APE1/Ref-1 knockdown in pancreatic ductal adenocarcinoma – characterizing gene expression changes and identifying novel pathways using single-cell RNA sequencing

Apurinic/apyrimidinic endonuclease 1/redox factor-1 (APE1/Ref-1 or APE1) is a multifunctional protein that regulates numerous transcription factors associated with cancer-related pathways. Because APE1 is essential for cell viability, generation of APE1-knockout cell lines and determining a comprehensive list of genes regulated by APE1 has not been possible. To circumvent this challenge, we utilized single-cell RNA sequencing to identify differentially expressed genes (DEGs) in relation to APE1 protein levels within the cell. Using a straightforward yet novel statistical design, we identified 2837 genes whose expression is significantly changed following APE1 knockdown. Using this gene expression profile, we identified multiple new pathways not previously linked to APE1, including the EIF2 signaling and mechanistic target of Rapamycin pathways and a number of mitochondrial-related pathways. We demonstrate that APE1 has an effect on modifying gene expression up to a threshold of APE1 expression, demonstrating that it is not necessary to completely knockout APE1 in cells to accurately study APE1 function. We validated the findings using a selection of the DEGs along with siRNA knockdown and qRT-PCR. Testing additional patient-derived pancreatic cancer cells reveals particular genes (ITGA1, TNFAIP2, COMMD7, RAB3D) that respond to APE1 knockdown similarly across all the cell lines. Furthermore, we verified that the redox function of APE1 was responsible for driving gene expression of mitochondrial genes such as PRDX5 and genes that are important for proliferation such as SIPA1 and RAB3D by treating with APE1 redox-specific inhibitor, APX3330. Our study identifies several novel genes and pathways affected by APE1, as well as tumor subtype specificity. These findings will allow for hypothesis-driven approaches to generate combination therapies using, for example, APE1 inhibitor APX3330 with other approved FDA drugs in an innovative manner for pancreatic and other cancer treatments

Primate social cognition: uniquely primate, uniquely social, or just unique?

Primates undoubtedly have impressive abilities in perceiving, recognising, understanding and interpreting other individuals, their ranks and relationships; they learn rapidly in social situations, employ both deceptive and cooperative tactics to manipulate companions, and distinguish others’ knowledge from ignorance. Some evidence suggests that great apes recognize the cognitive basis of manipulative tactics and have a deeper appreciation of intention and cooperation than monkeys; and only great apes among primates show any understanding of the concept of self. None of these abilities is unique to primates, however. We distinguish (1) a package of quantitative advantages in social sophistication, evident in several broad mammalian taxa, in which neocortical enlargement is associated with social group size; from (2) a qualitative difference in understanding found in several distantly related but large-brained species, including great apes, some corvids, and perhaps elephants, dolphins, and domestic dogs. Convergence of similar abilities in widely divergent taxa should enable their cognitive basis and evolutionary origins to be determined. Cortical enlargement seems to have been evolutionarily selected by social challenges, although it confers intellectual benefits in other domains also; most likely the mechanism is more efficient memory. The taxonomic distribution of qualitatively special social skills does not point to an evolutionary origin in social challenges, and may be more closely linked to a need to acquire novel ways of dealing with the physical world; but at present research on this question remains in its infancy. In the case of great apes, their ability to learn new manual routines by parsing action components may also account for their qualitatively different social skills, suggesting that any strict partition of physical and social cognition is likely to be misleading

Gaze following in an asocial reptile (Eublepharis macularius)

Gaze following is the ability to utilise information from another's gaze. It is most often seen in a social context or as a reflexive response to interesting external stimuli. Social species can potentially reveal utilisable knowledge about another's future intentions by attending to the target of their gaze. However, in even more fundamental situations, being sensitive to another's gaze can also be useful such as when it can facilitate greater foraging efficiency or lead to earlier predator detection. While gaze sensitivity has been shown to be prevalent in a number of social species, little is currently known about the potential for gaze following in asocial species. The current study investigated whether an asocial reptile, the leopard gecko (Eublepharis macularius), could reliably use the visual indicators of attention to follow the gaze of a conspecific around a barrier. We operated three trial conditions and found subjects (N = 6) responded significantly more to the conspecific demonstrator looking up at a laser stimulus projected onto an occluder during the experimental condition compared to either of two control conditions. The study's findings point toward growing evidence for gaze-following ability in reptiles, who are typically categorised as asocial. Furthermore, our findings support developing comparative social cognition research showing the origins of gaze following and other cognitive behaviours that may be more widely distributed across taxonomic groups than hitherto thought

Heterogeneous mass distribution of the rubble-pile asteroid (101955) Bennu

The gravity field of a small body provides insight into its internal mass distribution. We used two approaches to measure the gravity field of the rubble-pile asteroid (101955) Bennu: (i) tracking and modeling the spacecraft in orbit about the asteroid and (ii) tracking and modeling pebble-sized particles naturally ejected from Bennu’s surface into sustained orbits. These approaches yield statistically consistent results up to degree and order 3, with the particle-based field being statistically significant up to degree and order 9. Comparisons with a constant-density shape model show that Bennu has a heterogeneous mass distribution. These deviations can be modeled with lower densities at Bennu’s equatorial bulge and center. The lower-density equator is consistent with recent migration and redistribution of material. The lower-density center is consistent with a past period of rapid rotation, either from a previous Yarkovsky-O’Keefe-Radzievskii-Paddack cycle or arising during Bennu’s accretion following the disruption of its parent body

