Disentangling cell-intrinsic and extrinsic factors underlying gene expression evolution.

Chimeras have played a foundational role in biology, for example by enabling the classification of developmental processes into those driven intrinsically by individual cells versus those driven extrinsically by their extracellular environment. Here, we extend this framework to decompose evolutionary divergence in gene expression and other quantitative traits into cell-intrinsic, extrinsic, and intrinsic-extrinsic interaction components. Applying this framework to reciprocal rat-mouse chimeras, we found that the majority of gene expression divergence is attributable to cell-intrinsic factors, though extrinsic factors also play an integral role. For example, a rat-like extracellular environment extrinsically up-regulates the expression of a key transcriptional regulator of the endoplasmic reticulum (ER) stress response in some but not all cell types, which in turn strongly predicts extrinsic up-regulation of its target genes and of the ER stress response pathway as a whole. This effect is also seen at the protein level, suggesting propagation through multiple regulatory levels. We also demonstrate that our framework is applicable to a cellular trait, neuronal differentiation, and estimated the intrinsic and extrinsic contributions to its divergence. Finally, we show that imprinted genes are dramatically mis-expressed in species-mismatched environments, suggesting that mismatch between rapidly evolving intrinsic and extrinsic mechanisms controlling gene imprinting may contribute to barriers to interspecies chimerism. Overall, our conceptual framework opens new avenues to investigate the mechanistic basis of evolutionary divergence in gene expression and other quantitative traits in any multicellular organism.

Synthetic human gonadal tissues for toxicology.

The process of mammalian reproduction involves the development of fertile germ cells in the testis and ovary, supported by the surrounders. Fertilization leads to embryo development and ultimately the birth of offspring inheriting parental genome information. Any disruption in this process can result in disorders such as infertility and cancer. Chemical toxicity affecting the reproductive system and embryogenesis can impact birth rates, overall health, and fertility, highlighting the need for animal toxicity studies during drug development. However, the translation of animal data to human health remains challenging due to interspecies differences. In vitro culture systems offer a promising solution to bridge this gap, allowing the study of mammalian cells in an environment that mimics the physiology of the human body. Current advances on in vitro culture systems, such as organoids, enable the development of biomaterials that recapitulate the physiological state of reproductive organs. Application of these technologies to human gonadal cells would provide effective tools for drug screening and toxicity testing, and these models would be a powerful tool to study reproductive biology and pathology. This review focuses on the 2D/3D culture systems of human primary testicular and ovarian cells, highlighting the novel approaches for in vitro study of human reproductive toxicology, specifically in the context of testis and ovary.

Genome engineering with Cas9 and AAV repair templates generates frequent concatemeric insertions of viral vectors.

CRISPR-Cas9 paired with adeno-associated virus serotype 6 (AAV6) is among the most efficient tools for producing targeted gene knockins. Here, we report that this system can lead to frequent concatemeric insertions of the viral vector genome at the target site that are difficult to detect. Such errors can cause adverse and unreliable phenotypes that are antithetical to the goal of precision genome engineering. The concatemeric knockins occurred regardless of locus, vector concentration, cell line or cell type, including human pluripotent and hematopoietic stem cells. Although these highly abundant errors were found in more than half of the edited cells, they could not be readily detected by common analytical methods. We describe strategies to detect and thoroughly characterize the concatemeric viral vector insertions, and we highlight analytical pitfalls that mask their prevalence. We then describe strategies to prevent the concatemeric inserts by cutting the vector genome after transduction. This approach is compatible with established gene editing pipelines, enabling robust genetic knockins that are safer, more reliable and more reproducible.

Sexually dimorphic dynamics of the microtubule network in medaka (Oryzias latipes) germ cells.

