Research Opportunities

Understanding the role of transposable elements as gene regulators is important, because they make up 50% of the genome, but are relatively understudied in comparison to genes which make up 2% of the genome. In our lab, we take on the exciting challenge of understanding the role of locus-specific Transposable elements as regulators of gene expression in development by studying the activity of transposable elements in single cells using our unique method CELLO-seq using long read sequencing. 

In this PhD project, you will learn a diverse set of techniques (CRISPR, embryonic stem cell cultures, third generation sequencing technologies and in-depth quantitative analysis) and work together with others in an team comprised of molecular biologists, developmental biologists, biochemists, and data scientists.  We will teach you how to perform high-quality science and design your own experiments to develop your own project and make use of the training you received. This research, carried out together with collaborators at the University of Oxford, the University of Edinburgh, and elsewhere, should lead to new discoveries and insights that inform our quantitative understanding of locus-specific transposable elements as new regulators of gene expression in development. These discoveries will advance this novel exciting field while contributing to the next generation of single cell long read methods.   

Asthma is a common, complex, and chronic disease that is characterized by inflammation of the airways, airway hyperresponsiveness, and bronchospasms. It has major health disparities, and unfortunately populations that bear the greatest burden of disease are minimally represented in genomics research. The Consortium on Asthma among African-ancestry Populations in the Americas (CAAPA) seeks to discover genes and mechanisms conferring risk to asthma in populations of African ancestry, utilizing multi-omic data. A multi-omics approach in nasal epithelium using RNASeq and DNA methylation in CAAPA led to the confirmation of well-known T2 mechanisms in asthma risk, but also identified novel wound healing and medication response signatures, providing new information about the biological mechanisms underlying asthma in the underrepresented African ancestry populations. We have a greatly expanded opportunity including serum proteomics, RNASeq on PBMCs, and additional DNA methylation to test if an expanded systems biology / integrative omics approach can further refine axes of dysregulation in CAAPA and develop models to predict asthma endotypes that are derived off ‘local’ and ‘systemic’ signatures of asthma pertaining to the nasal epithelium and serum/PBMCs, respectively. 

Germline genomes are immortal. Their genetic information is transmitted to the next generation and ensures that continuation of life. To protect the integrity of their genomic information, germ cells employ a specialized small RNA-based defense system, PIWI-interacting small RNAs (piRNAs) and their PIWI protein partners. The interest of the Karam Teixera lab in germ cell biology and evolution and the focus of the Haase lab on mechanisms of small silencing RNAs converge on piRNA-guided surveillance of genome integrity. The collaborative project of an NIH OxCam Scholar is designed to combine strength of both labs in genetics, biochemistry and genomics, and offers training in experimental techniques and basic computational analyses of next-generation sequencing data. Results from this graduate study will further our understanding of how germ cells ensure genome integrity and the survival of future generations.

Many pathogens can infect a wide range of potential hosts. Understanding the factors that control pathogen host range is critical for understanding host-pathogen biology and for identifying potential reservoirs of disease. A major determinant of a pathogen’s host range is the compatibility between the pathogen’s effectors and key host proteins, such as host receptors required for infection or host immune proteins whose function the pathogen specifically neutralizes. We are developing and utilizing a new approach to systematically explore which animals carry host proteins that are susceptible to particular pathogen effectors. For a known targeted host protein, we identify thousands of homologs from across the space of sequenced genomes, and then synthesize the surface of the homologs bound by the effector and test whether the effector can bind them.

This project will involve selecting an important human pathogen, such as malaria, HIV, plague, or any other pathogen of interest to the student, and applying our systematic approach to determining its potential host range. We are also interested in exploring other applications of this novel approach, such as testing a single host protein against a range of pathogen effectors to determine the space of potential future pathogens. Please get in touch if you have ideas anywhere in this space!

Persistent inflammation is a pathogenic determinant in many common human diseases, including rheumatoid arthritis, Crohn’s disease, multiple sclerosis, and psoriasis, while playing a key role in the development of type-2 diabetes, obesity, certain forms of cancer, and neurodegenerative conditions such as Parkinson’s and Alzheimer’s diseases. The laboratory of Dr. Blackshear has identified tristetraprolin (TTP) as a protein that acts to restrict inflammation in mice by destabilising the mRNA of pro-inflammatory cytokines such as TNF, GM-CSF, CXCL1 and CXCL2. Mice where an instability-conferring element within TTP’s own mRNA was deleted using homologous recombination were remarkably resistant to inflammatory disease. Most importantly, these mice did not exhibit any pathology, presumably because of the relatively modest over-expression of TTP that was otherwise subject to normal regulation.  

