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Uechi L, Vasudevan S, Vilenski D, Branciamore S, Frankhouser D, O'Meally D, Meshinchi S, Marcucci G, Kuo YH, Rockne R, Kravchenko-Balasha N. Transcriptome free energy can serve as a dynamic patient-specific biomarker in acute myeloid leukemia. NPJ Syst Biol Appl 2024; 10:32. [PMID: 38527998 DOI: 10.1038/s41540-024-00352-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2023] [Accepted: 02/26/2024] [Indexed: 03/27/2024] Open
Abstract
Acute myeloid leukemia (AML) is prevalent in both adult and pediatric patients. Despite advances in patient categorization, the heterogeneity of AML remains a challenge. Recent studies have explored the use of gene expression data to enhance AML diagnosis and prognosis, however, alternative approaches rooted in physics and chemistry may provide another level of insight into AML transformation. Utilizing publicly available databases, we analyze 884 human and mouse blood and bone marrow samples. We employ a personalized medicine strategy, combining state-transition theory and surprisal analysis, to assess the RNA transcriptome of individual patients. The transcriptome is transformed into physical parameters that represent each sample's steady state and the free energy change (FEC) from that steady state, which is the state with the lowest free energy.We found the transcriptome steady state was invariant across normal and AML samples. FEC, representing active molecular processes, varied significantly between samples and was used to create patient-specific barcodes to characterize the biology of the disease. We discovered that AML samples that were in a transition state had the highest FEC. This disease state may be characterized as the most unstable and hence the most therapeutically targetable since a change in free energy is a thermodynamic requirement for disease progression. We also found that distinct sets of ongoing processes may be at the root of otherwise similar clinical phenotypes, implying that our integrated analysis of transcriptome profiles may facilitate a personalized medicine approach to cure AML and restore a steady state in each patient.
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Affiliation(s)
- Lisa Uechi
- Division of Mathematical Oncology and Computational Systems Biology, Department of Computational and Quantitative Medicine, Beckman Research Institute, City of Hope National Medical Center, Duarte, CA, 91010, USA
| | - Swetha Vasudevan
- The Institute of Biomedical and Oral Research, Faculty of Dental Medicine, The Hebrew University of Jerusalem, P.O.B. 12272, Ein Kerem, Jerusalem, 91120, Israel
| | - Daniela Vilenski
- The Institute of Biomedical and Oral Research, Faculty of Dental Medicine, The Hebrew University of Jerusalem, P.O.B. 12272, Ein Kerem, Jerusalem, 91120, Israel
| | - Sergio Branciamore
- Division of Mathematical Oncology and Computational Systems Biology, Department of Computational and Quantitative Medicine, Beckman Research Institute, City of Hope National Medical Center, Duarte, CA, 91010, USA
| | - David Frankhouser
- Division of Mathematical Oncology and Computational Systems Biology, Department of Computational and Quantitative Medicine, Beckman Research Institute, City of Hope National Medical Center, Duarte, CA, 91010, USA
| | - Denis O'Meally
- Department of Diabetes and Cancer Discovery Science, Arthur Riggs Diabetes and Metabolism Research Institute, Beckman Research Institute, City of Hope National Medical Center, Duarte, CA, 91010, USA
| | - Soheil Meshinchi
- Clinical Research Division, Fred Hutchinson Cancer Center, 1100 Fairview Ave N, D5-112, Seattle, WA, 98109, USA
| | - Guido Marcucci
- Department of Hematological Malignancies Translational Science, Gehr Family Center for Leukemia Research, Beckman Research Institute, City of Hope National Medical Center, Duarte, CA, USA
| | - Ya-Huei Kuo
- Department of Hematological Malignancies Translational Science, Gehr Family Center for Leukemia Research, Beckman Research Institute, City of Hope National Medical Center, Duarte, CA, USA
| | - Russell Rockne
- Division of Mathematical Oncology and Computational Systems Biology, Department of Computational and Quantitative Medicine, Beckman Research Institute, City of Hope National Medical Center, Duarte, CA, 91010, USA.
| | - Nataly Kravchenko-Balasha
- The Institute of Biomedical and Oral Research, Faculty of Dental Medicine, The Hebrew University of Jerusalem, P.O.B. 12272, Ein Kerem, Jerusalem, 91120, Israel.
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Sheva K, Roy Chowdhury S, Kravchenko-Balasha N, Meirovitz A. Molecular Changes in Breast Cancer Induced by Radiation Therapy. Int J Radiat Oncol Biol Phys 2024:S0360-3016(24)00435-8. [PMID: 38508467 DOI: 10.1016/j.ijrobp.2024.03.019] [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: 06/13/2023] [Revised: 02/29/2024] [Accepted: 03/10/2024] [Indexed: 03/22/2024]
Abstract
PURPOSE Breast cancer treatments are based on prognostic clinicopathologic features that form the basis for therapeutic guidelines. Although the utilization of these guidelines has decreased breast cancer-associated mortality rates over the past three decades, they are not adequate for individualized therapy. Radiation therapy (RT) is the backbone of breast cancer treatment. Although a highly successful therapeutic modality clinically, from a biological perspective, preclinical studies have shown RT to have the potential to alter tumor cell phenotype, immunogenicity, and the surrounding microenvironment, potentially changing the behavior of cancer cells and resulting in a significant variation in RT response. This review presents the recent advances in revealing the complex molecular changes induced by RT in the treatment of breast cancer and highlights the complexities of translating this information into clinically relevant tools for improved prognostic insights and the revelation of novel approaches for optimizing RT. METHODS AND MATERIALS Current literature was reviewed with a focus on recent advances made in the elucidation of tumor-associated radiation-induced molecular changes across molecular, genetic, and proteomic bases. This review was structured with the aim of providing an up-to-date overview over the very broad and complex subject matter of radiation-induced molecular changes and radioresistance, familiarizing the reader with the broader issue at hand. RESULTS The subject of radiation-induced molecular changes in breast cancer has been broached from various physiological focal points including that of the immune system, immunogenicity and the abscopal effect, tumor hypoxia, breast cancer classification and subtyping, molecular heterogeneity, and molecular plasticity. It is becoming increasingly apparent that breast cancer clinical subtyping alone does not adequately account for variation in RT response or radioresistance. Multiple components of the tumor microenvironment and immune system, delivered RT dose and fractionation schedules, radiation-induced bystander effects, and intrinsic tumor physiology and heterogeneity all contribute to the resultant RT outcome. CONCLUSIONS Despite recent advances and improvements in anticancer therapies, tumor resistance remains a significant challenge. As new analytical techniques and technologies continue to provide crucial insight into the complex molecular mechanisms of breast cancer and its treatment responses, it is becoming more evident that personalized anticancer treatment regimens may be vital in overcoming radioresistance.
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Affiliation(s)
- Kim Sheva
- The Legacy Heritage Oncology Center & Dr Larry Norton Institute, Soroka University Medical Center, Ben Gurion University of the Negev, Faculty of Medicine, Be'er Sheva, Israel.
| | - Sangita Roy Chowdhury
- The Institute of Biomedical and Oral Research, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Nataly Kravchenko-Balasha
- The Institute of Biomedical and Oral Research, The Hebrew University of Jerusalem, Jerusalem, Israel.
| | - Amichay Meirovitz
- The Legacy Heritage Oncology Center & Dr Larry Norton Institute, Soroka University Medical Center, Ben Gurion University of the Negev, Faculty of Medicine, Be'er Sheva, Israel.
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Alkhatib H, Conage-Pough J, Roy Chowdhury S, Shian D, Zaid D, Rubinstein AM, Sonnenblick A, Peretz-Yablonsky T, Granit A, Carmon E, Kohale IN, Boughey JC, Goetz MP, Wang L, White FM, Kravchenko-Balasha N. Patient-specific signaling signatures predict optimal therapeutic combinations for triple negative breast cancer. Mol Cancer 2024; 23:17. [PMID: 38229082 PMCID: PMC10790458 DOI: 10.1186/s12943-023-01921-9] [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: 11/02/2023] [Accepted: 12/20/2023] [Indexed: 01/18/2024] Open
Abstract
Triple negative breast cancer (TNBC) is a heterogeneous group of tumors which lack estrogen receptor, progesterone receptor, and HER2 expression. Targeted therapies have limited success in treating TNBC, thus a strategy enabling effective targeted combinations is an unmet need. To tackle these challenges and discover individualized targeted combination therapies for TNBC, we integrated phosphoproteomic analysis of altered signaling networks with patient-specific signaling signature (PaSSS) analysis using an information-theoretic, thermodynamic-based approach. Using this method on a large number of TNBC patient-derived tumors (PDX), we were able to thoroughly characterize each PDX by computing a patient-specific set of unbalanced signaling processes and assigning a personalized therapy based on them. We discovered that each tumor has an average of two separate processes, and that, consistent with prior research, EGFR is a major core target in at least one of them in half of the tumors analyzed. However, anti-EGFR monotherapies were predicted to be ineffective, thus we developed personalized combination treatments based on PaSSS. These were predicted to induce anti-EGFR responses or to be used to develop an alternative therapy if EGFR was not present.In-vivo experimental validation of the predicted therapy showed that PaSSS predictions were more accurate than other therapies. Thus, we suggest that a detailed identification of molecular imbalances is necessary to tailor therapy for each TNBC. In summary, we propose a new strategy to design personalized therapy for TNBC using pY proteomics and PaSSS analysis. This method can be applied to different cancer types to improve response to the biomarker-based treatment.
