Skip to main content

A disease-specific iPS cell resource for studying rare and intractable diseases



Disease-specific induced pluripotent stem cells (iPSCs) are useful tools for pathological analysis and diagnosis of rare diseases. Given the limited available resources, banking such disease-derived iPSCs and promoting their widespread use would be a promising approach for untangling the mysteries of rare diseases. Herein, we comprehensively established iPSCs from patients with designated intractable diseases in Japan and evaluated their properties to enrich rare disease iPSC resources.


Patients with designated intractable diseases were recruited for the study and blood samples were collected after written informed consent was obtained from the patients or their guardians. From the obtained samples, iPSCs were established using the episomal method. The established iPSCs were deposited in a cell bank.


We established 1,532 iPSC clones from 259 patients with 139 designated intractable diseases. The efficiency of iPSC establishment did not vary based on age and sex. Most iPSC clones originated from non-T and non-B hematopoietic cells. All iPSC clones expressed key transcription factors, OCT3/4 (range 0.27–1.51; mean 0.79) and NANOG (range 0.15–3.03; mean 1.00), relative to the reference 201B7 iPSC clone.


These newly established iPSCs are readily available to the researchers and can prove to be a useful resource for research on rare intractable diseases.


Rare diseases are defined as those that affect a relatively small number of people in the population. According to the definition of the European Union (EU), rare diseases are those that affect less than one person per 2,000 people (0.05% of the EU population), and in the United States (US), they are known to affect less than 200,000 people (about 0.06% of the US population) [1] The total number of rare diseases is estimated to be more than 7,000 [1]. For such rare diseases, patients usually cannot receive proper diagnosis and consensus therapeutic strategies have not been established. Global consortia and databases have been established to overcome these issues and establish diagnostic and therapeutic approaches [2, 3].

One of the challenges in the research and treatment of rare diseases is that the small number of patients makes it difficult to design studies for the development of diagnostic and therapeutic approaches; specifically, large-scale controlled trials are often difficult to conduct. In addition, access to patient samples is often limited. To overcome these problems, induced pluripotent stem cell (iPSC)-based disease modeling is a promising approach [4, 5]. iPSCs can be easily established from patient's somatic cells such as peripheral blood mononuclear cells (PBMCs) [6, 7], fibroblasts [8, 9], and urine [10]. Since iPSCs inherit the genetic information of their donor, they are particularly useful for the analysis of genetic diseases, which are estimated to account for approximately 80% of rare diseases [11]. Recent advances in differentiation technology have enabled the differentiation of iPSCs into a wide variety of cell types [12]. In addition, the development of 3D organoid methods has enabled the modeling of complex structures of human organs, such as the brain, liver, and kidney [13,14,15]. Indeed, in several rare diseases, structural abnormalities of the cerebrum have been reproduced using iPSC-derived cerebral organoids [16, 17].

However, the treatment of patients with rare and intractable diseases is often time-consuming, placing a heavy mental, physical, and financial burden on the patients and their families. Therefore, in Japan, a system of designated intractable diseases was introduced in 2015 to reduce the economic burden of patients with rare intractable diseases [18]. The criteria for classifying a disease as a designated intractable disease are as follows: (1) rarity (less than 0.1% of the Japanese population), (2) unknown etiology, (3) no effective treatment, (4) need for long-term treatment, and (5) existence of objective diagnostic criteria. Patients with designated intractable diseases are eligible to receive subsidies for medical expenses in exchange for providing medical information in a format designated for each disease to the Ministry of Health, Labor, and Welfare, Japan. As of December 2021, 338 diseases had been classified as designated intractable diseases. This system also serves as a comprehensive database, covering more than 90% of all newly designated intractable disease cases in Japan [18]. It also serves as a traceable database because medical information is continuously collected after registration.

Because iPSCs derived from patients with designated intractable diseases are accompanied by reliable medical history information, they can prove to be a useful resource for the analysis of rare diseases. Therefore, in this study, we established iPSCs from patients with designated intractable diseases in Japan as a resource to promote the research pertaining to the rare diseases. We recruited 259 patients with 139 designated diseases and established 1,532 clones on a unified platform. All iPSCs have been deposited at the RIKEN BioResource Center, where they would be available for academic use; notably, although these iPSCs are not available for direct selling, they can still be used for commercial research. We believe that these iPSCs can be effectively utilized as a resource for the construction of pathological models for a wide range of rare diseases.


