1
|
Kaczanowska S, Murty T, Alimadadi A, Contreras CF, Duault C, Subrahmanyam PB, Reynolds W, Gutierrez NA, Baskar R, Wu CJ, Michor F, Altreuter J, Liu Y, Jhaveri A, Duong V, Anbunathan H, Ong C, Zhang H, Moravec R, Yu J, Biswas R, Van Nostrand S, Lindsay J, Pichavant M, Sotillo E, Bernstein D, Carbonell A, Derdak J, Klicka-Skeels J, Segal JE, Dombi E, Harmon SA, Turkbey B, Sahaf B, Bendall S, Maecker H, Highfill SL, Stroncek D, Glod J, Merchant M, Hedrick CC, Mackall CL, Ramakrishna S, Kaplan RN. Immune determinants of CAR-T cell expansion in solid tumor patients receiving GD2 CAR-T cell therapy. Cancer Cell 2024; 42:35-51.e8. [PMID: 38134936 PMCID: PMC10947809 DOI: 10.1016/j.ccell.2023.11.011] [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] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/10/2023] [Revised: 09/18/2023] [Accepted: 11/22/2023] [Indexed: 12/24/2023]
Abstract
Chimeric antigen receptor T cells (CAR-Ts) have remarkable efficacy in liquid tumors, but limited responses in solid tumors. We conducted a Phase I trial (NCT02107963) of GD2 CAR-Ts (GD2-CAR.OX40.28.z.iC9), demonstrating feasibility and safety of administration in children and young adults with osteosarcoma and neuroblastoma. Since CAR-T efficacy requires adequate CAR-T expansion, patients were grouped into good or poor expanders across dose levels. Patient samples were evaluated by multi-dimensional proteomic, transcriptomic, and epigenetic analyses. T cell assessments identified naive T cells in pre-treatment apheresis associated with good expansion, and exhausted T cells in CAR-T products with poor expansion. Myeloid cell assessment identified CXCR3+ monocytes in pre-treatment apheresis associated with good expansion. Longitudinal analysis of post-treatment samples identified increased CXCR3- classical monocytes in all groups as CAR-T numbers waned. Together, our data uncover mediators of CAR-T biology and correlates of expansion that could be utilized to advance immunotherapies for solid tumor patients.
Collapse
Affiliation(s)
- Sabina Kaczanowska
- Pediatric Oncology Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Tara Murty
- Center for Cancer Cell Therapy, Stanford Cancer Institute, Stanford University School of Medicine, Stanford, CA, USA
| | - Ahmad Alimadadi
- La Jolla Institute for Immunology, La Jolla, CA, USA; Immunology Center of Georgia, Augusta University, Augusta, GA, USA; Georgia Cancer Center, Medical College of Georgia at Augusta University, Augusta, GA, USA
| | - Cristina F Contreras
- Pediatric Oncology Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA; Department of Oncology, University of Oxford, Oxford, UK
| | - Caroline Duault
- Stanford Human Immune Monitoring Center, Stanford University School of Medicine, Stanford, CA, USA
| | - Priyanka B Subrahmanyam
- Stanford Human Immune Monitoring Center, Stanford University School of Medicine, Stanford, CA, USA
| | - Warren Reynolds
- Center for Cancer Cell Therapy, Stanford Cancer Institute, Stanford University School of Medicine, Stanford, CA, USA
| | | | - Reema Baskar
- Department of Pathology, Stanford University, Stanford, CA, USA
| | - Catherine J Wu
- Broad Institute, Cambridge, MA, USA; Dana-Farber Cancer Institute, Boston, MA, USA
| | | | | | - Yang Liu
- Broad Institute, Cambridge, MA, USA
| | | | - Vandon Duong
- Center for Cancer Cell Therapy, Stanford Cancer Institute, Stanford University School of Medicine, Stanford, CA, USA
| | - Hima Anbunathan
- Center for Cancer Cell Therapy, Stanford Cancer Institute, Stanford University School of Medicine, Stanford, CA, USA
| | - Claire Ong
- Pediatric Oncology Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Hua Zhang
- Pediatric Oncology Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Radim Moravec
- Cancer Therapy Evaluation Program, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Joyce Yu
- Dana-Farber Cancer Institute, Boston, MA, USA
| | | | | | | | - Mina Pichavant
- Immunology Center of Georgia, Augusta University, Augusta, GA, USA
| | - Elena Sotillo
- Center for Cancer Cell Therapy, Stanford Cancer Institute, Stanford University School of Medicine, Stanford, CA, USA
| | - Donna Bernstein
- Pediatric Oncology Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Amanda Carbonell
- Pediatric Oncology Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Joanne Derdak
- Pediatric Oncology Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Jacquelyn Klicka-Skeels
- Pediatric Oncology Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Julia E Segal
- Pediatric Oncology Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Eva Dombi
- Pediatric Oncology Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Stephanie A Harmon
- Artificial Intelligence Resource, Molecular Imaging Branch, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Baris Turkbey
- Artificial Intelligence Resource, Molecular Imaging Branch, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Bita Sahaf
- Center for Cancer Cell Therapy, Stanford Cancer Institute, Stanford University School of Medicine, Stanford, CA, USA
| | - Sean Bendall
- Georgia Cancer Center, Medical College of Georgia at Augusta University, Augusta, GA, USA
| | - Holden Maecker
- Immunology Center of Georgia, Augusta University, Augusta, GA, USA
| | - Steven L Highfill
- Center for Cellular Engineering, Department of Transfusion Medicine, National Institutes of Health Clinical Center, Bethesda, MD, USA
| | - David Stroncek
- Center for Cellular Engineering, Department of Transfusion Medicine, National Institutes of Health Clinical Center, Bethesda, MD, USA
| | - John Glod
- Pediatric Oncology Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Melinda Merchant
- Pediatric Oncology Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Catherine C Hedrick
- La Jolla Institute for Immunology, La Jolla, CA, USA; Immunology Center of Georgia, Augusta University, Augusta, GA, USA; Georgia Cancer Center, Medical College of Georgia at Augusta University, Augusta, GA, USA
| | - Crystal L Mackall
- Center for Cancer Cell Therapy, Stanford Cancer Institute, Stanford University School of Medicine, Stanford, CA, USA
| | - Sneha Ramakrishna
- Center for Cancer Cell Therapy, Stanford Cancer Institute, Stanford University School of Medicine, Stanford, CA, USA.
| | - Rosandra N Kaplan
- Pediatric Oncology Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA.
| |
Collapse
|
2
|
Favaro P, Glass DR, Borges L, Baskar R, Reynolds W, Ho D, Bruce T, Tebaykin D, Scanlon VM, Shestopalov I, Bendall SC. Unravelling human hematopoietic progenitor cell diversity through association with intrinsic regulatory factors. bioRxiv 2023:2023.08.30.555623. [PMID: 37693547 PMCID: PMC10491219 DOI: 10.1101/2023.08.30.555623] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/12/2023]
Abstract
Hematopoietic stem and progenitor cell (HSPC) transplantation is an essential therapy for hematological conditions, but finer definitions of human HSPC subsets with associated function could enable better tuning of grafts and more routine, lower-risk application. To deeply phenotype HSPCs, following a screen of 328 antigens, we quantified 41 surface proteins and functional regulators on millions of CD34+ and CD34- cells, spanning four primary human hematopoietic tissues: bone marrow, mobilized peripheral blood, cord blood, and fetal liver. We propose more granular definitions of HSPC subsets and provide new, detailed differentiation trajectories of erythroid and myeloid lineages. These aspects of our revised human hematopoietic model were validated with corresponding epigenetic analysis and in vitro clonal differentiation assays. Overall, we demonstrate the utility of using molecular regulators as surrogates for cellular identity and functional potential, providing a framework for description, prospective isolation, and cross-tissue comparison of HSPCs in humans.
Collapse
Affiliation(s)
- Patricia Favaro
- Department of Pathology, Stanford University
- These authors contributed equally
| | - David R. Glass
- Department of Pathology, Stanford University
- Immunology Graduate Program, Stanford University
- Present address: Vaccine and Infectious Diseases Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
- These authors contributed equally
| | - Luciene Borges
- Department of Pathology, Stanford University
- Present address: Boehringer Ingelheim Pharmaceuticals, Inc., Ridgefield, CT, USA
- These authors contributed equally
| | - Reema Baskar
- Department of Pathology, Stanford University
- Present address: Genome Institute of Singapore
| | | | - Daniel Ho
- Department of Pathology, Stanford University
| | | | | | - Vanessa M. Scanlon
- Department of Laboratory Medicine, Yale School of Medicine
- Present address: Center for Regenerative Medicine and Skeletal Biology, University of Connecticut Health
| | | | - Sean C. Bendall
- Department of Pathology, Stanford University
- Immunology Graduate Program, Stanford University
- Lead author
| |
Collapse
|
3
|
Murty T, Kaczanowska S, Alimadadi A, Contreras C, Duault C, Balasubrahmanyan P, Reynolds W, Gutierrez N, Baskar R, Wu C, Michor F, Altreuter J, Liu Y, Jhaveri A, Duong V, Anbunathan H, Moravec R, Hong J, Biswas R, Van Nostrand S, Lindsay J, Pichavant M, Sotillo E, Sahaf B, Bendall S, Maecker H, Highfill S, Stroncek D, Merchant M, Glod J, Hedrick C, Mackall C, Ramakrishna S, Kaplan R. Abstract 2142: Immune determinants of CAR-T expansion in solid tumor patients receiving GD2 CAR-T cell therapy. Cancer Res 2023. [DOI: 10.1158/1538-7445.am2023-2142] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/07/2023]
Abstract
Abstract
Chimeric antigen receptor T cells (CAR-Ts) have demonstrated remarkable efficacy in leukemia and lymphomas but limited responses in solid tumors. We conducted a phase I trial (NCT02107963) of GD2 CAR-Ts (GD2-CAR.OX40.28.z.ICD9), demonstrating feasibility and safety of administering GD2 CAR-Ts in children and young adults with neuroblastoma and, for the first time, osteosarcoma. 15 patients aged 8-28 years were enrolled on four dose levels, of which 13 patients were infused. No dose-limiting toxicities were observed, and administration of up to 1x107 GD2-CAR-T/kg was feasible and safe for children and young adults with neuroblastoma and osteosarcoma. At Day 28 following GD2 CAR-T infusion, 23.1% (3/13) of evaluable patients had progressive disease and 76.9% (10/13) had stable disease (SD). 3/10 SD patients remained stable at 60 days post-infusion of GD2 CAR-T, but all patients eventually progressed. Since a major barrier to CAR-T efficacy is inadequate CAR-T expansion, we evaluated CAR-T levels and found that patients stratified into good and poor expander groups, observed across dose levels and associated with pro-inflammatory cytokine signatures in patients. To understand the immune cell contributors to CAR-T expansion, patient pre-treatment apheresis, CAR-T product, and post-infusion samples were evaluated by high-dimensional proteomic (CyTOF), transcriptomic (RNAseq), and epigenetic (ATACseq) analyses. In patient apheresis, good CAR-T expansion associated with more open chromatin and with both proteomic and transcriptomic enrichment of naïve T cells, while poor CAR-T expansion associated with increased levels of T effector memory (TEMRA) cells and enrichment of myeloid derived suppressor cell (MDSC) transcriptomic signatures. CAR-T products across patients, regardless of CAR-T expansion, demonstrated increased T cell activation proteomic signatures, with enhanced exhaustion transcriptomic signatures in poor expanders compared to good. The most robust cellular correlate to good CAR-T expansion was a population of CXCR3-expressing monocytes in pre-treatment apheresis. Interestingly, this CXCR3+ monocyte population reduced in post-infusion timepoints of good expanders, resembling levels found in poor expanders. Our findings were validated in TARGET-OS patient data in The Cancer Genome Atlas, where high CXCR3 expression was found to be associated with survival benefit in osteosarcoma patients. CXCR3 has been extensively studied on T cells, but its function on myeloid populations is yet to be fully explored. These results are the first to demonstrate that the peripheral immune environment prior to CAR-T administration may effectively predict and modulate CAR-T expansion in patients.