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Affiliation(s)
- Heba Alkhatib
- The Institute of Biomedical and Oral Research, The Hebrew University of Jerusalem, 9103401, Jerusalem, Israel
| | - Jason Conage-Pough
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
| | - Sangita Roy Chowdhury
- The Institute of Biomedical and Oral Research, The Hebrew University of Jerusalem, 9103401, Jerusalem, Israel
| | - Denen Shian
- The Institute of Biomedical and Oral Research, The Hebrew University of Jerusalem, 9103401, Jerusalem, Israel
| | - Deema Zaid
- The Institute of Biomedical and Oral Research, The Hebrew University of Jerusalem, 9103401, Jerusalem, Israel
| | - Ariel M Rubinstein
- The Institute of Biomedical and Oral Research, The Hebrew University of Jerusalem, 9103401, Jerusalem, Israel
| | - Amir Sonnenblick
- Tel Aviv Sourasky Medical Center, Tel Aviv, Israel
- Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Tamar Peretz-Yablonsky
- Sharett Institute of Oncology, Hebrew University-Hadassah Medical Center, 9103401, Jerusalem, Israel
| | - Avital Granit
- Sharett Institute of Oncology, Hebrew University-Hadassah Medical Center, 9103401, Jerusalem, Israel
| | - Einat Carmon
- Department of Surgery, Samson Assuta Ashdod University Hospital, Ashdod, Israel
| | - Ishwar N Kohale
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
| | - Judy C Boughey
- Department of Surgery, Mayo Clinic, Rochester, MN, 55905, USA
| | - Matthew P Goetz
- Department of Oncology, Mayo Clinic, Rochester, MN, 55905, USA
| | - Liewei Wang
- Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic, Rochester, MN, 55905, USA
| | - Forest M White
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA.
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA.
| | - Nataly Kravchenko-Balasha
- The Institute of Biomedical and Oral Research, The Hebrew University of Jerusalem, 9103401, Jerusalem, Israel.
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Rabah N, Ait Mohand FE, Kravchenko-Balasha N. Understanding Glioblastoma Signaling, Heterogeneity, Invasiveness, and Drug Delivery Barriers. Int J Mol Sci 2023; 24:14256. [PMID: 37762559 PMCID: PMC10532387 DOI: 10.3390/ijms241814256] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2023] [Revised: 09/13/2023] [Accepted: 09/14/2023] [Indexed: 09/29/2023] Open
Abstract
The most prevalent and aggressive type of brain cancer, namely, glioblastoma (GBM), is characterized by intra- and inter-tumor heterogeneity and strong spreading capacity, which makes treatment ineffective. A true therapeutic answer is still in its infancy despite various studies that have made significant progress toward understanding the mechanisms behind GBM recurrence and its resistance. The primary causes of GBM recurrence are attributed to the heterogeneity and diffusive nature; therefore, monitoring the tumor's heterogeneity and spreading may offer a set of therapeutic targets that could improve the clinical management of GBM and prevent tumor relapse. Additionally, the blood-brain barrier (BBB)-related poor drug delivery that prevents effective drug concentrations within the tumor is discussed. With a primary emphasis on signaling heterogeneity, tumor infiltration, and computational modeling of GBM, this review covers typical therapeutic difficulties and factors contributing to drug resistance development and discusses potential therapeutic approaches.
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Affiliation(s)
| | | | - Nataly Kravchenko-Balasha
- The Institute of Biomedical and Oral Research, Hebrew University of Jerusalem, Jerusalem 91120, Israel; (N.R.); (F.-E.A.M.)
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AbdEl-haq M, Kumar A, Ait Mohand FE, Kravchenko-Balasha N, Rottenberg Y, Domb AJ. Paclitaxel Delivery to the Brain for Glioblastoma Treatment. Int J Mol Sci 2023; 24:11722. [PMID: 37511480 PMCID: PMC10380674 DOI: 10.3390/ijms241411722] [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: 06/11/2023] [Revised: 07/14/2023] [Accepted: 07/18/2023] [Indexed: 07/30/2023] Open
Abstract
The development of paclitaxel-loaded polymeric nanoparticles for the treatment of brain tumors was investigated. Poly(lactide-glycolide) (PLGA) nanoparticles containing 10% w/w paclitaxel with a particle size of 216 nm were administered through intranasal and intravenous routes to male Sprague-Dawley rats at a dose of 5 mg/kg. Both routes of administration showed appreciable accumulation of paclitaxel in brain tissue, liver, and kidney without any sign of toxicity. The anti-proliferative effect of the nanoparticles on glioblastoma tumor cells was comparable to that of free paclitaxel.
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Affiliation(s)
- Muhammad AbdEl-haq
- Institute of Drug Research, School of Pharmacy-Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem 91120, Israel
| | - Awanish Kumar
- Institute of Drug Research, School of Pharmacy-Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem 91120, Israel
| | - Fatima-ezzahra Ait Mohand
- The Institute of Biomedical and Oral Research, Faculty of Dental Medicine, The Hebrew University of Jerusalem, Jerusalem 91120, Israel (N.K.-B.)
| | - Nataly Kravchenko-Balasha
- The Institute of Biomedical and Oral Research, Faculty of Dental Medicine, The Hebrew University of Jerusalem, Jerusalem 91120, Israel (N.K.-B.)
| | - Yakir Rottenberg
- Sharett Institute of Oncology, Hadassah-Hebrew University Medical Center, Jerusalem 91120, Israel;
| | - Abraham J. Domb
- Institute of Drug Research, School of Pharmacy-Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem 91120, Israel
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Sharon S, Daher-Ghanem N, Zaid D, Gough MJ, Kravchenko-Balasha N. The immunogenic radiation and new players in immunotherapy and targeted therapy for head and neck cancer. Front Oral Health 2023; 4:1180869. [PMID: 37496754 PMCID: PMC10366623 DOI: 10.3389/froh.2023.1180869] [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] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2023] [Accepted: 06/27/2023] [Indexed: 07/28/2023] Open
Abstract
Although treatment modalities for head and neck cancer have evolved considerably over the past decades, survival rates have plateaued. The treatment options remained limited to definitive surgery, surgery followed by fractionated radiotherapy with optional chemotherapy, and a definitive combination of fractionated radiotherapy and chemotherapy. Lately, immunotherapy has been introduced as the fourth modality of treatment, mainly administered as a single checkpoint inhibitor for recurrent or metastatic disease. While other regimens and combinations of immunotherapy and targeted therapy are being tested in clinical trials, adapting the appropriate regimens to patients and predicting their outcomes have yet to reach the clinical setting. Radiotherapy is mainly regarded as a means to target cancer cells while minimizing the unwanted peripheral effect. Radiotherapy regimens and fractionation are designed to serve this purpose, while the systemic effect of radiation on the immune response is rarely considered a factor while designing treatment. To bridge this gap, this review will highlight the effect of radiotherapy on the tumor microenvironment locally, and the immune response systemically. We will review the methodology to identify potential targets for therapy in the tumor microenvironment and the scientific basis for combining targeted therapy and radiotherapy. We will describe a current experience in preclinical models to test these combinations and propose how challenges in this realm may be faced. We will review new players in targeted therapy and their utilization to drive immunogenic response against head and neck cancer. We will outline the factors contributing to head and neck cancer heterogeneity and their effect on the response to radiotherapy. We will review in-silico methods to decipher intertumoral and intratumoral heterogeneity and how these algorithms can predict treatment outcomes. We propose that (a) the sequence of surgery, radiotherapy, chemotherapy, and targeted therapy should be designed not only to annul cancer directly, but to prime the immune response. (b) Fractionation of radiotherapy and the extent of the irradiated field should facilitate systemic immunity to develop. (c) New players in targeted therapy should be evaluated in translational studies toward clinical trials. (d) Head and neck cancer treatment should be personalized according to patients and tumor-specific factors.
