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Jahan J, Joshi S, Oca IMD, Toelle A, Lopez-Yang C, Chacon CV, Beyer AM, Garcia CA, Jarajapu YP. The role of telomerase reverse transcriptase in the mitochondrial protective functions of Angiotensin-(1-7) in diabetic CD34 + cells. Biochem Pharmacol 2024; 222:116109. [PMID: 38458330 PMCID: PMC11007670 DOI: 10.1016/j.bcp.2024.116109] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2023] [Revised: 01/08/2024] [Accepted: 03/05/2024] [Indexed: 03/10/2024]
Abstract
Angiotensin (Ang)-(1-7) stimulates vasoprotective functions of diabetic (DB) CD34+ hematopoietic stem/progenitor cells partly by decreasing reactive oxygen species (ROS), increasing nitric oxide (NO) levels and decreasing TGFβ1 secretion. Telomerase reverse transcriptase (TERT) translocates to mitochondria and regulates ROS generation. Alternative splicing of TERT results in variants α-, β- and α-β-TERT, which may oppose functions of full-length (FL) TERT. This study tested if the protective functions of Ang-(1-7) or TGFβ1-silencing are mediated by mitoTERT and that diabetes decreases FL-TERT expression by inducing splicing. CD34+ cells were isolated from the peripheral blood mononuclear cells of nondiabetic (ND, n = 68) or DB (n = 74) subjects. NO and mitoROS levels were evaluated by flow cytometry. TERT splice variants and mitoDNA-lesions were characterized by qPCR. TRAP assay was used for telomerase activity. Decoy peptide was used to block mitochondrial translocation (mitoXTERT). TERT inhibitor or mitoXTERT prevented the effects of Ang-(1-7) on NO or mitoROS levels in DB-CD34+ cells. FL-TERT expression and telomerase activity were lower and mitoDNA-lesions were higher in DB cells compared to ND and were reversed by Ang-(1-7) or TGFβ1-silencing. The prevalence of TERT splice variants, with predominant β-TERT expression, was higher and the expression of FL-TERT was lower in DB cells (n = 25) compared to ND (n = 30). Ang-(1-7) or TGFβ1-silencing decreased TERT-splicing and increased FL-TERT. Blocking of β-splicing increased FL-TERT and protected mitoDNA in DB-cells. The findings suggest that diabetes induces TERT-splicing in CD34+ cells and that β-TERT splice variant largely contributes to the mitoDNA oxidative damage.
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Affiliation(s)
- Jesmin Jahan
- Department of Pharmaceutical Sciences, College of Health Professions, North Dakota State University, Fargo, ND, USA
| | - Shrinidh Joshi
- Department of Pharmaceutical Sciences, College of Health Professions, North Dakota State University, Fargo, ND, USA
| | | | - Andrew Toelle
- Department of Pharmaceutical Sciences, College of Health Professions, North Dakota State University, Fargo, ND, USA
| | | | | | - Andreas M Beyer
- Department of Medicine and Physiology, Medical College of Wisconsin, Milwaukee, WI, USA
| | | | - Yagna Pr Jarajapu
- Department of Pharmaceutical Sciences, College of Health Professions, North Dakota State University, Fargo, ND, USA.
