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Srdic-Rajic T, Metlas R. Antibody VH domain sequence analysis by a bioinformatics approach based on electronic amino acid properties may help to predict paratop location. Immunol Lett 2021; 241:55-57. [PMID: 34785254 DOI: 10.1016/j.imlet.2021.11.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2021] [Revised: 10/15/2021] [Accepted: 11/11/2021] [Indexed: 11/28/2022]
Abstract
Gene as the basic functional unit of DNA encodes information about the product such as protein. The majority of proteins realize function through protein-protein interactions involving short protein motifs. However, some proteins such as antibodies are established by the rearrangement of several (V-D-J) gene segments with the potential addition of nontemplated nucleotides that may change information encoded by the respective gene segment used. Antibody VH domain sequence analysis by ISM bioinformatics approach that is based on amino acids physicochemical features, enable to distinguish the contribution of the information encoded by VH gene or generated during VDJ gene recombination for antibody-antigen interaction. The data presented in this report revealed the significance of CDRH3 for the interaction of antibody specific for immunogenic molecules while CDRH3 contribution is minor for antibody interaction with nonimmunogenic molecules such as haptens and native mammalian dsDNA. Thus, paratopes might be located in the CDRH3 or VH regions.
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Affiliation(s)
- Tatjana Srdic-Rajic
- Department of Experimental Oncology, Institute for oncology and radiology of Serbia, Belgrade,Serbia
| | - Radmila Metlas
- Center for Multidisciplinary Research, Institute of Nuclear Sciences VINCA, Belgrade, Serbia.
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NOTCH3 T6746C and TP53 P72R Polymorphisms Are Associated with the Susceptibility to Diffuse Cutaneous Systemic Sclerosis. BIOMED RESEARCH INTERNATIONAL 2020; 2020:8465971. [PMID: 32185220 PMCID: PMC7060860 DOI: 10.1155/2020/8465971] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/18/2019] [Revised: 12/15/2019] [Accepted: 01/21/2020] [Indexed: 02/06/2023]
Abstract
Introduction. NOTCH pathway and TP53 protein are involved in the development of fibrosis and autoimmune disorders, respectively. The aim of this study was to evaluate the role of single nucleotide polymorphisms (SNPs) of NOTCH3 and TP53 genes and serum anti-TP53 antibodies with the susceptibility, clinical subset of systemic sclerosis (SSc), and clinical profile of SSc patient, particularly with lung involvement and disease activity. Objects and Methods. 124 white Polish SSc patients (101 with limited cutaneous SSc-lcSSc, and 23 with diffuse cutaneous SSc-dcSSc) and 100 healthy individuals were included in the study. Patients were assessed for the presence of autoantibodies and interstitial lung disease. Two SNPs at position 6746 of NOTCH3 and TP53 genes and serum anti-TP53 antibodies with the susceptibility, clinical subset of systemic sclerosis (SSc), and clinical profile of SSc patient, particularly with lung involvement and disease activity. Results The genotypic frequencies of the NOTCH3 and p=0.03; χ 2 = 4.63). There was no significant difference between SSc patients and the control population in allele frequencies of both SNPs. The CT + CC genotypes of NOTCH3 and p=0.03; p=0.03; p=0.03; TP53 genes and serum anti-TP53 antibodies with the susceptibility, clinical subset of systemic sclerosis (SSc), and clinical profile of SSc patient, particularly with lung involvement and disease activity. p=0.03. Conclusion The CT + CC genotypes of NOTCH3 gene and PR + RR genotypes of the TP53 gene increased the risk of dcSSc development. Moreover, genotypes of CT + CC were associated with the active form of SSc suggesting the role of the NOTCH pathway in the pathogenesis of this disease.NOTCH3 and TP53 genes and serum anti-TP53 antibodies with the susceptibility, clinical subset of systemic sclerosis (SSc), and clinical profile of SSc patient, particularly with lung involvement and disease activity.