Study approval

This study was approved by the Ethics Committees of Kyoto University (G687), Shonan Kamakura General Hospital, and National Hospital Organization (NHO) (H26-NHO (shitei)-05) in Japan. Written informed consent was obtained from all patients or their guardians in accordance with the Declaration of Helsinki.

Donor recruitment and sample collection

At the Shonan Kamakura General Hospital, electronic medical records were searched for patients with designated intractable diseases, and medical coordinators and doctors obtained written informed consent from the candidates. In the NHO, each hospital belonging to the organization recruited patients with target diseases and sent their medical information to the headquarter. The headquarter scrutinized the medical information and selected eligible patients only if they met the criteria for the target disease. Subsequently, physicians from each hospital obtained written informed consent and collected the blood samples. Anonymization was performed at each facility. Peripheral blood mononuclear cells were isolated from the donor blood and cryopreserved. All donors underwent blood tests to exclude the presence of infection with hepatitis B, hepatitis C, human T-cell leukemia type 1, and human immunodeficiency viruses.

Establishment and maintenance of iPSCs

iPSCs were established from blood cells using previously described methods with marginal modifications [6]. Briefly, frozen peripheral blood mononuclear cells were thawed and cultured in StemSpan-ACF medium (STEMCELL Technologies, Vancouver, British Columbia, Canada) supplemented with stem cell factor (SCF; 100 ng/mL), thyroperoxidase (TPO; 100 ng/mL), Flt3 ligand (100 ng/mL), IL-6 (50 ng/mL), and IL-3 (10 ng/mL) for five days. SCF, TPO, Flt3 ligand, IL-6, and IL-3 were purchased from R&D Systems (Minneapolis, MN, USA). The episomal plasmids pCE-hOCT3/4, pCE-hSK, pCE-hUL, pCE-mp53DD, and pCXBEBNA1 were then co-transfected into 2 × 106 cultured PBMCs in a Nucleofector 2b device, using the Human CD34 cell Nucleofector kit (Lonza, Basel, Switzerland). The cells were dispensed into two-fold serial dilutions (six times) and plated into six wells of 6-well plates coated with Laminin511 E8 fragment matrix (iMatrix-511, Nippi, Tokyo, Japan) containing 1.5 mL of StemSpan-ACF medium containing the above-mentioned cytokines. Subsequently, 1.5 mL of complete StemFit AK03 medium was added every two days for three times, and the culture medium was replaced with 1.5 mL of complete StemFit AK03 medium at day 8 after the transduction. The colonies were picked up 2–3 weeks after the transduction and plated into 12-well plates coated with iMatrix-511 and cultured in 0.8 mL of complete StemFit AK03 medium containing Y27362 (10 μM, Wako, Osaka, Japan) for one day; the medium was then replaced with 0.8 mL of complete StemFit AK03 medium without Y27362. Five to seven days later, the cells were passaged again. Six clones were selected to generate passage two (P2) stocks. iPSCs were cultured on iMatrix-511-coated tissue culture plates using StemFit AK03 medium at 37 °C in an atmosphere containing 5% CO2 and 21% O2. Cells were passaged by dissociating them using TrypLE Select (Life Technologies, Gaithersburg, MD, USA). All clones were confirmed to be free of mycoplasma contamination prior to their deposition in the cell bank.


Morphological images were captured using an Olympus CKX41 microscope with a PlanApo 10 × /0.75 objective lens (Olympus, Tokyo, Japan) and a Nikon digital camera DS-Fil.

DNA and RNA extraction and cDNA synthesis

Genomic DNA and total RNA were extracted using the AllPrep DNA/RNA Mini Kit (Qiagen), following the manufacturer’s instructions. Genomic DNA was diluted to 25 ng/mL using distilled water. cDNA was synthesized using PrimeScript™ RT Master Mix (TaKaRa) from 500 ng of total RNA and diluted 1:10 in RNase-free water for OCT3/4 and NANOG mRNA expression analysis.

OCT3/4 and NANOG mRNA expression analysis

The mRNA expression of pluripotent stem cell markers, OCT3/4 and NANOG, was confirmed by quantitative real-time PCR (qRT-PCR) with TaqMan™ assay using StepOnePlus™ Real-Time PCR System (Thermo Fisher). Primer and probe sequences are listed in Supplementary Table S1. The expression values of the target genes were processed using the ΔΔCt method by normalization to GAPDH expression from the same cDNA templates, and the average of relative quantities (RQ) in comparison to the control 201B7 line are shown.

