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Jinna N, Rida P, Su T, Gong Z, Yao S, LaBarge M, Natarajan R, Jovanovic-Talisman T, Ambrosone C, Seewaldt V. The DARC Side of Inflamm-Aging: Duffy Antigen Receptor for Chemokines (DARC/ACKR1) as a Potential Biomarker of Aging, Immunosenescence, and Breast Oncogenesis among High-Risk Subpopulations. Cells 2022; 11:cells11233818. [PMID: 36497078 PMCID: PMC9740232 DOI: 10.3390/cells11233818] [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] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2022] [Revised: 11/09/2022] [Accepted: 11/23/2022] [Indexed: 11/30/2022] Open
Abstract
The proclivity of certain pre-malignant and pre-invasive breast lesions to progress while others do not continues to perplex clinicians. Clinicians remain at a crossroads with effectively managing the high-risk patient subpopulation owing to the paucity of biomarkers that can adequately risk-stratify and inform clinical decisions that circumvent unnecessary administration of cytotoxic and invasive treatments. The immune system mounts the most important line of defense against tumorigenesis and progression. Unfortunately, this defense declines or "ages" over time-a phenomenon known as immunosenescence. This results in "inflamm-aging" or the excessive infiltration of pro-inflammatory chemokines, which alters the leukocyte composition of the tissue microenvironment, and concomitant immunoediting of these leukocytes to diminish their antitumor immune functions. Collectively, these effects can foster the sequelae of neoplastic transformation and progression. The erythrocyte cell antigen, Duffy antigen receptor for chemokines(DARC/ACKR1), binds and internalizes chemokines to maintain homeostatic levels and modulate leukocyte trafficking. A negative DARC status is highly prevalent among subpopulations of West African genetic ancestry, who are at higher risk of developing breast cancer and disease progression at a younger age. However, the role of DARC in accelerated inflamm-aging and malignant transformation remains underexplored. Herein, we review compelling evidence suggesting that DARC may be protective against inflamm-aging and, therefore, reduce the risk of a high-risk lesion progressing to malignancy. We also discuss evidence supporting that immunotherapeutic intervention-based on DARC status-among high-risk subpopulations may evade malignant transformation and progression. A closer look into this unique role of DARC could glean deeper insight into the immune response profile of individual high-risk patients and their predisposition to progress as well as guide the administration of more "cyto-friendly" immunotherapeutic intervention to potentially "turn back the clock" on inflamm-aging-mediated oncogenesis and progression.
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Affiliation(s)
- Nikita Jinna
- Department of Population Science, City of Hope Comprehensive Cancer Center, Duarte, CA 91010, USA
| | - Padmashree Rida
- Department of Science, Rowland Hall, Salt Lake City, UT 84102, USA
| | - Tianyi Su
- Department of Science, Rowland Hall, Salt Lake City, UT 84102, USA
| | - Zhihong Gong
- Department of Cancer Prevention and Control, Roswell Park Comprehensive Cancer Center, Buffalo, NY 14263, USA
| | - Song Yao
- Department of Cancer Prevention and Control, Roswell Park Comprehensive Cancer Center, Buffalo, NY 14263, USA
| | - Mark LaBarge
- Department of Population Science, City of Hope Comprehensive Cancer Center, Duarte, CA 91010, USA
| | - Rama Natarajan
- Department of Diabetes Complications and Metabolism, City of Hope Comprehensive Cancer Center, Duarte, CA 91010, USA
| | | | - Christine Ambrosone
- Department of Cancer Prevention and Control, Roswell Park Comprehensive Cancer Center, Buffalo, NY 14263, USA
| | - Victoria Seewaldt
- Department of Population Science, City of Hope Comprehensive Cancer Center, Duarte, CA 91010, USA
- Correspondence:
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Jinna N, Rida P, Smart M, LaBarge M, Jovanovic-Talisman T, Natarajan R, Seewaldt V. Adaptation to Hypoxia May Promote Therapeutic Resistance to Androgen Receptor Inhibition in Triple-Negative Breast Cancer. Int J Mol Sci 2022; 23:ijms23168844. [PMID: 36012111 PMCID: PMC9408190 DOI: 10.3390/ijms23168844] [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: 07/22/2022] [Revised: 08/03/2022] [Accepted: 08/06/2022] [Indexed: 12/27/2022] Open
Abstract
Triple-negative breast cancer (TNBC) surpasses other BC subtypes as the most challenging to treat due to its lack of traditional BC biomarkers. Nearly 30% of TNBC patients express the androgen receptor (AR), and the blockade of androgen production and AR signaling have been the cornerstones of therapies for AR-positive TNBC. However, the majority of women are resistant to AR-targeted therapy, which is a major impediment to improving outcomes for the AR-positive TNBC subpopulation. The hypoxia signaling cascade is frequently activated in the tumor microenvironment in response to low oxygen levels; activation of the hypoxia signaling cascade allows tumors to survive despite hypoxia-mediated interference with cellular metabolism. The activation of hypoxia signaling networks in TNBC promotes resistance to most anticancer drugs including AR inhibitors. The activation of hypoxia network signaling occurs more frequently in TNBC compared to other BC subtypes. Herein, we examine the (1) interplay between hypoxia signaling networks and AR and (2) whether hypoxia and hypoxic stress adaptive pathways promote the emergence of resistance to therapies that target AR. We also pose the well-supported question, “Can the efficacy of androgen-/AR-targeted treatments be enhanced by co-targeting hypoxia?” By critically examining the evidence and the complex entwinement of these two oncogenic pathways, we argue that the simultaneous targeting of androgen biosynthesis/AR signaling and hypoxia may enhance the sensitivity of AR-positive TNBCs to AR-targeted treatments, derail the emergence of therapy resistance, and improve patient outcomes.
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Affiliation(s)
- Nikita Jinna
- Department of Population Science, City of Hope Comprehensive Cancer Center, Duarte, CA 91010, USA
| | | | - Max Smart
- Rowland Hall, Salt Lake City, UT 84102, USA
| | - Mark LaBarge
- Department of Population Science, City of Hope Comprehensive Cancer Center, Duarte, CA 91010, USA
| | | | - Rama Natarajan
- Department of Diabetes Complications and Metabolism, City of Hope Comprehensive Cancer Center, Duarte, CA 91010, USA
| | - Victoria Seewaldt
- Department of Population Science, City of Hope Comprehensive Cancer Center, Duarte, CA 91010, USA
- Correspondence:
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Ding YC, Hurley S, Park JS, Steele L, Rakoff M, Zhu Y, Zhao J, LaBarge M, Bernstein L, Chen S, Reynolds P, Neuhausen SL. Methylation biomarkers of polybrominated diphenyl ethers (PBDEs) and association with breast cancer risk at the time of menopause. Environ Int 2021; 156:106772. [PMID: 34425644 PMCID: PMC8385228 DOI: 10.1016/j.envint.2021.106772] [Citation(s) in RCA: 3] [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] [Subscribe] [Scholar Register] [Received: 02/02/2021] [Revised: 07/09/2021] [Accepted: 07/12/2021] [Indexed: 05/27/2023]
Abstract
BACKGROUND Exposure to polybrominated diphenyl ethers (PBDEs) may influence risk of developing post-menopausal breast cancer. Although mechanisms are poorly understood, epigenetic regulation of gene expression may play a role. OBJECTIVES To identify DNA methylation (DNAm) changes associated with PBDE serum levels and test the association of these biomarkers with breast cancer risk. METHODS We studied 397 healthy women (controls) and 133 women diagnosed with breast cancer (cases) between ages 40 and 58 years who participated in the California Teachers Study. PBDE levels were measured in blood. Infinium Human Methylation EPIC Bead Chips were used to measure DNAm. Using multivariable linear regression models, differentially methylated CpG sites (DMSs) and regions (DMRs) associated with serum PBDE levels were identified using controls. For top-ranked DMSs and DMRs, targeted next-generation bisulfite sequencing was used to measure DNAm for 133 invasive breast cancer cases and 301 age-matched controls. Conditional logistic regression was used to evaluate associations between DMSs and DMRs and breast cancer risk. RESULTS We identified 15 DMSs and 10 DMRs statistically significantly associated with PBDE levels (FDR < 0.05). Methylation changes in a DMS at BMP8B and DMRs at TP53 and A2M-AS1 were statistically significantly (FDR < 0.05) associated with breast cancer risk. CONCLUSION We show for the first time that serum PBDE levels are associated with differential methylation and that PBDE-associated DNAm changes in blood are associated with breast cancer risk.
