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ResearchIn-Press PreviewEndocrinologyNephrology Open Access | 10.1172/jci.insight.204385

Not all reference samples are equal in single-cell transcriptomics of human kidney tissue

Rajasree Menon,1 Paul L. Kimmel,2 Edgar A. Otto,3 Lalita Subramanian,3 Christopher L. O'Connor,3 Bradley Godfrey,3 Cathy Smith,3 Fadhl Alakwaa,3 Celine C. Berthier,3 Minnie M. Sarwal,4 E. Steve Woodle,5 Laura Pyle,6 Ye Ji Choi,6 Patricia Ladd,7 John R. Sedor,8 Sylvia E. Rosas,9 Sushrut S. Waikar,10 Abhijit S. Naik,3 Ricardo Melo Ferreira,11 Michael T. Eadon,11 Markus Bitzer,3 Petter Bjornstad,6 Jeffrey B. Hodgin,12 and Matthias Kretzler13

1Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, United States of America

2Department of Medicine, Geoge Washington University, Washington DC, United States of America

3Division of Nephrology, University of Michigan Medical School, Ann Arbor, United States of America

4Division of Transplant Surgery, University of California, San Francisco, San Francisco, United States of America

5Department of Surgery, University of Cincinnati College of Medicine, Cincinnati, United States of America

6Division of Metabolism, Endocrinology and Nutrition, University of Washington, Seattle, United States of America

7Division of Renal Diseases and Hypertension, University of Colorado School of Medicine, Aurora, United States of America

8Medical Specialties and Lerner Research Institutes, Case Western Reserve University, Cleveland, United States of America

9Kidney and Hypertension unit, Harvard Medical School, Boston, United States of America

10Section of Nephrology, Boston Medical Center, Boston, United States of America

11Department of Medicine, Indiana University School of Medicine, Indianapolis, United States of America

12Department of Pathology, University of Michigan, Ann Arbor, United States of America

13Department of Computational Medicine and Bioinformatics, University of Michigan Medical School, Ann Arbor, United States of America

Find articles by Menon, R. in: PubMed | Google Scholar |

1Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, United States of America

2Department of Medicine, Geoge Washington University, Washington DC, United States of America

3Division of Nephrology, University of Michigan Medical School, Ann Arbor, United States of America

4Division of Transplant Surgery, University of California, San Francisco, San Francisco, United States of America

5Department of Surgery, University of Cincinnati College of Medicine, Cincinnati, United States of America

6Division of Metabolism, Endocrinology and Nutrition, University of Washington, Seattle, United States of America

7Division of Renal Diseases and Hypertension, University of Colorado School of Medicine, Aurora, United States of America

8Medical Specialties and Lerner Research Institutes, Case Western Reserve University, Cleveland, United States of America

9Kidney and Hypertension unit, Harvard Medical School, Boston, United States of America

10Section of Nephrology, Boston Medical Center, Boston, United States of America

11Department of Medicine, Indiana University School of Medicine, Indianapolis, United States of America

12Department of Pathology, University of Michigan, Ann Arbor, United States of America

13Department of Computational Medicine and Bioinformatics, University of Michigan Medical School, Ann Arbor, United States of America

Find articles by Kimmel, P. in: PubMed | Google Scholar

1Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, United States of America

2Department of Medicine, Geoge Washington University, Washington DC, United States of America

3Division of Nephrology, University of Michigan Medical School, Ann Arbor, United States of America

4Division of Transplant Surgery, University of California, San Francisco, San Francisco, United States of America

5Department of Surgery, University of Cincinnati College of Medicine, Cincinnati, United States of America

6Division of Metabolism, Endocrinology and Nutrition, University of Washington, Seattle, United States of America

7Division of Renal Diseases and Hypertension, University of Colorado School of Medicine, Aurora, United States of America

8Medical Specialties and Lerner Research Institutes, Case Western Reserve University, Cleveland, United States of America

9Kidney and Hypertension unit, Harvard Medical School, Boston, United States of America

10Section of Nephrology, Boston Medical Center, Boston, United States of America

11Department of Medicine, Indiana University School of Medicine, Indianapolis, United States of America