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Pellegrino M, Traversi G, Arena A, Cappa M, Rosado MM, Andreani M, Delfino DV, Moretti F, Fierabracci A. Effect of p53 activation through targeting MDM2/MDM4 heterodimer on T regulatory and effector cells in the peripheral blood of Type 1 diabetes patients. PLoS One 2020; 15:e0228296. [PMID: 31995625 PMCID: PMC6988923 DOI: 10.1371/journal.pone.0228296] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2019] [Accepted: 01/10/2020] [Indexed: 12/13/2022] Open
Abstract
Various immunotherapies for the treatment of type 1 diabetes are currently under investigation. Some of these aim to rescue the remaining beta cells from autoimmune attack caused by the disease. Among the strategies employed, p53 has been envisaged as a possible target for immunomodulation. We studied the possible effect of p53 activation on Treg subsets and Treg/Teff balance in type 1 diabetes patients' PBMC. Upon p53 activation, we observed an increase in CD8+ Treg and activated CD8+ Teff whilst CD8+ Teff cells significantly decreased in healthy PBMC when stimulated with anti-CD3/CD28. No effect was detected on percentages of CD4+ Treg, while a reduction was seen in CD4+ Teff cells and an increase in activated CD4+ Teff cells. In patients' PBMC, upon p53 activation followed by 6 days of anti-CD3/CD28 stimulation, CD8+ Treg and activated CD8+ Teff were increased while CD8+ Teff were decreased. No differences were detected in the CD4+ counterparts. CD8+ Teff PD1+, CD8+ Teff PD1low were increased upon p53 activation in type 1 diabetics compared to controls while CD8+ Teff PD1high were increased in both groups. The same increased percentages were detected for CD4+ counterparts. CD4+ Treg PD1high cells were decreased in diabetics upon p53 activation at day 6 of anti-CD3/CD28 stimulation. In conclusion, a Teff dysregulation is observed upon p53 activation suggesting that molecules promoting p53 cannot be used for therapy in type 1 diabetics.
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Affiliation(s)
- Marsha Pellegrino
- Infectivology and Clinical Trials Research Department, Bambino Gesù Children’s Hospital, IRCCS, Rome, Italy
| | - Gianandrea Traversi
- Infectivology and Clinical Trials Research Department, Bambino Gesù Children’s Hospital, IRCCS, Rome, Italy
| | - Andrea Arena
- Infectivology and Clinical Trials Research Department, Bambino Gesù Children’s Hospital, IRCCS, Rome, Italy
| | - Marco Cappa
- Endocrinology Department, Bambino Gesù Children’s Hospital, IRCCS, Rome, Italy
| | - M. Manuela Rosado
- Research Laboratories, Bambino Gesù Children’s Hospital, IRCCS, Rome, Italy
| | - Marco Andreani
- Transplantation Immunogenetics Laboratory, Bambino Gesù Children’s Hospital, IRCCS, Rome, Italy
| | - Domenico V. Delfino
- Section of Pharmacology, Department of Medicine, University of Perugia, Perugia, Italy
| | - Fabiola Moretti
- Institute of Cell Biology and Neurobiology, National Research Council of Italy (CNR), Rome, Italy
| | - Alessandra Fierabracci
- Infectivology and Clinical Trials Research Department, Bambino Gesù Children’s Hospital, IRCCS, Rome, Italy
- * E-mail:
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Herkel J, Schrader J, Erez N, Lohse AW, Cohen IR. Activation of the Akt-CREB signalling axis by a proline-rich heptapeptide confers resistance to stress-induced cell death and inflammation. Immunology 2017; 151:474-480. [PMID: 28419468 DOI: 10.1111/imm.12745] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2017] [Revised: 03/31/2017] [Accepted: 04/08/2017] [Indexed: 12/15/2022] Open
Abstract
Cell stress of various kinds can lead to the induction of cell death and a damaging inflammatory response. Hence, a goal of therapeutic cell-stress management is to develop agents that might effectively regulate undesirable cell death and inflammation. To that end, we developed a synthetic peptide of seven amino acids based on structural mimicry to a functional domain of p53, a key factor in the responses of cells to stressful stimuli. This heptapeptide, which we term Stressin-1, was found to inhibit both cell death and the secretion of inflammatory mediators by various cell types in response to different stressful agents in vitro. The combined anti-inflammatory and anti-apoptotic activities of Stressin-1 were associated with a cellular signalling cascade that induced activation of Akt kinase and activation of the cAMP response element-binding protein (CREB) transcription factor. These immediate signalling events led to the inhibition of the signal transducer and activator of transcription and nuclear factor-κB pathways 24 hr later. Unexpectedly, we found no evidence for a direct involvement of p53 in the effects produced by Stressin-1. Intraperitoneal administration of 100 μg of Stressin-1 to lethally irradiated mice significantly protected them from death. These findings show that activating the Akt-CREB axis with Stressin-1 can counteract some of the undesirable effects of various cell stresses. Stressin-1 may have clinical usefulness.
