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305 Leveraging multi-timepoint blood samples to characterize cancer-associated mutations in the blood over time
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- Taralynn Mack, Kelly Von Beck, Alexander Silver, Michael Savona, Alexander Bick Vanderbilt
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- Journal:
- Journal of Clinical and Translational Science / Volume 7 / Issue s1 / April 2023
- Published online by Cambridge University Press:
- 24 April 2023, p. 91
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OBJECTIVES/GOALS: Clonal hematopoiesis of indeterminate potential (CHIP) is a common age-related condition that confers an increased risk of blood cancer, cardiovascular disease, and overall mortality. Larger proportions of blood cells with the CHIP mutation (clones) lead to worse outcomes. The goal of this study was to characterize CHIP clonal behavior over time. METHODS/STUDY POPULATION: While DNA biobanks have the ability to identify large cohorts of individuals with CHIP, they typically only contain blood from a single timepoint, limiting the ability to infer how CHIP clones change over time. In this preliminary study, we utilized multi-timepoint blood samples from 101 individuals with CHIP in Vanderbilt’s biobank (BioVU) to characterize clonal behavior over time. Using a CHIP gene-specific sequencing pipeline, we were able to characterize each individual’s CHIP mutation(s) and how the fraction of cells with the CHIP mutation expanded/reduced over time. By Spring 2023, we will also include ~300 additional individuals with CHIP in this study. RESULTS/ANTICIPATED RESULTS: CHIP mutations occurred 48% of the time in DNMT3A and 23% of the time in TET2, consistent with previous studies. 21% of individuals had more than one CHIP mutation. The mean difference in time between the two timepoints was 5.2 years (SD=2.9). Surprisingly, we observed both clonal expansion and clonal reduction across timepoints with 30% of DNMT3A, 0.6% of TET2, and 46% of JAK2 clones shrinking over time. The fastest average expansion was seen in TET2 clones (2% growth/year) and the slowest in DNMT3A clones (0.4% growth/year), but there was a significant amount of variation between individuals. In DNMT3A clones, there were no differences observed between loss of function mutations, missense mutations or DNMT3A R882 hotspot mutations. Clonal competition was observed in individuals with multiple driver mutations. DISCUSSION/SIGNIFICANCE: We used multi-timepoint blood samples to quantify the change in CHIP cell fraction over time on a per individual basis and observed novel clonal behavior and competition. Understanding the factors that influence the rate of CHIP progression can lead to personalized disease risk assessment for individuals with CHIP.
Contributors
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- By Aakash Agarwala, Linda S. Aglio, Rae M. Allain, Paul D. Allen, Houman Amirfarzan, Yasodananda Kumar Areti, Amit Asopa, Edwin G. Avery, Patricia R. Bachiller, Angela M. Bader, Rana Badr, Sibinka Bajic, David J. Baker, Sheila R. Barnett, Rena Beckerly, Lorenzo Berra, Walter Bethune, Sascha S. Beutler, Tarun Bhalla, Edward A. Bittner, Jonathan D. Bloom, Alina V. Bodas, Lina M. Bolanos-Diaz, Ruma R. Bose, Jan Boublik, John P. Broadnax, Jason C. Brookman, Meredith R. Brooks, Roland Brusseau, Ethan O. Bryson, Linda A. Bulich, Kenji Butterfield, William R. Camann, Denise M. Chan, Theresa S. Chang, Jonathan E. Charnin, Mark