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Billingsley JL, Yevdokimova V, Ayoub K, Benoit YD. Colorectal Cancer Is Borrowing Blueprints from Intestinal Ontogenesis. Cancers (Basel) 2023; 15:4928. [PMID: 37894295 PMCID: PMC10604965 DOI: 10.3390/cancers15204928] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2023] [Revised: 10/02/2023] [Accepted: 10/10/2023] [Indexed: 10/29/2023] Open
Abstract
Colorectal tumors are heterogenous cellular systems harboring small populations of self-renewing and highly tumorigenic cancer stem cells (CSCs). Understanding the mechanisms fundamental to the emergence of CSCs and colorectal tumor initiation is crucial for developing effective therapeutic strategies. Two recent studies have highlighted the importance of developmental gene expression programs as potential therapeutic targets to suppress pro-oncogenic stem cell populations in the colonic epithelium. Specifically, a subset of aberrant stem cells was identified in preneoplastic intestinal lesions sharing significant transcriptional similarities with fetal gut development. In such aberrant stem cells, Sox9 was shown as a cornerstone for altered cell plasticity, the maintenance of premalignant stemness, and subsequent colorectal tumor initiation. Independently, chemical genomics was used to identify FDA-approved drugs capable of suppressing neoplastic self-renewal based on the ontogenetic root of a target tumor and transcriptional programs embedded in pluripotency. Here, we discuss the joint conclusions from these two approaches, underscoring the importance of developmental networks in CSCs as a novel paradigm for identifying therapeutics targeting colorectal cancer stemness.
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Affiliation(s)
- Jacob L. Billingsley
- Department of Cellular and Molecular Medicine, University of Ottawa, Ottawa, ON K1H 8M5, Canada; (J.L.B.); (V.Y.); (K.A.)
| | - Veronika Yevdokimova
- Department of Cellular and Molecular Medicine, University of Ottawa, Ottawa, ON K1H 8M5, Canada; (J.L.B.); (V.Y.); (K.A.)
| | - Kristina Ayoub
- Department of Cellular and Molecular Medicine, University of Ottawa, Ottawa, ON K1H 8M5, Canada; (J.L.B.); (V.Y.); (K.A.)
| | - Yannick D. Benoit
- Department of Cellular and Molecular Medicine, University of Ottawa, Ottawa, ON K1H 8M5, Canada; (J.L.B.); (V.Y.); (K.A.)
- School of Pharmaceutical Sciences, University of Ottawa, Ottawa, ON K1H 8M5, Canada
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2
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Kameneva P, Melnikova VI, Kastriti ME, Kurtova A, Kryukov E, Murtazina A, Faure L, Poverennaya I, Artemov AV, Kalinina TS, Kudryashov NV, Bader M, Skoda J, Chlapek P, Curylova L, Sourada L, Neradil J, Tesarova M, Pasqualetti M, Gaspar P, Yakushov VD, Sheftel BI, Zikmund T, Kaiser J, Fried K, Alenina N, Voronezhskaya EE, Adameyko I. Serotonin limits generation of chromaffin cells during adrenal organ development. Nat Commun 2022; 13:2901. [PMID: 35614045 PMCID: PMC9133002 DOI: 10.1038/s41467-022-30438-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2020] [Accepted: 04/23/2022] [Indexed: 11/12/2022] Open
Abstract
Adrenal glands are the major organs releasing catecholamines and regulating our stress response. The mechanisms balancing generation of adrenergic chromaffin cells and protecting against neuroblastoma tumors are still enigmatic. Here we revealed that serotonin (5HT) controls the numbers of chromaffin cells by acting upon their immediate progenitor "bridge" cells via 5-hydroxytryptamine receptor 3A (HTR3A), and the aggressive HTR3Ahigh human neuroblastoma cell lines reduce proliferation in response to HTR3A-specific agonists. In embryos (in vivo), the physiological increase of 5HT caused a prolongation of the cell cycle in "bridge" progenitors leading to a smaller chromaffin population and changing the balance of hormones and behavioral patterns in adulthood. These behavioral effects and smaller adrenals were mirrored in the progeny of pregnant female mice subjected to experimental stress, suggesting a maternal-fetal link that controls developmental adaptations. Finally, these results corresponded to a size-distribution of adrenals found in wild rodents with different coping strategies.