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2
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Siqueira E, Kim BH, Reser L, Chow R, Delaney K, Esteller M, Ross MM, Shabanowitz J, Hunt DF, Guil S, Ausió J. Analysis of the interplay between MeCP2 and histone H1 during in vitro differentiation of human ReNCell neural progenitor cells. Epigenetics 2023; 18:2276425. [PMID: 37976174 PMCID: PMC10769555 DOI: 10.1080/15592294.2023.2276425] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2023] [Accepted: 10/18/2023] [Indexed: 11/19/2023] Open
Abstract
An immortalized neural cell line derived from the human ventral mesencephalon, called ReNCell, and its MeCP2 knock out were used. With it, we characterized the chromatin compositional transitions undergone during differentiation, with special emphasis on linker histones. While the WT cells displayed the development of dendrites and axons the KO cells did not, despite undergoing differentiation as monitored by NeuN. ReNCell expressed minimal amounts of histone H1.0 and their linker histone complement consisted mainly of histone H1.2, H1.4 and H1.5. The overall level of histone H1 exhibited a trend to increase during the differentiation of MeCP2 KO cells. The phosphorylation levels of histone H1 proteins decreased dramatically during ReNCell's cell differentiation independently of the presence of MeCP2. Immunofluorescence analysis showed that MeCP2 exhibits an extensive co-localization with linker histones. Interestingly, the average size of the nucleus decreased during differentiation but in the MeCP2 KO cells, the smaller size of the nuclei at the start of differentiation increased by almost 40% after differentiation by 8 days (8 DIV). In summary, our data provide a compelling perspective on the dynamic changes of H1 histones during neural differentiation, coupled with the intricate interplay between H1 variants and MeCP2.Abbreviations: ACN, acetonitrile; A230, absorbance at 230 nm; bFGF, basic fibroblast growth factor; CM, chicken erythrocyte histone marker; CNS, central nervous system; CRISPR, clustered regulated interspaced short palindromic repeatsDAPI, 4,'6-diaminidino-2-phenylindole; DIV, days in vitro (days after differentiation is induced); DMEM, Dulbecco's modified Eagle medium; EGF, epidermal growth factor; ESC, embryonic stem cell; GAPDH, glyceraldehyde-3-phosphate dehydrogenase; GFAP, glial fibrillary acidic proteinHPLC, high-performance liquid chromatography; IF, immunofluorescence; iPSCs, induced pluripotent stem cells; MAP2, microtubule-associated protein 2; MBD, methyl-binding domain; MeCP2, methyl-CpG binding protein 2; MS, mass spectrometry; NCP, nucleosome core particle; NeuN, neuron nuclear antigen; NPC, neural progenitor cellPAGE, polyacrylamide gel electrophoresis; PBS, phosphate buffered saline; PFA, paraformaldehyde; PTM, posttranslational modification; RP-HPLC, reversed phase HPLC; ReNCells, ReNCells VM; RPLP0, ribosomal protein lateral stalk subunit P0; RT-qPCR, reverse transcription quantitative polymerase-chain reaction; RTT, Rett Syndrome; SDS, sodium dodecyl sulphate; TAD, topologically associating domain; Triple KO, triple knockout.
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Affiliation(s)
- Edilene Siqueira
- Josep Carreras Leukaemia Research Institute (IJC), Badalona, Barcelona, Catalonia, Spain
- National Council for Scientific and Technological Development (CNPq), Brasilia, Federal District, Brazil
| | - Bo-Hyun Kim
- Department of Biochemistry and Microbiology, University of Victoria, Victoria, BC, Canada
| | - Larry Reser
- Department of Chemistry, University of Virginia, Charlottesville, Virginia, USA
| | - Robert Chow
- Department of Biology, University of Victoria, Victoria, BC, Canada
| | - Kerry Delaney
- Department of Biology, University of Victoria, Victoria, BC, Canada
| | - Manel Esteller
