What makes us different from chimps

We sincerely thank all three reviewers for their constructive criticism and overall positive feedback, which has helped us a lot to improve our manuscript. We also would like to thank the Reviewing Editor for kindly preparing the summary and essence of the reviewers' comments. First, quantification of the length of prometaphase-metaphase in human and chimpanzee apical progenitors APs of day 52 D52 cerebral organoids Figure 5—figure supplement 2.

Interestingly, comparison with the day 30 D30 cerebral organoid data that were already included in the original version of our manuscripts reveals that human AP metaphase is shorter at D52 than D30 and not any more different in length from D52 chimpanzee APs. As the proportion of proliferative divisions of human APs would be expected to decrease, and the proportion of differentiative divisions to increase, from D30 to D52, these data are consistent with the concept that a longer metaphase reflects a greater tendency for proliferative than differentiative AP divisions.

Second, determination of AP cell cycle parameters by cumulative EdU labeling Figure 5—figure supplement 4. As a long S-phase has previously been shown to be a hallmark of proliferative as opposed to neurogenic AP divisions Arai et al. Yet, differences in cell cycle parameters between human and chimpanzee apical progenitors APs , especially at the relatively early stages of cortical development examined in the present study, could impact the extent of basal progenitor BP generation and hence SVZ formation.

Interestingly, this difference is essentially accounted for by a longer S-phase of human APs The difference between human and chimpanzee APs with regard to the progression of mitosis Figure 5 is in line with the longer S-phase finding, as the longer metaphase plate stage may similarly impact the mode of AP division and thus the fate of the AP progeny.

These differences in cell cycle and mitosis parameters between human and chimpanzee APs are consistent with the anticipated differences in cortical development between the two species, as is now discussed in greater detail in the revised manuscript Discussion, last paragraph. We agree with reviewer 1 that it is worth emphasizing the validity of the organoid system to study cortical development in different primates, as well as the technical advancement, and have done so in the Introduction last paragraph.

As to the issue of dissecting mitotic phases of TBR2 basal progenitors by live high-resolution time-lapse imaging: we could not analyze these cell divisions in numbers sufficient for quantification due to their lower abundance as compared to APs, as also pointed out by the reviewer.

These cell populations were therefore only analyzed by tissue immunofluorescence and RNA-seq Figures 1 — 2. We agree that a proteomics analysis of mitotic APs would be very interesting, but — as implied by the reviewer — is beyond the scope of the present study.

As mentioned in the legend to Figure 2 , 5 organoids per species were used at day 28 and 17 organoids per species were used at days B More details are needed to understand the variation within each specie. For sample numbers, please see response above. For further details, please see revised Methods. In line with this, we have preliminary data suggesting that cortical development in chimpanzee cerebral organoids proceeds slightly faster than in human cerebral organoids unpublished data.

However, these differences emerge only at later stages of organoid development and not at the stages included in the present study. Thus, the cortical regions compared between the two species were all positive for the deep-layer neuron marker Ctip2 Figure 1A,B and negative for the upper-layer neuron marker Satb2 at DD54, and they were all Ctip2-negative at D28, indicating that the human and chimpanzee cerebral organoids were at a comparable stage in their development at these two time points.

We therefore think that it would not be appropriate to normalize the time in culture for gestation length, at least not with regard to the relatively early stages of cortical development investigated in the present study.

It is difficult to precisely determine whether the organoid developmental clock parallels the in vivo clock. Qualitatively, we and others Lancaster et al. Nature ; Qian et al. Cell ; Pasca et al. Nature Methods have observed a general time-dependent progression of neurogenesis and transition to gliogenesis in human cerebral organoids prepared by various recently published protocols.

As to the issue how reliably that clock operates from culture to culture: We have analyzed human cerebral organoids from two independent iPSC lines and chimp cerebral organoids from two independent iPSC lines, and find that cortical development proceeds reproducibly from culture to culture.

The figure has been revised such that the error bars now appear in both directions. The quantification of the Pax6 Tbr2— cells at day Figure 2B , which yields a significantly lower value for chimpanzee than human, was performed across the entire cortical wall, i. This information has now been added to the Methods section. As requested by the reviewer, Figure 2A has been revised and now includes representative insets indicating Pax6 Tbr2 cells at higher magnification, which illustrate the greater proportion of Pax6 Tbr2 cells in chimpanzee than human.