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Affiliation(s)
- Yuan Chun Ding
- Department of Population Sciences, Beckman Research Institute of City of Hope, Duarte, CA, USA
| | - Susan Hurley
- Department of Epidemiology and Biostatistics, University of California San Francisco, San Francisco, CA, USA; Office of Environmental Health Hazard Assessment, California Environmental Protection Agency, Oakland, CA, USA
| | - June-Soo Park
- Environmental Chemistry Laboratory, Department of Toxic Substances Control, Berkeley, CA, USA
| | - Linda Steele
- Department of Population Sciences, Beckman Research Institute of City of Hope, Duarte, CA, USA
| | - Michele Rakoff
- Breast Cancer Care and Research Fund, Los Angeles, CA, USA
| | - Yun Zhu
- Department of Epidemiology, College of Public Health and Health Professions and College of Medicine, University of Florida, Gainesville, FL, USA
| | - Jinying Zhao
- Department of Epidemiology, College of Public Health and Health Professions and College of Medicine, University of Florida, Gainesville, FL, USA
| | - Mark LaBarge
- Department of Population Sciences, Beckman Research Institute of City of Hope, Duarte, CA, USA
| | - Leslie Bernstein
- Department of Population Sciences, Beckman Research Institute of City of Hope, Duarte, CA, USA
| | - Shiuan Chen
- Department of Cancer Biology, Beckman Research Institute of City of Hope, Duarte, CA, USA
| | - Peggy Reynolds
- Department of Epidemiology and Biostatistics, University of California San Francisco, San Francisco, CA, USA
| | - Susan L Neuhausen
- Department of Population Sciences, Beckman Research Institute of City of Hope, Duarte, CA, USA.
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Sedrak MS, Sun C, Muss H, Freedman RA, Magnuson A, Gross CP, Tew WP, Klepin HD, Wildes TM, Dotan E, O'Connor T, Fenton MA, Sharma R, Chapman A, Owusu C, Chow S, Kim H, Katheria V, LaBarge M, Dale W, Armenian S, Neuhausen S, Cohen HJ. Abstract PS8-03: Inflammation and coagulation biomarkers associated with physical resilience in older women receiving chemotherapy for early breast cancer. Cancer Res 2021. [DOI: 10.1158/1538-7445.sabcs20-ps8-03] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Background: Physical resilience, the ability to resist decline and maintain functional status despite a stressor such as chemotherapy, is a central aspect of successful aging. Understanding clinical and biological factors associated with resilience in older women receiving chemotherapy for early breast cancer may facilitate the development of targeted interventions to maintain an individual’s robustness.Methods: Women age ≥65 (N=406) with Stage I-III breast cancer who were part of a clinical study of neo/adjuvant chemotherapy in older women were recruited from 16 sites (NCT01472094, R01AG037037). The Deficit Accumulation Index (DAI), a continuous score (0-1) calculated based on 51-items from geriatric assessment data (Cohen et al Cancer 2017), was measured before and after receipt of chemotherapy. DAI was categorized as robust (0.0<0.2), prefrail (0.2<0.35) and frail (≥0.35). Baseline blood biomarkers of inflammation (interleukin-6 [IL-6], C-reactive protein [CRP]) and coagulation (D-dimer) were measured and defined as elevated if values were ≥median values in this cohort. The population of interest was older women who were robust prior to initiation of chemotherapy. The primary outcome was resilience (Yes/No); yes, defined as retaining robustness [DAI 0.0<0.2] before and ≤1 month after chemotherapy. Demographic, disease, and pretreatment variables associated with resilience in univariate analysis with p<0.1 were further adjusted using multivariable logistic regression to examine the associations between baseline biomarkers and resilience. Results: Before starting chemotherapy, 324 of 406 (80%) older women were robust. The median age was 70 (range 65-86), 61% had stage II or III disease, 29% had HER2+ disease, 22% had TNBC, 37% received an anthracycline-based regimen, 49% had planned duration of treatment > 12 weeks, and 74% received primary prophylaxis with WBC growth factors. Among these 324 robust older women, 253 (78%) remained robust (resilient) at the end of chemotherapy, 63 (19%) became prefrail, and 8 (3%) became frail. In univariate analyses, patients treated with anthracycline (OR=0.63, p=0.09), planned duration of treatment > 12 weeks (OR=0.56, p=0.04), elevated IL-6 ≥2.7 pg/ml (OR=0.59, p=0.05), elevated CRP ≥4.3 μg/ml (OR=0.57, p=0.04), elevated D-dimer ≥0.7 μg/ml (OR=0.61, p=0.07), or at least one elevated biomarker (OR=0.18, p<0.001) at baseline were less likely to be resilient after systemic chemotherapy. Adjusting for anthracyclines and treatment duration, patients who had one or more elevated biomarker were still significantly less likely to be resilient (OR=0.15, 95 CI 0.04-0.49, p=0.002) compared to those with no elevated biomarkers at baseline.
Conclusions: In this cohort of older women with early breast cancer who were robust prior to initiation of chemotherapy, 22% became prefrail or frail at end of treatment. Resilience to chemotherapy was related to inflammatory and coagulation biomarkers. Further research is needed to examine the mechanism underlying why some older women are resilient and retain their robustness after receiving treatment, whereas others experience decline, and further explore the role of inflammation/coagulation in this phenomenon.
Table 1. Multivariable associations between baseline blood biomarkers and resilienceResilient (n=253) No. %Non-resilient (n=71) No. %Multivariable OR (95%CI)P value# of elevated biomarkers*064 (25)4 (6)1.00190 (36)29 (41)0.16 (0.05-0.55)0.004255 (22)22 (31)0.14 (0.04-0.49)0.002344 (17)16 (23)0.14 (0.04-0.51)0.003No elevated biomarker64 (25)4 (6)1.00At least one elevated189 (75)67 (94)0.15 (0.04-0.49)0.002*Biomarkers were defined as elevated using the entire cohort median value as cut off points (IL-6 ≥2.7 pg/ml, CRP ≥4.3 μg/ml, and D-dimer ≥0.7 μg/ml). Combined effects of biomarkers were examined by creating a four-level categorical combination variable: 0=all three biomarkers are <median; 1=one of the biomarkers ≥median; 2=two of the biomarkers ≥median; and, 3=all three biomarkers ≥median. A dichotomized variable was also created comparing none (all three biomarkers are <median) vs at least one biomarker elevated (≥median).
Citation Format: Mina S Sedrak, Canlan Sun, Hyman Muss, Rachel A. Freedman, Allison Magnuson, Cary P. Gross, William P. Tew, Heidi D. Klepin, Tanya M. Wildes, Efrat Dotan, Tracey O'Connor, Mary Ann Fenton, Ruby Sharma, Andrew Chapman, Cynthia Owusu, Selina Chow, Heeyoung Kim, Vani Katheria, Mark LaBarge, William Dale, Saro Armenian, Susan Neuhausen, Harvey J. Cohen. Inflammation and coagulation biomarkers associated with physical resilience in older women receiving chemotherapy for early breast cancer [abstract]. In: Proceedings of the 2020 San Antonio Breast Cancer Virtual Symposium; 2020 Dec 8-11; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2021;81(4 Suppl):Abstract nr PS8-03.
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Affiliation(s)
| | | | - Hyman Muss
- 2UNC Lineberger Comprehensive Cancer Center, Chapel Hill, NC
| | | | | | | | | | | | | | | | | | | | - Ruby Sharma
- 12Monter Cancer Center of the North Shore-LIJ Cancer Institute, New York, NY
| | - Andrew Chapman
- 13Sidney Kimmel Cancer Center Jefferson Health, Philadelphia, PA
| | - Cynthia Owusu
- 14Case Western Reserve Comprehensive Cancer Center, Cleveland, OH
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Stampfer MR, Fresques T, Lee SY, LaBarge M, Garbe J. Abstract 5818: The immortalization process as a therapeutic target. Cancer Res 2020. [DOI: 10.1158/1538-7445.am2020-5818] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Normal human somatic cells have a finite lifespan and intact tumor suppressor barriers, whereas most carcinoma cells have gained immortality and overcome multiple tumor suppressor barriers. We have developed a comprehensive human mammary epithelial cell (HMEC) culture system to examine the alterations involved in the transition from normal finite to malignant immortal; such data can suggest prevention strategies. Our studies have indicated that HMEC initially encounter a stress-associated senescence barrier (stasis) enforced by retinoblastoma (RB). Errors in the RB pathway allow stasis bypass; similar errors are seen early in progression in vivo. Replicative senescence due to telomere erosion is a second extremely stringent barrier, with critically short telomeres leading to genomic instability. Overcoming this barrier requires reactivation of endogenous telomerase, similar to what is seen in high-grade DCIS in vivo. Resulting immortal HMEC are resistant to oncogene-induced-senescence, and exposure to oncogenes that cause finite cells to senesce, can now give rise to malignancy, underscoring the critical importance of the immortalization step in progression. Also like DCIS, the molecular properties of our non/pre-malignant immortal HMEC lines are more similar to malignant immortal than normal finite cells, highlighting the abnormal, cancer-like qualities of immortalized cells. We suggest this similarity is due to a novel process that we have discovered to be involved in cancer-associated immortal transformation, that we have called conversion. HMEC that gain an error permissive for telomerase reactivation still need to undergo additional changes to assume the cancer-associated immortal phenotype: expression of sufficient telomerase activity to maintain short telomeres, mean TRF ~4 kb (which is shorter than what is present in normal finite cells). Conversion appears initiated by a mean TRF of <4 kb, and may entail changes in telomere structure. Possibly, the observed similar alterations in immortal cells ± malignancy results from changes induced by conversion. Importantly, cancer-associated immortalization is unique to cells progressing to cancer, and its inhibition may thus be a valuable therapeutic target. Surprisingly, little has been done to explore this possibility, we believe because: 1) small short-lived animals like mice do not stringently repress telomerase in adult cells; lacking a significant immortalization barrier, they cannot model this critical step in human carcinogenesis; 2) Immortally transformed cells are commonly referred to as normal or untransformed; 3) hTERT immortalization does not model cancer-associated immortalization; there is no conversion to short telomeres. Our preliminary data suggest potential approaches to inhibiting conversion.
