INTRODUCTION
The cellular mechanisms responsible for the broad array of human cytomegalovirus (HCMV)-induced birth defects are at best ill defined. Epidemiological study has found HCMV congenital infections occur in ∼40,000 pregnancies in the United States annually (
1). Ninety to 95% of congenitally infected infants are asymptomatic at birth. The 2 to 4,000 congenitally infected infants symptomatic at birth display a broad spectrum of central and peripheral nervous system (CNS and PNS, respectively) disorders, including microcephaly, mental retardation, vision loss, and, in ∼30% to 50% of all cases, sensorineural hearing loss (SNHL). During early childhood, an additional 4 to 6,000 of the asymptomatic but congenitally infected infants develop negative consequences. These late-onset manifestations are principally learning disabilities and/or SNHL (
2–8). The ∼8,000 newly diagnosed problematic cases each year (∼1:500 births) represent an incidence as high as or higher than that of other more well-known causes of birth defects including fetal alcohol and Down syndromes (
9–12). Birth defects can have tragic consequences for the lives of afflicted children and their families. For some of these afflictions the source is known; however, in the case of HCMV-induced birth defects, little is known. In the hope of reducing and treating HCMV-induced birth defects, there is a pressing need to understand the undoubtedly complex and likely multifaceted interactions between the virus and host which are responsible for the manifestations.
Small-animal model studies of cytomegaloviruses have made significant contributions to the body of knowledge (
13–18), but virus species specificity and differences in placental architecture limit their utility (reviewed in reference
17). Tissue culture experiments utilizing human foreskin fibroblasts (HFFs) and lab-adapted virus strains have also elucidated many HCMV virus-host cell interactions. HFFs provide an excellent model for certain virus-host interactions; however, given the infection's drastic effects on neurologic systems, studies in neural lineage cells are necessary.
The degree of differentiation of neural cell types influences their susceptibility to HCMV infection (
19–24). We along with others have found neonatal-derived neural progenitor cells (nd-NPCs) fully permissive for HCMV (
25–30). Unfortunately, nd-NPCs have a propensity to differentiate toward glia, producing mixed-cell-type populations. Fortunately, large populations of almost pure cell types can be generated using either embryonic stem (ES) cell or induced pluripotent stem cell (iPSC) technologies. Interestingly, NPCs derived from 10-week gestation tissue were substantially more permissive to infection (
30) than either ES- or iPS-derived NPCs (
31–38; also our unpublished results). This suggests that the more primitive stage of development of the ES- and iPS-derived cells influences their interactions with the virus.
All of the infection studies performed to date on undifferentiated ES or iPS cells (including ours described herein) find both cell types to be essentially nonpermissive for infection, as measured by
de novo expression of immediate early (IE) antigens (Ags) (
31,
33,
35,
37). However, the susceptibility to infection of these cells is much less clear. Two studies did not examine susceptibility (
31,
35); others found ES cells to be refractory to virus binding (
33), as is true in the mouse system (
39). Penkert and Kalejta (
37) found ES cells susceptible to infection. This last study also reported that ES cells could maintain viral genomes from which new viral Ags were expressed after differentiation.
Cerebral organoids (
40–42) are a model system allowing study of three-dimensional (3D) cell cultures that closely mimic
in vivo development, including growth and development of cortical structures over time. These cultures have been used to study changes that occur during microcephaly resulting from a genetic mutation (
41), as well as the architectural changes that occur due to Zika virus infection, which targets developing NPCs (
43,
44). We mock or HCMV infected a monolayer of iPSCs and subjected them to an organoid-generating developmental protocol. At 52 days postinfection (p.i.), virus-infected organoids expressed IE1 protein, demonstrating the continuous presence of viral genomes in these cultures. Infection induced dramatic changes in the organoids, including the presence of regions of necrosis, the presence of larger vacuoles and cysts, and a decrease in overall cellularity. Development in the organoids was affected, with the numbers of both developing and fully formed cortical structure sites decreased. In addition, in contrast to mock-infected organoids, virus-infected organoids displayed clear indicators of pathology, including changes in the architectural organization and depth of the lamination within the cortical structures, and aberrant/delayed expression of the neural marker β-tubulin III.
