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Wen RM, Qiu Z, Marti GEW, Peterson EE, Marques FJG, Bermudez A, Wei Y, Nolley R, Lam N, Polasko AL, Chiu CL, Zhang D, Cho S, Karageorgos GM, McDonough E, Chadwick C, Ginty F, Jung KJ, Machiraju R, Mallick P, Crowley L, Pollack JR, Zhao H, Pitteri SJ, Brooks JD. AZGP1 deficiency promotes angiogenesis in prostate cancer. J Transl Med 2024; 22:383. [PMID: 38659028 PMCID: PMC11044612 DOI: 10.1186/s12967-024-05183-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2023] [Accepted: 04/08/2024] [Indexed: 04/26/2024] Open
Abstract
BACKGROUND Loss of AZGP1 expression is a biomarker associated with progression to castration resistance, development of metastasis, and poor disease-specific survival in prostate cancer. However, high expression of AZGP1 cells in prostate cancer has been reported to increase proliferation and invasion. The exact role of AZGP1 in prostate cancer progression remains elusive. METHOD AZGP1 knockout and overexpressing prostate cancer cells were generated using a lentiviral system. The effects of AZGP1 under- or over-expression in prostate cancer cells were evaluated by in vitro cell proliferation, migration, and invasion assays. Heterozygous AZGP1± mice were obtained from European Mouse Mutant Archive (EMMA), and prostate tissues from homozygous knockout male mice were collected at 2, 6 and 10 months for histological analysis. In vivo xenografts generated from AZGP1 under- or over-expressing prostate cancer cells were used to determine the role of AZGP1 in prostate cancer tumor growth, and subsequent proteomics analysis was conducted to elucidate the mechanisms of AZGP1 action in prostate cancer progression. AZGP1 expression and microvessel density were measured in human prostate cancer samples on a tissue microarray of 215 independent patient samples. RESULT Neither the knockout nor overexpression of AZGP1 exhibited significant effects on prostate cancer cell proliferation, clonal growth, migration, or invasion in vitro. The prostates of AZGP1-/- mice initially appeared to have grossly normal morphology; however, we observed fibrosis in the periglandular stroma and higher blood vessel density in the mouse prostate by 6 months. In PC3 and DU145 mouse xenografts, over-expression of AZGP1 did not affect tumor growth. Instead, these tumors displayed decreased microvessel density compared to xenografts derived from PC3 and DU145 control cells, suggesting that AZGP1 functions to inhibit angiogenesis in prostate cancer. Proteomics profiling further indicated that, compared to control xenografts, AZGP1 overexpressing PC3 xenografts are enriched with angiogenesis pathway proteins, including YWHAZ, EPHA2, SERPINE1, and PDCD6, MMP9, GPX1, HSPB1, COL18A1, RNH1, and ANXA1. In vitro functional studies show that AZGP1 inhibits human umbilical vein endothelial cell proliferation, migration, tubular formation and branching. Additionally, tumor microarray analysis shows that AZGP1 expression is negatively correlated with blood vessel density in human prostate cancer tissues. CONCLUSION AZGP1 is a negative regulator of angiogenesis, such that loss of AZGP1 promotes angiogenesis in prostate cancer. AZGP1 likely exerts heterotypical effects on cells in the tumor microenvironment, such as stromal and endothelial cells. This study sheds light on the anti-angiogenic characteristics of AZGP1 in the prostate and provides a rationale to target AZGP1 to inhibit prostate cancer progression.
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Affiliation(s)
- Ru M Wen
- Department of Urology, Stanford University School of Medicine, Stanford, CA, 94305, USA.
| | - Zhengyuan Qiu
- Department of Urology, Stanford University School of Medicine, Stanford, CA, 94305, USA
| | - G Edward W Marti
- Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, CA, 94305, USA
| | - Eric E Peterson
- Department of Urology, Stanford University School of Medicine, Stanford, CA, 94305, USA
| | - Fernando Jose Garcia Marques
- Department of Radiology, Stanford University School of Medicine, Stanford, CA, 94305, USA
- Canary Center at Stanford for Cancer Early Detection, Stanford University School of Medicine, Stanford, CA, 94305, USA
| | - Abel Bermudez
- Department of Radiology, Stanford University School of Medicine, Stanford, CA, 94305, USA
- Canary Center at Stanford for Cancer Early Detection, Stanford University School of Medicine, Stanford, CA, 94305, USA
| | - Yi Wei
- Department of Urology, Stanford University School of Medicine, Stanford, CA, 94305, USA
| | - Rosalie Nolley
- Department of Urology, Stanford University School of Medicine, Stanford, CA, 94305, USA
| | - Nathan Lam
- Department of Urology, Stanford University School of Medicine, Stanford, CA, 94305, USA
| | - Alex LaPat Polasko
- Department of Urology, Stanford University School of Medicine, Stanford, CA, 94305, USA
| | - Chun-Lung Chiu
- Department of Urology, Stanford University School of Medicine, Stanford, CA, 94305, USA
| | - Dalin Zhang
- Department of Urology, Stanford University School of Medicine, Stanford, CA, 94305, USA
| | - Sanghee Cho
- GE HealthCare Technology and Innovation Center, Niskayuna, NY, 12309, USA
| | | | | | - Chrystal Chadwick
- GE HealthCare Technology and Innovation Center, Niskayuna, NY, 12309, USA
| | - Fiona Ginty
- GE HealthCare Technology and Innovation Center, Niskayuna, NY, 12309, USA
| | - Kyeong Joo Jung
- Department of Computer Science and Engineering, The Ohio State University, Columbus, OH, 43210, USA
| | - Raghu Machiraju
- Department of Computer Science and Engineering, The Ohio State University, Columbus, OH, 43210, USA
| | - Parag Mallick
- Canary Center at Stanford for Cancer Early Detection, Stanford University School of Medicine, Stanford, CA, 94305, USA
| | - Laura Crowley
- Department of Biochemistry, Stanford University School of Medicine, Stanford, CA, 94305, USA
- Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, CA, USA
| | - Jonathan R Pollack
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
| | - Hongjuan Zhao
- Department of Urology, Stanford University School of Medicine, Stanford, CA, 94305, USA
| | - Sharon J Pitteri
- Department of Radiology, Stanford University School of Medicine, Stanford, CA, 94305, USA
- Canary Center at Stanford for Cancer Early Detection, Stanford University School of Medicine, Stanford, CA, 94305, USA
| | - James D Brooks
- Department of Urology, Stanford University School of Medicine, Stanford, CA, 94305, USA.
- Canary Center at Stanford for Cancer Early Detection, Stanford University School of Medicine, Stanford, CA, 94305, USA.
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2
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Karageorgos GM, Cho S, McDonough E, Chadwick C, Ghose S, Owens J, Jung KJ, Machiraju R, West R, Brooks JD, Mallick P, Ginty F. Deep learning-based automated pipeline for blood vessel detection and distribution analysis in multiplexed prostate cancer images. Front Bioinform 2024; 3:1296667. [PMID: 38323039 PMCID: PMC10844485 DOI: 10.3389/fbinf.2023.1296667] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2023] [Accepted: 12/18/2023] [Indexed: 02/08/2024] Open
Abstract
Introduction: Prostate cancer is a highly heterogeneous disease, presenting varying levels of aggressiveness and response to treatment. Angiogenesis is one of the hallmarks of cancer, providing oxygen and nutrient supply to tumors. Micro vessel density has previously been correlated with higher Gleason score and poor prognosis. Manual segmentation of blood vessels (BVs) In microscopy images is challenging, time consuming and may be prone to inter-rater variabilities. In this study, an automated pipeline is presented for BV detection and distribution analysis in multiplexed prostate cancer images. Methods: A deep learning model was trained to segment BVs by combining CD31, CD34 and collagen IV images. In addition, the trained model was used to analyze the size and distribution patterns of BVs in relation to disease progression in a cohort of prostate cancer patients (N = 215). Results: The model was capable of accurately detecting and segmenting BVs, as compared to ground truth annotations provided by two reviewers. The precision (P), recall (R) and dice similarity coefficient (DSC) were equal to 0.93 (SD 0.04), 0.97 (SD 0.02) and 0.71 (SD 0.07) with respect to reviewer 1, and 0.95 (SD 0.05), 0.94 (SD 0.07) and 0.70 (SD 0.08) with respect to reviewer 2, respectively. BV count was significantly associated with 5-year recurrence (adjusted p = 0.0042), while both count and area of blood vessel were significantly associated with Gleason grade (adjusted p = 0.032 and 0.003 respectively). Discussion: The proposed methodology is anticipated to streamline and standardize BV analysis, offering additional insights into the biology of prostate cancer, with broad applicability to other cancers.
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Affiliation(s)
| | | | | | | | | | | | - Kyeong Joo Jung
- Department of Computer Science and Engineering, The Ohio State University, Columbus, OH, United States
| | - Raghu Machiraju
- Department of Computer Science and Engineering, The Ohio State University, Columbus, OH, United States
| | - Robert West
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, United States
| | - James D. Brooks
- Department of Urology, Stanford University School of Medicine, Stanford, CA, United States
| | - Parag Mallick
- Canary Center for Cancer Early Detection, Department of Radiology, Stanford University School of Medicine, Stanford, CA, United States
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3
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Barker AD, Alba MM, Mallick P, Agus DB, Lee JSH. An Inflection Point in Cancer Protein Biomarkers: What Was and What's Next. Mol Cell Proteomics 2023:100569. [PMID: 37196763 PMCID: PMC10388583 DOI: 10.1016/j.mcpro.2023.100569] [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] [Received: 11/25/2022] [Revised: 04/26/2023] [Accepted: 05/08/2023] [Indexed: 05/19/2023] Open
Abstract
Biomarkers remain the highest value proposition in cancer medicine today - especially protein biomarkers. Yet despite decades of evolving regulatory frameworks to facilitate the review of emerging technologies, biomarkers have been mostly about promise with very little to show for improvements in human health. Cancer is an emergent property of a complex system and deconvoluting the integrative and dynamic nature of the overall system through biomarkers is a daunting proposition. The last two decades have seen an explosion of multi-omics profiling and a range of advanced technologies for precision medicine, including the emergence of liquid biopsy, exciting advances in single cell analysis, artificial intelligence (machine and deep learning) for data analysis and many other advanced technologies that promise to transform biomarker discovery. Combining multiple omics modalities to acquire a more comprehensive landscape of the disease state, we are increasingly developing biomarkers to support therapy selection and patient monitoring. Furthering precision medicine, especially in oncology, necessitates moving away from the lens of reductionist thinking towards viewing and understanding that complex diseases are, in fact, complex adaptive systems. As such, we believe it is necessary to re-define biomarkers as representations of biological system states at different hierarchical levels of biological order. This definition could include traditional molecular, histologic, radiographic, or physiological characteristics, as well as emerging classes of digital markers and complex algorithms. To succeed in the future, we must move past purely observational individual studies and instead start building a mechanistic framework to enable integrative analysis of new studies within the context of prior studies. Identifying information in complex systems and applying theoretical constructs, such as information theory, to study cancer as a disease of dysregulated communication could prove to be "game changing" for the clinical outcome of cancer patients.
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Affiliation(s)
- Anna D Barker
- Lawrence J. Ellison Institute for Transformative Medicine, Los Angeles, CA; Complex Adaptive Systems Initiative and School of Life Sciences, Arizona State University, Tempe, Arizona
| | - Mario M Alba
- Pharmacology and Pharmaceutical Sciences, School of Pharmacy, University of Southern California, Los Angeles, CA
| | - Parag Mallick
- Canary Center at Stanford for Cancer Early Detection, Stanford University, Stanford, CA; Department of Radiology, Stanford University, Stanford, CA
| | - David B Agus
- Lawrence J. Ellison Institute for Transformative Medicine, Los Angeles, CA; Keck School of Medicine, University of Southern California, Los Angeles, CA; Viterbi School of Engineering, University of Southern California, Los Angeles, CA
| | - Jerry S H Lee
- Lawrence J. Ellison Institute for Transformative Medicine, Los Angeles, CA; Keck School of Medicine, University of Southern California, Los Angeles, CA; Viterbi School of Engineering, University of Southern California, Los Angeles, CA
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4
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Mallick P. Single‐Molecule Detection of Isoform‐Specific Tau Phosphorylation. Alzheimers Dement 2022. [DOI: 10.1002/alz.065032] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
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5
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Abramson A, Chan CT, Khan Y, Mermin-Bunnell A, Matsuhisa N, Fong R, Shad R, Hiesinger W, Mallick P, Gambhir SS, Bao Z. A flexible electronic strain sensor for the real-time monitoring of tumor regression. Sci Adv 2022; 8:eabn6550. [PMID: 36112679 PMCID: PMC9481124 DOI: 10.1126/sciadv.abn6550] [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] [Received: 12/10/2021] [Accepted: 07/12/2022] [Indexed: 05/02/2023]
Abstract
Assessing the efficacy of cancer therapeutics in mouse models is a critical step in treatment development. However, low-resolution measurement tools and small sample sizes make determining drug efficacy in vivo a difficult and time-intensive task. Here, we present a commercially scalable wearable electronic strain sensor that automates the in vivo testing of cancer therapeutics by continuously monitoring the micrometer-scale progression or regression of subcutaneously implanted tumors at the minute time scale. In two in vivo cancer mouse models, our sensor discerned differences in tumor volume dynamics between drug- and vehicle-treated tumors within 5 hours following therapy initiation. These short-term regression measurements were validated through histology, and caliper and bioluminescence measurements taken over weeklong treatment periods demonstrated the correlation with longer-term treatment response. We anticipate that real-time tumor regression datasets could help expedite and automate the process of screening cancer therapies in vivo.
