvine, Irvine, CA USA
| | - Kehui Wang
- Department of Pathology and Laboratory Medicine, University of California, Irvine, Irvine, CA USA
| | - Robert A Edwards
- Department of Pathology and Laboratory Medicine, University of California, Irvine, Irvine, CA USA
| | - Felix Grun
- Department of Developmental and Cell Biology, University of California, Irvine, Irvine, CA USA
| | - Yung Lyou
- Department of Microbiology and Molecular Genetics, University of California, Irvine, Irvine, CA USA
| | - Marian L Waterman
- Department of Microbiology and Molecular Genetics, University of California, Irvine, Irvine, CA USA
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