Publications & Press

Peer-reviewed journal articles

Many of the articles below are available for free (open access). Please contact the lab for copies of materials that are not freely available.

Cruz NM, Song X, Czerniecki SM, Gulieva RE, Churchill AJ, Kim YK, Winston K, Diaz M, Fu H, Finn LS, Pei Y, Himmelfarb J, Freedman BS (2017). Organoid cystogenesis reveals a critical role of microenvironment in human polycystic kidney disease. Nature Materials, doi: 10.1038/NMAT4994. In permissive microenvironments, kidney organoids with PKD mutations swell up to sizes easily seen by the naked eye.

Kim YK, Refaeli I, Brooks CR, Jing P, Gulieva RE, Hughes MR, Cruz NM, Liu Y, Churchill AJ, Wang Y, Fu H, Pippin JW, Lin LY, Shankland SJ, Vogl AW, McNagny KM, Freedman BS (2017). Gene-edited human kidney organoids reveal mechanisms of disease in podocyte development. Stem Cells, DOI: 10.1002/stem.2707. CRISPR’d organoids reveal how the podocyte gets its legs.

Shankland SJ, Freedman BS, Pippin JW (2017). Can podocytes be regenerated in adults? Curr Opin Nephrol Hypertens. 26(3):154-164. In this review paper, we discuss the ability of podocytes, the kidney’s filtering cells, to regenerate naturally, and the ramifications of these findings for clinical nephrology.

Tögel F, Valerius MT, Freedman BS, Iatrino R, Grinstein M, Bonventre JV (2017). Repair after nephron ablation reveals limitations of neonatal neonephrogenesis. JCI Insight 2(2):e88848. In this study, we show that mammalian kidneys cannot regenerate new nephrons, even when injury occurs only shortly after birth.

Pang P, Abbott M, Chang SL, Abdi M, Chauhan N, Mistri M, Ghofrani J, Fucci QA, Walker C, Leonardi C, Grady S, Halim A, Hoffman R, Lu T, Cao H, Tullius SG, Malek S, Kumar S, Steele G, Kibel A, Freedman BS, Waikar SS, Siedlecki AM (2017). Human vascular progenitor cells derived from renal arteries are endothelial-like and assist in the repair of injured renal capillary networks. Kidney Int. 91(1): 129-143. A study by our collaborator Dr. Siedlecki identifying a new population of adult stem cells for repairing blood vessels.

Freedman BS, Zeidel ML, Steinman TI (2016). Technology and the future of kidney careNephrol. News Issues 30(11): 24-28 (review). A look at kidney medicine 30 years in the future.

Freedman BS (2015). Modeling kidney disease with iPS Cells. Biomarker Insights 2015:Suppl. 1 153-169 doi: 10.4137/BMI.S20054.  A summary of recent progress in the field, including differentiation of kidney organoids and the use of genome editing techniques such as CRISPR.

Freedman BS, Brooks CR, Lam AQ, Fu H, Morizane R, Agrawal V, et al. (2015). Modelling kidney disease with CRISPR-mutant kidney organoids derived from human pluripotent epiblast spheroids. Nat. Commun. 6:8715 doi: 10.1038/ncomms9715.  This study describes a new, simple protocol for generating human mini-kidney organoids from stem cells, and uses gene-edited kidney organoids to re-create human kidney disease in a petri dish.

Morizane R, Lam AQ, Freedman BS, Kishi S, Valerius TM, Bonventre JV (2015). Nephron organoids derived from human pluripotent stem cells model kidney development and injury. Nat. Biotech doi:10.1038/nbt.3392. A new protocol for differentiating ES and iPS cells into kidney organoids that resemble kidney tissue.

Freedman BS, Steinman TI (2015). Stem cells represent a new area of kidney careNephrol. News Issues 29(8): 18-20 (review). An analysis of the potential for iPS cells in kidney clinical research and medicine.

Lam AQ, Freedman BS, Bonventre JV (2014). Directed differentiation of pluripotent stem cells to kidney cells. Semin Nephrol 34(4): 445-461 (review). A summary of recent progress and remaining challenges in using human pluripotent stem cells for kidney regeneration and disease modeling.

Lam AQ*, Freedman BS*, Morizane R*, Valerius MT, Bonventre JV (2014). Rapid and efficient differentiation of human pluripotent stem cells into intermediate mesoderm which forms tubules expressing kidney proximal tubular markers. J Am Soc Nephrol 25(6): 1211-1225This paper introduces a new protocol for rapidly converting ES and iPS cells into mesoderm and subsequently kidney progenitor cells. 

Freedman BS,* Lam AQ,* Sundsbak JL, Iatrino R, Su X, Koon SJ, Wu M, Daheron L, Harris PC, Zhou J, Bonventre JV (2013). Reduced ciliary polycystin-2 in iPS cells from PKD patients with PKD1 mutations. J Am Soc Nephrol 24: 1571-1586. In this paper, we generated iPS cells from patients with autosomal dominant and recessive PKD, and used them to identify a possible therapeutic approach.