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Affiliation(s)
- Polina Kameneva
- Department of Neuroimmunology, Center for Brain Research, Medical University Vienna, Vienna, Austria
- Department of Physiology and Pharmacology, Karolinska Institute, Stockholm, Sweden
| | - Victoria I Melnikova
- Koltsov Institute of Developmental Biology, Russian Academy of Sciences, Moscow, Russia
| | - Maria Eleni Kastriti
- Department of Neuroimmunology, Center for Brain Research, Medical University Vienna, Vienna, Austria
- Department of Physiology and Pharmacology, Karolinska Institute, Stockholm, Sweden
| | - Anastasia Kurtova
- Koltsov Institute of Developmental Biology, Russian Academy of Sciences, Moscow, Russia
| | - Emil Kryukov
- Department of Neuroimmunology, Center for Brain Research, Medical University Vienna, Vienna, Austria
- Department of Physiology and Pharmacology, Karolinska Institute, Stockholm, Sweden
| | - Aliia Murtazina
- Department of Physiology and Pharmacology, Karolinska Institute, Stockholm, Sweden
| | - Louis Faure
- Department of Neuroimmunology, Center for Brain Research, Medical University Vienna, Vienna, Austria
| | - Irina Poverennaya
- Department of Neuroimmunology, Center for Brain Research, Medical University Vienna, Vienna, Austria
| | - Artem V Artemov
- Department of Neuroimmunology, Center for Brain Research, Medical University Vienna, Vienna, Austria
- National Medical Research Center for Endocrinology, Moscow, Russia
| | - Tatiana S Kalinina
- Federal state budgetary institution "Research Zakusov Institute of Pharmacology" (FSBI "Zakusov Institute of Pharmacology"), Russian Academy of Sciences, Moscow, Russia
| | - Nikita V Kudryashov
- Federal state budgetary institution "Research Zakusov Institute of Pharmacology" (FSBI "Zakusov Institute of Pharmacology"), Russian Academy of Sciences, Moscow, Russia
- Sechenov First Moscow State Medical University (Sechenov University), Moscow, Russia
| | - Michael Bader
- Max-Delbrück Center for Molecular Medicine (MDC), 13125, Berlin-Buch, Germany
- German Center for Cardiovascular Research (DZHK), Partner Site Berlin, Germany
- Charité-Universitätsmedizin Berlin, 10117, Berlin, Germany
- Institute for Biology, University of Lübeck, 23562, Lübeck, Germany
| | - Jan Skoda
- Department of Experimental Biology, Faculty of Science, Masaryk University, Brno, Czech Republic
- International Clinical Research Center, St. Anne's University Hospital, Brno, Czech Republic
| | - Petr Chlapek
- Department of Experimental Biology, Faculty of Science, Masaryk University, Brno, Czech Republic
- International Clinical Research Center, St. Anne's University Hospital, Brno, Czech Republic
| | - Lucie Curylova
- Department of Experimental Biology, Faculty of Science, Masaryk University, Brno, Czech Republic
- International Clinical Research Center, St. Anne's University Hospital, Brno, Czech Republic
| | - Lukas Sourada
- Department of Experimental Biology, Faculty of Science, Masaryk University, Brno, Czech Republic
- International Clinical Research Center, St. Anne's University Hospital, Brno, Czech Republic
| | - Jakub Neradil
- Department of Experimental Biology, Faculty of Science, Masaryk University, Brno, Czech Republic
- International Clinical Research Center, St. Anne's University Hospital, Brno, Czech Republic
| | - Marketa Tesarova
- Central European Institute of Technology, Brno University of Technology, Brno, Czech Republic
| | - Massimo Pasqualetti
- Unit of Cell and Developmental Biology, Department of Biology, University of Pisa, Pisa, Italy
- Center for Neuroscience and Cognitive Systems @UniTn, Istituto Italiano di Tecnologia, Rovereto, Italy
| | | | - Vasily D Yakushov
- Severtsov Institute of Ecology and Evolution, Russian Academy of Sciences, Moscow, Russia
| | - Boris I Sheftel
- Severtsov Institute of Ecology and Evolution, Russian Academy of Sciences, Moscow, Russia
| | - Tomas Zikmund
- Central European Institute of Technology, Brno University of Technology, Brno, Czech Republic
| | - Jozef Kaiser
- Central European Institute of Technology, Brno University of Technology, Brno, Czech Republic
| | - Kaj Fried
- Department of Neuroscience, Karolinska Institute, Stockholm, Sweden
| | - Natalia Alenina
- Max-Delbrück Center for Molecular Medicine (MDC), 13125, Berlin-Buch, Germany
- German Center for Cardiovascular Research (DZHK), Partner Site Berlin, Germany
| | - Elena E Voronezhskaya
- Koltsov Institute of Developmental Biology, Russian Academy of Sciences, Moscow, Russia.