However, studies of TTP’s biochemical and molecular activities have been hampered by the existence of three other members of the same protein family in the mouse.  Each of these proteins exhibits similar biochemical activities in cell transfection experiments and in cell-free assays, but knockout mice of each have led to dramatically different phenotypes, involving early development, hematopoiesis, and placental function rather than inflammation.  For this reason, we will use the fruit-fly Drosophila melanogaster, which expresses only a single TTP family member, known as TIS11. Using genetics, biochemistry, transcriptomics, and proteomics we will explore the role of TIS11 and extrapolate findings to experiments in mammalian systems at NIEHS.

Population genomic approaches across diverse species have traditionally used short read sequence data to investigate population structure and signatures of selection. In the recent past, long reads are more traditionally used to build reference genomes to which the short read data can be aligned and evaluated. However, the cost of long read sequencing as well as the DNA input required to generate high quality long read data is dropping rapidly. We foresee a future where population genomics transitions to long read data.

Using these emerging technologies, this project will begin to evaluate what new insights are gained for the Anopheles gambiae species complex, a set of mosquito species famous as the vector of malaria and known to exhibit porous species boundaries and abundant structural variation.  We anticipate that long-read approaches for haplotype phasing and structural variant discovery will enable much clearer resolution of gene flow within species, introgression between species, and alleles under directional or balancing selection.  Insights gained from this project are likely to influence approaches taken for other species that are known to have similar complexities (e.g., Heliconius butterflies, African cichlid fishes).

This project will involve developing and applying new computational methods for analysing long-read sequencing data in an Anopheles population genomics context. The collaborating laboratories at the Sanger Institute and NHGRI are experts in these respective areas and well-suited to provide the appropriate mentorship.

Genome-wide association studies (GWAS) aim to identify the genetic basis of phenotypic traits using the variation that exists within natural populations. Uniquely for infectious diseases, the inter-individual heterogeneity in disease phenotype is linked to both host and pathogen genetic variation. Traditionally, genetic studies of infectious diseases have sought to explain between-individual variation in disease phenotypes by assessing genetic factors separately in humans or pathogens, under the assumption that these factors are independent. Although reasonable for some variants, there is strong theoretical and empirical evidence that genetic interactions between host and viruses play a major role in viral disease aetiology.

In this project you will integrate host and viral genomic data from the same patients to better understand viral pathogenesis and between-individual heterogeneity in disease outcomes. By analysis of paired host-virus genomic data from well-characterised cohorts you will gain novel insights on (a) host polymorphisms linked with viral sequence variation, (b) virus sites under strong host genetic selective pressures, (c) host and virus genetic factors independently contributing to disease phenotypes and (d) host-virus genetic interactions contributing to disease phenotypes. The findings have the potential to: (I) revolutionize our understanding of host-virus interactions and human biology; (II) aid in development of more effective vaccines, drug targets and immunotherapies; and (III) permit better use of therapies through patient stratification. In the age of “Big Data” and “Personalised Medicine”, analysis of paired host-pathogen genomic data will become increasingly important to uncover the mechanisms driving pathogen adaptations and heterogeneity of infection outcomes.

Inhibitors of DNA repair have emerged as powerful agents in cancer therapy, either as monotherapies that exploit synthetic lethal interactions between DNA repair pathways, or by increasing the efficacy of chemo- and radiotherapies. Principal in this strategy is inhibition of Poly(ADP-ribose)-polymerases (PARPs), enzymes that regulate DNA strand break repair, and PARP inhibitors (PARPi) are being used to treat tumours with defects in homologous recombination (HR). However, this strategy is restricted to treating ovarian cancers, with limited information on why PARPi are toxic to HR-defective cells, or additional synthetic lethal interactions that will broaden their application to treat other tumours.

By combining our expertise in PARP biology and DNA repair (e.g. Ronson, et al. Nat Commun 9: 746) with cutting edge genome editing, proteomics and cell biology, this project will address this fundamentally important question by characterising novel cancer-related genes that are synthetic lethal with PARP dysfunction. Through a genome-wide CRISPR-Cas9 screen, we identified a novel gene (PASL9) that is synthetic lethal with PARPi. Our data indicate PASL9 is critical to resolve replication-associated DNA damage through a mechanism that is mutated in colorectal cancers. Through multidisciplinary hypothesis-driven research, this research will: a) Define the nature of synthetic lethality between PARPs and PASL9; b) Establish the repair mechanism regulated by PASL9; c) Assess PASL9 as a target to treat colorectal cancer. These studies will define the mechanistic basis of how PARPs and PASL9 maintain genome stability and define novel strategies to exploit PARPi to treat a variety of tumours.