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Affiliation(s)
- Johannes Herkel
- Department of Medicine, University Medical Centre Hamburg-Eppendorf, Hamburg, Germany
| | - Jörg Schrader
- Department of Medicine, University Medical Centre Hamburg-Eppendorf, Hamburg, Germany
| | - Neta Erez
- Department of Pathology, Sackler School of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Ansgar W Lohse
- Department of Medicine, University Medical Centre Hamburg-Eppendorf, Hamburg, Germany
| | - Irun R Cohen
- Department of Immunology, The Weizmann Institute of Science, Rehovot, Israel
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Fierabracci A, Pellegrino M. The Double Role of p53 in Cancer and Autoimmunity and Its Potential as Therapeutic Target. Int J Mol Sci 2016; 17:ijms17121975. [PMID: 27897991 PMCID: PMC5187775 DOI: 10.3390/ijms17121975] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2016] [Revised: 11/07/2016] [Accepted: 11/17/2016] [Indexed: 01/22/2023] Open
Abstract
p53 is a sequence-specific short-lived transcription factor expressed at low concentrations in various tissues while it is upregulated in damaged, tumoral or inflamed tissue. In normally proliferating cells, p53 protein levels and function are tightly controlled by main regulators, i.e., MDM2 (mouse double minute 2) and MDM4 proteins. p53 plays an important role due to its ability to mediate tumor suppression. In addition to its importance as a tumor suppressor, p53 coordinates diverse cellular responses to stress and damage and plays an emerging role in various physiological processes, including fertility, cell metabolism, mitochondrial respiration, autophagy, cell adhesion, stem cell maintenance and development. Interestingly, it has been recently implicated in the suppression of autoimmune and inflammatory diseases in both mice and humans. In this review based on current knowledge on the functional properties of p53 and its regulatory pathways, we discuss the potential utility of p53 reactivation from a therapeutic perspective in oncology and chronic inflammatory disorders leading to autoimmunity.
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Affiliation(s)
- Alessandra Fierabracci
- Infectivology and Clinical Trials Area, Children's Hospital Bambino Gesù, 00146 Rome, Italy.
| | - Marsha Pellegrino
- Infectivology and Clinical Trials Area, Children's Hospital Bambino Gesù, 00146 Rome, Italy.
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Dreyfus DH. Gene sharing between Epstein–Barr virus and human immune response genes. Immunol Res 2016; 65:37-45. [DOI: 10.1007/s12026-016-8814-x] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
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7
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Fattal I, Shental N, Ben-Dor S, Molad Y, Gabrielli A, Pokroy-Shapira E, Oren S, Livneh A, Langevitz P, Zandman-Goddard G, Sarig O, Margalit R, Gafter U, Domany E, Cohen IR. Guanine polynucleotides are self-antigens for human natural autoantibodies and are significantly reduced in the human genome. Immunology 2015; 146:401-10. [PMID: 26227667 DOI: 10.1111/imm.12514] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2015] [Revised: 07/16/2015] [Accepted: 07/21/2015] [Indexed: 11/28/2022] Open
Abstract
In the course of investigating anti-DNA autoantibodies, we examined IgM and IgG antibodies to poly-G and other oligonucleotides in the sera of healthy persons and those diagnosed with systemic lupus erythematosus (SLE), scleroderma (SSc), or pemphigus vulgaris (PV); we used an antigen microarray and informatic analysis. We now report that all of the 135 humans studied, irrespective of health or autoimmune disease, manifested relatively high amounts of IgG antibodies binding to the 20-mer G oligonucleotide (G20); no participants entirely lacked this reactivity. IgG antibodies to homo-nucleotides A20, C20 or T20 were present only in the sera of SLE patients who were positive for antibodies to dsDNA. The prevalence of anti-G20 antibodies led us to survey human, mouse and Drosophila melanogaster (fruit fly) genomes for runs of T20 and G20 or more: runs of T20 appear > 170,000 times compared with only 93 runs of G20 or more in the human genome; of these runs, 40 were close to brain-associated genes. Mouse and fruit fly genomes showed significantly lower T20/G20 ratios than did human genomes. Moreover, sera from both healthy and SLE mice contained relatively little or no anti-G20 antibodies; so natural anti-G20 antibodies appear to be characteristic of humans. These unexpected observations invite investigation of the immune functions of anti-G20 antibodies in human health and disease and of runs of G20 in the human genome.