Citation Format: Tara Murty, Sabina Kaczanowska, Ahmad Alimadadi, Cristina Contreras, Caroline Duault, Priyanka Balasubrahmanyan, Warren Reynolds, Norma Gutierrez, Reema Baskar, Catherine Wu, Franziska Michor, Jennifer Altreuter, Yang Liu, Aashna Jhaveri, Vandon Duong, Hima Anbunathan, Radim Moravec, Joyce Hong, Roshni Biswas, Stephen Van Nostrand, James Lindsay, Mina Pichavant, Elena Sotillo, Bita Sahaf, Sean Bendall, Holden Maecker, Steven Highfill, David Stroncek, Melinda Merchant, John Glod, Catherine Hedrick, Crystal Mackall, Sneha Ramakrishna, Rosandra Kaplan. Immune determinants of CAR-T expansion in solid tumor patients receiving GD2 CAR-T cell therapy [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 2142.
Collapse
|
4
|
Ramakrishna S, Kaczanowska S, Murty T, Contreras CF, Merchant M, Glod J, Gutierrez N, Alimadadi A, Stroncek D, Highfill S, Duault C, Subrahmanyam PB, Holmes T, Reynolds W, Baskar R, Barge A, Lyon H, Moravec R, Ranasinghe S, Yu J, Biswas R, Pollack S, Van Nostrand S, Lindsay J, Pichavant M, Sahaf B, Bendall SC, Gentles AJ, Maecker H, Hedrick CC, Mackall C, Kaplan R. Abstract CT142: GD2.Ox40.CD28.z CAR T cell trial in neuroblastoma and osteosarcoma. Cancer Res 2022. [DOI: 10.1158/1538-7445.am2022-ct142] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Background: Chimeric antigen receptor T cells (CARTs) hold promising therapeutic potential for refractory tumors. GD2 is a tumor antigen expressed on neuroblastoma and osteosarcoma. In initial studies, T cells expressing 1st generation GD2-CARTs were shown to be safe and mediated modest antitumor activity in some patients with refractory neuroblastoma.
Methods: We developed a 3rd generation GD2-CART (GD2-CAR.OX40.28.z.ICD9) and conducted a phase I trial (NCT02107963) to determine the feasibility of producing and safety of administering escalating doses of GD2-CARTs in children and young adults with GD2+ solid tumors, including neuroblastoma and osteosarcoma, following cyclophosphamide-based lymphodepletion. Patient samples were evaluated for cytokine profile kinetics, immune phenotype analysis with mass cytometry (CyTOF), transcriptomic evaluation with RNA-sequencing (RNA-seq), epigenetic determination with Assay for Transposase-Accessible Chromatin using sequencing (ATAC-seq), and functional studies with flow cytometry.
Results: 15 patients aged 8-28 years were enrolled on four dose levels, of which 13 patients were infused. No dose-limiting toxicities were observed and administration of up to 1x107 GD2-CART/kg was feasible and safe for children and young adults with neuroblastoma and osteosarcoma. 15.4% (2/13) of patients experienced grade-1 cytokine release syndrome (CRS) and no neurological toxicity was observed. We measured the expansion and persistence of adoptively transferred GD2-CARTs in the peripheral blood. GD2-CARTs expanded in all patients receiving treatment, half of whom had expansion similar to that seen in clinically active CD19 and CD22 CARTs, but the GD2-CARTs had limited persistence. At Day 28 following GD2-CART infusion, 23.1% (3/13) of evaluable patients had progressive disease and 76.9% (10/13) had stable disease (SD). 3/10 SD patients remained stable at 60 days post-GD2-CART, but all patients eventually progressed. Since a major barrier to CART efficacy is inadequate CART expansion, we comprehensively evaluated for phenotypic, transcriptomic, and epigenetic immune profiles of patient apheresis, CART product, and post-treatment peripheral blood samples to identify determinants of CART expansion. GD2-CART expansion is significantly correlated with several T cell markers, and a larger baseline naïve and central memory T cell pool. Unique myeloid populations are associated with CART expansion. ATACseq identifies epigenetic differences in pre-treatment apheresis that may predict good CAR expansion in patients.
Conclusions: GD2-CART therapy following cyclophosphamide conditioning was well tolerated at all four dose levels in pediatric and young adult patients with neuroblastoma and osteosarcoma. Subsequent multi-dimensional analyses suggest key mechanisms underlying CART biology and function and highlight the potential of defining and applying molecular signatures in apheresis and CART product as biomarkers and prognostic indicators of CART expansion, with promise for advancing immunotherapies for solid tumor patients in the future.
Citation Format: Sneha Ramakrishna, Sabina Kaczanowska, Tara Murty, Cristina F. Contreras, Melinda Merchant, John Glod, Norma Gutierrez, Ahmad Alimadadi, David Stroncek, Steven Highfill, Caroline Duault, Priyanka B. Subrahmanyam, Tyson Holmes, Warren Reynolds, Reema Baskar, Antoine Barge, Hayley Lyon, Radim Moravec, Srinika Ranasinghe, Joyce Yu, Roshni Biswas, Samuel Pollack, Stephen Van Nostrand, James Lindsay, Mina Pichavant, Bita Sahaf, Sean C. Bendall, Andrew J. Gentles, Holden Maecker, Catherine C. Hedrick, Crystal Mackall, Rosandra Kaplan. GD2.Ox40.CD28.z CAR T cell trial in neuroblastoma and osteosarcoma [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr CT142.
Collapse
Affiliation(s)
- Sneha Ramakrishna
- 1Center for Cancer Cell Therapy, Stanford Cancer Institute, Stanford University School of Medicine, Stanford, CA
| | - Sabina Kaczanowska
- 2Pediatric Oncology Branch, Center for Cancer Research, NCI, NIH, Bethesda, MD
| | - Tara Murty
- 1Center for Cancer Cell Therapy, Stanford Cancer Institute, Stanford University School of Medicine, Stanford, CA
| | | | | | - John Glod
- 2Pediatric Oncology Branch, Center for Cancer Research, NCI, NIH, Bethesda, MD
| | | | | | - David Stroncek
- 5Center for Cellular Engineering, Department of Transfusion Medicine, NIH Clinical Center, Bethesda, MD
| | - Steven Highfill
- 5Center for Cellular Engineering, Department of Transfusion Medicine, NIH Clinical Center, Bethesda, MD
| | - Caroline Duault
- 6Institute for Immunity, Transplantation, and Infection, Stanford University School of Medicine, Stanford, CA
| | - Priyanka B. Subrahmanyam
- 6Institute for Immunity, Transplantation, and Infection, Stanford University School of Medicine, Stanford, CA
| | - Tyson Holmes
- 7Stanford Human Immune Monitoring Center, Stanford University School of Medicine, Stanford, CA
| | - Warren Reynolds
- 8Center for Cancer Cell Therapy, Stanford Cancer Institute, Stanford University School of Medicine, Palo Alto, CA
| | - Reema Baskar
- 9Stanford University School of Medicine, Stanford, CA
| | - Antoine Barge
- 10Department of Medicine (Biomedical Informatics/Quantitative Sciences unit), Stanford University School of Medicine, Stanford, CA
| | | | | | | | - Joyce Yu
- 13Dana-Farber Cancer Institute, Boston, MA
| | | | | | | | | | | | - Bita Sahaf
- 1Center for Cancer Cell Therapy, Stanford Cancer Institute, Stanford University School of Medicine, Stanford, CA
| | - Sean C. Bendall
- 14Department of Pathology, Stanford University, Stanford, CA
| | - Andrew J. Gentles
- 10Department of Medicine (Biomedical Informatics/Quantitative Sciences unit), Stanford University School of Medicine, Stanford, CA
| | - Holden Maecker
- 6Institute for Immunity, Transplantation, and Infection, Stanford University School of Medicine, Stanford, CA
| | | | - Crystal Mackall
- 1Center for Cancer Cell Therapy, Stanford Cancer Institute, Stanford University School of Medicine, Stanford, CA
| | - Rosandra Kaplan
- 2Pediatric Oncology Branch, Center for Cancer Research, NCI, NIH, Bethesda, MD
| |
Collapse
|
5
|
Baskar R, Chen AF, Favaro P, Reynolds W, Mueller F, Borges L, Jiang S, Park HS, Kool ET, Greenleaf WJ, Bendall SC. Integrating transcription-factor abundance with chromatin accessibility in human erythroid lineage commitment. Cell Rep Methods 2022; 2:100188. [PMID: 35463156 PMCID: PMC9017139 DOI: 10.1016/j.crmeth.2022.100188] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/28/2021] [Revised: 01/20/2022] [Accepted: 03/01/2022] [Indexed: 01/01/2023]
Abstract
Master transcription factors (TFs) directly regulate present and future cell states by binding DNA regulatory elements and driving gene-expression programs. Their abundance influences epigenetic priming to different cell fates at the chromatin level, especially in the context of differentiation. In order to link TF protein abundance to changes in TF motif accessibility and open chromatin, we developed InTAC-seq, a method for simultaneous quantification of genome-wide chromatin accessibility and intracellular protein abundance in fixed cells. Our method produces high-quality data and is a cost-effective alternative to single-cell techniques. We showcase our method by purifying bone marrow (BM) progenitor cells based on GATA-1 protein levels and establish high GATA-1-expressing BM cells as both epigenetically and functionally similar to erythroid-committed progenitors.