Citation Format: Martha R. Stampfer, Tara Fresques, Sun-Young Lee, Mark LaBarge, James Garbe. The immortalization process as a therapeutic target [abstract]. In: Proceedings of the Annual Meeting of the American Association for Cancer Research 2020; 2020 Apr 27-28 and Jun 22-24. Philadelphia (PA): AACR; Cancer Res 2020;80(16 Suppl):Abstract nr 5818.
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Affiliation(s)
| | - Tara Fresques
- 1Lawrence Berkeley National Laboratory, Berkeley, CA
| | - Sun-Young Lee
- 1Lawrence Berkeley National Laboratory, Berkeley, CA
| | | | - James Garbe
- 1Lawrence Berkeley National Laboratory, Berkeley, CA
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6
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Hoshino A, Kim HS, Bojmar L, Gyan KE, Cioffi M, Hernandez J, Zambirinis CP, Rodrigues G, Molina H, Heissel S, Mark MT, Steiner L, Benito-Martin A, Lucotti S, Di Giannatale A, Offer K, Nakajima M, Williams C, Nogués L, Pelissier Vatter FA, Hashimoto A, Davies AE, Freitas D, Kenific CM, Ararso Y, Buehring W, Lauritzen P, Ogitani Y, Sugiura K, Takahashi N, Alečković M, Bailey KA, Jolissant JS, Wang H, Harris A, Schaeffer LM, García-Santos G, Posner Z, Balachandran VP, Khakoo Y, Raju GP, Scherz A, Sagi I, Scherz-Shouval R, Yarden Y, Oren M, Malladi M, Petriccione M, De Braganca KC, Donzelli M, Fischer C, Vitolano S, Wright GP, Ganshaw L, Marrano M, Ahmed A, DeStefano J, Danzer E, Roehrl MHA, Lacayo NJ, Vincent TC, Weiser MR, Brady MS, Meyers PA, Wexler LH, Ambati SR, Chou AJ, Slotkin EK, Modak S, Roberts SS, Basu EM, Diolaiti D, Krantz BA, Cardoso F, Simpson AL, Berger M, Rudin CM, Simeone DM, Jain M, Ghajar CM, Batra SK, Stanger BZ, Bui J, Brown KA, Rajasekhar VK, Healey JH, de Sousa M, Kramer K, Sheth S, Baisch J, Pascual V, Heaton TE, La Quaglia MP, Pisapia DJ, Schwartz R, Zhang H, Liu Y, Shukla A, Blavier L, DeClerck YA, LaBarge M, Bissell MJ, Caffrey TC, Grandgenett PM, Hollingsworth MA, Bromberg J, Costa-Silva B, Peinado H, Kang Y, Garcia BA, O'Reilly EM, Kelsen D, Trippett TM, Jones DR, Matei IR, Jarnagin WR, Lyden D. Extracellular Vesicle and Particle Biomarkers Define Multiple Human Cancers. Cell 2020; 182:1044-1061.e18. [PMID: 32795414 DOI: 10.1016/j.cell.2020.07.009] [Citation(s) in RCA: 607] [Impact Index Per Article: 151.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2020] [Revised: 04/23/2020] [Accepted: 07/09/2020] [Indexed: 01/08/2023]
Abstract
There is an unmet clinical need for improved tissue and liquid biopsy tools for cancer detection. We investigated the proteomic profile of extracellular vesicles and particles (EVPs) in 426 human samples from tissue explants (TEs), plasma, and other bodily fluids. Among traditional exosome markers, CD9, HSPA8, ALIX, and HSP90AB1 represent pan-EVP markers, while ACTB, MSN, and RAP1B are novel pan-EVP markers. To confirm that EVPs are ideal diagnostic tools, we analyzed proteomes of TE- (n = 151) and plasma-derived (n = 120) EVPs. Comparison of TE EVPs identified proteins (e.g., VCAN, TNC, and THBS2) that distinguish tumors from normal tissues with 90% sensitivity/94% specificity. Machine-learning classification of plasma-derived EVP cargo, including immunoglobulins, revealed 95% sensitivity/90% specificity in detecting cancer. Finally, we defined a panel of tumor-type-specific EVP proteins in TEs and plasma, which can classify tumors of unknown primary origin. Thus, EVP proteins can serve as reliable biomarkers for cancer detection and determining cancer type.
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Affiliation(s)
- Ayuko Hoshino
- Children's Cancer and Blood Foundation Laboratories, Departments of Pediatrics, and Cell and Developmental Biology, Drukier Institute for Children's Health, Meyer Cancer Center, Weill Cornell Medicine, New York, NY, USA; School of Life Science and Technology, Tokyo Institute of Technology, Yokohama, Japan; Japan Science and Technology Agency, PRESTO, Tokyo, Japan.
| | - Han Sang Kim
- Children's Cancer and Blood Foundation Laboratories, Departments of Pediatrics, and Cell and Developmental Biology, Drukier Institute for Children's Health, Meyer Cancer Center, Weill Cornell Medicine, New York, NY, USA; Yonsei Cancer Center, Division of Medical Oncology, Department of Internal Medicine, Brain Korea 21 Plus Project for Medical Sciences, Severance Biomedical Science Institute, Yonsei University College of Medicine, Seoul, Korea
| | - Linda Bojmar
- Children's Cancer and Blood Foundation Laboratories, Departments of Pediatrics, and Cell and Developmental Biology, Drukier Institute for Children's Health, Meyer Cancer Center, Weill Cornell Medicine, New York, NY, USA; Department of Biomedical and Clinical Sciences, Linköping University, Linköping, Sweden; Department of Immunology, Genetics and Pathology, Uppsala University, Rudbeck Laboratory, Uppsala, Sweden
| | - Kofi Ennu Gyan
- Children's Cancer and Blood Foundation Laboratories, Departments of Pediatrics, and Cell and Developmental Biology, Drukier Institute for Children's Health, Meyer Cancer Center, Weill Cornell Medicine, New York, NY, USA; Tri-Institutional PhD Program in Computational Biology and Medicine, New York, NY, USA
| | - Michele Cioffi
- Children's Cancer and Blood Foundation Laboratories, Departments of Pediatrics, and Cell and Developmental Biology, Drukier Institute for Children's Health, Meyer Cancer Center, Weill Cornell Medicine, New York, NY, USA
| | - Jonathan Hernandez
- Children's Cancer and Blood Foundation Laboratories, Departments of Pediatrics, and Cell and Developmental Biology, Drukier Institute for Children's Health, Meyer Cancer Center, Weill Cornell Medicine, New York, NY, USA; Hepatopancreatobiliary Service, Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, NY, USA; Surgical Oncology Program, National Cancer Institute, National Institutes of Health, Bethesda, MD USA
| | - Constantinos P Zambirinis
- Children's Cancer and Blood Foundation Laboratories, Departments of Pediatrics, and Cell and Developmental Biology, Drukier Institute for Children's Health, Meyer Cancer Center, Weill Cornell Medicine, New York, NY, USA; Hepatopancreatobiliary Service, Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Gonçalo Rodrigues
- Children's Cancer and Blood Foundation Laboratories, Departments of Pediatrics, and Cell and Developmental Biology, Drukier Institute for Children's Health, Meyer Cancer Center, Weill Cornell Medicine, New York, NY, USA; Graduate Program in Areas of Basic and Applied Biology, Abel Salazar Biomedical Sciences Institute, University of Porto, Porto, Portugal
| | - Henrik Molina
- Proteomics Resource Center, The Rockefeller University, New York, NY, USA
| | - Søren Heissel
- Proteomics Resource Center, The Rockefeller University, New York, NY, USA
| | - Milica Tesic Mark
- Proteomics Resource Center, The Rockefeller University, New York, NY, USA
| | - Loïc Steiner
- Children's Cancer and Blood Foundation Laboratories, Departments of Pediatrics, and Cell and Developmental Biology, Drukier Institute for Children's Health, Meyer Cancer Center, Weill Cornell Medicine, New York, NY, USA; Swiss Institute for Experimental Cancer Research, School of Life Sciences, Ecole Polytechnique Federale de Lausanne, Lausanne, Switzerland
| | - Alberto Benito-Martin
- Children's Cancer and Blood Foundation Laboratories, Departments of Pediatrics, and Cell and Developmental Biology, Drukier Institute for Children's Health, Meyer Cancer Center, Weill Cornell Medicine, New York, NY, USA
| | - Serena Lucotti
- Children's Cancer and Blood Foundation Laboratories, Departments of Pediatrics, and Cell and Developmental Biology, Drukier Institute for Children's Health, Meyer Cancer Center, Weill Cornell Medicine, New York, NY, USA
| | - Angela Di Giannatale
- Children's Cancer and Blood Foundation Laboratories, Departments of Pediatrics, and Cell and Developmental Biology, Drukier Institute for Children's Health, Meyer Cancer Center, Weill Cornell Medicine, New York, NY, USA; Department of Pediatric Haematology/Oncology, IRCCS Bambino Gesù Children's Hospital, Rome, Italy
| | - Katharine Offer
- Children's Cancer and Blood Foundation Laboratories, Departments of Pediatrics, and Cell and Developmental Biology, Drukier Institute for Children's Health, Meyer Cancer Center, Weill Cornell Medicine, New York, NY, USA
| | - Miho Nakajima
- Children's Cancer and Blood Foundation Laboratories, Departments of Pediatrics, and Cell and Developmental Biology, Drukier Institute for Children's Health, Meyer Cancer Center, Weill Cornell Medicine, New York, NY, USA
| | - Caitlin Williams
- Children's Cancer and Blood Foundation Laboratories, Departments of Pediatrics, and Cell and Developmental Biology, Drukier Institute for Children's Health, Meyer Cancer Center, Weill Cornell Medicine, New York, NY, USA
| | - Laura Nogués