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Affiliation(s)
- Ittai Fattal
- Department of Immunology, The Weizmann Institute of Science, Rehovot, Israel.,Department of Physics of Complex Systems, The Weizmann Institute of Science, Rehovot, Israel.,Department of Nephrology, Rabin Medical Centre, Petach Tikva, Israel
| | - Noam Shental
- Department of Computer Science, The Open University of Israel, Raanana, Israel
| | - Shifra Ben-Dor
- Bioinformatics and Biological Computing Unit, The Weizmann Institute of Science, Rehovot, Israel
| | - Yair Molad
- The Rheumatology Unit, Rabin Medical Centre, Beilinson Hospital, Petach Tikva, Israel.,Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Armando Gabrielli
- Istituto di, Dipartimento di Scienze Cliniche e Molecolari- Clinica Medica, Università Politecnica delle Marche, Ancona, Italy
| | - Elisheva Pokroy-Shapira
- The Rheumatology Unit, Rabin Medical Centre, Beilinson Hospital, Petach Tikva, Israel.,Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Shirly Oren
- The Rheumatology Unit, Rabin Medical Centre, Beilinson Hospital, Petach Tikva, Israel.,Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Avi Livneh
- Department of Medicine F, Sheba Medical Centre, Tel Hashomer, Israel
| | - Pnina Langevitz
- The Rheumatology Unit, Sheba Medical Centre, Tel Hashomer, Israel
| | | | - Ofer Sarig
- Department of Dermatology, Tel Aviv Sourasky Medical Centre, Tel Aviv, Israel
| | - Raanan Margalit
- Science in Action Ltd, Weizmann Science Park, Ness-Ziona, Israel
| | - Uzi Gafter
- Department of Nephrology, Rabin Medical Centre, Petach Tikva, Israel
| | - Eytan Domany
- Department of Physics of Complex Systems, The Weizmann Institute of Science, Rehovot, Israel
| | - Irun R Cohen
- Department of Immunology, The Weizmann Institute of Science, Rehovot, Israel
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Fattal I, Shental N, Molad Y, Gabrielli A, Pokroy-Shapira E, Oren S, Livneh A, Langevitz P, Pauzner R, Sarig O, Gafter U, Domany E, Cohen IR. Epstein-Barr virus antibodies mark systemic lupus erythematosus and scleroderma patients negative for anti-DNA. Immunology 2014; 141:276-85. [PMID: 24164500 DOI: 10.1111/imm.12200] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2013] [Revised: 10/20/2013] [Accepted: 10/21/2013] [Indexed: 01/01/2023] Open
Abstract
Systemic lupus erythematosus (SLE) is an autoimmune disease that can attack many different body organs; the triggering event is unknown. SLE has been associated with more than 100 different autoantibody reactivities - anti-dsDNA is prominent. Nevertheless, autoantibodies to dsDNA occur in only two-thirds of SLE patients. We previously reported the use of an antigen microarray to characterize SLE serology. We now report the results of an expanded study of serology in SLE patients and scleroderma (SSc) patients compared with healthy controls. The analysis validated and extended previous findings: two-thirds of SLE patients reacted to a large spectrum of self-molecules that overlapped with their reactivity to dsDNA; moreover, some SLE patients manifested a deficiency of natural IgM autoantibodies. Most significant was the finding that many SLE patients who were negative for autoantibodies to dsDNA manifested abnormal antibody responses to Epstein-Barr virus (EBV): these subjects made IgG antibodies to EBV antigens to which healthy subjects did not respond or they failed to make antibodies to EBV antigens to which healthy subjects did respond. This observation suggests that SLE may be associated with a defective immune response to EBV. The SSc patients shared many of these serological abnormalities with SLE patients, but differed from them in increased IgG autoantibodies to topoisomerase and centromere B; 84% of SLE patients and 58% of SSc patients could be detected by their abnormal antibodies to EBV. Hence an aberrant immune response to a ubiquitous viral infection such as EBV might set the stage for an autoimmune disease.
