Integrated Collection of Stem Cell Bank Data, a Data Portal for Standardized Stem Cell Information

Deep learning for quantifying spatial patterning and formation process of early differentiated human-induced pluripotent stem cells with micropattern images

Micropatterning is reliable method for quantifying pluripotency of human-induced pluripotent stem cells (hiPSCs) that differentiate to form a spatial pattern of sorted, ordered and nonoverlapped three germ layers on the micropattern. In this study, we propose a deep learning method to quantify spatial patterning of the germ layers in the early differentiation stage of hiPSCs using micropattern images. We propose decoding and encoding U-net structures learning labelled Hoechst (DNA-stained) hiPSC regions with corresponding Hoechst and bright-field micropattern images to segment hiPSCs on Hoechst or bright-field images. We also propose a U-net structure to extract extraembryonic regions on a micropattern, and an algorithm to compares intensities of the fluorescence images staining respective germ-layer cells and extract their regions. The proposed method thus can quantify the pluripotency of a hiPSC line with spatial patterning including cell numbers, areas and distributions of germ-layer and extraembryonic cells on a micropattern, and reveal the formation process of hiPSCs and germ layers in the early differentiation stage by segmenting live-cell bright-field images. In our assay, the cell-number accuracy achieved 86% and 85%, and the cell region accuracy 89% and 81% for segmenting Hoechst and bright-field micropattern images, respectively. Applications to micropattern images of multiple hiPSC lines, micropattern sizes, groups of markers, living and fixed cells show the proposed method can be expected to be a useful protocol and tool to quantify pluripotency of a new hiPSC line before providing it to the scientific community.

The Management of Data for the Banking, Qualification, and Distribution of Induced Pluripotent Stem Cells: Lessons Learned from the European Bank for Induced Pluripotent Stem Cells

The European Bank for induced pluripotent Stem Cells (EBiSC) was established in 2014 as a non-profit project for the banking, quality control, and distribution of human iPSC lines for research around the world. EBiSC iPSCs are deposited from diverse laboratories internationally and, hence, a key activity for EBiSC is standardising not only the iPSC lines themselves but also the data associated with them. This includes enabling unique nomenclature for the cells, as well as applying uniformity to the data provided by the cell line generator versus quality control data generated by EBiSC, and providing mechanisms to share personal data in a secure and GDPR-compliant manner. A joint approach implemented by EBiSC and the human pluripotent stem cell registry (hPSCreg®) has provided a solution that enabled hPSCreg® to improve its registration platform for iPSCs and EBiSC to have a pipeline for the import, standardisation, storage, and management of data associated with EBiSC iPSCs. In this work, we describe the experience of cell line data management for iPSC banking throughout the course of EBiSC's development as a central European banking infrastructure and present a model for how this could be implemented by other iPSC repositories to increase the FAIRness of iPSC research globally.

A double encryption protection algorithm for stem cell bank privacy data based on improved AES and chaotic encryption technology

The unique infinite self-renewal ability and multidirectional differentiation potential of stem cells provide a strong support for the clinical treatment. In light of the growing demands for stem cell storage, how to ensure personal privacy security and comply with strict ethical supervision requirements is particularly important. In order to solve the problem of low security of traditional encryption algorithm, we proposed a double encryption protection (DEP) algorithm for stem cell bank privacy data based on improved AES and chaotic encryption technology. Firstly, we presented the hash value key decomposition algorithm, through the hash value dynamic coding, cyclic shift, conversion calculation to get the key of each subsystem in the built algorithm. Secondly, DEP algorithm for privacy data is realized with two level of encryption. The first level of encryption protection algorithm used AES as the main framework, adding dynamic coding and byte filling based on DNA coding, and carries out dynamic shift of rows and simplified mixing of columns. The second level of encryption protection algorithm conducted random encoding, operation, diffusion and decoding based on the results of our proposed sequence conversion algorithm. Finally, we raised two evaluation indexes, the number of characters change rate (NCCR) and the unified average change intensity of text (UACIT) to measure the sensitivity of encryption algorithms to changes in plain information. The experimental results of using DEP shown that the average values of histogram variance, information entropy, NCCR and UACIT are116.7883, 7.6688, 32.52% and 99.67%, respectively. DEP algorithm has a large key space, high key sensitivity, and enables dynamic encryption of private data in stem cell bank. The encryption scheme provided in this study ensures the security of the private information of stem cell bank in private cloud environment, and also provides a new method for the encryption of similar high confidentiality data.

Human-specific genetics: new tools to explore the molecular and cellular basis of human evolution

Our ancestors acquired morphological, cognitive and metabolic modifications that enabled humans to colonize diverse habitats, develop extraordinary technologies and reshape the biosphere. Understanding the genetic, developmental and molecular bases for these changes will provide insights into how we became human. Connecting human-specific genetic changes to species differences has been challenging owing to an abundance of low-effect size genetic changes, limited descriptions of phenotypic differences across development at the level of cell types and lack of experimental models. Emerging approaches for single-cell sequencing, genetic manipulation and stem cell culture now support descriptive and functional studies in defined cell types with a human or ape genetic background. In this Review, we describe how the sequencing of genomes from modern and archaic hominins, great apes and other primates is revealing human-specific genetic changes and how new molecular and cellular approaches - including cell atlases and organoids - are enabling exploration of the candidate causal factors that underlie human-specific traits.

Human pluripotent stem cell registry: Operations, role and current directions

The human plutiripotent stem cell registry (hPSCreg) is a global database for human embryonic and induced pluripotent stem cells (hESC, hiPSC). The publicly accessible Registry (https://hpscreg.eu) was set up to provide a transparent resource of quality‐assessed hPSC lines as well as to increase reproducibility of research and interoperability of data.

Decellularized Organ-Derived Scaffold Is a Promising Carrier for Human Induced Pluripotent Stem Cells-Derived Hepatocytes

Human induced pluripotent stem cells (hiPSCs) are a promising cell source for elucidating disease pathology and therapy. The mass supply of hiPSC-derived cells is technically feasible. Carriers that can contain a large number of hiPSC-derived cells and evaluate their functions in vivo-like environments will become increasingly important for understanding disease pathogenesis or treating end-stage organ failure. hiPSC-derived hepatocyte-like cells (hiPSC-HLCs; 5 × 10⁸) were seeded into decellularized organ-derived scaffolds under circumfusion culture. The scaffolds were implanted into immunodeficient microminiature pigs to examine their applicability in vivo. The seeded hiPSC-HLCs demonstrated increased albumin secretion and up-regulated cytochrome P450 activities compared with those in standard two-dimensional culture conditions. Moreover, they showed long-term survival accompanied by neovascularization in vivo. The decellularized organ-derived scaffold is a promising carrier for hiPSC-derived cells for ex vivo and in vivo use and is an essential platform for regenerative medicine and research.