- Josep Carreras Leukaemia Research Institute (IJC), Badalona, Barcelona, Catalonia, Spain
- Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Catalonia, Spain
- Physiological Sciences Department, School of Medicine and Health Sciences, University of Barcelona (UB), Barcelona, Catalonia, Spain
| | - Mark M. Ross
- Department of Chemistry, University of Virginia, Charlottesville, Virginia, USA
| | - Jeffrey Shabanowitz
- Department of Chemistry, University of Virginia, Charlottesville, Virginia, USA
| | - Donald F. Hunt
- Department of Chemistry, University of Virginia, Charlottesville, Virginia, USA
- Department of Pathology, University of Virginia, Charlottesville, Virginia, USA
| | - Sonia Guil
- Josep Carreras Leukaemia Research Institute (IJC), Badalona, Barcelona, Catalonia, Spain
- GermansTrias i Pujol Health Science Research Institute, Badalona, Barcelona, Catalonia, Spain
| | - Juan Ausió
- Department of Biochemistry and Microbiology, University of Victoria, Victoria, BC, Canada
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3
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Grzybkowska A, Anczykowska K, Antosiewicz J, Olszewski S, Dzitkowska-Zabielska M, Tomczyk M. Identification of Optimal Reference Genes for qRT-PCR Normalization for Physical Activity Intervention and Omega-3 Fatty Acids Supplementation in Humans. Int J Mol Sci 2023; 24:ijms24076734. [PMID: 37047706 PMCID: PMC10094777 DOI: 10.3390/ijms24076734] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2023] [Revised: 03/29/2023] [Accepted: 03/30/2023] [Indexed: 04/14/2023] Open
Abstract
The quantitative polymerase chain reaction (qRT-PCR) technique gives promising opportunities to detect and quantify RNA targets and is commonly used in many research fields. This study aimed to identify suitable reference genes for physical exercise and omega-3 fatty acids supplementation intervention. Forty healthy, physically active men were exposed to a 12-week eicosapentaenoic acid (EPA) and docosahexaenoic acid (DHA) supplementation and standardized endurance training protocol. Blood samples were collected before and after the intervention and mRNA levels of six potential reference genes were tested in the leukocytes of 18 eligible participants using the qRT-PCR method: GAPDH (Glyceraldehyde-3-phosphate dehydrogenase), ACTB (Beta actin), TUBB (Tubulin Beta Class I), RPS18 (Ribosomal Protein S18), UBE2D2 (Ubiquitin-conjugating enzyme E2 D2), and HPRT1 (Hypoxanthine Phosphoribosyltransferase 1). The raw quantification cycle (Cq) values were then analyzed using RefFinder, an online tool that incorporates four different algorithms: NormFinder, geNorm, BestKeeper, and the comparative delta-Ct method. Delta-Ct, NormFinder, BestKeeper, and RefFinder comprehensive ranking have found GAPDH to be the most stably expressed gene. geNorm has identified TUBB and HPRT as the most stable genes. All algorithms have found ACTB to be the least stably expressed gene. A combination of the three most stably expressed genes, namely GAPDH, TUBB, and HPRT, is suggested for obtaining the most reliable results.
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Affiliation(s)
- Agata Grzybkowska
- Faculty of Physical Education, Gdansk University of Physical Education and Sport, 80-336 Gdansk, Poland
| | - Katarzyna Anczykowska
- Faculty of Physical Education, Gdansk University of Physical Education and Sport, 80-336 Gdansk, Poland
| | - Jędrzej Antosiewicz
- Department of Bioenergetics and Physiology of Exercise, Medical University of Gdansk, 80-211 Gdansk, Poland
| | - Szczepan Olszewski
- Department of Bioenergetics and Physiology of Exercise, Medical University of Gdansk, 80-211 Gdansk, Poland
| | - Magdalena Dzitkowska-Zabielska
- Faculty of Physical Education, Gdansk University of Physical Education and Sport, 80-336 Gdansk, Poland