Residual plasmid analysis

The residual plasmids used for establishing the iPSCs were analyzed by TaqMan quantitative PCR using a StepOnePlus™ Real-Time PCR System (Thermo Fisher). Primer and probe sequences of CMV and EBNA1 were designed based on CAG-promoter region and the cording region of EBNA1 gene (Supplementary Table S1). The residual plasmid numbers were determined by a standard curve method with pCE-OCT3/4 episomal plasmid of known quantity using 50 ng genomic DNA of established iPSC at passages 4 to 6.

Cell type of origin analysis

The cell type of origin, including T cell, B cell, or non-T/non-B cell lineage, on established iPSC was analyzed by TaqMan™ quantitative PCR using StepOnePlus™ Real-Time PCR System (Thermo Fisher). The primer and probe sequences of T cell receptor (TCR) and joining region of immunoglobulin heavy chain (JH) were designed based on the sequences of TRD, T cell receptor delta locus, and IGH, immunoglobulin heavy chain locus, respectively (Supplementary Table S1). Quantitative PCR was performed using TRD, IGH, and RNaseP1 primers and probes using 20 ng genomic DNA of established iPSC at passages 4 to 6, and the number of TRD and IGH loci was analyzed using CopyCaller™ Software (Thermo Fisher) with the number of RNaseP1 loci as an internal standard. The cell type of origin was determined as T cell lineage if the number of TRD loci was 1 or 0, as B cell lineage if the number of IGH loci was 1 or 0, and as non-T/non-B cell lineage otherwise.


Statistical analysis was performed using Prism version 9.0 (GraphPad, San Diego, CA, USA). Each analysis method has been described in the figure legends. Statistical significance was set at p < 0.05.


Donor recruitment system and donor details

In this study, we established a pipeline from donor recruitment through iPSC establishment to iPSC deposition in a cell bank (Fig. 1A). At the start of donor recruitment, 306 intractable diseases were designated by the Japanese Ministry of Health, Labour, and Welfare. Donors with these diseases were targeted for recruitment as they had an annual medical summary required for aid. Medical institutions that participated in disease recruitment selected patients with the target diseases from electronic medical records to determine potential donors. As a result, 259 donors with 139 designated intractable diseases were recruited, and a total of 1,532 iPSC clones were established. Donor eligibility was confirmed on the basis of the diagnostic criteria for each disease.

Fig. 1
figure 1

Characteristics of iPSC donors. See also Supplementary Table S2. A Workflow from donor recruitment to depositing iPSCs in Riken Bioresource Bank. B Age distribution of recruited donors

The average age of the donors was 45.53 years. The age distribution of the patients is shown in Fig. 1B. There were 125 males and 134 females, with a sex ratio of 0.93. Designated intractable diseases were originally classified according to the International Classification of Diseases (ICD)-10. The diseases and cases from which iPSCs were established in this study were classified according to ICD-10 (Table 1). Various disease categories have been established, but the most commonly observed category is “congenital malformations, deformations, and chromosomal abnormalities” (major category XVII). Notably, the definition of designated intractable diseases has a medical administrative aspect and differs from the ICD-10 disease classification. For example, lysosomal diseases are comprehensively considered as designated intractable diseases, but can be divided into more than 30 individual disease units. Detailed donor information, including sex, age range, diagnosis, and ICD-10 classification, is presented in Supplementary Table S2.

Table 1 Number of donors grouped by disease category based on ICD-10


Frozen peripheral blood mononuclear cells (PBMCs) were thawed and reprogrammed by introducing episomal vectors encoding OCT3/4, SOX2, KLF4, LIN28, LMYC, and p53 dominant-negative fragments (Fig. 2A). In all recruited cases, iPSC clones were successfully established and no cases of reprogramming failure were recorded. For 13 donors, only five or fewer iPSC lines could be deposited, but for the remaining 246 donors (95.0%), six iPSC lines were successfully established and deposited. The average reprogramming efficiency was 0.06%, and there was no significant difference in reprogramming efficiency according to sex (Fig. 2B). No correlation between age and reprogramming efficiency was observed partly because of the large variation (Supplementary Fig. 1A). The mean doubling time of established iPSC clones was 29.67 ± 8.38 hours, which also did not show any correlation with age (Supplementary Fig. 1B). Male-derived iPSC lines had slightly longer doubling times (female: 29.29 ± 8.11 hours vs. male: 30.07 ± 8.64 hours; Fig. 2C). Interestingly, a few outliers with extremely long doubling times were observed, however, these were clones obtained from the same donors. The doubling times of the other clones from donors with such outliers were also longer than the average (Supplementary Fig. 1C). This is presumably due to a donor-derived characteristic; however, whether this was observed due to the genetic characteristics of the donor or the nature or condition of the source PBMCs remains unknown. Clones with extremely prolonged doubling times may require further evaluation, because of the possibility that genetic mutations or structural changes in the genome have occurred during the reprogramming process. In conclusion, we successfully established iPSCs from all recruited donors, and these iPSC lines were capable of proliferating in vitro, albeit with some variability.