DISCUSSION
There is a plethora of literature (reviewed in reference
54) describing the gross morphological CNS changes associated with congenital HCMV infection utilizing ultrasound, computed tomography (CT) scans, and other imaging techniques; however, it has only been in the relatively recent past that molecular, cellular, and histopathological analyses from a substantial number of clinical samples have provided a clearer picture of the extent of the pathological changes and the cell types that are infected in the developing brain (
48–50). These clinical studies have corroborated tissue culture experiments (including our own), which have found NPCs permissive for infection (
25–38). Clinical sample analyses have revealed that multiple other cell types, including neurons, neuroblasts, glia, and meningeal cells, can be Ag
+. Stem cells in the ventricular/germinal zones of infected brain specimens, analogous to NPCs, most often displayed signs of infection. However, despite a broad range of cell types expressing viral Ags, Ag positivity is, at best, only scattered (
38,
48–50). Histopathological analysis of clinical specimens found signs of microcephaly and cortical lesions, with areas of focal necrosis and cellular loss. Descriptions of delayed maturation and abnormal cortical lamination, in some instances with necrosis, have also been reported (
48–50). Our results in 3D organoid culture have recapitulated some of the changes observed in these analyses.
In the last 5 years, 3D organoid cultures have proven their value for the study of the development and pathology of genetic mutations and exposure to external stimuli, including drugs, pathogens, and chemicals, for multiple organ types (
55). In 2013, Lancaster and colleagues were the first to describe the development of a cerebral organoid system, starting from either ES or iPS cells (
41). Lancaster et al. demonstrated that these cultures were capable of developing into discrete regions, including the cerebral cortex. Cortical structures organized into laminations as development progressed. Lancaster et al. also explored the utility of the system to study developmental changes that occur due to genetic mutation. Since the introduction of these protocols, two groups have used cerebral organoids to study the developmental ramifications of Zika virus infection (
43,
44). Given HCMV's documented effects on the central and peripheral nervous systems following congenital infection (
54), we believed that cerebral organoids could provide a model for examining whether harbored genomes and expression of viral genes during differentiation affected neurological development. Our results demonstrate detrimental effects on organoid development due to HCMV infection.
We used iPSC lines derived from the same neonatal tissue used for our nd-NPC studies (
25,
45). This provided a baseline for comparison to the reprogrammed cells. These iPSCs were susceptible to the clinical isolate TR but expressed no new viral Ag for the first 48 hpi (
Fig. 1 and
2). Some studies have found ES and iPS cells susceptible to infection (
37), while other studies report the opposite (
33). The discrepancy may lie in the cell lines and viral isolates used for the studies. We have found two different iPSC lines largely susceptible to the clinical isolate TR (
Fig. 1). However, only one of these, SC27, was susceptible to HCMV Towne, while SC30 was not. Berger and colleagues (
33) saw no binding or penetration of their clinical isolates into two ES cell lines. In contrast, Penkert and Kalejta (
37) found two different ES cell lines that were susceptible to both AD169 and FIX strain infection but that transported limited tegument proteins to the nucleus and expressed no new viral Ags. Penkert and Kalejta went on to show that these cells harbored genomes for an extended period. The literature agrees that in their most primitive, undifferentiated state, stem cells do not support new viral gene expression and are not permissive for infection.
Several labs have described neural differentiation of ES and iPS cells to prerosette neural stem cells (NSCs) and the slightly later derivative NPCs (
31–38). These studies agreed that NSCs and NPCs were both susceptible and permissive for HCMV infection, expressing new viral Ags soon after infection. However, the very detailed study of Belzile and colleagues, which utilized several different ES cell lines to differentiate NSC populations, found marked variability in their permissiveness, potentially hinging on the expression of the neural marker FORSE-1 (
32). Berger and colleagues found that susceptibility and permissiveness hinged on the onset of expression of the platelet-derived growth factor receptor alpha (PDGFRα) protein on the cell surface (
33). Receptor display on the surface of any given cell line may influence susceptibility.
