CometChip: A High-throughput 96-Well Platform for Measuring DNA Damage in Microarrayed Human Cells

DNA damaging agents can promote aging, disease and cancer and they are ubiquitous in the environment and produced within human cells as normal cellular metabolites. Ironically, at high doses DNA damaging agents are also used to treat cancer. The ability to quantify DNA damage responses is thus critical in the public health, pharmaceutical and clinical domains. Here, we describe a novel platform that exploits microfabrication techniques to pattern cells in a fixed microarray The ‘CometChip’ is based upon the well-established single cell gel electrophoresis assay (a.k.a. the comet assay), which estimates the level of DNA damage by evaluating the extent of DNA migration through a matrix in an electrical field. The type of damage measured by this assay includes abasic sites, crosslinks, and strand breaks. Instead of being randomly dispersed in agarose in the traditional assay, cells are captured into an agarose microwell array by gravity. The platform also expands from the size of a standard microscope slide to a 96-well format, enabling parallel processing. Here we describe the protocols of using the chip to evaluate DNA damage caused by known genotoxic agents and the cellular repair response followed after exposure. Through the integration of biological and engineering principles, this method potentiates robust and sensitive measurements of DNA damage in human cells and provides the necessary throughput for genotoxicity testing, drug development, epidemiological studies and clinical assays.National Institute of Environmental Health Sciences (Training Grant in Environmental Toxicology T32-ES007020)Massachusetts Institute of Technology. Center for Environmental Health Sciences (P30-ES002109)National Institute of Environmental Health Sciences (5-UO1-ES016045)National Institute of Environmental Health Sciences (1-R21-ES019498)National Institute of Environmental Health Sciences (R44-ES021116

Inter-group cooperation in humans and other animals

Social interactions are often characterised by cooperation within groups and conflict or competition between groups. In certain circumstances, however, cooperation can arise between social groups. Here we examine the circumstances under which inter-group cooperation is expected to emerge and present examples with particular focus on groups in two well-studied but dissimilar taxa: humans and social insects. Drivers for the evolution of inter-group cooperation include overarching threats from predators, competitors or adverse conditions, and group-level resource asymmetries. Resources can differ between groups in both quantity and type. Where the difference is in type, inequalities can lead to specialisation and division of labour between groups, a phenomenon characteristic of human societies, but rarely seen in other animals. The ability to identify members of one’s own group is essential for social coherence; we consider the proximate roles of identity effects in shaping inter-group cooperation and allowing membership of multiple groups. Finally, we identify numerous valuable avenues for future research that will improve our understanding of the processes shaping inter-group cooperation

Evolutionary Hypotheses and Moral Skepticism

Proponents of evolutionary debunking arguments aim to show that certain genealogical explanations of our moral faculties, if true, undermine our claim to moral knowledge. Criticisms of these arguments generally take the debunker’s genealogical explanation for granted. The task of the anti-debunker is thought to be that of reconciling the (supposed) truth of this hypothesis with moral knowledge. In this paper, I shift the critical focus instead to the debunker’s empirical hypothesis and argue that the skeptical strength of an evolutionary debunking argument is dependent upon the evidence for that hypothesis—evidence which, upon further inspection, proves far from compelling. Following that, however, I suggest that the same considerations which spell trouble for the empirical hypotheses of traditional debunking arguments can also be taken to give rise to an alternative—and better supported—style of debunking argument