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Affiliation(s)
- Alex Abramson
- Department of Chemical Engineering, Stanford University, Stanford, CA 94305, USA
| | - Carmel T. Chan
- Department of Radiology, Stanford University, Stanford, CA 94305, USA
- Molecular Imaging Program at Stanford (MIPS) and Bio-X Program, Stanford University, Stanford CA, 94305, USA
| | - Yasser Khan
- Department of Chemical Engineering, Stanford University, Stanford, CA 94305, USA
| | - Alana Mermin-Bunnell
- Department of Chemical Engineering, Stanford University, Stanford, CA 94305, USA
- Department of Bioengineering, Stanford University, Stanford, CA 94305, USA
| | - Naoji Matsuhisa
- Department of Chemical Engineering, Stanford University, Stanford, CA 94305, USA
| | - Robyn Fong
- Department of Cardiothoracic Surgery, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Rohan Shad
- Department of Cardiothoracic Surgery, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - William Hiesinger
- Department of Cardiothoracic Surgery, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Parag Mallick
- Department of Radiology, Stanford University, Stanford, CA 94305, USA
- Canary Center at Stanford for Cancer Early Detection, Stanford University, Stanford, CA 94305, USA
| | - Sanjiv Sam Gambhir
- Department of Radiology, Stanford University, Stanford, CA 94305, USA
- Molecular Imaging Program at Stanford (MIPS) and Bio-X Program, Stanford University, Stanford CA, 94305, USA
- Department of Bioengineering, Stanford University, Stanford, CA 94305, USA
- Canary Center at Stanford for Cancer Early Detection, Stanford University, Stanford, CA 94305, USA
- Department of Medicine, Stanford University, Stanford, CA 94305, USA
| | - Zhenan Bao
- Department of Chemical Engineering, Stanford University, Stanford, CA 94305, USA
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6
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Satpathy SK, Panigrahi UK, Biswal R, Mallick P. Tuning the Optical Properties of ZnO Nanorods Through Gd Doping. Proc Natl Acad Sci , India, Sect A Phys Sci 2022. [DOI: 10.1007/s40010-022-00798-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/14/2022]
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7
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Gardner L, Kostarelos K, Mallick P, Dive C, Hadjidemetriou M. Nano-omics: nanotechnology-based multidimensional harvesting of the blood-circulating cancerome. Nat Rev Clin Oncol 2022; 19:551-561. [PMID: 35739399 DOI: 10.1038/s41571-022-00645-x] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/10/2022] [Indexed: 02/08/2023]
Abstract
Over the past decade, the development of 'simple' blood tests that enable cancer screening, diagnosis or monitoring and facilitate the design of personalized therapies without the need for invasive tumour biopsy sampling has been a core ambition in cancer research. Data emerging from ongoing biomarker development efforts indicate that multiple markers, used individually or as part of a multimodal panel, are required to enhance the sensitivity and specificity of assays for early stage cancer detection. The discovery of cancer-associated molecular alterations that are reflected in blood at multiple dimensions (genome, epigenome, transcriptome, proteome and metabolome) and integration of the resultant multi-omics data have the potential to uncover novel biomarkers as well as to further elucidate the underlying molecular pathways. Herein, we review key advances in multi-omics liquid biopsy approaches and introduce the 'nano-omics' paradigm: the development and utilization of nanotechnology tools for the enrichment and subsequent omics analysis of the blood-circulating cancerome.
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Affiliation(s)
- Lois Gardner
- Nanomedicine Lab, Faculty of Biology, Medicine and Health, The University of Manchester, Manchester, UK
- Cancer Research UK Manchester Institute Cancer Biomarker Centre, The University of Manchester, Manchester, UK
| | - Kostas Kostarelos
- Nanomedicine Lab, Faculty of Biology, Medicine and Health, The University of Manchester, Manchester, UK
- Catalan Institute of Nanoscience & Nanotechnology (ICN2), UAB Campus, Barcelona, Spain
| | - Parag Mallick
- Canary Center at Stanford for Cancer Early Detection, Stanford University, California, USA
| | - Caroline Dive
- Cancer Research UK Manchester Institute Cancer Biomarker Centre, The University of Manchester, Manchester, UK
| | - Marilena Hadjidemetriou
- Nanomedicine Lab, Faculty of Biology, Medicine and Health, The University of Manchester, Manchester, UK.
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8
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Reffai A, Mesmoudi M, Derkaoui T, Ghailani Nourouti N, Barakat A, Sellal N, Mallick P, Bennani Mechita M. Epidemiological Profile and Clinicopathological, Therapeutic, and Prognostic Characteristics of Nasopharyngeal Carcinoma in Northern Morocco. Cancer Control 2021; 28:10732748211050587. [PMID: 34664512 PMCID: PMC8529313 DOI: 10.1177/10732748211050587] [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] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Background Nasopharyngeal carcinoma is a multifactorial disease mainly affecting the
Asian and North African populations including Morocco. This study aimed to
determine the epidemiological profile of nasopharyngeal carcinoma in
Northern Morocco as well as its clinicopathological, therapeutic, and
prognostic characteristics. Methods 129 patients with nasopharyngeal carcinoma followed at the regional center of
oncology of Tangier in the period between April 2017 and July 2019, and
diagnosed elsewhere from March 2000 to February 2019, were included in this
study. Statistical analysis of the data was realized using Statistical
Package for the Social Sciences (SPSS) software. Results Nasopharyngeal carcinoma (NPC) represented 5% of all cases with a median age
of 50. The most affected age group was 40–54 years (41.1%). Of all patients,
65.9% were men and 34.1% were women with a sex ratio of 1.93 (Male/Female).
Undifferentiated nasopharyngeal carcinomas were the most common histological
type affecting 96.12% of patients. At diagnosis, the majority of patients
(82.2%) had an advanced stage of NPC (III, VIa, b, c) including 5.4% of
metastatic cases (IVc). Most cases (86%) had lymph node involvement with
cervical mass being the most common clinical presentation. 81.4% of patients
received radiotherapy combined with chemotherapy. Among these patients,
54.3% had concurrent radiochemotherapy preceded by induction chemotherapy.
The 5-year overall survival (OS) was 86.8% for all patients. It represented
91.3% for early stages, 87.9% for locally advanced stages, and 57.1% for the
metastatic stage significantly. The disease-free survival (DFS) at 5 years
was 87.6% knowing that relapse occurred in 16 cases. Conclusions Nasopharyngeal carcinoma is a particular disease with a late declaration. It
is common in Morocco as is the case in other endemic areas with a high
prevalence. Patients’ survival is significantly influenced by disease
staging.
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Affiliation(s)
- Ayman Reffai
- Biomedical Genomics and Oncogenetics Research Laboratory, Faculty of Science and Technology of Tangier (FSTT), 531748Abdelmalek Essaadi University (UAE), Tangier, Morocco
| | - Mohamed Mesmoudi
- Biomedical Genomics and Oncogenetics Research Laboratory, Faculty of Science and Technology of Tangier (FSTT), 531748Abdelmalek Essaadi University (UAE), Tangier, Morocco.,Ahmed Ben Zayed Al Nahyan Center of Cancer Treatment, Tangier, Morocco
| | - Touria Derkaoui
- Biomedical Genomics and Oncogenetics Research Laboratory, Faculty of Science and Technology of Tangier (FSTT), 531748Abdelmalek Essaadi University (UAE), Tangier, Morocco
| | - Naima Ghailani Nourouti
- Biomedical Genomics and Oncogenetics Research Laboratory, Faculty of Science and Technology of Tangier (FSTT), 531748Abdelmalek Essaadi University (UAE), Tangier, Morocco
| | - Amina Barakat
- Biomedical Genomics and Oncogenetics Research Laboratory, Faculty of Science and Technology of Tangier (FSTT), 531748Abdelmalek Essaadi University (UAE), Tangier, Morocco
| | - Nabila Sellal
- Ahmed Ben Zayed Al Nahyan Center of Cancer Treatment, Tangier, Morocco
| | - Parag Mallick
- Canary Center for Cancer Early Detection, School of Medicine, 10624Stanford University, Stanford, CA, USA
| | - Mohcine Bennani Mechita
- Biomedical Genomics and Oncogenetics Research Laboratory, Faculty of Science and Technology of Tangier (FSTT), 531748Abdelmalek Essaadi University (UAE), Tangier, Morocco
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9
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Stawicki CM, Rinker TE, Burns M, Tonapi SS, Galimidi RP, Anumala D, Robinson JK, Klein JS, Mallick P. Modular fluorescent nanoparticle DNA probes for detection of peptides and proteins. Sci Rep 2021; 11:19921. [PMID: 34620912 PMCID: PMC8497506 DOI: 10.1038/s41598-021-99084-4] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2021] [Accepted: 09/20/2021] [Indexed: 02/08/2023] Open
Abstract
Fluorescently labeled antibody and aptamer probes are used in biological studies to characterize binding interactions, measure concentrations of analytes, and sort cells. Fluorescent nanoparticle labels offer an excellent alternative to standard fluorescent labeling strategies due to their enhanced brightness, stability and multivalency; however, challenges in functionalization and characterization have impeded their use. This work introduces a straightforward approach for preparation of fluorescent nanoparticle probes using commercially available reagents and common laboratory equipment. Fluorescent polystyrene nanoparticles, Thermo Fisher Scientific FluoSpheres, were used in these proof-of-principle studies. Particle passivation was achieved by covalent attachment of amine-PEG-azide to carboxylated particles, neutralizing the surface charge from - 43 to - 15 mV. A conjugation-annealing handle and DNA aptamer probe were attached to the azide-PEG nanoparticle surface either through reaction of pre-annealed handle and probe or through a stepwise reaction of the nanoparticles with the handle followed by aptamer annealing. Nanoparticles functionalized with DNA aptamers targeting histidine tags and VEGF protein had high affinity (EC50s ranging from 3 to 12 nM) and specificity, and were more stable than conventional labels. This protocol for preparation of nanoparticle probes relies solely on commercially available reagents and common equipment, breaking down the barriers to use nanoparticles in biological experiments.
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Affiliation(s)
| | - Torri E Rinker
- Nautilus Biotechnology, 201 Industrial Rd #310, San Carlos, CA, 94070, USA.
| | - Markus Burns
- Nautilus Biotechnology, 201 Industrial Rd #310, San Carlos, CA, 94070, USA
| | - Sonal S Tonapi
- Nautilus Biotechnology, 201 Industrial Rd #310, San Carlos, CA, 94070, USA
| | - Rachel P Galimidi
- Nautilus Biotechnology, 201 Industrial Rd #310, San Carlos, CA, 94070, USA
| | - Deepthi Anumala
- Nautilus Biotechnology, 201 Industrial Rd #310, San Carlos, CA, 94070, USA
| | - Julia K Robinson
- Nautilus Biotechnology, 201 Industrial Rd #310, San Carlos, CA, 94070, USA
| | - Joshua S Klein
- Nautilus Biotechnology, 201 Industrial Rd #310, San Carlos, CA, 94070, USA
| | - Parag Mallick
- Nautilus Biotechnology, 201 Industrial Rd #310, San Carlos, CA, 94070, USA
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10
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Satpathy S, Panigrahi U, Panda S, Thiruvengadam V, Biswal R, Luyten W, Mallick P. Influence of Gd doping on morphological, toxicity and magnetic properties of ZnO nanorods. Materials Today Communications 2021; 28:102725. [DOI: 10.1016/j.mtcomm.2021.102725] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/15/2023]
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11
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Lu P, Foley J, Zhu C, McNamara K, Sirinukunwattana K, Vennam S, Varma S, Fehri H, Srivastava A, Zhu S, Rittscher J, Mallick P, Curtis C, West R. Transcriptome and genome evolution during HER2-amplified breast neoplasia. Breast Cancer Res 2021; 23:73. [PMID: 34266469 PMCID: PMC8281634 DOI: 10.1186/s13058-021-01451-6] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2020] [Accepted: 07/03/2021] [Indexed: 01/05/2023] Open
Abstract
Background The acquisition of oncogenic drivers is a critical feature of cancer progression. For some carcinomas, it is clear that certain genetic drivers occur early in neoplasia and others late. Why these drivers are selected and how these changes alter the neoplasia’s fitness is less understood. Methods Here we use spatially oriented genomic approaches to identify transcriptomic and genetic changes at the single-duct level within precursor neoplasia associated with invasive breast cancer. We study HER2 amplification in ductal carcinoma in situ (DCIS) as an event that can be both quantified and spatially located via fluorescence in situ hybridization (FISH) and immunohistochemistry on fixed paraffin-embedded tissue. Results By combining the HER2-FISH with the laser capture microdissection (LCM) Smart-3SEQ method, we found that HER2 amplification in DCIS alters the transcriptomic profiles and increases diversity of copy number variations (CNVs). Particularly, interferon signaling pathway is activated by HER2 amplification in DCIS, which may provide a prolonged interferon signaling activation in HER2-positive breast cancer. Multiple subclones of HER2-amplified DCIS with distinct CNV profiles are observed, suggesting that multiple events occurred for the acquisition of HER2 amplification. Notably, DCIS acquires key transcriptomic changes and CNV events prior to HER2 amplification, suggesting that pre-amplified DCIS may create a cellular state primed to gain HER2 amplification for growth advantage. Conclusion By using genomic methods that are spatially oriented, this study identifies several features that appear to generate insights into neoplastic progression in precancer lesions at a single-duct level. Supplementary Information The online version contains supplementary material available at 10.1186/s13058-021-01451-6.
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Affiliation(s)
- Peipei Lu
- Department of Pathology, Stanford University, Stanford, CA, USA.
| | - Joseph Foley
- Department of Pathology, Stanford University, Stanford, CA, USA
| | - Chunfang Zhu
- Department of Pathology, Stanford University, Stanford, CA, USA
| | - Katherine McNamara
- Department of Medicine and Genetics, Stanford University, Stanford, CA, USA
| | - Korsuk Sirinukunwattana
- Institute of Biomedical Engineering, Department of Engineering Science, University of Oxford, Oxford, UK.,Big Data Institute/Li Ka Shing Centre for Health Information and Discovery, University of Oxford, Oxford, UK
| | - Sujay Vennam
- Department of Pathology, Stanford University, Stanford, CA, USA
| | - Sushama Varma
- Department of Pathology, Stanford University, Stanford, CA, USA
| | - Hamid Fehri
- Institute of Biomedical Engineering, Department of Engineering Science, University of Oxford, Oxford, UK.,Big Data Institute/Li Ka Shing Centre for Health Information and Discovery, University of Oxford, Oxford, UK
| | - Arunima Srivastava
- Department of Computer Science and Engineering, The Ohio State University, Columbus, OH, USA
| | - Shirley Zhu
- Department of Pathology, Stanford University, Stanford, CA, USA
| | - Jens Rittscher
- Institute of Biomedical Engineering, Department of Engineering Science, University of Oxford, Oxford, UK
| | - Parag Mallick
- Department of Radiology, Stanford University, Stanford, CA, USA
| | - Christina Curtis
- Department of Medicine and Genetics, Stanford University, Stanford, CA, USA
| | - Robert West
- Department of Pathology, Stanford University, Stanford, CA, USA
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12
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Satpathy S, Panigrahi U, Panda S, Biswal R, Luyten W, Mallick P. Structural, optical, antimicrobial and ferromagnetic properties of Zn1−xLaxO nanorods synthesized by chemical route. Journal of Alloys and Compounds 2021; 865:158937. [DOI: 10.1016/j.jallcom.2021.158937] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/15/2023]
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13
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Panigrahi UK, Sahu B, Behuria HG, Sahu SK, Dhal SP, Hussain S, Mallick P. Synthesis, characterization and bioactivity of thio-acetamide modified ZnO nanoparticles embedded in zinc acetate matrix. Nano Ex 2021. [DOI: 10.1088/2632-959x/abdad8] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
Abstract
ZnO nanoparticles embedded in zinc acetate matrix were synthesized by chemical route. The effect of thio-acetamide concentration during its synthesis was probed by structural, morphological, optical and bioactivity studies. XRD characterization indicated the formation of dominant phase of zinc acetate along with the low intensity peak of wurtzite ZnO. Morphological transition from bulky-like feature to flower-like feature via flake-like feature, is evidenced with increasing thio-acetamide molar concentrations. The optical band gap of samples decreased from ∼3.29 to 3.24 eV whereas the emitted color shifted from near green to blue region with increasing of molar concentration of thio-acetamide from 0 to 30% in the sample. The nanoparticles exhibited antimicrobial activity against seven (7) common human pathogenic bacteria including drug resistant varieties K. pneumonaie and S. aureus. The nanoparticles formed pores in the biological model membranes made from egg-phosphatidyl choline. Our study reveals that the thio-acetamide modified ZnO nanoparticles embedded in zinc acetate matrix could be used as potential drug lead to fight drug resistance against K. pneumoniae and S. aureus.