Several factors instructed our experimental design and encouraged us to undertake these experiments. First, the SC27 and SC30 iPSCs were susceptible to TR in their undifferentiated state. Obviously, studying the effects of HCMV infection on development would be impossible if the virus was incapable of entering the initial cell population. Second, infecting an already formed organoid would have presented challenges related to quantification of equal exposure to input virus. Accurate calculations of the multiplicity of infection (MOI) would have been nearly impossible without disassociating the structure, rendering its structural study impossible. Also, the spherical structure would have inhibited equal exposure of all cells to input virus since cells on the interior of a sphere would likely be less exposed. Third, infection of iPSCs was not lytic, with only scattered (<1%) undifferentiated iPSCs expressing very low levels of IE1. Our experiments with infection of nd-NPCs found that differentiated neural cell types were not only highly susceptible but also almost universally permissive for infection, with lysis of all cells over a restricted time course of infection. Infecting already differentiated organoids was likely to be equivalently severe and provide little, or no, opportunity to study development for an extended period (in our studies, to 52 days p.i.). The results of Cosset and colleagues (
35) using engineered neural tissues found that infection of already differentiated cells resulted in complete cellular lysis by 15 days p.i. These results may well model the development of microcephaly in severely affected fetuses. We hoped to examine infection's effects on the development of cortical structures over a longer period of time; therefore, we infected iPSCs prior to commencing the organoid differentiation and growth protocol. Fourth, performing the organoid differentiation protocol on infected iPSCs grown on coverslips identified new viral gene expression, the establishment of viral replication centers, and the shedding of virus to cocultured HFFs from a small subset of these differentiated cells (
Fig. 2). Intriguingly, commencement of expression of new viral Ags in the infected iPSCs paralleled the protocol-defined withdrawal of fibroblast growth factor (FGF) from the medium, suggesting that maintenance of “stem-ness” inhibited the progression of infection. These results suggested that an organoid generated from an infected iPSC population would harbor functional viral genomes, permitting the study of the effect of viral gene expression on development over a long duration.
Congenital Zika virus infection is known to induce birth defects pathologically similar to those observed after congenital HCMV infection, with microcephaly being the most pronounced effect observed (
54). Two recent papers used cerebral organoid systems to study the effects of Zika virus infection on cortical development (
43,
44). Both studies differentiated organoids for 10 days prior to infection, presumably to permit development of large NPC populations, which have been shown to be preferentially infected by Zika virus. Parallel to our findings, both studies reported increased necrosis in infected organoids. Unlike our studies, the authors noted preferential killing of NPCs. The loss of the progenitor populations may have led to the observed decreased neuronal cell layer volumes and concomitant decreases in average overall size of Zika virus-infected organoids. In contrast to these Zika virus studies, we observed no statistically significant change in the sizes of organoids after HCMV infection. Approximations of organoid size, using whole-organoid stereoscopic images, revealed only slight differences in the average size of mock- and HCMV-infected organoids, with the individual areas of the members of the two groups overlapping considerably (
Fig. 3B). We also found no correlation between developmental score and organoid size in either mock- or virus-infected organoids, suggesting that, even if HCMV infection did have a minor effect on growth, this effect did not impact the developmental scores.
Admittedly, we had difficulty finding Ag
+ cells in sectioned virus-infected organoids. We are unsure if processing or Ag visualization was to blame; however, whole virus-infected organoids stained prior to sectioning displayed focal regions of Ag
+ cells (
Fig. 3C). This staining was very similar to that reported in clinical tissue samples, with only scattered Ag
+ cells observed throughout cortical sections (
38,
48–50). One study described an 8-μm section with anywhere from 1 to 300 IE
+ cells (
38). This suggests that the significant developmental ramifications we observed were not dependent on expression of new viral Ags in every cell or the shedding of significant quantities of virus.
As described in the results section and shown in
Table 1 and
Fig. 4, we saw clear changes in development in virus-infected organoids compared to that of their mock-infected counterparts. There were fewer cortical structures. Laminated areas present in virus-infected organoids were thinner and less developed. Some developmental sites in virus-infected organoids contained fragmented cell clusters, indicating underdevelopment. β-Tubulin III staining of the latter regions revealed gaps in the underlying neural cell layer (
Fig. 4B), reminiscent of dysplastic lesions observed in clinical samples. In addition, virus-infected organoids had areas of necrosis and sometimes contained vacuoles within the cortical structures themselves. Last, cysts were seen in the virus-infected organoids. These pathologies were rarely seen in mock-infected organoids. Our findings parallel literature descriptions of cortical lesions in infected clinical samples, with areas of focal necrosis and cellular loss, descriptions of delayed maturation, and abnormal cortical lamination (
48–50). Importantly, ∼73% of mock-infected organoids had developmental scores of +++ or above. None of the virus-infected organoids scored above ++. Lancaster and Knoblich (
40) reported that in a population of EBs showing radial organization, further differentiation to organoids yielded true-cortical structures in 30% to 80% of the population. Our mock-infected organoid population was at the upper end of this range (73%), whereas the virus-infected organoids fell far below that 30% threshold (at best 8%), a statistically significant difference in development due to infection (
Fig. 4C).