- Children's Cancer and Blood Foundation Laboratories, Departments of Pediatrics, and Cell and Developmental Biology, Drukier Institute for Children's Health, Meyer Cancer Center, Weill Cornell Medicine, New York, NY, USA; Microenvironment and Metastasis Laboratory, Department of Molecular Oncology, Spanish National Cancer Research Center (CNIO), Madrid, Spain
| | - Fanny A Pelissier Vatter
- Children's Cancer and Blood Foundation Laboratories, Departments of Pediatrics, and Cell and Developmental Biology, Drukier Institute for Children's Health, Meyer Cancer Center, Weill Cornell Medicine, New York, NY, USA
| | - Ayako Hashimoto
- Children's Cancer and Blood Foundation Laboratories, Departments of Pediatrics, and Cell and Developmental Biology, Drukier Institute for Children's Health, Meyer Cancer Center, Weill Cornell Medicine, New York, NY, USA; School of Life Science and Technology, Tokyo Institute of Technology, Yokohama, Japan; Department of Obstetrics and Gynecology, Faculty of Medicine, University of Tokyo, Tokyo, Japan
| | - Alexander E Davies
- Department of Veterinary Biosciences, College of Veterinary Medicine, The Ohio State University, Columbus, OH, USA
| | - Daniela Freitas
- Children's Cancer and Blood Foundation Laboratories, Departments of Pediatrics, and Cell and Developmental Biology, Drukier Institute for Children's Health, Meyer Cancer Center, Weill Cornell Medicine, New York, NY, USA; i3S-Institute for Research and Innovation in Health, University of Porto, Rua Alfredo Allen 208, Porto, Portugal
| | - Candia M Kenific
- Children's Cancer and Blood Foundation Laboratories, Departments of Pediatrics, and Cell and Developmental Biology, Drukier Institute for Children's Health, Meyer Cancer Center, Weill Cornell Medicine, New York, NY, USA
| | - Yonathan Ararso
- Children's Cancer and Blood Foundation Laboratories, Departments of Pediatrics, and Cell and Developmental Biology, Drukier Institute for Children's Health, Meyer Cancer Center, Weill Cornell Medicine, New York, NY, USA
| | - Weston Buehring
- Children's Cancer and Blood Foundation Laboratories, Departments of Pediatrics, and Cell and Developmental Biology, Drukier Institute for Children's Health, Meyer Cancer Center, Weill Cornell Medicine, New York, NY, USA
| | - Pernille Lauritzen
- Children's Cancer and Blood Foundation Laboratories, Departments of Pediatrics, and Cell and Developmental Biology, Drukier Institute for Children's Health, Meyer Cancer Center, Weill Cornell Medicine, New York, NY, USA
| | - Yusuke Ogitani
- Children's Cancer and Blood Foundation Laboratories, Departments of Pediatrics, and Cell and Developmental Biology, Drukier Institute for Children's Health, Meyer Cancer Center, Weill Cornell Medicine, New York, NY, USA
| | - Kei Sugiura
- School of Life Science and Technology, Tokyo Institute of Technology, Yokohama, Japan; Graduate School of Pharmaceutical Sciences, The University of Tokyo, Tokyo, Japan
| | - Naoko Takahashi
- School of Life Science and Technology, Tokyo Institute of Technology, Yokohama, Japan
| | - Maša Alečković
- Department of Molecular Biology, Princeton University, Princeton, NJ, USA
| | - Kayleen A Bailey
- Children's Cancer and Blood Foundation Laboratories, Departments of Pediatrics, and Cell and Developmental Biology, Drukier Institute for Children's Health, Meyer Cancer Center, Weill Cornell Medicine, New York, NY, USA
| | - Joshua S Jolissant
- Children's Cancer and Blood Foundation Laboratories, Departments of Pediatrics, and Cell and Developmental Biology, Drukier Institute for Children's Health, Meyer Cancer Center, Weill Cornell Medicine, New York, NY, USA; Hepatopancreatobiliary Service, Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Huajuan Wang
- Children's Cancer and Blood Foundation Laboratories, Departments of Pediatrics, and Cell and Developmental Biology, Drukier Institute for Children's Health, Meyer Cancer Center, Weill Cornell Medicine, New York, NY, USA
| | - Ashton Harris
- Children's Cancer and Blood Foundation Laboratories, Departments of Pediatrics, and Cell and Developmental Biology, Drukier Institute for Children's Health, Meyer Cancer Center, Weill Cornell Medicine, New York, NY, USA
| | - L Miles Schaeffer
- Children's Cancer and Blood Foundation Laboratories, Departments of Pediatrics, and Cell and Developmental Biology, Drukier Institute for Children's Health, Meyer Cancer Center, Weill Cornell Medicine, New York, NY, USA
| | - Guillermo García-Santos
- Children's Cancer and Blood Foundation Laboratories, Departments of Pediatrics, and Cell and Developmental Biology, Drukier Institute for Children's Health, Meyer Cancer Center, Weill Cornell Medicine, New York, NY, USA; Department of General and Gastrointestinal Surgery, Hospital Universitario Central de Asturias (HUCA), Oviedo, Spain
| | - Zoe Posner
- Children's Cancer and Blood Foundation Laboratories, Departments of Pediatrics, and Cell and Developmental Biology, Drukier Institute for Children's Health, Meyer Cancer Center, Weill Cornell Medicine, New York, NY, USA
| | - Vinod P Balachandran
- Hepatopancreatobiliary Service, Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, NY, USA; Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Yasmin Khakoo
- Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - G Praveen Raju
- Department of Neurology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Avigdor Scherz
- Department of Plant and Environmental Sciences, Weizmann Institute of Science, Rehovot, Israel
| | - Irit Sagi
- Department of Biological Regulation, Weizmann Institute of Science, Rehovot, Israel
| | - Ruth Scherz-Shouval
- Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot, Israel
| | - Yosef Yarden
- Department of Biological Regulation, Weizmann Institute of Science, Rehovot, Israel
| | - Moshe Oren
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Mahathi Malladi
- Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Mary Petriccione
- Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Kevin C De Braganca
- Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Maria Donzelli
- Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Cheryl Fischer
- Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Stephanie Vitolano
- Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Geraldine P Wright
- Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Lee Ganshaw
- Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Mariel Marrano
- Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Amina Ahmed
- Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Joe DeStefano
- Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Enrico Danzer
- Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, NY, USA; Pediatric Surgical Service, Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Michael H A Roehrl
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA; Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Norman J Lacayo
- Lucile Packard Children's Hospital Stanford, Stanford, CA, USA
| | - Theresa C Vincent
- Department of Immunology, Genetics and Pathology, Uppsala University, Rudbeck Laboratory, Uppsala, Sweden; Department of Microbiology, New York University School of Medicine, New York, NY, USA
| | - Martin R Weiser
- Colorectal Service, Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Mary S Brady
- Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Paul A Meyers
- Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Leonard H Wexler
- Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Srikanth R Ambati
- Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Alexander J Chou
- Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Emily K Slotkin
- Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Shakeel Modak
- Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Stephen S Roberts
- Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Ellen M Basu
- Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Daniel Diolaiti
- Perlmutter Cancer Center, New York University Langone Health, New York, NY, USA
| | - Benjamin A Krantz
- Perlmutter Cancer Center, New York University Langone Health, New York, NY, USA; Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Fatima Cardoso
- Breast Unit, Champalimaud Clinical Center/Champalimaud Foundation, Lisbon, Portugal
| | - Amber L Simpson
- Hepatopancreatobiliary Service, Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Michael Berger
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA; Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Charles M Rudin
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Diane M Simeone
- Perlmutter Cancer Center, New York University Langone Health, New York, NY, USA
| | - Maneesh Jain
- Fred and Pamela Buffett Cancer Center, University of Nebraska Medical Center, Omaha, NE, USA
| | - Cyrus M Ghajar
- Public Health Sciences Division/Translational Research Program, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Surinder K Batra