Why male orangutans do not kill infants

Infanticide is widespread among mammals, is particularly common in primates, and has been shown to be an adaptive male strategy under certain conditions. Although no infanticides in wild orangutans have been reported to date, several authors have suggested that infanticide has been an important selection pressure influencing orangutan behavior and the evolution of orangutan social systems. In this paper, we critically assess this suggestion. We begin by investigating whether wild orangutans have been studied for a sufficiently long period that we might reasonably expect to have detected infanticide if it occurs. We consider whether orangutan females exhibit counterstrategies typically employed by other mammalian females. We also assess the hypothesis that orangutan females form special bonds with particular “protector males” to guard against infanticide. Lastly, we discuss socioecological reasons why orangutan males may not benefit from infanticide. We conclude that there is limited evidence for female counterstrategies and little support for the protector male hypothesis. Aspects of orangutan paternity certainty, lactational amenorrhea, and ranging behavior may explain why infanticide is not a strategy regularly employed by orangutan males on Sumatra or Borneo

Male-Mediated Gene Flow in Patrilocal Primates

BACKGROUND: Many group-living species display strong sex biases in dispersal tendencies. However, gene flow mediated by apparently philopatric sex may still occur and potentially alters population structure. In our closest living evolutionary relatives, dispersal of adult males seems to be precluded by high levels of territoriality between males of different groups in chimpanzees, and has only been observed once in bonobos. Still, male-mediated gene flow might occur through rare events such as extra-group matings leading to extra-group paternity (EGP) and female secondary dispersal with offspring, but the extent of this gene flow has not yet been assessed. METHODOLOGY/PRINCIPAL FINDINGS: Using autosomal microsatellite genotyping of samples from multiple groups of wild western chimpanzees (Pan troglodytes verus) and bonobos (Pan paniscus), we found low genetic differentiation among groups for both males and females. Characterization of Y-chromosome microsatellites revealed levels of genetic differentiation between groups in bonobos almost as high as those reported previously in eastern chimpanzees, but lower levels of differentiation in western chimpanzees. By using simulations to evaluate the patterns of Y-chromosomal variation expected under realistic assumptions of group size, mutation rate and reproductive skew, we demonstrate that the observed presence of multiple and highly divergent Y-haplotypes within western chimpanzee and bonobo groups is best explained by successful male-mediated gene flow. CONCLUSIONS/SIGNIFICANCE: The similarity of inferred rates of male-mediated gene flow and published rates of EGP in western chimpanzees suggests this is the most likely mechanism of male-mediated gene flow in this subspecies. In bonobos more data are needed to refine the estimated rate of gene flow. Our findings suggest that dispersal patterns in these closely related species, and particularly for the chimpanzee subspecies, are more variable than previously appreciated. This is consistent with growing recognition of extensive behavioral variation in chimpanzees and bonobos

Great Apes and Biodiversity Offset Projects in Africa: The Case for National Offset Strategies

The development and private sectors are increasingly considering “biodiversity offsets” as a strategy to compensate for their negative impacts on biodiversity, including impacts on great apes and their habitats in Africa. In the absence of national offset policies in sub-Saharan Africa, offset design and implementation are guided by company internal standards, lending bank standards or international best practice principles. We examine four projects in Africa that are seeking to compensate for their negative impacts on great ape populations. Our assessment of these projects reveals that not all apply or implement best practices, and that there is little standardization in the methods used to measure losses and gains in species numbers. Even if they were to follow currently accepted best-practice principles, we find that these actions may still fail to contribute to conservation objectives over the long term. We advocate for an alternative approach in which biodiversity offset and compensation projects are designed and implemented as part of a National Offset Strategy that (1) takes into account the cumulative impacts of development in individual countries, (2) identifies priority offset sites, (3) promotes aggregated offsets, and (4) integrates biodiversity offset and compensation projects with national biodiversity conservation objectives. We also propose supplementary principles necessary for biodiversity offsets to contribute to great ape conservation in Africa. Caution should still be exercised, however, with regard to offsets until further field-based evidence of their effectiveness is available

On the Interplay Between Statistical Concepts and Computational Models in Omics Applications

Technological advancements have lead to the generation of enormous amounts of data. In order to capitalize on this trend, however, both computational and statistical challenges must be tackled. While computational efficiency is important, interpretability of models and algorithms are essential to ensuring the validity of any conclusions drawn. Nowhere is this more clear than in the case of biomedical data, where inferences drawn from large datasets are used to inform future directions of research, diagnose diseases, and generate leads for the development of new pharmaceuticals. This work examines the interplay between statistical concepts and computational models in three applications. Specifically, quantifying protein expression of fluorescent images, classifying somatic mutations in cancer, and combining p-values computed from genomic summary statistics. Across these applications, there are three recurring themes: accounting for technical and biological variation in data processing, evaluating the performance of a model in its end use case, and integrating results with outside data. Within these applications and themes, many statistical concepts are employed including Bayes theorem, and type I error rate control alongside computational models such a convolutional neural networks and Monte Carlo sampling algorithms. The results of these investigations inform much broader application areas such as biomedical imaging, modeling genomic sequences, and hypothesis testing in high-dimensions. Specific contributions in the application of Convolutional Neural Networks include demonstrating their ability to replicate the quantification of protein expression images from various manually-generated or deterministic label sets as well as the creation of a modeling framework for sequencing-based cancer diagnostics and the prioritization of unvalidated somatic mutations. In the area of hypothesis testing, novel algorithms are proposed that enable the use of a powerful and interpretable technique of combining p-values in the large-scale setting of genome-wide association studies