The dearth of true-cortical structures we observed indicated that HCMV infection of an organoid's progenitor cells induced a population-wide effect in a differentiated organoid. β-Tubulin III staining within organoids also points to a population-wide effect resulting from infection. This marker is present in the axons of postmitotic, differentiated neurons (
53). The presence of β-tubulin III within a structure indicates the level/extent of differentiation of that structure. Logically, nestin staining, which marks the presence of NPCs, would developmentally precede β-tubulin III expression in an area. Compared to staining in mock-infected organoids, staining for β-tubulin III within the true-cortical structures of the virus-infected organoids was frequently reduced or absent (
Fig. 6A). Neuronal projections in virus-infected organoids, marked by β-tubulin III in the outer laminated layer (
Fig. 6A, arrows), were only intermittently and weakly stained compared to staining in mock-infected organoids. The only three true-cortical structures found among the nine virus-infected organoids stained for these markers displayed three different staining patterns. The first (
Fig. 6A, third row) displayed decreased levels of both proteins, with no characteristic cytoplasmic nestin staining visible. Fortuitously, we were able to capture images of the same structure for both H&E and marker analyses (
Fig. 4B, frame i). H&E analysis revealed an architecturally altered structure containing vacuoles throughout and a mass of necrotic cells within the ventricle. The necrotic cells may be indicative of virus-induced death of NPCs. The absence of specific cytoplasmic nestin staining could be a result of HCMV-induced downregulation of nestin expression, as we have reported previously (
45). In the second true-cortical structure, only nestin, which marks NPCs, was observed (
Fig. 6A, fourth row). This suggests delayed development within this structure such that postmitotic neurons were either not yet formed or not yet expressing β-tubulin III. In the last true-cortical structure (
Fig. 6A, bottom row), both nestin and β-tubulin III were present, indicating a progression in differentiation to postmitotic neurons; however, projections were not as frequent as in the mock-infected controls and were often aberrant in appearance. Several studies done in two-dimensional (2D) culture systems reported the inability of infected NPCs to properly differentiate down a neural pathway (
27,
31,
32,
34) and that infected neurons had defective neurite outgrowth (
31,
56) and degeneration of β-tubulin III signal integrity in their processes (
31,
56). Our studies substantiate these findings.
We were unable to compare the depths of β-tubulin III layers in true-cortical structures between mock-infected and virus-infected organoids due to an insufficient sample size found among the virus-infected organoids. To better understand the relationship between the depth of β-tubulin III layers and development, we compared the depths between cortical developmental sites and true-cortical structures in mock-infected controls. The statistically significant decrease in the inner-layer depth in true-cortical structures might seem counterintuitive. However, two explanations seem plausible in the context of development. First, as cortical structures continue to develop, the underlying layers may become more compact as they become more organized, with the cell bodies more architecturally aligned. Second, as the cerebral cortex develops, more mature neurons migrate out from the ventricular zones and into the laminated exterior. True-cortical structures in the mock-infected organoids had higher cell densities in the exterior of the structures, with fewer cells localized directly next to the scaffold (
Fig. 4A, frames iii and v). The decrease in inner-layer depth may indicate the outward migration of these cells. We look forward to exploring these developmental processes more thoroughly in our future studies.
