Amrita Sarkar, Ph.D.

faculty photo
Research Assistant Professor of Pediatrics
Staff Scientist, Division of Hematology, Children’s Hospital of Philadelphia
Department: Pediatrics

Contact information
Children's Hospital of Philadelphia
3615 Civic Center Boulevard, 3rd Floor, Suite 312B
Philadelphia, PA 19107
Lab: 2515901971
Education:
B.Sc (Physiology)
University of Calcutta, Kolkata, India, 2008.
M.Sc (Human Physiology and Pharmacology)
University of Calcutta, Kolkata, India, 2010.
Ph.D (Physiology and Pharmacology)
Department of Physiology, University of Calcutta, Kolkata, India, 2014.
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Description of Research Expertise

o Practice of handling human subject:
 Blood collection from human vein (certified Phlebotomists).
 Experiment with normal, HIT, COVID-19, VITT and APS patient plasma sample.
o Practice of handling experimental laboratory animals (Rat, mice, guineapig, Rabbit, Toad):
 Handling mouse: Colonies maintenance, breeding and genotyping
 Dosage routes: Intraperitoneal, intramuscular, intravenous, intraarticular, intradermal, subcutaneous injection and gavage (force feeding) of drug/ minerals/ microRNA/ siRNA/adenovirus/nano-formulation.
 Anatomical measurements: Paw, knee, ankle diameter measurement from in rat and mice.
 Physiological parameters: Insulin and Glucose tolerance test in mice model. Echocardiography of mice, X-ray study, blood hematological parameters count.
 Surgery: Osteoporosis development, Cecal ligation puncture procedure (CLP model), Lung surgery model, Liver Surgery model, Cremaster model. Liver, lung surgery in mice model, along with injury, Cremaster muscle surgery along with injury of vessel in mice model.
 Model development: Osteoarthritis, Rheumatoid arthritis model development; Diabetes and Diabetic cardiomyophy model (Type I and Type II), Inflammation and nociception models in mice, Hyperimmunization model development (guineapig); LPS induced Sepsis model, Thrombosis model, In vitro COVID-19 and Vaccine induced thrombotic thrombocytopenia (VITT) model.
 Fluid collection: Synovial fluid collection from joint and its analysis through ELISA, Blood collection (hepatic vein, vena cava, retro-orbital, cardiac, tail vein, jugular vein, marginal ear vein (rabbit), iliac vein)
 Toxicity studies: in animal (Hemolysis, hemorrhagic study, acute toxicity study).
 Pharmacological Studies: Drug dose response in isolated guineapig heart auricle, Drug dose response in isolated rat phrenic nerve, Drug dose response in toad heart.
 Biochemical analysis: Physiological markers analysis from blood, urine from rat and mice model. Oxidative stress molecule analysis from rat and mice blood. Free DNA measurement from mice plasma, free DNA assessment from mice plasma.
o Cell culture techniques:
 Isolation, culture and treatment of primary cell culture (synoviocyte culture both in human and rat, primary neonatal rat cardiomyocyte, primary adult mice and rat cardiomyocyte, Lymphocyte isolation from spleen, heart and blood), B, T cell and mice and human monocyte isolation and culture using isolation kit.
 Handling and treatment of HIG-82 (synoviocytes) cell line, H9C2 and C2C12 (cardiomyocyte) cell line, A20 (B lymphoma) cell line, HUVEC primary cell line, mouse aortic endothelial cells line, porcine WT kidney endothelial cells, porcine aortic endothelial cells.
 High and low glucose treatment and analysis in cardiomyocyte (both primary and stable cell line).
 Hybridoma cells for antibody production.
 MTT assay for cell apoptosis determination.