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Atallah MB, Tandon V, Hiam KJ, Boyce H, Hori M, Atallah W, Spitzer MH, Engleman E, Mallick P. ImmunoGlobe: enabling systems immunology with a manually curated intercellular immune interaction network. BMC Bioinformatics 2020; 21:346. [PMID: 32778050 PMCID: PMC7430879 DOI: 10.1186/s12859-020-03702-3] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2020] [Accepted: 07/27/2020] [Indexed: 01/03/2023] Open
Abstract
BACKGROUND While technological advances have made it possible to profile the immune system at high resolution, translating high-throughput data into knowledge of immune mechanisms has been challenged by the complexity of the interactions underlying immune processes. Tools to explore the immune network are critical for better understanding the multi-layered processes that underlie immune function and dysfunction, but require a standardized network map of immune interactions. To facilitate this we have developed ImmunoGlobe, a manually curated intercellular immune interaction network extracted from Janeway's Immunobiology textbook. RESULTS ImmunoGlobe is the first graphical representation of the immune interactome, and is comprised of 253 immune system components and 1112 unique immune interactions with detailed functional and characteristic annotations. Analysis of this network shows that it recapitulates known features of the human immune system and can be used uncover novel multi-step immune pathways, examine species-specific differences in immune processes, and predict the response of immune cells to stimuli. ImmunoGlobe is publicly available through a user-friendly interface at www.immunoglobe.org and can be downloaded as a computable graph and network table. CONCLUSION While the fields of proteomics and genomics have long benefited from network analysis tools, no such tool yet exists for immunology. ImmunoGlobe provides a ground truth immune interaction network upon which such tools can be built. These tools will allow us to predict the outcome of complex immune interactions, providing mechanistic insight that allows us to precisely modulate immune responses in health and disease.
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Affiliation(s)
- Michelle B Atallah
- Canary Center at Stanford, Department of Radiology, Stanford University School of Medicine, Stanford, CA, USA
| | | | - Kamir J Hiam
- Departments of Otolaryngology and Microbiology & Immunology, Helen Diller Family Comprehensive Cancer Center, Parker Institute for Cancer Immunotherapy, Chan Zuckerberg Biohub, University of California, San Francisco, CA, USA
| | - Hunter Boyce
- Canary Center at Stanford, Department of Radiology, Stanford University School of Medicine, Stanford, CA, USA
| | - Michelle Hori
- Canary Center at Stanford, Department of Radiology, Stanford University School of Medicine, Stanford, CA, USA
| | - Waleed Atallah
- Canary Center at Stanford, Department of Radiology, Stanford University School of Medicine, Stanford, CA, USA
| | - Matthew H Spitzer
- Departments of Otolaryngology and Microbiology & Immunology, Helen Diller Family Comprehensive Cancer Center, Parker Institute for Cancer Immunotherapy, Chan Zuckerberg Biohub, University of California, San Francisco, CA, USA
| | - Edgar Engleman
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
| | - Parag Mallick
- Canary Center at Stanford, Department of Radiology, Stanford University School of Medicine, Stanford, CA, USA.
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15
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Panigrahi UK, Sathe V, Babu PD, Mitra A, Mallick P. Effect of Mg doping on the improvement of photoluminescence and magnetic properties of NiO nanoparticles. Nano Express 2020. [DOI: 10.1088/2632-959x/aba285] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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16
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Boyce HB, Mallick P. Geostatistical visualization of ecological interactions in tumors. Proceedings (IEEE Int Conf Bioinformatics Biomed) 2020; 2019:2741-2749. [PMID: 32368363 DOI: 10.1109/bibm47256.2019.8983076] [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] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
Recent advances in our understanding of cancer progression have highlighted the roles played by molecular heterogeneity and by the tumor microenvironment in driving drug resistance and metastasis. The coupling of single-cell measurement technologies with algorithms, such as t-sne and SPADE, have enabled deep investigation of tumor heterogeneity. However, such techniques only capture molecular heterogeneity and do not enable the quantification nor visualization of intercellular interactions. They additionally do not allow the visualization of ecological niches that are critical to understanding tumor behavior. Novel computational tools to quantify and visualize spatial patterns in the tumor microenvironment are critically needed. Here, we take a tumor ecology perspective to examine how predation, mutualism, commensalism, and parasitism may impact tumor development and spatial patterning. We additionally quantify local spatial heterogeneity and the emergent global spatial behavior of the models using geostatistics. By visualizing emergent spatial patterns we demonstrate the potential utility of a geostatistical analysis in differentiating amongst cell-cell interactions in the tumor microenvironment. These studies introduce both an ecological framework for characterizing intercellular interactions in cancer and a novel way of quantifying and visualizing spatial patterns in cancer.
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Affiliation(s)
- Hunter Bryan Boyce
- Program in Biomedical Informatics, Stanford University, Stanford, CA, USA
| | - Parag Mallick
- Canary Center at Stanford for Cancer Early Detection, Stanford University, Palo Alto, CA, USA
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17
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Srivastava A, Sharpnack M, Huang K, Mallick P, Machiraju R. PTR Explorer: An approach to identify and explore Post Transcriptional Regulatory mechanisms using proteogenomics. Pac Symp Biocomput 2020; 25:475-486. [PMID: 31797620] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Integration of transcriptomic and proteomic data should reveal multi-layered regulatory processes governing cancer cell behaviors. Traditional correlation-based analyses have demonstrated limited ability to identify the post-transcriptional regulatory (PTR) processes that drive the non-linear relationship between transcript and protein abundances. In this work, we ideate an integrative approach to explore the variety of post-transcriptional mechanisms that dictate relationships between genes and corresponding proteins. The proposed workflow utilizes the intuitive technique of scatterplot diagnostics or scagnostics, to characterize and examine the diverse scatterplots built from transcript and protein abundances in a proteogenomic experiment. The workflow includes representing gene-protein relationships as scatterplots, clustering on geometric scagnostic features of these scatterplots, and finally identifying and grouping the potential gene-protein relationships according to their disposition to various PTR mechanisms. Our study verifies the efficacy of the implemented approach to excavate possible regulatory mechanisms by utilizing comprehensive tests on a synthetic dataset. We also propose a variety of 2D pattern-specific downstream analyses methodologies such as mixture modeling, and mapping miRNA post-transcriptional effects to explore each mechanism further. This work suggests that the proposed methodology has the potential for discovering and categorizing post-transcriptional regulatory mechanisms, manifesting in proteogenomic trends. These trends subsequently provide evidence for cancer specificity, miRNA targeting, and identification of regulation impacted by biological functionality and different types of degradation. (Supplementary Material - https://github.com/arunima2/PTRE_PSB_2020).
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Affiliation(s)
- Arunima Srivastava
- Dept. of Computer Science and Engineering, The Ohio State University, 2015 Neil Ave, Columbus, OH, USA,
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18
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Nikolov M, White B, Pegoraro A, Hope D, Eljanne M, Eddy J, Janmey P, Mallick P, Dang K. Abstract 2451: Physical, genomic, and proteomic characterization of a cancer cell line panel in an integrated dataset. Cancer Res 2019. [DOI: 10.1158/1538-7445.am2019-2451] [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
Introduction: Recent work has linked cancer phenotype (e.g., metastatic ability) to physical properties (e.g., nuclear deformability), as well as genetic alterations (e.g., mutations in lamin genes affecting nuclear stiffness). However, while the genomics of immortalized human cell lines - important models for studying cancer disease pathogenesis and progression - have been relatively well studied, an integrative analysis of physical cell phenotypes with genomic, transcriptomic, and proteomics assays, spanning tissues of origins and culture environments (CE), has been lacking. The Physical Sciences in Oncology Network (PS-ON), a trans-disciplinary project established by the NCI, has generated a curated open dataset that is accessible to researchers via various database interfaces to address this need.
Methods: A panel of 39 cancerous and non-malignant cell lines frequently used in cancer research were selected to cover a set of nine tissues: breast, lung, pancreas, brain, prostate, colon, ovary, blood, and skin. Thirty of these cell lines (from all tissues except blood) were assayed by traction and atomic force microscopy and imaging to measure their cell morphology, proliferation, motility, and nuclear volume. Measurements were performed in seven CE of varying physical properties (e.g., stiffness) to recapitulate a range of realistic tissue conditions and frequently used reagents. All 39 cell lines were assayed via whole exome sequencing, mRNA-seq, and miRNA-seq (in a single CE), while nine cell lines were subjected to proteomic analysis (across seven CEs).
Results: All raw measurements and summary metrics from the study were incorporated into a data model compatible with established data stores (e.g., GDC, miRBase) and integrated in an open-access relational database (RDB). We performed several integrative analyses using the RDB. A broad set of interactions emerged between cell line CE characteristics (e.g., integrin ligands), the phenotypes of cells (e.g., motility) and gene expression, with effect-size varying by cell-line tissue of origin and cancer diagnosis. For instance, motility was significantly (FDR < 5%) correlated with expression of a small set of genes across tissues (e.g., BNP1 and PFKP in both skin and prostate cancers).
Conclusion: This PS-ON cell line characterization allows correlative analyses across CE, cells’ morphological and proliferation properties, and omics data. The integrated RDB facilitates these analyses via a unified interface and data model for the large collection of files comprising the resource. We demonstrated the utility of the RDB by using it to infer the relationship between differential gene expression, CE and resulting phenotypes, with potentially important downstream effects on hallmarks of cancer malignancy.
Citation Format: Milen Nikolov, Brian White, Adrian Pegoraro, Debra Hope, Mariam Eljanne, James Eddy, Paul Janmey, Parag Mallick, Kristen Dang. Physical, genomic, and proteomic characterization of a cancer cell line panel in an integrated dataset [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr 2451.
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Affiliation(s)
| | | | | | - Debra Hope
- 3National Institutes of Health, Bethesda, MD
| | | | | | - Paul Janmey
- 4University of Pennsylvania, Philadelphia, PA
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19
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Panigrahi UK, Das PK, Babu PD, Mishra NC, Mallick P. Structural, optical and magnetic properties of Ni1−xZnxO/Ni nanocomposite. SN Appl Sci 2019. [DOI: 10.1007/s42452-019-0461-0] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
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20
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Amodei D, Egertson J, MacLean BX, Johnson R, Merrihew GE, Keller A, Marsh D, Vitek O, Mallick P, MacCoss MJ. Improving Precursor Selectivity in Data-Independent Acquisition Using Overlapping Windows. J Am Soc Mass Spectrom 2019; 30:669-684. [PMID: 30671891 PMCID: PMC6445824 DOI: 10.1007/s13361-018-2122-8] [Citation(s) in RCA: 74] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/20/2018] [Revised: 12/03/2018] [Accepted: 12/05/2018] [Indexed: 05/22/2023]
Abstract
A major goal of proteomics research is the accurate and sensitive identification and quantification of a broad range of proteins within a sample. Data-independent acquisition (DIA) approaches that acquire MS/MS spectra independently of precursor information have been developed to overcome the reproducibility challenges of data-dependent acquisition and the limited breadth of targeted proteomics strategies. Typical DIA implementations use wide MS/MS isolation windows to acquire comprehensive fragment ion data. However, wide isolation windows produce highly chimeric spectra, limiting the achievable sensitivity and accuracy of quantification and identification. Here, we present a DIA strategy in which spectra are collected with overlapping (rather than adjacent or random) windows and then computationally demultiplexed. This approach improves precursor selectivity by nearly a factor of 2, without incurring any loss in mass range, mass resolution, chromatographic resolution, scan speed, or other key acquisition parameters. We demonstrate a 64% improvement in sensitivity and a 17% improvement in peptides detected in a 6-protein bovine mix spiked into a yeast background. To confirm the method's applicability to a realistic biological experiment, we also analyze the regulation of the proteasome in yeast grown in rapamycin and show that DIA experiments with overlapping windows can help elucidate its adaptation toward the degradation of oxidatively damaged proteins. Our integrated computational and experimental DIA strategy is compatible with any DIA-capable instrument. The computational demultiplexing algorithm required to analyze the data has been made available as part of the open-source proteomics software tools Skyline and msconvert (Proteowizard), making it easy to apply as part of standard proteomics workflows. Graphical Abstract.
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Affiliation(s)
- Dario Amodei
- Department of Radiology, Stanford University, 3155 Porter Drive, Palo Alto, CA USA
| | - Jarrett Egertson
- Department of Genome Sciences, University of Washington, 3720 15th Ave. NE, Seattle, WA USA
| | - Brendan X. MacLean
- Department of Genome Sciences, University of Washington, 3720 15th Ave. NE, Seattle, WA USA
| | - Richard Johnson
- Department of Genome Sciences, University of Washington, 3720 15th Ave. NE, Seattle, WA USA
| | - Gennifer E. Merrihew
- Department of Genome Sciences, University of Washington, 3720 15th Ave. NE, Seattle, WA USA
| | - Austin Keller
- Department of Genome Sciences, University of Washington, 3720 15th Ave. NE, Seattle, WA USA
| | - Don Marsh
- Department of Genome Sciences, University of Washington, 3720 15th Ave. NE, Seattle, WA USA
| | - Olga Vitek
- College of Computer and Information Science, Northeastern University, 440 Huntington Ave, Boston, MA USA
| | - Parag Mallick
- Department of Radiology, Stanford University, 3155 Porter Drive, Palo Alto, CA USA
| | - Michael J. MacCoss
- Department of Genome Sciences, University of Washington, 3720 15th Ave. NE, Seattle, WA USA
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21
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Srivastava A, Adusumilli R, Boyce H, Garijo D, Ratnakar V, Mayani R, Yu T, Machiraju R, Gil Y, Mallick P. Semantic workflows for benchmark challenges: Enhancing comparability, reusability and reproducibility. Pac Symp Biocomput 2019; 24:208-219. [PMID: 30864323 PMCID: PMC6417805] [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] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
Benchmark challenges, such as the Critical Assessment of Structure Prediction (CASP) and Dialogue for Reverse Engineering Assessments and Methods (DREAM) have been instrumental in driving the development of bioinformatics methods. Typically, challenges are posted, and then competitors perform a prediction based upon blinded test data. Challengers then submit their answers to a central server where they are scored. Recent efforts to automate these challenges have been enabled by systems in which challengers submit Docker containers, a unit of software that packages up code and all of its dependencies, to be run on the cloud. Despite their incredible value for providing an unbiased test-bed for the bioinformatics community, there remain opportunities to further enhance the potential impact of benchmark challenges. Specifically, current approaches only evaluate end-to-end performance; it is nearly impossible to directly compare methodologies or parameters. Furthermore, the scientific community cannot easily reuse challengers' approaches, due to lack of specifics, ambiguity in tools and parameters as well as problems in sharing and maintenance. Lastly, the intuition behind why particular steps are used is not captured, as the proposed workflows are not explicitly defined, making it cumbersome to understand the flow and utilization of data. Here we introduce an approach to overcome these limitations based upon the WINGS semantic workflow system. Specifically, WINGS enables researchers to submit complete semantic workflows as challenge submissions. By submitting entries as workflows, it then becomes possible to compare not just the results and performance of a challenger, but also the methodology employed. This is particularly important when dozens of challenge entries may use nearly identical tools, but with only subtle changes in parameters (and radical differences in results). WINGS uses a component driven workflow design and offers intelligent parameter and data selection by reasoning about data characteristics. This proves to be especially critical in bioinformatics workflows where using default or incorrect parameter values is prone to drastically altering results. Different challenge entries may be readily compared through the use of abstract workflows, which also facilitate reuse. WINGS is housed on a cloud based setup, which stores data, dependencies and workflows for easy sharing and utility. It also has the ability to scale workflow executions using distributed computing through the Pegasus workflow execution system. We demonstrate the application of this architecture to the DREAM proteogenomic challenge.