Gametogenesis is the process through which germ cells differentiate into sexually dimorphic gametes, eggs and sperm. In the teleost fish medaka (Oryzias latipes), a germ cell-intrinsic sex determinant, foxl3, triggers germline feminization by activating two genetic pathways that regulate folliculogenesis and meiosis. Here, we identified a pathway involving a dome-shaped microtubule structure that may be the basis of oocyte polarity. This structure was first established in primordial germ cells in both sexes, but was maintained only during oogenesis and was destabilized in differentiating spermatogonia under the influence of Sertoli cells expressing dmrt1. Although foxl3 was dispensable for this pathway, dazl was involved in the persistence of the microtubule dome at the time of gonocyte development. In addition, disruption of the microtubule dome caused dispersal of bucky ball RNA, suggesting the structure may be prerequisite for the Balbiani body. Collectively, the present findings provide mechanistic insight into the establishment of sex-specific polarity through the formation of a microtubule structure in germ cells, as well as clarifying the genetic pathways implementing oocyte-specific characteristics.

Ran-GTP assembles a specialized spindle structure for accurate chromosome segregation in medaka early embryos.

Despite drastic cellular changes during cleavage, a mitotic spindle assembles in each blastomere to accurately segregate duplicated chromosomes. Mechanisms of mitotic spindle assembly have been extensively studied using small somatic cells. However, mechanisms of spindle assembly in large vertebrate embryos remain little understood. Here, we establish functional assay systems in medaka (Oryzias latipes) embryos by combining CRISPR knock-in with auxin-inducible degron technology. Live imaging reveals several unexpected features of microtubule organization and centrosome positioning that achieve rapid, accurate cleavage. Importantly, Ran-GTP assembles a dense microtubule network at the metaphase spindle center that is essential for chromosome segregation in early embryos. This unique spindle structure is remodeled into a typical short, somatic-like spindle after blastula stages, when Ran-GTP becomes dispensable for chromosome segregation. We propose that despite the presence of centrosomes, the chromosome-derived Ran-GTP pathway has essential roles in functional spindle assembly in large, rapidly dividing vertebrate early embryos, similar to acentrosomal spindle assembly in oocytes.

In Vitro Storage of Functional Sperm at Room Temperature in Zebrafish and Medaka.

The longevity of sperm in teleost such as zebrafish and medaka is short when isolated even in saline-balanced solution at a physiological temperature. In contrast, some internal fertilizers exhibit the long-term storage of sperm, >10 months, in the female reproductive tract. This evidence implies that sperm in teleost possesses the ability to survive for a long time under suitable conditions; however, these conditions are not well understood. In this study, we show that the sperm of zebrafish can survive and maintain fertility in L-15-based storage medium supplemented with bovine serum albumin, fetal bovine serum, glucose, and lactic acid for 28 days at room temperature. The fertilized embryos developed to normal fertile adults. This storage medium was effective in medaka sperm stored for 7 days at room temperature. These results suggest that sperm from external fertilizer zebrafish and medaka has the ability to survive for at least 4 and 1 week, respectively, in the body fluid-like medium at a physiological temperature. This sperm storage method allows researchers to ship sperm by low-cost methods and to investigate key factors for motility and fertile ability in those sperm.

Generation, characterization, and differentiation of induced pluripotent stem-like cells in the domestic cat.

Induced pluripotent stem (iPS) cells are generated from somatic cells and can differentiate into various cell types. Therefore, these cells are expected to be a powerful tool for modeling diseases and transplantation therapy. Generation of domestic cat iPS cells depending on leukemia inhibitory factor has been reported; however, this strategy may not be optimized. Considering that domestic cats are excellent models for studying spontaneous diseases, iPS cell generation is crucial. In this study, we aimed to derive iPS cells from cat embryonic fibroblasts retrovirally transfected with mouse Oct3/4, Klf4, Sox2, and c-Myc. After transfection, embryonic fibroblasts were reseeded onto inactivated SNL 76/7 and cultured in a medium supplemented with basic fibroblast growth factor. Flat, compact, primary colonies resembling human iPS colonies were observed. Additionally, primary colonies were more frequently observed in the KnockOut Serum Replacement medium than in the fetal bovine serum (FBS) medium. However, enhanced maintenance and proliferation of iPS-like cells occurred in the FBS medium. These iPS-like cells expressed embryonic stem cell markers, had normal karyotypes, proliferated beyond 45 passages, and differentiated into all three germ layers in vitro. Notably, expression of exogenous Oct3/4, Klf4, and Sox2 was silenced in these cells. However, the iPS-like cells failed to form teratomas. In conclusion, this is the first study to establish and characterize cat iPS-like cells, which can differentiate into different cell types depending on the basic fibroblast growth factor.