Collapse
Affiliation(s)
- Reema Baskar
- Department of Pathology, Stanford University, Stanford, CA 94305, USA
- Cancer Biology Program, Stanford University, Stanford, CA 94305, USA
| | - Amy F. Chen
- Department of Genetics, Stanford University, Stanford, CA 94305, USA
| | - Patricia Favaro
- Department of Pathology, Stanford University, Stanford, CA 94305, USA
| | - Warren Reynolds
- Department of Pathology, Stanford University, Stanford, CA 94305, USA
| | - Fabian Mueller
- Department of Genetics, Stanford University, Stanford, CA 94305, USA
| | - Luciene Borges
- Department of Pathology, Stanford University, Stanford, CA 94305, USA
| | - Sizun Jiang
- Department of Pathology, Stanford University, Stanford, CA 94305, USA
| | - Hyun Shin Park
- Department of Chemistry, Stanford University, Stanford, CA 94305, USA
| | - Eric T. Kool
- Department of Chemistry, Stanford University, Stanford, CA 94305, USA
- ChEM-H Institute, Stanford University, Stanford, CA 94305, USA
| | - William J. Greenleaf
- Department of Genetics, Stanford University, Stanford, CA 94305, USA
- Department of Applied Physics, Stanford University, Stanford, CA 94305, USA
- Chan Zuckerberg Biohub, San Francisco, CA, USA
| | - Sean C. Bendall
- Department of Pathology, Stanford University, Stanford, CA 94305, USA
| |
Collapse
|
6
|
Baskar R, Kimmey SC, Bendall SC. Revealing new biology from multiplexed, metal-isotope-tagged, single-cell readouts. Trends Cell Biol 2022; 32:501-512. [PMID: 35181197 DOI: 10.1016/j.tcb.2022.01.012] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2021] [Revised: 01/19/2022] [Accepted: 01/20/2022] [Indexed: 11/26/2022]
Abstract
Mass cytometry (MC) is a recent technology that pairs plasma-based ionization of cells in suspension with time-of-flight (TOF) mass spectrometry to sensitively quantify the single-cell abundance of metal-isotope-tagged affinity reagents to key proteins, RNA, and peptides. Given the ability to multiplex readouts (~50 per cell) and capture millions of cells per experiment, MC offers a robust way to assay rare, transitional cell states that are pertinent to human development and disease. Here, we review MC approaches that let us probe the dynamics of cellular regulation across multiple conditions and sample types in a single experiment. Additionally, we discuss current limitations and future extensions of MC as well as computational tools commonly used to extract biological insight from single-cell proteomic datasets.
Collapse
Affiliation(s)
- Reema Baskar
- Department of Pathology, School of Medicine, Stanford University, Stanford, CA, USA
| | - Sam C Kimmey
- Department of Pathology, School of Medicine, Stanford University, Stanford, CA, USA
| | - Sean C Bendall
- Department of Pathology, School of Medicine, Stanford University, Stanford, CA, USA.
| |
Collapse
|
7
|
Hartmann FJ, Mrdjen D, McCaffrey E, Glass DR, Greenwald NF, Bharadwaj A, Khair Z, Verberk SGS, Baranski A, Baskar R, Graf W, Van Valen D, Van den Bossche J, Angelo M, Bendall SC. Single-cell metabolic profiling of human cytotoxic T cells. Nat Biotechnol 2021; 39:186-197. [PMID: 32868913 PMCID: PMC7878201 DOI: 10.1038/s41587-020-0651-8] [Citation(s) in RCA: 131] [Impact Index Per Article: 43.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2020] [Accepted: 07/23/2020] [Indexed: 12/12/2022]
Abstract
Cellular metabolism regulates immune cell activation, differentiation and effector functions, but current metabolic approaches lack single-cell resolution and simultaneous characterization of cellular phenotype. In this study, we developed an approach to characterize the metabolic regulome of single cells together with their phenotypic identity. The method, termed single-cell metabolic regulome profiling (scMEP), quantifies proteins that regulate metabolic pathway activity using high-dimensional antibody-based technologies. We employed mass cytometry (cytometry by time of flight, CyTOF) to benchmark scMEP against bulk metabolic assays by reconstructing the metabolic remodeling of in vitro-activated naive and memory CD8+ T cells. We applied the approach to clinical samples and identified tissue-restricted, metabolically repressed cytotoxic T cells in human colorectal carcinoma. Combining our method with multiplexed ion beam imaging by time of flight (MIBI-TOF), we uncovered the spatial organization of metabolic programs in human tissues, which indicated exclusion of metabolically repressed immune cells from the tumor-immune boundary. Overall, our approach enables robust approximation of metabolic and functional states in individual cells.
Collapse
Affiliation(s)
- Felix J Hartmann
- Department of Pathology, School of Medicine, Stanford University, Palo Alto, CA, USA
| | - Dunja Mrdjen
- Department of Pathology, School of Medicine, Stanford University, Palo Alto, CA, USA
| | - Erin McCaffrey
- Department of Pathology, School of Medicine, Stanford University, Palo Alto, CA, USA
- Immunology Graduate Program, Stanford University, Palo Alto, CA, USA
| | - David R Glass
- Department of Pathology, School of Medicine, Stanford University, Palo Alto, CA, USA
- Immunology Graduate Program, Stanford University, Palo Alto, CA, USA
| | - Noah F Greenwald
- Department of Pathology, School of Medicine, Stanford University, Palo Alto, CA, USA
| | - Anusha Bharadwaj
- Department of Pathology, School of Medicine, Stanford University, Palo Alto, CA, USA
| | - Zumana Khair
- Department of Pathology, School of Medicine, Stanford University, Palo Alto, CA, USA
| | - Sanne G S Verberk
- Department of Molecular Cell Biology and Immunology, Amsterdam Cardiovascular Sciences, Cancer Center Amsterdam, Amsterdam UMC, Vrije Universiteit Amsterdam, Amsterdam, Netherlands
| | - Alex Baranski
- Department of Pathology, School of Medicine, Stanford University, Palo Alto, CA, USA
| | - Reema Baskar
- Department of Pathology, School of Medicine, Stanford University, Palo Alto, CA, USA
| | - William Graf
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
| | - David Van Valen
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Jan Van den Bossche
- Department of Molecular Cell Biology and Immunology, Amsterdam Cardiovascular Sciences, Cancer Center Amsterdam, Amsterdam UMC, Vrije Universiteit Amsterdam, Amsterdam, Netherlands
| | - Michael Angelo
- Department of Pathology, School of Medicine, Stanford University, Palo Alto, CA, USA
| | - Sean C Bendall
- Department of Pathology, School of Medicine, Stanford University, Palo Alto, CA, USA.
| |
Collapse
|
8
|
Fayemi OE, Baskar R, Adekunle AS, Sherif EM, Ebenso EE. SPEEK/ZnO Nanocomposite Modified Gold Electrode for Electrochemical Detection of Dopamine. ELECTROANAL 2020. [DOI: 10.1002/elan.202060210] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
- Omolola E. Fayemi
- Department of Chemistry, School of Physical and Chemical Sciences, Faculty of Natural and Agricultural Sciences North-West University (Mafikeng Campus) Private Bag X2046 Mmabatho 2735 South Africa
- Material Science Innovation and Modelling (MaSIM) Research Focus Area, Faculty of Natural and Agricultural Sciences North-West University (Mafikeng Campus) Private Bag X2046 Mmabatho 2735 South Africa
| | - R. Baskar
- Material Science Innovation and Modelling (MaSIM) Research Focus Area, Faculty of Natural and Agricultural Sciences North-West University (Mafikeng Campus) Private Bag X2046 Mmabatho 2735 South Africa
- Department of Chemistry Indian Institute of Technology, Madras Chennai 600036, Tamil Nadu India
| | | | - El‐Sayed M. Sherif
- Mechanical Engineering Department, College of Engineering King Saud University P.O.Box800 Al-Riyadh 11421 SaudiArabia
- Electrochemistry and Corrosion Laboratory, Department of Physical Chemistry National Research Centre El-Buhouth St., Dokki 12622 Cairo Egypt
| | - Eno E. Ebenso
- Department of Chemistry, School of Physical and Chemical Sciences, Faculty of Natural and Agricultural Sciences North-West University (Mafikeng Campus) Private Bag X2046 Mmabatho 2735 South Africa
- Material Science Innovation and Modelling (MaSIM) Research Focus Area, Faculty of Natural and Agricultural Sciences North-West University (Mafikeng Campus) Private Bag X2046 Mmabatho 2735 South Africa
- Department of Chemistry, College of Science, Engineering and Technology University of South Africa Florida, Roodepoort South Africa 1710
| |
Collapse
|
9
|
Kim Y, Caleron A, Glass D, Tsai A, Favaro P, Baskar R, Hartmann F, Greenleaf W, Bendall S. 2015 – A HIGHLY MULTIPLEXED SINGLE CELL PROTEOMIC SCREEN REVEALS THE PHENOTYPIC AND FUNCTIONAL LANDSCAPE OF THE HUMAN LYMPHO-MYELOID DIFFERENTIATION AXIS. Exp Hematol 2020. [DOI: 10.1016/j.exphem.2020.09.177] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
|
10
|
Grandi FC, Baskar R, Smeriglio P, Murkherjee S, Indelli PF, Amanatullah DF, Goodman S, Chu C, Bendall S, Bhutani N. Single-cell mass cytometry reveals cross-talk between inflammation-dampening and inflammation-amplifying cells in osteoarthritic cartilage. Sci Adv 2020; 6:eaay5352. [PMID: 32201724 PMCID: PMC7069698 DOI: 10.1126/sciadv.aay5352] [Citation(s) in RCA: 39] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/28/2019] [Accepted: 12/17/2019] [Indexed: 05/06/2023]
Abstract
Aging or injury leads to degradation of the cartilage matrix and the development of osteoarthritis (OA). Because of a paucity of single-cell studies of OA cartilage, little is known about the interpatient variability in its cellular composition and, more importantly, about the cell subpopulations that drive the disease. Here, we profiled healthy and OA cartilage samples using mass cytometry to establish a single-cell atlas, revealing distinct chondrocyte progenitor and inflammation-modulating subpopulations. These rare populations include an inflammation-amplifying (Inf-A) population, marked by interleukin-1 receptor 1 and tumor necrosis factor receptor II, whose inhibition decreased inflammation, and an inflammation-dampening (Inf-D) population, marked by CD24, which is resistant to inflammation. We devised a pharmacological strategy targeting Inf-A and Inf-D cells that significantly decreased inflammation in OA chondrocytes. Using our atlas, we stratified patients with OA in three groups that are distinguished by the relative proportions of inflammatory to regenerative cells, making it possible to devise precision therapeutic approaches.