12Department of Pathology, University of Michigan, Ann Arbor, United States of America

13Department of Computational Medicine and Bioinformatics, University of Michigan Medical School, Ann Arbor, United States of America

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1Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, United States of America

2Department of Medicine, Geoge Washington University, Washington DC, United States of America

3Division of Nephrology, University of Michigan Medical School, Ann Arbor, United States of America

4Division of Transplant Surgery, University of California, San Francisco, San Francisco, United States of America

5Department of Surgery, University of Cincinnati College of Medicine, Cincinnati, United States of America

6Division of Metabolism, Endocrinology and Nutrition, University of Washington, Seattle, United States of America

7Division of Renal Diseases and Hypertension, University of Colorado School of Medicine, Aurora, United States of America

8Medical Specialties and Lerner Research Institutes, Case Western Reserve University, Cleveland, United States of America

9Kidney and Hypertension unit, Harvard Medical School, Boston, United States of America

10Section of Nephrology, Boston Medical Center, Boston, United States of America

11Department of Medicine, Indiana University School of Medicine, Indianapolis, United States of America

12Department of Pathology, University of Michigan, Ann Arbor, United States of America

13Department of Computational Medicine and Bioinformatics, University of Michigan Medical School, Ann Arbor, United States of America

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1Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, United States of America

2Department of Medicine, Geoge Washington University, Washington DC, United States of America

3Division of Nephrology, University of Michigan Medical School, Ann Arbor, United States of America

4Division of Transplant Surgery, University of California, San Francisco, San Francisco, United States of America

5Department of Surgery, University of Cincinnati College of Medicine, Cincinnati, United States of America

6Division of Metabolism, Endocrinology and Nutrition, University of Washington, Seattle, United States of America

7Division of Renal Diseases and Hypertension, University of Colorado School of Medicine, Aurora, United States of America

8Medical Specialties and Lerner Research Institutes, Case Western Reserve University, Cleveland, United States of America

9Kidney and Hypertension unit, Harvard Medical School, Boston, United States of America

10Section of Nephrology, Boston Medical Center, Boston, United States of America

11Department of Medicine, Indiana University School of Medicine, Indianapolis, United States of America

12Department of Pathology, University of Michigan, Ann Arbor, United States of America

13Department of Computational Medicine and Bioinformatics, University of Michigan Medical School, Ann Arbor, United States of America

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1Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, United States of America

2Department of Medicine, Geoge Washington University, Washington DC, United States of America

3Division of Nephrology, University of Michigan Medical School, Ann Arbor, United States of America

4Division of Transplant Surgery, University of California, San Francisco, San Francisco, United States of America

5Department of Surgery, University of Cincinnati College of Medicine, Cincinnati, United States of America

6Division of Metabolism, Endocrinology and Nutrition, University of Washington, Seattle, United States of America

7Division of Renal Diseases and Hypertension, University of Colorado School of Medicine, Aurora, United States of America

8Medical Specialties and Lerner Research Institutes, Case Western Reserve University, Cleveland, United States of America

9Kidney and Hypertension unit, Harvard Medical School, Boston, United States of America

10Section of Nephrology, Boston Medical Center, Boston, United States of America

11Department of Medicine, Indiana University School of Medicine, Indianapolis, United States of America

12Department of Pathology, University of Michigan, Ann Arbor, United States of America

13Department of Computational Medicine and Bioinformatics, University of Michigan Medical School, Ann Arbor, United States of America

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1Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, United States of America

2Department of Medicine, Geoge Washington University, Washington DC, United States of America

3Division of Nephrology, University of Michigan Medical School, Ann Arbor, United States of America

4Division of Transplant Surgery, University of California, San Francisco, San Francisco, United States of America

5Department of Surgery, University of Cincinnati College of Medicine, Cincinnati, United States of America

6Division of Metabolism, Endocrinology and Nutrition, University of Washington, Seattle, United States of America

7Division of Renal Diseases and Hypertension, University of Colorado School of Medicine, Aurora, United States of America