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Affiliation(s)
- Arunima Srivastava
- Computer Science and Engineering, The Ohio State University, 2015 Neil Ave Columbus, OH 43210,
| | - Ravali Adusumilli
- Canary Center for Cancer Early Detection, Stanford University, 3155 Porter Dr., Palo Alto, CA, 94305,
| | - Hunter Boyce
- Canary Center for Cancer Early Detection, Stanford University, 3155 Porter Dr., Palo Alto, CA, 94305,
| | - Daniel Garijo
- Information Sciences Institute, University of Southern California, Marina del Rey, Los Angeles, CA 90292,
| | - Varun Ratnakar
- Information Sciences Institute, University of Southern California, Marina del Rey, Los Angeles, CA 90292,
| | - Rajiv Mayani
- Information Sciences Institute, University of Southern California, Marina del Rey, Los Angeles, CA 90292, mayani@,isi.edu
| | - Thomas Yu
- Sage Bionetworks, 2901 Third Ave., Suite 330, Seattle WA 98121,
| | - Raghu Machiraju
- Computer Science and Engineering, The Ohio State University, 2015 Neil Ave Columbus, OH 43210,
| | - Yolanda Gil
- Information Sciences Institute, University of Southern California, Marina del Rey, Los Angeles, CA 90292,
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22
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Tiemann K, Garri C, Lee SB, Malihi PD, Park M, Alvarez RM, Yap LP, Mallick P, Katz JE, Gross ME, Kani K. Loss of ER retention motif of AGR2 can impact mTORC signaling and promote cancer metastasis. Oncogene 2018; 38:3003-3018. [PMID: 30575818 DOI: 10.1038/s41388-018-0638-9] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2017] [Revised: 10/29/2018] [Accepted: 11/21/2018] [Indexed: 12/16/2022]
Abstract
Anterior gradient 2 (AGR2) is a member of the protein disulfide isomerase (PDI) family, which plays a role in the regulation of protein homeostasis and the unfolded protein response pathway (UPR). AGR2 has also been characterized as a proto-oncogene and a potential cancer biomarker. Cellular localization of AGR2 is emerging as a key component for understanding the role of AGR2 as a proto-oncogene. Here, we provide evidence that extracellular AGR2 (eAGR2) promotes tumor metastasis in various in vivo models. To further characterize the role of the intracellular-resident versus extracellular protein, we performed a comprehensive protein-protein interaction screen. Based on these results, we identify AGR2 as an interacting partner of the mTORC2 pathway. Importantly, our data indicates that eAGR2 promotes increased phosphorylation of RICTOR (T1135), while intracellular AGR2 (iAGR2) antagonizes its levels and phosphorylation. Localization of AGR2 also has opposing effects on the Hippo pathway, spheroid formation, and response to chemotherapy in vitro. Collectively, our results identify disparate phenotypes predicated on AGR2 localization. Our findings also provide credence for screening of eAGR2 to guide therapeutic decisions.
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Affiliation(s)
- Katrin Tiemann
- University of Southern California, Keck School of Medicine, Lawrence J. Ellison Institute for Transformative Medicine, Los Angeles, CA, USA
| | - Carolina Garri
- University of Southern California, Keck School of Medicine, Lawrence J. Ellison Institute for Transformative Medicine, Los Angeles, CA, USA
| | - Sang Bok Lee
- University of Southern California, Keck School of Medicine, Lawrence J. Ellison Institute for Transformative Medicine, Los Angeles, CA, USA
| | - Paymaneh D Malihi
- University of Southern California, Keck School of Medicine, Lawrence J. Ellison Institute for Transformative Medicine, Los Angeles, CA, USA
| | - Mincheol Park
- University of Southern California, Keck School of Medicine, Lawrence J. Ellison Institute for Transformative Medicine, Los Angeles, CA, USA
| | - Ruth M Alvarez
- University of Southern California, Keck School of Medicine, Lawrence J. Ellison Institute for Transformative Medicine, Los Angeles, CA, USA
| | - Li Peng Yap
- Department of Radiology, Keck School of Medicine, Los Angeles, CA, USA
| | - Parag Mallick
- Stanford University, Department of Radiology, Los Angeles, CA, USA
| | - Jonathan E Katz
- University of Southern California, Keck School of Medicine, Lawrence J. Ellison Institute for Transformative Medicine, Los Angeles, CA, USA
| | - Mitchell E Gross
- University of Southern California, Keck School of Medicine, Lawrence J. Ellison Institute for Transformative Medicine, Los Angeles, CA, USA
| | - Kian Kani
- University of Southern California, Keck School of Medicine, Lawrence J. Ellison Institute for Transformative Medicine, Los Angeles, CA, USA.
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23
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Rath B, Nanayakkara A, Mallick P, Samal PK. SUSY Quantum Mechanics for PT Symmetric Systems. Proc Natl Acad Sci , India, Sect A Phys Sci 2018. [DOI: 10.1007/s40010-017-0415-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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24
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Srivastava A, Kulkarni C, Huang K, Parwani A, Mallick P, Machiraju R. Imitating Pathologist Based Assessment With Interpretable and Context Based Neural Network Modeling of Histology Images. Biomed Inform Insights 2018; 10:1178222618807481. [PMID: 30450002 PMCID: PMC6236488 DOI: 10.1177/1178222618807481] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/15/2018] [Accepted: 09/25/2018] [Indexed: 11/21/2022]
Abstract
Convolutional neural networks (CNNs) have gained steady popularity as a tool to
perform automatic classification of whole slide histology images. While CNNs
have proven to be powerful classifiers in this context, they fail to explain
this classification, as the network engineered features used for modeling and
classification are ONLY interpretable by the CNNs themselves. This work aims at
enhancing a traditional neural network model to perform histology image
modeling, patient classification, and interpretation of the distinctive features
identified by the network within the histology whole slide images (WSIs). We
synthesize a workflow which (a) intelligently samples the training data by
automatically selecting only image areas that display visible disease-relevant
tissue state and (b) isolates regions most pertinent to the trained CNN
prediction and translates them to observable and qualitative features such as
color, intensity, cell and tissue morphology and texture. We use the Cancer
Genome Atlas’s Breast Invasive Carcinoma (TCGA-BRCA) histology dataset to build
a model predicting patient attributes (disease stage and node status) and the
tumor proliferation challenge (TUPAC 2016) breast cancer histology image
repository to help identify disease-relevant tissue state (mitotic activity). We
find that our enhanced CNN based workflow both increased patient attribute
predictive accuracy (~2% increase for disease stage and ~10% increase for node
status) and experimentally proved that a data-driven CNN histology model
predicting breast invasive carcinoma stages is highly sensitive to features such
as color, cell size, and shape, granularity, and uniformity. This work
summarizes the need for understanding the widely trusted models built using deep
learning and adds a layer of biological context to a technique that functioned
as a classification only approach till now.
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Affiliation(s)
- Arunima Srivastava
- Department of Computer Science and Engineering, The Ohio State University, Columbus, OH, USA
| | - Chaitanya Kulkarni
- Department of Computer Science and Engineering, The Ohio State University, Columbus, OH, USA
| | - Kun Huang
- School of Medicine, Indiana University, Indianapolis, IN, USA
| | - Anil Parwani
- Department of Pathology, The Ohio State University, Columbus, OH, USA
| | - Parag Mallick
- Canary Center at Stanford for Cancer Early Detection, Stanford University, Palo Alto, CA, USA
| | - Raghu Machiraju
- Department of Computer Science and Engineering, The Ohio State University, Columbus, OH, USA
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25
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Hughes NP, Xu L, Nielsen CH, Chang E, Hori SS, Natarajan A, Lee S, Kjær A, Kani K, Wang SX, Mallick P, Gambhir SS. A blood biomarker for monitoring response to anti-EGFR therapy. Cancer Biomark 2018; 22:333-344. [PMID: 29689709 DOI: 10.3233/cbm-171149] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [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: 12/24/2022]
Abstract
BACKGROUND AND OBJECTIVE To monitor therapies targeted to epidermal growth factor receptors (EGFR) in non-small cell lung cancer (NSCLC), we investigated Peroxiredoxin 6 (PRDX6) as a biomarker of response to anti-EGFR agents. METHODS We studied cells that are sensitive (H3255, HCC827) or resistant (H1975, H460) to gefitinib. PRDX6 was examined with either gefitinib or vehicle treatment using enzyme-linked immunosorbent assays. We created xenograft models from one sensitive (HCC827) and one resistant cell line (H1975) and monitored serum PRDX6 levels during treatment. RESULTS PRDX6 levels in cell media from sensitive cell lines increased significantly after gefitinib treatment vs. vehicle, whereas there was no significant difference for resistant lines. PRDX6 accumulation over time correlated positively with gefitinib sensitivity. Serum PRDX6 levels in gefitinib-sensitive xenograft models increased markedly during the first 24 hours of treatment and then decreased dramatically during the following 48 hours. Differences in serum PRDX6 levels between vehicle and gefitinib-treated animals could not be explained by differences in tumor burden. CONCLUSIONS Our results show that changes in serum PRDX6 during the course of gefitinib treatment of xenograft models provide insight into tumor response and such an approach offers several advantages over imaging-based strategies for monitoring response to anti-EGFR agents.
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Affiliation(s)
- Nicholas P Hughes
- Molecular Imaging Program at Stanford, Department of Radiology, Stanford University School of Medicine, Stanford, CA, USA.,Molecular Imaging Program at Stanford, Department of Radiology, Stanford University School of Medicine, Stanford, CA, USA
| | - Lingyun Xu
- Molecular Imaging Program at Stanford, Department of Radiology, Stanford University School of Medicine, Stanford, CA, USA.,Canary Center at Stanford for Cancer Early Detection, Palo Alto, CA, USA.,Molecular Imaging Program at Stanford, Department of Radiology, Stanford University School of Medicine, Stanford, CA, USA
| | - Carsten H Nielsen
- Molecular Imaging Program at Stanford, Department of Radiology, Stanford University School of Medicine, Stanford, CA, USA.,Department of Clinical Physiology, Nuclear Medicine and PET, Center for Diagnostic Investigations, Rigshospitalet, Copenhagen, Denmark.,Cluster for Molecular Imaging, Faculty of Health Sciences, University of Copenhagen, Copenhagen, Denmark.,Molecular Imaging Program at Stanford, Department of Radiology, Stanford University School of Medicine, Stanford, CA, USA
| | - Edwin Chang
- Molecular Imaging Program at Stanford, Department of Radiology, Stanford University School of Medicine, Stanford, CA, USA.,Canary Center at Stanford for Cancer Early Detection, Palo Alto, CA, USA.,Molecular Imaging Program at Stanford, Department of Radiology, Stanford University School of Medicine, Stanford, CA, USA
| | - Sharon S Hori
- Molecular Imaging Program at Stanford, Department of Radiology, Stanford University School of Medicine, Stanford, CA, USA.,Canary Center at Stanford for Cancer Early Detection, Palo Alto, CA, USA
| | - Arutselvan Natarajan
- Molecular Imaging Program at Stanford, Department of Radiology, Stanford University School of Medicine, Stanford, CA, USA.,Canary Center at Stanford for Cancer Early Detection, Palo Alto, CA, USA
| | - Samantha Lee
- Canary Center at Stanford for Cancer Early Detection, Palo Alto, CA, USA
| | - Andreas Kjær
- Department of Clinical Physiology, Nuclear Medicine and PET, Center for Diagnostic Investigations, Rigshospitalet, Copenhagen, Denmark.,Cluster for Molecular Imaging, Faculty of Health Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Kian Kani
- Lawrence J. Ellison Institute of Transformative Medicine, University of Southern California, Los Angeles, CA, USA
| | - Shan X Wang
- Department of Bioengineering, Stanford University, Stanford, CA, USA.,Department of Materials Science and Engineering, Stanford University, Stanford, CA, USA
| | - Parag Mallick
- Molecular Imaging Program at Stanford, Department of Radiology, Stanford University School of Medicine, Stanford, CA, USA.,Canary Center at Stanford for Cancer Early Detection, Palo Alto, CA, USA
| | - Sanjiv Sam Gambhir
- Molecular Imaging Program at Stanford, Department of Radiology, Stanford University School of Medicine, Stanford, CA, USA.,Canary Center at Stanford for Cancer Early Detection, Palo Alto, CA, USA.,Department of Bioengineering, Stanford University, Stanford, CA, USA.,Department of Materials Science and Engineering, Stanford University, Stanford, CA, USA
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26
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Sharpnack MF, Ranbaduge N, Srivastava A, Cerciello F, Codreanu SG, Liebler DC, Mascaux C, Miles WO, Morris R, McDermott JE, Sharpnack JL, Amann J, Maher CA, Machiraju R, Wysocki VH, Govindan R, Mallick P, Coombes KR, Huang K, Carbone DP. Proteogenomic Analysis of Surgically Resected Lung Adenocarcinoma. J Thorac Oncol 2018; 13:1519-1529. [PMID: 30017829 DOI: 10.1016/j.jtho.2018.06.025] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [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: 01/24/2018] [Revised: 06/12/2018] [Accepted: 06/27/2018] [Indexed: 12/31/2022]
Abstract
INTRODUCTION Despite apparently complete surgical resection, approximately half of resected early-stage lung cancer patients relapse and die of their disease. Adjuvant chemotherapy reduces this risk by only 5% to 8%. Thus, there is a need for better identifying who benefits from adjuvant therapy, the drivers of relapse, and novel targets in this setting. METHODS RNA sequencing and liquid chromatography/liquid chromatography-mass spectrometry proteomics data were generated from 51 surgically resected non-small cell lung tumors with known recurrence status. RESULTS We present a rationale and framework for the incorporation of high-content RNA and protein measurements into integrative biomarkers and show the potential of this approach for predicting risk of recurrence in a group of lung adenocarcinomas. In addition, we characterize the relationship between mRNA and protein measurements in lung adenocarcinoma and show that it is outcome specific. CONCLUSIONS Our results suggest that mRNA and protein data possess independent biological and clinical importance, which can be leveraged to create higher-powered expression biomarkers.