Generation of Self-Fertilizing Hermaphroditic Fish from Gonochoristic Fish, Medaka (Oryzias latipes).

INTRODUCTION: Hermaphroditism is a mode of reproduction involving an individual animal that possesses both a testis and an ovary either sequentially or simultaneously. The mechanism creating hermaphrodites remains unknown. Previously, we identified foxl3 as the germline sex determination gene in a gonochoristic fish, medaka (Oryzias latipes). foxl3 loss-of-function (foxl3-/-) females produce functional sperm as well as eggs in the ovary. However, these two gametes are not self-fertilizing because of the histological separation of each gamete production. In this study, we attempted to generate self-fertilizing medaka from female medaka by modifying germline sex using foxl3-/- mutants and by using exogenous androgen to induce partial sex reversal of somatic cells. METHODS: foxl3-/- XX females were treated with 11-ketotestosterone (11-KT), a potent teleost fish androgen, at the sexually mature stage for 30 days (90-120 dph). Then, the fish were kept under normal conditions until they were either being dissected or crossed with infertile males. RESULTS AND DISCUSSION: We showed that the foxl3-/- XX female medaka can be transformed into a self-fertilizing hermaphrodite by inducing the formation of a male-like structure with exogenous 11-KT. Self-fertilization occurs in either the ovarian cavity, the oviduct, or both where sperm is released from a tubule-like structure which is likely derived from germinal epithelium, suggesting that timely modification of 2 independent mechanisms, regulation of germline sex and partial sex reversal of somatic cells, are critical to change the reproduction mode. Our results will provide insights in developmental and evolutional occurrence of hermaphrodite vertebrates, facilitate an innovative technique to improve the efficient selection of fish with desirable traits, and contribute to the rescue of endangered species.

Zygotic nanos3 Mutant Medaka (Oryzias latipes) Displays Gradual Loss of Germ Cells and Precocious Spermatogenesis During Gonadal Development.

Nanos is one of the components of germ plasm and is evolutionarily conserved from flies to mammals. In medaka (Oryzias latipes), maternally provided nanos3 is essential for maintenance of primordial germ cells (PGCs). Here, we generated nanos3 loss-of-function mutants by using transcription activator-like effector nuclease (TALEN) and examined the function of zygotic nanos3 in medaka. Zygotic nanos3 homozygous (-/-) mutants derived from nanos3 heterozygous mothers formed germ cells. However, after hatching, the number of germ cells decreased considerably, resulting in infertility of both nanos3-/- females and males. Surprisingly, both nanos3-/- XX and XY mutants underwent precocious spermatogenesis during early gonadal development, as seen in loss-of-function mutants of foxl3, the germline sex-determination gene, in medaka. Therefore, in addition to the maintenance of germ cells, these results suggest that zygotic nanos3 affects the proper regulation of germline sex in XX medaka.

Streamlined and quantitative detection of chimerism using digital PCR.