Based on their location in the SVZ and their marker expression, the Pax6 Tbr2 cells are likely to be basal progenitors committed to neuron production and endowed with self-renewal capacity. We are aware that these two experiments 45d and 62d appear as outlier populations. Based on our previous single cell transcriptome analysis of human organoids Camp, Badsha et al. Instead it likely reflects the relative composition of cells and patterned regions of those particular organoids, and our limited sampling of cells per organoid.

The organoid protocol that we used Lancaster et al. All organoids analyzed in this study contained one or more stratified cortical-like regions surrounding a ventricle. These cortical-like regions are often patterned as dorsal telencephalon FOXG1 and OTX2- , however we have observed cortical regions that express ventral telencephalon or hindbrain markers Camp, Badsha et al.

For the 62d organoid, we observed one relatively large cortical-like region, which we microdissected and used for the scRNA-seq analysis. Based on the clustering pattern and marker gene expression, we concluded that cells from this 62d organoid were from a hindbrain-like region. In contrast, a different 61d organoid from the same batch contained many cerebral cortex cells, arguing against a developmental time-point phenomenon for the 62d organoid.

We have also observed an abundance of mesenchymal cells in some organoids, and have shown that these mesenchymal cells surround the periphery of cortical regions.

In the case of the 45d organoid, we captured many of these mesenchymal cells and, unfortunately, no cerebral cortex cells. It will be interesting to understand how the transcriptomes and genetic networks change as a function of age in human and chimpanzee cerebral organoids. However, we would need many more cells and time points to address this challenging question. The APs studied in Figures 4 and 5 are indeed Pax6 Tbr2— cells, because in line with the data shown in Figure 2B , virtually all mitotic figures at the ventricular surface are Pax6 Tbr2—.

It is therefore not necessary to use Pax6 and Tbr2 reporter plasmids. Moreover, mitosis at the apical, ventricular surface, as is the case for the dividing cells analyzed in Figures 4 and 5 , is the defining criterion of an AP.

Although the absolute length of prometaphase-metaphase of mouse APs is shorter than that of hominid APs, the chromosome dynamics e. Also, other mitotic phases prophase, telophase, see Figure 5—figure supplement 1 are essentially the same for mouse and hominid APs. Therefore, we believe that it is legitimate to relate the longer prometaphase-metaphase of proliferating than neurogenic mouse APs to the longer prometaphase-metaphase of human than chimpanzee APs.

Moreover, the shortening of metaphase of human APs with the progression of organoid cortical development from D30 to D52 Figure 5—figure supplement 2 , when proliferative AP divisions would be expected to decrease, is also consistent with the concept, derived from the dissection of mouse AP mitosis, that a longer metaphase reflects a greater tendency for proliferative than differentiative AP divisions. We have now further clarified this in the revised text Results.

However, in Figure 5—figure supplement 1 , no significant difference is shown. There appears to be a misunderstanding. Hence, the fact that the mouse prophase image was taken The length of prophase is essentially the same for mouse and hominid APs, as shown in Figure 5—figure supplement 1. To prevent such misunderstanding, we have now made this more clear in the figure legends. Rather, the longer S-phase of human APs We used the same set of genes as described in Camp, Badsha et al.

Specifically we used the top genes that correlated with PC1 from PCA on fetal cortex progenitor cells. This generally gave two clear groups of cells that either expressed the genes highly or had low expression of these genes. There were additional sub-clusters of cells that partially expressed the genes. This assignment was consistent with an unbiased assignment using the method published by Scialdone et al. We therefore excluded ambiguous cells and S-phase cells, which did not have a clear transcriptional signature in our experiment.

There are 10 genes that overlap between the genes highlighted in yellow in the top left quadrant of Figure 3E and the genes highlighted in Figure 8D. The most differentially expressed genes between human and chimpanzee APs, which are also specific to APs, are listed above.

It is possible that prometaphase-metaphase duration could be prolonged by over-expressing these genes in chimpanzee organoid.

Note that we have now specified these 10 genes in the text Results, last paragraph. It would be very interesting indeed to compare the various mitotic phases of human and chimpanzee basal progenitors by live high-resolution time-lapse imaging. However, as also pointed out by reviewer 1, the abundance of basal progenitors in the cerebral organoids is much lower than that of APs, and the numbers of basal progenitors in mitosis were not sufficient for a reliable quantitative comparison.