In the future we hope to use this highly tractable organoid system to study the effects of infection at later times during development. We plan to expand to different clinical isolates, especially those derived from congenitally infected infants, and different iPSC lines, looking more closely at neural marker patterning as the organoids grow. We intend to carefully characterize the nature of the cell death observed and the cellular constituents that compose the honeycomb-tissue. Taking cues from our earlier studies with NPC infection (
45) and the recent work of Cosset and colleagues (
35), who examined changes to transcriptional profiles after infection of engineered neural tissue anchored on hydrophilic membranes, we will also ask questions regarding the fate of organoid development in the absence of particular cellular proteins (absent infection). Our results have demonstrated parallels between the pathologies present in clinical specimens and the 3D organoid system. We plan to extend our studies and hope that others can exploit this system to examine informative avenues surrounding the mechanisms responsible for HCMV-induced birth defects.
MATERIALS AND METHODS
Cells and virus used.
Two iPSC cell lines (SC27 and SC30) were obtained from our colleague, Phil Schwartz. Cells were grown as single cells in feeder-free monolayers in StemPro human ES cell (hESC) serum- and feeder-free (SFM) medium (Life Technologies) with basic FGF (bFGF) (final concentration, 20 ng/ml; Prospec) as described in Stover et al. (
57). The same neonatal tissue used in our previous nd-NPC studies (
25,
45,
46) was used to generate these iPSC lines. These lines were dedifferentiated according to standard lentivirus transduction protocols of either nd-NPC (SC27) or fibroblast (SC30) cultures as described previously (
57,
58).
The clinical isolate TR (for triple resistant; generously provided at passage 4 by Jay Nelson, Oregon Health and Science University [
47]) was used in these studies. TR was propagated for fewer than 4 additional passages on human foreskin fibroblasts (HFFs) as previously described (
59). To obtain high-titer TR stocks, viral supernatants were pelleted using high-speed ultracentrifugation through a 20% sucrose cushion. All TR stocks were tested to ensure maintenance of the clinical cassette of gene products as defined in Murphy et al. (
47). HFFs were used as a control for permissive infection and were cultured as previously described (
60).
Infection conditions.
SC27 and SC30 iPSCs were grown until confluent on six-well dishes coated with Matrigel. After cells reached confluence, wells were split 1:6 (seeding ∼2.5 × 105 cells/well) onto Matrigel-coated coverslips and allowed to settle overnight. Subconfluent cultures were then infected at an MOI of 5. In initial tests for susceptibility, coverslips were harvested at 5 and 24 h p.i. and stained for viral entry with Ab against either pp65 or pp71 tegument protein and for de novo protein synthesis with Ab against IE1. Subconfluent HFFs were infected as a control for permissive infection.
SC30 iPSCs used for infection and subsequent organoid development were split 1:6 as described above and plated onto either Matrigel-coated wells or wells containing glass coverslips. Cells were allowed to grow to confluence in these wells (∼1.5 × 106 cells/confluent well). After reaching confluence, cells were infected at an MOI of 5 and subjected to the organoid differentiation protocol described below. Cells infected on coverslips were carried through the same changes in medium components as described below for the differentiation protocol. These cells were monitored for the expression of viral Ags and the development of viral replication centers at the designated time points p.i. by immunofluorescence and phase-contrast microscopy. The differentiation on coverslips was performed on cultures infected at both subconfluent and confluent densities with very similar results.
iPSC/HFF coculture.
At day 14 days p.i. (day 13 postdifferentiation), iPSCs carried through the organoid differentiation protocol on coverslips were trypsinized and counted, and 500 cells were seeded per well of a 12-well dish containing subconfluent HFFs on coverslips. Coverslips were harvested at 5, 7, and 12 days postcoculturing. After fixation and permeabilization, cells were stained for the presence of viral Ag+ foci with Abs against IE1 and UL44.
iPSC coverslip immunofluorescence.
Coverslips were harvested at given time points p.i., rinsed with 1× phosphate-buffered saline (PBS), and fixed in 3% formaldehyde diluted in 2.5% sucrose–1× PBS at 37°C for 5 min. The cells were then washed three times with 1× PBS, permeabilized with 1% Triton in 2.5% sucrose–1× PBS–0.3 M glycine for 5 min at room temperature (RT), and quickly rinsed again with 1× PBS. Coverslips were blocked with 30% fetal bovine serum (FBS) in blocking solution 3 (1% bovine serum albumin [BSA], 0.05% Tween 20 in 1× PBS) for 30 min at RT in a humidity chamber. The cells were rinsed in 1× PBS and then incubated with primary Abs diluted in blocking solution 3 for 15 min. After thorough washing in 1× PBS, coverslips were incubated with secondary Abs diluted in blocking solution 3 for 15 min. The coverslips were rinsed again with 1× PBS and mounted in Vectashield antifade solution containing 4′,6′-diamidino-2-phenylindole (DAPI; Vector Laboratories). Epifluorescence analysis and imaging were performed on a Nikon Eclipse E800 fluorescence microscope equipped with a Nikon DS-Ri1 camera and Nikon Elements software. Figures were prepared using Adobe Photoshop and Illustrator software.