- Center of Translational Medicine, Medical University of Gdansk, 80-952 Gdansk, Poland
| | - Maja Tomczyk
- Faculty of Physical Education, Gdansk University of Physical Education and Sport, 80-336 Gdansk, Poland
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Vetrivel S, Zhang R, Engel M, Oßwald A, Watts D, Chen A, Wielockx B, Sbiera S, Reincke M, Riester A. Characterization of Adrenal miRNA-Based Dysregulations in Cushing's Syndrome. Int J Mol Sci 2022; 23:ijms23147676. [PMID: 35887024 PMCID: PMC9320303 DOI: 10.3390/ijms23147676] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2022] [Revised: 07/04/2022] [Accepted: 07/10/2022] [Indexed: 02/05/2023] Open
Abstract
MiRNAs are important epigenetic players with tissue- and disease-specific effects. In this study, our aim was to investigate the putative differential expression of miRNAs in adrenal tissues from different forms of Cushing’s syndrome (CS). For this, miRNA-based next-generation sequencing was performed in adrenal tissues taken from patients with ACTH-independent cortisol-producing adrenocortical adenomas (CPA), from patients with ACTH-dependent pituitary Cushing’s disease (CD) after bilateral adrenalectomy, and from control subjects. A confirmatory QPCR was also performed in adrenals from patients with other CS subtypes, such as primary bilateral macronodular hyperplasia and ectopic CS. Sequencing revealed significant differences in the miRNA profiles of CD and CPA. QPCR revealed the upregulated expression of miR-1247-5p in CPA and PBMAH (log2 fold change > 2.5, p < 0.05). MiR-379-5p was found to be upregulated in PBMAH and CD (log2 fold change > 1.8, p < 0.05). Analyses of miR-1247-5p and miR-379-5p expression in the adrenals of mice which had been exposed to short-term ACTH stimulation showed no influence on the adrenal miRNA expression profiles. For miRNA-specific target prediction, RNA-seq data from the adrenals of CPA, PBMAH, and control samples were analyzed with different bioinformatic platforms. The analyses revealed that both miR-1247-5p and miR-379-5p target specific genes in the WNT signaling pathway. In conclusion, this study identified distinct adrenal miRNAs as being associated with CS subtypes.
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Affiliation(s)
- Sharmilee Vetrivel
- Medizinische Klinik und Poliklinik IV, LMU Klinikum, Ludwig-Maximilians-University, 80336 Munich, Germany; (S.V.); (R.Z.); (A.O.); (M.R.)
| | - Ru Zhang
- Medizinische Klinik und Poliklinik IV, LMU Klinikum, Ludwig-Maximilians-University, 80336 Munich, Germany; (S.V.); (R.Z.); (A.O.); (M.R.)
| | - Mareen Engel
- Department of Stress Neurobiology and Neurogenetics, Max Planck Institute of Psychiatry, 80804 Munich, Germany; (M.E.); (A.C.)
| | - Andrea Oßwald
- Medizinische Klinik und Poliklinik IV, LMU Klinikum, Ludwig-Maximilians-University, 80336 Munich, Germany; (S.V.); (R.Z.); (A.O.); (M.R.)
| | - Deepika Watts
- Institute of Clinical Chemistry and Laboratory Medicine, Technische Universität Dresden, 01307 Dresden, Germany; (D.W.); (B.W.)
| | - Alon Chen
- Department of Stress Neurobiology and Neurogenetics, Max Planck Institute of Psychiatry, 80804 Munich, Germany; (M.E.); (A.C.)
- Department of Neurobiology, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Ben Wielockx
- Institute of Clinical Chemistry and Laboratory Medicine, Technische Universität Dresden, 01307 Dresden, Germany; (D.W.); (B.W.)
| | - Silviu Sbiera
- Department of Internal Medicine I, Division of Endocrinology and Diabetes, University Hospital, University of Würzburg, 97080 Würzburg, Germany;
| | - Martin Reincke
- Medizinische Klinik und Poliklinik IV, LMU Klinikum, Ludwig-Maximilians-University, 80336 Munich, Germany; (S.V.); (R.Z.); (A.O.); (M.R.)
| | - Anna Riester
- Medizinische Klinik und Poliklinik IV, LMU Klinikum, Ludwig-Maximilians-University, 80336 Munich, Germany; (S.V.); (R.Z.); (A.O.); (M.R.)
