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Vikram R Paralkar, MD
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Assistant Professor of Medicine (Hematology-Oncology)
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Investigator, Abramson Family Cancer Research Institute, University of Pennsylvania
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Member, Hematologic Malignancies Program, Abramson Cancer Center, University of Pennsylvania
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Member, Spatial and Architectural Epigenetics Interest Group, Penn Epigenetics Institute, University of Pennsylvania
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Core Member, Penn Epigenetics Institute, University of Pennsylvania
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Department: Medicine
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Graduate Group Affiliations
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Contact information
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BRB II/III Room 551
36 421 Curie Boulevard
Philadelphia, PA 19104
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36 421 Curie Boulevard
Philadelphia, PA 19104
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Office: 215-573-9252
3e Lab: 215-573-9831
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3e Lab: 215-573-9831
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Education:
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3a DG Ruparel College, Mumbai, India, 1998.
21 7 MD c
3f Seth GS Medical College, Mumbai, India, 2004.
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Permanent link21 8 HSC c
3a DG Ruparel College, Mumbai, India, 1998.
21 7 MD c
3f Seth GS Medical College, Mumbai, India, 2004.
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1b RESEARCH INTERESTS:
1a0 Research in the Paralkar Lab spans the spectrum from human patient sample studies and mouse models to cutting-edge molecular biology tools, high-throughput sequencing approaches, and novel computational algorithms, all with the goal of gaining insight into how the transcription of coding genes and noncoding ribosomal DNA genes is regulated in hematopoietic stem cells, myeloid progenitors, and in leukemia.
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11 KEYWORDS:
51 Hematopoiesis, Leukemia, Gene regulation, Ribosome biogenesis, Stem cells
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19 RESEARCH DETAILS:
3a 1)rRNA Transcription in Hematopoiesis and Leukemia
194 Ribosomal RNA (rRNA) forms the majority of cellular RNA, and its transcription in the nucleolus by RNA Polymerase I from ribosomal DNA (rDNA) repeats accounts for the bulk of all transcription. rRNA transcription rates vary dramatically between different normal cell types in the hematopoietic tree, and leukemic cells have characteristic prominent nucleoli, indicating robust ribosome synthesis.
16e The rate of ribosome production has far-reaching influence on the fate of the cell, and dictates its size, proliferation, and ability to translate global or specific mRNAs. Little is known however about how rRNA transcription is regulated and fine-tuned across normal and malignant tissues, and whether this regulation can be targeted for leukemia treatment.
1a7 The Paralkar Lab has identified that key hematopoietic and leukemic transcription factors bind to rDNA and regulate rRNA transcription, and we are interested in understanding how the binding of cell-type-specific transcription factors regulates the activity of Polymerase I and the transcription of rRNA in normal hematopoiesis, and how this regulation is co-opted in leukemia to drive abundant ribosome biogenesis.
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45 2) Stemness and Differentiation in Hematopoiesis and Leukemia
273 Normal hematopoiesis requires an intricate balance in the bone marrow between the ability of stem cells to maintain themselves for decades of life while producing billions of mature blood cells every day. This balance is maintained by the combinatorial activity of transcription factors and chromatin proteins that dictate the transcription of coding gene networks instructing fate choice decisions. Several of the critical factors involved in these decisions are mutated in acute and chronic leukemias, and their mutations tip the equilibrium in the bone marrow towards accumulation of aberrant progenitor populations.
cd The Paralkar Lab is interested in gaining a detailed mechanistic understanding of how chromatin proteins regulate the stemness-differentiation balance, and how mutations in them produce malignancy.
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3f 3) Bioinformatic Pipelines for Genetics and Epigenetics
22e Current bioinformatic pipelines for high-throughput studies like whole genome sequencing, RNA-seq, ChIP-seq, and single cell RNA-seq are limited in their ability to map repetitive elements of the genome like ribosomal DNA. Such loci therefore tend to be ignored in genome wide analyses. Given that rRNA accounts for the bulk of the transcriptional output of the cell, the inability to map datasets to rDNA has historically been a major limitation, and has created a significant knowledge gap in our understanding of the most abundant RNA in the cell.
101 The Paralkar Lab has developed customized genomes and computational pipelines to map datasets to rDNA, and we are interested in developing advanced tools to map and interpret the genetic and epigenetic profiles of rDNA in normal and malignant cells.
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15 TEAM MEMBERS:
30 Charles Antony, PhD - Research Associate
37 Melanie Auerbach, BS - Administrative Assistant
3b Meredith Arterburn, BS - Cancer Biology PhD Student
31 Sanae Dezhabad - Undergraduate Researcher
30 Victoria Feist, BS - Research Specialist
31 Subin George MS - Computational Biologist
37 Jill Henrich, BS - Cancer Biology PhD Candidate
38 Putzer Hung, MD/PhD - Hematology-Oncology Fellow
3a Aishwarya Pawar, MS - Cancer Biology PhD Candidate
41 Eleanor Sams, BS - Genetics and Epigenetics PhD Candidate
58 Lucille Wang, BS - Developmental, Stem Cell, and Regenerative Biology PhD Student
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Description of Clinical Expertise
36 Acute and Chronic Myeloid Malignancies71
Description of Research Expertise
49 PARALKAR LAB WEBSITE: https://paralkarlab.med.upenn.edu/8
1b RESEARCH INTERESTS:
1a0 Research in the Paralkar Lab spans the spectrum from human patient sample studies and mouse models to cutting-edge molecular biology tools, high-throughput sequencing approaches, and novel computational algorithms, all with the goal of gaining insight into how the transcription of coding genes and noncoding ribosomal DNA genes is regulated in hematopoietic stem cells, myeloid progenitors, and in leukemia.