- Fred and Pamela Buffett Cancer Center, University of Nebraska Medical Center, Omaha, NE, USA
| | - Ben Z Stanger
- Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Jack Bui
- Department of Pathology, University of California San Diego, La Jolla, CA, USA
| | - Kristy A Brown
- Department of Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Vinagolu K Rajasekhar
- Orthopedic Service, Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - John H Healey
- Orthopedic Service, Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Maria de Sousa
- Children's Cancer and Blood Foundation Laboratories, Departments of Pediatrics, and Cell and Developmental Biology, Drukier Institute for Children's Health, Meyer Cancer Center, Weill Cornell Medicine, New York, NY, USA; Graduate Program in Areas of Basic and Applied Biology, Abel Salazar Biomedical Sciences Institute, University of Porto, Porto, Portugal
| | - Kim Kramer
- Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Sujit Sheth
- Department of Pediatrics, Weill Cornell Medicine, New York, NY, USA
| | - Jeanine Baisch
- Department of Pediatrics, Weill Cornell Medicine, New York, NY, USA; Drukier Institute for Children's Health, Weill Cornell Medicine, New York, NY, USA
| | - Virginia Pascual
- Department of Pediatrics, Weill Cornell Medicine, New York, NY, USA; Drukier Institute for Children's Health, Weill Cornell Medicine, New York, NY, USA
| | - Todd E Heaton
- Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, NY, USA; Pediatric Surgical Service, Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Michael P La Quaglia
- Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, NY, USA; Pediatric Surgical Service, Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - David J Pisapia
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Robert Schwartz
- Division of Gastroenterology & Hepatology, Weill Cornell Medicine, New York, NY, USA
| | - Haiying Zhang
- Children's Cancer and Blood Foundation Laboratories, Departments of Pediatrics, and Cell and Developmental Biology, Drukier Institute for Children's Health, Meyer Cancer Center, Weill Cornell Medicine, New York, NY, USA
| | - Yuan Liu
- Thoracic Surgery Service, Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Arti Shukla
- Department of Pathology and Laboratory Medicine, University of Vermont, Burlington, VT, USA
| | - Laurence Blavier
- Department of Pediatrics and Biochemistry and Molecular Medicine, University of Southern California, CA, USA
| | - Yves A DeClerck
- Department of Pediatrics and Biochemistry and Molecular Medicine, University of Southern California, CA, USA
| | - Mark LaBarge
- Department of Population Sciences, Beckman Research Institute at City of Hope, Duarte, CA, USA
| | - Mina J Bissell
- Life Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Thomas C Caffrey
- Fred and Pamela Buffett Cancer Center, University of Nebraska Medical Center, Omaha, NE, USA
| | - Paul M Grandgenett
- Fred and Pamela Buffett Cancer Center, University of Nebraska Medical Center, Omaha, NE, USA
| | - Michael A Hollingsworth
- Fred and Pamela Buffett Cancer Center, University of Nebraska Medical Center, Omaha, NE, USA
| | - Jacqueline Bromberg
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA; Department of Medicine, Weill Cornell Medicine, New York, NY, USA
| | | | - Hector Peinado
- Microenvironment and Metastasis Laboratory, Department of Molecular Oncology, Spanish National Cancer Research Center (CNIO), Madrid, Spain
| | - Yibin Kang
- Department of Molecular Biology, Princeton University, Princeton, NJ, USA
| | - Benjamin A Garcia
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Eileen M O'Reilly
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - David Kelsen
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Tanya M Trippett
- Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - David R Jones
- Thoracic Surgery Service, Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Irina R Matei
- Children's Cancer and Blood Foundation Laboratories, Departments of Pediatrics, and Cell and Developmental Biology, Drukier Institute for Children's Health, Meyer Cancer Center, Weill Cornell Medicine, New York, NY, USA
| | - William R Jarnagin
- Hepatopancreatobiliary Service, Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, NY, USA.
| | - David Lyden
- Children's Cancer and Blood Foundation Laboratories, Departments of Pediatrics, and Cell and Developmental Biology, Drukier Institute for Children's Health, Meyer Cancer Center, Weill Cornell Medicine, New York, NY, USA.
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7
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Keenan AB, Jenkins SL, Jagodnik KM, Koplev S, He E, Torre D, Wang Z, Dohlman AB, Silverstein MC, Lachmann A, Kuleshov MV, Ma'ayan A, Stathias V, Terryn R, Cooper D, Forlin M, Koleti A, Vidovic D, Chung C, Schürer SC, Vasiliauskas J, Pilarczyk M, Shamsaei B, Fazel M, Ren Y, Niu W, Clark NA, White S, Mahi N, Zhang L, Kouril M, Reichard JF, Sivaganesan S, Medvedovic M, Meller J, Koch RJ, Birtwistle MR, Iyengar R, Sobie EA, Azeloglu EU, Kaye J, Osterloh J, Haston K, Kalra J, Finkbiener S, Li J, Milani P, Adam M, Escalante-Chong R, Sachs K, Lenail A, Ramamoorthy D, Fraenkel E, Daigle G, Hussain U, Coye A, Rothstein J, Sareen D, Ornelas L, Banuelos M, Mandefro B, Ho R, Svendsen CN, Lim RG, Stocksdale J, Casale MS, Thompson TG, Wu J, Thompson LM, Dardov V, Venkatraman V, Matlock A, Van Eyk JE, Jaffe JD, Papanastasiou M, Subramanian A, Golub TR, Erickson SD, Fallahi-Sichani M, Hafner M, Gray NS, Lin JR, Mills CE, Muhlich JL, Niepel M, Shamu CE, Williams EH, Wrobel D, Sorger PK, Heiser LM, Gray JW, Korkola JE, Mills GB, LaBarge M, Feiler HS, Dane MA, Bucher E, Nederlof M, Sudar D, Gross S, Kilburn DF, Smith R, Devlin K, Margolis R, Derr L, Lee A, Pillai A. The Library of Integrated Network-Based Cellular Signatures NIH Program: System-Level Cataloging of Human Cells Response to Perturbations. Cell Syst 2018; 6:13-24. [PMID: 29199020 PMCID: PMC5799026 DOI: 10.1016/j.cels.2017.11.001] [Citation(s) in RCA: 241] [Impact Index Per Article: 40.2] [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: 07/27/2017] [Revised: 09/13/2017] [Accepted: 11/01/2017] [Indexed: 12/19/2022]
Abstract
The Library of Integrated Network-Based Cellular Signatures (LINCS) is an NIH Common Fund program that catalogs how human cells globally respond to chemical, genetic, and disease perturbations. Resources generated by LINCS include experimental and computational methods, visualization tools, molecular and imaging data, and signatures. By assembling an integrated picture of the range of responses of human cells exposed to many perturbations, the LINCS program aims to better understand human disease and to advance the development of new therapies. Perturbations under study include drugs, genetic perturbations, tissue micro-environments, antibodies, and disease-causing mutations. Responses to perturbations are measured by transcript profiling, mass spectrometry, cell imaging, and biochemical methods, among other assays. The LINCS program focuses on cellular physiology shared among tissues and cell types relevant to an array of diseases, including cancer, heart disease, and neurodegenerative disorders. This Perspective describes LINCS technologies, datasets, tools, and approaches to data accessibility and reusability.
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Affiliation(s)
- Alexandra B Keenan
- BD2K-LINCS DCIC, Mount Sinai Center for Bioinformatics, Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Sherry L Jenkins
- BD2K-LINCS DCIC, Mount Sinai Center for Bioinformatics, Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Kathleen M Jagodnik
- BD2K-LINCS DCIC, Mount Sinai Center for Bioinformatics, Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Simon Koplev
- BD2K-LINCS DCIC, Mount Sinai Center for Bioinformatics, Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Edward He
- BD2K-LINCS DCIC, Mount Sinai Center for Bioinformatics, Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Denis Torre
- BD2K-LINCS DCIC, Mount Sinai Center for Bioinformatics, Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Zichen Wang
- BD2K-LINCS DCIC, Mount Sinai Center for Bioinformatics, Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Anders B Dohlman
- BD2K-LINCS DCIC, Mount Sinai Center for Bioinformatics, Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Moshe C Silverstein
- BD2K-LINCS DCIC, Mount Sinai Center for Bioinformatics, Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Alexander Lachmann
- BD2K-LINCS DCIC, Mount Sinai Center for Bioinformatics, Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Maxim V Kuleshov
- BD2K-LINCS DCIC, Mount Sinai Center for Bioinformatics, Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Avi Ma'ayan
- BD2K-LINCS DCIC, Mount Sinai Center for Bioinformatics, Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA.