Fig. 2
figure 2

Establishment of iPSC lines. See also Supplementary Fig. 1. A Flowchart depicting iPSC establishment. B Relationship between sex and reprogramming efficiency (%). C Relationship between sex and doubling time of established iPSC lines. (total n = 1,039; female n = 535; male n = 504). B, C Statistical analysis was performed using Mann–Whitney U test

Evaluation of the basic properties of iPSCs

Next, we evaluated the basic properties of the established iPSCs. All iPSC clones had a morphology consistent with that of in vitro human pluripotent stem cells (representative images are shown in Fig. 3A). To determine the type of cells in the PBMCs from which each iPSC clone was derived, genomic recombination of the T cell receptor (TCR) and joining region of immunoglobulin heavy chain (JH) of iPSCs were evaluated. Interestingly, the majority (97.8%) of the iPSC clones had no recombination in both TCR and JH regions, indicating that they originated from non-T non-B hematopoietic cells (Fig. 3B).

Fig. 3
figure 3

Basic characterization of established iPSCs. See also Supplementary Fig. 2. A Representative phase contrast images of iPSC colonies. iPSC clones from the patients with (i) Duchenne muscular dystrophy, (ii) Alexander disease, (iii) Dravet syndrome and (iv) Smith-Magenis syndrome are shown. Scale bars = 100 μm. Estimation of the cell type from which iPSCs originated; n = 1,532. C Estimation of the number of residual copies of episomal vectors remaining in iPSCs, calculated based on the quantitative values of EBNA and CAG promotors. Dashed lines are drawn at the line corresponding to one copy of remaining vector per cell; n = 1,532. D Correlation between OCT3/4 and NANOG expression in each clone. The single regression equation is plotted on the graph; n = 1,532. E, F Comparison of OCT3/4 (E) and NANOG (F) expression by sex (female n = 798, male n = 734). Values for each clone have been plotted relative to the expression levels in control 201B7 iPSCs. Statistical analysis was performed using the unpaired t-test (E) and Mann–Whitney U test (F)

The copy number of the episomal vectors remaining in the iPSC clones was also measured. Because all vectors used for reprogramming contained the CAG promoter and EBNA1 sequence, we evaluated the copy numbers of these two sequences per cell at passage 2. As a result, we observed that 96.3% of the clones had less than one copy of both CAG and EBNA promoters per cell (Fig. 3C). Thus, in most iPSC lines, the effect of plasmid persistence was deemed to be negligible.

Expression of pluripotency-associated genes

We next assessed the expression of OCT3/4 and NANOG, which are transcription factors expressed in undifferentiated pluripotent stem cells (Fig. 3D) [19, 20]. A weak correlation was observed between the expression levels of OCT3/4 and NANOG in each iPSC line. No clones lacked the expression of OCT3/4 or NANOG, but a large variation in their expression levels was observed among the clones (relative to the average expression levels of OCT3/4 and NANOG in control 201B7, wherein the expression levels of OCT3/4 ranged between 0.27–1.51 (mean 0.79) and that of NANOG ranged between 0.15–3.03 (mean 1.00)). Interestingly, the expression levels of both OCT3/4 and NANOG were significantly higher in female-derived clones (Fig. 3E and F). The association between age and the expression levels of these transcription factors was not evident (Supplementary Fig. 2A and B). Overall, all iPSC lines expressed the considerable amount of transcription factors specific to undifferentiated pluripotent stem cells.

Database construction

Finally, to promote the use of our iPSC resource, we have built a database that provides access to the information pertaining to iPSCs produced in our resource projects, including this study (CiCLeD: CiRA iPS Cell Line Database). Brief information regarding the donors and iPSC clones described in this study can be freely accessed from CiCLeD constructed at the following URL (


In this study, we established iPSCs from patients registered with designated intractable diseases, which is Japan's intractable disease support system, resulting in the establishment of a disease iPSC resource consisting of iPSCs established from patients with intractable diseases in a wide range of disease areas. The diseases from which iPSCs were established were diverse in terms of ICD-10 classification. The established iPSCs have been deposited in a public cell bank Riken Bioresource Center, and all researchers can potentially use these iPSCs for their own research pertaining to diseases.

