Brain organoids: an ensemble of bioassays to investigate human neurodevelopment and disease

AbstractUnderstanding etiology of human neurological and psychiatric diseases is challenging. Genomic changes, protracted development, and histological features unique to human brain development limit the disease aspects that can be investigated using model organisms. Hence, in order to study phenotypes associated with human brain development, function, and disease, it is necessary to use alternative experimental systems that are accessible, ethically justified, and replicate human context. Human pluripotent stem cell (hPSC)-derived brain organoids offer such a system, which recapitulates features of early human neurodevelopment in vitro, including the generation, proliferation, and differentiation of neural progenitors into neurons and glial cells and the complex interactions among the diverse, emergent cell types of the developing brain in three-dimensions (3-D). In recent years, numerous brain organoid protocols and related techniques have been developed to recapitulate aspects of embryonic and fetal brain development in a reproducible and predictable manner. Altogether, these different organoid technologies provide distinct bioassays to unravel novel, disease-associated phenotypes and mechanisms. In this review, we summarize how the diverse brain organoid methods can be utilized to enhance our understanding of brain disorders.Facts

• Brain organoids offer an in vitro approach to study aspects of human brain development and disease.
• Diverse brain organoid techniques offer bioassays to investigate new phenotypes associated with human brain disorders that are difficult to study in monolayer cultures.
• Brain organoids have been particularly useful to study phenomena and diseases associated with neural progenitor morphology, survival, proliferation, and differentiation.

Open question

• Future brain organoid research needs to aim at later stages of neurodevelopment, linked with neuronal activity and connections, to unravel further disease-associated phenotypes.
• Continued improvement of existing organoid protocols is required to generate standardized methods that recapitulate in vivo-like spatial diversity and complexity.

Subject terms: Neuroscience, Neurological disorders

     

Trends and challenges in modeling glioma using 3D human brain organoids

The human brain organoids derived from pluripotent cells are a new class of three-dimensional tissue systems that recapitulates several neural epithelial aspects. Brain organoids have already helped efficient modeling of crucial elements of brain development and disorders. Brain organoids’ suitability in modeling glioma has started to emerge, offering another usefulness of brain organoids in disease modeling. Although the current state-of-the organoids mostly reflect the immature state of the brain, with their vast cell diversity, human brain-like cytoarchitecture, feasibility in culturing, handling, imaging, and tractability can offer enormous potential in reflecting the glioma invasion, integration, and interaction with different neuronal cell types. Here, we summarize the current trend of employing brain organoids in glioma modeling and discuss the immediate challenges. Solving them might lay a foundation for using brain organoids as a pre-clinical 3D substrate to dissect the glioma invasion mechanisms in detail.Subject terms: Cancer stem cells, CNS cancer     

Organoid systems to study the human female reproductive tract and pregnancy

Both the proper functioning of the female reproductive tract (FRT) and normal placental development are essential for women’s health, wellbeing, and pregnancy outcome. The study of the FRT in humans has been challenging due to limitations in the in vitro and in vivo tools available. Recent developments in 3D organoid technology that model the different regions of the FRT include organoids of the ovaries, fallopian tubes, endometrium and cervix, as well as placental trophoblast. These models are opening up new avenues to investigate the normal biology and pathology of the FRT. In this review, we discuss the advances, potential, and limitations of organoid cultures of the human FRT.Subject terms: Cell biology, Physiology, Diseases

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Generation of three-dimensional retinal organoids expressing rhodopsin and S- and M-cone opsins from mouse stem cells

Purpose

Three-dimensional retinal organoids can be differentiated from embryonic stem cells/induced pluripotent stem cells (ES/iPS cells) under defined medium conditions. We modified the serum-free floating culture of embryoid body-like aggregates with quick reaggregation (SFEBq) culture procedure to obtain retinal organoids expressing more rod photoreceptors and S- and M-cone opsins.

Efficient and error-free fluorescent gene tagging in human organoids without double-strand DNA cleavage

CRISPR-associated nucleases are powerful tools for precise genome editing of model systems, including human organoids. Current methods describing fluorescent gene tagging in organoids rely on the generation of DNA double-strand breaks (DSBs) to stimulate homology-directed repair (HDR) or non-homologous end joining (NHEJ)-mediated integration of the desired knock-in. A major downside associated with DSB-mediated genome editing is the required clonal selection and expansion of candidate organoids to verify the genomic integrity of the targeted locus and to confirm the absence of off-target indels. By contrast, concurrent nicking of the genomic locus and targeting vector, known as in-trans paired nicking (ITPN), stimulates efficient HDR-mediated genome editing to generate large knock-ins without introducing DSBs. Here, we show that ITPN allows for fast, highly efficient, and indel-free fluorescent gene tagging in human normal and cancer organoids. Highlighting the ease and efficiency of ITPN, we generate triple fluorescent knock-in organoids where 3 genomic loci were simultaneously modified in a single round of targeting. In addition, we generated model systems with allele-specific readouts by differentially modifying maternal and paternal alleles in one step. ITPN using our palette of targeting vectors, publicly available from Addgene, is ideally suited for generating error-free heterozygous knock-ins in human organoids.