8Medical Specialties and Lerner Research Institutes, Case Western Reserve University, Cleveland, United States of America

9Kidney and Hypertension unit, Harvard Medical School, Boston, United States of America

10Section of Nephrology, Boston Medical Center, Boston, United States of America

11Department of Medicine, Indiana University School of Medicine, Indianapolis, United States of America

12Department of Pathology, University of Michigan, Ann Arbor, United States of America

13Department of Computational Medicine and Bioinformatics, University of Michigan Medical School, Ann Arbor, United States of America

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1Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, United States of America

2Department of Medicine, Geoge Washington University, Washington DC, United States of America

3Division of Nephrology, University of Michigan Medical School, Ann Arbor, United States of America

4Division of Transplant Surgery, University of California, San Francisco, San Francisco, United States of America

5Department of Surgery, University of Cincinnati College of Medicine, Cincinnati, United States of America

6Division of Metabolism, Endocrinology and Nutrition, University of Washington, Seattle, United States of America

7Division of Renal Diseases and Hypertension, University of Colorado School of Medicine, Aurora, United States of America

8Medical Specialties and Lerner Research Institutes, Case Western Reserve University, Cleveland, United States of America

9Kidney and Hypertension unit, Harvard Medical School, Boston, United States of America

10Section of Nephrology, Boston Medical Center, Boston, United States of America

11Department of Medicine, Indiana University School of Medicine, Indianapolis, United States of America

12Department of Pathology, University of Michigan, Ann Arbor, United States of America

13Department of Computational Medicine and Bioinformatics, University of Michigan Medical School, Ann Arbor, United States of America

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1Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, United States of America

2Department of Medicine, Geoge Washington University, Washington DC, United States of America

3Division of Nephrology, University of Michigan Medical School, Ann Arbor, United States of America

4Division of Transplant Surgery, University of California, San Francisco, San Francisco, United States of America

5Department of Surgery, University of Cincinnati College of Medicine, Cincinnati, United States of America

6Division of Metabolism, Endocrinology and Nutrition, University of Washington, Seattle, United States of America

7Division of Renal Diseases and Hypertension, University of Colorado School of Medicine, Aurora, United States of America

8Medical Specialties and Lerner Research Institutes, Case Western Reserve University, Cleveland, United States of America

9Kidney and Hypertension unit, Harvard Medical School, Boston, United States of America

10Section of Nephrology, Boston Medical Center, Boston, United States of America

11Department of Medicine, Indiana University School of Medicine, Indianapolis, United States of America

12Department of Pathology, University of Michigan, Ann Arbor, United States of America

13Department of Computational Medicine and Bioinformatics, University of Michigan Medical School, Ann Arbor, United States of America

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1Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, United States of America

2Department of Medicine, Geoge Washington University, Washington DC, United States of America

3Division of Nephrology, University of Michigan Medical School, Ann Arbor, United States of America

4Division of Transplant Surgery, University of California, San Francisco, San Francisco, United States of America

5Department of Surgery, University of Cincinnati College of Medicine, Cincinnati, United States of America

6Division of Metabolism, Endocrinology and Nutrition, University of Washington, Seattle, United States of America

7Division of Renal Diseases and Hypertension, University of Colorado School of Medicine, Aurora, United States of America

8Medical Specialties and Lerner Research Institutes, Case Western Reserve University, Cleveland, United States of America

9Kidney and Hypertension unit, Harvard Medical School, Boston, United States of America

10Section of Nephrology, Boston Medical Center, Boston, United States of America

11Department of Medicine, Indiana University School of Medicine, Indianapolis, United States of America

12Department of Pathology, University of Michigan, Ann Arbor, United States of America

13Department of Computational Medicine and Bioinformatics, University of Michigan Medical School, Ann Arbor, United States of America

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1Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, United States of America

2Department of Medicine, Geoge Washington University, Washington DC, United States of America

3Division of Nephrology, University of Michigan Medical School, Ann Arbor, United States of America

4Division of Transplant Surgery, University of California, San Francisco, San Francisco, United States of America