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Affiliation(s)
- Shay Sharon
- Department of Oral and Maxillofacial Surgery, Hadassah Medical Center, Faculty of Dental Medicine, The Hebrew University of Jerusalem, Jerusalem, Israel
- The Institute of Biomedical and Oral Research, The Hebrew University of Jerusalem, Jerusalem, Israel
- Department of Oral and Maxillofacial Surgery, Boston University and Boston Medical Center, Boston, MA, United States
| | - Narmeen Daher-Ghanem
- The Institute of Biomedical and Oral Research, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Deema Zaid
- The Institute of Biomedical and Oral Research, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Michael J. Gough
- Earle A. Chiles Research Institute, Robert W. Franz Cancer Center, Providence Portland Medical Center, Portland, OR, United States
| | - Nataly Kravchenko-Balasha
- The Institute of Biomedical and Oral Research, The Hebrew University of Jerusalem, Jerusalem, Israel
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Aldwaik RK, Shian D, Thapa R, Vasudevan S, Ashqar MAA, Reich E, Kravchenko-Balasha N, Klutstein M. Overexpressed kinetochore genes are used by cancer cells as genome destabilizers and transformation catalysts. Transl Oncol 2023; 34:101703. [PMID: 37295219 DOI: 10.1016/j.tranon.2023.101703] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2023] [Revised: 05/14/2023] [Accepted: 05/23/2023] [Indexed: 06/12/2023] Open
Abstract
Cancer cells have an altered transcriptome, which contributes to their abnormal behavior. Many tumors have high levels of kinetochore genes, which play important roles in genome stability. This overexpression could be utilized to destabilize cancer cell genomes, however this has not been proven specifically. We investigated the link between kinetochore gene overexpression, chromosomal number variations (CNVs) and genomic instability. Data on RNA expression and CNV from 12 different cancer types were evaluated using information theory. In all cancer types, we looked at the relationship between RNA expression and CNVs. Kinetochore gene expression was found to be substantially linked with CNV levels. In all cancer types, with the exception of thyroid cancer, highly expressed kinetochore genes were enriched in the most dominant cancer-specific co-expression subnetworks characterizing the largest patient subgroups. Except for thyroid cancer, kinetochore inner protein CENPA was among the transcripts most strongly associated with CNV values in all cancer types studied, with significantly higher expression levels in patients with high CNVs than in patients with low CNVs. CENPA function was investigated further in cell models by transfecting genomically stable (HCT116) and unstable (MCF7 and HT29) cancer cell lines using CENPA overexpression vectors. This overexpression increased the number of abnormal cell divisions in the stable cancer cell line HCT116 and, to a lesser extent, in the unstable cell lines MCF7 and HT29. Overexpression improved anchorage-independent growth properties of all cell lines. Our findings suggest that overexpression of kinetochore genes in general, and CENPA in particular, can cause genomic instability and cancer progression.
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Affiliation(s)
- Reem Kamal Aldwaik
- The Institute of Biomedical and Oral Research, Faculty of Dental Medicine, The Hebrew University of Jerusalem, P.O.B. 12272, Ein Kerem, Jerusalem 91120, Israel
| | - Denen Shian
- The Institute of Biomedical and Oral Research, Faculty of Dental Medicine, The Hebrew University of Jerusalem, P.O.B. 12272, Ein Kerem, Jerusalem 91120, Israel
| | - Roshina Thapa
- The Institute of Biomedical and Oral Research, Faculty of Dental Medicine, The Hebrew University of Jerusalem, P.O.B. 12272, Ein Kerem, Jerusalem 91120, Israel
| | - Swetha Vasudevan
- The Institute of Biomedical and Oral Research, Faculty of Dental Medicine, The Hebrew University of Jerusalem, P.O.B. 12272, Ein Kerem, Jerusalem 91120, Israel
| | - Mimi Abo-Ayoub Ashqar
- The Institute of Biomedical and Oral Research, Faculty of Dental Medicine, The Hebrew University of Jerusalem, P.O.B. 12272, Ein Kerem, Jerusalem 91120, Israel
| | - Eli Reich
- The Institute of Biomedical and Oral Research, Faculty of Dental Medicine, The Hebrew University of Jerusalem, P.O.B. 12272, Ein Kerem, Jerusalem 91120, Israel
| | - Nataly Kravchenko-Balasha
- The Institute of Biomedical and Oral Research, Faculty of Dental Medicine, The Hebrew University of Jerusalem, P.O.B. 12272, Ein Kerem, Jerusalem 91120, Israel.
| | - Michael Klutstein
- The Institute of Biomedical and Oral Research, Faculty of Dental Medicine, The Hebrew University of Jerusalem, P.O.B. 12272, Ein Kerem, Jerusalem 91120, Israel.
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Carmon I, Zecharyahu L, Elayyan J, Meka SRK, Reich E, Kandel L, Bilkei-Gorzo A, Zimmer A, Mechoulam R, Kravchenko-Balasha N, Dvir-Ginzberg M. HU308 Mitigates Osteoarthritis by Stimulating Sox9-Related Networks of Carbohydrate Metabolism. J Bone Miner Res 2023; 38:154-170. [PMID: 36350089 PMCID: PMC10098743 DOI: 10.1002/jbmr.4741] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/27/2022] [Revised: 10/14/2022] [Accepted: 10/21/2022] [Indexed: 11/11/2022]
Abstract
Osteoarthritis (OA) is characterized by progressive, irreversible erosion of articular cartilage accompanied by severe pain and immobility. This study aimed to assess the effect and mechanism of action of HU308, a selective cannabinoid receptor type 2 (CB2) agonist, in preventing OA-related joint damage. To test the assumption that HU308 could prevent OA-related joint damage, Cnr2 null mice and wild type (WT) mice were aged to reach 20 months and analyzed for joint structural features. OA was induced in WT mice via a post-traumatic procedure or aging, followed by HU308 local (intra-articular) or systemic (intraperitoneal) administration, respectively. Additional analyses of time and dose courses for HU308 were carried out in human primary chondrocytes, analyzed by RNA sequencing, RT-PCR, chromatin immunoprecipitation, and immunoblotting. Our results showed that Cnr2 null mice exhibited enhanced age-related OA severity and synovitis compared to age-matched WT mice. Systemic administration of HU308 to 16-month-old mice improved pain sensitivity and maintained joint integrity, which was consistent with the intra-articular administration of HU308 in post-traumatic OA mice. When assessing human chondrocytes treated with HU308, we uncovered a dose- and time-related increase in ACAN and COL2A1 expression, which was preceded by increased SOX9 expression due to pCREB transcriptional activity. Finally, transcriptomic analysis of patient-derived human chondrocytes identified patient subpopulations exhibiting HU308-responsive trends as judged by enhanced SOX9 expression, accompanied by enriched gene networks related to carbohydrate metabolism. Collectively, the results showed that HU308 reduced trauma and age-induced OA via CB2-pCREB dependent activation of SOX9, contributing to augmented gene networks related to carbohydrate metabolism. © 2022 The Authors. Journal of Bone and Mineral Research published by Wiley Periodicals LLC on behalf of American Society for Bone and Mineral Research (ASBMR).