A major downside of double-strand break-mediated genome editing is the need to verify the genomic integrity of the targeted locus and confirm the absence of off-target indels. This study shows that in-trans paired nicking is a mutation-free CRISPR strategy to introduce precise knock-ins into human organoids; its genomic fidelity allows all knock-in cells to be pooled, accelerating the establishment of new organoid models.     

The rise of coastal Middle Bronze Age Levant – A multidisciplinary approach for investigating in Sidon,Lebanon

Objectives

The Levantine Middle Bronze Age (MBA, circa 2000–1500 BCE) marks a period of increased trade and regional interaction, spurred on by technological developments. In light of previous research exhibiting limited mobility in Sidon, further investigation was conducted using biodistance analysis to understand local population history and site development.

Materials and Methods

Dental nonmetric traits, a proxy for genetic information, were explored using ASUDAS on a sub-sample of primary inhumations (n = 35). The biodistance matrix was generated using Gower distance measures, and further tested using PERMDISP, PERMANOVA, Mantel test and hierarchical cluster analysis. The data was also contrasted to ⁸⁷Sr/⁸⁶Sr and δ¹⁸O as well as δ¹³C and δ¹⁵N values.

Results

There were no significant diachronic differences in isotopes values, and there was biological continuity (n = 35, Mantel test r = 0.11, p = 0.02, comparing local phases and biodistance). The analysis also suggested of a sub-group of individuals with biological proximity shared a more limited range of mobility and dietary habits.

Conclusions

The isotopes (⁸⁷Sr/⁸⁶Sr, δ¹⁸O, δ¹³C, δ¹⁵N) and biodistance analysis conducted on the Sidon College site skeletal assemblage exhibits stability and continuity of the people, despite the site's increasing role in the maritime network. This continuity may have been a key factor in Sidon's success, allowing it to accumulate wealth and resources for centuries to come.

     

Hemochromatosis in Two Female Olive Baboons (Papio anubis)

This report describes hemochromatosis associated with chronic parenteral iron dextran administration in 2 female olive baboons (Papio anubis). These baboons were enrolled on an experimental protocol that induced and maintained anemia by periodic phlebotomy for use in studying potential treatments for sickle cell anemia. The 2 baboons both presented with clinical signs consistent with iron overload, including decreased appetite, weight loss, elevated liver enzymes, and hepatosplenomegaly. Histopathologic findings supported a morphologic diagnosis of systemic hemosiderosis, as evidenced by the overwhelming presence of iron in the reticuloendothelial system and liver after the application of Prussian blue stain. This finding, combined with the clinical presentation, lead to a final diagnosis of hemochromatosis. This case report suggests that providing anemic patients with chronic parenteral iron supplementation in the absence of iron deficiency can result in iatrogenic iron overload and subsequent systemic toxicity. Furthermore, these subjects may present with hemochromatosis and its associated clinical signs many years after cessation of iron supplementation.