Xiao B,* Freedman BS,* Miller KE, Heald R, and Marko JF  (2012). Histone H1 compacts DNA under force and during chromatin assembly. Mol Biol Cell 23(24):4864-71. This paper measures that histone H1 compacts individual molecules of DNA under force, protecting them from shear stress during complex nuclear remodeling processes.

Fu H, Freedman BS, Lim CT, Heald R, and J Yan (2011). Atomic force microscope imaging of chromatin assembled in Xenopus laevis egg extract. Chromosoma 120(3):245-54. This paper introduces a novel method to examine chromatin structure under physiological conditions, in contrast to the highly purified and simplified conditions typically used in the lab.

Freedman BS, Miller KE, and R Heald (2010). Xenopus egg extracts increase dynamics of histone H1 on sperm chromatin. PLoS ONE 5(9): e13111. This paper shows that histone H1 rapidly binds and releases chromatin in physiological cytoplasm, but gets stuck on chromatin in non-physiological buffer. This paper is freely available.

Freedman BS and R Heald  (2010). Functional comparison of H1 histones in Xenopus reveals isoform-specific regulation by Cdk1 and RanGTP. Current Biology 20(11):1048-1052. This paper shows that negative charges and cyclin-dependent phosphorylation of histone H1 at mitosis actually enhance its binding to chromosomes, contrary to the existing dogma in the field.

Maresca TJ, Freedman BS, and R Heald (2005). Histone H1 is essential for mitotic chromosome architecture and segregation in Xenopus laevis egg extracts. J. Cell Biol. 169(6):859-869. This paper shows that mitotic chromosomes assembled without histone H1 are long and “stringy,” causing problems during cell division. This paper is freely available.

* = co-first authors

 

Press

Why the UW is sending a kidney into outer space. Columns Magazine, September 28, 2017. How kidney-on-a-chip and kidney organoids are bringing Star Trek closer to reality.

Cell Shorts | Illuminating the kidney. Allen Institute ‘Cell Shorts’ video series, July 2017.  A beautiful video on how our lab is using new iPS cell lines from the Allen Institute to illuminate kidney disease and regeneration.

Gene Editing May Offer Clues, Future Treatments for Kidney Disease. ASN Kidney News 9:5, May 2017.  Dr. Freedman is quoted regarding the potential of gene editing techniques, such as CRISPR, for diagnosing, studying, and ultimately treating kidney disease.

Paul Allen’s Latest Science Project: a Psychedelic Way to Peer Inside Cells. The Seattle Times, April 5, 2017; Machine Learning Predicts the Look of Stem Cells, Nature News. April 5, 2017. In these articles, Dr. Freedman is quoted on how the Allen Institute’s Cell Collection and Cell Explorer tools can be used to study disease processes.

NephMadness 2017: the Case for CRISPR-Cas9. AJKD Blog. April 3, 2017. In this blog post, Dr. Freedman provides a fun synopsis of why CRISPR-Cas9 gene editing is of paramount importance for kidney medicine.

With CRISPR, Modeling Disease in Mini Organs. The Scientist. May 6, 2016. An article capturing the zeitgeist of using genetically edited organoids for understanding and treating diseases like cystic fibrosis, cancer, and polycystic kidney.

New gene editing technology: What it could mean for the future of PKD. PKD Foundation Webinar Wednesdays Series, March 18, 2016. In layman’s terms, this webinar explains the fundamentals of gene editing with CRISPR and how it might impact PKD therapy.

Support NKF Research. National Kidney Foundation, January 19, 2016. A great video explaining what we do and the vital role you can play by supporting the National Kidney Foundation.

Modelling Disease in Kidney Organoids. Nature Reviews Nephrology 12:4 (2016). doi: 10.1038/nrneph.2015.181. Highlighting the generation of kidney organoids with disease phenotypes using CRISPR.

A New Gene Editing Technique Turns Human Pluripotent Stem Cells into a Model System for Polycystic Kidney Disease. American Society for Cell Biology, December 14, 2015. How using gene editing enables us to re-create PKD in human organoids.

Scientists Grow ‘Mini-Kidneys’ in Petri Dishes. Futurity News, October 27, 2015. Focusing on the discovery of human kidney organoids from pluripotent stem cells as a new tool for disease modeling and regeneration.

The PKD Research Experience. PKD Connection, October 26, 2015. Dr. Freedman describes what it’s like to do science in a column for the PKD Foundation – over 400 shares on Facebook!

Engineering Kidneys for Treatments and Transplants. National Kidney Foundation, January 15, 2015. Over 400 shares and 1,000 likes on Facebook! It’s great getting comments and feedback from patients.

Kidney Cells Generated from Stem Cells. MedPage Today, January 12, 2014. Our first success towards creating kidney cells from human pluripotent stem cells.

Research Findings Point to New Therapeutic Approach for Common Cause of Kidney Failure. ASN, Sept. 5, 2013. Our first success towards modeling PKD phenotypes with human pluripotent stem cells.

Induced Pluripotent Stem Cells from Polycystic Kidney Disease Patients: a Novel Tool to Model the Pathogenesis of Cystic Kidney Disease. JASN, Oct. 2013. A commentary on our article generating iPS cells from patients with PKD and showing the first kidney-relevant phenotype in these cells.