o Antibody production from hybridoma cells:
 Antibody production, purification from plasma and hybridoma sup.
 Antibody labelling.
 IgG purification, digestion and Fc-modification, preparation of F(ab’)2 fragment.
o B cell Biology:
 Evaluation of B cell expression in heart section using immunohistochemistry, immunofluorescence staining.
 Evaluation of B cell expression on heart tissue using western blot and immunoprecipitation technique
 Evaluation of B cell expression using flow cytometry.
 Evaluation of B cell expression and B cell homing from circulation to heart using B cell specific gene therapy.
o Bioflux microfluidics:
 Microfluidics model and drug interaction after photochemical injury in cell culture using human, mouse, porcine endothelial cells for in vitro thrombosis model.
o COVID and VITT experiment:
 Handling COVID and VITT plasma and run them in microfluidics system for thrombosis experiment.
o Molecular Biology:
 Isolation of total RNA and cDNA synthesis.
 RT-PCR, Real Time PCR.
 Agarose or polyacrylamide gel electrophoresis
 Primer design for RT-PCR and qPCR
 Microarray analysis.
o Protein Biochemistry:
 Protein estimation and preparation.
 Protein expression and interaction: Gel electrophoresis (PAGE and SDS), Western blot, immuno-precipitation and co-immuno- precipitation.
 Sandwich ELISA.
 HPLC, UV Scan, CD spectra analysis, Fluorescence study, X-RD analysis, FTIR analysis, EDAX, MALDI-TOF, LC-MS/MS, Dialysis of protein sample for salting in and out.
o Carbohydrate analysis:
 Thin Layer Chromatography, Paper chromatography, acid hydrolysis for carbohydrate separation and identification.
o Tissue handling and staining:
 Tissue dehydration and block preparation and sectioning
 Hematoxylin and eosin staining; immunohistochemical (single and double color staining), immunofluorescence staining and imaging of tissue sections.

o Cell staining:
 Immunocytochemistry and immunofluorescence (double color) staining and imaging.
 Confocal imaging of live cells using trackers for colocalization.
 Synoviocyte apoptosis measurement by annexin V-FITC through fluorescent microscopy.
 Immunofluorescence study for apoptosis detection.
o Flow cytometry:
 Antibody expression detection using 4 colors and 8 colors together, Cell apoptosis study.
o Microscopy:
 Bright light microscopy, fluorescence microscopy, scanning electron microscopy, Live cell imaging using EVOS, confocal microscopy both with cells and in live mice under anesthesia and in live cell and animal.
o Nanoformulation and Nanotechnology:
 Gold nanoparticle preparation and tagging with protein, tagging with fish oil lipid and peptide and encapsulation within liposome to target specific to arthritis in both animal model and synoviocyte cell cultures.
 Liposome preparation and characterisation
 Characterization of nanoparticle- DLS, Zeta, TEM and SEM imaging, EDAX, Contact angle to analyse hydrophobicity or hydrophilicity of the particle.
o Bacteriology:
 Colony forming unit from mouse blood and organs.
o Software Specific Skills:
 Origin lab Pro.
 GraphPad Prism.
 Bioinformatics tools: BLAST-protein and nucleotide.
 Microsoft Office, Excel, Power Point.
 Adobe Photoshop, Image J (western blot, immunocytochemistry, immunofluorescence, confocal analaysis)
o Hands on training
• Human Cell Culture, FPLC (Chromatography), Gel Filtration, X- Ray Crystallography by hanging drop vapour diffusion method from Goa BITS Pillani, Goa, India.

Selected Publications

Mazharian A, Bertin O, Sarkar A, Augros J, Bornert A, Loubière C, Jönsson F, Warwicker J, Abbott WM, Dushek O, Vayne C, Rauova L, Fütterer K, Rollin J, Poncz M, Senis YA.: G6b-B antibody-based cis-acting platelet receptor inhibitors (CAPRIs) as a new family of anti-thrombotic therapeutics. bioRxiv 14(1): doi: 10.1101/2024.05.10.593500, May 2024.

Ngo AT, Skidmore A, Oberg J, Yarovoi I, Sarkar A, Levine N, Bochenek V, Zhao G, Rauova L, Kowalska MA, Eckart K, Mangalmurti NS, Rux A, Cines DB, Poncz M, Gollomp K.: Platelet factor 4 limits neutrophil extracellular trap- and cell-free DNA-induced thrombogenicity and endothelial injury. JCI Insight 8(7): e171054, Nov 2023.