Culturing cerebral organoids.
Organoid culturing was performed as described in Lancaster and Knoblich (
40), with minor modifications. iPSCs were maintained in monolayer, single-cell culture as described above in Stempro hESC SFM containing 20 ng/ml bFGF. Confluent monolayers were infected as described above. At 24 hpi, cells were lifted, counted, and seeded to begin embryoid body (EB) formation with 9,000 cells per well with low-bFGF (4 ng/ml) and rho-associated coiled-coil protein kinase (ROCK) inhibitor. After 4 days, bFGF and ROCK inhibitor was removed. Neural induction, Matrigel embedding, and transfer to differentiation medium without vitamin A were performed as described previously (
40). After an additional 4 days, vitamin A was added. One week later, the organoids were placed onto an orbital rotator to circulate the medium. At 52 days after seeding to form EBs, organoids were harvested.
Organoid size measurements.
Stereoscopic images of all mock- and virus-infected organoids were captured at ×4 magnification after fixation. Using the Nikon Elements-BR software polygon area tool, the approximately circular circumference of the tissue of each organoid was traced to generate an area measurement in pixels, which was subsequently converted to millimeters. Sizes of individual organoids were graphed using GraphPad Prism software, with the color of each symbol corresponding to the developmental score assigned in
Table 1.
Organoid fixation, embedding, and sectioning.
Organoids were fixed in 4% paraformaldehyde diluted in 1× PBS at 4°C for 20 min and then washed three times at room temperature (RT) with 1× PBS. Organoids were then sunk in 30% sucrose diluted in 1× PBS at 4°C. Note that organoids could be preserved at this stage via flash freezing in liquid nitrogen and subsequent storage at −80°C. After sucrose treatment, the organoids were submerged in a 1:1 mixture of optimum cutting temperature (OCT) embedding material–30% sucrose and placed on an orbital rotator at RT for 30 min. Organoids were then embedded in pure OCT, flash frozen in liquid nitrogen, serially sectioned on a cryotome to 14-μm sections, and mounted on positively charged microscope slides. Sections were stored at −20°C until further processing was required.
Hematoxylin and eosin staining and analysis.
The histopathologies of mock- and HCMV-infected organoids were evaluated as described below. The first, middle, and last slides of serially sectioned organoids (encompassing an average of 27 sections) were thawed at RT and rinsed in 1× PBS for 1 min. The slides were then carried through a standard H&E staining protocol. Coverslips were affixed with Permount. Images of each H&E-stained section were captured on a Nikon Eclipse E800 microscope equipped with a Nikon DS-Ri1 camera and Nikon Elements software using a 4× objective. Image captures were used for quantitative morphometric analysis of organoid histopathology. Larger organoids were imaged using multiple overlapping fields. These images were stitched together using the tiling function of Adobe Photoshop to obtain single-image montages for analysis. Two independent investigators scored the deidentified images and arrived at essentially identical rankings. In addition to the 4× images, higher-magnification images (20 to 60×) were also used to analyze H&E-stained sections for pathological changes, including evidence and magnitude of cell death, degree of structural/architectural organization, and cellular morphology throughout the organoid. The depths of lamination in both cortical development sites and true-cortical structures were noted. The thickness and continuity of the cortical structure scaffold were examined. Additional assessment criteria included the abundance of neurons and support cells throughout the organoid, the presence and size of vacuolations and cysts, and the level of death and disorganization of cells adjacent to cortical structures. From our observations, we assigned scores ranging from + to ++++ to each organoid. Scores corresponded to very poor/no significant development (+), poor development (++), modest development (+++), and normal development (++++) (
Table 1). Positive indications of development increased scores more than negative pathologies reduced scores.
Organoid immunofluorescence.