| | - Vasileios Stathias
- BD2K-LINCS DCIC, Department of Molecular and Cellular Pharmacology, University of Miami, Miami, FL 33146, USA
| | - Raymond Terryn
- BD2K-LINCS DCIC, Department of Molecular and Cellular Pharmacology, University of Miami, Miami, FL 33146, USA
| | - Daniel Cooper
- BD2K-LINCS DCIC, Department of Molecular and Cellular Pharmacology, University of Miami, Miami, FL 33146, USA
| | - Michele Forlin
- BD2K-LINCS DCIC, Department of Molecular and Cellular Pharmacology, University of Miami, Miami, FL 33146, USA
| | - Amar Koleti
- BD2K-LINCS DCIC, Department of Molecular and Cellular Pharmacology, University of Miami, Miami, FL 33146, USA
| | - Dusica Vidovic
- BD2K-LINCS DCIC, Department of Molecular and Cellular Pharmacology, University of Miami, Miami, FL 33146, USA
| | - Caty Chung
- BD2K-LINCS DCIC, Department of Molecular and Cellular Pharmacology, University of Miami, Miami, FL 33146, USA
| | - Stephan C Schürer
- BD2K-LINCS DCIC, Department of Molecular and Cellular Pharmacology, University of Miami, Miami, FL 33146, USA
| | - Jouzas Vasiliauskas
- BD2K-LINCS DCIC, Department of Environmental Health, University of Cincinnati, Cincinnati, OH 45220, USA
| | - Marcin Pilarczyk
- BD2K-LINCS DCIC, Department of Environmental Health, University of Cincinnati, Cincinnati, OH 45220, USA
| | - Behrouz Shamsaei
- BD2K-LINCS DCIC, Department of Environmental Health, University of Cincinnati, Cincinnati, OH 45220, USA
| | - Mehdi Fazel
- BD2K-LINCS DCIC, Department of Environmental Health, University of Cincinnati, Cincinnati, OH 45220, USA
| | - Yan Ren
- BD2K-LINCS DCIC, Department of Environmental Health, University of Cincinnati, Cincinnati, OH 45220, USA
| | - Wen Niu
- BD2K-LINCS DCIC, Department of Environmental Health, University of Cincinnati, Cincinnati, OH 45220, USA
| | - Nicholas A Clark
- BD2K-LINCS DCIC, Department of Environmental Health, University of Cincinnati, Cincinnati, OH 45220, USA
| | - Shana White
- BD2K-LINCS DCIC, Department of Environmental Health, University of Cincinnati, Cincinnati, OH 45220, USA
| | - Naim Mahi
- BD2K-LINCS DCIC, Department of Environmental Health, University of Cincinnati, Cincinnati, OH 45220, USA
| | - Lixia Zhang
- BD2K-LINCS DCIC, Department of Environmental Health, University of Cincinnati, Cincinnati, OH 45220, USA
| | - Michal Kouril
- BD2K-LINCS DCIC, Department of Environmental Health, University of Cincinnati, Cincinnati, OH 45220, USA
| | - John F Reichard
- BD2K-LINCS DCIC, Department of Environmental Health, University of Cincinnati, Cincinnati, OH 45220, USA
| | - Siva Sivaganesan
- BD2K-LINCS DCIC, Department of Environmental Health, University of Cincinnati, Cincinnati, OH 45220, USA
| | - Mario Medvedovic
- BD2K-LINCS DCIC, Department of Environmental Health, University of Cincinnati, Cincinnati, OH 45220, USA
| | - Jaroslaw Meller
- BD2K-LINCS DCIC, Department of Environmental Health, University of Cincinnati, Cincinnati, OH 45220, USA
| | - Rick J Koch
- DToxS, Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Marc R Birtwistle
- DToxS, Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Ravi Iyengar
- DToxS, Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Eric A Sobie
- DToxS, Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Evren U Azeloglu
- DToxS, Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Julia Kaye
- NeuroLINCS, Gladstone Institute of Neurological Disease and the Departments of Neurology and Physiology, University of California San Francisco, San Francisco, CA 94158, USA
| | - Jeannette Osterloh
- NeuroLINCS, Gladstone Institute of Neurological Disease and the Departments of Neurology and Physiology, University of California San Francisco, San Francisco, CA 94158, USA
| | - Kelly Haston
- NeuroLINCS, Gladstone Institute of Neurological Disease and the Departments of Neurology and Physiology, University of California San Francisco, San Francisco, CA 94158, USA
| | - Jaslin Kalra
- NeuroLINCS, Gladstone Institute of Neurological Disease and the Departments of Neurology and Physiology, University of California San Francisco, San Francisco, CA 94158, USA
| | - Steve Finkbiener
- NeuroLINCS, Gladstone Institute of Neurological Disease and the Departments of Neurology and Physiology, University of California San Francisco, San Francisco, CA 94158, USA
| | - Jonathan Li
- NeuroLINCS, Department of Biological Engineering, MIT, Cambridge, MA 02142, USA
| | - Pamela Milani
- NeuroLINCS, Department of Biological Engineering, MIT, Cambridge, MA 02142, USA
| | - Miriam Adam
- NeuroLINCS, Department of Biological Engineering, MIT, Cambridge, MA 02142, USA
| | | | - Karen Sachs
- NeuroLINCS, Department of Biological Engineering, MIT, Cambridge, MA 02142, USA
| | - Alex Lenail
- NeuroLINCS, Department of Biological Engineering, MIT, Cambridge, MA 02142, USA
| | - Divya Ramamoorthy
- NeuroLINCS, Department of Biological Engineering, MIT, Cambridge, MA 02142, USA
| | - Ernest Fraenkel
- NeuroLINCS, Department of Biological Engineering, MIT, Cambridge, MA 02142, USA
| | - Gavin Daigle
- NeuroLINCS, Department of Neuroscience, Johns Hopkins University, Baltimore, MD 21205, USA
| | - Uzma Hussain
- NeuroLINCS, Department of Neuroscience, Johns Hopkins University, Baltimore, MD 21205, USA
| | - Alyssa Coye
- NeuroLINCS, Department of Neuroscience, Johns Hopkins University, Baltimore, MD 21205, USA
| | - Jeffrey Rothstein
- NeuroLINCS, Department of Neuroscience, Johns Hopkins University, Baltimore, MD 21205, USA
| | - Dhruv Sareen
- NeuroLINCS, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
| | - Loren Ornelas
- NeuroLINCS, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
| | - Maria Banuelos
- NeuroLINCS, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
| | - Berhan Mandefro
- NeuroLINCS, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
| | - Ritchie Ho
- NeuroLINCS, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
| | - Clive N Svendsen
- NeuroLINCS, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
| | - Ryan G Lim
- NeuroLINCS, Departments of Psychiatry and Human Behavior and Neurobiology and Behavior, University of California Irvine, Irvine, CA 92697, USA
| | - Jennifer Stocksdale
- NeuroLINCS, Departments of Psychiatry and Human Behavior and Neurobiology and Behavior, University of California Irvine, Irvine, CA 92697, USA
| | - Malcolm S Casale
- NeuroLINCS, Departments of Psychiatry and Human Behavior and Neurobiology and Behavior, University of California Irvine, Irvine, CA 92697, USA
| | - Terri G Thompson
- NeuroLINCS, Departments of Psychiatry and Human Behavior and Neurobiology and Behavior, University of California Irvine, Irvine, CA 92697, USA
| | - Jie Wu
- NeuroLINCS, Departments of Psychiatry and Human Behavior and Neurobiology and Behavior, University of California Irvine, Irvine, CA 92697, USA
| | - Leslie M Thompson
- NeuroLINCS, Departments of Psychiatry and Human Behavior and Neurobiology and Behavior, University of California Irvine, Irvine, CA 92697, USA
| | - Victoria Dardov
- NeuroLINCS, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
| | | | - Andrea Matlock
- NeuroLINCS, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
| | | | - Jacob D Jaffe
- LINCS PCCSE, The Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA
| | | | - Aravind Subramanian
- LINCS Center for Transcriptomics, The Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA
| | - Todd R Golub
- LINCS Center for Transcriptomics, The Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA; Dana-Farber Cancer Institute, Boston, MA 02215, USA; Howard Hughes Medical Institute, Chevy Chase, MD 20815, USA; Harvard Medical School, Boston, MA 02115, USA
| | - Sean D Erickson
- HMS LINCS Center, Harvard Medical School, Boston, MA 02115, USA
| | | | - Marc Hafner
- HMS LINCS Center, Harvard Medical School, Boston, MA 02115, USA
| | | | - Jia-Ren Lin
- HMS LINCS Center, Harvard Medical School, Boston, MA 02115, USA
| | - Caitlin E Mills
- HMS LINCS Center, Harvard Medical School, Boston, MA 02115, USA
| | | | - Mario Niepel
- HMS LINCS Center, Harvard Medical School, Boston, MA 02115, USA
| | | | | | - David Wrobel
- HMS LINCS Center, Harvard Medical School, Boston, MA 02115, USA
| | - Peter K Sorger
- HMS LINCS Center, Harvard Medical School, Boston, MA 02115, USA
| | - Laura M Heiser
- MEP-LINCS Center, Oregon Health & Science University, Portland, OR 97239, USA
| | - Joe W Gray
- MEP-LINCS Center, Oregon Health & Science University, Portland, OR 97239, USA
| | - James E Korkola
- MEP-LINCS Center, Oregon Health & Science University, Portland, OR 97239, USA
| | - Gordon B Mills
- MEP-LINCS Center, Department of Systems Biology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Mark LaBarge
- MEP-LINCS Center, Department of Population Sciences, Beckman Research Institute at City of Hope, Duarte, CA 91011, USA; MEP-LINCS Center, Center for Cancer Biomarkers Research, University of Bergen, Bergen 5009, Norway
| | - Heidi S Feiler
- MEP-LINCS Center, Oregon Health & Science University, Portland, OR 97239, USA
| | - Mark A Dane
- MEP-LINCS Center, Oregon Health & Science University, Portland, OR 97239, USA
| | - Elmar Bucher
- MEP-LINCS Center, Oregon Health & Science University, Portland, OR 97239, USA
| | - Michel Nederlof
- MEP-LINCS Center, Oregon Health & Science University, Portland, OR 97239, USA; MEP-LINCS Center, Quantitative Imaging Systems LLC, Portland, OR 97239, USA
| | - Damir Sudar
- MEP-LINCS Center, Oregon Health & Science University, Portland, OR 97239, USA; MEP-LINCS Center, Quantitative Imaging Systems LLC, Portland, OR 97239, USA
| | - Sean Gross
- MEP-LINCS Center, Oregon Health & Science University, Portland, OR 97239, USA
| | - David F Kilburn
- MEP-LINCS Center, Oregon Health & Science University, Portland, OR 97239, USA