5Department of Surgery, University of Cincinnati College of Medicine, Cincinnati, United States of America

6Division of Metabolism, Endocrinology and Nutrition, University of Washington, Seattle, United States of America

7Division of Renal Diseases and Hypertension, University of Colorado School of Medicine, Aurora, United States of America

8Medical Specialties and Lerner Research Institutes, Case Western Reserve University, Cleveland, United States of America

9Kidney and Hypertension unit, Harvard Medical School, Boston, United States of America

10Section of Nephrology, Boston Medical Center, Boston, United States of America

11Department of Medicine, Indiana University School of Medicine, Indianapolis, United States of America

12Department of Pathology, University of Michigan, Ann Arbor, United States of America

13Department of Computational Medicine and Bioinformatics, University of Michigan Medical School, Ann Arbor, United States of America

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1Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, United States of America

2Department of Medicine, Geoge Washington University, Washington DC, United States of America

3Division of Nephrology, University of Michigan Medical School, Ann Arbor, United States of America

4Division of Transplant Surgery, University of California, San Francisco, San Francisco, United States of America

5Department of Surgery, University of Cincinnati College of Medicine, Cincinnati, United States of America

6Division of Metabolism, Endocrinology and Nutrition, University of Washington, Seattle, United States of America

7Division of Renal Diseases and Hypertension, University of Colorado School of Medicine, Aurora, United States of America

8Medical Specialties and Lerner Research Institutes, Case Western Reserve University, Cleveland, United States of America

9Kidney and Hypertension unit, Harvard Medical School, Boston, United States of America

10Section of Nephrology, Boston Medical Center, Boston, United States of America

11Department of Medicine, Indiana University School of Medicine, Indianapolis, United States of America

12Department of Pathology, University of Michigan, Ann Arbor, United States of America

13Department of Computational Medicine and Bioinformatics, University of Michigan Medical School, Ann Arbor, United States of America

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1Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, United States of America

2Department of Medicine, Geoge Washington University, Washington DC, United States of America

3Division of Nephrology, University of Michigan Medical School, Ann Arbor, United States of America

4Division of Transplant Surgery, University of California, San Francisco, San Francisco, United States of America

5Department of Surgery, University of Cincinnati College of Medicine, Cincinnati, United States of America

6Division of Metabolism, Endocrinology and Nutrition, University of Washington, Seattle, United States of America

7Division of Renal Diseases and Hypertension, University of Colorado School of Medicine, Aurora, United States of America

8Medical Specialties and Lerner Research Institutes, Case Western Reserve University, Cleveland, United States of America

9Kidney and Hypertension unit, Harvard Medical School, Boston, United States of America

10Section of Nephrology, Boston Medical Center, Boston, United States of America

11Department of Medicine, Indiana University School of Medicine, Indianapolis, United States of America

12Department of Pathology, University of Michigan, Ann Arbor, United States of America

13Department of Computational Medicine and Bioinformatics, University of Michigan Medical School, Ann Arbor, United States of America

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1Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, United States of America

2Department of Medicine, Geoge Washington University, Washington DC, United States of America

3Division of Nephrology, University of Michigan Medical School, Ann Arbor, United States of America

4Division of Transplant Surgery, University of California, San Francisco, San Francisco, United States of America

5Department of Surgery, University of Cincinnati College of Medicine, Cincinnati, United States of America

6Division of Metabolism, Endocrinology and Nutrition, University of Washington, Seattle, United States of America

7Division of Renal Diseases and Hypertension, University of Colorado School of Medicine, Aurora, United States of America

8Medical Specialties and Lerner Research Institutes, Case Western Reserve University, Cleveland, United States of America

9Kidney and Hypertension unit, Harvard Medical School, Boston, United States of America

10Section of Nephrology, Boston Medical Center, Boston, United States of America

11Department of Medicine, Indiana University School of Medicine, Indianapolis, United States of America

12Department of Pathology, University of Michigan, Ann Arbor, United States of America

13Department of Computational Medicine and Bioinformatics, University of Michigan Medical School, Ann Arbor, United States of America

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1Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, United States of America