Applying the medical history survey system of designated intractable diseases to the clinical information of iPSC donors will make it possible to obtain medical information in a uniform form for each disease and track donors in the future. In addition, if the patient database is accompanied by iPSC data, it would be possible to correlate disease phenotypes with the phenotypes at the cellular and genetic levels, thus providing very useful data for disease research. Unfortunately, medical information has been currently deposited in Japanese; therefore, it is necessary to make the dataset available globally in English.

It is already widely known that iPSCs are useful in rare disease research. As many rare diseases are hereditary, the establishment of iPSCs from the somatic cells of patients with rare genetic diseases can provide pluripotent stem cells that reflect the patient's genomic information. By differentiating these iPSCs into diseased cells, the pathology of each individual patient can be reproduced in vitro and analyzed in detail. Using patient-derived iPSCs, we can analyze the pathology of the rarest cases in details and reach a diagnosis. In fact, based on iPSC-derived phenotyping, it is possible to identify special genetic mutations that cannot be identified by whole-exon sequencing [21]. However, only about 300 designated intractable diseases, including rare intractable diseases, of the more than 7,000 rare diseases have been covered in the current study. In addition, not all disease-iPSCs included in designated intractable diseases have been established. Therefore, it is necessary to make continuous efforts to establish, evaluate, and deposit iPSCs for rare diseases, including designated intractable diseases.

Interestingly, there were sex-based differences in the expression levels of NANOG, an important transcription factor in PSCs. SRY gene on the Y chromosome is known to cause sex-dependent differences in global gene expression in human PSCs [22]. In addition, sex-based differences are known to cause differences in global demethylation during reprogramming [23]. Functional differences in differentiated cells derived from human PSCs have also been suggested previously [24]. These are small-scale studies, and our large cohort study suggests that sex-dependent differences can also affect those factors that are very important for the maintenance of pluripotency. The causes of this phenomenon and its consequences in terms of cell function remain to be elucidated.

The majority of iPSCs established from PBMCs lacked TCR and JH recombination, and were therefore considered to have been originated from non-T non-B cells. As the PBMC fraction also contains natural killer cells and monocytes in addition to T and B cells, these cells are thought to be the origin of iPSCs. This significant bias in the origin of iPSCs may be due to the fact that the cytokine setting used for the preculture of PBMCs did not include specific stimuli to proliferate T cells or B cells; for example, IL-2 anti-CD3 and anti-CD40 antibodies were not used. However, it was recently reported that preculture of PBMCs with similar cytokines expanded CD71-positive erythroblasts, and that these erythroblasts were the source of iPSCs [25]. Unfortunately, because we did not evaluate PBMCs prior to reprogramming, it is unclear as to which of these possibilities is more plausible.

In conclusion, we have established a large-scale iPSC panel of rare intractable diseases in Japan and deposited them in a public cell bank. These iPSCs are now widely available to the researchers and can prove to be a useful resource for research on rare intractable diseases. This study is a unique attempt to combine the basic resource of iPSCs for rare disease research with medical economic support measures for patients with intractable diseases. The future aim of such a system is to directly combine iPS cell-derived data with clinical findings and apply it to personalized medicine, including treatment and preventive medicine.

Availability of data and materials

The datasets used and/or analyzed in this study are available in the CiCLED database. All iPSC clones can be distributed through the RIKEN BioResource Center to the extent consistent with Japanese law.



European Union


The United States


Induced pluripotent stem cell


International classification of diseases


T cell receptor


Joining region of immunoglobulin heavy chain


National Hospital Organization


T cell receptor delta locus


Immunoglobulin heavy chain locus


  1. Haendel M, Vasilevsky N, Unni D, Bologa C, Harris N, Rehm H, et al. How many rare diseases are there? Nat Rev Drug Discov. 2020;19(2):77–8.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  2. Austin CP, Cutillo CM, Lau LPL, Jonker AH, Rath A, Julkowska D, et al. Future of Rare Diseases Research 2017–2027: an IRDiRC Perspective. Clin Transl Sci. 2018;11(1):21–7.

    Article  PubMed  Google Scholar 

  3. Boycott KM, Lau LP, Cutillo CM, Austin CP. International collaborative actions and transparency to understand, diagnose, and develop therapies for rare diseases. EMBO Mol Med. 2019;11(5):e10486.