| | - Igor Adameyko
- Department of Neuroimmunology, Center for Brain Research, Medical University Vienna, Vienna, Austria.
- Department of Physiology and Pharmacology, Karolinska Institute, Stockholm, Sweden.
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3
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Feng J, Zhao D, Lv F, Yuan Z. Epigenetic Inheritance From Normal Origin Cells Can Determine the Aggressive Biology of Tumor-Initiating Cells and Tumor Heterogeneity. Cancer Control 2022; 29:10732748221078160. [PMID: 35213254 PMCID: PMC8891845 DOI: 10.1177/10732748221078160] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022] Open
Abstract
The acquisition of genetic- and epigenetic-abnormalities during transformation has been recognized as the two fundamental factors that lead to tumorigenesis and determine the aggressive biology of tumor cells. However, there is a regularity that tumors derived from less-differentiated normal origin cells (NOCs) usually have a higher risk of vascular involvement, lymphatic and distant metastasis, which can be observed in both lymphohematopoietic malignancies and somatic cancers. Obviously, the hypothesis of genetic- and epigenetic-abnormalities is not sufficient to explain how the linear relationship between the cellular origin and the biological behavior of tumors is formed, because the cell origin of tumor is an independent factor related to tumor biology. In a given system, tumors can originate from multiple cell types, and tumor-initiating cells (TICs) can be mapped to different differentiation hierarchies of normal stem cells, suggesting that the heterogeneity of the origin of TICs is not completely chaotic. TIC’s epigenome includes not only genetic- and epigenetic-abnormalities, but also established epigenetic status of genes inherited from NOCs. In reviewing previous studies, we found much evidence supporting that the status of many tumor-related “epigenetic abnormalities” in TICs is consistent with that of the corresponding NOC of the same differentiation hierarchy, suggesting that they may not be true epigenetic abnormalities. So, we speculate that the established statuses of genes that control NOC’s migration, adhesion and colonization capabilities, cell-cycle quiescence, expression of drug transporters, induction of mesenchymal formation, overexpression of telomerase, and preference for glycolysis can be inherited to TICs through epigenetic memory and be manifested as their aggressive biology. TICs of different origins can maintain different degrees of innate stemness from NOC, which may explain why malignancies with stem cell phenotypes are usually more aggressive.