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11 KEYWORDS:
51 Hematopoiesis, Leukemia, Gene regulation, Ribosome biogenesis, Stem cells
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19 RESEARCH DETAILS:
3a 1)rRNA Transcription in Hematopoiesis and Leukemia
194 Ribosomal RNA (rRNA) forms the majority of cellular RNA, and its transcription in the nucleolus by RNA Polymerase I from ribosomal DNA (rDNA) repeats accounts for the bulk of all transcription. rRNA transcription rates vary dramatically between different normal cell types in the hematopoietic tree, and leukemic cells have characteristic prominent nucleoli, indicating robust ribosome synthesis.
16e The rate of ribosome production has far-reaching influence on the fate of the cell, and dictates its size, proliferation, and ability to translate global or specific mRNAs. Little is known however about how rRNA transcription is regulated and fine-tuned across normal and malignant tissues, and whether this regulation can be targeted for leukemia treatment.
1a7 The Paralkar Lab has identified that key hematopoietic and leukemic transcription factors bind to rDNA and regulate rRNA transcription, and we are interested in understanding how the binding of cell-type-specific transcription factors regulates the activity of Polymerase I and the transcription of rRNA in normal hematopoiesis, and how this regulation is co-opted in leukemia to drive abundant ribosome biogenesis.
8
45 2) Stemness and Differentiation in Hematopoiesis and Leukemia
273 Normal hematopoiesis requires an intricate balance in the bone marrow between the ability of stem cells to maintain themselves for decades of life while producing billions of mature blood cells every day. This balance is maintained by the combinatorial activity of transcription factors and chromatin proteins that dictate the transcription of coding gene networks instructing fate choice decisions. Several of the critical factors involved in these decisions are mutated in acute and chronic leukemias, and their mutations tip the equilibrium in the bone marrow towards accumulation of aberrant progenitor populations.
cd The Paralkar Lab is interested in gaining a detailed mechanistic understanding of how chromatin proteins regulate the stemness-differentiation balance, and how mutations in them produce malignancy.
8
3f 3) Bioinformatic Pipelines for Genetics and Epigenetics
22e Current bioinformatic pipelines for high-throughput studies like whole genome sequencing, RNA-seq, ChIP-seq, and single cell RNA-seq are limited in their ability to map repetitive elements of the genome like ribosomal DNA. Such loci therefore tend to be ignored in genome wide analyses. Given that rRNA accounts for the bulk of the transcriptional output of the cell, the inability to map datasets to rDNA has historically been a major limitation, and has created a significant knowledge gap in our understanding of the most abundant RNA in the cell.
101 The Paralkar Lab has developed customized genomes and computational pipelines to map datasets to rDNA, and we are interested in developing advanced tools to map and interpret the genetic and epigenetic profiles of rDNA in normal and malignant cells.
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15 TEAM MEMBERS:
30 Charles Antony, PhD - Research Associate
37 Melanie Auerbach, BS - Administrative Assistant
3b Meredith Arterburn, BS - Cancer Biology PhD Student
31 Sanae Dezhabad - Undergraduate Researcher
30 Victoria Feist, BS - Research Specialist
31 Subin George MS - Computational Biologist
37 Jill Henrich, BS - Cancer Biology PhD Candidate
38 Putzer Hung, MD/PhD - Hematology-Oncology Fellow
3a Aishwarya Pawar, MS - Cancer Biology PhD Candidate
41 Eleanor Sams, BS - Genetics and Epigenetics PhD Candidate
58 Lucille Wang, BS - Developmental, Stem Cell, and Regenerative Biology PhD Student
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17b Sams EI, Feist VK, Gray EM, George SS, Antony C, Henrich JA, Wald J, Dunagin MC, Wang Z, Erlitzki N, Raj A, Signer RAJ, Paralkar VR: Dynamics of ribosomal RNA transcription and abundance in normal and leukemic hematopoiesis. BioRxiv Page: 2025.08.01.668217, Aug 2025 Notes: doi: 10.1101/2025.08.01.668217.
10f Jalnapurkar SS, Pawar AS, George SS, Antony C, Somers P, Grana J, Feist VK, Gurbuxani S, Paralkar VR: PHF6 suppresses self-renewal of leukemic stem cells in AML. Leukemia 38(9): 1938-1948, Jul 2024.
d0 Paralkar VR: Transcription factor regulation of ribosomal RNA in hematopoiesis. Current Opinion in Hematology 31(4): 199-206, Apr 2024.
f4 Antony C, Somers P, Gray EM, Pimkin M, Paralkar VR: FISH-Flow to quantify nascent and mature ribosomal RNA in mouse and human cells. STAR Protocols 4(3): 102463, Sep 2023.