Sarkar A, Khandelwal S, Koma GT, Kim H, Gruel Y, Rollin J, Passam F, Wool GD, Arepally GM, Cines DB, Rauova L, Poncz M.: Treatment of thrombocytopenia and thrombosis in HIT in mice using deglycosylated KKO: a novel therapeutic? Blood Adv 7(6): 4112-4123, Aug 2023.

Ngo ATP, Sarkar A, Yarovoi I, Levine ND, Bochenek V, Zhao G, Rauova L, Kowalska MA, Eckart K, Mangalmurti NS, Rux A, Cines DB, Poncz M, Gollomp K.: Neutrophil extracellular trap stabilization by platelet factor 4 reduces thrombogenicity and endothelial cell injury. bioRxiv 1(9): doi: 10.1101/2023.01.09.522931, Jan 2023.

Apostolidis SA, Sarkar A, Giannini HM, Goel RR, Mathew D, Suzuki A, Baxter AE, Greenplate AR, Alanio C, Abdel-Hakeem M, Oldridge DA, Giles JR, Wu JE, Chen Z, Huang YJ, Belman J, Pattekar A, Manne S, Kuthuru O, Dougherty J, Weiderhold B, Weisman AR, Ittner CAG, Gouma S, Dunbar D, Frank I, Huang AC, Vella LA; UPenn COVID Processing Unit; Reilly JP, Hensley SE, Rauova L, Zhao L, Meyer NJ, Poncz M, Abrams CS, Wherry EJ.: Signaling Through FcγRIIA and the C5a-C5aR Pathway Mediate Platelet Hyperactivation in COVID-19. Front Immunol 13(1): 834988, Mar 2022.

Khandelwal S, Barnes A, Rauova L, Sarkar A, Rux AH, Yarovoi SV, Zaitsev SS, Lambris JD, Myoung SS, Johnson A, Lee GM, Duarte M, Poncz M, Arepally GM, Cines DB.: Complement mediates binding and procoagulant effects of ultralarge HIT immune complexes. Blood 138(4): 2106-2116, Nov 2021.

Apostolidis SA, Sarkar A, Giannini HM, Goel RR, Mathew D, Suzuki A, Baxter AE, Greenplate AR, Alanio C, Abdel-Hakeem M, Oldridge DA, Giles J, Wu JE, Chen Z, Huang YJ, Pattekar A, Manne S, Kuthuru O, Dougherty J, Weiderhold B, Weisman AR, Ittner CAG, Gouma S, Dunbar D, Frank I, Huang AC, Vella LA; UPenn COVID Processing Unit; Reilly JP, Hensley SE, Rauova L, Zhao L, Meyer NJ, Poncz M, Abrams CS, Wherry EJ.: Signaling through FcγRIIA and the C5a-C5aR pathway mediates platelet hyperactivation in COVID-19. bioRxiv 5(1): doi: 10.1101/2021.05.01.442279, May 2021.

Cines DB, Zaitsev S, Rauova L, Rux AH, Stepanova V, Krishnaswamy S, Sarkar A, Kowalska MA, Zhao G, Mast AE, Blumberg LJ, McCrae KR, Poncz M, Hubbard JJ, Pyzik M, Blumberg RS.: FcRn augments induction of tissue factor activity by IgG-containing immune complexes. Blood 135(1): 2085-2093, Jun 2020.

Johnston I, Sarkar A, Hayes V, Koma GT, Arepally GM, Chen J, Chung DW, López JA, Cines DB, Rauova L, Poncz M.: Recognition of PF4-VWF complexes by heparin-induced thrombocytopenia antibodies contributes to thrombus propagation. Blood 135(6): 1270-1280, Apr 2020.

Gollomp K, Sarkar A, Harikumar S, Seeholzer SH, Arepally GM, Hudock K, Rauova L, Kowalska MA, Poncz M.: Fc-modified HIT-like monoclonal antibody as a novel treatment for sepsis. Blood 135(3): 743-754, Mar 2020.

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Last updated: 07/02/2025
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