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Affiliation(s)
- Jiliang Feng
- Clinical-Pathology Center, Capital Medical University Affiliated Beijing Youan Hospital, Beijing, China
| | - Dawei Zhao
- Medical Imaging Department, Capital Medical University Affiliated Beijing Youan Hospital, Beijing, China
| | - Fudong Lv
- Clinical-Pathology Center, Capital Medical University Affiliated Beijing Youan Hospital, Beijing, China
| | - Zhongyu Yuan
- Clinical-Pathology Center, Capital Medical University Affiliated Beijing Youan Hospital, Beijing, China
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Feng J, Zhu R, Yin Y, Wang S, Zhou L, Lv F, Zhao D. Re-Recognizing the Cellular Origin of the Primary Epithelial Tumors of the Liver. J Hepatocell Carcinoma 2021; 8:1537-1563. [PMID: 34917552 PMCID: PMC8668194 DOI: 10.2147/jhc.s334935] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2021] [Accepted: 11/25/2021] [Indexed: 11/29/2022] Open
Abstract
The primary epithelial tumors of the liver (PETL) are composed of a series of heterogeneous tumors. Although the classification of PETLs has been updated several times by the World Health Organization, the cellular origins of some tumors in this family remain to be precisely depicted. In addition, certain tumors in different categories have similar histology, molecular phenotypes and biological characteristics, suggesting that they may have the same cellular origin. In this work, a narrative review method was adopted to review the relevant papers. By comparing the expression profiles of biomarkers of liver epithelium at different lineages and stages of differentiation, the cells-of-origin of some major members of the PETL family were reassessed. We propose that 1) hepatic adenomas, hepatocellular carcinomas (HCCs) and pure fetal hepatoblastomas (HBs) share the same spectrum in their cellular origin including the hepatocytic-committed progenitors (HCP) and their differentiated descendants. 2) Bile duct adenomas, peribiliary cysts and intrahepatic cholangiocellular carcinomas (ICCs) can share the same spectrum in their cellular origin including the cholangiocytic-committed progenitors (CCP) and their differentiated descendants. 3) The cells-of-origin of embryonal HBs include liver stem cells (LSCs), hepatoblasts, and transitional cells between them. Embryonal HB with small cell element, small cell undifferentiated HB and small cell neuroendocrine carcinoma of the liver can have the same or similar cells-of-origin from LSC. Embryonal HB lacking the small cell component of the LSC phenotype and presenting both hepatocytic and bile duct/ductule components may originate from actual hepatoblasts/hepatic progenitor cells (HPCs) as the combined HCC-ICC does. 4) Teratoid hepatoblastoma and mixed epithelial/mesenchymal HBs can be derived from the LSCs or even less committed extrahepatic pluripotent stem cell. 5) Many members of the PETLs family, including those derived from LSCs, hepatoblasts/HPCs, early HCPs and CCPs, have neuroendocrine potentiality. Except for those primary hepatic neuroendocrine tumor (PHNET) exhibit hepatocytic and/or cholangiocytic phenotypes, other PHNETs subtype may be derived from the descendants of LSC that differentiate towards the upper digestive tract, pancreas or other lineages.
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Affiliation(s)
- Jiliang Feng
- Clinical-Pathology Center, Beijing You-An Hospital, Capital Medical University, Beijing, 100069, People’s Republic of China
- Correspondence: Jiliang Feng Clinical-Pathology Center, Beijing You-An Hospital, Capital Medical University, No. 8, Xitoutiao, Youanmenwai Street, FengTai District, Beijing, 100069, People’s Republic of ChinaTel +86-10-83997342Fax +86-10-83997343 Email
| | - Ruidong Zhu
- General Surgical Center, Beijing You-An Hospital, Capital Medical University, Beijing, 100069, People’s Republic of China
| | - Yu Yin
- Department of Pathology, Anhui Medical University, Hefei, 230032, People’s Republic of China
| | - Shanshan Wang
- Clinical-Pathology Center, Beijing You-An Hospital, Capital Medical University, Beijing, 100069, People’s Republic of China
| | - Lei Zhou
- Department of Pathology, First Affiliated Hospital of Bengbu Medical College/Bengbu Medical College, Bengbu, 233004, People’s Republic of China
| | - Fudong Lv
- Clinical-Pathology Center, Beijing You-An Hospital, Capital Medical University, Beijing, 100069, People’s Republic of China
| | - Dawei Zhao
- Department of Medical Imaging, Capital Medical University, Beijing, 100069, People’s Republic of China
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Alsheikh HAM, Metge BJ, Pruitt HC, Kammerud SC, Chen D, Wei S, Shevde LA, Samant RS. Disruption of STAT5A and NMI signaling axis leads to ISG20-driven metastatic mammary tumors. Oncogenesis 2021; 10:45. [PMID: 34078871 PMCID: PMC8172570 DOI: 10.1038/s41389-021-00333-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2021] [Revised: 04/23/2021] [Accepted: 05/07/2021] [Indexed: 12/12/2022] Open
Abstract