2Department of Medicine, Geoge Washington University, Washington DC, United States of America

3Division of Nephrology, University of Michigan Medical School, Ann Arbor, United States of America

4Division of Transplant Surgery, University of California, San Francisco, San Francisco, United States of America

5Department of Surgery, University of Cincinnati College of Medicine, Cincinnati, United States of America

6Division of Metabolism, Endocrinology and Nutrition, University of Washington, Seattle, United States of America

7Division of Renal Diseases and Hypertension, University of Colorado School of Medicine, Aurora, United States of America

8Medical Specialties and Lerner Research Institutes, Case Western Reserve University, Cleveland, United States of America

9Kidney and Hypertension unit, Harvard Medical School, Boston, United States of America

10Section of Nephrology, Boston Medical Center, Boston, United States of America

11Department of Medicine, Indiana University School of Medicine, Indianapolis, United States of America

12Department of Pathology, University of Michigan, Ann Arbor, United States of America

13Department of Computational Medicine and Bioinformatics, University of Michigan Medical School, Ann Arbor, United States of America

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1Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, United States of America

2Department of Medicine, Geoge Washington University, Washington DC, United States of America

3Division of Nephrology, University of Michigan Medical School, Ann Arbor, United States of America

4Division of Transplant Surgery, University of California, San Francisco, San Francisco, United States of America

5Department of Surgery, University of Cincinnati College of Medicine, Cincinnati, United States of America

6Division of Metabolism, Endocrinology and Nutrition, University of Washington, Seattle, United States of America

7Division of Renal Diseases and Hypertension, University of Colorado School of Medicine, Aurora, United States of America

8Medical Specialties and Lerner Research Institutes, Case Western Reserve University, Cleveland, United States of America

9Kidney and Hypertension unit, Harvard Medical School, Boston, United States of America

10Section of Nephrology, Boston Medical Center, Boston, United States of America

11Department of Medicine, Indiana University School of Medicine, Indianapolis, United States of America

12Department of Pathology, University of Michigan, Ann Arbor, United States of America

13Department of Computational Medicine and Bioinformatics, University of Michigan Medical School, Ann Arbor, United States of America

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1Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, United States of America

2Department of Medicine, Geoge Washington University, Washington DC, United States of America

3Division of Nephrology, University of Michigan Medical School, Ann Arbor, United States of America

4Division of Transplant Surgery, University of California, San Francisco, San Francisco, United States of America

5Department of Surgery, University of Cincinnati College of Medicine, Cincinnati, United States of America

6Division of Metabolism, Endocrinology and Nutrition, University of Washington, Seattle, United States of America

7Division of Renal Diseases and Hypertension, University of Colorado School of Medicine, Aurora, United States of America

8Medical Specialties and Lerner Research Institutes, Case Western Reserve University, Cleveland, United States of America

9Kidney and Hypertension unit, Harvard Medical School, Boston, United States of America

10Section of Nephrology, Boston Medical Center, Boston, United States of America

11Department of Medicine, Indiana University School of Medicine, Indianapolis, United States of America

12Department of Pathology, University of Michigan, Ann Arbor, United States of America

13Department of Computational Medicine and Bioinformatics, University of Michigan Medical School, Ann Arbor, United States of America

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1Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, United States of America

2Department of Medicine, Geoge Washington University, Washington DC, United States of America

3Division of Nephrology, University of Michigan Medical School, Ann Arbor, United States of America

4Division of Transplant Surgery, University of California, San Francisco, San Francisco, United States of America

5Department of Surgery, University of Cincinnati College of Medicine, Cincinnati, United States of America

6Division of Metabolism, Endocrinology and Nutrition, University of Washington, Seattle, United States of America

7Division of Renal Diseases and Hypertension, University of Colorado School of Medicine, Aurora, United States of America

8Medical Specialties and Lerner Research Institutes, Case Western Reserve University, Cleveland, United States of America

9Kidney and Hypertension unit, Harvard Medical School, Boston, United States of America

10Section of Nephrology, Boston Medical Center, Boston, United States of America

11Department of Medicine, Indiana University School of Medicine, Indianapolis, United States of America

