Erratum: Dendritic spine formation and synapse maturation in transcription factor-induced human iPSC-derived neurons.

[This corrects the article DOI: 10.1016/j.isci.2023.106285.].

Dendritic spine formation and synapse maturation in transcription factor-induced human iPSC-derived neurons.

Synaptic maturation is reportedly limited in human induced pluripotent stem cell (iPSC)-derived neurons. Notably, their ability to reach postnatal-like stages and form dendritic spines has been difficult to demonstrate unless using long-term cultured organoids. Recent transcription factor (TF)-based induction methods allow the accelerated generation of differentiated neurons, which offers an unprecedented opportunity to address further progression into late developmental stages. Herein, we report on a comprehensive time-course study of TF-induced iPSC neurons cultured in vitro through an intrinsic maturation program following neurogenesis. Moreover, we determined the transcriptional and morphological sequences of key developmental events associated with spinogenesis, including the conversion of drebrin to its brain-specific isoform A and the N-methyl-D-aspartate (NMDA) receptor subunit switch. TF-induced iPSC neurons successfully acquired structural and functional synaptic maturity, which will critically expand their utility in modeling higher brain functions and disorders.

Development of fibrin hydrogel-based in vitro bioassay system for assessment of skin permeability to and pro-inflammatory activity mediated by zinc ion released from nanoparticles.

Nanoparticles (NPs) are promising products in industry and medicine due to their unique physicochemical properties. In particular, zinc oxide (ZnO) NPs are extensively incorporated into sunscreens to protect the skin from exposure to ultraviolet radiation. However, there are several health concerns about skin penetration and the resultant toxicity. As methodologies for evaluating NP toxicity are under development, it is difficult to fully assess the toxicity of ZnO NPs toward humans. In this study, we developed a platform to simultaneously detect skin permeability to and pro-inflammatory activity mediated by zinc ion released from NPs. First, we generated a stable reporter cell line expressing green fluorescent protein (GFP) under the control of interleukin-8 (IL-8) promoter activity. The expression levels of GFP induced by zinc reflected the endogenous IL-8 expression levels and the pro-inflammatory responses. Next, we found that fibrin hydrogel can reproduce permeability to zinc ion of a human skin equivalent model and is therefore a promising material to assess skin permeability to zinc ion. Then, we constructed a fibrin hydrogel-based in vitro bioassay system for the simultaneous detection of skin permeability to and pro-inflammatory activity mediated by zinc ion released from NPs by using a stable reporter cell line and a fibrin hydrogel layer. This bioassay system is a promising in vitro permeation test due to its technical simplicity and good predictability. Overall, we believe that our bioassay system can be widely used in the cosmetics and pharmaceutical industries.

Novel Bioprinting Application for the Production of Reference Material Containing a Defined Copy Number of Target DNA.

Nucleic acid amplification methods, such as polymerase chain reaction (PCR), are extensively used in many applications to detect target DNA because of their high sensitivity, good reproducibility, and wide dynamic range of quantification. However, analytical quality control when detecting low copy number target DNA is often missing because of a lack of appropriate reference materials. Recent advances in analytical sciences require a method to accurately quantify DNA at the single molecule level. Herein, we have developed a novel method to produce reference material containing a defined copy number of target DNA (referred to as "cell number-based DNA reference material"). In this method, a suspension of cells carrying a single target DNA sequence was ejected by an inkjet head, and the number of cells in each droplet was counted using highly sensitive cameras. The resulting solutions contained a defined copy number of target DNA and could be used as reference materials. The use of the newly developed reference material was compared with that of diluted solutions of target DNA to evaluate the performance of qualitative real-time PCR in terms of the limit of detection (LOD). Our results demonstrated that cell number-based DNA reference material provides more accurate information regarding performance quality. The reference material produced by this method is a promising tool to evaluate assay performance.

High-precision three-dimensional inkjet technology for live cell bioprinting.