Molecular dynamics of developmental processes are repurposed by cancer cells to support cancer initiation and progression. Disruption of the delicate balance between cellular differentiation and plasticity during mammary development leads to breast cancer initiation and metastatic progression. STAT5A is essential for differentiation of secretory mammary alveolar epithelium. Active STAT5A characterizes breast cancer patients for favorable prognosis. N-Myc and STAT Interactor protein (NMI) was initially discovered as a protein that interacts with various STATs; however, the relevance of these interactions to normal mammary development and cancer was not known. We observe that NMI protein is expressed in the mammary ductal epithelium at the onset of puberty and is induced in pregnancy. NMI protein is decreased in 70% of patient specimens with metastatic breast cancer compared to primary tumors. Here we present our finding that NMI and STAT5A cooperatively mediate normal mammary development. Loss of NMI in vivo caused a decrease in STAT5A activity in normal mammary epithelial as well as breast cancer cells. Analysis of STAT5A mammary specific controlled genetic program in the context of NMI knockout revealed ISG20 (interferon stimulated exonuclease gene 20, a protein involved in rRNA biogenesis) as an unfailing negatively regulated target. Role of ISG20 has never been described in metastatic process of mammary tumors. We observed that overexpression of ISG20 is increased in metastases compared to matched primary breast tumor tissues. Our observations reveal that NMI-STAT5A mediated signaling keeps a check on ISG20 expression via miR-17–92 cluster. We show that uncontrolled ISG20 expression drives tumor progression and metastasis.
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Affiliation(s)
| | - Brandon J Metge
- Department of Pathology, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Hawley C Pruitt
- Department of Pathology, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Sarah C Kammerud
- Department of Pathology, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Dongquan Chen
- Department of Medicine, University of Alabama at Birmingham, Birmingham, AL, USA.,O'Neal Comprehensive Cancer Center, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Shi Wei
- Department of Pathology, University of Alabama at Birmingham, Birmingham, AL, USA.,O'Neal Comprehensive Cancer Center, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Lalita A Shevde
- Department of Pathology, University of Alabama at Birmingham, Birmingham, AL, USA.,O'Neal Comprehensive Cancer Center, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Rajeev S Samant
- Department of Pathology, University of Alabama at Birmingham, Birmingham, AL, USA. .,O'Neal Comprehensive Cancer Center, University of Alabama at Birmingham, Birmingham, AL, USA. .,Birmingham VA Medical Center, Birmingham, AL, USA.
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6
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Fawzy MS, Toraih EA, El-Wazir A, Hosny MM, Badran DI, El Kelish A. Long intergenic non-coding RNA, regulator of reprogramming (LINC-ROR) over-expression predicts poor prognosis in renal cell carcinoma. Arch Med Sci 2021; 17:1016-1027. [PMID: 34336029 PMCID: PMC8314397 DOI: 10.5114/aoms.2019.85201] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/19/2018] [Accepted: 07/14/2018] [Indexed: 11/17/2022] Open
Abstract
INTRODUCTION Long intergenic non-coding RNA, regulator of reprogramming (LINC-ROR) is a newly identified cytoplasmic long non-coding RNA (lncRNA) implicated in cell longevity and apoptosis. We aimed in the current work for the first time to investigate the association of the expression profiles of LINC-ROR and three stem-related transcriptional factors with clinicopathological data and their impact on renal cell carcinoma (RCC) progression in a sample of RCC patients. MATERIAL AND METHODS Expression levels of LINC-ROR and stemness-related factors: SOX2, NANOG, and POU5F1 were detected in 60 formalin-fixed, paraffin-embedded tissues, and their paired adjacent non-cancer tissues (n = 60) by using real-time qRT-PCR analysis. Additionally, the expression profiles were compared with the available clinicopathological features. RESULTS The genes studied were markedly up-regulated in RCC (medians and interquartile ranges were 30.3 (1.84-235.5), 10.2 (1.84-53.9), 5.39 (0.94-23.5), and 12.5 (1.61-43.2) for LINC-ROR, SOX2, NANOG, and POU5F1, respectively) relative to paired non-cancer tissue. High expression levels were associated with poor prognosis in terms of tumour undifferentiation (for LINC-ROR, SOX2, and NANOG), lymph node infiltration (for SOX2), postoperative recurrence (for LINC-ROR and SOX2), and shorter overall survival (OS) and progression-free survival (for all genes studied). The best curve for OS prediction was constructed with LINC-ROR data (area under the receiver operating characteristic curve (AUC) = 0.804 at a cut-off value of 72.7, sensitivity 78.9%, and specificity 80.5%). CONCLUSIONS Collectively, aberrant LINC-ROR and pluripotent gene expression may be recognised as prognostic markers for RCC. Future functional studies are highly recommended to validate the study findings.