Glass slides with organoid serial sections were thawed at RT. The slides were rinsed in 1× PBS for 5 min and then permeabilized with 1% Triton X-100 in 0.3 M glycine–1× PBS for 5 min at RT and rinsed in 1× PBS. All subsequent incubations were performed in a humidity chamber at RT. Blocking solution 1 was added (30% FBS, 0.2% Triton X-100, 0.3 M glycine in 1× PBS) for 1 h. Slides were washed for 10 min with 1× PBS, after which they were incubated in primary Ab diluted in blocking solution 2 (1% BSA, 0.05% Tween 20, 0.2% Triton X-100 in 1× PBS) for 90 min and then washed twice for 10 min with 1× PBS. Slides were then incubated in secondary Ab and Hoechst (to visualize nuclei), also diluted in blocking solution 2, for 90 min. Three final 10-min washes in 1× PBS were performed prior to mounting in Vectashield antifade solution containing DAPI. Epifluorescence analysis, image capture, and figure preparation were performed as described above.
Detection of viral IE1 in organoids utilized whole-organoid staining. Staining was performed as described above for organoid sections, with the following differences: incubation in both primary and secondary Abs for 6 days at 4°C, with longer washes after each Ab incubation (3 times for 30 min in 1× PBS at RT). Whole organoids were then processed for sectioning as described above. For analysis, sections were thawed, blocked as described above, then incubated with Hoechst diluted in blocking solution 2 for 30 min, washed, and mounted as described above. For confocal analysis, organoids were imaged on a Nikon Andor spinning-disk confocal microscope using a Xyla sCMOS camera. Image capture and preparation were performed using Imaris software.
Antibodies.
Primary Abs included the following: anti-β-tubulin III (IgG2B) (T8660; Sigma), anti-nestin (IgG1) (MAB5326; Millipore), anti-IE1 and MCP (IgG2A; both kind gifts from Bill Britt), anti-pp65 and -UL44 (IgG1) (clones CH12 and CH13, respectively; Virusys), anti-pp71 (IgG1) (clone IE233, a kind gift from Rob Kalejta), and rabbit anti-Oct4 (GTX101497; Genetex). Secondary Abs used were the following: goat anti-mouse IgG1 and IgG2A Alex Fluor 488-coupled Abs (Molecular Probes), goat anti-mouse IgG1, IgG2A, and IgG2B tetramethyl rhodamine isothiocyanate (TRITC)-coupled Abs (Southern Biotech), goat anti-rabbit Alex Fluor 488-coupled Ab (Molecular Probes), and donkey anti-rabbit TRITC-coupled Ab (Jackson Laboratory).
Cortical development site/structure lamination and β-tubulin III+ inner-layer depth analyses.
Organoid sections were stained for the neuron- and NPC-specific markers β-tubulin III and nestin, respectively (
51–53). Immunofluorescent images (×20 magnification) of cortical development sites and true-cortical structures were captured and then imported into ImageJ. Images were analyzed for two parameters using the line segment tool (
Fig. 5B and
6A, brackets). First, the depth of the outer lamination layer was measured, as defined by the outside edge of the cortical development sites and true-cortical structures to the outermost edge of the β-tubulin III
+ neurons. In essence, this was a measure of the depth of projections of β-tubulin III toward the outer surface. Nestin staining was used to help define the interior edge of this lamination/projection outer layer. Second, the depth of the strongly staining β-tubulin III interior layer, indicative of neuron cell bodies, was measured. For consistency within a given organoid, depth measurements were taken along regions of the structure where continuous β-tubulin III staining was observed. At least five separate measurements along the lamination layers of the structure/site were used to generate an average depth in pixels. Pixel depth was then converted to micrometers using the parameters of the camera/objective used. Average depth measurements for a given site were used for statistical analysis. Six sites representing four different mock-infected organoids and seven sites representing four different virus-infected organoids were used for cortical development site analysis. Nine structures from three different mock-infected organoids were used for true-cortical structure analysis. Because only one structure in one virus-infected organoid stained positively for both β-tubulin III and nestin, statistically relevant true-cortical structure layer comparisons could not be performed between mock- and virus-infected organoids.
Statistical analyses.
An unpaired, two-tailed Student t test assuming unequal variance and using Welch’s correction was performed for all statistical analyses.