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Affiliation(s)
- Michael F Sharpnack
- Department of Biomedical Informatics, The Ohio State University, Columbus, Ohio
| | - Nilini Ranbaduge
- Department of Chemistry, The Ohio State University, Columbus, Ohio
| | - Arunima Srivastava
- Department of Computer Science and Engineering, The Ohio State University, Columbus, Ohio
| | | | - Simona G Codreanu
- Department of Chemistry, Vanderbilt University, Nashville, Tennessee
| | - Daniel C Liebler
- Department of Biochemistry, Vanderbilt University, Nashville, Tennessee
| | - Celine Mascaux
- Department of Multidisciplinary Oncology and Therapeutic Innovations, Assistance Publique des Hôpitaux de Marseille, France; Aix-Marseille University, Marseille, France
| | - Wayne O Miles
- Center for Regenerative Medicine, Massachusetts General Hospital, Boston, Massachusetts
| | - Robert Morris
- Center for Regenerative Medicine, Massachusetts General Hospital, Boston, Massachusetts
| | - Jason E McDermott
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA
| | - James L Sharpnack
- Department of Statistics, University of California, Davis, California
| | - Joseph Amann
- Comprehensive Cancer Center, The Ohio State University, Columbus, Ohio
| | - Christopher A Maher
- Department of Medicine, Washington University in St. Louis, St. Louis, Missouri
| | - Raghu Machiraju
- Department of Computer Science and Engineering, The Ohio State University, Columbus, Ohio
| | - Vicki H Wysocki
- Department of Chemistry, The Ohio State University, Columbus, Ohio
| | - Ramaswami Govindan
- Department of Medicine, Washington University in St. Louis, St. Louis, Missouri
| | - Parag Mallick
- Department of Radiology, Stanford University, Palo Alto, California
| | - Kevin R Coombes
- Department of Biomedical Informatics, The Ohio State University, Columbus, Ohio
| | - Kun Huang
- Department of Biomedical Informatics, The Ohio State University, Columbus, Ohio
| | - David P Carbone
- Comprehensive Cancer Center, The Ohio State University, Columbus, Ohio.
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27
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Abstract
Machine learning methods for learning network structure are applied to quantitative proteomics experiments and reverse-engineer intracellular signal transduction networks. They provide insight into the rewiring of signaling within the context of a disease or a phenotype. To learn the causal patterns of influence between proteins in the network, the methods require experiments that include targeted interventions that fix the activity of specific proteins. However, the interventions are costly and add experimental complexity. We describe an active learning strategy for selecting optimal interventions. Our approach takes as inputs pathway databases and historic data sets, expresses them in form of prior probability distributions on network structures, and selects interventions that maximize their expected contribution to structure learning. Evaluations on simulated and real data show that the strategy reduces the detection error of validated edges as compared with an unguided choice of interventions and avoids redundant interventions, thereby increasing the effectiveness of the experiment.
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Affiliation(s)
- Robert O Ness
- 1 Department of Statistics, Purdue University , West Lafayette, Indiana
| | - Karen Sachs
- 2 Department of Immunology, School of Medicine, Stanford University , Palo Alto, California
| | - Parag Mallick
- 3 Canary Center for Cancer Early Detection, School of Medicine, Stanford University , Palo Alto, California
| | - Olga Vitek
- 4 College of Science, College of Computer and Information Science, Northeastern University , Boston, Massachusetts
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28
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Totten SM, Adusumilli R, Kullolli M, Tanimoto C, Brooks JD, Mallick P, Pitteri SJ. Multi-lectin Affinity Chromatography and Quantitative Proteomic Analysis Reveal Differential Glycoform Levels between Prostate Cancer and Benign Prostatic Hyperplasia Sera. Sci Rep 2018; 8:6509. [PMID: 29695737 PMCID: PMC5916935 DOI: 10.1038/s41598-018-24270-w] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2017] [Accepted: 03/29/2018] [Indexed: 02/06/2023] Open
Abstract
Currently prostate-specific antigen is used for prostate cancer (PCa) screening, however it lacks the necessary specificity for differentiating PCa from other diseases of the prostate such as benign prostatic hyperplasia (BPH), presenting a clinical need to distinguish these cases at the molecular level. Protein glycosylation plays an important role in a number of cellular processes involved in neoplastic progression and is aberrant in PCa. In this study, we systematically interrogate the alterations in the circulating levels of hundreds of serum proteins and their glycoforms in PCa and BPH samples using multi-lectin affinity chromatography and quantitative mass spectrometry-based proteomics. Specific lectins (AAL, PHA-L and PHA-E) were used to target and chromatographically separate core-fucosylated and highly-branched protein glycoforms for analysis, as differential expression of these glycan types have been previously associated with PCa. Global levels of CD5L, CFP, C8A, BST1, and C7 were significantly increased in the PCa samples. Notable glycoform-specific alterations between BPH and PCa were identified among proteins CD163, C4A, and ATRN in the PHA-L/E fraction and among C4BPB and AZGP1 glycoforms in the AAL fraction. Despite these modest differences, substantial similarities in glycoproteomic profiles were observed between PCa and BPH sera.
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Affiliation(s)
- Sarah M Totten
- Canary Center at Stanford for Cancer Early Detection, Department of Radiology, Stanford University School of Medicine, Palo Alto, CA, 94304, USA
| | - Ravali Adusumilli
- Canary Center at Stanford for Cancer Early Detection, Department of Radiology, Stanford University School of Medicine, Palo Alto, CA, 94304, USA
| | - Majlinda Kullolli
- Canary Center at Stanford for Cancer Early Detection, Department of Radiology, Stanford University School of Medicine, Palo Alto, CA, 94304, USA
| | - Cheylene Tanimoto
- Canary Center at Stanford for Cancer Early Detection, Department of Radiology, Stanford University School of Medicine, Palo Alto, CA, 94304, USA
| | - James D Brooks
- Department of Urology, Stanford University School of Medicine, Stanford, CA, 94305, USA
| | - Parag Mallick
- Canary Center at Stanford for Cancer Early Detection, Department of Radiology, Stanford University School of Medicine, Palo Alto, CA, 94304, USA
| | - Sharon J Pitteri
- Canary Center at Stanford for Cancer Early Detection, Department of Radiology, Stanford University School of Medicine, Palo Alto, CA, 94304, USA.
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29
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Sylman JL, Mitrugno A, Atallah M, Tormoen GW, Shatzel JJ, Tassi Yunga S, Wagner TH, Leppert JT, Mallick P, McCarty OJT. The Predictive Value of Inflammation-Related Peripheral Blood Measurements in Cancer Staging and Prognosis. Front Oncol 2018; 8:78. [PMID: 29619344 PMCID: PMC5871812 DOI: 10.3389/fonc.2018.00078] [Citation(s) in RCA: 58] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2018] [Accepted: 03/07/2018] [Indexed: 12/23/2022] Open
Abstract
In this review, we discuss the interaction between cancer and markers of inflammation (such as levels of inflammatory cells and proteins) in the circulation, and the potential benefits of routinely monitoring these markers in peripheral blood measurement assays. Next, we discuss the prognostic value and limitations of using inflammatory markers such as neutrophil-to-lymphocyte and platelet-to-lymphocyte ratios and C-reactive protein measurements. Furthermore, the review discusses the benefits of combining multiple types of measurements and longitudinal tracking to improve staging and prognosis prediction of patients with cancer, and the ability of novel in silico frameworks to leverage this high-dimensional data.
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Affiliation(s)
- Joanna L Sylman
- VA Palo Alto Health Care System, Palo Alto, CA, United States.,Biomedical Engineering, School of Medicine, Oregon Health & Science University, Portland, OR, United States.,Canary Center at Stanford, Department of Radiology, Stanford University School of Medicine, Stanford, CA, United States
| | - Annachiara Mitrugno
- Biomedical Engineering, School of Medicine, Oregon Health & Science University, Portland, OR, United States
| | - Michelle Atallah
- Canary Center at Stanford, Department of Radiology, Stanford University School of Medicine, Stanford, CA, United States
| | - Garth W Tormoen
- Department of Radiation Medicine, Oregon Health & Science University, Portland, OR, United States
| | - Joseph J Shatzel
- Division of Hematology and Medical Oncology, Oregon Health & Science University, Portland, OR, United States.,Cancer Early Detection & Advanced Research Center, Oregon Health & Science University, Portland, OR, United States
| | - Samuel Tassi Yunga
- Cancer Early Detection & Advanced Research Center, Oregon Health & Science University, Portland, OR, United States.,Knight Cancer Institute, Oregon Health & Science University, Portland, OR, United States
| | - Todd H Wagner
- VA Palo Alto Health Care System, Palo Alto, CA, United States.,Department of Surgery, Stanford University School of Medicine, Stanford, CA, United States
| | - John T Leppert
- VA Palo Alto Health Care System, Palo Alto, CA, United States.,Department of Urology, Stanford University School of Medicine, Stanford, CA, United States
| | - Parag Mallick
- Canary Center at Stanford, Department of Radiology, Stanford University School of Medicine, Stanford, CA, United States
| | - Owen J T McCarty
- Biomedical Engineering, School of Medicine, Oregon Health & Science University, Portland, OR, United States
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30
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Abstract
Recent advances in proteome informatics have led to an explosion in tools to analyze mass spectrometry data. These tools operate across the analysis pipeline doing everything from assessing quality control to matching peptides to spectra to quantification. Unfortunately, the vast majority of these tools are not able to operate directly on the proprietary formats generated by the diverse mass spectrometers. Consequently, the first step in many protocols is the conversion of data from vendor-specific binary files to open-format files. This protocol details the use of ProteoWizard's msConvert and msConvertGUI software for this conversion, taking format features, coding options, and vendor particularities into account. We specifically describe the various options available when doing conversions and the implications of each option.
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Affiliation(s)
- Ravali Adusumilli
- Canary Center at Stanford for Cancer Early Detection, Department of Radiology, Stanford University, Stanford, CA, USA
| | - Parag Mallick
- Canary Center at Stanford for Cancer Early Detection, Department of Radiology, Stanford University, Stanford, CA, USA. .,School of Medicine, Stanford University, 3155 Porter Drive, MC 5483, Palo Alto, CA, 94304, USA.
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31
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Lee JR, Appelmann I, Miething C, Shultz TO, Ruderman D, Kim D, Mallick P, Lowe SW, Wang SX. Longitudinal Multiplexed Measurement of Quantitative Proteomic Signatures in Mouse Lymphoma Models Using Magneto-Nanosensors. Theranostics 2018; 8:1389-1398. [PMID: 29507628 PMCID: PMC5835944 DOI: 10.7150/thno.20706] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2017] [Accepted: 12/12/2017] [Indexed: 01/23/2023] Open
Abstract
Cancer proteomics is the manifestation of relevant biological processes in cancer development. Thus, it reflects the activities of tumor cells, host-tumor interactions, and systemic responses to cancer therapy. To understand the causal effects of tumorigenesis or therapeutic intervention, longitudinal studies are greatly needed. However, most of the conventional mouse experiments are unlikely to accommodate frequent collection of serum samples with a large enough volume for multiple protein assays towards single-object analysis. Here, we present a technique based on magneto-nanosensors to longitudinally monitor the protein profiles in individual mice of lymphoma models using a small volume of a sample for multiplex assays. Methods: Drug-sensitive and -resistant cancer cell lines were used to develop the mouse models that render different outcomes upon the drug treatment. Two groups of mice were inoculated with each cell line, and treated with either cyclophosphamide or vehicle solution. Serum samples taken longitudinally from each mouse in the groups were measured with 6-plex magneto-nanosensor cytokine assays. To find the origin of IL-6, experiments were performed using IL-6 knock-out mice. Results: The differences in serum IL-6 and GCSF levels between the drug-treated and untreated groups were revealed by the magneto-nanosensor measurement on individual mice. Using the multiplex assays and mouse models, we found that IL-6 is secreted by the host in the presence of tumor cells upon the drug treatment. Conclusion: The multiplex magneto-nanosensor assays enable longitudinal proteomic studies on mouse tumor models to understand tumor development and therapy mechanisms more precisely within a single biological object.
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32
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Srivastava A, Kulkarni C, Mallick P, Huang K, Machiraju R. Building trans-omics evidence: using imaging and 'omics' to characterize cancer profiles. Pac Symp Biocomput 2018; 23:377-387. [PMID: 29218898] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Utilization of single modality data to build predictive models in cancer results in a rather narrow view of most patient profiles. Some clinical facet s relate strongly to histology image features, e.g. tumor stages, whereas others are associated with genomic and proteomic variations (e.g. cancer subtypes and disease aggression biomarkers). We hypothesize that there are coherent "trans-omics" features that characterize varied clinical cohorts across multiple sources of data leading to more descriptive and robust disease characterization. In this work, for l 05 breast cancer patients from the TCGA (The Cancer Genome Atlas), we consider four clinical attributes (AJCC Stage, Tumor Stage, ER-Status and PAM50 mRNA Subtypes), and build predictive models using three different modalities of data (histopathological images, transcriptomics and proteomics). Following which, we identify critical multi-level features that drive successful classification of patients for the various different cohorts. To build predictors for each data type, we employ widely used "best practice" techniques including CNN-based (convolutional neural network) classifiers for histopathological images and regression models for proteogenomic data. While, as expected, histology images outperformed molecular features while predicting cancer stages, and transcriptomics held superior discriminatory power for ER-Status and PAM50 subtypes, there exist a few cases where all data modalities exhibited comparable performance. Further, we also identified sets of key genes and proteins whose expression and abundance correlate across each clinical cohort including (i) tumor severity and progression (incl. GABARAP), (ii) ER-status (incl.ESRl) and (iii) disease subtypes (incl. FOXCl). Thus, we quantitatively assess the efficacy of different data types to predict critical breast cancer patient attributes and improve disease characterization.
