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Paul Brakeman

MD, PhD

  • Professor, Pediatrics
  • Pediatric Nephrologist

Biography

Dr. Brakeman is an Associate Professor based at the the UCSF Benioff Children's Hospital with a primary appointment in Pediatrics and a secondary apointment in the Division of Nephrology in the Department of Medicine.

The primary focus of his research is the engineering of human renal epithelial cells for use in a bioartificial kidney. Work is currently underway at UCSF on a multi-center project to develop a bioartificial implantable renal assist device based on hemofiltration. One of the important components of an implantable bioartificial device is an active renal proximal tubule cell bioreactor that can provide some of the metabolic activity of renal tubules. Another critical function of the cellular bioreactor will be the reabsorption of salt and water in order to reduce the volume of the filtrate generated as much as possible before elimination via the bladder. Dr. Brakeman's lab is focused on engineering human proximal tubules cells to enhance sodium and water reabsorption for use in the bioartificial kidney. In addition, he is actively evaluating the use of the proximal tubule cell bioreactor for use in toxicology and pharmaceutical evaluation of novel compounds.

Education & Training

  • John Hopkins University School of Medicine
  • University of California, San Francisco School of Medicine

Clinical Trials

  • Nephrotic Syndrome Study Network

    —

    Conditions: Minimal Change Disease,Membranous Nephropathy,Focal Segmental Glomerulosclerosis,Kidney Disease,Glomerulonephritis