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Affiliation(s)
- Idan Carmon
- Multidisciplinary Center for Cannabinoid Research, Hebrew University of Jerusalem, Jerusalem, Israel.,Institute of BioMedical and Oral Research, Faculty of Dental Medicine, Hebrew University of Jerusalem, Jerusalem, Israel
| | - Lital Zecharyahu
- Institute of BioMedical and Oral Research, Faculty of Dental Medicine, Hebrew University of Jerusalem, Jerusalem, Israel
| | - Jinan Elayyan
- Institute of BioMedical and Oral Research, Faculty of Dental Medicine, Hebrew University of Jerusalem, Jerusalem, Israel
| | - Sai R K Meka
- Multidisciplinary Center for Cannabinoid Research, Hebrew University of Jerusalem, Jerusalem, Israel.,Institute of BioMedical and Oral Research, Faculty of Dental Medicine, Hebrew University of Jerusalem, Jerusalem, Israel
| | - Eli Reich
- Institute of BioMedical and Oral Research, Faculty of Dental Medicine, Hebrew University of Jerusalem, Jerusalem, Israel
| | - Leonid Kandel
- Orthopedic Complex. Hebrew University- Hadassah Medical Center, Jerusalem, Israel
| | | | - Andreas Zimmer
- Institute of Molecular Psychiatry, University of Bonn, Bonn, Germany
| | - Raphael Mechoulam
- Multidisciplinary Center for Cannabinoid Research, Hebrew University of Jerusalem, Jerusalem, Israel
| | - Nataly Kravchenko-Balasha
- Institute of BioMedical and Oral Research, Faculty of Dental Medicine, Hebrew University of Jerusalem, Jerusalem, Israel
| | - Mona Dvir-Ginzberg
- Multidisciplinary Center for Cannabinoid Research, Hebrew University of Jerusalem, Jerusalem, Israel.,Institute of BioMedical and Oral Research, Faculty of Dental Medicine, Hebrew University of Jerusalem, Jerusalem, Israel
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Alkhatib H, Rubinstein AM, Vasudevan S, Flashner-Abramson E, Stefansky S, Chowdhury SR, Oguche S, Peretz-Yablonsky T, Granit A, Granot Z, Ben-Porath I, Sheva K, Feldman J, Cohen NE, Meirovitz A, Kravchenko-Balasha N. Computational quantification and characterization of independently evolving cellular subpopulations within tumors is critical to inhibit anti-cancer therapy resistance. Genome Med 2022; 14:120. [PMID: 36266692 PMCID: PMC9583500 DOI: 10.1186/s13073-022-01121-y] [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] [Received: 01/20/2022] [Accepted: 09/28/2022] [Indexed: 11/22/2022] Open
Abstract
Background Drug resistance continues to be a major limiting factor across diverse anti-cancer therapies. Contributing to the complexity of this challenge is cancer plasticity, in which one cancer subtype switches to another in response to treatment, for example, triple-negative breast cancer (TNBC) to Her2-positive breast cancer. For optimal treatment outcomes, accurate tumor diagnosis and subsequent therapeutic decisions are vital. This study assessed a novel approach to characterize treatment-induced evolutionary changes of distinct tumor cell subpopulations to identify and therapeutically exploit anticancer drug resistance. Methods In this research, an information-theoretic single-cell quantification strategy was developed to provide a high-resolution and individualized assessment of tumor composition for a customized treatment approach. Briefly, this single-cell quantification strategy computes cell barcodes based on at least 100,000 tumor cells from each experiment and reveals a cell-specific signaling signature (CSSS) composed of a set of ongoing processes in each cell. Results Using these CSSS-based barcodes, distinct subpopulations evolving within the tumor in response to an outside influence, like anticancer treatments, were revealed and mapped. Barcodes were further applied to assign targeted drug combinations to each individual tumor to optimize tumor response to therapy. The strategy was validated using TNBC models and patient-derived tumors known to switch phenotypes in response to radiotherapy (RT). Conclusions We show that a barcode-guided targeted drug cocktail significantly enhances tumor response to RT and prevents regrowth of once-resistant tumors. The strategy presented herein shows promise in preventing cancer treatment resistance, with significant applicability in clinical use. Supplementary Information The online version contains supplementary material available at 10.1186/s13073-022-01121-y.
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Affiliation(s)
- Heba Alkhatib
- The institute of Biomedical and Oral Research, The Hebrew University of Jerusalem, 9103401, Jerusalem, Israel
| | - Ariel M Rubinstein
- The institute of Biomedical and Oral Research, The Hebrew University of Jerusalem, 9103401, Jerusalem, Israel
| | - Swetha Vasudevan
- The institute of Biomedical and Oral Research, The Hebrew University of Jerusalem, 9103401, Jerusalem, Israel
| | - Efrat Flashner-Abramson
- The institute of Biomedical and Oral Research, The Hebrew University of Jerusalem, 9103401, Jerusalem, Israel
| | - Shira Stefansky
- The institute of Biomedical and Oral Research, The Hebrew University of Jerusalem, 9103401, Jerusalem, Israel
| | - Sangita Roy Chowdhury
- The institute of Biomedical and Oral Research, The Hebrew University of Jerusalem, 9103401, Jerusalem, Israel
| | - Solomon Oguche
- The institute of Biomedical and Oral Research, The Hebrew University of Jerusalem, 9103401, Jerusalem, Israel
| | - Tamar Peretz-Yablonsky
- Sharett Institute of Oncology, Hebrew University-Hadassah Medical Center, 9103401, Jerusalem, Israel
| | - Avital Granit
- Sharett Institute of Oncology, Hebrew University-Hadassah Medical Center, 9103401, Jerusalem, Israel
| | - Zvi Granot
- Department of Developmental Biology and Cancer Research, Institute for Medical Research-Israel-Canada, The Hebrew University-Hadassah Medical School, 91120, Jerusalem, Israel
| | - Ittai Ben-Porath
- Department of Developmental Biology and Cancer Research, Institute for Medical Research-Israel-Canada, The Hebrew University-Hadassah Medical School, 91120, Jerusalem, Israel
| | - Kim Sheva
- The Legacy Heritage Oncology Center & Dr. Larry Norton Institute, Soroka University Medical Center, Ben Gurion University of the Negev, Faculty of Medicine, 8410101, Beer Sheva, Israel
| | - Jon Feldman
- Sharett Institute of Oncology, Hebrew University-Hadassah Medical Center, 9103401, Jerusalem, Israel
| | - Noa E Cohen
- School of Software Engineering and Computer Science, Azrieli College of Engineering, 9103501, Jerusalem, Israel
| | - Amichay Meirovitz
- The Legacy Heritage Oncology Center & Dr. Larry Norton Institute, Soroka University Medical Center, Ben Gurion University of the Negev, Faculty of Medicine, 8410101, Beer Sheva, Israel.
| | - Nataly Kravchenko-Balasha
- The institute of Biomedical and Oral Research, The Hebrew University of Jerusalem, 9103401, Jerusalem, Israel.
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10
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Jubran MR, Vilenski D, Flashner-Abramson E, Shnaider E, Vasudevan S, Rubinstein AM, Meirovitz A, Sharon S, Polak D, Kravchenko-Balasha N. Overcoming resistance to EGFR monotherapy in HNSCC by identification and inhibition of individualized cancer processes. Am J Cancer Res 2022; 12:1204-1219. [PMID: 35154483 PMCID: PMC8771558 DOI: 10.7150/thno.64347] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [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: 06/28/2021] [Accepted: 12/01/2021] [Indexed: 11/11/2022] Open
Abstract
Therapeutic strategies for advanced head and neck squamous carcinoma (HNSCC) consist of multimodal treatment, including Epidermal Growth Factor Receptor (EGFR) inhibition, immune-checkpoint inhibition, and radio (chemo) therapy. Although over 90% of HNSCC tumors overexpress EGFR, attempts to replace cytotoxic treatments with anti-EGFR agents have failed due to alternative signaling pathways and inter-tumor heterogeneity. Methods: Using protein expression data obtained from hundreds of HNSCC tissues and cell lines we compute individualized signaling signatures using an information-theoretic approach. The approach maps each HNSCC malignancy according to the protein-protein network reorganization in every tumor. We show that each patient-specific signaling signature (PaSSS) includes several distinct altered signaling subnetworks. Based on the resolved PaSSSs we design personalized drug combinations. Results: We show that simultaneous targeting of central hub proteins from each altered subnetwork is essential to selectively enhance the response of HNSCC tumors to anti-EGFR therapy and inhibit tumor growth. Furthermore, we demonstrate that the PaSSS-based drug combinations lead to induced expression of T cell markers and IFN-γ secretion, pointing to higher efficiency of the immune response. Conclusion: The PaSSS-based approach advances our understanding of how individualized therapies should be tailored to HNSCC tumors.
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11
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Sharon S, Duhen T, Bambina S, Baird J, Leidner R, Bell B, Casap N, Crittenden M, Vasudevan S, Jubran M, Kravchenko-Balasha N, Gough M. Explant Modeling of the Immune Environment of Head and Neck Cancer. Front Oncol 2021; 11:611365. [PMID: 34221953 PMCID: PMC8249923 DOI: 10.3389/fonc.2021.611365] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2020] [Accepted: 05/25/2021] [Indexed: 01/10/2023] Open
Abstract
Patients exhibit distinct responses to immunotherapies that are thought to be linked to their tumor immune environment. However, wide variations in outcomes are also observed in patients with matched baseline tumor environments, indicating that the biological response to treatment is not currently predictable using a snapshot analysis. To investigate the relationship between the immune environment of tumors and the biological response to immunotherapies, we characterized four murine head and neck squamous cell carcinoma (HNSCC) models on two genetic backgrounds. Using tumor explants from those models, we identified correlations between the composition of infiltrating immune cells and baseline cytokine profiles prior to treatment. Following treatment with PD-1 blockade, CTLA-4 blockade, or OX40 stimulation, we observed inter-individual variability in the response to therapy between genetically identical animals bearing the same tumor. These distinct biological responses to treatment were not linked to the initial tumor immune environment, meaning that outcome would not be predictable from a baseline analysis of the tumor infiltrates. We similarly performed the explant assay on patient HNSCC tumors and found significant variability between the baseline environment of the tumors and their response to therapy. We propose that tumor explants provide a rapid biological assay to assess response to candidate immunotherapies that may allow matching therapies to individual patient tumors. Further development of explant approaches may allow screening and monitoring of treatment responses in HNSCC.