In recent years, bioprinting has emerged as a promising technology for the construction of three-dimensional (3D) tissues to be used in regenerative medicine or in vitro screening applications. In the present study, we present the development of an inkjet-based bioprinting system to arrange multiple cells and materials precisely into structurally organized constructs. A novel inkjet printhead has been specially designed for live cell ejection. Droplet formation is powered by piezoelectric membrane vibrations coupled with mixing movements to prevent cell sedimentation at the nozzle. Stable drop-on-demand dispensing and cell viability were validated over an adequately long time to allow the fabrication of 3D tissues. Reliable control of cell number and spatial positioning was demonstrated using two separate suspensions with different cell types printed sequentially. Finally, a process for constructing stratified Mille-Feuille-like 3D structures is proposed by alternately superimposing cell suspensions and hydrogel layers with a controlled vertical resolution. The results show that inkjet technology is effective for both two-dimensional patterning and 3D multilayering and has the potential to facilitate the achievement of live cell bioprinting with an unprecedented level of precision.

Chimeric antibodies.

Here we describe a detailed protocol for the one-step preparation of antigen-specific human chimeric immunoglobulin G (IgG) monoclonal antibodies (mAbs) using an in vitro antibody design method referred to as the ADLib (Autonomously Diversifying Library) system. This method employs a chicken B cell line DT40-based library in which the variable regions of the Ig gene loci have been highly diversified by treatment with the histone deacetylase inhibitors. DT40 cells express both membrane-bound and secreted forms of chicken IgM. This property allows a rapid screening and selection of antibody-producing B cells from the library by using magnetic beads conjugated with any antigen of interest. To apply the ADLib system to the direct generation of human chimeric antibody, we have inserted a DNA segment coding for the constant region of human IgG into the chicken IgM heavy-chain locus of DT40 cells by homologous gene targeting. By a mechanism of alternative splicing, the resulting DT40 strain simultaneously expresses chimeric human IgG that contain the same Ig variable region sequences as the membrane-bound chicken IgM displayed at the cell surface. Application of the ADLib system to this human Ig-inserted DT40 strain enables the one-step isolation of human chimeric IgG that is specific for any antigen of interest and can be easily purified for immediate use.

Role of α7-nicotinic acetylcholine receptor in normal and cancer stem cells.

The α7-nicotinic acetylcholine receptor (α7-nAChR) is widely known as a neurotransmitter receptor in nervous systems. α7-nAChR is also present in a variety of non-neuronal tissues, where it has been implicated in the regulation of essential cellular functions including proliferation, survival, differentiation and communication. We have recently found in breast cancer that α7-nAChR is involved in the proliferation of cancer stem cells, which constitute a minor subpopulation responsible for tumor development and metastasis. Since growing evidence suggests that α7-nAChR is present not only in mature tissues and organs but also in undifferentiated stem cells and progenitor cells, α7-nAChR emerges as a key mediator in the regulation of self-renewal and differentiation. We provide here an overview of the recent works on the expression and function of α7-nAChR in normal and cancer stem cells, and their relevance to disease-related cellular dysfunction. Understanding the role of α7-nAChR in stem cells would be of great interest for its application potential in drug discovery and in regenerative medicine.

B-cell display-based one-step method to generate chimeric human IgG monoclonal antibodies.

The recent development of screening strategies based on the generation and display of large libraries of antibody fragments has allowed considerable advances for the in vitro isolation of monoclonal antibodies (mAbs). We previously developed a technology referred to as the 'ADLib (Autonomously Diversifying Library) system', which allows the rapid screening and isolation in vitro of antigen-specific monoclonal antibodies (mAbs) from libraries of immunoglobulin M (IgM) displayed by the chicken B-cell line DT40. Here, we report a novel application of the ADLib system to the production of chimeric human mAbs. We have designed gene knock-in constructs to generate DT40 strains that coexpress chimeric human IgG and chicken IgM via B-cell-specific RNA alternative splicing. We demonstrate that the application of the ADLib system to these strains allows the one-step selection of antigen-specific human chimeric IgG. In addition, the production of chimeric IgG can be selectively increased when we modulate RNA processing by overexpressing the polyadenylation factor CstF-64. This method provides a new way to efficiently design mAbs suitable for a wide range of purposes including antibody therapy.