Collapse
Affiliation(s)
- Fiorella Carla Grandi
- Department of Orthopedic Surgery, School of Medicine, Stanford University, Stanford, CA 94303, USA
| | - Reema Baskar
- Department of Pathology, School of Medicine, Stanford University, Stanford, CA 94303, USA
| | - Piera Smeriglio
- Department of Orthopedic Surgery, School of Medicine, Stanford University, Stanford, CA 94303, USA
| | - Shravani Murkherjee
- Department of Orthopedic Surgery, School of Medicine, Stanford University, Stanford, CA 94303, USA
| | | | - Derek F. Amanatullah
- Department of Orthopedic Surgery, School of Medicine, Stanford University, Stanford, CA 94303, USA
| | - Stuart Goodman
- Department of Orthopedic Surgery, School of Medicine, Stanford University, Stanford, CA 94303, USA
| | - Constance Chu
- Department of Orthopedic Surgery, School of Medicine, Stanford University, Stanford, CA 94303, USA
- Palo Alto Veterans Administration Health Care System, Palo Alto, CA 94304, USA
| | - Sean Bendall
- Department of Pathology, School of Medicine, Stanford University, Stanford, CA 94303, USA
| | - Nidhi Bhutani
- Department of Orthopedic Surgery, School of Medicine, Stanford University, Stanford, CA 94303, USA
- Corresponding author.
| |
Collapse
|
11
|
Baskar R, Fienberg HG, Khair Z, Favaro P, Kimmey S, Green DR, Nolan GP, Plevritis S, Bendall SC. TRAIL-induced variation of cell signaling states provides nonheritable resistance to apoptosis. Life Sci Alliance 2019; 2:e201900554. [PMID: 31704709 PMCID: PMC6848270 DOI: 10.26508/lsa.201900554] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2019] [Revised: 10/24/2019] [Accepted: 10/25/2019] [Indexed: 02/06/2023] Open
Abstract
TNFα-related apoptosis-inducing ligand (TRAIL), specifically initiates programmed cell death, but often fails to eradicate all cells, making it an ineffective therapy for cancer. This fractional killing is linked to cellular variation that bulk assays cannot capture. Here, we quantify the diversity in cellular signaling responses to TRAIL, linking it to apoptotic frequency across numerous cell systems with single-cell mass cytometry (CyTOF). Although all cells respond to TRAIL, a variable fraction persists without apoptotic progression. This cell-specific behavior is nonheritable where both the TRAIL-induced signaling responses and frequency of apoptotic resistance remain unaffected by prior exposure. The diversity of signaling states upon exposure is correlated to TRAIL resistance. Concomitantly, constricting the variation in signaling response with kinase inhibitors proportionally decreases TRAIL resistance. Simultaneously, TRAIL-induced de novo translation in resistant cells, when blocked by cycloheximide, abrogated all TRAIL resistance. This work highlights how cell signaling diversity, and subsequent translation response, relates to nonheritable fractional escape from TRAIL-induced apoptosis. This refined view of TRAIL resistance provides new avenues to study death ligands in general.
Collapse
Affiliation(s)
- Reema Baskar
- Cancer Biology Program, Stanford University School of Medicine, Stanford, CA, USA
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
| | - Harris G Fienberg
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
- Immunology Program, Stanford University School of Medicine, Stanford, CA, USA
| | - Zumana Khair
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
| | - Patricia Favaro
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
| | - Sam Kimmey
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
- Developmental Biology Program, Stanford University School of Medicine, Stanford, CA, USA
| | | | - Garry P Nolan
- Baxter Laboratory, Stanford University School of Medicine, Stanford, CA, USA
| | - Sylvia Plevritis
- Cancer Biology Program, Stanford University School of Medicine, Stanford, CA, USA
| | - Sean C Bendall
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
- Immunology Program, Stanford University School of Medicine, Stanford, CA, USA
| |
Collapse
|
12
|
Kimmey SC, Borges L, Baskar R, Bendall SC. Parallel analysis of tri-molecular biosynthesis with cell identity and function in single cells. Nat Commun 2019; 10:1185. [PMID: 30862852 PMCID: PMC6414513 DOI: 10.1038/s41467-019-09128-7] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2018] [Accepted: 02/05/2019] [Indexed: 12/02/2022] Open
Abstract
Cellular products derived from the activity of DNA, RNA, and protein synthesis collectively control cell identity and function. Yet there is little information on how these three biosynthesis activities are coordinated during transient and sparse cellular processes, such as activation and differentiation. Here, we describe Simultaneous Overview of tri-Molecule Biosynthesis (SOM3B), a molecular labeling and simultaneous detection strategy to quantify DNA, RNA, and protein synthesis in individual cells. Comprehensive interrogation of biosynthesis activities during transient cell states, such as progression through cell cycle or cellular differentiation, is achieved by partnering SOM3B with parallel quantification of select biomolecules with conjugated antibody reagents. Here, we investigate differential de novo DNA, RNA, and protein synthesis dynamics in transformed human cell lines, primary activated human immune cells, and across the healthy human hematopoietic continuum, all at a single-cell resolution.
Collapse
Affiliation(s)
- Samuel C Kimmey
- Department of Developmental Biology, Stanford University School of Medicine, Stanford, CA, 94305, USA
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, 94305, USA
| | - Luciene Borges
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, 94305, USA
| | - Reema Baskar
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, 94305, USA
- Cancer Biology PhD Program, Stanford University School of Medicine, Stanford, CA, 94305, USA
| | - Sean C Bendall
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, 94305, USA.
| |
Collapse
|
13
|
Sivarajasekar N, Balasubramani K, Baskar R, Sivamani S, Ganesh Moorthy I. Eco-Friendly Acetaminophen Sequestration Using Waste Cotton Seeds: Equilibrium, Optimization and Validation Studies. J WATER CHEM TECHNO+ 2019. [DOI: 10.3103/s1063455x18060048] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
|
14
|
Kliver S, Rayko M, Komissarov A, Bakin E, Zhernakova D, Prasad K, Rushworth C, Baskar R, Smetanin D, Schmutz J, Rokhsar DS, Mitchell-Olds T, Grossniklaus U, Brukhin V. Assembly of the Boechera retrofracta Genome and Evolutionary Analysis of Apomixis-Associated Genes. Genes (Basel) 2018; 9:genes9040185. [PMID: 29597328 PMCID: PMC5924527 DOI: 10.3390/genes9040185] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [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: 02/14/2018] [Revised: 03/21/2018] [Accepted: 03/22/2018] [Indexed: 11/16/2022] Open
Abstract
Closely related to the model plant Arabidopsis thaliana, the genus Boechera is known to contain both sexual and apomictic species or accessions. Boechera retrofracta is a diploid sexually reproducing species and is thought to be an ancestral parent species of apomictic species. Here we report the de novo assembly of the B. retrofracta genome using short Illumina and Roche reads from 1 paired-end and 3 mate pair libraries. The distribution of 23-mers from the paired end library has indicated a low level of heterozygosity and the presence of detectable duplications and triplications. The genome size was estimated to be equal 227 Mb. N50 of the assembled scaffolds was 2.3 Mb. Using a hybrid approach that combines homology-based and de novo methods 27,048 protein-coding genes were predicted. Also repeats, transfer RNA (tRNA) and ribosomal RNA (rRNA) genes were annotated. Finally, genes of B. retrofracta and 6 other Brassicaceae species were used for phylogenetic tree reconstruction. In addition, we explored the histidine exonuclease APOLLO locus, related to apomixis in Boechera, and proposed model of its evolution through the series of duplications. An assembled genome of B. retrofracta will help in the challenging assembly of the highly heterozygous genomes of hybrid apomictic species.
Collapse
Affiliation(s)
- Sergei Kliver
- Dobzhansky Center for Genome Bioinformatics, St. Petersburg State Universit, Sredniy Prospekt, 41, Vasilievsky Island, 199004 St. Petersburg, Russia.