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Affiliation(s)
- Shay Sharon
- Department of Oral and Maxillofacial Surgery, Hadassah and Hebrew University Medical Center, Jerusalem, Israel
| | - Thomas Duhen
- Earle A. Chiles Research Institute, Robert W. Franz Cancer Center, Providence Portland Medical Center, Portland, OR, United States
| | - Shelly Bambina
- Earle A. Chiles Research Institute, Robert W. Franz Cancer Center, Providence Portland Medical Center, Portland, OR, United States
| | - Jason Baird
- Earle A. Chiles Research Institute, Robert W. Franz Cancer Center, Providence Portland Medical Center, Portland, OR, United States
| | - Rom Leidner
- Earle A. Chiles Research Institute, Robert W. Franz Cancer Center, Providence Portland Medical Center, Portland, OR, United States
| | - Bryan Bell
- Earle A. Chiles Research Institute, Robert W. Franz Cancer Center, Providence Portland Medical Center, Portland, OR, United States
| | - Nardy Casap
- Department of Oral and Maxillofacial Surgery, Hadassah and Hebrew University Medical Center, Jerusalem, Israel
| | - Marka Crittenden
- Earle A. Chiles Research Institute, Robert W. Franz Cancer Center, Providence Portland Medical Center, Portland, OR, United States
- The Oregon Clinic, Portland, OR, United States
| | - Swetha Vasudevan
- The Institute of Biomedical and Oral Research, Hebrew University of Jerusalem, Jerusalem, Israel
| | - Maria Jubran
- The Institute of Biomedical and Oral Research, Hebrew University of Jerusalem, Jerusalem, Israel
| | | | - Michael Gough
- Earle A. Chiles Research Institute, Robert W. Franz Cancer Center, Providence Portland Medical Center, Portland, OR, United States
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12
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Vasudevan S, Flashner-Abramson E, Alkhatib H, Roy Chowdhury S, Adejumobi IA, Vilenski D, Stefansky S, Rubinstein AM, Kravchenko-Balasha N. Overcoming resistance to BRAF V600E inhibition in melanoma by deciphering and targeting personalized protein network alterations. NPJ Precis Oncol 2021; 5:50. [PMID: 34112933 PMCID: PMC8192524 DOI: 10.1038/s41698-021-00190-3] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2020] [Accepted: 05/13/2021] [Indexed: 12/11/2022] Open
Abstract
BRAFV600E melanoma patients, despite initially responding to the clinically prescribed anti-BRAFV600E therapy, often relapse, and their tumors develop drug resistance. While it is widely accepted that these tumors are originally driven by the BRAFV600E mutation, they often eventually diverge and become supported by various signaling networks. Therefore, patient-specific altered signaling signatures should be deciphered and treated individually. In this study, we design individualized melanoma combination treatments based on personalized network alterations. Using an information-theoretic approach, we compute high-resolution patient-specific altered signaling signatures. These altered signaling signatures each consist of several co-expressed subnetworks, which should all be targeted to optimally inhibit the entire altered signaling flux. Based on these data, we design smart, personalized drug combinations, often consisting of FDA-approved drugs. We validate our approach in vitro and in vivo showing that individualized drug combinations that are rationally based on patient-specific altered signaling signatures are more efficient than the clinically used anti-BRAFV600E or BRAFV600E/MEK targeted therapy. Furthermore, these drug combinations are highly selective, as a drug combination efficient for one BRAFV600E tumor is significantly less efficient for another, and vice versa. The approach presented herein can be broadly applicable to aid clinicians to rationally design patient-specific anti-melanoma drug combinations.
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Affiliation(s)
- S Vasudevan
- The Institute of Biomedical and Oral Research, Hebrew University of Jerusalem, Jerusalem, Israel
| | - E Flashner-Abramson
- The Institute of Biomedical and Oral Research, Hebrew University of Jerusalem, Jerusalem, Israel
| | - Heba Alkhatib
- The Institute of Biomedical and Oral Research, Hebrew University of Jerusalem, Jerusalem, Israel
| | - Sangita Roy Chowdhury
- The Institute of Biomedical and Oral Research, Hebrew University of Jerusalem, Jerusalem, Israel
| | - I A Adejumobi
- The Institute of Biomedical and Oral Research, Hebrew University of Jerusalem, Jerusalem, Israel
| | - D Vilenski
- The Institute of Biomedical and Oral Research, Hebrew University of Jerusalem, Jerusalem, Israel
| | - S Stefansky
- The Institute of Biomedical and Oral Research, Hebrew University of Jerusalem, Jerusalem, Israel
| | - A M Rubinstein
- The Institute of Biomedical and Oral Research, Hebrew University of Jerusalem, Jerusalem, Israel
| | - N Kravchenko-Balasha
- The Institute of Biomedical and Oral Research, Hebrew University of Jerusalem, Jerusalem, Israel.
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13
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Zahavi T, Salmon-Divon M, Salgado R, Elkin M, Hermano E, Rubinstein AM, Francis PA, Di Leo A, Viale G, de Azambuja E, Ameye L, Sotiriou C, Salmon A, Kravchenko-Balasha N, Sonnenblick A. Heparanase: a potential marker of worse prognosis in estrogen receptor-positive breast cancer. NPJ Breast Cancer 2021; 7:67. [PMID: 34050190 PMCID: PMC8163849 DOI: 10.1038/s41523-021-00277-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2020] [Accepted: 05/11/2021] [Indexed: 01/09/2023] Open
Abstract
Heparanase promotes tumor growth in breast tumors. We now evaluated heparanase protein and gene-expression status and investigated its impact on disease-free survival in order to gain better insight into the role of heparanase in ER-positive (ER+) breast cancer prognosis and to clarify its role in cell survival following chemotherapy. Using pooled analysis of gene-expression data, we found that heparanase was associated with a worse prognosis in estrogen receptor-positive (ER+) tumors (log-rank p < 10-10) and predictive to chemotherapy resistance (interaction p = 0.0001) but not hormonal therapy (Interaction p = 0.62). These results were confirmed by analysis of data from a phase III, prospective randomized trial which showed that heparanase protein expression is associated with increased risk of recurrence in ER+ breast tumors (log-rank p = 0.004). In vitro experiments showed that heparanase promoted tumor progression and increased cell viability via epithelial-mesenchymal transition, stemness, and anti-apoptosis pathways in luminal breast cancer. Taken together, our results demonstrated that heparanase is associated with worse outcomes and increased cell viability in ER+ BC.
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Affiliation(s)
- Tamar Zahavi
- Tel Aviv Sourasky Medical Center, Tel Aviv, Israel
- Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
- Department of Molecular Biology, Adelson School of Medicine, Ariel University, Ariel, Israel
| | - Mali Salmon-Divon
- Department of Molecular Biology, Adelson School of Medicine, Ariel University, Ariel, Israel
| | - Roberto Salgado
- Division of Research, Peter MacCallum Cancer Centre, Melbourne, VIC, Australia
- Department of Pathology, GZA-ZNA Hospitals, Antwerp, Belgium
| | - Michael Elkin
- Department of Oncology, Hadassah Medical Organization and Faculty of Medicine, Hebrew University of Jerusalem, Jerusalem, Israel
| | - Esther Hermano
- Department of Oncology, Hadassah Medical Organization and Faculty of Medicine, Hebrew University of Jerusalem, Jerusalem, Israel
| | - Ariel M Rubinstein
- The Institute of Biomedical and Oral Research, Hebrew University of Jerusalem, Jerusalem, Israel
| | - Prudence A Francis
- Peter MacCallum Cancer Centre, University of Melbourne, Melbourne, VIC, Australia
- Breast Cancer Trials Australia & New Zealand, Newcastle, NSW, Australia
- International Breast Cancer Study Group, Bern, Switzerland
| | - Angelo Di Leo
- Sandro Pitigliani Department of Medical Oncology, Hospital of Prato, Prato, Italy
| | - Giuseppe Viale
- The University of Milan, and IEO European Institute of Oncology IRCCS, Milan, Italy
| | - Evandro de Azambuja
- Institut Jules Bordet and l'Université Libre de Bruxelles (U.L.B), Brussels, Belgium
| | - Lieveke Ameye
- Institut Jules Bordet and l'Université Libre de Bruxelles (U.L.B), Brussels, Belgium
| | - Christos Sotiriou
- Institut Jules Bordet and l'Université Libre de Bruxelles (U.L.B), Brussels, Belgium
| | | | | | - Amir Sonnenblick
- Tel Aviv Sourasky Medical Center, Tel Aviv, Israel.
- Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel.
