Noncoding RNAs in leprosy neuropathy?

Background

Leprosy is a chronic disease affecting the peripheral nerves, skin, eyes and upper respiratory tract caused by Mycobacterium leprae infection. One devastating consequence of leprosy is peripheral neuropathy, primarily caused by infection of Schwann cells, the glial cells of the peripheral nervous system. Although antibiotic treatment is increasingly curative, nerve damage is essentially irreversible and new cases are frequent, particularly in low/middle income countries (>200k new cases per year). Treatment is hindered because infections are often asymptomatic for 5-20 years. Despite its neglected nature, leprosy has considerable potential for contributing fundamentally to the broader fields of research on mycobacterial diseases, immunobiology, glial cell biology and neurodegenerative diseases.

M. leprae preferentially invades Schwann cells of adult peripheral nerves. The Rambukkana lab showed that when bacterial load is high M. leprae reprograms adult Schwann cells epigenetically, inducing a progenitor/stem cell–like cell with immunomodulatory properties. It is this remarkable reprogramming of a human cell type by a bacterium that we wish to study in this project. M. leprae is also remarkable in that >50% of its genome is devoid of protein-coding genes containing, instead, large numbers of non-coding pseudogenes many of which are transcribed. These long noncoding RNAs (lncRNAs) could participate in the pathogenesis of leprosy neuropathy. This could occur either directly (transcriptionally) if translocated to the host cell nucleus, or indirectly (post-transcriptionally) if competing for host cell microRNAs in the host cell cytoplasm. By using small RNA/microRNA sequencing analysis the Rambukkana lab has identified 6 short (15-30nt) M. leprae RNAs each present in the cytoplasm of Schwann cells after 2 weeks’ incubation with the bacterium.

The Ponting lab is investigating the molecular mechanisms of long and short noncoding RNAs. In separate projects, nuclear lncRNAs were found both to be transcribed in the vicinity of transcription factor genes and to be bound to their protein products, thereby modulating the transcription of target genes. Additionally, the group studies cytoplasmic lncRNAs that – through their binding of microRNAs – modulate the abundance of transcripts and proteins of mitochondrial complex I, thereby altering its enzymatic activity. The group has extensive experience in using computational approaches to identifying lncRNAs and microRNAs, and predicting their molecular mechanisms. This combined expertise in experimental and computational noncoding RNA biology, together with the longstanding expertise in M. leprae biology of the Rambukkana lab, forms the basis of this inter-disciplinary project in precision medicine.

Aims

What M. leprae and host RNAs contribute to the pathogenesis of nerve damage?

Our two groups’ preliminary data implicate transcribed M. leprae pseudogenes and short RNAs in modulating the levels of host mRNAs. The three stages of this PhD project are: (I) computational approaches predicting M. leprae long and short noncoding RNAs (based on M. leprae genome sequence) modulating Schwann cell function (Ponting lab); (II) experimental approaches to investigate these predictions (Rambukkana lab); and, (III) joint experimental and computational genomics approaches to determine the transcriptional or post-transcriptional responses of host Schwann cells from altering these M. leprae noncoding RNAs’ abundance (both labs). The initial computational stage will combine short and long RNA sequencing of M. leprae infected Schwann cells with detection of M. leprae short hairpin sequences. The middle experimental phase will test predicted interactions of M. leprae and host RNAs. In the final stage, deep bulk and single-cell transcriptomics will determine the cellular response to altering M. leprae ncRNA abundance.

Training Outcomes

The successful PhD student applicant will be trained in cutting-edge Quantitative Skills (computational omics, statistics, network analyses) applied to diverse data types, and Interdisciplinary Skills linking experimental (human and bacterial cellular and molecular biology; single cell biology; RNA biology; neurobiology) and computational approaches.

This MRC programme is joint between the Universities of Edinburgh and Glasgow. You will be registered at the host institution of the primary supervisor detailed in your project selection.

All applications should be made via the University of Edinburgh, irrespective of project location:

http://www.ed.ac.uk/studying/postgraduate/degrees/index.php?r=site/view&id=919

Please note you must apply to one of the projects and you are encouraged to contact the primary supervisor prior to making your application. Additional information on the application process if available from the link above.

For more information about Precision Medicine visit:

http://www.ed.ac.uk/usher/precision-medicine