- All-Russia Research Institute for Agricultural Microbiology, Podbelskogo sh. 3, Pushkin, 196608 St. Petersburg, Russia.
| | - Mike Rayko
- Dobzhansky Center for Genome Bioinformatics, St. Petersburg State Universit, Sredniy Prospekt, 41, Vasilievsky Island, 199004 St. Petersburg, Russia.
| | - Alexey Komissarov
- Dobzhansky Center for Genome Bioinformatics, St. Petersburg State Universit, Sredniy Prospekt, 41, Vasilievsky Island, 199004 St. Petersburg, Russia.
| | - Evgeny Bakin
- Dobzhansky Center for Genome Bioinformatics, St. Petersburg State Universit, Sredniy Prospekt, 41, Vasilievsky Island, 199004 St. Petersburg, Russia.
| | - Daria Zhernakova
- Dobzhansky Center for Genome Bioinformatics, St. Petersburg State Universit, Sredniy Prospekt, 41, Vasilievsky Island, 199004 St. Petersburg, Russia.
| | - Kasavajhala Prasad
- Department of Biology, Colorado State University, Fort Collins, CO 80523; USA.
| | - Catherine Rushworth
- University and Jepson Herbaria, University of California, Berkeley, NC 94720; USA.
| | - R Baskar
- Department of Biotechnology, Indian Institute of Technology. Sardar Patel road, 600036 Chennai, India.
| | - Dmitry Smetanin
- Department of Plant and Microbial Biology Zurich-Basel Plant Science Center, University of Zurich, Zollikerstrasse 107, 8008 Zurich; Switzerland.
| | - Jeremy Schmutz
- Department of Energy Joint Genome Institute, Walnut Creek, CA 94598; USA.
- HudsonAlpha Institute of Biotechnology, Huntsville, AL 35806; USA.
| | - Daniel S Rokhsar
- Department of Energy Joint Genome Institute, Walnut Creek, CA 94598; USA.
| | | | - Ueli Grossniklaus
- Department of Plant and Microbial Biology Zurich-Basel Plant Science Center, University of Zurich, Zollikerstrasse 107, 8008 Zurich; Switzerland.
| | - Vladimir Brukhin
- Dobzhansky Center for Genome Bioinformatics, St. Petersburg State Universit, Sredniy Prospekt, 41, Vasilievsky Island, 199004 St. Petersburg, Russia.
- Department of Plant Embryology and Reproductive Biology, Komarov Botanical Institute RAS, 197376 St. Petersburg, Russia.
| |
Collapse
|
15
|
Bhushan S, Singh AK, Mohanraj N, Krishnamoorthy J, Baskar R. Reproductive age affects the somatic mutation rates in the transgenerational progenies in Arabidopsis. Mech Dev 2017. [DOI: 10.1016/j.mod.2017.04.398] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
|
16
|
Venkatasubbu GD, Baskar R, Anusuya T, Seshan CA, Chelliah R. Toxicity mechanism of titanium dioxide and zinc oxide nanoparticles against food pathogens. Colloids Surf B Biointerfaces 2016; 148:600-606. [PMID: 27694049 DOI: 10.1016/j.colsurfb.2016.09.042] [Citation(s) in RCA: 63] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2016] [Revised: 09/12/2016] [Accepted: 09/27/2016] [Indexed: 11/29/2022]
Abstract
Food preservation is an important field of research. It extends the shelf life of major food products. Our current study is based on food preservation through TiO2 and ZnO nanoparticles. TiO2 and ZnO are biocompatible nanomaterial. The biocompatibility of the materials were established through toxicity studies on cell lines. Titanium dioxide and Zinc Oxide nanoparticle were synthesized by wet chemical process. They are characterized by X-Ray diffraction and TEM. The antibacterial activities of both the materials were analysed to ensure their effectiveness as food preservative against Salmonella typhi, Klebsiella pneumoniae and Shigella flexneri. The results indicates that TiO2 and ZnO nanoparticle inhibits Salmonella, Klebsiella and Shigella. The mode of action is by the generation of ROS in cases of Salmonella, Klebsiella. Mode of action in Shigella is still unclear. It was also proved that TiO2 and ZnO nanoparticle are biocompatible materials.
Collapse
Affiliation(s)
| | - R Baskar
- Department of Biotechnology, University of Madras, Chennai, Tamil Nadu, India
| | - T Anusuya
- Department of Nanotechnology, SRM University, Kattankulathur, Tamil Nadu, India
| | - C Arun Seshan
- Crystal Growth Centre, Anna University, Chennai, Tamil Nadu, India
| | | |
Collapse
|
17
|
Brichkina A, Nguyen NT, Baskar R, Wee S, Gunaratne J, Robinson RC, Bulavin DV. Proline isomerisation as a novel regulatory mechanism for p38MAPK activation and functions. Cell Death Differ 2016; 23:1592-601. [PMID: 27233083 DOI: 10.1038/cdd.2016.45] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2015] [Revised: 04/05/2016] [Accepted: 04/15/2016] [Indexed: 12/22/2022] Open
Abstract
The stress-induced p38 mitogen-activated protein kinase (MAPK) pathway plays an essential role in multiple physiological processes, including cancer. In turn, p38MAPK phosphorylation at Thr180 and Tyr182 is a key regulatory mechanism for its activation and functions. Here we show that this mechanism is actively regulated through isomerisation of Pro224. Different cyclophilins can isomerise this proline residue and modulate the ability of upstream kinases to phosphorylate Thr180 and Tyr182. In vivo mutation of Pro224 to Ile in endogenous p38MAPK significantly reduced its phosphorylation and activity. This resulted in attenuation of p38MAPK signalling, which in turn caused an enhanced apoptosis and sensitivity to a DNA-damaging drug, cisplatin. We further found a reduction in size and number of lesions in homozygous mice carrying the p38MAPK P224I substitution in a K-ras model of lung tumorigenesis. We propose that cyclophilin-dependent isomerisation of p38MAPK is an important novel mechanism in regulating p38MAPK phosphorylation and functions. Thus, inhibition of this process, including with drugs that are in clinical trials, may improve the efficacy of current anti-cancer therapeutic regimes.
Collapse
Affiliation(s)
- A Brichkina
- Institute of Molecular and Cell Biology, A*STAR (Agency for Science, Technology and Research), Biopolis, Singapore 138673, Singapore
| | - N Tm Nguyen
- Institute of Molecular and Cell Biology, A*STAR (Agency for Science, Technology and Research), Biopolis, Singapore 138673, Singapore
| | - R Baskar
- Institute of Molecular and Cell Biology, A*STAR (Agency for Science, Technology and Research), Biopolis, Singapore 138673, Singapore
| | - S Wee
- Institute of Molecular and Cell Biology, A*STAR (Agency for Science, Technology and Research), Biopolis, Singapore 138673, Singapore
| | - J Gunaratne
- Institute of Molecular and Cell Biology, A*STAR (Agency for Science, Technology and Research), Biopolis, Singapore 138673, Singapore
| | - R C Robinson
- Institute of Molecular and Cell Biology, A*STAR (Agency for Science, Technology and Research), Biopolis, Singapore 138673, Singapore.,Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 117597, Singapore
| | - D V Bulavin
- Institute for Research on Cancer and Aging of Nice (IRCAN), INSERM, U1081-UMR CNRS 7284, University of Nice - Sophia Antipolis, Centre Antoine Lacassagne, Nice, France
| |
Collapse
|
18
|
Baskar R, Umamaheswari K, Jeyakumar D, Alli M. Molecular diagnosis and antifungal susceptibility profiles of rare isolates of filamentous fungi among patients with cancer from South India. Int J Infect Dis 2016. [DOI: 10.1016/j.ijid.2016.02.679] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
|
19
|
Sivarajasekar N, Baskar R. Adsorption of basic red 9 on activated waste Gossypium hirsutum seeds: Process modeling, analysis and optimization using statistical design. J IND ENG CHEM 2014. [DOI: 10.1016/j.jiec.2013.10.058] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
|
20
|
Umamaheswari K, Baskar R, Chandru K, Rajendiran N, Chandirasekar S. Antibacterial activity of gold nanoparticles and their toxicity assessment. BMC Infect Dis 2014. [PMCID: PMC4080108 DOI: 10.1186/1471-2334-14-s3-p64] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
|
21
|
Baskar R, Baby C, Moni M, Subramanian K. Synthesis, characterization and dynamic NMR studies of a novel chalcone based N-substituted morpholine derivative. J Mol Struct 2013. [DOI: 10.1016/j.molstruc.2013.02.029] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
|
22
|
Baskar R, Gopiraman M, Kesavan D, Kim IS, Subramanian K. Synthesis, Characterization, and Electrochemical Studies of Novel Biphenyl Based Compounds. Ind Eng Chem Res 2012. [DOI: 10.1021/ie201470j] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- R. Baskar
- Department
of Chemistry, Anna University, Chennai,
India
| | - M. Gopiraman
- Nano Fusion Technology
Research
Group, Department of Functional Machinery and Mechanics, Faculty of
Textile Science and Technology, Shinshu University, Nagano 386-8567, Japan
- Department of Chemistry, National Institute of Technology, Tiruchirappalli,
India
| | - D. Kesavan
- Department of Chemistry, National Institute of Technology, Tiruchirappalli,
India
| | - Ick Soo Kim
- Nano Fusion Technology
Research
Group, Department of Functional Machinery and Mechanics, Faculty of
Textile Science and Technology, Shinshu University, Nagano 386-8567, Japan
| | - K. Subramanian
- Department
of Chemistry, Anna University, Chennai,
India
| |
Collapse
|
23
|
Baskar R, Subramanian K. Synthesis, characterization and fluorescence studies of novel bi-phenyl based acrylate and methacrylate. Spectrochim Acta A Mol Biomol Spectrosc 2011; 79:1992-1997. [PMID: 21703915 DOI: 10.1016/j.saa.2011.05.105] [Citation(s) in RCA: 6] [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] [Subscribe] [Scholar Register] [Received: 03/28/2011] [Revised: 05/26/2011] [Accepted: 05/30/2011] [Indexed: 05/31/2023]
Abstract
4-[(1E)-3-(biphenyl-4-yl)buta-1,3-dien-1-yl]phenyl prop-2-enoate (ACH) and 4-[(1E)-3-(biphenyl-4-yl)buta-1,3-dien-1-yl]phenyl 2-methylprop-2-enoate (MCH) was synthesized from biphenyl in three steps and their structures were confirmed by elemental analysis, IR, NMR (1H, 13C, DEPT135, 1H-1H COSY, 1H-13C HSQC and 1H-13C HMBC) spectroscopic techniques. In this present study, various physicochemical characteristics we demonstrate solubility, color, absorbance and fluorescence property of novel biphenyl based acrylate and methacrylate measured in different solvents like benzene, dichloromethane, tetrahydrofuran, acetonitrile, dimethylsulfoxide and ethanol.