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14
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Dagan H, Flashner-Abramson E, Vasudevan S, Jubran MR, Cohen E, Kravchenko-Balasha N. Exploring Alzheimer's Disease Molecular Variability via Calculation of Personalized Transcriptional Signatures. Biomolecules 2020; 10:biom10040503. [PMID: 32225014 PMCID: PMC7226317 DOI: 10.3390/biom10040503] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [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: 01/30/2020] [Revised: 03/23/2020] [Accepted: 03/24/2020] [Indexed: 12/27/2022] Open
Abstract
Despite huge investments and major efforts to develop remedies for Alzheimer’s disease (AD) in the past decades, AD remains incurable. While evidence for molecular and phenotypic variability in AD have been accumulating, AD research still heavily relies on the search for AD-specific genetic/protein biomarkers that are expected to exhibit repetitive patterns throughout all patients. Thus, the classification of AD patients to different categories is expected to set the basis for the development of therapies that will be beneficial for subpopulations of patients. Here we explore the molecular heterogeneity among a large cohort of AD and non-demented brain samples, aiming to address the question whether AD-specific molecular biomarkers can progress our understanding of the disease and advance the development of anti-AD therapeutics. We studied 951 brain samples, obtained from up to 17 brain regions of 85 AD patients and 22 non-demented subjects. Utilizing an information-theoretic approach, we deciphered the brain sample-specific structures of altered transcriptional networks. Our in-depth analysis revealed that 7 subnetworks were repetitive in the 737 diseased and 214 non-demented brain samples. Each sample was characterized by a subset consisting of ~1–3 subnetworks out of 7, generating 52 distinct altered transcriptional signatures that characterized the 951 samples. We show that 30 different altered transcriptional signatures characterized solely AD samples and were not found in any of the non-demented samples. In contrast, the rest of the signatures characterized different subsets of sample types, demonstrating the high molecular variability and complexity of gene expression in AD. Importantly, different AD patients exhibiting similar expression levels of AD biomarkers harbored distinct altered transcriptional networks. Our results emphasize the need to expand the biomarker-based stratification to patient-specific transcriptional signature identification for improved AD diagnosis and for the development of subclass-specific future treatment.
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Affiliation(s)
- Hila Dagan
- The Rachel and Selim Benin School of Computer Science and Engineering, Hebrew University, Jerusalem 9190416, Israel;
| | - Efrat Flashner-Abramson
- Department for Bio-Medical Research, Faculty of Dental Medicine, Hebrew University of Jerusalem, Jerusalem 91120, Israel; (E.F.-A.); (S.V.); (M.R.J.)
| | - Swetha Vasudevan
- Department for Bio-Medical Research, Faculty of Dental Medicine, Hebrew University of Jerusalem, Jerusalem 91120, Israel; (E.F.-A.); (S.V.); (M.R.J.)
| | - Maria R. Jubran
- Department for Bio-Medical Research, Faculty of Dental Medicine, Hebrew University of Jerusalem, Jerusalem 91120, Israel; (E.F.-A.); (S.V.); (M.R.J.)
| | - Ehud Cohen
- Department of Biochemistry and Molecular Biology, The Institute for Medical Research Israel—Canada, The Hebrew University School of Medicine, Jerusalem 9112102, Israel;
| | - Nataly Kravchenko-Balasha
- Department for Bio-Medical Research, Faculty of Dental Medicine, Hebrew University of Jerusalem, Jerusalem 91120, Israel; (E.F.-A.); (S.V.); (M.R.J.)
- Correspondence:
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15
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Kravchenko-Balasha N. Translating Cancer Molecular Variability into Personalized Information Using Bulk and Single Cell Approaches. Proteomics 2020; 20:e1900227. [PMID: 32072740 DOI: 10.1002/pmic.201900227] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2019] [Revised: 01/13/2020] [Indexed: 12/17/2022]
Abstract
Cancer research is striving toward new frontiers of assigning the correct personalized drug(s) to a given patient. However, extensive tumor heterogeneity poses a major obstacle. Tumors of the same type often respond differently to therapy, due to patient-specific molecular aberrations and/or untargeted tumor subpopulations. It is frequently not possible to determine a priori which patients will respond to a certain therapy or how an efficient patient-specific combined therapy should be designed. Large-scale datasets have been growing at an accelerated pace and various technologies and analytical tools for single cell and bulk level analyses are being developed to extract significant individualized signals from such heterogeneous data. However, personalized therapies that dramatically alter the course of the disease remain scarce, and most tumors still respond poorly to medical care. In this review, the basic concepts of bulk and single cell approaches are discussed, as well as their emerging role in individualized designs of drug therapies, including the advantages and limitations of their applications in personalized medicine.
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Affiliation(s)
- Nataly Kravchenko-Balasha
- Department for Bio-Medical Research, Faculty of Dental Medicine, Hebrew University of Jerusalem, Jerusalem, 91120, Israel
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16
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Flashner-Abramson E, Vasudevan S, Adejumobi IA, Sonnenblick A, Kravchenko-Balasha N. Decoding cancer heterogeneity: studying patient-specific signaling signatures towards personalized cancer therapy. Theranostics 2019; 9:5149-5165. [PMID: 31410207 PMCID: PMC6691586 DOI: 10.7150/thno.31657] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [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: 11/20/2018] [Accepted: 05/05/2019] [Indexed: 01/25/2023] Open
Abstract
The past years have witnessed a rapid increase in the amount of large-scale tumor datasets. The challenge has now become to find a way to obtain useful information from these masses of data that will allow to determine which combination of FDA-approved drugs is best suited to treat the specific tumor. Various statistical analyses are being developed to extract significant signals from cancer datasets. However, tumors are still being assigned to pre-defined categories (breast luminal A, triple negative, etc.), conceptually contradicting the vast heterogeneity that is known to exist among tumors, and likely overlooking unique tumors that must be addressed and treated individually. We present herein an approach based on information theory that, rather than searches for what makes a tumor similar to other tumors, addresses tumors individually and unbiasedly, and impartially decodes the critical patient-specific molecular network reorganization in every tumor. Methods: Using a large dataset obtained from ~3500 tumors of 11 types we decipher the altered protein network structure in each tumor, namely the patient-specific signaling signature. Each signature can harbor several altered protein subnetworks. We suggest that simultaneous targeting of central proteins from every altered subnetwork is essential to efficiently disturb the altered signaling in each tumor. We experimentally validate our ability to dissect sample-specific signaling signatures and to rationally design personalized drug combinations. Results: We unraveled a surprisingly simple order that underlies the extreme apparent complexity of tumor tissues, demonstrating that only 17 altered protein subnetworks characterize ~3500 tumors of 11 types. Each tumor was described by a specific subset of 1-4 subnetworks out of 17, i.e. a tumor-specific altered signaling signature. We show that the majority of tumor-specific signaling signatures are extremely rare, and are shared by only 5 tumors or less, supporting a personalized, comprehensive study of tumors in order to design the optimal combination therapy for every patient. We validate the results by confirming that the processes identified in the 11 original cancer types characterize patients harboring a different cancer type as well. We show experimentally, using different cancer cell lines, that the individualized combination therapies predicted by us achieved higher rates of killing than the clinically prescribed treatments. Conclusions: We present a new strategy to deal with the inter-tumor heterogeneity and to break down the high complexity of cancer systems into simple, easy to crack, patient-specific signaling signatures that guide the rational design of personalized drug therapies.
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17
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Kravchenko-Balasha N, Aframian DJ. A novel strategy for diagnosing viral vs
bacterial infection: implications for oral diseases. Oral Dis 2018; 24:491-493. [DOI: 10.1111/odi.12629] [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] [Received: 12/16/2016] [Revised: 12/20/2016] [Accepted: 12/20/2016] [Indexed: 11/26/2022]
Affiliation(s)
- N Kravchenko-Balasha
- Bio-Medical Sciences Department; Institute of Dental Sciences; Faculty of Dental Medicine; The Hebrew University; Jerusalem Israel
| | - DJ Aframian
- Department of Oral Medicine, Sedation and Maxillofacial Imaging; Faculty of Dental Medicine; Hadassah Medical Center; The Hebrew University; Jerusalem Israel
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18
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Kravchenko-Balasha N, Johnson H, White FM, Heath JR, Levine RD. A Thermodynamic-Based Interpretation of Protein Expression Heterogeneity in Different Glioblastoma Multiforme Tumors Identifies Tumor-Specific Unbalanced Processes. J Phys Chem B 2016; 120:5990-7. [PMID: 27035264 DOI: 10.1021/acs.jpcb.6b01692] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
We describe a thermodynamic-motivated, information theoretic analysis of proteomic data collected from a series of 8 glioblastoma multiforme (GBM) tumors. GBMs are considered here as prototypes of heterogeneous cancers. That heterogeneity is viewed here as manifesting in different unbalanced biological processes that are associated with thermodynamic-like constraints. The analysis yields a molecular description of a stable steady state that is common across all tumors. It also resolves molecular descriptions of unbalanced processes that are shared by several tumors, such as hyperactivated phosphoprotein signaling networks. Further, it resolves unbalanced processes that provide unique classifiers of tumor subgroups. The results of the theoretical interpretation are compared against those of statistical multivariate methods and are shown to provide a superior level of resolution for identifying unbalanced processes in GBM tumors. The identification of specific constraints for each GBM tumor suggests tumor-specific combination therapies that may reverse this imbalance.