Preeclampsia is a multi-system hypertensive disorder of pregnancy that is caused by placental dysfunction.  The placenta releases extracellular vesicles (EVs) into the maternal circulation from early pregnancy all the way to term as part of its normal function. These EVs have proteins on the surface and contain genetic cargo, capable of altering maternal cellular function. It is known that the release, protein and genetic content of EVs is altered in preeclampsia. We have optimised an ex-vivo placental perfusion technique that permits isolation of trophoblast EVs. We have isolated EVs from normal and preeclampsia subjected these to proteomic and sequencing analysis. It is apparent that there are significant differences in miRNA and other non-coding RNA between EVs from normal and PE placentae. These differences have been validated by RT-PCR. We now wish to investigate the downstream cellular effects of the miRNAs/non-coding sequences, in cell models (endothelial, hepatic etc.) using transfected HEK293 cells. KEK293 cells constitutively produce exosomes. The transfected HEK293 cell will produce exosomes enriched for the RNA species of interest and allow specific miRNA effects to be determined using deep sequencing and proteomics analyses of the target cell. Analysis will require the candidate to be trained in bioinformatics approaches.

Simultaneously, we will interrogate a cohort of clinical samples for circulating miRNAs and investigate their role as a potential biomarker of placental function/disease. The NDWRH sits within the Women’s Centre at the John Radcliffe hospital and delivers 8000 women per year. 

Maintaining genome integrity through DNA repair is critical for human health and defects in these pathways result in cancer, neurodegeneration and premature ageing. Understanding DNA repair mechanisms will provide insights into the underlying causes of these conditions and strategies for their treatment. For example, inhibitors of Poly(ADP-ribose) polymerases (PARPs), enzymes that regulate DNA strand break repair, are used to treat DNA repair deficient tumours, with the potential to treat other malignancies.

However, despite the use of PARP inhibitors in the clinic, the substrates modified by these enzymes and how they regulate DNA repair are ill-defined. For example, although histones are targets for ADP-ribosylation (ADPr) following DNA damage, how this regulates genome stability either directly, or through competition with other histone post-translational modifications (PTMs) is unclear.  This, in part, is due to the absence of an experimental platform in which PARPs and histone ADPr sites can be manipulated in tandem. These criteria are met in the eukaryotic model organism Dictyostelium and we have identified histone ADPr sites modified in response to DNA damage in this organism. We will exploit the unique ability to introduce site-specific ADPr mutations into endogenous Dictyostelium histone genes to define how ADPr regulates DNA repair either directly, or through influencing other histone PTMs. We will identify novel proteins that specifically interact with ADPr histones and characterise these factors in human cells. Together, this work will uncover how cells maintain genome integrity that will inform novel strategies to refine the use of PARP inhibitors in the clinic.

Germline genomes are immortal.  Their genetic information is transmitted to the next generation and ensures that continuation of life.  To protect the integrity of their genomic information, germ cells employ a specialized small RNA-based defense system, PIWI-interacting small RNAs (piRNAs) and their PIWI protein partners.  The interest of the Karam Teixera lab in germ cell biology and evolution and the focus of the Haase lab on mechanisms of small silencing RNAs converge on piRNA-guided surveillance of genome integrity. The collaborative project of an OxCam Scholar is designed to combine strength of both labs in genetics, biochemistry and genomics, and offers training in experimental techniques and basic computational analyses of next-generation sequencing data.  Results from this graduate study will further our understanding of how germ cells ensure genome integrity and the survival of future generations. 

It is well recognized that acquired genetic mutations are an important cause of cancer, but recent studies have suggested that such somatic mutations are also associated with atherosclerosis. Somatic mutations have been found in blood from 10% of people over 70 years of age and 20% of people over 90 years of age and appear associated with an increased risk of atherosclerotic disease. Although age is a known independent risk factor for atherosclerosis, the basis for this has not been known.  It now appears likely that these mutations, several of which are found in genes known to regulate inflammation and immunity, are either a direct contributor to, or a potential biomarker for, this age-associated risk. The challenge now is to identify molecular mechanisms linking these somatic mutations with atherosclerosis.

This PhD project will investigate the cellular and molecular basis of the association between age associated DNA mutations and atherosclerotic disease risk. To do this will require cross-disciplinary collaboration, so this project brings together two highly complementary groups to address this important new biomedical challenge. At the National Heart, Lung and Blood Institute of the NIH, Chris Hourigan works on these acquired mutations in the context of a blood cancer called acute myeloid leukemia. At Oxford, Chris O’Callaghan works on molecular mechanisms involved in atherosclerosis and the genetic control of those mechanisms, especially in vessel wall inflammation.

This is a very exciting new field and has potential to identify new drug targets and so benefit patients with atherosclerosis. The experience gained by this doctorate will be highly relevant to other fields and will include cellular and molecular biology, high throughput sequencing approaches including single cell approaches and analysis of genetic variation.

*This project is available for the 2021 Oxford-NIH Pilot Programme*