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Affiliation(s)
- Ittai Fattal
- Department of Immunology, The Weizmann Institute of Science, Rehovot, Israel; Department of Physics of Complex Systems, The Weizmann Institute of Science, Rehovot, Israel; Department of Nephrology, Rabin Medical Centre, Petach Tikva, Israel
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Kawashima H, Takatori H, Suzuki K, Iwata A, Yokota M, Suto A, Minamino T, Hirose K, Nakajima H. Tumor suppressor p53 inhibits systemic autoimmune diseases by inducing regulatory T cells. THE JOURNAL OF IMMUNOLOGY 2013; 191:3614-23. [PMID: 24006461 DOI: 10.4049/jimmunol.1300509] [Citation(s) in RCA: 51] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
The tumor suppressor p53 plays a central role in tumor suppression by inducing apoptosis, cell cycle arrest, senescence, and DNA repair. In addition to the antitumor functions of p53, accumulating evidence using systemic p53-deficient mice suggests that p53 suppresses autoimmunity. However, it remains unknown how p53 suppresses autoimmunity. In this study, we generated T cell-specific p53-deficient mice (CD4-Cre p53(fl/fl) mice, or p53 conditional knockout [cKO] mice) and found that aged p53-cKO mice spontaneously developed inflammatory lesions in various organs, including lung, liver, stomach, thyroid gland, submandibular gland, and kidney. Additionally, anti-nuclear Abs and autoantibodies against gastric parietal cells were detected in p53-cKO mice but not in control p53(fl/fl) mice (p53 wild-type mice). Importantly, the number of Foxp3(+)CD4(+) regulatory T cells (Tregs) in the spleen and lung as well as in vitro differentiation of induced Tregs was significantly reduced in p53-cKO mice as compared with that in p53 wild-type mice. Regarding the mechanisms underlying p53-mediated Treg induction, p53 enhanced the transcription of Foxp3 by binding to the promoter and the conserved noncoding DNA sequence-2 of the Foxp3 gene. Taken together, these results suggest that p53 expressed in T cells functions as a suppressor for autoimmunity by inducing Treg differentiation.
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Affiliation(s)
- Hirotoshi Kawashima
- Department of Allergy and Clinical Immunology, Graduate School of Medicine, Chiba University, Chiba 260-8670, Japan
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Immune System Computation and the Immunological Homunculus. MODEL DRIVEN ENGINEERING LANGUAGES AND SYSTEMS 2006. [DOI: 10.1007/11880240_35] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
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Abstract
The discoveries of DNA mimicry by proteins inspired by Ugi experiments led by Dale Mosbaugh and his colleagues have sparked dramatic insights for our understanding of DNA and protein interactions. Currently only a small number protein mimics of DNA are known or suspected, including Ugi, HI1450, Ocr, TAF1, MfpA, and Dinl. These proteins are structurally diverse, but together they share common themes we define here. These mimics tend to resemble distorted rather than normal B-DNA, possibly to prevent cross-reactions with other DNA metabolizing proteins that should not be inhibited. Side-chain carboxylates of glutamates and aspartates functionally replace phosphates and thereby generate an overall charge pattern resembling the DNA phosphate backbone. Most protein mimics of DNA have strikingly hydrophobic cores that likely stabilize the protein fold despite substantial charge localization and a relatively small internal volume enforced by the restrictions from DNA size. These common characteristics for protein mimicry of DNA should prove useful for future identifications of DNA mimics, which seem likely to be found in bacteriophages, conjugative plasmids, eukaryotic viruses, and transcription machinery. We also suggest approaches to the design of novel DNA mimics to inhibit specific pathways and could be important for basic science applications and for use as therapeutic agents. Moreover, mimicry in general is of critical importance in that it provides an elegant mechanism by which interfaces can be reused to force sequential rather than simultaneous complex formations such as seen in systems involving polar protein assemblies and DNA repair machinery.
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Affiliation(s)
- Christopher D Putnam
- Ludwig Institute for Cancer Research, Department of Medicine, University of California, San Diego School of Medicine, La Jolla, 92093-0669, USA
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