Distinct roles of HDAC1 and HDAC2 in transcription and recombination at the immunoglobulin loci in the chicken B cell line DT40.

The class I histone deacetylases HDAC1 and HDAC2 are highly conserved except for their C-terminal domain, but are presumed to have distinct functions in various tissues. We investigated the division of roles between HDAC1 and HDAC2 for the control of transcription and recombination at the immunoglobulin (Ig) gene in DT40. HDAC1(-/-) knock-out cells showed an increased incidence of gene conversion and of deletion/insertion events at the Ig light chain locus (IgL), but not at the heavy chain locus (IgH). Irrespective of recombinational activity, the transcription levels at IgL and IgH were decreased in HDAC1(-/-) cells, while other genes actively transcribed in B cells were slightly up-regulated compared to the levels in wild-type cells. These observations were strikingly different from the previously reported effects in HDAC2(-/-) cells, which showed a significant enhancement of transcriptional and recombinational activities at both IgL and IgH. Swapping experiments of the C-terminal unconserved domain of HDAC2 with its HDAC1 counterpart by gene knock-in demonstrated that this domain was not responsible for the phenotypic differences of HDAC1(-/-) and HDAC2(-/-). This suggests that other features such as modifications in the N-terminal catalytic domain could be important to determine the functional differences of these enzymes despite their structural similarities.

Histone H3 lysine 4 trimethylation marks meiotic recombination initiation sites.

The function of histone modifications in initiating and regulating the chromosomal events of the meiotic prophase remains poorly understood. In Saccharomyces cerevisiae, we examined the genome-wide localization of histone H3 lysine 4 trimethylation (H3K4me3) along meiosis and its relationship to gene expression and position of the programmed double-strand breaks (DSBs) that initiate interhomologue recombination, essential to yield viable haploid gametes. We find that the level of H3K4me3 is constitutively higher close to DSB sites, independently of local gene expression levels. Without Set1, the H3K4 methylase, 84% of the DSB sites exhibit a severely reduced DSB frequency, the reduction being quantitatively correlated with the local level of H3K4me3 in wild-type cells. Further, we show that this differential histone mark is already established in vegetative cells, being higher in DSB-prone regions than in regions with no or little DSB. Taken together, our results demonstrate that H3K4me3 is a prominent and preexisting mark of active meiotic recombination initiation sites. Novel perspectives to dissect the various layers of the controls of meiotic DSB formation are discussed.

Modulation of immunoglobulin gene conversion frequency and distribution by the histone deacetylase HDAC2 in chicken DT40.

Modifications of histones are reportedly associated with the regulation of immunoglobulin (Ig) gene diversification mechanisms, but the extent of their involvement in promoting sequence alterations at the Ig variable (V) regions still remains to be elucidated. We have previously demonstrated that Ig gene conversion in the B cell line DT40 is accompanied by the local hyperacetylation of histones, and that its frequency is highly increased in cells treated with the histone deacetylase (HDAC) inhibitor trichostatin A (TSA). In this report, we describe the enhancing effects of the homozygous deletion of HDAC2 (HDAC2-/-) on Ig gene conversion. Remarkably, sequence analysis revealed that the distribution of the gene conversion tracts induced throughout the Ig V regions in HDAC2-/- was significantly different from the diversification patterns in TSA-treated wild-type cultures. Furthermore, we found that the effects of HDAC2-/- and of the treatment with TSA were additive as regards histone acetylation, Ig gene transcription, gene conversion frequency and distribution of gene conversion tracts. These results underscore the potential participation of HDAC-mediated histone acetylation in Ig diversification, but also suggest a specific role of HDAC2 to control the spatial targeting of Ig gene conversion.

Specific transcriptional responses induced by 8-methoxypsoralen and UVA in yeast.

