Raga Krishnakumar

Biography

Raga Krishnakumar’s main area of research is detecting, understanding and regulating mammalian cell fate, including fate changes with response to environmental stimuli such as infectious agents or stress conditions. Specifically, she is interested in how we can generate and deploy therapeutic cells for a variety of disease states and conditions that are pertinent both to national security and public health. She applies an integrated approach of high-throughput experimentation, data analytics and functional assays to identify mechanisms by which to generate context-specific therapeutic cells. In addition, she is involved in a number of projects at Sandia as a computational biologist, including the identification and classification of mobile elements in bacterial genomes, and real-time selective sequencing of specific nucleic acids in mixed samples using the Oxford Nanopore MinION long-read sequencer.

Education

Bachelor’s Degree: Bachelor of Arts (honors) in Natural Sciences (Biochemistry), University of Cambridge, UK (2001 – 2004)

Doctoral Degree: : Ph.D. in Biochemistry, Cell and Molecular Biology, Cornell University (2004 – 2010); PI: W. Lee Kraus

Postdoctoral Fellowships:

• Postdoctoral Fellow, Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, University of California San Francisco (2010 – 2016); PI: Robert Blelloch
• Postdoctoral Appointee, Systems Biology Department, Sandia National Laboratories (2016); PIs: Michael Bartsch and Kelly Williams).

Raga Krishnakumar did her undergraduate studies at the University of Cambridge, UK. She majored in Natural Sciences with a specialization in Biochemistry. She then did her Ph.D. work with Dr. Lee Kraus at Cornell University in Ithaca, NY, where she focused on the role of two nucleosome-binding proteins – Poly ADP-ribose polymerase-1 (PARP-1) and histone H1 – in the regulation of chromatin structure and transcription in breast cancer cells and cardiomyocytes. Her work was funded in part by an American Heart Association predoctoral fellowship. She completed her Ph.D. in 2010.

Following this, Krishnakumar did her postdoctoral work at the University of California San Francisco (UCSF) in the laboratory of Dr. Robert Blelloch. She led two main projects during her postdoc. First, in collaboration with a graduate student in the lab, she found that microRNA activity is suppressed in mature oocytes due to limiting amounts of the effector Argonaute protein. The second project focused on the epigenetic regulation of mouse embryonic stem (ES) cell differentiation, specifically showing that a transcription factor, Foxd3, that is central to regulating the timing of differentiation through enhancer priming. In addition, during her postdoc, Krishnakumar trained as a computational biologist and bioinformatician, and acquired both the coding and statistics knowledge required to perform in-depth analysis of large data sets. Her postdoctoral work was funded in part by an A.P. Giannini postdoctoral fellowship.

Research Interests

Engineering Therapeutic Mesenchymal Stem Cells

Krishnakumar’s goal is to harness the incredible versatility of mesenchymal stem cells (MSCs) as antibacterial, immunomodulatory and regenerative cells for therapeutic purposes, with a special focus on bacterial infection in mammalian systems. Krishnakumar and her team are characterizing the molecular signatures (transcriptomic, epigenomic and proteomic) that correlate with functional outcomes in order to a) be able to successfully isolate properly therapeutic MSCs and b) convert other cell types into stably therapeutic MSCs. They are generating computational models using our large omic data sets combined with readouts on functional outcomes that inform them on how specific cells will behave based on their molecular profile, and how they can customize the behavior of these cells by targeting specific genomic regions and pathways.

Identifying and Classifying Bacterial Mobile Genomic Elements

Understanding the mechanisms underlying the trajectories of bacterial mobile elements is of crucial importance, since bacteria use these elements to acquire drug-resistance and toxicity genes. In collaboration with Kelly Williams, Krishnakumar has worked on the classification of bacterial mobile elements identified by two pieces of software developed at Sandia – Islander and Comparator. Specifically, she is interested in understanding how mobile elements differ from their host genomes in terms of composition and size and has used this information to generate a model that identifies false positive elements. Her work focuses specifically on genomic islands, which are characteristically modular in their nature (they have groups of genes that travel and function together). She has therefore developed a clustering protocol to group islands elements based on a range of similarity, from near-identical to islands that share some modules but have evolved divergently for some time.

Real-time Selective Sequencing Using the MinION Nanopore Sequencer

Given the short timelines often associated with pathogenesis in infectious disease, rapid identification and diagnosis of agents is critical for successful treatment of affected patients, and the prevention of spreading, both within single individuals and throughout the population at large. In an effort to address this, in collaboration with Michael Bartsch, she has characterized the performance of the long-read nanopore sequencer from Oxford Nanopore Technologies, the MinION, across genomes with a range of nucleotide bias. She examined the likelihood of both stochastic and deterministic errors as a result of the evolving hardware and base calling software. Her team is also one of the few groups worldwide making us of the ability of the MinION to perform interactive sequencing (i.e. real-time decision making on whether to sequence a particular strand based on the pattern of the leading segment). They have established a program that performs real-time thresholding and basecalling, and decides which strands of nucleic acid to prioritize for sequencing, allowing them to relatively enrich a specific region of interest over background. Through collaborations, they are currently looking at potential real-world applications for this technology. 