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Affiliation(s)
- Arunima Srivastava
- Department of Computer Science and Engineering, The Ohio State University, 2015 Neil Avenue, Columbus, OH 43210, USA,
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33
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Das PK, Biswal R, Choudhary RJ, Ganesan V, Mallick P. Evolution of surface topography and optical band gap of ZnO film deposited on NiO/Si(100). SURF INTERFACE ANAL 2017. [DOI: 10.1002/sia.6365] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- P. K. Das
- Department of Physics; North Orissa University; Baripada 757003 India
| | - R. Biswal
- Department of Applied Physics and Ballistics; Fakir Mohan University; Balasore 756019 India
| | - R. J. Choudhary
- UGC-DAE Consortium for Scientific Research; Khandwa Road Indore 452 017 India
| | - V. Ganesan
- UGC-DAE Consortium for Scientific Research; Khandwa Road Indore 452 017 India
| | - P. Mallick
- Department of Physics; North Orissa University; Baripada 757003 India
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34
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Sharpnack MF, Chen B, Aran D, Kosti I, Sharpnack DD, Carbone DP, Mallick P, Huang K. Global Transcriptome Analysis of RNA Abundance Regulation by ADAR in Lung Adenocarcinoma. EBioMedicine 2017; 27:167-175. [PMID: 29273356 PMCID: PMC5828651 DOI: 10.1016/j.ebiom.2017.12.005] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2017] [Revised: 11/27/2017] [Accepted: 12/05/2017] [Indexed: 01/13/2023] Open
Abstract
Despite tremendous advances in targeted therapies against lung adenocarcinoma, the majority of patients do not benefit from personalized treatments. A deeper understanding of potential therapeutic targets is crucial to increase the survival of patients. One promising target, ADAR, is amplified in 13% of lung adenocarcinomas and in-vitro studies have demonstrated the potential of its therapeutic inhibition to inhibit tumor growth. ADAR edits millions of adenosines to inosines within the transcriptome, and while previous studies of ADAR in cancer have solely focused on protein-coding edits, > 99% of edits occur in non-protein coding regions. Here, we develop a pipeline to discover the regulatory potential of RNA editing sites across the entire transcriptome and apply it to lung adenocarcinoma tumors from The Cancer Genome Atlas. This method predicts that 1413 genes contain regulatory edits, predominantly in non-coding regions. Genes with the largest numbers of regulatory edits are enriched in both apoptotic and innate immune pathways, providing a link between these known functions of ADAR and its role in cancer. We further show that despite a positive association between ADAR RNA expression and apoptotic and immune pathways, ADAR copy number is negatively associated with apoptosis and several immune cell types' signatures. ADAR potentially regulates the mRNA abundance of thousands of genes. Editing of the APOL1 3′ UTR is associated with its upregulation and patient poor overall survival. ADAR-regulated genes are enriched for apoptosis and immune pathways.
Lung cancer is the most deadly cancer globally and current targeted treatments only benefit a minority of patients. Inhibiting the ADAR oncogene has shown promising preclinical results; however, little is known about ADAR's functions in cancer. We investigate a key function of ADAR, mRNA regulation via RNA editing, and provide evidence that it is linked to tumor immunity and cell death in human lung adenocarcinoma. Our results provide a motivation to explore combination immunotherapies that include ADAR inhibition.
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Affiliation(s)
- Michael F Sharpnack
- Department of Biomedical Informatics, The Ohio State University, Columbus, OH, United States
| | - Bin Chen
- Institute for Computational Health Sciences, University of California San Francisco, San Francisco, CA, United States
| | - Dvir Aran
- Institute for Computational Health Sciences, University of California San Francisco, San Francisco, CA, United States
| | - Idit Kosti
- Institute for Computational Health Sciences, University of California San Francisco, San Francisco, CA, United States
| | | | - David P Carbone
- Comprehensive Cancer Center, The Ohio State University, Columbus, OH, United States
| | - Parag Mallick
- Canary Center for Cancer Early Detection, Stanford University, Palo Alto, CA, United States.
| | - Kun Huang
- Department of Biomedical Informatics, The Ohio State University, Columbus, OH, United States; Current Address: Department of Medicine, Indiana University School of Medicine, Indianapolis, IN, United States.
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35
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Lee JR, Chan CT, Ruderman D, Chuang HY, Gaster RS, Atallah M, Mallick P, Lowe SW, Gambhir SS, Wang SX. Longitudinal Monitoring of Antibody Responses against Tumor Cells Using Magneto-nanosensors with a Nanoliter of Blood. Nano Lett 2017; 17:6644-6652. [PMID: 28990786 PMCID: PMC5851288 DOI: 10.1021/acs.nanolett.7b02591] [Citation(s) in RCA: 7] [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] [Indexed: 05/03/2023]
Abstract
Each immunoglobulin isotype has unique immune effector functions. The contribution of these functions in the elimination of pathogens and tumors can be determined by monitoring quantitative temporal changes in isotype levels. Here, we developed a novel technique using magneto-nanosensors based on the effect of giant magnetoresistance (GMR) for longitudinal monitoring of total and antigen-specific isotype levels with high precision, using as little as 1 nL of serum. Combining in vitro serologic measurements with in vivo imaging techniques, we investigated the role of the antibody response in the regression of firefly luciferase (FL)-labeled lymphoma cells in spleen, kidney, and lymph nodes in a syngeneic Burkitt's lymphoma mouse model. Regression status was determined by whole body bioluminescent imaging (BLI). The magneto-nanosensors revealed that anti-FL IgG2a and total IgG2a were elevated and sustained in regression mice compared to non-regression mice (p < 0.05). This platform shows promise for monitoring immunotherapy, vaccination, and autoimmunity.
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Affiliation(s)
- Jung-Rok Lee
- Division of Mechanical and Biomedical Engineering, Ewha Womans University, Seoul 03760, South Korea
- Department of Materials Science and Engineering, Stanford University, Stanford, California 94305, United States
| | - Carmel T. Chan
- Department of Medicine, Department of Radiology, Stanford University, Stanford, California 94305, United States
| | - Daniel Ruderman
- Ellison Institute of Transformative Medicine of USC, USC Keck School of Medicine, Los Angeles, California 90211, United States
| | - Hui-Yen Chuang
- Department of Medicine, Department of Radiology, Stanford University, Stanford, California 94305, United States
| | - Richard S. Gaster
- Department of Bioengineering, Stanford University, Stanford, California 94305, United States
- Pliant Therapeutics, Redwood City, California 94063, United States
| | - Michelle Atallah
- Cancer Biology Program, Stanford School of Medicine, Stanford, California 94305, United States
| | - Parag Mallick
- Department of Medicine, Department of Radiology, Stanford University, Stanford, California 94305, United States
| | - Scott W. Lowe
- Cancer Biology and Genetics Program, Memorial Sloan Kettering Cancer Center, New York, New York 10065, United States
| | - Sanjiv S. Gambhir
- Department of Medicine, Department of Radiology, Stanford University, Stanford, California 94305, United States
| | - Shan X. Wang
- Department of Materials Science and Engineering, Stanford University, Stanford, California 94305, United States
- Department of Medicine, Department of Radiology, Stanford University, Stanford, California 94305, United States
- Department of Electrical Engineering, Stanford University, Stanford, California 94305, United States
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36
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Yeh CY, Adusumilli R, Kullolli M, Mallick P, John EM, Pitteri SJ. Assessing biological and technological variability in protein levels measured in pre-diagnostic plasma samples of women with breast cancer. Biomark Res 2017; 5:30. [PMID: 29075496 PMCID: PMC5645980 DOI: 10.1186/s40364-017-0110-y] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [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: 08/03/2017] [Accepted: 10/03/2017] [Indexed: 12/30/2022] Open
Abstract
Background Quantitative proteomics allows for the discovery and functional investigation of blood-based pre-diagnostic biomarkers for early cancer detection. However, a major limitation of proteomic investigations in biomarker studies remains the biological and technical variability in the analysis of complex clinical samples. Moreover, unlike ‘omics analogues such as genomics and transcriptomics, proteomics has yet to achieve reproducibility and long-term stability on a unified technological platform. Few studies have thoroughly investigated protein variability in pre-diagnostic samples of cancer patients across multiple platforms. Methods We obtained ten blood plasma “case” samples collected up to 2 years prior to breast cancer diagnosis. Each case sample was paired with a matched control plasma from a full biological sister without breast cancer. We measured protein levels using both mass-spectrometry and antibody-based technologies to: (1) assess the technical considerations in different protein assays when analyzing limited clinical samples, and (2) evaluate the statistical power of potential diagnostic analytes. Results Although we found inherent technical variation in the three assays used, we detected protein dependent biological signal from the limited samples. The three assay types yielded 32 proteins with statistically significantly (p < 1E-01) altered expression levels between cases and controls, with no proteins retaining statistical significance after false discovery correction. Conclusions Technical, practical, and study design considerations are essential to maximize information obtained in limited pre-diagnostic samples of cancer patients. This study provides a framework that estimates biological effect sizes critical for consideration in designing studies for pre-diagnostic blood-based biomarker detection. Electronic supplementary material The online version of this article (10.1186/s40364-017-0110-y) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Christine Y Yeh
- Department of Biomedical Informatics, Stanford University School of Medicine, Stanford, CA 93405 USA.,Department of Radiology, Canary Center at Stanford for Cancer Early Detection, Stanford University School of Medicine, Palo Alto, CA 94304 USA.,Department of Genetics, Stanford University School of Medicine, Stanford, CA 93405 USA
| | - Ravali Adusumilli
- Department of Radiology, Canary Center at Stanford for Cancer Early Detection, Stanford University School of Medicine, Palo Alto, CA 94304 USA
| | - Majlinda Kullolli
- Department of Radiology, Canary Center at Stanford for Cancer Early Detection, Stanford University School of Medicine, Palo Alto, CA 94304 USA
| | - Parag Mallick
- Department of Radiology, Canary Center at Stanford for Cancer Early Detection, Stanford University School of Medicine, Palo Alto, CA 94304 USA.,Stanford Cancer Institute, Stanford University School of Medicine, Stanford, CA 94305 USA
| | - Esther M John
- Stanford Cancer Institute, Stanford University School of Medicine, Stanford, CA 94305 USA.,Cancer Prevention Institute of California, Fremont, CA 94538 USA
| | - Sharon J Pitteri
- Department of Radiology, Canary Center at Stanford for Cancer Early Detection, Stanford University School of Medicine, Palo Alto, CA 94304 USA.,Stanford Cancer Institute, Stanford University School of Medicine, Stanford, CA 94305 USA
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37
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Kani K, Garri C, Tiemann K, Malihi PD, Punj V, Nguyen AL, Lee J, Hughes LD, Alvarez RM, Wood DM, Joo AY, Katz JE, Agus DB, Mallick P. JUN-Mediated Downregulation of EGFR Signaling Is Associated with Resistance to Gefitinib in EGFR-mutant NSCLC Cell Lines. Mol Cancer Ther 2017; 16:1645-1657. [PMID: 28566434 DOI: 10.1158/1535-7163.mct-16-0564] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [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: 08/25/2016] [Revised: 03/08/2017] [Accepted: 05/08/2017] [Indexed: 12/27/2022]
Abstract
Mutations or deletions in exons 18-21 in the EGFR) are present in approximately 15% of tumors in patients with non-small cell lung cancer (NSCLC). They lead to activation of the EGFR kinase domain and sensitivity to molecularly targeted therapeutics aimed at this domain (gefitinib or erlotinib). These drugs have demonstrated objective clinical response in many of these patients; however, invariably, all patients acquire resistance. To examine the molecular origins of resistance, we derived a set of gefitinib-resistant cells by exposing lung adenocarcinoma cell line, HCC827, with an activating mutation in the EGFR tyrosine kinase domain, to increasing gefitinib concentrations. Gefitinib-resistant cells acquired an increased expression and activation of JUN, a known oncogene involved in cancer progression. Ectopic overexpression of JUN in HCC827 cells increased gefitinib IC50 from 49 nmol/L to 8 μmol/L (P < 0.001). Downregulation of JUN expression through shRNA resensitized HCC827 cells to gefitinib (IC50 from 49 nmol/L to 2 nmol/L; P < 0.01). Inhibitors targeting JUN were 3-fold more effective in the gefitinib-resistant cells than in the parental cell line (P < 0.01). Analysis of gene expression in patient tumors with EGFR-activating mutations and poor response to erlotinib revealed a similar pattern as the top 260 differentially expressed genes in the gefitinib-resistant cells (Spearman correlation coefficient of 0.78, P < 0.01). These findings suggest that increased JUN expression and activity may contribute to gefitinib resistance in NSCLC and that JUN pathway therapeutics merit investigation as an alternate treatment strategy. Mol Cancer Ther; 16(8); 1645-57. ©2017 AACR.
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Affiliation(s)
- Kian Kani
- Lawrence J. Ellison Institute for Transformative Medicine, Keck School of Medicine, University of Southern California, Los Angeles, California.
- Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California Keck School of Medicine, Los Angeles, California
| | - Carolina Garri
- Lawrence J. Ellison Institute for Transformative Medicine, Keck School of Medicine, University of Southern California, Los Angeles, California
| | - Katrin Tiemann
- Lawrence J. Ellison Institute for Transformative Medicine, Keck School of Medicine, University of Southern California, Los Angeles, California
| | - Paymaneh D Malihi
- Lawrence J. Ellison Institute for Transformative Medicine, Keck School of Medicine, University of Southern California, Los Angeles, California
| | - Vasu Punj
- Division of Hematology, Department of Medicine, University of Southern California, Los Angeles, California
| | - Anthony L Nguyen
- Lawrence J. Ellison Institute for Transformative Medicine, Keck School of Medicine, University of Southern California, Los Angeles, California
| | - Janet Lee
- Lawrence J. Ellison Institute for Transformative Medicine, Keck School of Medicine, University of Southern California, Los Angeles, California
| | - Lindsey D Hughes
- Lawrence J. Ellison Institute for Transformative Medicine, Keck School of Medicine, University of Southern California, Los Angeles, California
| | - Ruth M Alvarez
- Lawrence J. Ellison Institute for Transformative Medicine, Keck School of Medicine, University of Southern California, Los Angeles, California
| | - Damien M Wood
- Lawrence J. Ellison Institute for Transformative Medicine, Keck School of Medicine, University of Southern California, Los Angeles, California
| | - Ah Young Joo
- Lawrence J. Ellison Institute for Transformative Medicine, Keck School of Medicine, University of Southern California, Los Angeles, California
| | - Jonathan E Katz
- Lawrence J. Ellison Institute for Transformative Medicine, Keck School of Medicine, University of Southern California, Los Angeles, California
| | - David B Agus
- Lawrence J. Ellison Institute for Transformative Medicine, Keck School of Medicine, University of Southern California, Los Angeles, California
- Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California Keck School of Medicine, Los Angeles, California
| | - Parag Mallick
- Lawrence J. Ellison Institute for Transformative Medicine, Keck School of Medicine, University of Southern California, Los Angeles, California.