| | - Rebecca Smith
- MEP-LINCS Center, Oregon Health & Science University, Portland, OR 97239, USA
| | - Kaylyn Devlin
- MEP-LINCS Center, Oregon Health & Science University, Portland, OR 97239, USA
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Engelsen A, Wnup-Lipinska K, Tiron C, Pelissier F, Jokela T, Haaland G, Gausdal G, Sandal T, Frink R, Liang X, Hinz S, Ahmed L, Hellesøy M, Mickelm D, Minna J, LaBarge M, Brekken R, Lorens J. 362 Phenotypic plasticity in epithelial progenitors and mesenchymal carcinoma is regulated by Axl signaling. Eur J Cancer 2014. [DOI: 10.1016/s0959-8049(14)70488-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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Jokela T, Stampfer M, Lorens J, LaBarge M. Abstract A095: The microenvironmental basis of AXL regulation. Mol Cancer Res 2014. [DOI: 10.1158/1557-3125.advbc-a095] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
AXL tyrosine kinase expression is a strong negative prognostic factor for survival of human breast cancer, and its expression is significant in metastases. Breast cancer metastasis is promoted by epithelial-mesenchymal transition (EMT), where epithelial cells lose their cell-to-cell contacts and polarity, resulting in transformation to a fibroblastic migratory phenotype. During EMT process, AXL is highly expressed, and knockdown of AXL completely prevents the invasion of breast cancer cells via EMT-based mechanisms. EMT is promoted by specific transcription factors like slug or oncogenes like Ras, but interestingly, without extracellular signaling feedback, cells will lose the EMT state and invasion capability.
In this study we characterize extracellular stimuli that stabilize AXL expression and the EMT-phenotype in human mammary epithelial cells. In Vitro studies were implemented with HMEC-derived cell lines, which have traceable origins and were derived through defined immortalization steps. Mammary epithelial cells were induced into an EMT phenotype by Slug-overexpression and exposure to different microenvironments. AXL and other EMT markers were monitored in each cell passage. Results have shown that with Slug-expressing cells lose the EMT phenotype after a few cell passages. When Slug induced HMECs were cultured on Micro Environment microArrays (MEArray), specific microenvironments were revealed that increased and stabilized AXL expression. Our results show that microenvironmental signals are essential to induce and maintain the EMT phenotype.
Citation Format: Tiina Jokela, Martha Stampfer, James Lorens, Mark LaBarge. The microenvironmental basis of AXL regulation. [abstract]. In: Proceedings of the AACR Special Conference on Advances in Breast Cancer Research: Genetics, Biology, and Clinical Applications; Oct 3-6, 2013; San Diego, CA. Philadelphia (PA): AACR; Mol Cancer Res 2013;11(10 Suppl):Abstract nr A095.
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Affiliation(s)
- Tiina Jokela
- 1Lawrence Berkeley National Laboratory, Berkeley, CA,
| | | | | | - Mark LaBarge
- 1Lawrence Berkeley National Laboratory, Berkeley, CA,
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Stampfer M, Vrba L, Fuchs L, Brothman A, LaBarge M, Futscher B, Garbe J. Abstract B008: Efficient immortalization of normal human mammary epithelial cells using two pathologically relevant agents does not require gross genomic alterations. Mol Cancer Res 2013. [DOI: 10.1158/1557-3125.advbc-b008] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Most human carcinomas contain genomically unstable cells with multiple genomic errors, and express telomerase activity. Widespread instability can first be observed in vivo at the pre-malignant stage, such as DCIS, and in vitro as finite lifespan cells with critically shortened telomeres approach replicative senescence. We have proposed that telomere-dysfunction induced genomic instability in pre-malignant finite cells may be needed to generate the errors required for telomerase reactivation and immortalization, while also generating many additional “passenger” errors that will be carried forward into resulting carcinomas. Genomic errors that occur prior to immortalization may influence the cancer phenotype and form the basis for ongoing genomic instability in the malignant cells. Further, the prevalence of many genomic errors in primary human carcinomas makes it difficult to identify the driver errors responsible for immortalization using only in vivo tissues. Although immortalization is crucial for human carcinoma development, little is known about the processes that allow telomerase reactivation during malignant progression. This knowledge gap is due, in part, to the paucity of experimentally tractable model systems that can examine human epithelial cell immortalization as it might occur in vivo. For example, most murine models lack a significant replicative senescence/immortalization barrier; immortalization employing hTERT precludes examination of the errors responsible for telomerase reactivation during carcinogenesis; a reproducible human mammary epithelial cell immortalization model employing agents implicated in in vivo carcinogenesis has been lacking. We achieved efficient non-clonal immortalization of normal human mammary epithelial cells (HMEC) by directly targeting the two main senescence barriers encountered by cultured HMEC. The stress-associated stasis barrier, enforced by elevated levels of p16INK4A, was bypassed using shRNA to p16. The replicative senescence barrier due to critically shortened telomeres was bypassed in post-stasis HMEC by c-Myc transduction. These results demonstrate that just two pathologically relevant oncogenic agents are sufficient to immortally transform normal human epithelial cells. The non-clonal immortalized lines generated by direct targeting of the senescence barriers exhibited normal karyotypes at early passages, supporting our hypothesis that the genomic instability commonly present in human carcinomas may not be required per se for immortal transformation, but is needed to generate errors that overcome tumor suppressive barriers. This method of achieving efficient HMEC immortalization, in the absence of “passenger” genomic errors, should facilitate examination of telomerase regulation during human carcinoma progression. Additionally, immortalization, associated with telomerase reactivation, is necessary for progression of all subtypes of human beast carcinomas, and could therefore be a valuable therapeutic target. Our reproducible method for immortalization can permit exploration of agents that may prevent or reverse the immortalization process. That transduction of just shRNA to p16 and c-Myc can immortally transform normal HMEC validates our model of the two main tumor-suppressive senescence barriers (Garbe et al, Cancer Res 2009): stasis, a stress-associated arrest independent of telomere length and extent of replication, and replicative senescence due to telomere dysfunction.
Citation Format: Martha Stampfer, Lukas Vrba, Laura Fuchs, Arthur Brothman, Mark LaBarge, Bernard Futscher, James Garbe. Efficient immortalization of normal human mammary epithelial cells using two pathologically relevant agents does not require gross genomic alterations. [abstract]. In: Proceedings of the AACR Special Conference on Advances in Breast Cancer Research: Genetics, Biology, and Clinical Applications; Oct 3-6, 2013; San Diego, CA. Philadelphia (PA): AACR; Mol Cancer Res 2013;11(10 Suppl):Abstract nr B008.
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Affiliation(s)
| | | | | | | | - Mark LaBarge
- 1Lawrence Berkeley National Laboratory, Berkeley, CA,
| | | | - James Garbe
- 1Lawrence Berkeley National Laboratory, Berkeley, CA,
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Tiron C, Pelissier F, Wnuk-Lipinska K, Stefansson I, Virtakoivu R, Miyano M, Sandal T, Micklem D, Garbe J, Stampfer M, Ivaska J, Akslen L, LaBarge M, Lorens J. Abstract 4888: Axl receptor signaling in required for stem cell traits and metastasis in breast cancer. Cancer Res 2013. [DOI: 10.1158/1538-7445.am2013-4888] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Epithelial-to-mesenchymal transition (EMT) endows carcinoma cells with migratory, survival and stem cell-like attributes that facilitate therapeutic resistance and metastasis. Expression of the Axl receptor tyrosine kinase in aggressive breast cancer correlates with EMT, poor survival and is prevalent in patient metastases. Induction of EMT in immortalized mammary epithelial cells by EMT-transcription factors, TGFbeta or hypoxia upregulates Axl and establishes an autocrine-signaling loop with its ligand, Gas6. Axl receptor signaling is required to maintain EMT-related invasive, drug resistance and cancer stem cell (CSC) traits of malignant breast cancer cells. Targeting Axl signaling with RNAi or pharmacological agents blocks the EMT/CSC gene program and inhibits malignant functions including invasiveness, drug resistance, mammosphere formation, in vivo tumor initiation, and spontaneous metastasis in orthotopic breast cancer models. These results suggest that Axl expression is requisite for the maintenance of EMT and stem cell-like traits during malignant progression. The EMT program is characteristic of normal adult mammary epithelial stem/progenitor cells. Congruently, we show that the Axl receptor expressed on mammary epithelial stem/progenitor cells, and Axl signaling is necessary for mammary epithelial multipotent progenitor activity. Thus Axl receptor signaling represents a novel regulatory pathway linking normal mammary stem/progenitor cells and breast cancer stem cells. Hence, clinical Axl inhibitors represent a novel therapeutic avenue to target EMT/CSC traits of aggressive breast cancer.