Research Activities & Funding

  • The Role of Nectin in Congenital Obstructive Nephropathy

    —

    Sponsor: NIH K08DK068358

    Role: Principal Investigator

Publications

  • Kim EJ, Chen C, Gologorsky R, Santandreu A, Torres A, Wright N, Goodin MS, Moyer J, Chui BW, Blaha C, Brakeman P, Vartanian S, Tang Q, David Humes H, Fissell WH, Roy S. Feasibility of an implantable bioreactor for renal cell therapy using silicon nanopore membranes. Nat Commun. 2023 08 29; 14(1):4890. PubMed
  • Onder AM, Ansari MAY, Deng F, Grinsell MM, Patterson L, Jetton J, Fathallah-Shaykh S, Ranch D, Aviles D, Copelovitch L, Ellis E, Chadha V, Elmaghrabi A, Lin JJ, Butani L, Haddad M, Marsenic O, Brakeman P, Quigley R, Shin HS, Garro R, Raina R, Langman CB. Persistent Increase in Serum Ferritin Levels despite Converting to Permanent Vascular Access in Pediatric Hemodialysis Patients: Pediatric Nephrology Research Consortium Study. J Clin Med. 2023 Jun 25; 12(13). PubMed
  • Varnell C, Harshman LA, Liu C, Smith L, Al-Akash S, Barletta GM, Brakeman P, Chaudhuri A, Fadakar P, Galea L, Garro R, Gluck C, Kershaw DB, Matossian D, Patel HP, Peterson C, Pruette C, Ranabothu S, Rodig N, Singer P, Sebestyen VanSickle J, Weng PL, Danziger-Isakov L, Seifert ME, Hooper DK. COVID-19 in pediatric kidney transplantation: a follow-up report of the Improving Renal Outcomes Collaborative. Pediatr Nephrol. 2023 02; 38(2):537-547. PubMed
  • Lombel RM, Brakeman PR, Sack BS, Butani L. Urologic Considerations in Pediatric Chronic Kidney Disease. Adv Chronic Kidney Dis. 2022 05; 29(3):308-317. PubMed
  • Onder AM, Flynn JT, Ansari MAY, Deng F, DeFreitas M, Katsoufis C, Grinsell MM, Patterson L, Jetton J, Fathallah-Shaykh S, Ranch D, Aviles D, Copelovitch L, Ellis E, Chadha V, Elmaghrabi A, Lin JJ, Butani L, Haddad M, Marsenic O, Brakeman P, Quigley R, Shin HS, Garro R, Raina R, Langman CB, Wood E, Pediatric Nephrology Research Consortium. Conversion to permanent vascular access is associated with improved markers of hemodialysis efficacy in children: Pediatric nephrology research consortium study. Clin Nephrol. 2021 Nov; 96(5):270-280. PubMed
  • Ganesan LL, O'Brien FJ, Sirich TL, Plummer NS, Sheth R, Fajardo C, Brakeman P, Sutherland SM, Meyer TW. Association of Plasma Uremic Solute Levels with Residual Kidney Function in Children on Peritoneal Dialysis. Clin J Am Soc Nephrol. 2021 10; 16(10):1531-1538. PubMed
  • Varnell C, Harshman LA, Smith L, Liu C, Chen S, Al-Akash S, Barletta GM, Belsha C, Brakeman P, Chaudhuri A, Fadakar P, Garro R, Gluck C, Goebel J, Kershaw D, Matossian D, Nailescu C, Patel HP, Pruette C, Ranabothu S, Rodig N, Smith J, Sebestyen VanSickle J, Weng P, Danziger-Isakov L, Hooper DK, Seifert M. COVID-19 in pediatric kidney transplantation: The Improving Renal Outcomes Collaborative. Am J Transplant. 2021 08; 21(8):2740-2748. PubMed
  • O'Brien FJ, Sirich TL, Taussig A, Fung E, Ganesan LL, Plummer NS, Brakeman P, Sutherland SM, Meyer TW. Plasma pseudouridine levels reflect body size in children on hemodialysis. Pediatr Nephrol. 2020 02; 35(2):305-312. PubMed
  • Onder AM, Flynn JT, Billings AA, Deng F, DeFreitas M, Katsoufis C, Grinsell MM, Patterson L, Jetton J, Fathallah-Shaykh S, Ranch D, Aviles D, Copelovitch L, Ellis E, Chadha V, Elmaghrabi A, Lin JJ, Butani L, Haddad M, Marsenic O, Brakeman P, Quigley R, Shin HS, Garro R, Liu H, Rahimikollu J, Raina R, Langman CB, Wood E, Midwest Pediatric Nephrology Consortium. Predictors of time to first cannulation for arteriovenous fistula in pediatric hemodialysis patients: Midwest Pediatric Nephrology Consortium study. Pediatr Nephrol. 2020 02; 35(2):287-295. PubMed
  • Yu W, Marshall WF, Metzger RJ, Brakeman PR, Morsut L, Lim W, Mostov KE. Simple Rules Determine Distinct Patterns of Branching Morphogenesis. Cell Syst. 2019 09 25; 9(3):221-227. PubMed