- Department of Radiology, Stanford University, Stanford, California
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38
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Sylman JL, Mitrugno A, Tormoen GW, Wagner TH, Mallick P, McCarty OJT. Platelet count as a predictor of metastasis and venous thromboembolism in patients with cancer. Converg Sci Phys Oncol 2017; 3. [PMID: 29081989 DOI: 10.1088/2057-1739/aa6c05] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Platelets are anucleate cells in the blood at concentrations of 150,000 to 400,000 cells/µL and play a key role in hemostasis. Several studies have suggested that platelets contribute to cancer progression and cancer-associated thrombosis. In this review, we provide an overview of the biochemical and biophysical mechanisms by which platelets interact with cancer cells and review the evidence supporting a role for platelet-enhanced metastasis of cancer, and venous thromboembolism (VTE) in patients with cancer. We discuss the potential for and limitations of platelet counts to discriminate cancer disease burden and prognosis. Lastly, we consider more advanced diagnostic approaches to improve studies on the interaction between the hemostatic system and cancer cells.
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Affiliation(s)
- Joanna L Sylman
- Biomedical Engineering, School of Medicine, Oregon Health and Science University, Portland, OR.,VA Palo Alto Health Care System, Palo Alto, CA.,Canary Center at Stanford, Department of Radiology, Stanford University School of Medicine, Stanford, CA
| | - Annachiara Mitrugno
- Biomedical Engineering, School of Medicine, Oregon Health and Science University, Portland, OR
| | - Garth W Tormoen
- Department of Radiation Medicine, Oregon Health & Science University, 3181 SW Sam Jackson Park Rd, Portland, OR
| | - Todd H Wagner
- VA Palo Alto Health Care System, Palo Alto, CA.,Department of Surgery, Stanford University School of Medicine, Stanford, CA
| | - Parag Mallick
- Canary Center at Stanford, Department of Radiology, Stanford University School of Medicine, Stanford, CA
| | - Owen J T McCarty
- Biomedical Engineering, School of Medicine, Oregon Health and Science University, Portland, OR
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Abstract
Proteins play a key role in all aspects of cellular homeostasis. Proteomics, the large-scale study of proteins, provides in-depth data on protein properties, including abundances and post-translational modification states, and as such provides a rich avenue for the investigation of biological and disease processes. While proteomic tools such as mass spectrometry have enabled exquisitely sensitive sample analysis, sample preparation remains a critical unstandardized variable that can have a significant impact on downstream data readouts. Consistency in sample preparation and handling is therefore paramount in the collection and analysis of proteomic data.Here we describe methods for performing protein extraction from cell culture or tissues, digesting the isolated protein into peptides via in-solution enzymatic digest, and peptide cleanup with final preparations for analysis via liquid chromatography-mass spectrometry. These protocols have been optimized and standardized for maximum consistency and maintenance of sample integrity.
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Affiliation(s)
- Michelle Atallah
- Canary Center at Stanford for Cancer Early Detection, Stanford University, 3155 Porter Drive, Palo Alto, CA, 94304, USA
| | - Mark R Flory
- Canary Center at Stanford for Cancer Early Detection, Stanford University, 3155 Porter Drive, Palo Alto, CA, 94304, USA
| | - Parag Mallick
- Canary Center at Stanford for Cancer Early Detection, Stanford University, 3155 Porter Drive, Palo Alto, CA, 94304, USA.
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40
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Park SM, Lee JY, Hong S, Lee SH, Dimov IK, Lee H, Suh S, Pan Q, Li K, Wu AM, Mumenthaler SM, Mallick P, Lee LP. Dual transcript and protein quantification in a massive single cell array. Lab Chip 2016; 16:3682-8. [PMID: 27546183 PMCID: PMC5221609 DOI: 10.1039/c6lc00762g] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
Recently, single-cell molecular analysis has been leveraged to achieve unprecedented levels of biological investigation. However, a lack of simple, high-throughput single-cell methods has hindered in-depth population-wide studies with single-cell resolution. We report a microwell-based cytometric method for simultaneous measurements of gene and protein expression dynamics in thousands of single cells. We quantified the regulatory effects of transcriptional and translational inhibitors on cMET mRNA and cMET protein in cell populations. We studied the dynamic responses of individual cells to drug treatments, by measuring cMET overexpression levels in individual non-small cell lung cancer (NSCLC) cells with induced drug resistance. Across NSCLC cell lines with a given protein expression, distinct patterns of transcript-protein correlation emerged. We believe this platform is applicable for interrogating the dynamics of gene expression, protein expression, and translational kinetics at the single-cell level - a paradigm shift in life science and medicine toward discovering vital cell regulatory mechanisms.
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Affiliation(s)
- Seung-Min Park
- Department of Bioengineering, University of California, Berkeley, California, USA.
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41
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Patsch K, Chiu CL, Engeln M, Agus DB, Mallick P, Mumenthaler SM, Ruderman D. Single cell dynamic phenotyping. Sci Rep 2016; 6:34785. [PMID: 27708391 PMCID: PMC5052535 DOI: 10.1038/srep34785] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2015] [Accepted: 09/19/2016] [Indexed: 12/25/2022] Open
Abstract
Live cell imaging has improved our ability to measure phenotypic heterogeneity. However, bottlenecks in imaging and image processing often make it difficult to differentiate interesting biological behavior from technical artifact. Thus there is a need for new methods that improve data quality without sacrificing throughput. Here we present a 3-step workflow to improve dynamic phenotype measurements of heterogeneous cell populations. We provide guidelines for image acquisition, phenotype tracking, and data filtering to remove erroneous cell tracks using the novel Tracking Aberration Measure (TrAM). Our workflow is broadly applicable across imaging platforms and analysis software. By applying this workflow to cancer cell assays, we reduced aberrant cell track prevalence from 17% to 2%. The cost of this improvement was removing 15% of the well-tracked cells. This enabled detection of significant motility differences between cell lines. Similarly, we avoided detecting a false change in translocation kinetics by eliminating the true cause: varied proportions of unresponsive cells. Finally, by systematically seeking heterogeneous behaviors, we detected subpopulations that otherwise could have been missed, including early apoptotic events and pre-mitotic cells. We provide optimized protocols for specific applications and step-by-step guidelines for adapting them to a variety of biological systems.
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Affiliation(s)
- Katherin Patsch
- Lawrence J. Ellison Institute for Transformative Medicine, University of Southern California, Los Angeles, California, USA
| | - Chi-Li Chiu
- Lawrence J. Ellison Institute for Transformative Medicine, University of Southern California, Los Angeles, California, USA
| | - Mark Engeln
- Lawrence J. Ellison Institute for Transformative Medicine, University of Southern California, Los Angeles, California, USA
| | - David B Agus
- Lawrence J. Ellison Institute for Transformative Medicine, University of Southern California, Los Angeles, California, USA
| | - Parag Mallick
- Department of Radiology, Canary Center at Stanford for Cancer Early Detection, Stanford University, Palo Alto, CA, USA
| | - Shannon M Mumenthaler
- Lawrence J. Ellison Institute for Transformative Medicine, University of Southern California, Los Angeles, California, USA
| | - Daniel Ruderman
- Lawrence J. Ellison Institute for Transformative Medicine, University of Southern California, Los Angeles, California, USA
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42
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Liu S, Bainer R, Yui Y, Flinders C, Mallick P, Weaver V, Mumenthaler S. Abstract A23: Characterization of diverging molecular and phenotypic responses under changing extracellular matrix stiffness in MCF10A cells. Cancer Res 2016. [DOI: 10.1158/1538-7445.tme16-a23] [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
Tissue stiffness has emerged as an important regulator in the maintenance of normal cellular processes. In general, solid tumors are known to be much stiffer than normal tissue, with increased extracellular matrix (ECM) density being indicative of a higher risk for many cancers, including those of the breast. Over the course of breast cancer progression, the ECM becomes increasingly stiffer, a phenomenon which is known to be a driver of malignancy. In a 3D culture system using self-assembling peptide (SAP) gels, we grew MCF10A acini under a dynamic range of stiffness environments (140-5800 Pa). Under normal breast tissue elasticity, mammary epithelial cells form rounded, polarized acini with cleared lumens. However, in tumor-like stiffnesses, the same cells form non-polarized, collapsed structures that invade into the gel. To investigate the specific genes and pathways affected by stiffness, we have conducted tandem mass spectrometry to identify protein expression changes in MCF10A cells grown on SAP gels of increasing stiffness. Interestingly, the resulting analysis showed that cells grown on higher stiffnesses exhibit greater variation in protein expression. These divergent force-regulated molecular pathways are involved in a variety of cellular functions, including cell adhesion and migration, metabolism, and the immune response, among others. This study underscores the significance of mechanical forces exerted by the ECM, and signifies the first large-scale proteomic screen carried out to analyze heterogeneous cellular responses to changing stiffness environments.
Citation Format: Sonya Liu, Russell Bainer, Yoshihiro Yui, Colin Flinders, Parag Mallick, Valerie Weaver, Shannon Mumenthaler. Characterization of diverging molecular and phenotypic responses under changing extracellular matrix stiffness in MCF10A cells. [abstract]. In: Proceedings of the AACR Special Conference: Function of Tumor Microenvironment in Cancer Progression; 2016 Jan 7–10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2016;76(15 Suppl):Abstract nr A23.
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Affiliation(s)
- Sonya Liu
- 1University of Southern California, Los Angeles, CA,
| | - Russell Bainer
- 2University of California, San Francisco, San Francisco, CA,
| | - Yoshihiro Yui
- 2University of California, San Francisco, San Francisco, CA,
| | | | | | - Valerie Weaver
- 2University of California, San Francisco, San Francisco, CA,
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43
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van de Ven SMWY, Bemis KD, Lau K, Adusumilli R, Kota U, Stolowitz M, Vitek O, Mallick P, Gambhir SS. Protein biomarkers on tissue as imaged via MALDI mass spectrometry: A systematic approach to study the limits of detection. Proteomics 2016; 16:1660-9. [PMID: 26970438 DOI: 10.1002/pmic.201500515] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [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: 12/10/2015] [Revised: 02/23/2016] [Accepted: 03/05/2016] [Indexed: 01/05/2023]
Abstract
MALDI mass spectrometry imaging (MSI) is emerging as a tool for protein and peptide imaging across tissue sections. Despite extensive study, there does not yet exist a baseline study evaluating the potential capabilities for this technique to detect diverse proteins in tissue sections. In this study, we developed a systematic approach for characterizing MALDI-MSI workflows in terms of limits of detection, coefficients of variation, spatial resolution, and the identification of endogenous tissue proteins. Our goal was to quantify these figures of merit for a number of different proteins and peptides, in order to gain more insight in the feasibility of protein biomarker discovery efforts using this technique. Control proteins and peptides were deposited in serial dilutions on thinly sectioned mouse xenograft tissue. Using our experimental setup, coefficients of variation were <30% on tissue sections and spatial resolution was 200 μm (or greater). Limits of detection for proteins and peptides on tissue were in the micromolar to millimolar range. Protein identification was only possible for proteins present in high abundance in the tissue. These results provide a baseline for the application of MALDI-MSI towards the discovery of new candidate biomarkers and a new benchmarking strategy that can be used for comparing diverse MALDI-MSI workflows.
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Affiliation(s)
- Stephanie M W Y van de Ven
- Canary Center at Stanford, Department of Radiology, Stanford University School of Medicine, Stanford, CA, USA.,Molecular Imaging Program at Stanford, Stanford University School of Medicine, Stanford, CA, USA
| | - Kyle D Bemis
- Department of Statistics, Purdue University, West Lafayette, IN, USA
| | - Kenneth Lau
- Canary Center at Stanford, Department of Radiology, Stanford University School of Medicine, Stanford, CA, USA
| | - Ravali Adusumilli
- Canary Center at Stanford, Department of Radiology, Stanford University School of Medicine, Stanford, CA, USA.,Molecular Imaging Program at Stanford, Stanford University School of Medicine, Stanford, CA, USA
| | - Uma Kota
- Canary Center at Stanford, Department of Radiology, Stanford University School of Medicine, Stanford, CA, USA.,Thermo Fisher Scientific, San Jose, CA, USA
| | - Mark Stolowitz
- Canary Center at Stanford, Department of Radiology, Stanford University School of Medicine, Stanford, CA, USA.,Molecular Imaging Program at Stanford, Stanford University School of Medicine, Stanford, CA, USA
| | - Olga Vitek
- College of Science, College of Computer and Information Science, Northeastern University, Boston, MA, USA
| | - Parag Mallick
- Canary Center at Stanford, Department of Radiology, Stanford University School of Medicine, Stanford, CA, USA.,Molecular Imaging Program at Stanford, Stanford University School of Medicine, Stanford, CA, USA
| | - Sanjiv S Gambhir
- Canary Center at Stanford, Department of Radiology, Stanford University School of Medicine, Stanford, CA, USA.,Molecular Imaging Program at Stanford, Stanford University School of Medicine, Stanford, CA, USA.,Department of Bioengineering, Stanford University School of Medicine, Stanford, CA, USA.,Department of Materials Science & Engineering, Stanford, CA, USA
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44
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Flinders C, Lam L, Rubbi L, Ferrari R, Fitz-Gibbon S, Chen PY, Thompson M, Christofk H, B Agus D, Ruderman D, Mallick P, Pellegrini M. Epigenetic changes mediated by polycomb repressive complex 2 and E2a are associated with drug resistance in a mouse model of lymphoma. Genome Med 2016; 8:54. [PMID: 27146673 PMCID: PMC4857420 DOI: 10.1186/s13073-016-0305-0] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [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: 08/20/2015] [Accepted: 04/13/2016] [Indexed: 11/10/2022] Open
Abstract
Background The genetic origins of chemotherapy resistance are well established; however, the role of epigenetics in drug resistance is less well understood. To investigate mechanisms of drug resistance, we performed systematic genetic, epigenetic, and transcriptomic analyses of an alkylating agent-sensitive murine lymphoma cell line and a series of resistant lines derived by drug dose escalation. Methods Dose escalation of the alkylating agent mafosfamide was used to create a series of increasingly drug-resistant mouse Burkitt’s lymphoma cell lines. Whole genome sequencing, DNA microarrays, reduced representation bisulfite sequencing, and chromatin immunoprecipitation sequencing were used to identify alterations in DNA sequence, mRNA expression, CpG methylation, and H3K27me3 occupancy, respectively, that were associated with increased resistance. Results Our data suggest that acquired resistance cannot be explained by genetic alterations. Based on integration of transcriptional profiles with transcription factor binding data, we hypothesize that resistance is driven by epigenetic plasticity. We observed that the resistant cells had H3K27me3 and DNA methylation profiles distinct from those of the parental lines. Moreover, we observed DNA methylation changes in the promoters of genes regulated by E2a and members of the polycomb repressor complex 2 (PRC2) and differentially expressed genes were enriched for targets of E2a. The integrative analysis considering H3K27me3 further supported a role for PRC2 in mediating resistance. By integrating our results with data from the Immunological Genome Project (Immgen.org), we showed that these transcriptional changes track the B-cell maturation axis. Conclusions Our data suggest a novel mechanism of drug resistance in which E2a and PRC2 drive changes in the B-cell epigenome; these alterations attenuate alkylating agent treatment-induced apoptosis. Electronic supplementary material The online version of this article (doi:10.1186/s13073-016-0305-0) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Colin Flinders
- Department of Biological Chemistry, University of California, Los Angeles, CA, 90095, USA.,Center for Applied Molecular Medicine, University of Southern California, Los Angeles, CA, 90033, USA
| | - Larry Lam
- Department of Molecular, Cellular and Developmental Biology, University of California, Los Angeles, CA, 90095, USA
| | - Liudmilla Rubbi
- Department of Molecular, Cellular and Developmental Biology, University of California, Los Angeles, CA, 90095, USA
| | - Roberto Ferrari
- Department of Molecular, Cellular and Developmental Biology, University of California, Los Angeles, CA, 90095, USA
| | - Sorel Fitz-Gibbon
- Department of Molecular, Cellular and Developmental Biology, University of California, Los Angeles, CA, 90095, USA
| | - Pao-Yang Chen
- Department of Molecular, Cellular and Developmental Biology, University of California, Los Angeles, CA, 90095, USA
| | - Michael Thompson
- Department of Molecular, Cellular and Developmental Biology, University of California, Los Angeles, CA, 90095, USA
| | - Heather Christofk
- Department of Molecular and Medical Pharmacology, University of California, Los Angeles, CA, 90095, USA
| | - David B Agus
- Department of Medicine, University of Southern California, Los Angeles, CA, 90033, USA.,Center for Applied Molecular Medicine, University of Southern California, Los Angeles, CA, 90033, USA
| | - Daniel Ruderman
- Department of Medicine, University of Southern California, Los Angeles, CA, 90033, USA.,Center for Applied Molecular Medicine, University of Southern California, Los Angeles, CA, 90033, USA
| | - Parag Mallick
- Canary Center, Stanford University, Palo Alto, CA, 94305, USA. .,Center for Applied Molecular Medicine, University of Southern California, Los Angeles, CA, 90033, USA.