Collapse
Affiliation(s)
- R Baskar
- Department of Chemistry, Anna University, Chennai, India
| | | |
Collapse
|
24
|
Reddy SS, Ramatholisamma P, Ramesh B, Baskar R, Saralakumari D. Beneficiary effect of Tinospora cordifolia against high-fructose diet induced abnormalities in carbohydrate and lipid metabolism in Wistar rats. Horm Metab Res 2009; 41:741-6. [PMID: 19764107 DOI: 10.1055/s-0029-1220922] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Abstract
High intake of dietary fructose has been shown to exert a number of adverse metabolic eff ects in humans and experimental animals. The present study was designed to investigate the eff ect of the aqueous extract of Tinospora cordifolia stem (TCAE) on the adverse eff ects of fructose loading toward carbohydrate and lipid metabolism in rats. Adult male Wistar rats of body weight around 200 g were divided into four groups, two of which were fed with starch diet and the other two with high fructose (66 %) diet. Plant extract of TC (400 mg/kg/day) was administered orally to each group of the starch fed rats and the highfructose fed rats. At the end of 60 days of experimental period, biochemical parameters related to carbohydrate and lipid metabolism were assayed. Hyperglycemia, hyperinsulinemia, hypertriglyceridemia, insulin resistance, and elevated levels of hepatic total lipids, cholesterol, triglycerides, and free fatty acids (p < 0.05) observed in fructose-fed rats were completely prevented with TCAE treatment. Alterations in the activities of enzymes of glucose metabolism (hexokinase, phosphofructokinase, pyruvate kinase, glucose-6-phosphatase, fructose-1,6-bisphosphatase, and glucose-6-phosphate dehydrogenase) and lipid metabolism (fatty acid synthetase, lipoprotein lipase, and malic enzyme) as observed in the high fructose-fed rats were prevented with TCAE administration. In conclusion, our fi ndings indicate improvement of glucose and lipid metabolism in high-fructose fed rats by treatment with Tinospora cordifolia, and suggest that the plant can be used as an adjuvant for the prevention and/or management of insulin resistance and disorders related to it.
Collapse
Affiliation(s)
- S Sreenivasa Reddy
- Department of Biochemistry, Sri Krishnadevaraya University, Anantapur, Andhra Pradesh, India
| | | | | | | | | |
Collapse
|
25
|
Subhasree B, Baskar R, Laxmi Keerthana R, Lijina Susan R, Rajasekaran P. Evaluation of antioxidant potential in selected green leafy vegetables. Food Chem 2009. [DOI: 10.1016/j.foodchem.2009.01.029] [Citation(s) in RCA: 85] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
|
26
|
Karuna R, Reddy SS, Baskar R, Saralakumari D. Antioxidant potential of aqueous extract of Phyllanthus amarus in rats. Indian J Pharmacol 2009; 41:64-7. [PMID: 20336219 PMCID: PMC2841234 DOI: 10.4103/0253-7613.51342] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.5] [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: 07/12/2008] [Revised: 09/29/2008] [Accepted: 03/30/2009] [Indexed: 11/13/2022] Open
Abstract
OBJECTIVE Increased levels of oxidative stress may be implicated in the etiology of many pathological conditions. Protective antioxidant action imparted by many plant extracts and plant products make them promising therapeutic drugs for free radical induced pathologies. In this study we assessed the antioxidant potential of Phyllanthus amarus (Euphorbiaceae). MATERIALS AND METHODS EXPERIMENTAL RATS WERE DIVIDED INTO TWO GROUPS: Control and Phyllanthus amarus (P. amarus) treated. Treated rats received P. amarus aqueous extract (PAAEt) at a dose of 200 mg/kg body wt/day for 8 weeks. After the treatment period of 8 weeks lipid peroxidation (LPO), vitamin C, uric acid and reduced glutathione (GSH) were estimated in plasma and antioxidant enzymes: Glutathione peroxidase (GPx), catalase (CAT) and superoxide dismutase (SOD) were also assayed. Genotoxicity of PAAEt was assessed by single cell gel electrophoresis (SCGE) of lymphocytes under both in vitro and in vivo conditions. The protective role of PAAEt against hydrogen peroxide (H(2)O(2)), streptozotocin (STZ) and nitric oxide generating system induced lymphocyte DNA damage was also assessed by SCGE. RESULTS PAAEt treated rats showed a significant decrease in plasma LPO and a significant increase in plasma vitamin C, uric acid, GSH levels and GPx, CAT and SOD activities. SCGE experiment reveals that PAAEt was devoid of genotoxicity and had a significant protective effect against H(2)O(2), STZ and nitric oxide (NO) induced lymphocyte DNA damage. CONCLUSION The results suggest the non-toxic nature of PAAEt and consumption of PAAEt can be linked to improved antioxidant status and reduction in the risk of oxidative stress.
Collapse
Affiliation(s)
- R. Karuna
- Department of Biochemistry, Sri Krishnadevaraya University, Anantapur - 515 003, Andhra Pradesh, India
| | - S. Sreenivasa Reddy
- Department of Biochemistry, Sri Krishnadevaraya University, Anantapur - 515 003, Andhra Pradesh, India
| | - R. Baskar
- Department of Biochemistry, Sri Krishnadevaraya University, Anantapur - 515 003, Andhra Pradesh, India
| | - D. Saralakumari
- Department of Biochemistry, Sri Krishnadevaraya University, Anantapur - 515 003, Andhra Pradesh, India
| |
Collapse
|
27
|
Abstract
The study was aimed to examine if oral administration of the aqueous extract of the whole plant OCIMUM SANCTUM (OS) protects against the development of insulin resistance in fructose fed rats. Male Wister rats were randomly divided into four groups of eight animals each: group-S (starch diet), group-F (fructose diet), group-F+OS (fructose diet along with OCIMUM SANCTUM extract at a dose of 200 mg/kg), group-S+OS (starch diet along with OCIMUM SANCTUM). During the experimental period of 60 days body weight, plasma glucose, insulin, and triglycerides were measured at an interval of 15 days. Insulin sensitivity was assessed at the end of experimental period by measuring glucose-insulin index, which is the product of the areas under the curve of glucose and insulin during oral glucose tolerance test. The nontoxic nature of OS was revealed by unaltered body weight, plasma glucose, insulin, and triglyceride levels in group-S+OS when compared with group-S. A significant gain in body weight, hyperglycemia, hyperinsulinemia, hypertriglyceridemia, and insulin resistance were observed in group-F when compared with group-S. OS treatment prevented the observed fructose induced alterations in group-F+OS. In conclusion, our results suggests that oral administration of OS aqueous extract could delay the development of insulin resistance in rats and may be used as an adjuvant therapy for treating diabetic patients with insulin resistance.
Collapse
Affiliation(s)
- S S Reddy
- Department of Biochemistry, Sri Krishnadevaraya University, Anantapur, Andhra Pradesh, India
| | | | | | | |
Collapse
|
28
|
Baskar S, Baskar R, Lee N, Kaushik A, Theophilus PK. Precipitation of iron in microbial mats of the spring waters of Borra Caves, Vishakapatnam, India: some geomicrobiological aspects. ACTA ACUST UNITED AC 2007. [DOI: 10.1007/s00254-007-1159-y] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
|
29
|
Baskar R, Rajeswari V, Kumar TS. In vitro antioxidant studies in leaves of Annona species. Indian J Exp Biol 2007; 45:480-5. [PMID: 17569293] [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] [Subscribe] [Scholar Register] [Indexed: 05/15/2023]
Abstract
Antioxidant potential of leaves of three different species of Annona was studied by using different in vitro models eg., 1,1-diphenyl-2-picryl hydrazyl (DPPH), 2,2-azinobis-(3-ethylbenzothizoline-6-sulphonate) (ABTS), nitric oxide, superoxide, hydroxy radical and lipid peroxidation. The ethanolic extract of A. muricata at 500 microg/ml showed maximum scavenging activity (90.05%) of ABTS radical cation followed by the scavenging of hydroxyl radical (85.88%) and nitric oxide (72.60%) at the same concentration. However, the extract showed only moderate lipid peroxidation inhibition activity. In contrast, the extract of A. reticulata showed better activity in quenching DPPH (89.37%) and superoxide radical (80.88%) respectively. A.squamosa extract exhibited least inhibition in all in vitro antioxidant models excepting hydroxyl radical (79.79%). These findings suggest that the extracts of A. muricata possess potent in vitro antioxidant activity as compared to leaves of A. squamosa and A. reticulata suggesting its role as an effective free radical scavenger, augmenting its therapeutic
Collapse
Affiliation(s)
- R Baskar
- Department of Biotechnology, Kumaraguru College of Technology, Coimbatore 641 006, India.
| | | | | |
Collapse
|
30
|
Sailaja YR, Baskar R, Srinivas Rao CS, Saralakumari D. Membrane lipids and protein-bound carbohydrates status during the maturation of reticulocytes to erythrocytes in type 2 diabetics. Clin Chim Acta 2004; 341:185-92. [PMID: 14967175 DOI: 10.1016/j.cccn.2003.12.003] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2003] [Revised: 12/01/2003] [Accepted: 12/01/2003] [Indexed: 12/16/2022]
Abstract
BACKGROUND The reticulocyte maturation process is an ideal model for the study of biochemical alterations seen during final stage of erythropoiesis under disease conditions. In this study, determined whether type 2 diabetes has any effect on membrane lipids and protein-bound carbohydrates during the maturation of reticulocytes to erythrocytes. SUBJECTS AND METHODS Lipids (cholesterol and phospholipids) and protein-bound carbohydrates (hexose, hexosamine and sialic acid) were extracted and estimated in plasma, membrane of reticulocytes and erythrocytes from 20 treated but uncontrolled type 2 diabetic volunteers and age matched controls. RESULTS Plasma, membranes of reticulocytes and erythrocytes of diabetics showed increase in cholesterol (35.7%, 8.7% and 16.4%); phospholipids (43.4%, 18.8% and 8.2%); hexose (34.1%, 19.3% and 8.2%) and decrease in hexosamine (11.9%, 7.3% and 14.7%); and sialic acid (34.1%, 19.3% and 32.0%) compared to controls. As reticulocytes matured to erythrocytes, cholesterol, phospholipids, hexosamine and sialic acid levels were decreased; C/P ratio and hexose levels were increased in both controls and diabetics. However, these alterations were more intensified in diabetics. CONCLUSION These alterations in diabetic patients may indicate the existence of one or both of the following conditions: acceleration of maturation processes and/or decreased red blood cell life span.