  • Onder AM, Flynn JT, Billings AA, Deng F, DeFreitas M, Katsoufis C, Grinsell MM, Patterson LT, Jetton J, Fathallah-Shaykh S, Ranch D, Aviles D, Copelovitch L, Ellis E, Chadha V, Elmaghrabi A, Lin JJ, Butani L, Haddad M, Couloures OM, Brakeman P, Quigley R, Shin HS, Garro R, Liu H, Rahimikollu J, Raina R, Langman CB, Wood EG, Midwest Pediatric Nephrology Consortium. Correction to: Predictors of patency for arteriovenous fistulae and grafts in pediatric hemodialysis patients. Pediatr Nephrol. 2019 Aug; 34(8):1483-1484. PubMed
  • Ferrell N, Sandoval RM, Molitoris BA, Brakeman P, Roy S, Fissell WH. Application of physiological shear stress to renal tubular epithelial cells. Methods Cell Biol. 2019; 153:43-67. PubMed
  • Zinter MS, Spicer AC, Liu KD, Orwoll BE, Alkhouli MF, Brakeman PR, Calfee CS, Matthay MA, Sapru A. Positive Cumulative Fluid Balance Is Associated With Mortality in Pediatric Acute Respiratory Distress Syndrome in the Setting of Acute Kidney Injury. Pediatr Crit Care Med. 2019 04; 20(4):323-331. PubMed
  • Jayagopal A, Brakeman PR, Soler P, Ferrell N, Fissell W, Kroetz DL, Roy S. Apical Shear Stress Enhanced Organic Cation Transport in Human OCT2/MATE1-Transfected Madin-Darby Canine Kidney Cells Involves Ciliary Sensing. J Pharmacol Exp Ther. 2019 06; 369(3):523-530. PubMed
  • Gomez Mendez LM, Cascino MD, Katsumoto TR, Brakeman P, Brunetta P, Jayne D, Dall'Era M, Rovin B, Garg J. Outcome of participants with nephrotic syndrome in combined clinical trials of lupus nephritis. Lupus Sci Med. 2019; 6(1):e000308. PubMed
  • Onder AM, Flynn JT, Billings AA, Deng F, DeFreitas M, Katsoufis C, Grinsell MM, Patterson LT, Jetton J, Fathallah-Shaykh S, Ranch D, Aviles D, Copelovitch L, Ellis E, Chanda V, Elmaghrabi A, Lin JJ, Butani L, Haddad M, Couloures OM, Brakeman P, Quigley R, Stella Shin H, Garro R, Liu H, Rahimikollu J, Raina R, Langman CB, Wood EG, Midwest Pediatric Nephrology Consortium. Predictors of patency for arteriovenous fistulae and grafts in pediatric hemodialysis patients. Pediatr Nephrol. 2019 02; 34(2):329-339. PubMed
  • Gomez Mendez LM, Cascino MD, Garg J, Katsumoto TR, Brakeman P, Dall'Era M, Looney RJ, Rovin B, Dragone L, Brunetta P. Peripheral Blood B Cell Depletion after Rituximab and Complete Response in Lupus Nephritis. Clin J Am Soc Nephrol. 2018 10 08; 13(10):1502-1509. PubMed
  • Wang MK, Chuang KW, Li Y, Gaither T, Brakeman P, Gonzalez L, Brennan J, Baskin LS. Renal function outcomes in pediatric patients with symptomatic reflux into the transplanted kidney treated with redo ureteroneocystostomy. J Pediatr Urol. 2018 06; 14(3):275.e1-275.e5. PubMed
  • Gao L, Yang Z, Hiremath C, Zimmerman SE, Long B, Brakeman PR, Mostov KE, Bryant DM, Luby-Phelps K, Marciano DK. Afadin orients cell division to position the tubule lumen in developing renal tubules. Development. 2017 10 01; 144(19):3511-3520. PubMed
  • Oates A, Benedict KA, Sun K, Brakeman PR, Lim J, Kim C. Laser acupuncture reduces pain in pediatric kidney biopsies: a randomized controlled trial. Pain. 2017 01; 158(1):103-109. PubMed
  • Brakeman P, Miao S, Cheng J, Lee CZ, Roy S, Fissell WH, Ferrell N. A modular microfluidic bioreactor with improved throughput for evaluation of polarized renal epithelial cells. Biomicrofluidics. 2016 Nov; 10(6):064106. PubMed
  • Kim S, Heller J, Iqbal Z, Kant R, Kim EJ, Durack J, Saeed M, Do L, Hetts S, Wilson M, Brakeman P, Fissell WH, Roy S. Preliminary Diffusive Clearance of Silicon Nanopore Membranes in a Parallel Plate Configuration for Renal Replacement Therapy. ASAIO J. 2016 Mar-Apr; 62(2):169-75. PubMed
  • Tran CS, Eran Y, Ruch TR, Bryant DM, Datta A, Brakeman P, Kierbel A, Wittmann T, Metzger RJ, Mostov KE, Engel JN. Host cell polarity proteins participate in innate immunity to Pseudomonas aeruginosa infection. Cell Host Microbe. 2014 May 14; 15(5):636-43. PubMed
  • Wong T, Matthay KK, Boscardin WJ, Hawkins RA, Brakeman PR, DuBois SG. Acute changes in blood pressure in patients with neuroblastoma treated with ¹³¹I-metaiodobenzylguanidine (MIBG). Pediatr Blood Cancer. 2013 Sep; 60(9):1424-30. PubMed