Iron is an essential micronutrient that plays an important role in cellular proliferation, oxygen transport, and cellular energy generation.^13,26,31 The highest levels of iron in the body is found in the erythrocytes, followed by the liver, reticuloendothelial system, and skeletal muscle.⁹ Three main mechanisms regulate iron: 1) dietary absorption through the proximal duodenum; 2) recycling of senescent red blood cells by macrophages; and 3) storage in the liver. The liver produces the hormone hepcidin, which is the primary negative regulator of systemic iron metabolism.³⁸ Hepcidin controls the release of iron from enterocytes and macrophages into the circulation by binding to and degrading ferroportin, the only mammalian iron exporter.³⁵ When plasma iron levels are high, hepatocytes increase hepcidin synthesis. The increased hepcidin subsequently suppresses gastrointestinal absorption of exogenous iron and iron release from macrophages into circulation.³¹Approximately 1 to 2 mg of iron is lost per day through enterocyte and skin sloughing.³⁸ Iron can also be lost by hemorrhage, menstruation, and parasitic infestation.³⁸ Other than these, the body has no active mechanism for iron excretion. Iron overload can result from acute iron toxicity or chronic accumulation of iron over time.³⁵ Iron is primarily stored in the liver in the form of ferritin, and excess iron is transformed into hemosiderin, an oxidized form of ferritin. Hemosiderin is an iron-containing pigment found primarily in macrophages and hepatocytes.³⁵Hemosiderosis occurs when iron accumulates in tissues, but causes no subsequent organ injury or dysfunction. It is not typically pathologic and can be reversed.⁹ In contrast, hemochromatosis occurs when iron accumulation results in organ injury and dysfunction.³⁵ The 2 types of hemochromatosis are primary and secondary. Primary hemochromatosis, also known as hereditary hemochromatosis, is the result of inherited mutations in genes that are important for iron homeostasis. The most common gene involved in primary hemochromatosis is HFE, an autosomal recessive trait.¹¹ Almost all forms of primary hemochromatosis involve low levels of hepcidin expression.¹¹ Secondary hemochromatosis can occur due to iron-loading anemias such as thalassemia and sideroblastic anemia, chronic liver disease (for example, hepatitis C), and iatrogenic causes, such as excess iron in the diet or parenteral administration.¹⁶ Hemolytic anemia and repeated blood transfusions can also result in secondary hemochromatosis.³⁵ In primary hemochromatosis, iron typically accumulates in the liver, pancreas, heart, and endocrine glands for many years.^16,24 In contrast, secondary hemochromatosis patients often accumulate iron in the reticuloendothelial system, bone marrow, and lymph nodes¹⁶ over a shorter time period,²⁴ with excess iron accumulating in the hepatocytes after the reticuloendothelial system has become saturated with iron.¹⁶ Symptoms of iron overload can vary among individuals due to the number of organ systems affected. These symptoms may include lethargy, arthralgia, skin hyperpigmentation, abdominal pain, abnormal liver chemistry tests, and hepatomegaly.¹⁵ In the current report, we describe 2 cases of hemochromatosis in female baboons after chronic parenteral administration of iron dextran as part of an anemia maintenance protocol used to study sickle cell anemia treatments.     

Shifts in office and virtual primary care during the early COVID-19 pandemic in Ontario,Canada

BACKGROUND:Globally, primary care changed dramatically as a result of the coronavirus disease 2019 (COVID-19) pandemic. We aimed to understand the degree to which office and virtual primary care changed, and for which patients and physicians, during the initial months of the pandemic in Ontario, Canada.METHODS:This population-based study compared comprehensive, linked primary care physician billing data from Jan. 1 to July 28, 2020, with the same period in 2019. We identified Ontario residents with at least 1 office or virtual (telephone or video) visit during the study period. We compared trends in total physician visits, office visits and virtual visits before COVID-19 with trends after pandemic-related public health measures changed the delivery of care, according to various patient and physician characteristics. We used interrupted time series analysis to compare trends in the early and later halves of the COVID-19 period.RESULTS:Compared with 2019, total primary care visits between March and July 2020 decreased by 28.0%, from 7.66 to 5.51 per 1000 people/day. The smallest declines were among patients with the highest expected health care use (8.3%), those who could not be attributed to a primary care physician (10.2%), and older adults (19.1%). In contrast, total visits in rural areas increased by 6.4%. Office visits declined by 79.1% and virtual care increased 56-fold, comprising 71.1% of primary care physician visits. The lowest uptake of virtual care was among children (57.6%), rural residents (60.6%) and physicians with panels of ≥ 2500 patients (66.0%).INTERPRETATION:Primary care in Ontario saw large shifts from office to virtual care over the first 4 months of the COVID-19 pandemic. Total visits declined least among those with higher health care needs. The determinants and consequences of these major shifts in care require further study.