- Correspondence: ; Tel.: +49-89-440052111
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Wedemeyer MA, Muskens I, Strickland BA, Aurelio O, Martirosian V, Wiemels JL, Weisenberger DJ, Wang K, Mukerjee D, Rhie SK, Zada G. Epigenetic dysregulation in meningiomas. Neurooncol Adv 2022; 4:vdac084. [PMID: 35769412 PMCID: PMC9234763 DOI: 10.1093/noajnl/vdac084] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023] Open
Abstract
Background Meningiomas are the most common primary brain tumor. Though typically benign with a low mutational burden, tumors with benign histology may behave aggressively and there are no proven chemotherapies. Although DNA methylation patterns distinguish subgroups of meningiomas and have higher predictive value for tumor behavior than histologic classification, little is known about differences in DNA methylation between meningiomas and surrounding normal dura tissue. Methods Whole-exome sequencing and methylation array profiling were performed on 12 dura/meningioma pairs (11 WHO grade I and 1 WHO grade II). Single-nucleotide polymorphism (SNP) genotyping and methylation array profiling were performed on an additional 19 meningiomas (9 WHO grade I, 5 WHO grade II, 4 WHO grade III). Results Using multimodal studies of meningioma/dura pairs, we identified 4 distinct DNA methylation patterns. Diffuse DNA hypomethylation of malignant meningiomas readily facilitated their identification from lower-grade tumors by unsupervised clustering. All clusters and 12/12 meningioma-dura pairs exhibited hypomethylation of the gene promoters of a module associated with the craniofacial patterning transcription factor FOXC1 and its upstream lncRNA FOXCUT. Furthermore, we identified an epigenetic continuum of increasing hypermethylation of polycomb repressive complex target promoters with increasing histopathologic grade. Conclusion These findings support future investigations of the role of epigenetic dysregulation of FOXC1 and cranial patterning genes in meningioma formation as well as studies of the utility of polycomb inhibitors for the treatment of malignant meningiomas.
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Affiliation(s)
- Michelle A Wedemeyer
- Department of Neurosurgery, University of California San Francisco, Benioff Children’s Hospitals, San Francisco, California, USA
| | - Ivo Muskens
- Children’s Cancer Research Laboratory, Center of Genetic Epidemiology, Keck School of Medicine, University of Southern California, Los Angeles, California, USA
| | - Ben A Strickland
- Department of Neurosurgery, Keck School of Medicine, University of Southern California, Los Angeles, California, USA
| | - Oscar Aurelio
- Department of Neurosurgery, Keck School of Medicine, University of Southern California, Los Angeles, California, USA,Brain Tumor Center, University of Southern California, Los Angeles, California, USA
| | - Vahan Martirosian
- Brain Tumor Center, University of Southern California, Los Angeles, California, USA
| | - Joseph L Wiemels
- Children’s Cancer Research Laboratory, Center of Genetic Epidemiology, Keck School of Medicine, University of Southern California, Los Angeles, California, USA
| | - Daniel J Weisenberger
- Department of Biochemistry and Molecular Medicine, Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, California, USA
| | - Kai Wang
- Department of Pathology and Laboratory Medicine, Children’s Hospital of Philadelphia Research Institute, Philadelphia, Pennsylvania, USA
| | - Debraj Mukerjee
- Department of Neurosurgery, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Suhn K Rhie
- Suhn K. Rhie, PhD, Department of Biochemistry and Molecular Medicine, Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, California, USA ()
| | - Gabriel Zada
- Corresponding Authors: Gabriel Zada, MD, MS, Department of Neurosurgery, Keck School of Medicine, University of Southern California, 1200 N State Street, Los Angeles, CA 90033, USA ()
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Dwivedi N, Mondal S, P. K. S, T. S, Sachdeva K, Bathula C, K. V, K. S. N, Damodar S, Dhar SK, Das M. Relative quantification of BCL2 mRNA for diagnostic usage needs stable uncontrolled genes as reference. PLoS One 2020; 15:e0236338. [PMID: 32785215 PMCID: PMC7423076 DOI: 10.1371/journal.pone.0236338] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2020] [Accepted: 07/02/2020] [Indexed: 01/21/2023] Open