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Affiliation(s)
- Manal S. Fawzy
- Department of Medical Biochemistry and Molecular Biology, Faculty of Medicine, Suez Canal University, Ismailia, Egypt
- Department of Biochemistry, Faculty of Medicine, Northern Border University, Arar, Saudi Arabia
| | - Eman A. Toraih
- Genetics Unit, Department of Histology and Cell Biology, Faculty of Medicine, Suez Canal University, Ismailia, Egypt
- Center of Excellence of Molecular and Cellular Medicine, Suez Canal University, Ismailia, Egypt
| | - Aya El-Wazir
- Genetics Unit, Department of Histology and Cell Biology, Faculty of Medicine, Suez Canal University, Ismailia, Egypt
- Center of Excellence of Molecular and Cellular Medicine, Suez Canal University, Ismailia, Egypt
| | - Marwa M. Hosny
- Department of Medical Biochemistry and Molecular Biology, Faculty of Medicine, Suez Canal University, Ismailia, Egypt
| | - Dahlia I. Badran
- Department of Medical Biochemistry and Molecular Biology, Faculty of Medicine, Suez Canal University, Ismailia, Egypt
| | - Amr El Kelish
- Botany Department, Faculty of Science, Suez Canal University, Ismailia, Egypt
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Bedognetti D, Ceccarelli M, Galluzzi L, Lu R, Palucka K, Samayoa J, Spranger S, Warren S, Wong KK, Ziv E, Chowell D, Coussens LM, De Carvalho DD, DeNardo DG, Galon J, Kaufman HL, Kirchhoff T, Lotze MT, Luke JJ, Minn AJ, Politi K, Shultz LD, Simon R, Thórsson V, Weidhaas JB, Ascierto ML, Ascierto PA, Barnes JM, Barsan V, Bommareddy PK, Bot A, Church SE, Ciliberto G, De Maria A, Draganov D, Ho WS, McGee HM, Monette A, Murphy JF, Nisticò P, Park W, Patel M, Quigley M, Radvanyi L, Raftopoulos H, Rudqvist NP, Snyder A, Sweis RF, Valpione S, Zappasodi R, Butterfield LH, Disis ML, Fox BA, Cesano A, Marincola FM. Toward a comprehensive view of cancer immune responsiveness: a synopsis from the SITC workshop. J Immunother Cancer 2019; 7:131. [PMID: 31113486 PMCID: PMC6529999 DOI: 10.1186/s40425-019-0602-4] [Citation(s) in RCA: 49] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2019] [Accepted: 04/23/2019] [Indexed: 12/13/2022] Open
Abstract
Tumor immunology has changed the landscape of cancer treatment. Yet, not all patients benefit as cancer immune responsiveness (CIR) remains a limitation in a considerable proportion of cases. The multifactorial determinants of CIR include the genetic makeup of the patient, the genomic instability central to cancer development, the evolutionary emergence of cancer phenotypes under the influence of immune editing, and external modifiers such as demographics, environment, treatment potency, co-morbidities and cancer-independent alterations including immune homeostasis and polymorphisms in the major and minor histocompatibility molecules, cytokines, and chemokines. Based on the premise that cancer is fundamentally a disorder of the genes arising within a cell biologic process, whose deviations from normality determine the rules of engagement with the host's response, the Society for Immunotherapy of Cancer (SITC) convened a task force of experts from various disciplines including, immunology, oncology, biophysics, structural biology, molecular and cellular biology, genetics, and bioinformatics to address the complexity of CIR from a holistic view. The task force was launched by a workshop held in San Francisco on May 14-15, 2018 aimed at two preeminent goals: 1) to identify the fundamental questions related to CIR and 2) to create an interactive community of experts that could guide scientific and research priorities by forming a logical progression supported by multiple perspectives to uncover mechanisms of CIR. This workshop was a first step toward a second meeting where the focus would be to address the actionability of some of the questions identified by working groups. In this event, five working groups aimed at defining a path to test hypotheses according to their relevance to human cancer and identifying experimental models closest to human biology, which include: 1) Germline-Genetic, 2) Somatic-Genetic and 3) Genomic-Transcriptional contributions to CIR, 