Primary care is considered the cornerstone of most health systems worldwide, and in higher-income countries, primary care visits are about 30 times more frequent than hospital admissions.¹ Health systems with greater availability of primary care are associated with increased access to care, reduced health inequities, better outcomes and lower costs.² Despite the centrality of primary care to health care systems, little is known about how it has been affected by coronavirus disease 19 (COVID-19).On Mar. 11, 2020, the World Health Organization declared COVID-19 a global pandemic.³ On Mar. 15, Ontario’s Chief Medical Officer of Health issued a directive to ramp down elective surgeries and other nonemergent health services, and on Mar. 19, health care providers and organizations were directed to stop or substantially reduce all nonessential or elective services until further notice.⁴ The Ontario Ministry of Health and the Ontario Medical Association negotiated the addition of temporary billing codes in the province’s schedule of benefits to facilitate virtual care, effective as of Mar. 14 (Appendix 1, available at www.cmaj.ca/lookup/doi/10.1503/cmaj.202303/tab-related-content). In mid to late May 2020, the province undertook a phased resumption of certain in-person health professional services and surgeries.⁴Initial reports from ongoing COVID-19-related surveys of primary care providers in Canada and the United States showed major disruptions to care, decreased payments, challenges keeping offices functioning, lack of personal protective equipment and widespread uptake of virtual care.^5,6 The degree to which virtual care — such as phone calls, video visits and secure text messages — replaced in-person office visits is not known. It is also not known which patients and physicians were most affected by the challenges to office-based practice or the change to virtual visits. We aimed to understand the degree to which office and virtual primary care changed, and for which patients and physicians, during the initial months of the COVID-19 pandemic in Ontario, Canada.     

Human iNSC-derived brain organoid model of lysosomal storage disorder in Niemann–Pick disease type C

Recent studies on developing three-dimensional (3D) brain organoids from stem cells have allowed the generation of in vitro models of neural disease and have enabled the screening of drugs because these organoids mimic the complexity of neural tissue. Niemann-Pick disease, type C (NPC) is a neurodegenerative lysosomal storage disorder caused by mutations in the NPC1 or NPC2. The pathological features underlying NPC are characterized by the abnormal accumulation of cholesterol in acidic compartments, including late endosomes and lysosomes. Due to the inaccessibility of brain tissues from human NPC patients, we developed NPC brain organoids with induced neural stem cells from NPC patient-derived fibroblasts. NPC organoids exhibit significantly reduced size and proliferative ability, which are accompanied by accumulation of cholesterol, impairment in neuronal differentiation, and autophagic flux and dysfunction of lysosomes; therefore, NPC organoids can recapitulate the main phenotypes of NPC patients. Furthermore, these pathological phenotypes observed in NPC organoids were reversed by treatment with valproic acid and HPBCD, which are known to be an effective treatment for several neurodegenerative diseases. Our data present patient-specific phenotypes in 3D organoid-based models of NPC and highlight the application of this model to drug screening in vitro.Subject terms: Disease model, Lipid-storage diseases, Neural stem cells     

Establishment of intestinal organoid cultures modeling injury-associated epithelial regeneration

The capacity of 3D organoids to mimic physiological tissue organization and functionality has provided an invaluable tool to model development and disease in vitro. However, conventional organoid cultures primarily represent the homeostasis of self-organizing stem cells and their derivatives. Here, we established a novel intestinal organoid culture system composed of 8 components, mainly including VPA, EPZ6438, LDN193189, and R-Spondin 1 conditioned medium, which mimics the gut epithelium regeneration that produces hyperplastic crypts following injury; therefore, these organoids were designated hyperplastic intestinal organoids (Hyper-organoids). Single-cell RNA sequencing identified different regenerative stem cell populations in our Hyper-organoids that shared molecular features with in vivo injury-responsive Lgr5⁺ stem cells or Clu⁺ revival stem cells. Further analysis revealed that VPA and EPZ6438 were indispensable for epigenome reprogramming and regeneration in Hyper-organoids, which functioned through epigenetically regulating YAP signaling. Furthermore, VPA and EPZ6438 synergistically promoted regenerative response in gut upon damage in vivo. In summary, our results demonstrated a new in vitro organoid model to study epithelial regeneration, highlighting the importance of epigenetic reprogramming that pioneers tissue repair.Subject terms: Intestinal stem cells, Regeneration     

Prenatal household size and composition are associated with infant fecal bacterial diversity in Cebu,Philippines

Objectives

The gut microbiome (GM) connects physical and social environments to infant health. Since the infant GM affects immune system development, there is interest in understanding how infants acquire microbes from mothers and other household members.

Materials and Methods

As a part of the Cebu Longitudinal Health and Nutrition Survey (CLHNS), we paired fecal samples (proxy for the GM) collected from infants living in Metro Cebu, Philippines at 2 weeks (N = 39) and 6 months (N = 36) with maternal interviews about prenatal household composition. We hypothesized that relationships between prenatal household size and composition and infant GM bacterial diversity (as measured in fecal samples) would vary by infant age, as well as by household member age and sex. We also hypothesized that infant GM bacterial abundances would differ by prenatal household size and composition.

Results

Data from 16 S rRNA bacterial gene sequencing show that prenatal household size was the most precise estimator of infant GM bacterial diversity, and that the direction of the association between this variable and infant GM bacterial diversity changed between the two time points. The abundances of bacterial families in the infant GM varied by prenatal household variables.