Citation Format: Crina Tiron, Fanny Pelissier, Katarzyna Wnuk-Lipinska, Ingunn Stefansson, Reeta Virtakoivu, Masaru Miyano, Tone Sandal, David Micklem, James Garbe, Martha Stampfer, Johanna Ivaska, Lars Akslen, Mark LaBarge, James Lorens. Axl receptor signaling in required for stem cell traits and metastasis in breast cancer. [abstract]. In: Proceedings of the 104th Annual Meeting of the American Association for Cancer Research; 2013 Apr 6-10; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2013;73(8 Suppl):Abstract nr 4888. doi:10.1158/1538-7445.AM2013-4888
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Affiliation(s)
| | | | | | | | | | - Masaru Miyano
- 3Lawrence Berkeley National Laboratory, Berkeley, CA
| | | | | | - James Garbe
- 3Lawrence Berkeley National Laboratory, Berkeley, CA
| | | | | | | | - Mark LaBarge
- 3Lawrence Berkeley National Laboratory, Berkeley, CA
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Tiron C, Pelissier F, Wnuk-Lipinska K, Stefansson I, Virtakoivu R, Miyano M, Sandal T, Micklem D, Garbe J, Stampfer M, Ivaska J, Akslen L, LaBarge M, Lorens J. Abstract C76: Axl signaling is required for stem cell traits and metastasis in breast cancer. Cancer Res 2013. [DOI: 10.1158/1538-7445.tim2013-c76] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Epithelial-to-mesenchymal transition (EMT) endows carcinoma cells with migratory, survival and stem cell-like attributes that facilitate therapeutic resistance and metastasis. Expression of the Axl receptor tyrosine kinase in breast cancer correlates with EMT, poor survival and is prevalent in patient metastases. Axl upregulation in mammary epithelial cells by EMT-transcription factors, TGFbeta or hypoxia, establishes an autocrine-signaling loop with its ligand, Gas6. Inhibition of Axl signaling blocks EMT/ cancer stem cell traits including invasiveness, drug resistance, mammosphere formation, in vivo tumor initiation, and prevents spontaneous metastasis in orthotopic breast cancer models. Congruently, we show that Axl is expressed on mammary epithelial stem/progenitor cells and regulates multipotent progenitor activity. Thus Axl signal transduction represents a novel regulatory pathway linking normal mammary stem/progenitor cells and breast cancer stem cell activity. Clinical Axl-inhibitors represent a novel therapeutic opportunity to treat aggressive breast cancer.
Citation Format: Crina Tiron, Fanny Pelissier, Katarzyna Wnuk-Lipinska, Ingunn Stefansson, Reeta Virtakoivu, Masaru Miyano, Tone Sandal, David Micklem, James Garbe, Martha Stampfer, Johanna Ivaska, Lars Akslen, Mark LaBarge, James Lorens. Axl signaling is required for stem cell traits and metastasis in breast cancer. [abstract]. In: Proceedings of the AACR Special Conference on Tumor Invasion and Metastasis; Jan 20-23, 2013; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2013;73(3 Suppl):Abstract nr C76.
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Affiliation(s)
| | | | | | | | | | - Masaru Miyano
- 3Lawrence Berkeley National Laboratory, Berkeley, CA,
| | | | | | - James Garbe
- 3Lawrence Berkeley National Laboratory, Berkeley, CA,
| | | | | | | | - Mark LaBarge
- 3Lawrence Berkeley National Laboratory, Berkeley, CA,
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Garbe JC, Vrba L, Jackson MW, Futscher B, LaBarge M, Stampfer MR. Abstract A41: Vulnerability of human mammary epithelial cells to oncogenic transformation. Cancer Res 2011. [DOI: 10.1158/1538-7445.fbcr11-a41] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Breast cancers display great phenotypic and molecular diversity. Based on these differences, ∼5 breast cancer subtypes have been categorized; importantly, these subtypes show major differences in clinical parameters. Etiology and progression likely differ in subtypes; significant variables may include the type of cell from which the cancer originated, and the specific genomic alterations that subverted normal processes to confer malignancy. However, large gaps exist in our knowledge of target cell identity or molecular events responsible for any breast cancer subtype. Understanding the molecular alterations that lead to the different breast cancer types could facilitate design of clinical interventions in the carcinogenic progression. Our laboratory has addressed this issue with a long-term program to develop an experimentally tractable HMEC culture system for investigating multi-step breast carcinogenesis. Normal finite HMEC have been exposed to pathologically relevant oncogenic agents, generating cells at different stages in transformation with properties consistent with what is known about breast cancer progression in vivo. However, thus far almost all in vitro transformed HMEC lines represent a limited subset of the phenotypes observed in breast cancer cells in vivo. We hypothesized that this limited phenotype could result from targeting cells in culture conditions that restrict most normal HMEC growth, and proposed using HMEC grown in our new media that support growth of cells with luminal, myoepithelial, and progenitor lineage markers. We also hypothesized that unstressed HMEC (without p16INK4a induction) would be more vulnerable to transformation and yield a greater range of transformed phenotypes. Our transformation protocols were based on our model of the tumor-suppressive senescence barriers encountered by cultured HMEC (Garbe et al, Cancer Res 2009). To bypass stasis (stress-induced senescence mediated by Rb/p16) we exposed normal HMEC to shRNA to p16. To bypass telomere dysfunction due to telomere attrition, we used cMyc, an hTERT transactivator. Our data show that p16sh, then cMyc, given to unstressed normal HMEC, produced rapid uniform immortalization. cMyc did not immortalize p16(−) post-stasis HMEC that had high stress exposure prior to epigenetic silencing of p16. HMEC that had become p16(-) post-stasis by different means exhibited additional significant differences, e.g., epigenetic alterations and telomerase activity. Unstressed pre-stasis HMEC were also uniformly immortalized by hTERT, and showed rare clonal immortalization with cMyc alone. Rare clonal immortalization by p16sh alone occurred during the period of genomic instability at telomere dysfunction. Immortalized lines showed many phenotypic differences, but those derived from young women exhibited mainly basal markers. Our recent work showing age-associated changes in lineage markers could be relevant to the observed age-associated increased luminal breast cancer incidence and to generating luminal lines. Applying our p16sh/cMyc protocol to an older woman's HMEC produced an immortal line with luminal properties. Altogether, we have shown that different pathways to transformation are associated with different molecular properties, opening the possibility of individualized therapy for these distinct means of becoming malignant. Future studies will evaluate the effects of specific oncogenic exposures on different normal HMEC types from young and older women.
Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the Second AACR International Conference on Frontiers in Basic Cancer Research; 2011 Sep 14-18; San Francisco, CA. Philadelphia (PA): AACR; Cancer Res 2011;71(18 Suppl):Abstract nr A41.
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Affiliation(s)
| | | | | | | | - Mark LaBarge
- 1Lawrence Berkeley National Laboratory, Berkeley, CA
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Hitoshi Y, Lorens J, Kitada SI, Fisher J, LaBarge M, Ring HZ, Francke U, Reed JC, Kinoshita S, Nolan GP. Toso, a cell surface, specific regulator of Fas-induced apoptosis in T cells. Immunity 1998; 8:461-71. [PMID: 9586636 DOI: 10.1016/s1074-7613(00)80551-8] [Citation(s) in RCA: 179] [Impact Index Per Article: 6.9] [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: 02/07/2023]
Abstract
Fas is a surface receptor that can transmit signals for apoptosis. Using retroviral cDNA library-based functional cloning we identified a gene, toso, that blocks Fas-mediated apoptosis. Toso expression was confined to lymphoid cells and was enhanced after cell-specific activation processes in T cells. Toso appeared limited to inhibition of apoptosis mediated by members of the TNF receptor family and was capable of inhibiting T cell self-killing induced by TCR activation processes that up-regulate Fas ligand. We mapped the effect of Toso to inhibition of caspase-8 processing, the most upstream caspase activity in Fas-mediated signaling, potentially through activation of cFLIP. Toso therefore serves as a novel regulator of Fas-mediated apoptosis and may act as a regulator of cell fate in T cells and other hematopoietic lineages.
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Affiliation(s)
- Y Hitoshi
- Department of Molecular Pharmacology, Stanford University School of Medicine, California 94305, USA
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