4) Determinant(s) of Immunogenic Cell Death that modulate CIR, and 5) Experimental Models that best represent CIR and its conversion to an immune responsive state. This manuscript summarizes the contributions from each group and should be considered as a first milestone in the path toward a more contemporary understanding of CIR. We appreciate that this effort is far from comprehensive and that other relevant aspects related to CIR such as the microbiome, the individual's recombined T cell and B cell receptors, and the metabolic status of cancer and immune cells were not fully included. These and other important factors will be included in future activities of the taskforce. The taskforce will focus on prioritization and specific actionable approach to answer the identified questions and implementing the collaborations in the follow-up workshop, which will be held in Houston on September 4-5, 2019.
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Affiliation(s)
| | | | - Lorenzo Galluzzi
- Department of Radiation Oncology, Weill Cornell Medical College, New York, NY, USA
- Sandra and Edward Meyer Cancer Center, New York, NY, USA
- Université Paris Descartes/Paris V, Paris, France
| | | | - Karolina Palucka
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, USA
| | | | - Stefani Spranger
- Koch Institute for Integrative Cancer Research at MIT, Cambridge, MT, USA
| | | | - Kwok-Kin Wong
- Perlmutter Cancer Center, New York Langone Health, New York, NY, USA
| | - Elad Ziv
- University of California, San Francisco, San Francisco, CA, USA
| | - Diego Chowell
- Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | | | - Daniel D De Carvalho
- Department of Medical Biophysics, Princess Margaret Cancer Centre University Health Network, University of Toronto, Toronto, Canada
| | - David G DeNardo
- Washington University School of Medicine in St. Louis, St. Louis, MO, USA
| | - Jérôme Galon
- INSERM, Laboratory of Integrative Cancer Immunology, Equipe Labellisée Ligue Contre le Cancer, Sorbonne Université, Sorbonne Paris Cité, Université Paris Descartes, Université Paris Diderot; Centre de Recherche des Cordeliers, F-75006, Paris, France
| | - Howard L Kaufman
- Massachusetts General Hospital, Boston, MA, USA and Replimune, Inc., Woburn, MA, USA
| | - Tomas Kirchhoff
- Perlmutter Comprehensive Cancer Center, New York University School of Medicine, New York University Langone Health New York, New York, NY, USA
| | - Michael T Lotze
- UPMC Hillman Cancer Center, University of Pittsburgh, Pittsburgh, PA, USA
| | | | - Andy J Minn
- Abramson Family Cancer Research Institute, University of Pennsylvania, Philadelphia, PA, USA
| | | | | | | | | | | | | | | | | | | | | | - Adrian Bot
- Kite, a Gilead Company, Santa Monica, CA, USA
| | | | | | - Andrea De Maria
- Università degli Studi di Genova and Ospedale Policlinico San Martino IRCCS, Genoa, Italy
| | | | - Winson S Ho
- Department of Neurosurgery, Division of Pediatric Neurosurgery, Primary Children's Hospital, University of Utah, Salt Lake City, UT, USA
| | - Heather M McGee
- Department of Radiation Oncology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Anne Monette
- Lady Davis Institute for Medical Research, Jewish General Hospital, Montreal, QC, Canada
| | | | - Paola Nisticò
- IRCCS Istituto Nazionale Tumori Regina Elena, Rome, Italy
| | - Wungki Park
- Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | | | | | - Laszlo Radvanyi
- Ontario Institute for Cancer Research, Toronto, Ontario, Canada
| | | | - Nils-Petter Rudqvist
- Department of Radiation Oncology, Weill Cornell Medical College, New York, NY, USA
| | | | | | - Sara Valpione
- CRUK Manchester Institute and The Christie NHS Foundation Trust, The University of Manchester, Manchester, UK
| | - Roberta Zappasodi
- Ludwig Collaborative and Swim Across America Laboratory, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Parker Institute for Cancer Immunotherapy, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | | | | | - Bernard A Fox
- Earle A. Chiles Research Institute, Robert W. Franz Cancer Center, Providence Cancer Institute, Portland, OR, USA