Conclusions

Results highlight the contributions of various household sources to the bacterial diversity of the infant GM, and suggest that prenatal household size is a useful measure for estimating infant GM bacterial diversity in this cohort. Future research should measure the effect of specific sources of household bacterial exposures, including social interactions with caregivers, on the infant GM.

     

The fluoride transporter FLUORIDE EXPORTER (FEX) is the major mechanism of tolerance to fluoride toxicity in plants1

Fluoride is everywhere in the environment, yet it is toxic to living things. How biological organisms detoxify fluoride has been unknown until recently. Fluoride-specific ion transporters in both prokaryotes (Fluoride channel; Fluc) and fungi (Fluoride Exporter; FEX) efficiently export fluoride to the extracellular environment. FEX homologs have been identified throughout the plant kingdom. Understanding the function of FEX in a multicellular organism will reveal valuable knowledge about reducing toxic effects caused by fluoride. Here, we demonstrate the conserved role of plant FEX (FLUORIDE EXPORTER) in conferring fluoride tolerance. Plant FEX facilitates the efflux of toxic fluoride ions from yeast cells and is required for fluoride tolerance in plants. A CRISPR/Cas9-generated mutation in Arabidopsis thaliana FEX renders the plant vulnerable to low concentrations (100-µM) of fluoride at every stage of development. Pollen is particularly affected, failing to develop even at extremely low levels of fluoride in the growth medium. The action of the FEX membrane transport protein is the major fluoride defense mechanism in plants.

Plants rely on a fluoride transporter to tolerate toxic fluoride ions.     

Knowledge graphs of ethical concerns of cerebral organoids

ObjectivesThe rapid development of cerebral organoid technology and the gradual maturity of cerebral organoids highlight the necessity of foresighted research on relevant ethical concerns. We employed knowledge graphs and conducted statistical analysis with CiteSpace for a comprehensive analysis of the status quo of the research on the ethical concerns of cerebral organoids from a bibliometric perspective.Materials and MethodsWe performed a statistical analysis of published papers on cerebral organoid ethics, keyword co‐occurrence graph, literature co‐citation and knowledge clustering graph to examine the status of the ethics research, internal relationship between technological development and ethical research, and ethical concerns of the academia. Finally, we used a keyword time zone graph and related statistics to analyze and predict the trends and popular topics of future cerebral organoids ethics research.ResultsWe demonstrated that although the ethical concerns of cerebral organoids have long been discussed, it was not until 2017 that the ethical issues began to receive more attention, when cerebral organoids were gradually mimicking the human brain more closely and increasingly being combined with chimera research. The recent key ethical concerns are primarily divided into three categories: concerns that are common in life sciences, specific to cerebral organoids, and present in cross‐fields. These increasing ethical concerns are inherently related to the continual development of technology. The analysis pointed out that future research should focus on the ethical concerns of consciousness that are unique to cerebral organoids, ethical concerns of cross‐fields, and construction and improvement of legislative and regulatory systems.ConclusionsAlthough research on cerebral organoids can benefit the biomedicine field, the relevant ethical concerns are significant and have received increasing attention, which are inherently related to the continual development of technology. Future studies in ethics regarding cerebral organoid research should focus on the ethical concerns of consciousness, and cross‐fields, as well as the improvement of regulatory systems.

We performed a statistical analysis of published papers on cerebral organoid ethics, keyword co‐occurrence graph, literature co‐citation and knowledge clustering graph to examine the status of the ethics research. We also used a keyword time zone graph and related statistics to analyse and predict the trends and popular topics of future cerebral organoids ethics research.     

Proteomic Analysis Reveals that Topoisomerase 2A is Associated with Defective Sperm Head Morphology

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Highlights

• •Human spermatozoa possess cells of poor morphology that lack nuclear integrity.
• •These cells can be isolated by density separation.
• •Mass spectrometry reveals their nuclei contain excess protein.
• •TOP2A is a promising marker of this poor nuclear development.

     

Tape stripping the stratum corneum for biomarkers of ultraviolet radiation exposure at sub-erythemal dosages: a study in human volunteers

Abstract

Purpose

Prevalence of skin cancer is rapidly increasing. There is a need for non-invasive biomarkers to assess efficacy of prevention strategies aiming at reduction of exposure to ultraviolet radiation (UVR). Recently, stratum corneum (SC) biomarkers were applied in various inflammatory skin diseases. Here, we explore their suitability as candidate biomarkers for UVR.