Animal chimeras are widely used for biomedical discoveries, from developmental biology to cancer research. However, the accurate quantitation of mixed cell types in chimeric and mosaic tissues is complicated by sample preparation bias, transgenic silencing, phenotypic similarity, and low-throughput analytical pipelines. Here, we have developed and characterized a droplet digital PCR single-nucleotide discrimination assay to detect chimerism among common albino and non-albino mouse strains. In addition, we validated that this assay is compatible with crude lysate from all solid organs, drastically streamlining sample preparation. This chimerism detection assay has many additional advantages over existing methods including its robust nature, minimal technical bias, and ability to report the total number of cells in a prepared sample. Moreover, the concepts discussed here are readily adapted to other genomic loci to accurately measure mixed cell populations in any tissue.

Dynamics of Spermatogenesis and Change in Testicular Morphology under 'Mating' and 'Non-Mating' Conditions in Medaka (Oryzias latipes).

Here, we report that the gross morphology of the testes changes under 'non-mating' or 'mating' conditions in medaka (Oryzias latipes). During these conditions, an efferent duct expands and a histological unit of spermatogenesis, the lobule, increases its number under 'non-mating' conditions. Based on BrdU labeling experiments, lower mitotic activity occurs in gonial cells under 'non-mating' conditions, which is consistent with the reduced number of germ cell cysts. Interestingly, the total number of type A spermatogonia was maintained, regardless of the mating conditions. In addition, the transition from mitosis to meiosis may have been retarded under the 'non-mating' conditions. The minimum time required for germ cells to become sperm, from the onset of commitment to spermatogenesis, was approximately 14 days in vivo. The time was not found to significantly differ between 'non-mating' and 'mating' conditions. The collective data suggest the presence of a mechanism wherein the homeostasis of spermatogenesis is altered in response to the mating conditions.

Observation of Medaka Larval Gonads by Immunohistochemistry and Confocal Laser Microscopy.

The combination of immunohistochemistry and confocal laser microscopy enables the observation of cellular structures and protein localization within cells using whole-mount tissues. However, such high-resolution imaging requires several steps, such as proper dissection before fixation and antibody staining, and the appropriate positioning of tissues on a glass slide for observation. Here, we describe the method developed by our laboratory for the immunohistochemistry of medaka embryonic and larval gonads, focusing on the dissection and mounting of tissues for confocal laser microscopy. Positioning the gonad just beneath the coverslips is essential to obtain high-resolution images at a level where cellular components of germ cells, such as germ plasm and nuclear structures, can be clearly observed using an oil immersion objective lens.

Generation of Functional Organs Using a Cell-Competitive Niche in Intra- and Inter-species Rodent Chimeras.

Interspecies organ generation via blastocyst complementation has succeeded in rodents, but not yet in evolutionally more distant species. Early developmental arrest hinders the formation of highly chimeric fetuses. We demonstrate that the deletion of insulin-like growth factor 1 receptor (Igf1r) in mouse embryos creates a permissive "cell-competitive niche" in several organs, significantly augmenting both mouse intraspecies and mouse/rat interspecies donor chimerism that continuously increases from embryonic day 11 onward, sometimes even taking over entire organs within intraspecies chimeras. Since Igf1r deletion allows the evasion of early developmental arrest, interspecies fetuses with high levels of organ chimerism can be generated via blastocyst complementation. This observation should facilitate donor cell contribution to host tissues, resulting in whole-organ generation via blastocyst complementation across wide evolutionary distances.

Critical roles of the ddx5 gene in zebrafish sex differentiation and oocyte maturation.