Our results, linking the longer prometaphase-metaphase of human than chimpanzee APs to proliferative AP divisions, may at first sight appear to be opposite to those of Pilaz et al. However, we would like to emphasize that the experimental system employed by Pilaz et al. The prometaphase-metaphase lengthening that we observed is a natural difference among three hominids and one rodent species, whereas Pilaz et al.

The perturbations by Pilaz et al. We have now clarified this issue in the revised text Discussion. Is there any evidence in the transcriptomic analyses of differences in genes controlling cell cycle re-entry? We agree with reviewer 3 that the 5-min lengthening of metaphase is unlikely to explain all of the difference between human and chimp in cerebral cortex growth during fetal development.

The issue raised by the reviewer in this context, i. Nat Comm and also by work from the Matsuzaki lab that has shown that a perfectly vertical AP cleavage plane can give rise to either AP or BP daughter cells. Therefore, the reviewer is entirely correct in suggesting that factors other than cleavage plane orientation also influence AP daughter cell fate. In fact, in line with the reviewer's suggestion, our observation that there are no significant differences in spindle orientation between human and chimp made us analyze other aspects of AP division, which led to the finding of the metaphase lengthening.

The embryoid bodies formed after the iPS cell dissociation and plating may vary in size due to the initial differential clumping of cells. However, thereafter, there is no overt difference between the two species in the size of the organoids formed after a similar period in culture.

In this context, we would like to point out that the lack of an overt difference in human vs. As to the issue of human vs. Also, there is no significantly greater abundance of cycling cells Ki67 cells in human as compared to chimpanzee cerebral organoid cortical regions Figure 2C,D , consistent with no major difference in NPC cell cycle re-entry between the two species.

Our data reveal that both types of differences are present. Compared to iPSCs, the length of prometaphase-metaphase is extended for both human and chimpanzee cerebral organoid APs Figure 6. This shows that a general lengthening of prometaphase-metaphase is caused by the transition from iPSCs to cerebral organoids.

However, the total length of prometaphase-metaphase is longer in human than in chimpanzee APs, indicating a species-specific difference Figure 5. In addition, when prometaphase and metaphase were analyzed individually, our data show that, while both human and chimpanzee APs show a lengthening of prometaphase as compared to iPSCs, only the human APs showed also a lengthening of metaphase Figure 6.

This constitutes a species-specific difference. Taken together these results show that the longer prometaphase-metaphase in human APs is due to a lengthening not only of prometaphase, as seen in the chimpanzee, but also of metaphase.

We agree with the reviewer that comparing organoids from other tissues would be interesting. However, this would require establishing other types of organoid systems in our lab to perform these complex and demanding experiments, and we think this would be out of the scope of the present study.

We agree with the reviewers that this is a very important point, and an interesting and challenging aspect of scRNA-seq data analysis, interpretation, and presentation. To perform differential gene expression analysis using the Bayesian approach developed by Karchenko et al. Therefore, we attempt to connect single cell transcriptome data with traditionally described cell types. In general, we do observe a continuum of transcriptome states across all cells, however we also find accumulations of cells that are similar with respect to the expression of groups of genes and steep transitions from such group of cells to other cells.

These cells likely represent a cellular state that is relatively more stable than the apparent intermediates. The genes similarly expressed within such a cell group generally correlate well with previously described cell type marker genes and we therefore think we have the resolution to discretely classify APs, BPs, and neurons. There are of course some cells that are in between the previous and next state on the continuum. These intermediate cells are relatively less abundant but we force them into a discrete cell type.

Since these cells are relatively rare and present in both human and chimpanzee, we do not think that we introduce a bias into the differential gene expression analysis by including these cells.

The funders had no role in study design, data collection and interpretation, or the decision to submit the work for publication. We thank Marta Florio for assistance with human tissue dissection.

SP was supported by the Paul G. Allen Family Foundation. Human subjects: Human fetal brain tissue weeks post conception wpc was obtained with informed written maternal consent followed by elective pregnancy termination. This article is distributed under the terms of the Creative Commons Attribution License , which permits unrestricted use and redistribution provided that the original author and source are credited.

Article citation count generated by polling the highest count across the following sources: Crossref , Scopus , PubMed Central. Phagocytosis requires rapid actin reorganization and spatially controlled force generation to ingest targets ranging from pathogens to apoptotic cells.

How actomyosin activity directs membrane extensions to engulf such diverse targets remains unclear. Here, we combine lattice light-sheet microscopy LLSM with microparticle traction force microscopy MP-TFM to quantify actin dynamics and subcellular forces during macrophage phagocytosis.