Abstract
Dysregulation of BCL2 is a pathophysiology observed in haematological malignancies. For implementation of available treatment-options it is preferred to know the relative quantification of BCL2 mRNA with appropriate reference genes. For the choice of reference genes-(i) Reference Genes were selected by assessing variation of >60,000 genes from 4 RNA-seq datasets of haematological malignancies followed by filtering based on their GO biological process annotations and proximity of their chromosomal locations to known disease translocations. Selected genes were experimentally validated across various haematological malignancy samples followed by stability comparison using geNorm, NormFinder, BestKeeper and RefFinder. (ii) 43 commonly used Reference Genes were obtained from literature through extensive systematic review. Levels of BCL2 mRNA was assessed by qPCR normalized either by novel reference genes from this study or GAPDH, the most cited reference gene in literature and compared. The analysis showed PTCD2, PPP1R3B and FBXW9 to be the most unregulated genes across lymph-nodes, bone marrow and PBMC samples unlike the Reference Genes used in literature. BCL2 mRNA level shows a consistent higher expression in haematological malignancy patients when normalized by these novel Reference Genes as opposed to GAPDH, the most cited Reference Gene. These reference genes should also be applicable in qPCR platforms using Taqman probes and other model systems including cell lines and rodent models. Absence of sample from healthy-normal individual in diagnostic cases call for careful selection of Reference Genes for relative quantification of a biomarker by qPCR.BCL2 can be used as molecular diagnostics only if normalized with a set of reference genes with stable yet low levels of expression across different types of haematological malignancies.
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MESH Headings
- Animals
- Biomarkers, Tumor/blood
- Biomarkers, Tumor/genetics
- Biomarkers, Tumor/isolation & purification
- Bone Marrow/pathology
- Cell Line, Tumor
- Datasets as Topic
- Disease Models, Animal
- Feasibility Studies
- Gene Expression Regulation, Neoplastic
- Genes, Essential
- Hematologic Neoplasms/blood
- Hematologic Neoplasms/diagnosis
- Hematologic Neoplasms/genetics
- Hematologic Neoplasms/pathology
- Humans
- Leukocytes, Mononuclear
- Proto-Oncogene Proteins c-bcl-2/blood
- Proto-Oncogene Proteins c-bcl-2/genetics
- Proto-Oncogene Proteins c-bcl-2/isolation & purification
- RNA, Messenger/blood
- RNA, Messenger/genetics
- RNA, Messenger/isolation & purification
- RNA-Seq/standards
- Real-Time Polymerase Chain Reaction/standards
- Reference Standards
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Affiliation(s)
- Nehanjali Dwivedi
- Tumor Immunology Program, MSMF, MSMC, Narayana Health City, Bangalore, India
- MAHE, Manipal, India
| | - Sreejeta Mondal
- Tumor Immunology Program, MSMF, MSMC, Narayana Health City, Bangalore, India
| | - Smitha P. K.
- Tumor Immunology Program, MSMF, MSMC, Narayana Health City, Bangalore, India
| | - Sowmya T.
- Tumor Immunology Program, MSMF, MSMC, Narayana Health City, Bangalore, India
| | - Kartik Sachdeva
- Tumor Immunology Program, MSMF, MSMC, Narayana Health City, Bangalore, India
| | - Christopher Bathula
- Tumor Immunology Program, MSMF, MSMC, Narayana Health City, Bangalore, India
| | - Vishnupriyan K.
- Tumor Immunology Program, MSMF, MSMC, Narayana Health City, Bangalore, India
| | - Nataraj K. S.
- Department of Haematology, MSMF, MSMC, Narayana Health City, Bangalore, India
| | - Sharat Damodar
- Department of Haematology, MSMF, MSMC, Narayana Health City, Bangalore, India
| | - Sujan K. Dhar
- Beyond Antibody, InCite Labs, MSMF, MSMC, Narayana Health City, Bangalore, India
| | - Manjula Das
- Tumor Immunology Program, MSMF, MSMC, Narayana Health City, Bangalore, India
- Beyond Antibody, InCite Labs, MSMF, MSMC, Narayana Health City, Bangalore, India
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