Collapse
Affiliation(s)
- Y R Sailaja
- Department of Biochemistry, Sri Krishnadevaraya University, Anantapur 515 003, Andhra Pradesh, India
| | | | | | | |
Collapse
|
31
|
Abstract
Free radical-induced lipid peroxidation has been associated with numerous disease processes including diabetes mellitus. The extent of lipid peroxidation (LPO) and antioxidant defense system [i.e., levels of glutathione (GSH), glucose-6-phosphate dehydrogenase (G6PDH), glutathione reductase (GR), glutathione peroxidase (GPx), glutathione-S-transferase (GST), and catalase (CAT)] were evaluated in reticulocytes and erythrocytes of type 2 diabetic males and age-matched controls. Type 2 diabetics have shown increased lipid peroxidation and decreased levels of GSH, GR, GPx, G6PDH, and GST both in reticulocytes and erythrocytes compared to controls, indicating the presence of oxidative stress and defective antioxidant systems in these patients. CAT activity is found to be enhanced in both the reticulocytes and erythrocytes of diabetics, with a greater percentage enhancement in reticulocytes. The extent of increase in lipid peroxidation is greater in erythrocytes compared to reticulocytes in these patients. Furthermore, the maturation of reticulocytes to erythrocytes resulted in decreased GSH and decreased activities of all antioxidant enzymes (except CAT) both in normals and type 2 diabetes individuals, indicating decreased scavenging capacity as reticulocytes mature to erythrocytes. These maturational alterations are further intensified in type 2 diabetics. The present study reveals that the alterations in lipid peroxidation and antioxidant system lean toward early senescence of erythrocytes in type 2 diabetic patients.
Collapse
Affiliation(s)
- Y R Sailaja
- Department of Biochemistry, Sri Krishnadevaraya University, Anantapur, India
| | | | | |
Collapse
|
32
|
Baskar R, Anantharaman N, Babu JS, Sundaram S. L-glutamic acid production in a novel three phase fluidized bed reactor using coimmobilized bio-catalyst. Biomed Sci Instrum 2001; 37:457-62. [PMID: 11347434] [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] [Subscribe] [Scholar Register] [Indexed: 04/16/2023]
Abstract
The production of L-Glutamic acid has been studied using coimmobilized whole cells of pseudomonas reptilivora and micrococcus glutamicus in a three phase fluidized bed bioreactor with selected production medium enriched with glucose. The effect of initial substrate concentration, temperature, pH and aeration rate on the yield of glutamic acid has been investigated. It has been found that the acid production increases exponentially with substrate concentration and mass transfer co-efficient varied linearly with temperature and aeration rate. The optimum temperature and pH are 31 degree Celsius and 7.2 respectively.
Collapse
Affiliation(s)
- R Baskar
- Department of Chemical Engineering, Regional Engineering College, Tiruchirappali-620 015, India
| | | | | | | |
Collapse
|
33
|
Baskar R, Chhabra P, Mascarenhas P, Nanjundiah V. A cell type-specific effect of calcium on pattern formation and differentiation in dictyostelium discoideum. Int J Dev Biol 2000; 44:491-8. [PMID: 11032184] [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] [Subscribe] [Scholar Register] [Indexed: 02/17/2023]
Abstract
Spatial gradients of sequestered and free cellular calcium (Ca2+) exist in the slug of Dictyostelium discoideum (Maeda and Maeda, 1973; Tirlapur et al., 1991; Azhar et al., 1995; Cubitt et al., 1995). When we vary intracellular Ca2+ with the help of calcium buffers and the ionophore Br-A23187, there are striking effects on slug morphology, patterning and cell differentiation. In the presence of a calcium ionophore, high external Ca2+ levels lead to an increase of intracellular sequestered and free Ca2+, the formation of long slugs, a decrease in the fraction of genetically defined prespore cells and 'stalky' fruiting bodies. Conversely, a lowering of external Ca2+ levels results in a decrease of intracellular Ca2+, the formation of short slugs, an increase in the prespore fraction and 'spory' fruiting bodies. We infer that Ca2+ plays a significant morphogenetic role in D. discoideum development, by selectively promoting the prestalk pathway relative to the prespore pathway.
Collapse
Affiliation(s)
- R Baskar
- Department of Molecular Reproduction, Development and Genetics, Indian Institute of Science, Bangalore
| | | | | | | |
Collapse
|
34
|
Abstract
The present investigation was carried out to study the effects of in utero exposure to low-level gamma radiation (0.25, 0.35, or 0.50 Gy) on the postnatal neurophysiology and neurochemistry of the mouse. Pregnant Swiss albino mice were irradiated on days 11.5, 12.5, 14.5, or 17.5 post coitus (PC) and allowed to deliver. Locomotor and exploratory activities, learning and memory functions, and emotional activities were tested at 3 months of age using behavior tests. A representative group of animals was killed and hippocampal biogenic amines, noradrenaline, dopamine, serotonin (5-HT), and 5-HT's metabolite 5-hydroxy indoleactetic acid (5-HIAA), were measured. Exposure to 0.25 Gy at any of the gestation days did not produce any significant impairment in brain functions. However, an increase in gamma irradiation to 0.50 Gy on all the gestation days produced significant impairment in locomotor (open-field test) and anxiolytic (light and dark area test) activities, learning (hole board test), memory functions (active avoidance test), and emotional activity (rearings). The late fetal period is relatively resistant to radiation-induced impairment of brain functions. Both of the organogenesis gestation days showed a higher sensitivity than the fetal gestation days studied. Even a lower dose of 0.35 Gy when exposed on the late organogenesis days 11.5 and 12.5 PC, produced significant reduction in locomotor and exploratory activities. Day 11.5 PC showed a higher sensitivity than the other PC days studied. Biogenic amines did not show significant change after any of the exposures on any of the gestation days. The results suggest a threshold between 0.25 to 0.35 Gy for postnatal neurobehavior changes.
Collapse
Affiliation(s)
- R Baskar
- Department of Radiobiology, Kasturba Medical College, Dr. T.M.A. Pai Research Center, Manipal 576 119, India.
| | | |
Collapse
|
35
|
Hongyo T, Li T, Syaifudin M, Baskar R, Ikeda H, Kanakura Y, Aozasa K, Nomura T. Specific c-kit mutations in sinonasal natural killer/T-cell lymphoma in China and Japan. Cancer Res 2000; 60:2345-7. [PMID: 10811105] [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] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/16/2023]
Abstract
Sinonasal lymphoma is one of the constituents of lethal midline granuloma, which is a clinical term for progressive, destructive lesions affecting the midline of the face. The majority of sinonasal lymphomas, especially those showing polymorphous patterns of proliferation and thus termed polymorphic reticulosis, recently were categorized as sinonasal natural killer/T-cell lymphomas. They are more prevalent in Asia than Europe or North America and are associated with EBV infection. Twenty-three cases with sinonasal natural killer/T-cell lymphomas were collected from two high-incidence regions: Beijing, China (14 cases) and Osaka, Japan (9 cases). c-kit mutations were analyzed on paraffin-embedded specimens by PCR-single-strand conformation polymorphism followed by direct sequencing; the c-kit proto-oncogene encodes a receptor of tyrosine kinase, which plays an important role in the regulation of normal and neoplastic hematopoiesis by the interaction with its specific ligand, termed stem cell factor. Twelve single nucleotide substitution mutations were seen in 23 cases. Ten of 14 Chinese cases (71.4%) had mutations at exon 11 or exon 17, whereas only two of nine Japanese cases (22.2%) had mutations, showing a significant difference in frequency between Chinese and Japanese cases. Furthermore, seven of eight mutations (92%) in exon 17 occurred at codon 825 and three of four mutations (75%) in exon 11 occurred at codon 561. Such a specificity has not been reported before, and these results, taken together, suggest that location-specific differences in etiological factors cause specific mutations in c-kit gene.
Collapse
Affiliation(s)
- T Hongyo
- Department of Radiation Biology, Faculty of Medicine, Osaka University, Japan
| | | | | | | | | | | | | | | |
Collapse
|
36
|
Abstract
Little is known about the timing of the maternal-to-zygotic transition during seed development in flowering plants. Because plant embryos can develop from somatic cells or microspores, maternal contributions are not considered to be crucial in early embryogensis. Early-acting embryo-lethal mutants in Arabidopsis, including emb30/gnom which affects the first zygotic division, have fuelled the perception that both maternal and paternal genomes are active immediately after fertilization. Here we show that none of the paternally inherited alleles of 20 loci that we tested is expressed during early seed development in Arabidopsis. For genes that are expressed at later stages, the paternally inherited allele becomes active three to four days after fertilization. The genes that we tested are involved in various processes and distributed throughout the genome, indicating that most, if not all, of the paternal genome may be initially silenced. Our findings are corroborated by genetic studies showing that emb30/gnom has a maternal-effect phenotype that is paternally rescuable in addition to its zygotic lethality. Thus, contrary to previous interpretations, early embryo and endosperm development are mainly under maternal control.
