9 results on '"Robert J. Kimmerling"'
Search Results
2. Publisher Correction: A pipeline for malignancy and therapy agnostic assessment of cancer drug response using cell mass measurements
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Robert J. Kimmerling, Mark M. Stevens, Selim Olcum, Anthony Minnah, Madeleine Vacha, Rachel LaBella, Matthew Ferri, Steven C. Wasserman, Juanita Fujii, Zayna Shaheen, Srividya Sundaresan, Drew Ribadeneyra, David S. Jayabalan, Sarita Agte, Adolfo Aleman, Joseph A. Criscitiello, Ruben Niesvizky, Marlise R. Luskin, Samir Parekh, Cara A. Rosenbaum, Anobel Tamrazi, and Clifford A. Reid
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Biology (General) ,QH301-705.5 - Published
- 2023
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3. Microfluidic active loading of single cells enables analysis of complex clinical specimens
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Nicholas L. Calistri, Robert J. Kimmerling, Seth W. Malinowski, Mehdi Touat, Mark M. Stevens, Selim Olcum, Keith L. Ligon, and Scott R. Manalis
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Science - Abstract
Single-cell detection methods are limited by the trade-off between flow rate and measurement precision. Here the authors introduce active loading, an optically triggered microfluidic system to concentrate diluted cell samples, which reduces clogging and decreases processing time in single-cell assays.
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- 2018
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4. Linking single-cell measurements of mass, growth rate, and gene expression
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Robert J. Kimmerling, Sanjay M. Prakadan, Alejandro J. Gupta, Nicholas L. Calistri, Mark M. Stevens, Selim Olcum, Nathan Cermak, Riley S. Drake, Kristine Pelton, Frederik De Smet, Keith L. Ligon, Alex K. Shalek, and Scott R. Manalis
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Single-cell RNA-Seq ,Mass ,Growth ,Serial suspended microchannel resonator ,Multi-omics ,Single cell ,Biology (General) ,QH301-705.5 ,Genetics ,QH426-470 - Abstract
Abstract Mass and growth rate are highly integrative measures of cell physiology not discernable via genomic measurements. Here, we introduce a microfluidic platform enabling direct measurement of single-cell mass and growth rate upstream of highly multiplexed single-cell profiling such as single-cell RNA sequencing. We resolve transcriptional signatures associated with single-cell mass and growth rate in L1210 and FL5.12 cell lines and activated CD8+ T cells. Further, we demonstrate a framework using these linked measurements to characterize biophysical heterogeneity in a patient-derived glioblastoma cell line with and without drug treatment. Our results highlight the value of coupled phenotypic metrics in guiding single-cell genomics.
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- 2018
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5. Determining therapeutic susceptibility in multiple myeloma by single-cell mass accumulation
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Arif E. Cetin, Mark M. Stevens, Nicholas L. Calistri, Mariateresa Fulciniti, Selim Olcum, Robert J. Kimmerling, Nikhil C. Munshi, and Scott R. Manalis
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Science - Abstract
Multiple myeloma is characterized by high rates of drug resistance and relapse. Here the authors utilize a functional assay to assess the ex vivo drug sensitivity of single multiple myeloma cells based on measuring the mass accumulation rate of individual cells.