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Affiliation(s)
- Nataly Kravchenko-Balasha
- NanoSystems Biology Cancer Center, Division of Chemistry, Caltech , Pasadena, California 91125, United States.,Bio-Medical Sciences Department, The Faculty of Dental Medicine, The Hebrew University of Jerusalem , Jerusalem 9112001, Israel
| | - Hannah Johnson
- Signaling Programme, The Babraham Institute , Cambridge CB22 3AT, United Kingdom
| | - Forest M White
- Department of Biological Engineering, MIT , Cambridge, Massachusetts 02139, United States
| | - James R Heath
- NanoSystems Biology Cancer Center, Division of Chemistry, Caltech , Pasadena, California 91125, United States
| | - R D Levine
- Department of Molecular and Medical Pharmacology, David Geffen School of Medicine and Department of Chemistry and Biochemistry, UCLA , Los Angeles, California 90095, United States.,The Institute of Chemistry, The Hebrew University of Jerusalem , Jerusalem 91904, Israel
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19
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Poovathingal SK, Kravchenko-Balasha N, Shin YS, Levine RD, Heath JR. Critical Points in Tumorigenesis: A Carcinogen-Initiated Phase Transition Analyzed via Single-Cell Proteomics. Small 2016; 12:1425-31. [PMID: 26780498 PMCID: PMC4886749 DOI: 10.1002/smll.201501178] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/27/2015] [Revised: 11/09/2015] [Indexed: 05/06/2023]
Abstract
A kinetic, single-cell proteomic study of chemically induced carcinogenesis is interpreted by treating the single-cell data as fluctuations of an open system transitioning between different steady states. In analogy to a first-order transition, phase coexistence and the loss of degrees of freedom are observed. The transition is detected well before the appearance of the traditional biomarker of the carcinogenic transformation.
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Affiliation(s)
- Suresh Kumar Poovathingal
- Division of Chemistry and Chemical Engineering, California Institute of Technology, MC 127-72, 1200 E. California Blvd, Pasadena, CA, 91125, USA
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Esch-sur-Alzette, L-4362, Luxembourg
| | - Nataly Kravchenko-Balasha
- Division of Chemistry and Chemical Engineering, California Institute of Technology, MC 127-72, 1200 E. California Blvd, Pasadena, CA, 91125, USA
- Department of Bio-Medical Sciences, Faculty of Dental Medicine, Hebrew University of Jerusalem, Jerusalem, 91120, Israel
| | - Young Shik Shin
- Division of Chemistry and Chemical Engineering, California Institute of Technology, MC 127-72, 1200 E. California Blvd, Pasadena, CA, 91125, USA
| | - Raphael David Levine
- Institute of Chemistry, The Hebrew University of Jerusalem, Jerusalem, 91904, Israel
- Department of Molecular and Medical Pharmacology, David Geffen School of Medicine, University of California, Los Angeles, CA, 90095, USA
| | - James R Heath
- Division of Chemistry and Chemical Engineering, California Institute of Technology, MC 127-72, 1200 E. California Blvd, Pasadena, CA, 91125, USA
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20
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Kravchenko-Balasha N, Simon S, Levine RD, Remacle F, Exman I. Computational surprisal analysis speeds-up genomic characterization of cancer processes. PLoS One 2014; 9:e108549. [PMID: 25405334 PMCID: PMC4236016 DOI: 10.1371/journal.pone.0108549] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2014] [Accepted: 08/31/2014] [Indexed: 01/18/2023] Open
Abstract
Surprisal analysis is increasingly being applied for the examination of transcription levels in cellular processes, towards revealing inner network structures and predicting response. But to achieve its full potential, surprisal analysis should be integrated into a wider range computational tool. The purposes of this paper are to combine surprisal analysis with other important computation procedures, such as easy manipulation of the analysis results – e.g. to choose desirable result sub-sets for further inspection –, retrieval and comparison with relevant datasets from public databases, and flexible graphical displays for heuristic thinking. The whole set of computation procedures integrated into a single practical tool is what we call Computational Surprisal Analysis. This combined kind of analysis should facilitate significantly quantitative understanding of different cellular processes for researchers, including applications in proteomics and metabolomics. Beyond that, our vision is that Computational Surprisal Analysis has the potential to reach the status of a routine method of analysis for practitioners. The resolving power of Computational Surprisal Analysis is here demonstrated by its application to a variety of cellular cancer process transcription datasets, ours and from the literature. The results provide a compact biological picture of the thermodynamic significance of the leading gene expression phenotypes in every stage of the disease. For each transcript we characterize both its inherent steady state weight, its correlation with the other transcripts and its variation due to the disease. We present a dedicated website to facilitate the analysis for researchers and practitioners.
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Affiliation(s)
- Nataly Kravchenko-Balasha
- NanoSystems Biology Cancer Center, Division of Chemistry, Caltech, Pasadena, California, United States of America
| | - Simcha Simon
- Software Engineering Department, The Jerusalem College of Engineering, Azrieli, Jerusalem, Israel
| | - R. D. Levine
- The Institute of Chemistry, The Hebrew University, Jerusalem, Israel
- Department of Molecular and Medical Pharmacology, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, California, United States of America
| | - F. Remacle
- The Institute of Chemistry, The Hebrew University, Jerusalem, Israel
- Département de Chimie, Université de Liège, Liège, Belgium
| | - Iaakov Exman
- Software Engineering Department, The Jerusalem College of Engineering, Azrieli, Jerusalem, Israel
- * E-mail:
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Cohen N, Kravchenko-Balasha N, Klein S, Levitzki A. Heterogeneity of gene expression in murine squamous cell carcinoma development-the same tumor by different means. PLoS One 2013; 8:e57748. [PMID: 23526950 PMCID: PMC3601100 DOI: 10.1371/journal.pone.0057748] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2012] [Accepted: 01/25/2013] [Indexed: 02/04/2023] Open
Abstract
Transformation is a complex process, involving many changes in the cell. In this work, we investigated the transcriptional changes that arose during the development of squamous cell carcinoma (SCC) in mice. Using microarray analysis, we looked at gene expression during different stages in cancer progression in 31 mice. By analyzing tumor progression in each mouse separately, we were able to define the global changes that were common to all 31 mice, as well as significant changes that occurred in fewer individuals. We found that different genes can contribute to the tumorigenic process in different mice, and that there are many ways to acquire the malignant properties defined by Hanahan and Weinberg as "hallmarks of cancer". Eventually, however, all these changes lead to a very similar cancerous phenotype. The finding that gene expression is strongly heterogeneous in tumors that were induced by a standardized protocol in closely related mice underscores the need for molecular characterization of human tumors and personalized therapy.
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Affiliation(s)
- Noam Cohen
- Unit of Cellular Signaling, Department of Biological Chemistry, The Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Nataly Kravchenko-Balasha
- Unit of Cellular Signaling, Department of Biological Chemistry, The Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Shoshana Klein
- Unit of Cellular Signaling, Department of Biological Chemistry, The Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Alexander Levitzki
- Unit of Cellular Signaling, Department of Biological Chemistry, The Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem, Israel
- * E-mail:
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Mizrachy-Schwartz S, Cohen N, Klein S, Kravchenko-Balasha N, Levitzki A. Up-regulation of AMP-activated protein kinase in cancer cell lines is mediated through c-Src activation. J Biol Chem 2011; 286:15268-77. [PMID: 21245141 PMCID: PMC3083231 DOI: 10.1074/jbc.m110.211813] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2010] [Indexed: 01/01/2023] Open
Abstract
We report that the activation level of AMP-dependent protein kinase AMPK is elevated in cancer cell lines as a hallmark of their transformed state. In OVCAR3 and A431 cells, c-Src signals through protein kinase Cα, phospholipase Cγ, and LKB1 to AMPK. AMPK controls internal ribosome entry site (IRES) dependent translation in these cells. We suggest that AMPK activation via PKC might be a general mechanism to regulate IRES-dependent translation in cancer cells.