Chrostowski, Fred Cobey, Adam B. Collins, Mercedes A. Concepcion, Christopher W. Connor, Bronwyn Cooper, Jeffrey B. Cooper, Martha Cordoba-Amorocho, Stephen B. Corn, Darin J. Correll, Gregory J. Crosby, Lisa J. Crossley, Deborah J. Culley, Tomas Cvrk, Michael N. D'Ambra, Michael Decker, Daniel F. Dedrick, Mark Dershwitz, Francis X. Dillon, Pradeep Dinakar, Alimorad G. Djalali, D. John Doyle, Lambertus Drop, Ian F. Dunn, Theodore E. Dushane, Sunil Eappen, Thomas Edrich, Jesse M. Ehrenfeld, Jason M. Erlich, Lucinda L. Everett, Elliott S. Farber, Khaldoun Faris, Eddy M. Feliz, Massimo Ferrigno, Richard S. Field, Michael G. Fitzsimons, Hugh L. Flanagan Jr., Vladimir Formanek, Amanda A. Fox, John A. Fox, Gyorgy Frendl, Tanja S. Frey, Samuel M. Galvagno Jr., Edward R. Garcia, Jonathan D. Gates, Cosmin Gauran, Brian J. Gelfand, Simon Gelman, Alexander C. Gerhart, Peter Gerner, Omid Ghalambor, Christopher J. Gilligan, Christian D. Gonzalez, Noah E. Gordon, William B. Gormley, Thomas J. Graetz, Wendy L. Gross, Amit Gupta, James P. Hardy, Seetharaman Hariharan, Miriam Harnett, Philip M. Hartigan, Joaquim M. Havens, Bishr Haydar, Stephen O. Heard, James L. Helstrom, David L. Hepner, McCallum R. Hoyt, Robert N. Jamison, Karinne Jervis, Stephanie B. Jones, Swaminathan Karthik, Richard M. Kaufman, Shubjeet Kaur, Lee A. Kearse Jr., John C. Keel, Scott D. Kelley, Albert H. Kim, Amy L. Kim, Grace Y. Kim, Robert J. Klickovich, Robert M. Knapp, Bhavani S. Kodali, Rahul Koka, Alina Lazar, Laura H. Leduc, Stanley Leeson, Lisa R. Leffert, Scott A. LeGrand, Patricio Leyton, J. Lance Lichtor, John Lin, Alvaro A. Macias, Karan Madan, Sohail K. Mahboobi, Devi Mahendran, Christine Mai, Sayeed Malek, S. Rao Mallampati, Thomas J. Mancuso, Ramon Martin, Matthew C. Martinez, J. A. Jeevendra Martyn, Kai Matthes, Tommaso Mauri, Mary Ellen McCann, Shannon S. McKenna, Dennis J. McNicholl, Abdel-Kader Mehio, Thor C. Milland, Tonya L. K. Miller, John D. Mitchell, K. Annette Mizuguchi, Naila Moghul, David R. Moss, Ross J. Musumeci, Naveen Nathan, Ju-Mei Ng, Liem C. Nguyen, Ervant Nishanian, Martina Nowak, Ala Nozari, Michael Nurok, Arti Ori, Rafael A. Ortega, Amy J. Ortman, David Oxman, Arvind Palanisamy, Carlo Pancaro, Lisbeth Lopez Pappas, Benjamin Parish, Samuel Park, Deborah S. Pederson, Beverly K. Philip, James H. Philip, Silvia Pivi, Stephen D. Pratt, Douglas E. Raines, Stephen L. Ratcliff, James P. Rathmell, J. Taylor Reed, Elizabeth M. Rickerson, Selwyn O. Rogers Jr., Thomas M. Romanelli, William H. Rosenblatt, Carl E. Rosow, Edgar L. Ross, J. Victor Ryckman, Mônica M. Sá Rêgo, Nicholas Sadovnikoff, Warren S. Sandberg, Annette Y. Schure, B. Scott Segal, Navil F. Sethna, Swapneel K. Shah, Shaheen F. Shaikh, Fred E. Shapiro, Torin D. Shear, Prem S. Shekar, Stanton K. Shernan, Naomi Shimizu, Douglas C. Shook, Kamal K. Sikka, Pankaj K. Sikka, David A. Silver, Jeffrey H. Silverstein, Emily A. Singer, Ken Solt, Spiro G. Spanakis, Wolfgang Steudel, Matthias Stopfkuchen-Evans, Michael P. Storey, Gary R. Strichartz, Balachundhar Subramaniam, Wariya Sukhupragarn, John Summers, Shine Sun, Eswar Sundar, Sugantha Sundar, Neelakantan Sunder, Faraz Syed, Usha B. Tedrow, Nelson L. Thaemert, George P. Topulos, Lawrence C. Tsen, Richard D. Urman, Charles A. Vacanti, Francis X. Vacanti, Joshua C. Vacanti, Assia Valovska, Ivan T. Valovski, Mary Ann Vann, Susan Vassallo, Anasuya Vasudevan, Kamen V. Vlassakov, Gian Paolo Volpato, Essi M. Vulli, J. Matthias Walz, Jingping Wang, James F. Watkins, Maxwell Weinmann, Sharon L. Wetherall, Mallory Williams, Sarah H. Wiser, Zhiling Xiong, Warren M. Zapol, Jie Zhou