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- 2017
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6. Trisomy of a Down Syndrome Critical Region Globally Amplifies Transcription via HMGN1 Overexpression
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Cody T. Mowery, Jaime M. Reyes, Lucia Cabal-Hierro, Kelly J. Higby, Kristen L. Karlin, Jarey H. Wang, Robert J. Kimmerling, Paloma Cejas, Klothilda Lim, Hubo Li, Takashi Furusawa, Henry W. Long, David Pellman, Bjoern Chapuy, Michael Bustin, Scott R. Manalis, Thomas F. Westbrook, Charles Y. Lin, and Andrew A. Lane
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Biology (General) ,QH301-705.5 - Abstract
Summary: Down syndrome (DS, trisomy 21) is associated with developmental abnormalities and increased leukemia risk. To reconcile chromatin alterations with transcriptome changes, we performed paired exogenous spike-in normalized RNA and chromatin immunoprecipitation sequencing in DS models. Absolute normalization unmasks global amplification of gene expression associated with trisomy 21. Overexpression of the nucleosome binding protein HMGN1 (encoded on chr21q22) recapitulates transcriptional changes seen with triplication of a Down syndrome critical region on distal chromosome 21, and HMGN1 is necessary for B cell phenotypes in DS models. Absolute exogenous-normalized chromatin immunoprecipitation sequencing (ChIP-Rx) also reveals a global increase in histone H3K27 acetylation caused by HMGN1. Transcriptional amplification downstream of HMGN1 is enriched for stage-specific programs of B cells and B cell acute lymphoblastic leukemia, dependent on the developmental cellular context. These data offer a mechanistic explanation for DS transcriptional patterns and suggest that further study of HMGN1 and RNA amplification in diverse DS phenotypes is warranted. : How trisomy 21 contributes to Down syndrome phenotypes, including increased leukemia risk, is not well understood. Mowery et al. use per-cell normalization approaches to reveal global transcriptional amplification in Down syndrome models. HMGN1 overexpression is sufficient to induce these alterations and promotes lineage-associated transcriptional programs, signaling, and B cell progenitor phenotypes. Keywords: Down syndrome, leukemia, HMGN1, spike-in normalization, RNA sequencing, ChIP-Rx, transcriptional amplification, trisomy 21, Down syndrome critical region, DSCR, B cells
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- 2018
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7. A microfluidic platform enabling single-cell RNA-seq of multigenerational lineages
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Robert J. Kimmerling, Gregory Lee Szeto, Jennifer W. Li, Alex S. Genshaft, Samuel W. Kazer, Kristofor R. Payer, Jacob de Riba Borrajo, Paul C. Blainey, Darrell J. Irvine, Alex K. Shalek, and Scott R. Manalis
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Science - Abstract
Existing single-cell RNA-seq methods provide the transcriptome of a cellular phenotype at a single time point. Here, Kimmerlinget al. present a microfluidic platform that enables off-chip single-cell RNA-seq after multigenerational lineage tracking under controlled culture conditions.
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- 2016
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8. Mass measurements during lymphocytic leukemia cell polyploidization decouple cell cycle- and cell size-dependent growth
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Robert J. Kimmerling, Scott R. Manalis, Joon Ho Kang, Teemu P. Miettinen, Selim Olcum, Kristofor R. Payer, Nicholas L. Calistri, and Luye Mu
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Pseudodiploid ,Population ,Cell ,Biosensing Techniques ,Cell Enlargement ,Polyploidy ,Mice ,Engineering ,Exponential growth ,Cell Line, Tumor ,medicine ,cell growth ,Animals ,Humans ,education ,Cell Proliferation ,mass measurement ,education.field_of_study ,Multidisciplinary ,Cell growth ,Chemistry ,Cell Cycle ,Cell Biology ,Metabolism ,Biological Sciences ,Microfluidic Analytical Techniques ,Cell cycle ,medicine.disease ,Leukemia, Lymphoid ,cell size ,Leukemia ,medicine.anatomical_structure ,Physical Sciences ,transport limitation ,Biophysics ,Cell Division - Abstract
Significance Cell size is believed to influence cell growth through limited transport efficiency in larger cells. However, this has not been experimentally investigated due to a lack of noninvasive, high-precision growth quantification methods suitable for measuring large cells. Here, we have engineered large versions of microfluidic mass sensors called suspended microchannel resonators in order to study the growth of single mammalian cells that range 100-fold in mass. Our measurements, which decouple growth effects caused by cell cycle and cell size, revealed that absolute cell size does not impose strict transport or other limitations that would inhibit growth and that cell cycle has a large influence on growth., Cell size is believed to influence cell growth and metabolism. Consistently, several studies have revealed that large cells have lower mass accumulation rates per unit mass (i.e., growth efficiency) than intermediate-sized cells in the same population. Size-dependent growth is commonly attributed to transport limitations, such as increased diffusion timescales and decreased surface-to-volume ratio. However, separating cell size- and cell cycle-dependent growth is challenging. To address this, we monitored growth efficiency of pseudodiploid mouse lymphocytic leukemia cells during normal proliferation and polyploidization. This was enabled by the development of large-channel suspended microchannel resonators that allow us to monitor buoyant mass of single cells ranging from 40 pg (small pseudodiploid cell) to over 4,000 pg, with a resolution ranging from ∼1% to ∼0.05%. We find that cell growth efficiency increases, plateaus, and then decreases as cell cycle proceeds. This growth behavior repeats with every endomitotic cycle as cells grow into polyploidy. Overall, growth efficiency changes 33% throughout the cell cycle. In contrast, increasing cell mass by over 100-fold during polyploidization did not change growth efficiency, indicating exponential growth. Consistently, growth efficiency remained constant when cell cycle was arrested in G2. Thus, cell cycle is a primary determinant of growth efficiency. As growth remains exponential over large size scales, our work finds no evidence for transport limitations that would decrease growth efficiency.