Treatment of eukaryotic cells with 8-methoxypsoralen plus UVA irradiation (8-MOP/UVA) induces pyrimidine monoadducts and interstrand crosslinks and initiates a cascade of events leading to cytotoxic, mutagenic and carcinogenic responses. Transcriptional activation plays an important part in these responses. Our previous study in Saccharomyces cerevisiae showed that the repair of these lesions involves the transient formation of DNA double-strand breaks and the enhanced expression of landmark DNA damage response genes such as RAD51, RNR2 and DUN1, as well as the Mec1/Rad53 kinase signaling cascade. We have now used DNA microarrays to examine genome-wide transcriptional changes produced after induction of 8-MOP/UVA photolesions. We found that 128 genes were strongly induced and 29 genes strongly repressed. Modifications in gene expression concern numerous biological processes. Compared to other genotoxic treatments, c. 42% of the response genes were specific to 8-MOP/UVA treatment. In addition to common DNA damage response genes and genes induced by environmental stresses, a large fraction of 8-MOP/UVA response genes correspond to membrane-related functions.

An ex vivo method for rapid generation of monoclonal antibodies (ADLib system).

Here, we describe a protocol for using the ADLib (Autonomously Diversifying Library) system to rapidly generate specific monoclonal antibodies using DT40, a chicken B-cell line that undergoes constitutive gene conversion at both light- and heavy-chain immunoglobulin loci. We previously developed the ADLib system on the basis of our finding that gene conversion in DT40 cells was enhanced by treatment of the cells with a histone deacetylase inhibitor, trichostatin A (TSA). TSA treatment evolves a diversified library of DT40 cells (ADLib), in which each cell has different surface IgM specificity. Antigen-specific DT40 cells are selected from ADLib using antigen-conjugated magnetic beads, and their specificity can be examined by various immunological assays, using culture supernatant containing secreted IgM. The whole process from selection to screening can be completed in about 1 week. Thus, the ADLib system will accelerate biological studies, including drug discovery and design.

Set1 is required for meiotic S-phase onset, double-strand break formation and middle gene expression.

The Set1 protein of Saccharomyces cerevisiae is a histone methyltransferase (HMTase) acting on lysine 4 of histone H3. Inactivation of the SET1 gene in a diploid leads to a sporulation defect. We have studied various processes that take place during meiotic differentiation in set1delta diploid cells. The absence of Set1 leads to a delay of meiotic S-phase onset, which reflects a defect in DNA replication initiation. The timely induction of meiotic DNA replication does not require the Set1 HMTase activity, but depends on the SET domain. In addition, set1delta displays a severe impairment of the DNA double-strand break formation, which is not only the consequence of the replication delay. Transcriptional profiling experiments show that the induction of middle meiotic genes, but not of early meiotic genes, is affected by the loss of Set1. In contrast to meiotic replication, the transcriptional induction of the middle meiotic genes appears to depend on the methylation of H3-K4. Our results unveil multiple roles of Set1 in meiotic differentiation and distinguish between HMTase-dependent and -independent Set1 functions.

Association of Mre11p with double-strand break sites during yeast meiosis.

The repair of DNA double-strand breaks (DSBs) requires the activity of the Mre11/Rad50/Xrs2(Nbs1) complex. In Saccharomyces cerevisiae, this complex is required for both the initiation of meiotic recombination by Spo11p-catalyzed programmed DSBs and for break end resection, which is necessary for repair by homologous recombination. We report that Mre11p transiently associates with the chromatin of Spo11-dependent DSB regions throughout the genome. Mutant analyses show that Mre11p binding requires the function of all genes required for DSB formation, with the exception of RAD50. However, Mre11p binding does not require DSB formation itself, since Mre11p transiently associates with DSB regions in the catalysis-negative mutant spo11-Y135F. Mre11p release from chromatin is blocked in mutants that accumulate unresected DSBs. We propose that Mre11p is a component of a pre-DSB complex that assembles on the DSB sites, thus ensuring a tight coupling between DSB formation by Spo11p and the processing of break ends.