- Edited by Charles Vacanti, Scott Segal, Pankaj Sikka, Richard Urman
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- Book:
- Essential Clinical Anesthesia
- Published online:
- 05 January 2012
- Print publication:
- 11 July 2011, pp xv-xxviii
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Measurements of the Refractive Indices of MOCVD and HVPE Grown AlGaN Films Using Prism-Coupling Techniques Correlated with Spectroscopic Reflection/Transmission Analysisa
- Norman A. Sanford, Lawrence H. Robins, Albert V. Davydov, Alexander J. Shapiro, Denis V. Tsvetkov, Vladimir A. Dmitriev, Silver Spring, Stacia Keller, Umesh K. Mishra, Steven P. DenBaars
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- Journal:
- MRS Online Proceedings Library Archive / Volume 743 / 2002
- Published online by Cambridge University Press:
- 11 February 2011, L11.21
- Print publication:
- 2002
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Waveguide prism-coupling methods were used to measure the ordinary and extraordinary refractive indices of AlxGa1-xN films grown on sapphire substrates by HVPE and MOCVD. Several discrete wavelengths ranging from 442 nm to 1064 nm were used and the results were fit to one-term Sellmeier equations. The maximum standard uncertainty in the refractive index measurements was ± 0.005 and the maximum standard uncertainty in the self-consistent calculation for film thickness was ± 15 nm. Analysis of normal-incidence spectroscopic transmittance and reflectance measurements, correlated with the prism-coupling results, was used to determine the ordinary refractive index as a continuous function of wavelength from the band gap wavelength of each sample (between 252 nm and 364 nm) to 2500 nm. The Al compositions of the samples were determined using energy-dispersive X-ray spectroscopy analysis (EDS). HVPE grown samples had compositions x = 0.279, 0.363, 0.593, and 0.657. MOCVD samples had x = 0.00, 0.419, 0.507, 0.618, 0.660, and 0.666. The maximum standard uncertainty in the absolute EDS-determined value for x was ± 0.02.
Pre-mRNA processing factors are required for nuclear export
- ALEXANDER S. BRODSKY, PAMELA A. SILVER
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RNA export from the nucleus is thought to be linked to proper processing and packaging into ribonucleoprotein protein complexes. A system to observe mRNA nuclear export in living yeast cells was developed by fusing the U1A RNA-binding protein to the green fluorescent protein to follow specific mRNAs with U1A hairpins engineered into them. RNAs encoding Rpl25, Pgk1, and Ssa4 were examined for the effects of 3′ UTRs, introns, RNA processing factors, nucleoporins, and transport factors on their export. All accumulated in the nucleus in mutants affecting components of the nuclear export machinery and certain nucleoporins. However, under conditions of stress, PGK1 and RPL25 transcripts accumulate in the nucleus whereas SSA4 RNA is exported. Moreover, when export is blocked, only RNAs containing the ASH1 3′ UTR accumulated in the nucleolus. Mutations in the splicing machinery selectively blocked export of only intron-containing RNAs. Mutations in RNA14, RNA15, and PAP1, which encode factors important for 3′ processing, also blocked export of all RNAs, including SSA4, thereby linking export to the process of polyadenlyation. Taken together, these data graphically display the connections between mRNA processing and nuclear export.