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- 2020
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9. High-throughput measurement of single-cell growth rates using serial microfluidic mass sensor arrays
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Mark A. Murakami, Robert J. Kimmerling, Nathan Cermak, Masaaki Ogawa, Francois Baleras, Steven C. Wasserman, Scott R. Manalis, Francisco Feijó Delgado, Arzu Sandikci, Selim Olcum, Vincent Agache, Kristofor R. Payer, Mark M. Stevens, David M. Weinstock, Yuki Kikuchi, Scott M. Knudsen, Massachusetts Institute of Technology. Department of Biological Engineering, Massachusetts Institute of Technology. Department of Biology, Massachusetts Institute of Technology. Department of Mechanical Engineering, Massachusetts Institute of Technology. Microsystems Technology Laboratories, Koch Institute for Integrative Cancer Research at MIT, Olcum, Selim A., Delgado, Francisco Feijo, Wasserman, Steven, Payer, Kristofor, Knudsen, Scott, Kimmerling, Robert John, Stevens, Mark M., Kikuchi, Yuki, Sandikci, Arzu, and Manalis, Scott R
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0301 basic medicine ,Resolution (mass spectrometry) ,Transducers ,Cell ,Microfluidics ,Antimicrobial peptides ,Drug Evaluation, Preclinical ,Biomedical Engineering ,Bioengineering ,02 engineering and technology ,medicine.disease_cause ,Sensitivity and Specificity ,Applied Microbiology and Biotechnology ,Article ,Enterococcus faecalis ,03 medical and health sciences ,Lab-On-A-Chip Devices ,medicine ,Escherichia coli ,Cell Proliferation ,biology ,Cell growth ,Reproducibility of Results ,Equipment Design ,Micro-Electrical-Mechanical Systems ,021001 nanoscience & nanotechnology ,biology.organism_classification ,Yeast ,High-Throughput Screening Assays ,3. Good health ,Cell biology ,Equipment Failure Analysis ,030104 developmental biology ,medicine.anatomical_structure ,Molecular Medicine ,0210 nano-technology ,Biotechnology - Abstract
Methods to rapidly assess cell growth would be useful for many applications, including drug susceptibility testing, but current technologies have limited sensitivity or throughput. Here we present an approach to precisely and rapidly measure growth rates of many individual cells simultaneously. We flow cells in suspension through a microfluidic channel with 10-12 resonant mass sensors distributed along its length, weighing each cell repeatedly over the 4-20 min it spends in the channel. Because multiple cells traverse the channel at the same time, we obtain growth rates for >60 cells/h with a resolution of 0.2 pg/h for mammalian cells and 0.02 pg/h for bacteria. We measure the growth of single lymphocytic cells, mouse and human T cells, primary human leukemia cells, yeast, Escherichia coli and Enterococcus faecalis. Our system reveals subpopulations of cells with divergent growth kinetics and enables assessment of cellular responses to antibiotics and antimicrobial peptides within minutes., United States. Army Research Office (Grant W911NF-09-D-0001), National Science Foundation (U.S.) (Grant 1129359), National Cancer Institute (U.S.) (Grant U54CA143874), National Cancer Institute (U.S.) (Grant P30-CA14051), National Cancer Institute (U.S.) (Grant R33-CA191143), National Institutes of Health (U.S.) (Grant T32-GM008334), National Institute of General Medical Sciences (U.S.) (Grant T32-GM008334)
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- 2016
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