The Gut Microbiome Shapes the Tumor Microenvironment by Tuning Innate Immunity

Immune checkpoint blockade has revolutionized cancer treatment but has only benefited a subset of patients. Among the variables that could contribute to interpatient heterogeneity is differential composition of the patients’ microbiome, which has been shown to affect anti-tumor immunity and immunotherapy efficacy in preclinical mouse models. We began by investigating whether there is an association between response to anti-PD-1 therapy and the composition of the gut microbiome (Chapter 3). We analyzed baseline stool samples from metastatic melanoma patients before immunotherapy treatment through an integration of 16S ribosomal RNA gene sequencing, metagenomic shotgun sequencing, and quantitative polymerase chain reaction for selected bacteria. A significant association was observed between commensal microbial composition and clinical response. Reconstitution of germ-free mice with fecal material from responding patients could lead to improved tumor control, augmented T cell responses, and greater efficacy of anti-PD-L1 therapy. These results suggest that the commensal microbiome may have a mechanistic impact on anti-tumor immunity in human cancer patients. Next, we explored the cellular mechanisms responsible for variable responses to cancer immunotherapy using mice stably colonized by patient commensals (Chapter 4). We rigorously evaluated the tumor immune infiltrate in representative responder and non-responder models using single cell gene expression, flow cytometry and functional tests to identify the source of resistance to immune checkpoint blockade. We found that variable tumor control with anti-PD-L1 was CD8+ T cell-dependent, and likely stemmed from distinct activation states of myeloid cells within the tumor microenvironment. Collectively, these results illustrate how the gut microbiome can impact the tumor microenvironment by tuning innate immunity and offer direction for future studies investigating the link between commensal bacteria and immunotherapy efficacy in patients

CometChip: A High-throughput 96-Well Platform for Measuring DNA Damage in Microarrayed Human Cells

DNA damaging agents can promote aging, disease and cancer and they are ubiquitous in the environment and produced within human cells as normal cellular metabolites. Ironically, at high doses DNA damaging agents are also used to treat cancer. The ability to quantify DNA damage responses is thus critical in the public health, pharmaceutical and clinical domains. Here, we describe a novel platform that exploits microfabrication techniques to pattern cells in a fixed microarray The ‘CometChip’ is based upon the well-established single cell gel electrophoresis assay (a.k.a. the comet assay), which estimates the level of DNA damage by evaluating the extent of DNA migration through a matrix in an electrical field. The type of damage measured by this assay includes abasic sites, crosslinks, and strand breaks. Instead of being randomly dispersed in agarose in the traditional assay, cells are captured into an agarose microwell array by gravity. The platform also expands from the size of a standard microscope slide to a 96-well format, enabling parallel processing. Here we describe the protocols of using the chip to evaluate DNA damage caused by known genotoxic agents and the cellular repair response followed after exposure. Through the integration of biological and engineering principles, this method potentiates robust and sensitive measurements of DNA damage in human cells and provides the necessary throughput for genotoxicity testing, drug development, epidemiological studies and clinical assays.National Institute of Environmental Health Sciences (Training Grant in Environmental Toxicology T32-ES007020)Massachusetts Institute of Technology. Center for Environmental Health Sciences (P30-ES002109)National Institute of Environmental Health Sciences (5-UO1-ES016045)National Institute of Environmental Health Sciences (1-R21-ES019498)National Institute of Environmental Health Sciences (R44-ES021116

CometChip enables parallel analysis of multiple DNA repair activities

DNA damage can be cytotoxic and mutagenic, and it is directly linked to aging, cancer, and other diseases. To counteract the deleterious effects of DNA damage, cells have evolved highly conserved DNA repair pathways. Many commonly used DNA repair assays are relatively low throughput and are limited to analysis of one protein or one pathway. Here, we have explored the capacity of the CometChip platform for parallel analysis of multiple DNA repair activities. Taking advantage of the versatility of the traditional comet assay and leveraging micropatterning techniques, the CometChip platform offers increased throughput and sensitivity compared to the traditional comet assay. By exposing cells to DNA damaging agents that create substrates of Base Excision Repair, Nucleotide Excision Repair, and Non-Homologous End Joining, we show that the CometChip is an effective method for assessing repair deficiencies in all three pathways. With these applications of the CometChip platform, we expand the utility of the comet assay for precise, high-throughput, parallel analysis of multiple DNA repair activities