12Department of Pathology, University of Michigan, Ann Arbor, United States of America

13Department of Computational Medicine and Bioinformatics, University of Michigan Medical School, Ann Arbor, United States of America

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1Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, United States of America

2Department of Medicine, Geoge Washington University, Washington DC, United States of America

3Division of Nephrology, University of Michigan Medical School, Ann Arbor, United States of America

4Division of Transplant Surgery, University of California, San Francisco, San Francisco, United States of America

5Department of Surgery, University of Cincinnati College of Medicine, Cincinnati, United States of America

6Division of Metabolism, Endocrinology and Nutrition, University of Washington, Seattle, United States of America

7Division of Renal Diseases and Hypertension, University of Colorado School of Medicine, Aurora, United States of America

8Medical Specialties and Lerner Research Institutes, Case Western Reserve University, Cleveland, United States of America

9Kidney and Hypertension unit, Harvard Medical School, Boston, United States of America

10Section of Nephrology, Boston Medical Center, Boston, United States of America

11Department of Medicine, Indiana University School of Medicine, Indianapolis, United States of America

12Department of Pathology, University of Michigan, Ann Arbor, United States of America

13Department of Computational Medicine and Bioinformatics, University of Michigan Medical School, Ann Arbor, United States of America

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1Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, United States of America

2Department of Medicine, Geoge Washington University, Washington DC, United States of America

3Division of Nephrology, University of Michigan Medical School, Ann Arbor, United States of America

4Division of Transplant Surgery, University of California, San Francisco, San Francisco, United States of America

5Department of Surgery, University of Cincinnati College of Medicine, Cincinnati, United States of America

6Division of Metabolism, Endocrinology and Nutrition, University of Washington, Seattle, United States of America

7Division of Renal Diseases and Hypertension, University of Colorado School of Medicine, Aurora, United States of America

8Medical Specialties and Lerner Research Institutes, Case Western Reserve University, Cleveland, United States of America

9Kidney and Hypertension unit, Harvard Medical School, Boston, United States of America

10Section of Nephrology, Boston Medical Center, Boston, United States of America

11Department of Medicine, Indiana University School of Medicine, Indianapolis, United States of America

12Department of Pathology, University of Michigan, Ann Arbor, United States of America

13Department of Computational Medicine and Bioinformatics, University of Michigan Medical School, Ann Arbor, United States of America

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1Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, United States of America

2Department of Medicine, Geoge Washington University, Washington DC, United States of America

3Division of Nephrology, University of Michigan Medical School, Ann Arbor, United States of America

4Division of Transplant Surgery, University of California, San Francisco, San Francisco, United States of America

5Department of Surgery, University of Cincinnati College of Medicine, Cincinnati, United States of America

6Division of Metabolism, Endocrinology and Nutrition, University of Washington, Seattle, United States of America

7Division of Renal Diseases and Hypertension, University of Colorado School of Medicine, Aurora, United States of America

8Medical Specialties and Lerner Research Institutes, Case Western Reserve University, Cleveland, United States of America

9Kidney and Hypertension unit, Harvard Medical School, Boston, United States of America

10Section of Nephrology, Boston Medical Center, Boston, United States of America

11Department of Medicine, Indiana University School of Medicine, Indianapolis, United States of America

12Department of Pathology, University of Michigan, Ann Arbor, United States of America

13Department of Computational Medicine and Bioinformatics, University of Michigan Medical School, Ann Arbor, United States of America

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1Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, United States of America

2Department of Medicine, Geoge Washington University, Washington DC, United States of America

3Division of Nephrology, University of Michigan Medical School, Ann Arbor, United States of America

4Division of Transplant Surgery, University of California, San Francisco, San Francisco, United States of America

5Department of Surgery, University of Cincinnati College of Medicine, Cincinnati, United States of America

6Division of Metabolism, Endocrinology and Nutrition, University of Washington, Seattle, United States of America

7Division of Renal Diseases and Hypertension, University of Colorado School of Medicine, Aurora, United States of America