101 George SS, Pimkin M, Paralkar VR: Construction and validation of customized genomes for human and mouse ribosomal DNA mapping. Journal of Biological Chemistry 299(6): 104766, Jun 2023.
15e Antony C, George SS, Blum J, Somers P, Thorsheim CL, Wu-Corts DJ, Ai Y, Gao L, Lv K, Tremblay MG, Moss T, Tan K, Wilusz JE, Ganley ARD, Pimkin M, Paralkar VR: Control of ribosomal RNA synthesis by hematopoietic transcription factors. Molecular Cell 82(20): 3826-3839, Oct 2022.
144 Lv K, Gong C, Antony C, Han X, Ren J, Donaghy R, Cheng Y, Pellegrino S, Warren AJ, Paralkar VR, Tong W: HectD1 controls hematopoietic stem cell regeneration by coordinating ribosome assembly and protein synthesis. Cell Stem Cell 28(7): 1-16, Jul 2021.
13c Xu P, Palmer LE, Lechauve C, Zhao G, Yao Y, Luan J, Vourekas A, Tan H, Peng J, Scheutz JD, Mourelatos Z, Wu G, Weiss MJ, Paralkar VR: Regulation of gene expression by miR-144/451 during mouse erythropoiesis. Blood 133(23): 2518-2528, Jun 2019.
126 Paralkar VR, Taborda CC, Huang P, Yao Y, Kossenkov AV, Prasad R, Luan J, Davies JO, Hughes JR, Hardison RC, Blobel GA, Weiss MJ: Unlinking an lncRNA from Its Associated cis Element. Molecular Cell 62(1): 104-10, Apr 2016.
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Selected Publications
1ae Pawar AS, Somers P, Alex A, Grana J, Feist VK, George SS, Jalnapurkar SS, Antony C, Verner R, White-Brown SK, Khera M, Mendoza-Figueroa MS, Liu KF, Morrissette JJD, Gurbuxani S, Paralkar VR: Leukemia mutated proteins PHF6 and PHIP form a chromatin complex that represses acute myeloid leukemia stemness. Genes and Development 39(19-20): 1219-1240, Oct 2025.17b Sams EI, Feist VK, Gray EM, George SS, Antony C, Henrich JA, Wald J, Dunagin MC, Wang Z, Erlitzki N, Raj A, Signer RAJ, Paralkar VR: Dynamics of ribosomal RNA transcription and abundance in normal and leukemic hematopoiesis. BioRxiv Page: 2025.08.01.668217, Aug 2025 Notes: doi: 10.1101/2025.08.01.668217.
10f Jalnapurkar SS, Pawar AS, George SS, Antony C, Somers P, Grana J, Feist VK, Gurbuxani S, Paralkar VR: PHF6 suppresses self-renewal of leukemic stem cells in AML. Leukemia 38(9): 1938-1948, Jul 2024.
d0 Paralkar VR: Transcription factor regulation of ribosomal RNA in hematopoiesis. Current Opinion in Hematology 31(4): 199-206, Apr 2024.
f4 Antony C, Somers P, Gray EM, Pimkin M, Paralkar VR: FISH-Flow to quantify nascent and mature ribosomal RNA in mouse and human cells. STAR Protocols 4(3): 102463, Sep 2023.
101 George SS, Pimkin M, Paralkar VR: Construction and validation of customized genomes for human and mouse ribosomal DNA mapping. Journal of Biological Chemistry 299(6): 104766, Jun 2023.
15e Antony C, George SS, Blum J, Somers P, Thorsheim CL, Wu-Corts DJ, Ai Y, Gao L, Lv K, Tremblay MG, Moss T, Tan K, Wilusz JE, Ganley ARD, Pimkin M, Paralkar VR: Control of ribosomal RNA synthesis by hematopoietic transcription factors. Molecular Cell 82(20): 3826-3839, Oct 2022.
144 Lv K, Gong C, Antony C, Han X, Ren J, Donaghy R, Cheng Y, Pellegrino S, Warren AJ, Paralkar VR, Tong W: HectD1 controls hematopoietic stem cell regeneration by coordinating ribosome assembly and protein synthesis. Cell Stem Cell 28(7): 1-16, Jul 2021.
13c Xu P, Palmer LE, Lechauve C, Zhao G, Yao Y, Luan J, Vourekas A, Tan H, Peng J, Scheutz JD, Mourelatos Z, Wu G, Weiss MJ, Paralkar VR: Regulation of gene expression by miR-144/451 during mouse erythropoiesis. Blood 133(23): 2518-2528, Jun 2019.
126 Paralkar VR, Taborda CC, Huang P, Yao Y, Kossenkov AV, Prasad R, Luan J, Davies JO, Hughes JR, Hardison RC, Blobel GA, Weiss MJ: Unlinking an lncRNA from Its Associated cis Element. Molecular Cell 62(1): 104-10, Apr 2016.
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