DEAD-box helicase 5 (Ddx5) functions as an ATP-dependent RNA helicase and as a transcriptional coactivator for several transcription factors; however, the developmental function of the ddx5 gene in vertebrates is not fully understood. We found that the zebrafish ddx5 gene was expressed in developing gonads. Using the genome editing technology transcription activator-like effector nuclease, we established a ddx5-disrupted zebrafish and examined the morphological phenotypes of the mutant. We found that the majority of ddx5-deficient mutants developed as fertile males with normal testes and a small number of ddx5-deficient mutants developed as infertile females with small ovaries. Apoptotic cell death at 31 days post fertilization was increased in thick immature gonads (presumptive developing ovaries) of the ddx5-deficient mutant compared to those of heterozygous wild-type fish, while the number of apoptotic cells in thin immature gonads (presumptive developing testes) was comparable between the mutant and wild-type animals. Histological analysis revealed that ovaries of adult ddx5-deficient females had fewer vitellogenic oocytes and a larger number of stage I and II oocytes. The amount of cyclic adenosine monophosphate in the ddx5-deficient ovaries was high compared to that of wild-type ovaries, presumably leading to the mitotic arrest of oocyte maturation. Therefore, the ddx5 gene is dispensable for testis development, but it is essential for female sex differentiation and oocyte maturation in zebrafish.

foxl3, a sexual switch in germ cells, initiates two independent molecular pathways for commitment to oogenesis in medaka.

Germ cells have the ability to differentiate into eggs and sperm and must determine their sexual fate. In vertebrates, the mechanism of commitment to oogenesis following the sexual fate decision in germ cells remains unknown. Forkhead-box protein L3 (foxl3) is a switch gene involved in the germline sexual fate decision in the teleost fish medaka (Oryzias latipes). Here, we show that foxl3 organizes two independent pathways of oogenesis regulated by REC8 meiotic recombination protein a (rec8a), a cohesin component, and F-box protein (FBP) 47 (fbxo47), a subunit of E3 ubiquitin ligase. In mutants of either gene, germ cells failed to undergo oogenesis but developed normally into sperm in testes. Disruption of rec8a resulted in arrest at a meiotic pachytenelike stage specifically in females, revealing a sexual difference in meiotic progression. Analyses of fbxo47 mutants showed that this gene regulates transcription factors that facilitate folliculogenesis: LIM homeobox 8 (lhx8b), factor in the germline α (figla), and newborn ovary homeobox (nobox). Interestingly, we found that the fbxo47 pathway ensures that germ cells do not deviate from an oogenic pathway until they reach diplotene stage. The mutant phenotypes together with the timing of their expression imply that germline feminization is established during early meiotic prophase I.

Seasonal changes in NRF2 antioxidant pathway regulates winter depression-like behavior.

Seasonal changes in the environment lead to depression-like behaviors in humans and animals. The underlying mechanisms, however, are unknown. We observed decreased sociability and increased anxiety-like behavior in medaka fish exposed to winter-like conditions. Whole brain metabolomic analysis revealed seasonal changes in 68 metabolites, including neurotransmitters and antioxidants associated with depression. Transcriptome analysis identified 3,306 differentially expressed transcripts, including inflammatory markers, melanopsins, and circadian clock genes. Further analyses revealed seasonal changes in multiple signaling pathways implicated in depression, including the nuclear factor erythroid-derived 2-like 2 (NRF2) antioxidant pathway. A broad-spectrum chemical screen revealed that celastrol (a traditional Chinese medicine) uniquely reversed winter behavior. NRF2 is a celastrol target expressed in the habenula (HB), known to play a critical role in the pathophysiology of depression. Another NRF2 chemical activator phenocopied these effects, and an NRF2 mutant showed decreased sociability. Our study provides important insights into winter depression and offers potential therapeutic targets involving NRF2.

Starvation causes female-to-male sex reversal through lipid metabolism in the teleost fish, medaka (Olyzias latipes).

The teleost fish, medaka (Oryzias latipes), employs the XX/XY genetic sex determination system. We show here that the phenotypic sex of medaka is affected by changes in lipid metabolism. Medaka larvae subjected to 5 days of starvation underwent female-to-male sex reversal. Metabolomic and RT-qPCR analyses indicated that pantothenate metabolism was suppressed by starvation. Consistently, inhibiting the pantothenate metabolic pathway caused sex reversal. The final metabolite in this pathway is coenzyme A, an essential factor for lipogenesis. Inhibiting fatty acid synthesis, the first step of lipogenesis, also caused sex reversal. The expression of dmrt1, a critical gene for male development, was suppressed by starvation, and a dmrt1 (Δ13) mutant did not show sex reversal under starvation. Collectively, these results indicate that fatty acid synthesis is involved in female-to-male sex reversal through ectopic expression of male gene dmrt1 under starvation.