8Medical Specialties and Lerner Research Institutes, Case Western Reserve University, Cleveland, United States of America

9Kidney and Hypertension unit, Harvard Medical School, Boston, United States of America

10Section of Nephrology, Boston Medical Center, Boston, United States of America

11Department of Medicine, Indiana University School of Medicine, Indianapolis, United States of America

12Department of Pathology, University of Michigan, Ann Arbor, United States of America

13Department of Computational Medicine and Bioinformatics, University of Michigan Medical School, Ann Arbor, United States of America

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1Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, United States of America

2Department of Medicine, Geoge Washington University, Washington DC, United States of America

3Division of Nephrology, University of Michigan Medical School, Ann Arbor, United States of America

4Division of Transplant Surgery, University of California, San Francisco, San Francisco, United States of America

5Department of Surgery, University of Cincinnati College of Medicine, Cincinnati, United States of America

6Division of Metabolism, Endocrinology and Nutrition, University of Washington, Seattle, United States of America

7Division of Renal Diseases and Hypertension, University of Colorado School of Medicine, Aurora, United States of America

8Medical Specialties and Lerner Research Institutes, Case Western Reserve University, Cleveland, United States of America

9Kidney and Hypertension unit, Harvard Medical School, Boston, United States of America

10Section of Nephrology, Boston Medical Center, Boston, United States of America

11Department of Medicine, Indiana University School of Medicine, Indianapolis, United States of America

12Department of Pathology, University of Michigan, Ann Arbor, United States of America

13Department of Computational Medicine and Bioinformatics, University of Michigan Medical School, Ann Arbor, United States of America

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1Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, United States of America

2Department of Medicine, Geoge Washington University, Washington DC, United States of America

3Division of Nephrology, University of Michigan Medical School, Ann Arbor, United States of America

4Division of Transplant Surgery, University of California, San Francisco, San Francisco, United States of America

5Department of Surgery, University of Cincinnati College of Medicine, Cincinnati, United States of America

6Division of Metabolism, Endocrinology and Nutrition, University of Washington, Seattle, United States of America

7Division of Renal Diseases and Hypertension, University of Colorado School of Medicine, Aurora, United States of America

8Medical Specialties and Lerner Research Institutes, Case Western Reserve University, Cleveland, United States of America

9Kidney and Hypertension unit, Harvard Medical School, Boston, United States of America

10Section of Nephrology, Boston Medical Center, Boston, United States of America

11Department of Medicine, Indiana University School of Medicine, Indianapolis, United States of America

12Department of Pathology, University of Michigan, Ann Arbor, United States of America

13Department of Computational Medicine and Bioinformatics, University of Michigan Medical School, Ann Arbor, United States of America

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Published May 20, 2026 - More info

JCI Insight. https://doi.org/10.1172/jci.insight.204385.
Copyright © 2026, Menon et al. This work is licensed under the Creative Commons Attribution 4.0 International License. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/.
Published May 20, 2026 - Version history
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Abstract

Identifying mechanisms of kidney disease commonly involves comparing diseased samples to healthy reference tissues; however, the effects of variability in tissue procurement, storage, and donor characteristics remain underexplored. In this study, we systematically evaluated three reference tissue types—tumor nephrectomy (TN), pre-transplant biopsies from living donors (LD), and percutaneous biopsies from healthy control volunteers (HC)—to determine their impact on differential gene expression across three diabetic kidney disease (DKD) states. We observed distinct injury markers, cell state proportions, and gene signatures associated with procurement method, sex, and donor age. Adjustment for these confounding factors significantly influenced pathway analysis results. Specifically, correcting for age and sex eliminated significant enrichment of interferon gamma response in the diabetes mellitus–resilient (DM-R) versus HC comparison. Processes related to biological aging were enriched in older reference tissues, potentially confounding disease-specific interpretations. Importantly, tumor necrosis factor signaling via nuclear factor-κB remained enriched in LD and TN samples relative to HC, even after accounting for confounders. These results underscore the critical importance of selecting appropriate control tissues and rigorously adjusting for confounding variables to reliably discern the molecular mechanisms underlying kidney diseases.

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