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Affiliation(s)
- Sarit Mizrachy-Schwartz
- From the Unit of Cellular Signaling, Department of Biological Chemistry, The Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem 91904, Israel
| | - Noam Cohen
- From the Unit of Cellular Signaling, Department of Biological Chemistry, The Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem 91904, Israel
| | - Shoshana Klein
- From the Unit of Cellular Signaling, Department of Biological Chemistry, The Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem 91904, Israel
| | - Nataly Kravchenko-Balasha
- From the Unit of Cellular Signaling, Department of Biological Chemistry, The Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem 91904, Israel
| | - Alexander Levitzki
- From the Unit of Cellular Signaling, Department of Biological Chemistry, The Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem 91904, Israel
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Kravchenko-Balasha N, Remacle F, Gross A, Rotter V, Levitzki A, Levine RD. Convergence of logic of cellular regulation in different premalignant cells by an information theoretic approach. BMC Syst Biol 2011; 5:42. [PMID: 21410932 PMCID: PMC3072338 DOI: 10.1186/1752-0509-5-42] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/21/2010] [Accepted: 03/16/2011] [Indexed: 11/10/2022]
Abstract
BACKGROUND Surprisal analysis is a thermodynamic-like molecular level approach that identifies biological constraints that prevents the entropy from reaching its maximum. To examine the significance of altered gene expression levels in tumorigenesis we apply surprisal analysis to the WI-38 model through its precancerous states. The constraints identified by the analysis are transcription patterns underlying the process of transformation. Each pattern highlights the role of a group of genes that act coherently to define a transformed phenotype. RESULTS We identify a major transcription pattern that represents a contraction of signaling networks accompanied by induction of cellular proliferation and protein metabolism, which is essential for full transformation. In addition, a more minor, "tumor signature" transcription pattern completes the transformation process. The variation with time of the importance of each transcription pattern is determined. Midway through the transformation, at the stage when cells switch from slow to fast growth rate, the major transcription pattern undergoes a total inversion of its weight while the more minor pattern does not contribute before that stage. CONCLUSIONS A similar network reorganization occurs in two very different cellular transformation models: WI-38 and the cervical cancer HF1 models. Our results suggest that despite differences in a list of transcripts expressed in different cancer models the rationale of the network reorganization remains essentially the same.
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Affiliation(s)
- Nataly Kravchenko-Balasha
- Unit of Cellular Signaling, Department of Biological Chemistry, The Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem 91904, Israel
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Kravchenko-Balasha N, Klein S, Safrai M, Levitzki A. Contribution of gross chromosomal changes to HPV16-induced transformation. Mol BioSyst 2011; 7:1501-11. [DOI: 10.1039/c0mb00284d] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
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Mizrachy-Schwartz S, Cohen N, Klein S, Kravchenko-Balasha N, Levitzki A. Amino acid starvation sensitizes cancer cells to proteasome inhibition. IUBMB Life 2010; 62:757-63. [DOI: 10.1002/iub.377] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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Kravchenko-Balasha N, Mizrachy-Schwartz S, Klein S, Levitzki A. Shift from apoptotic to necrotic cell death during human papillomavirus-induced transformation of keratinocytes. J Biol Chem 2009; 284:11717-27. [PMID: 19221178 DOI: 10.1074/jbc.m900217200] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
Oncogenic transformation is a complex, multistep process, which goes through several stages before complete malignant transformation occurs. To identify early processes in carcinogenesis, we used an in vitro model, based on the initiating event in cervical cancer, papillomavirus transformation of keratinocytes. We compared gene expression in primary keratinocytes (K) and papillomavirus-transformed keratinocytes from early (E) and late (L) passages and from benzo[a]pyrene-treated L cells (BP). The transformed cells exhibit similar transcriptional changes to clinical cervical carcinoma. The number of transcripts expressed progressively decreased during the evolution from K to BP cells. Bioinformatic analysis, validated by detailed biochemical analysis, revealed substantial contraction of both pro- and antiapoptotic networks during transformation. Nonetheless, L and BP cells were not resistant to apoptotic stimuli. At doses of cisplatin that led to 30-60% apoptosis of K and E cells, transformed L and BP cells underwent 80% necrotic cell death, which became the default response to genotoxic stress. Moreover, appreciable necrotic fractions were observed in the cervical carcinoma cell line, HeLa, in response to comparable doses of cisplatin. The shrinkage of biochemical networks, including the apoptotic network, may allow a cancer cell to economize on energy usage to facilitate enhanced proliferation but leaves it vulnerable to stress. This study supports the hypothesis that the process of cancer transformation may be accompanied by a shift from apoptosis to necrosis.
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Affiliation(s)
- Nataly Kravchenko-Balasha
- Unit of Cellular Signaling, Department of Biological Chemistry, Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Safra Campus, Givat Ram, Jerusalem 91904, Israel
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Geiger T, Sabanay H, Kravchenko-Balasha N, Geiger B, Levitzki A. Anomalous features of EMT during keratinocyte transformation. PLoS One 2008; 3:e1574. [PMID: 18253510 PMCID: PMC2215777 DOI: 10.1371/journal.pone.0001574] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2007] [Accepted: 01/09/2008] [Indexed: 12/28/2022] Open
Abstract
During the evolution of epithelial cancers, cells often lose their characteristic features and acquire a mesenchymal phenotype, in a process known as epithelial-mesenchymal transition (EMT). In the present study we followed early stages of keratinocyte transformation by HPV16, and observed diverse cellular changes, associated with EMT. We compared primary keratinocytes with early and late passages of HF1 cells, a cell line of HPV16-transformed keratinocytes. We have previously shown that during the progression from the normal cells to early HF1 cells, immortalization is acquired, while in the progression to late HF1, cells become anchorage independent. We show here that during the transition from the normal state to late HF1 cells, there is a progressive reduction in cytokeratin expression, desmosome formation, adherens junctions and focal adhesions, ultimately leading to poorly adhesive phenotype, which is associated with anchorage-independence. Surprisingly, unlike "conventional EMT", these changes are associated with reduced Rac1-dependent cell migration. We monitored reduced Rac1-dependent migration also in the cervical cancer cell line SiHa. Therefore we can conclude that up to the stage of tumor formation migratory activity is eliminated.
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Affiliation(s)
- Tamar Geiger
- Department of Biological Chemistry, Institute of Life Science, The Hebrew University, Jerusalem, Israel
| | - Helena Sabanay
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Nataly Kravchenko-Balasha
- Department of Biological Chemistry, Institute of Life Science, The Hebrew University, Jerusalem, Israel
| | - Benjamin Geiger
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Alexander Levitzki
- Department of Biological Chemistry, Institute of Life Science, The Hebrew University, Jerusalem, Israel
- * To whom correspondence should be addressed. E-mail:
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Mizrachy-Schwartz S, Kravchenko-Balasha N, Ben-Bassat H, Klein S, Levitzki A. Optimization of energy-consuming pathways towards rapid growth in HPV-transformed cells. PLoS One 2007; 2:e628. [PMID: 17622357 PMCID: PMC1913554 DOI: 10.1371/journal.pone.0000628] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2007] [Accepted: 06/26/2007] [Indexed: 12/16/2022] Open
Abstract
Cancer is a complex, multi-step process characterized by misregulated signal transduction and altered metabolism. Cancer cells divide faster than normal cells and their growth rates have been reported to correlate with increased metabolic flux during cell transformation. Here we report on progressive changes in essential elements of the biochemical network, in an in vitro model of transformation, consisting of primary human keratinocytes, human keratinocytes immortalized by human papillomavirus 16 (HPV16) and passaged repeatedly in vitro, and the extensively-passaged cells subsequently treated with the carcinogen benzo[a]pyrene. We monitored changes in cell growth, cell size and energy metabolism. The more transformed cells were smaller and divided faster, but the cellular energy flux was unchanged. During cell transformation the protein synthesis network contracted, as shown by the reduction in key cap-dependent translation factors. Moreover, there was a progressive shift towards internal ribosome entry site (IRES)-dependent translation. The switch from cap to IRES-dependent translation correlated with progressive activation of c-Src, an activator of AMP-activated protein kinase (AMPK), which controls energy-consuming processes, including protein translation. As cellular protein synthesis is a major energy-consuming process, we propose that the reduction in cell size and protein amount provide energy required for cell survival and proliferation. The cap to IRES-dependent switch seems to be part of a gradual optimization of energy-consuming mechanisms that redirects cellular processes to enhance cell growth, in the course of transformation.
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Affiliation(s)
- Sarit Mizrachy-Schwartz
- Unit of Cellular Signaling, Department of Biological Chemistry, The Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Nataly Kravchenko-Balasha
- Unit of Cellular Signaling, Department of Biological Chemistry, The Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Hannah Ben-Bassat
- The Laboratory of Experimental Surgery, Hadassah University Hospital, Jerusalem, Israel
- The Israel National Skin Bank, Hadassah University Hospital, Jerusalem, Israel
| | - Shoshana Klein
- Unit of Cellular Signaling, Department of Biological Chemistry, The Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Alexander Levitzki
- Unit of Cellular Signaling, Department of Biological Chemistry, The Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem, Israel
- * To whom correspondence should be addressed. E-mail:
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