    Article  PubMed  PubMed Central  Google Scholar 

  4. Anderson RH, Francis KR. Modeling rare diseases with induced pluripotent stem cell technology. Mol Cell Probes. 2018;40:52–9.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  5. Karagiannis P, Yamanaka S, Saito MK. Application of induced pluripotent stem cells to primary immunodeficiency diseases. Exp Hematol. 2019;71:43–50.

    Article  CAS  PubMed  Google Scholar 

  6. Okita K, Yamakawa T, Matsumura Y, Sato Y, Amano N, Watanabe A, et al. An efficient nonviral method to generate integration-free human-induced pluripotent stem cells from cord blood and peripheral blood cells. Stem Cells. 2013;31(3):458–66.

    Article  CAS  PubMed  Google Scholar 

  7. Ye L, Muench MO, Fusaki N, Beyer AI, Wang J, Qi Z, et al. Blood cell-derived induced pluripotent stem cells free of reprogramming factors generated by Sendai viral vectors. Stem Cells Transl Med. 2013;2(8):558–66.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  8. Nakagawa M, Koyanagi M, Tanabe K, Takahashi K, Ichisaka T, Aoi T, et al. Generation of induced pluripotent stem cells without Myc from mouse and human fibroblasts. Nat Biotechnol. 2008;26(1):101–6.

    Article  CAS  PubMed  Google Scholar 

  9. Takahashi K, Tanabe K, Ohnuki M, Narita M, Ichisaka T, Tomoda K, et al. Induction of pluripotent stem cells from adult human fibroblasts by defined factors. Cell. 2007;131(5):861–72.

    Article  CAS  PubMed  Google Scholar 

  10. Zhou T, Benda C, Duzinger S, Huang Y, Li X, Li Y, et al. Generation of induced pluripotent stem cells from urine. J Am Soc Nephrol. 2011;22(7):1221–8.

    Article  PubMed  PubMed Central  Google Scholar 

  11. Marwaha S, Knowles JW, Ashley EA. A guide for the diagnosis of rare and undiagnosed disease: beyond the exome. Genome Medicine. 2022;14(1):23.

    Article  PubMed  PubMed Central  Google Scholar 

  12. Karagiannis P, Takahashi K, Saito M, Yoshida Y, Okita K, Watanabe A, et al. Induced pluripotent stem cells and their use in human models of disease and development. Physiol Rev. 2019;99(1):79–114.

    Article  CAS  PubMed  Google Scholar 

  13. Eiraku M, Watanabe K, Matsuo-Takasaki M, Kawada M, Yonemura S, Matsumura M, et al. Self-organized formation of polarized cortical tissues from ESCs and its active manipulation by extrinsic signals. Cell Stem Cell. 2008;3(5):519–32.

    Article  CAS  PubMed  Google Scholar 

  14. Takasato M, Er PX, Chiu HS, Maier B, Baillie GJ, Ferguson C, et al. Kidney organoids from human iPS cells contain multiple lineages and model human nephrogenesis. Nature. 2015;526(7574):564–8.

    Article  CAS  PubMed  Google Scholar 

  15. Takebe T, Sekine K, Enomura M, Koike H, Kimura M, Ogaeri T, et al. Vascularized and functional human liver from an iPSC-derived organ bud transplant. Nature. 2013;499(7459):481–4.

    Article  CAS  PubMed  Google Scholar 

  16. Lancaster MA, Renner M, Martin CA, Wenzel D, Bicknell LS, Hurles ME, et al. Cerebral organoids model human brain development and microcephaly. Nature. 2013;501(7467):373–9.

    Article  CAS  PubMed  Google Scholar 

  17. Taniguchi-Ikeda M, Koyanagi-Aoi M, Maruyama T, Takaori T, Hosoya A, Tezuka H, et al. Restoration of the defect in radial glial fiber migration and cortical plate organization in a brain organoid model of Fukuyama muscular dystrophy. iScience. 2021;24(10):103140.

    Article  PubMed  PubMed Central  Google Scholar 

  18. Kanatani Y, Tomita N, Sato Y, Eto A, Omoe H, Mizushima H. National registry of designated intractable diseases in Japan: present status and future prospects. Neurol Med Chir (Tokyo). 2017;57(1):1–7.

    Article  PubMed  Google Scholar 

  19. Mitsui K, Tokuzawa Y, Itoh H, Segawa K, Murakami M, Takahashi K, et al. The homeoprotein Nanog is required for maintenance of pluripotency in mouse epiblast and ES cells. Cell. 2003;113(5):631–42.