Collapse
|
37
|
Kurooka M, Hongyo T, Nakajima H, Baskar R, Li LY, Fukuda K, Sutoh K, Miyata M, Matsuda H, Nomura T. High incidence of esophageal cancer in esophageal achalasia by the oral administration of N-amyl-N-methylnitrosamine and its prevention by nicardipine hydrochloride in mice. Cancer Lett 1998; 127:55-61. [PMID: 9619858 DOI: 10.1016/s0304-3835(98)00006-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Esophageal achalasia (EA) is a rare disease in man and animals and there are many discussions on its higher risk of esophageal cancer. N-Amyl-N-methylnitrosamine (AMN) which specifically induces esophageal tumors in mice and rats was given to three mutant mouse strains, i.e. 101/N, STX/Le and BXH-8, which develop a high incidence of EA. The incidence of EA in 101/N, STX/Le, BXH-8 and normal C57BL/6J mice was 38.5% (110/286), 30.1% (43/143), 91.8% (190/207) and 0% (0/167), respectively. The average numbers of AMN-induced esophageal tumors in EA(+) were significantly higher than those of EA(-) in all of the 101/N, STX/Le and BXH-8 mice. Furthermore, significantly larger size tumors and invasive squamous cell carcinomas were found in EA(+) mice than in EA(-) mice. These results indicate the higher sensitivity of EA for both tumor induction and promotion, possibly due to the longer retention of AMN. In fact, relaxation of the lower esophagus by a smooth muscle relaxing calcium-channel blocker, nicardipine hydrochloride, significantly prevented the induction of esophageal tumors.
Collapse
Affiliation(s)
- M Kurooka
- Department of Radiation Biology, Faculty of Medicine, Osaka University, Suita, Japan
| | | | | | | | | | | | | | | | | | | |
Collapse
|
38
|
Suresh R, Devi PU, Baskar R. Changes in mouse behavior induced by fetal exposure to diagnostic ultrasound. Indian J Exp Biol 1996; 34:895-7. [PMID: 9014530] [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] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
Pregnant Swiss albino mice were exposed to diagnostic ultrasound (3.5 MHz, 65mw, ISPTP = 1 W/cm2, ISATA = 240 W/cm2) for 10 min on day 14, 16 or 17 of gestation to assess any changes in physiological reflexes (pinna detachment, eye opening and fur development) and postnatal mortality. Changes in locomotor activity by open field test and dark/bright arena test and learning and memory by hole board test were also recorded. No change was observed in physiological reflexes and postnatal mortality. However there were significant alterations in behavior in all the three exposed groups. These results demonstrate that ultrasound exposure during the late fetal period can impair brain function in adult mouse.
Collapse
Affiliation(s)
- R Suresh
- Department of Anatomy, Kasturba Medical College, Manipal, India
| | | | | |
Collapse
|
39
|
Baskar R, Devi PU. Long-term effect of prenatal exposure to low level of gamma radiation on neurophysiology of mouse. Indian J Exp Biol 1996; 34:887-90. [PMID: 9014528] [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] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
Abdominal region of pregnant Swiss mice were exposed to 0.25, 0.35 or 0.50 Gy of gamma radiation on days 11.5, 12.5, 14.5 or 17.5 post coitus (pc). Changes in locomotory activity and learning performance, and hippocampal biogenic amines (noradrenaline, NA; dopamine, DA; 5-hydroxytryptomine, 5-HT; and 5-HTs metabolite 5-hydroxyindolacetic acid, 5-HIAA) were studied at 12 (adult) and 18 months (old) of age. Significant change in locomotory activity and learning performance was observed after exposure to 0.50 Gy at late organogenesis day (11.5 pc), when tested at 12 months of age, but not observed much change at 18 months. Biogenic amines did not show any significant change after any exposure dose at any of the gestation days. It was inferred from the results that gamma irradiation (0.50 Gy) at the late organogenesis (day 11.5 pc) can impair the brain functions in adults when normal faculties are functional.
Collapse
Affiliation(s)
- R Baskar
- Department of Radiobiology, Kasturba Medical College, Manipal, India
| | | |
Collapse
|
40
|
Abstract
The abdominal region of pregnant Swiss albino mice was exposed to single dose of 0.5 Gy gamma-radiation at gestation days from 1.5 to 17.5 days post-coitus (p.c). The animals were sacrificed on day 18 p.c. and foetuses were examined for resorption and embryonic death, foetal death, growth retardation, small head, low brain weight, micro-phthalmia and any other gross morphological abnormalities. The period of maximum sensitivity for each effect varied. The only demonstrable effect of irradiation during the pre-implantation period was an increase in prenatal mortality. Resorptions were maximal after exposure between days 2 and 4 p.c. The pre-implantation irradiated embryos which survived did not show any major foetal abnormalities. These results confirm earlier mouse studies using higher doses of X-rays. Small head, low brain weight and microphthalmia were prominent after exposure during the late organogenesis period, especially between days 9 and 13 p.c. But no other externally visible anomalies were detected. These findings demonstrate that mouse organogenesis is very sensitive to radiation-induced retardation of development, even at doses < 1 Gy. One exencephaly, one cleft palate and two cases of open eyelids were observed in the foetuses exposed on days 14.5 and 15.5 p.c.; the number of these cases was too small to indicate a causal relationship with exposure.
Collapse
Affiliation(s)
- P U Devi
- Department of Radiobiology, Kasturba Medical College, Manipal, India
| | | |
Collapse
|
41
|
Abstract
Investigations were undertaken to study the role of lupeol, a pentacyclic triterpene from Crataeva nurvala stem bark, in calcium oxalate experimental rat urolithiasis. A 2% solution of ammonium oxalate was administered by gastric intubation for inducing hyperoxaluric condition in adult male rats of Wistar strain. The duration of treatment was for 15 days. This resulted in increased urinary excretion of oxalate associated with reduction in citrate and glycosaminoglycans. The urinary marker enzymes which indicate renal tissue damage namely--lactate dehydrogenase, inorganic pyrophosphatase, alkaline phosphatase, gamma glutamyl transferase, beta-glucuronidase and N-acetyl beta-D glucosaminidase were found to be elevated. Lupeol administration (25 mg/kg body weight/day) reduced significantly the renal excretion of oxalate. It also reduced the extent of renal tubular damage as evidenced from the decreased levels of the above enzymes in urine. Such a reduction is likely to be beneficial in minimizing the deposition of stone-forming constituents in the kidney which provides antilithic effect.
Collapse
Affiliation(s)
- M M Malini
- Department of Biochemistry, University of Madras, India
| | | | | |
Collapse
|
42
|
Baskar R, Saravanan N, Varalakshmi P. Effect ofCrataeva nurvala bark decoction on enzymatic changes in liver of normal and stone forming rats. Indian J Clin Biochem 1995. [DOI: 10.1007/bf02871010] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
|
43
|
|
44
|
Devi PU, Baskar R, Hande MP. Effect of exposure to low-dose gamma radiation during late organogenesis in the mouse fetus. Radiat Res 1994; 138:133-8. [PMID: 8146293] [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] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
The abdominal region of pregnant Swiss mice was exposed to 0.05 to 0.50 Gy of gamma radiation on day 11.5 postcoitus. The animals were sacrificed on day 18 of gestation and the fetuses were examined for mortality, growth retardation, changes in head size and brain weight, and incidence of microphthalmia. No marked increase in fetal mortality or growth retardation was observed below 0.25 Gy; the increase in these parameters was significant only at 0.50 Gy. A significant reduction in head size and brain weight and a significant increase in the incidence of microphthalmia were observed at doses above 0.15 Gy. Detectable levels of microcephaly and microphthalmia were evident even at 0.10 Gy. A linear dose response was seen for these effects in the dose range of 0.05 to 0.15 Gy. It is concluded that the late period of organogenesis in the mouse, especially between days 10 and 12 postcoitus, is a particularly sensitive phase in the development of the skull, brain and eye.
Collapse
Affiliation(s)
- P U Devi
- Department of Radiobiology, Kasturba Medical College, Manipal, India
| | | | | |
Collapse
|
45
|
Devi VK, Baskar R, Varalakshmi P. Biochemical effects in normal and stone forming rats treated with the ripe kernel juice of plantain (musa paradisiaca). Anc Sci Life 1993; 12:451-61. [PMID: 22556626 PMCID: PMC3336560] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/1992] [Accepted: 05/06/1993] [Indexed: 11/13/2022] Open
Abstract
The effect of Musa paradisiaca stem kernel juice was investigated in experimental urolithiatic rats. Stone forming rats exhibited a significant elevation in the activities of two oxalate synthesizing enzymes - Glycollic acid oxidase and Lactate dehydrogenase. Deposition and excretion of stone forming constituents in kidney and urine were also increased in these rats. The enzyme activities and the level of crystalline components were lowered with the extract treatment. The extract also reduced the activities of urinary alkaline phosphatase, lactate dehydrogenase, r-glutamyl transferase, inorganic pyrophosphatase and β-glucuronidase in calculogenic rats. No appreciable changes were noticed with leucine amino peptidase activity in treated rats.
Collapse
Affiliation(s)
- V. Kalpana Devi
- Department of Medical Biochemistry, P.G. Institute of Basic Medical Sciences, Taramani, Madras – 600 113, INDIA
| | - R. Baskar
- Department of Medical Biochemistry, P.G. Institute of Basic Medical Sciences, Taramani, Madras – 600 113, INDIA
| | - P. Varalakshmi
- Department of Medical Biochemistry, P.G. Institute of Basic Medical Sciences, Taramani, Madras – 600 113, INDIA
| |
Collapse
|
46
|
Subha K, Baskar R, Varalakshmi P. Biochemical changes in kidneys of normal and stone forming rats with sodium pentosan polysulphate. Biochem Int 1992; 26:357-65. [PMID: 1373054] [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] [Subscribe] [Scholar Register] [Indexed: 03/25/2023]
Abstract
The influence of sodium pentosan polysulphate was studied on the deposition of stone forming constituents along with certain enzymes in the renal tissue of experimentally induced urolithiatic rats. Calcium, oxalate and phosphorus levels were elevated in kidneys of lithogenic rats, while SPP administration reduced these levels to near control values. The elevation in kidney LDH was significant in the stone forming groups and SPP had minimal effect. Increases in the activities of Na+, K(+)-and Ca(2+)-ATPases in the calculogenic groups was lowered considerably with SPP treatment. Inorganic pyrophosphatase activity was reduced significantly in the calculogenic as well as in the drug treated groups. Leucine aminopeptidase was decreased in the calculogenic group. SPP treatment elevated the enzyme activity in the treated groups. Reduction in kidney oxalate with SPP may prove useful in the medical management of urolithiasis.
Collapse
Affiliation(s)
- K Subha
- Department of Medical Biochemistry, University of Madras, India
| | | | | |
Collapse
|