We show that spatially localized forces leading to target constriction are prominent during phagocytosis of antibody-opsonized targets. Contractile myosin-II activity contributes to late-stage phagocytic force generation and progression, supporting a specific role in phagocytic cup closure.

Observations of partial target eating attempts and sudden target release via a popping mechanism suggest that constriction may be critical for resolving complex in vivo target encounters. Overall, our findings present a phagocytic cup shaping mechanism that is distinct from cytoskeletal remodeling in 2D cell motility and may contribute to mechanosensing and phagocytic plasticity. Recently it was reported that UCH37 activity is stimulated by branched ubiquitin chain architectures.

To understand how UCH37 achieves its unique debranching specificity, we performed biochemical and NMR structural analyses and found that UCH37 is activated by contacts with the hydrophobic patches of both distal ubiquitins that emanate from a branched ubiquitin.

In addition, RPN13, which recruits UCH37 to the proteasome, further enhances branched-chain specificity by restricting linear ubiquitin chains from having access to the UCH37 active site. In cultured human cells under conditions of proteolytic stress, we show that substrate clearance by the proteasome is promoted by both binding and deubiquitination of branched polyubiquitin by UCH Proteasomes containing UCH37 C88A , which is catalytically inactive, aberrantly retain polyubiquitinated species as well as the RAD23B substrate shuttle factor, suggesting a defect in recycling of the proteasome.

These findings provide a foundation to understand how proteasome degradation of substrates modified by a unique ubiquitin chain architecture is aided by a DUB. Key processes of biological condensates are diffusion and material exchange with their environment.

Experimentally, diffusive dynamics are typically probed via fluorescent labels. However, to date, a physics-based, quantitative framework for the dynamics of labeled condensate components is lacking.

Here, we derive the corresponding dynamic equations, building on the physics of phase separation, and quantitatively validate the related framework via experiments. We show that by using our framework, we can precisely determine diffusion coefficients inside liquid condensates via a spatio-temporal analysis of fluorescence recovery after photobleaching FRAP experiments.

We showcase the accuracy and precision of our approach by considering space- and time-resolved data of protein condensates and two different polyelectrolyte-coacervate systems. Interestingly, our theory can also be used to determine a relationship between the diffusion coefficient in the dilute phase and the partition coefficient, without relying on fluorescence measurements in the dilute phase. This enables us to investigate the effect of salt addition on partitioning and bypasses recently described quenching artifacts in the dense phase.

Our approach opens new avenues for theoretically describing molecule dynamics in condensates, measuring concentrations based on the dynamics of fluorescence intensities, and quantifying rates of biochemical reactions in liquid condensates. Cited Views 43, Annotations Open annotations.

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Figure 7. Figure 8 with 1 supplement see all. The following data sets were generated. Borrell V Reillo I Emerging roles of neural stem cells in cerebral cortex development and evolution Developmental Neurobiology 72 — Florio M Huttner WB Neural progenitors, neurogenesis and the evolution of the neocortex Development — Get in Touch Book a Presentation. From the field. Great Apes.

Our Champions. Youth Power. Work With Us. In fact, chimps are more closely related to humans than they are to gorillas. But the similarities we share go beyond our genetic makeup.

Check out these 10 ways chimpanzees and humans are the same! There are of course many differences between the two species—we stand on two legs, have larger brains and are relatively hairless. Now a little bit of a disclaimer for those of us who work in this field: these cells have limitations. They are cells in culture. We cannot really look at social experience, and their relevance to a living organism is oftentimes questionable.

But we can ask the question: are there differences that are detectable at a cellular and molecular level that help us understand the origin of humans? We have begun building a library with other collaborators around the world, and have reprogrammed somatic cells from many of these species into iPS cells. They retain common features of embryonic stem cells at the cellular level and they have the same genetic makeup as predicted based on the species.

In our first attempt to see if we could identify differences in these primitive cells, we did what is called a complete transcriptional mRNA analysis. If we compare the transcriptional genomes of chimpanzees and bonobos, there are very few differences.

So we pooled all our animals together and compared that combined nonhuman primate group to the human group. In analyzing these genomes, we detected two very interesting genes. Why are we interested in these two proteins? These two proteins are active suppressors of the activity of what we call mobile elements, which are genetic elements that exist in all of our genomes.