Periaortic Abdominal Fat Area as a Predictor of Surgical Difficulties during Extraperitoneal Laparoscopic Para-aortic Lymphadenectomy.

STUDY OBJECTIVE: To evaluate whether obesity is a marker of surgical difficulty during extraperitoneal para-aortic lymphadenectomy. DESIGN: Retrospective observational cohort study. SETTING: Tertiary medical center in the Kanazawa area of Japan. PATIENTS: Eighty-four patients with primary endometrial cancer who underwent extraperitoneal laparoscopic para-aortic lymphadenectomy (LPAND) between January 2005 and December 2017 were included. INTERVENTIONS: We investigated the correlation between operative times and body mass indexes, visceral fat areas, and periabdominal artery fat areas (PAFAs). The number of lymph nodes harvested was used as an indicator of the degree of surgical completion. MEASUREMENTS AND MAIN RESULTS: There was no correlation between the operative time and body mass index. Significant correlations were observed between operative time and visceral fat area (p = .026; r = 0.243) and between operative time and PAFA (p = .007; r = 0.293). A multivariate analysis showed that PAFA was a significant independent marker that could be used to predict prolonged operative times for extraperitoneal LPAND (p = .045; odds ratio, 3.05). The number of para-aortic lymph nodes harvested was not significant in the high- and low-PAFA groups (22 and 25, respectively; p = .525). CONCLUSION: PAFA is an adequate marker of prolonged operative time for extraperitoneal LPAND among patients with endometrial cancer.

Seasonal regulation of the lncRNA LDAIR modulates self-protective behaviours during the breeding season.

To cope with seasonal environmental changes, animals adapt their physiology and behaviour in response to photoperiod. However, the molecular mechanisms underlying these adaptive changes are not completely understood. Here, using genome-wide expression analysis, we show that an uncharacterized long noncoding RNA (lncRNA), LDAIR, is strongly regulated by photoperiod in Japanese medaka fish (Oryzias latipes). Numerous transcripts and signalling pathways are activated during the transition from short- to long-day conditions; however, LDAIR is one of the first genes to be induced and its expression shows a robust daily rhythm under long-day conditions. Transcriptome analysis of LDAIR knockout fish reveals that the LDAIR locus regulates a gene neighbourhood, including corticotropin releasing hormone receptor 2, which is involved in the stress response. Behavioural analysis of LDAIR knockout fish demonstrates that LDAIR affects self-protective behaviours under long-day conditions. Therefore, we propose that photoperiodic regulation of corticotropin releasing hormone receptor 2 by LDAIR modulates adaptive behaviours to seasonal environmental changes.

Novel components of germline sex determination acting downstream of foxl3 in medaka.

Germline sex determination is an essential process for the production of sexually dimorphic gametes. In medaka, Forkhead box L3 (foxl3) was previously identified as a germ cell-intrinsic regulator of sex determination that suppresses the initiation of spermatogenesis in female germ cells. To reveal the molecular mechanism of germline sex determination by foxl3, we conducted the following four analyses: Comparison of transcriptomes between wild-type and foxl3-mutant germ cells; epistatic analysis; identification of the FOXL3-binding motif; and ChIP-qPCR assay using a FOXL3-monoclonal antibody. We identified two candidate genes acting downstream of foxl3: Rec8a and fbxo47. It has been known that Rec8 regulates sister chromatid cohesion and Fbxo47 acts as a ubiquitin E3 ligase. These functions have not been, however, associated with sexual differentiation in germ cells. Our results uncover novel components acting downstream of foxl3, providing insights into the mechanism of germline sex determination.