| | - Matteo Pellegrini
- Department of Molecular, Cellular and Developmental Biology, University of California, Los Angeles, CA, 90095, USA.
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Bemis KD, Harry A, Eberlin LS, Ferreira CR, van de Ven SM, Mallick P, Stolowitz M, Vitek O. Probabilistic Segmentation of Mass Spectrometry (MS) Images Helps Select Important Ions and Characterize Confidence in the Resulting Segments. Mol Cell Proteomics 2016; 15:1761-72. [PMID: 26796117 PMCID: PMC4858953 DOI: 10.1074/mcp.o115.053918] [Citation(s) in RCA: 43] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2015] [Indexed: 11/24/2022] Open
Abstract
Mass spectrometry imaging is a powerful tool for investigating the spatial distribution of chemical compounds in a biological sample such as tissue. Two common goals of these experiments are unsupervised segmentation of images into newly discovered homogeneous segments and supervised classification of images into predefined classes. In both cases, the important secondary goals are to characterize the uncertainty associated with the segmentation and with the classification and to characterize the spectral features that define each segment or class. Recent analysis methods have focused on the spatial structure of the data to improve results. However, they either do not address these secondary goals or do this with separate post hoc procedures. We introduce spatial shrunken centroids, a statistical model-based framework for both supervised classification and unsupervised segmentation. It takes as input sets of previously detected, aligned, quantified, and normalized spectral features and expresses both spatial and multivariate nature of the data using probabilistic modeling. It selects informative subsets of spectral features that define each unsupervised segment or supervised class and quantifies and visualizes the uncertainty in spatial segmentations and in tissue classification. In the unsupervised setting, it also guides the choice of an appropriate number of segments. We demonstrate the usefulness of this framework in a supervised human renal cell carcinoma experimental dataset and several unsupervised experimental datasets, including a pig fetus cross-section, three rodent brains, and a controlled image with known ground truth. This framework is available for use within the open-source R package Cardinal as part of a full pipeline for the processing, visualization, and statistical analysis of mass spectrometry imaging experiments.
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Affiliation(s)
| | | | - Livia S Eberlin
- §Department of Chemistry, Purdue University, West Lafayette, IN 47907
| | | | - Stephanie M van de Ven
- ¶Canary Center at Canary Foundation, Stanford University School of Medicine, Palo Alto, CA 94304; College of Science and
| | - Parag Mallick
- ¶Canary Center at Canary Foundation, Stanford University School of Medicine, Palo Alto, CA 94304; College of Science and
| | - Mark Stolowitz
- ¶Canary Center at Canary Foundation, Stanford University School of Medicine, Palo Alto, CA 94304; College of Science and
| | - Olga Vitek
- **College of Computer and Information Science, Northeastern University, Boston, MA 02115
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Frieboes HB, Curtis LT, Wu M, Kani K, Mallick P. Simulation of the Protein-Shedding Kinetics of a Fully Vascularized Tumor. Cancer Inform 2015; 14:163-75. [PMID: 26715830 PMCID: PMC4687979 DOI: 10.4137/cin.s35374] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [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: 09/25/2015] [Revised: 11/09/2015] [Accepted: 11/15/2015] [Indexed: 12/12/2022] Open
Abstract
Circulating biomarkers are of significant interest for cancer detection and treatment personalization. However, the biophysical processes that determine how proteins are shed from cancer cells or their microenvironment, diffuse through tissue, enter blood vasculature, and persist in circulation remain poorly understood. Since approaches primarily focused on experimental evaluation are incapable of measuring the shedding and persistence for every possible marker candidate, we propose an interdisciplinary computational/experimental approach that includes computational modeling of tumor tissue heterogeneity. The model implements protein production, transport, and shedding based on tumor vascularization, cell proliferation, hypoxia, and necrosis, thus quantitatively relating the tumor and circulating proteomes. The results highlight the dynamics of shedding as a function of protein diffusivity and production. Linking the simulated tumor parameters to clinical tumor and vascularization measurements could potentially enable this approach to reveal the tumor-specific conditions based on the protein detected in circulation and thus help to more accurately manage cancer diagnosis and treatment.
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Affiliation(s)
- Hermann B Frieboes
- Department of Bioengineering, University of Louisville, Louisville, KY, USA. ; James Graham Brown Cancer Center, University of Louisville, Louisville, KY, USA
| | - Louis T Curtis
- Department of Bioengineering, University of Louisville, Louisville, KY, USA
| | - Min Wu
- Department of Engineering Sciences and Applied Mathematics, Northwestern University, Chicago, IL, USA
| | - Kian Kani
- Center for Applied Molecular Medicine, University of Southern California, Los Angeles, CA, USA
| | - Parag Mallick
- Canary Center at Stanford for Cancer Early Detection, Stanford University, Stanford, CA, USA
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47
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Bainer R, Yui Y, Mumenthaler S, Mallick P, Liu L, Wu HJ, Podlaha O, Michor F, Liphardt J, Licht J, Weaver V. Abstract PR09: Extracellular stiffness cues drive spatial reorganization of the genome to globally constrain RNA abundance. Cancer Res 2015. [DOI: 10.1158/1538-7445.compsysbio-pr09] [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
The stiffness of the extracellular matrix (ECM) drives mechanosignaling that regulates tissue development and malignancy. We previously showed that a stiff ECM disrupts tissue organization and enhances malignant progression by inducing cell invasion and migration. However, the specific transcriptional and molecular events in which mechanotransduction directs these phenotypes are not well understood. To clarify this process, we used a combination of genome-scale approaches to monitor changes in gene expression and protein abundance as a function of acinar morphogenesis and tissue homeostasis in three dimensional extracellular matrix hydrogels with tunable stiffness. Elevated ECM stiffness perturbed tissue homeostasis and reverted the transcriptional phenotype of differentiated mammary acini to resemble that observed in rapidly proliferating nonpolarized mammary cell aggregates. These findings suggest that tissue tension induces cellular changes that directly reflect higher-order tissue organizational states. We found that these changes involve the spatial rearrangement of peripheral chromatin, and that the expression levels of multiple histone deacetylases increase in organized tissues concurrently with elevated nuclear heterochromatin content, an effect that is abrogated in rigid ECM conditions. We support these observations by mapping mechanoresponsive peripheral heterochromatin elements via ChIPseq, enabling us to directly identify dynamic regions containing genes whose transcriptional activity is responsive to mechanical cues. Finally, using a combination of genomic, imaging, and molecular biology techniques we demonstrated that ECM compliance and tissue organization significantly influences global RNA abundance. Notably, this model presents formidable conceptual and practical challenges for the interpretation of genomic data. Collectively, this work indicates that tissue organization is critically dependent on the cellular mechanical environment, which qualitatively and quantitatively shapes the epigenetic and transcriptional landscape by mechanisms that have not yet been elucidated.
Note: This abstract was not presented at the conference.
Citation Format: Russell Bainer, Yoshihiro Yui, Shannon Mumenthaler, Parag Mallick, Lin Liu, Hua-Jun Wu, Ondrej Podlaha, Franziska Michor, Jan Liphardt, Jonathan Licht, Valerie Weaver. Extracellular stiffness cues drive spatial reorganization of the genome to globally constrain RNA abundance. [abstract]. In: Proceedings of the AACR Special Conference on Computational and Systems Biology of Cancer; Feb 8-11 2015; San Francisco, CA. Philadelphia (PA): AACR; Cancer Res 2015;75(22 Suppl 2):Abstract nr PR09.
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Affiliation(s)
| | | | | | | | - Lin Liu
- 4Dana-Farber Cancer Institute, Boston, MA,
| | - Hua-Jun Wu
- 4Dana-Farber Cancer Institute, Boston, MA,
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Chang E, Pohling C, Natarajan A, Witney T, Kaur J, Xu L, Gowrishankar G, de Souza A, Schick S, Chan L, Wu N, Khaw P, Mischel P, Abbasi T, Usmani S, Mallick P, Gambhir SS. DDEL-04AshwaMAX AND WITHAFERIN A INHIBITS GLIOMAS IN CELLULAR AND MURINE ORTHOTOPIC MODELS. Neuro Oncol 2015. [DOI: 10.1093/neuonc/nov212.04] [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: 11/14/2022] Open
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Venkatesh H, Johung T, Caretti V, Mallick P, Monje M. Abstract LB-036: Neuronal activity-regulated secretion of neuroligin-3 promotes glioma growth. Cancer Res 2015. [DOI: 10.1158/1538-7445.am2015-lb-036] [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
Active neurons exert a mitogenic effect on normal neural precursor and oligodendroglial precursor cells, the putative cellular origins of high-grade glioma (HGG). We demonstrate that active neurons similarly promote HGG proliferation and growth in vivo using optogenetic control of cortical neuronal activity in a patient-derived pediatric glioblastoma orthotopic xenograft model. Activity-regulated mitogen(s) are secreted, as the conditioned medium from optogenetically stimulated cortical slices promoted proliferation of pediatric and adult patient-derived HGG cultures. The synaptic protein neuroligin-3 (NLGN3) was identified as the leading candidate mitogen; soluble NLGN3 was sufficient and necessary to promote robust HGG cell proliferation. NLGN3 induced PI3K-mTOR pathway activity and feed-forward expression of NLGN3 in glioma cells, providing mechanistic insight into its surprising role as a mitogen. NLGN3 expression levels in human HGG negatively correlated with patient overall survival. These findings indicate the important role of active neurons in the brain tumor microenvironment and identify secreted NLGN3 as an unexpected mechanism promoting neuronal activity-regulated cancer growth.
Citation Format: Humsa Venkatesh, Tessa Johung, Viola Caretti, Parag Mallick, Michelle Monje. Neuronal activity-regulated secretion of neuroligin-3 promotes glioma growth. [abstract]. In: Proceedings of the 106th Annual Meeting of the American Association for Cancer Research; 2015 Apr 18-22; Philadelphia, PA. Philadelphia (PA): AACR; Cancer Res 2015;75(15 Suppl):Abstract nr LB-036. doi:10.1158/1538-7445.AM2015-LB-036
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Mumenthaler SM, Foo J, Choi NC, Heise N, Leder K, Agus DB, Pao W, Michor F, Mallick P. The Impact of Microenvironmental Heterogeneity on the Evolution of Drug Resistance in Cancer Cells. Cancer Inform 2015; 14:19-31. [PMID: 26244007 PMCID: PMC4504404 DOI: 10.4137/cin.s19338] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2015] [Revised: 05/03/2015] [Accepted: 05/12/2015] [Indexed: 12/15/2022] Open
Abstract
Therapeutic resistance arises as a result of evolutionary processes driven by dynamic feedback between a heterogeneous cell population and environmental selective pressures. Previous studies have suggested that mutations conferring resistance to epidermal growth factor receptor (EGFR) tyrosine kinase inhibitors (TKI) in non-small-cell lung cancer (NSCLC) cells lower the fitness of resistant cells relative to drug-sensitive cells in a drug-free environment. Here, we hypothesize that the local tumor microenvironment could influence the magnitude and directionality of the selective effect, both in the presence and absence of a drug. Using a combined experimental and computational approach, we developed a mathematical model of preexisting drug resistance describing multiple cellular compartments, each representing a specific tumor environmental niche. This model was parameterized using a novel experimental dataset derived from the HCC827 erlotinib-sensitive and -resistant NSCLC cell lines. We found that, in contrast to in the drug-free environment, resistant cells may hold a fitness advantage compared to parental cells in microenvironments deficient in oxygen and nutrients. We then utilized the model to predict the impact of drug and nutrient gradients on tumor composition and recurrence times, demonstrating that these endpoints are strongly dependent on the microenvironment. Our interdisciplinary approach provides a model system to quantitatively investigate the impact of microenvironmental effects on the evolutionary dynamics of tumor cells.
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Affiliation(s)
- Shannon M Mumenthaler
- Center for Applied Molecular Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Jasmine Foo
- School of Mathematics, University of Minnesota, Minneapolis, MN, USA
| | - Nathan C Choi
- Center for Applied Molecular Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Nicholas Heise
- School of Mathematics, University of Minnesota, Minneapolis, MN, USA
| | - Kevin Leder
- Department of Industrial and Systems Engineering, University of Minnesota, Minneapolis, MN, USA
| | - David B Agus
- Center for Applied Molecular Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - William Pao
- Department of Medicine, Vanderbilt-Ingram Cancer Center, Nashville, TN, USA
| | - Franziska Michor
- Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Parag Mallick
- Department of Radiology, Canary Center at Stanford for Cancer Early Detection, Stanford University, Palo Alto, CA, USA
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