In fact, 50 percent of the DNA in human genomes is made up of these mobile elements molecular parasites of the genome. So what are mobile elements? They are elements that exist in specific locations in the genome and, through unique mechanisms, they can make copies of themselves and jump from one part of the genome to another.

Barbara McClintock discovered these elements through her work on maize. Some of us study a specific form of mobile elements called a LINE-1 retrotransposon. They exist in thousands of copies in the genome, as a DNA that makes a strand of RNA and then makes proteins that binds back onto the RNA, helping the element copy itself. This combination of mRNA and proteins then moves back into the nucleus where the DNA resides and pastes itself into the genome at a new location.

These LINE elements continue to be active in our genome, and they are particularly active in neural progenitor cells. Not only do humans make more of these proteins, but as an apparent consequence, the lower levels of these L1 suppressors in chimpanzees and bonobos means the L1 elements are much more active in chimpanzees and bonobos than in humans. When searching the DNA libraries genomes that have been sequenced for chimps, bonobos, and humans, there are many more L1 DNA elements in the genomes of chimps and bonobos relative to humans.

This greater number of L1 elements in non-human primate genomes leads to an increase in DNA diversity and, thus, in the diversity of their offspring and potentially in their behavior. This led us to speculate that this decrease in genetic diversity that occurs in humans leads to a greater dependence on cultural adaptive changes to survive as a species rather than genetic adaptive changes. For example, if a virus were to infect a chimp or a bonobo population, in order for that species to survive it would require a member of the species with the genetic mutation that provided protection in some form from the virus.

Humans do not wait for the mutation from a member of the species that would provide protection from the virus. We build hospitals, we design antibodies, we transmit our knowledge through cultural information cultural evolution rather than relying on genetics genetic evolution for the spread and the survival of the species.

I n the s, my research group happened to discover the first known genetic difference between humans and chimpanzees.

And so I thought, well, they must be just like us. And, indeed, when I first looked at the major causes of death in adult captive chimpanzees, the number one killer was heart disease, heart attacks, and heart failure. Again, I thought, well, they are just like humans. But then when I started going over the textbook with the veterinarian, I noticed that not all the diseases were the same. So the question arises: are there human-specific diseases? There are a few criteria for human-specific diseases: they are very common in humans but rarely reported in great apes, even in captivity; and they cannot be experimentally reproduced in apes in the days when such studies were allowed.

The caveat, of course, is that reliable information is limited to data on a few thousand Great Apes in captivity. But these apes were cared for in NIH-funded facilities with full veterinary care — probably better medical care than most Americans get — and there were thorough necropsies. As it turned out, I was even wrong about heart disease. It was not until my spouse and collaborator Nissi Varki looked at the pathology that she realized that while heart disease is common in both humans and chimpanzees, it is caused by different pathological processes.

They developed massive scar tissue replacing their heart muscle, which is called interstitial myocardial fibrosis. There is now a special project called The Great Ape Heart Project, which is providing clinical, pathologic, and research strategies to aid in the understanding and treatment of cardiac disease in all of the ape species. There are actually two mysteries to be solved: why do humans not often suffer from the fibrotic heart disease that is so common in our closest evolutionary cousins?

Conversely, why do the Great Apes not often have the kind of heart disease that is common in humans? We put together a list of candidates of human-specific diseases that meet the criteria I mentioned earlier, and myocardial infarction is number one. Malignant malaria is number two. In studies done from the s to the s, people actually did horrible two-way cross-transfusions between chimpanzees and humans infected or not infected with malaria, and there was no evidence of cross-infection.

In fact, the parasites looked the same, but they were actually completely different. More modern work done by Francisco Ayala and others showed that, in fact, P. Pascal Gagneux and I wrote an article that explains what might have happened.

There are multiple forms of ape malaria that are mild throughout Africa. At some point, we escaped because of a change in the surface sialic acid molecule.

Another candidate for human-specific diseases is typhoid fever. More horrible studies were done in the s that showed that large doses of Salmonella typhi did not result in severe cases of typhoid fever in chimpanzees.

It can only bind to the human cell surface again, because of the sialic acid difference between the species. Another candidate is cholera, which is a major killer in humans. We then made experiments on monkeys, cats, poultry, dogs and various other animals. So, Vibrio cholerae does not induce diarrhea in adult animals other than in humans and many people are trying to figure out why.

There are many other candidates for human-specific diseases. Another difference is in carcinomas, cancers of epithelial origin.