    Article  CAS  PubMed  Google Scholar 

  20. Nichols J, Zevnik B, Anastassiadis K, Niwa H, Klewe-Nebenius D, Chambers I, et al. Formation of pluripotent stem cells in the mammalian embryo depends on the POU transcription factor Oct4. Cell. 1998;95(3):379–91.

    Article  CAS  PubMed  Google Scholar 

  21. Kawasaki Y, Oda H, Ito J, Niwa A, Tanaka T, Hijikata A, et al. Identification of a high-frequency somatic NLRC4 mutation as a cause of autoinflammation by pluripotent cell-based phenotype dissection. Arthritis Rheumatol (Hoboken, NJ). 2016;69(2):447–59.

    Article  Google Scholar 

  22. Ronen D, Benvenisty N. Sex-dependent gene expression in human pluripotent stem cells. Cell Rep. 2014;8(4):923–32.

    Article  CAS  PubMed  Google Scholar 

  23. Milagre I, Stubbs TM, King MR, Spindel J, Santos F, Krueger F, et al. Gender differences in global but not targeted demethylation in iPSC reprogramming. Cell Rep. 2017;18(5):1079–89.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  24. Li Y, Wen Y, Green M, Cabral EK, Wani P, Zhang F, et al. Cell sex affects extracellular matrix protein expression and proliferation of smooth muscle progenitor cells derived from human pluripotent stem cells. Stem Cell Res Ther. 2017;8(1):156.

    Article  PubMed  PubMed Central  Google Scholar 

  25. Agu CA, Soares FAC, Alderton A, Patel M, Ansari R, Patel S, et al. Successful generation of human induced pluripotent stem cell lines from blood samples held at room temperature for up to 48 hr. Stem Cell Reports. 2015;5(4):660–71.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

Download references


We thank the patients and their families for their cooperation in this study. We are grateful to Ms. Suga Hasegawa (CiRA, Kyoto University, Kyoto, Japan), Ms. Ayumi Matsunaga (iPS Cell Research Foundation, Kyoto, Japan), and Ms. Harumi Watanabe (CiRA, Kyoto University, Kyoto, Japan) for their administrative assistance. We also thank Ms. Tomoko Kohsaka (iPS Cell Research Foundation, Kyoto, Japan) for coordinating donor recruitment, Dr. Peter Karagiannis for language editing, and Dr. Keisuke Okita (CiRA, Kyoto University, Kyoto, Japan) for providing episomal vectors. We thank Dr. Naoto Utada and Ms. Etsuko Shimizu (Shonan Kamakura General Hospital, Kamakura, Japan) for their cooperation in donor recruitment at the Shonan Kamakura General Hospital. We thank following researchers (CiRA, Kyoto University, Kyoto, Japan) for assisting the reprogramming and quality evaluation of iPSCs: Ms. Ayako Nagahashi, Ms. Miho Saito, Dr. Koichi Igura, Ms. Monica Ono, Ms. Masami Yamashita, Ms. Minako Sakamoto, Ms. Yoshie Ishii, Dr. Yuri Kawasaki, Mr. Kazuki Kobayashi, Ms. Sayaka Nishimura, Ms. Misa Miyakawa, and Ms. Setsuko Inoue. We thank following physicians for conducting donor recruitment in National Hospital Organization (NHO): Dr. Morio Sawamura (NHO Shibukawa Medical Center, Shibukawa, Japan), Dr. Masahiro Suzuki (NHO Saitama National Hospital, Wako, Japan), Dr. Akira Hebisawa (NHO Tokyo National Hospital, Kiyose, Japan), Dr. Jun Tohyama (NHO Nishi-Niigata Chuo National Hospital, Niigata, Japan), Dr. Yoichi Takei (NHO Matsumoto Medical Center , Matsumoto, Japan), Dr. Satoru Sakagami (NHO Kanazawa Medical Center, Kanazawa, Japan), Dr. Michinori Funato (NHO Nagara Medical Center, Gifu, Japan), Dr. Katsumi Imai (NHO Shizuoka Institute of Epilepsy and Neurological Disorders, Shizuoka, Japan), Dr. Satoshi Kuru (NHO Suzuka National Hospital, Suzuka, Japan), Dr. Hatsumi Yamamoto (NHO Mie Chuo Medical Center, Tsu, Japan), Dr. Akira Shimatsu (NHO Kyoto Medical Center, Kyoto, Japan), Dr. Yoshikazu Inoue (NHO Kinki-chuo Chest Medical Center, Sakai, Japan), Dr. Yoshiki Adachi (NHO Matsue Medical Center, Matsue, Japan), Dr. Hiromi Matsubara (NHO Okayama Medical Center, Okayama, Japan), Dr. Yasushi Tanimoto (NHO Minami-Okayama Medical Center, Hayashima, Japan), Dr. Yoshinori Yamashita (NHO Kure Medical Center, Kure, Japan), Dr. Koichi Mandai (NHO Higashihiroshima Medical Center, Higashi-Hiroshima, Japan), Dr. Yasushi Okada (NHO Kyushu Medical Center, Fukuoka, Japan), Dr. Terufumi Shimoda (NHO Fukuoka National Hospital, Fukuoka, Japan), Dr. Tetsuyuki Kiyokawa (NHO Kumamoto Medical Center, Kumamoto, Japan), Dr. Michihisa Jogasaki (NHO Kagoshima Medical Center, Kagoshima, Japan), Dr. Kiyosu Taniguchi (NHO Mie National Hospital, Tsu, Japan), Dr. Yukihiko Saeki (NHO Osaka Minami Medical Center, Kawachi-Nagano, Japan), Dr. Kentro Ota (NHO Niigata National Hospital, Kashiwazaki, Japan), Dr. Takao Mitsui (NHO Tokushima National Hospital, Yoshinogawa, Japan), Dr. Shunji Matsuda (NHO Ehime Medical Center, Toon, Japan), Dr. Hideyuki Sawada (NHO Utano National Hospital, Kyoto, Japan), Dr. Yo Ishiguro (NHO Hirosaki General Medical Center, Hirosaki, Japan), and Dr. Tatsuo Matsunaga (NHO Tokyo Medical Center, Tokyo, Japan). We would like to thank late Dr. Mitsuru Kawai (NHO Higashisaitama National Hospital, Hasuda, Japan) for leading the donor recruitment process at NHO.