Publications

Selected Publications

• Publications may be viewed through the NCBI Collection.
• Krishnakumar R, Gamble MJ, Frizzell KM, Berrocal JG, Kininis M, Kraus WL. Reciprocal binding of PARP-1 and histone H1 at promoters specifies transcriptional outcomes. Science (New York, N.Y.). 2008; 319(5864):819-21.
• Zhang T, Berrocal JG, Frizzell KM, Gamble MJ, DuMond ME, Krishnakumar R, Yang T, Sauve AA, Kraus WL. Enzymes in the NAD+ salvage pathway regulate SIRT1 activity at target gene promoters. The Journal of biological chemistry. 2009; 284(30):20408-17.
• Frizzell KM, Gamble MJ, Berrocal JG, Zhang T, Krishnakumar R, Cen Y, Sauve AA,Kraus WL. Global analysis of transcriptional regulation by poly(ADP-ribose) polymerase-1 and poly(ADP-ribose) glycohydrolase in MCF-7 human breast cancer cells. The Journal of biological chemistry. 2009; 284(49):33926-38.
• Gamble MJ, Frizzell KM, Yang C, Krishnakumar R, Kraus WL. The histone variant macroH2A1 marks repressed autosomal chromatin, but protects a subset of its target genes from silencing. Genes & development. 2010; 24(1):21-32.
• Krishnakumar R, Kraus WL. The PARP side of the nucleus: molecular actions, physiological outcomes, and clinical targets. Molecular cell. 2010; 39(1):8-24.
• Krishnakumar R, Kraus WL. PARP-1 regulates chromatin structure and transcription through a KDM5B-dependent pathway. Molecular cell. 2010; 39(5):736-49.
• Zhang T, Berrocal JG, Yao J, DuMond ME, Krishnakumar R, Ruhl DD, Ryu KW, Gamble MJ, Kraus WL. Regulation of poly(ADP-ribose) polymerase-1-dependent gene expression through promoter-directed recruitment of a nuclear NAD+ synthase. The Journal of biological chemistry. 2012; 287(15):12405-16.
• Krishnakumar R, Blelloch RH. Epigenetics of cellular reprogramming. Current opinion in genetics & development. 2013; 23(5):548-55.
• Luo X, Chae M, Krishnakumar R, Danko CG, Kraus WL. Dynamic reorganization of the AC16 cardiomyocyte transcriptome in response to TNFα signaling revealed by integrated genomic analyses. BMC genomics. 2014; 15:155.
• Parchem RJ, Ye J, Judson RL, LaRussa MF, Krishnakumar R, Blelloch A, Oldham MC, Blelloch R. Two miRNA clusters reveal alternative paths in late-stage reprogramming. Cell stem cell. 2014; 14(5):617-31.
• Krishnakumar R, Chen AF, Pantovich MG, Danial M, Parchem RJ, Labosky PA, Blelloch R. FOXD3 Regulates Pluripotent Stem Cell Potential by Simultaneously Initiating and Repressing Enhancer Activity. Cell stem cell. 2016; 18(1):104-17.
• Freimer JW, Krishnakumar R, Cook MS, Blelloch R. Expression of Alternative Ago2 Isoform Associated with Loss of microRNA-Driven Translational Repression in Mouse Oocytes. Current biology: CB. 2018; 28(2):296-302.e3.
• Krishnakumar R, Sinha A, Bird SW, Jayamohan H, Edwards HS, Schoeniger JS, Patel KD, Branda SS, Bartsch MS. Systematic and stochastic influences on the performance of the MinION nanopore sequencer across a range of nucleotide bias. Scientific reports. 2018; 8(1):3159.
• Chen AF, Liu AJ, Krishnakumar R, Freimer JW, DeVeale B, Blelloch R. GRHL2-Dependent Enhancer Switching Maintains a Pluripotent Stem Cell Transcriptional Subnetwork after Exit from Naive Pluripotency. Cell stem cell.018.

Awards, Honors, and Memberships

• A.P. Giannini Medical Research Fellow, 3-year Postdoctoral Fellowship (2011-2014)
• NIH Ruth L. Kirschstein National Research Service Award (NRSA) Institutional Research Training Grant-Parent T32 (2011)
• Predoctoral Fellowship, American Heart Association (2008-2010)