HCA Data Explorer

Kidney organoid reproducibility across multiple human iPSC lines and diminished off target cells after transplantation revealed by single cell transcriptomics

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Updated August 30, 2022

Human iPSC-derived kidney organoids have the potential to revolutionize discovery, but assessing their consistency and reproducibility across iPSC lines, and reducing the generation of off-target cells remain an open challenge. Here, we used single cell RNA-Seq (scRNA-Seq) to profile 450,118 cells to show that organoid composition and development are comparable to human fetal and adult kidneys. Although cell classes were largely reproducible across iPSC lines, time points, protocols, and replicates, cell proportions were variable between different iPSC lines. Off-target cell proportions were the most variable. Prolonged in vitro culture did not alter cell types, but organoid transplantation under the mouse kidney capsule diminished off-target cells. Our work shows how scRNA-seq can help score organoids for reproducibility, faithfulness and quality, that kidney organoids derived from different iPSC lines are comparable surrogates for human kidney, and that transplantation enhances their formation by diminishing off-target cells. Overall design: We have 49 organoids in total. We include 4 donors (AS, ThF, N1, N2; 2 males, 2 females) at 4 timepoints: 1 replicate each at the iPSC (Day 0), 1 replicate for 2 donors (N1, N2), 2 for the other two (AS, ThF) at Day 7, 3 replicates each at Days 15 and 29. For one donor (AS), we include 2 experiments at D15 and D29. For one donor (ThF), we have extended culture experiments at D32 (3 replicates) and D51(1 replicate). For ThF, we generated D29 organoids (3 replicates) from a second protocol. We have 2 transplanted organoids at D29. Organoids were pooled on lanes using a randomized design to ensure that organoids replicates from an individual batch (donor, replicate, condition) were distributed across lanes.

Anna GrekaBroad Institute of MIT and Harvardagreka@broadinstitute.org
Anna Greka (Principal Investigator)1
1Broad Institute of MIT and Harvard
Rachel Schwartz

To reference this project, please use the following link:

https://explore.data.humancellatlas.org/projects/a60803bb-f7db-45cf-b529-95436152a801
None
INSDC Project Accessions:GEO Series Accessions:INSDC Study Accessions:

Analysis Portals

None

Project Label

transplantedKidneyOrganoids

Species

Homo sapiens

Sample Type

organoids

Anatomical Entity

2 anatomical entities

Organ Part

2 organ parts

Selected Cell Types

Unspecified

Model Organ

kidney

Disease Status (Specimen)

normal

Disease Status (Donor)

normal

Development Stage

2 development stages

Library Construction Method

10x 3' v2

Nucleic Acid Source

single cell

Paired End

false

Analysis Protocol

analysis_protocol_1

File Format

4 file formats

Cell Count Estimate

450.1k

Donor Count

2
fastq.gz279 file(s)mtx.gz9 file(s)tsv.gz18 file(s)xlsx1 file(s)