  • Yang Z, Zimmerman S, Brakeman PR, Beaudoin GM, Reichardt LF, Marciano DK. De novo lumen formation and elongation in the developing nephron: a central role for afadin in apical polarity. Development. 2013 Apr; 140(8):1774-84. PubMed
  • Gálvez-Santisteban M, Rodriguez-Fraticelli AE, Bryant DM, Vergarajauregui S, Yasuda T, Bañón-Rodríguez I, Bernascone I, Datta A, Spivak N, Young K, Slim CL, Brakeman PR, Fukuda M, Mostov KE, Martín-Belmonte F. Synaptotagmin-like proteins control the formation of a single apical membrane domain in epithelial cells. Nat Cell Biol. 2012 Aug; 14(8):838-49. PubMed
  • Hu JH, Yang L, Kammermeier PJ, Moore CG, Brakeman PR, Tu J, Yu S, Petralia RS, Li Z, Zhang PW, Park JM, Dong X, Xiao B, Worley PF. Preso1 dynamically regulates group I metabotropic glutamate receptors. Nat Neurosci. 2012 Jun; 15(6):836-44. PubMed
  • Marciano DK, Brakeman PR, Lee CZ, Spivak N, Eastburn DJ, Bryant DM, Beaudoin GM, Hofmann I, Mostov KE, Reichardt LF. p120 catenin is required for normal renal tubulogenesis and glomerulogenesis. Development. 2011 May; 138(10):2099-109. PubMed
  • Brakeman PR, Liu KD, Shimizu K, Takai Y, Mostov KE. Nectin proteins are expressed at early stages of nephrogenesis and play a role in renal epithelial cell morphogenesis. Am J Physiol Renal Physiol. 2009 Mar; 296(3):F564-74. PubMed
  • Yu W, Shewan AM, Brakeman P, Eastburn DJ, Datta A, Bryant DM, Fan QW, Weiss WA, Zegers MM, Mostov KE. Involvement of RhoA, ROCK I and myosin II in inverted orientation of epithelial polarity. EMBO Rep. 2008 Sep; 9(9):923-9. PubMed
  • Liu KD, Brakeman PR. Renal repair and recovery. Crit Care Med. 2008 Apr; 36(4 Suppl):S187-92. PubMed
  • Hirose R, Xu F, Dang K, Liu T, Behrends M, Brakeman PR, Wiener-Kronish J, Niemann CU. Transient hyperglycemia affects the extent of ischemia-reperfusion-induced renal injury in rats. Anesthesiology. 2008 Mar; 108(3):402-14. PubMed
  • Nguyen S, McCulloch C, Brakeman P, Portale A, Hsu CY. Being overweight modifies the association between cardiovascular risk factors and microalbuminuria in adolescents. Pediatrics. 2008 Jan; 121(1):37-45. PubMed
  • Brakeman P. Vesicoureteral reflux, reflux nephropathy, and end-stage renal disease. Adv Urol. 2008; 508949. PubMed
  • Liu KD, Datta A, Yu W, Brakeman PR, Jou TS, Matthay MA, Mostov KE. Rac1 is required for reorientation of polarity and lumen formation through a PI 3-kinase-dependent pathway. Am J Physiol Renal Physiol. 2007 Nov; 293(5):F1633-40. PubMed
  • Kim M, Datta A, Brakeman P, Yu W, Mostov KE. Polarity proteins PAR6 and aPKC regulate cell death through GSK-3beta in 3D epithelial morphogenesis. J Cell Sci. 2007 Jul 15; 120(Pt 14):2309-17. PubMed
  • Mostov K, Brakeman P, Datta A, Gassama A, Katz L, Kim M, Leroy P, Levin M, Liu K, Martin F, O'Brien LE, Verges M, Su T, Tang K, Tanimizu N, Yamaji T, Yu W. Formation of multicellular epithelial structures. Novartis Found Symp. 2005; 269:193-200; discussion 200-5, 223-30. PubMed
  • Foa L, Rajan I, Haas K, Wu GY, Brakeman P, Worley P, Cline H. The scaffold protein, Homer1b/c, regulates axon pathfinding in the central nervous system in vivo. Nat Neurosci. 2001 May; 4(5):499-506. PubMed
  • Tu JC, Xiao B, Naisbitt S, Yuan JP, Petralia RS, Brakeman P, Doan A, Aakalu VK, Lanahan AA, Sheng M, Worley PF. Coupling of mGluR/Homer and PSD-95 complexes by the Shank family of postsynaptic density proteins. Neuron. 1999 Jul; 23(3):583-92. PubMed
  • Brakeman PR, Lanahan AA, O'Brien R, Roche K, Barnes CA, Huganir RL, Worley PF. Homer: a protein that selectively binds metabotropic glutamate receptors. Nature. 1997 Mar 20; 386(6622):284-8. PubMed
  • Meltzer CC, Zubieta JK, Links JM, Brakeman P, Stumpf MJ, Frost JJ. MR-based correction of brain PET measurements for heterogeneous gray matter radioactivity distribution. J Cereb Blood Flow Metab. 1996 Jul; 16(4):650-8. PubMed
  • Keltner JR, Roos MS, Brakeman PR, Budinger TF. Magnetohydrodynamics of blood flow. Magn Reson Med. 1990 Oct; 16(1):139-49. PubMed
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