This work was supported by grants from the Core Center for iPS Cell Research of Research Center Network (JP21bm0104001 and 23bm1323001 to M.K.S. and S.Y.), Research on Intractable Diseases Using Disease-Specific iPSCs (16bm0609001h0005 to M.K.S. and S.Y.) for Realization of Regenerative Medicine from the Japan Agency for Medical Research and Development (AMED), the Program for Intractable Diseases Research utilizing Disease-specific iPSCs of AMED (JP21bm0804004 to M.K.S. and JP19bm0804001 to M.K.S. and S.Y.), and the iPS Cell Research Fund (to M.K.S.).

Author information

Authors and Affiliations



Conceptualization project administration and supervision (M.K.S. and S.Y.), methodology (M.K.S. and M.O.), validation (K.W.), formal analysis (M.K.S.), investigation (M.O. and I.A.), resources (N.T., A.N., K.O., S.I., and S.K.), visualization (K.S.), writing-original draft (M.K.S.), editing-review and editing (K.W. and M.K.S.), and funding acquisition (M.K.S. and S.Y.).

Corresponding author

Correspondence to Megumu K. Saito.

Ethics declarations

Ethics approval and consent to participate

This study was approved by the Ethics Committees of Kyoto University (G687), Tokushukai Shonan-Kamakura Hospital, and National Hospital Organization (NHO) (H26-NHO (shitei)-05) in Japan. Written informed consent was obtained from all patients or their guardians in accordance with the Declaration of Helsinki.

Consent for publication

Not applicable.

Competing interests

The authors declare that they have no competing interests.

Additional information

Publisher’s Note

Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.

Supplementary Information

Additional file 1:

Supplementary Table S1. qRT-PCR primers used for iPSC characterization.

Additional file 2:

Supplementary Table S2. Detailed donor information.

Additional file 3:

Supplementary Fig. 1. Reprograming efficiency and doubling time of iPSCs, related to Fig. 2. Supplementary Fig. 2. Relationship of OCT3/4 and NANOG expression and donor age, related to Fig. 3.

Rights and permissions

Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article's Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article's Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit

Reprints and Permissions

About this article

Check for updates. Verify currency and authenticity via CrossMark

Cite this article

Saito, M.K., Osawa, M., Tsuchida, N. et al. A disease-specific iPS cell resource for studying rare and intractable diseases. Inflamm Regener 43, 43 (2023).

Download citation

  • Received:

  • Accepted:

  • Published:

  • DOI:


  • iPS cells
  • Designated diseases
  • Rare and intractable diseases
  • Reprogramming