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8
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Samdani A, Vetrivel U. POAP: A GNU parallel based multithreaded pipeline of open babel and AutoDock suite for boosted high throughput virtual screening. Comput Biol Chem 2018. [PMID: 29533817 DOI: 10.1016/j.compbiolchem.2018.02.012] [Citation(s) in RCA: 49] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
High throughput virtual screening plays a crucial role in hit identification during the drug discovery process. With the rapid increase in the chemical libraries, virtual screening process becomes computationally challenging, thereby posing a demand for efficiently parallelized software pipelines. Here we present a GNU Parallel based pipeline-POAP that is programmed to run Open Babel and AutoDock suite under highly optimized parallelization. The ligand preparation module is a unique feature in POAP, as it offers extensive options for geometry optimization, conformer generation, parallelization and also quarantines erroneous datasets for seamless operation. POAP also features multi receptor docking that can be utilized for comparative virtual screening and drug repurposing studies. As demonstrated using different structural datasets, POAP proves to be an efficient pipeline that enables high scalability, seamless operability, dynamic file handling and optimal utilization of CPU's for computationally demanding tasks. POAP is distributed freely under GNU GPL license and can be downloaded at https://github.com/inpacdb/POAP.
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Affiliation(s)
- A Samdani
- Centre for Bioinformatics, Kamalnayan Bajaj Institute for Research in Vision and Ophthalmology, Vision Research Foundation, Sankara Nethralaya, Chennai, 600 006, Tamil Nadu, India; School of Chemical and Biotechnology, SASTRA University, Thanjavur, India
| | - Umashankar Vetrivel
- Centre for Bioinformatics, Kamalnayan Bajaj Institute for Research in Vision and Ophthalmology, Vision Research Foundation, Sankara Nethralaya, Chennai, 600 006, Tamil Nadu, India.
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Conditional knockout of N-Myc and STAT interactor disrupts normal mammary development and enhances metastatic ability of mammary tumors. Oncogene 2018; 37:1610-1623. [PMID: 29326438 PMCID: PMC5921859 DOI: 10.1038/s41388-017-0037-7] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2017] [Revised: 09/26/2017] [Accepted: 10/23/2017] [Indexed: 02/07/2023]
Abstract
The process of organ development requires a delicate balance between cellular plasticity and differentiation. This balance is disrupted in cancer initiation and progression. N-Myc and STAT interactor (NMI: human or Nmi: murine) has emerged as a relevant player in the etiology of breast cancer. However, a fundamental understanding of its relevance to normal mammary biology is lacking. To gain insight into its normal function in mammary gland, we generated a mammary-specific Nmi knockout mouse model. We observed that Nmi protein expression is induced in mammary epithelium at the onset of pregnancy, in luminal cells and persists throughout lactation. Nmi knockout results in a precocious alveolar phenotype. These alveoli exhibit an extensive presence of nuclear β-catenin and enhanced Wnt/β-catenin signaling. The Nmi knockout pubertal ductal tree shows enhanced invasion of the mammary fatpad and increased terminal end bud numbers. Tumors from Nmi null mammary epithelium show a significant enrichment of poorly differentiated cells with elevated stem/progenitor markers, active Wnt/β-catenin signaling, highly invasive morphology as well as, increased number of distant metastases. Our study demonstrates that Nmi has a distinct role in the differentiation process of mammary luminal epithelial cell compartment and developmental aberrations resulting from Nmi absence contribute to metastasis and demonstrates that aberration in normal developmental program can lead to metastatic disease, highlighting the contribution and importance of luminal progenitor cells in driving metastatic disease.
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