Biology subjects

Mitchell, T. J.

Publications and source records attributed to Mitchell, T. J..

22 records · Page 2Linked to original sources

bioRxiv2019

Macrophages utilize mitochondrial fission to enhance mROS production during responses to Streptococcus pneumoniae

Immunometabolism and regulation of mitochondrial reactive oxygen species (mROS) are critical determinants of the immune effector phenotype of differentiated macrophages. Mitochondrial function requires dynamic fission and fusion, but whether effector function is associated with altered dynamics during bacterial responses is unknown. We show that macrophage mitochondria undergo fission after 12 h of progressive ingestion of live Streptococcus pneumoniae (pneumococci). Fission is associated with progressive reduction in oxidative phosphorylation but increased mROS generation. Fission is enhanced by mROS production, PI3K{gamma} signaling and by cathepsin B, but not by inflammasome activation or IL-1{beta} generation. Reduced fission following PI3K{gamma} or cathepsin B inhibition is associated with reduced mROS generation and bacterial killing. Fission is associated with Parkin recruitment to mitochondria, but not mitophagy. Fission occurs upstream of apoptosis induction and independently of caspase activation. During macrophage innate responses to live bacteria mitochondria shift from oxidative phosphorylation and ATP generation to mROS production and microbicidal responses with a progressive shift towards mitochondrial fission.

immunology↗

bioRxiv2019

3D-printed moulds of renal tumours for image-guided tissue sampling in the clinical setting

PURPOSESpatial heterogeneity of tumours is a major challenge in precision oncology. The relationship between molecular and imaging heterogeneity is still poorly understood, as it relies on the accurate co-registration of medical images and tissue biopsies. tumour moulds can guide the localization of biopsies, but their creation is time consuming, technologically challenging, and difficult to interface with routine clinical practice. These hurdles have so far hindered the progress in the area of multiscale integration of tumour heterogeneity data. METHODSWe have developed an open source computational framework to automatically produce patient-specific 3D-printed moulds that can be used in the clinical setting. Our approach achieves accurate co-registration of sampling location between tissue and imaging, and integrates seamlessly with clinical, imaging and pathology workflows. RESULTSWe applied our framework to patients with renal cancer undergoing radical nephrectomy. We created personalised moulds for five patients, obtaining Dice similarity coefficients between imaging and tissue sections ranging from 0.86 to 0.93 for tumour regions, and between 0.70 and 0.76 for healthy kidney. The framework required minimal manual intervention, producing the final mould design in just minutes, while automatically taking into account clinical considerations such as a preference for specific cutting planes. CONCLUSIONOur work provides a robust and automated interface between imaging and tissue samples, enabling the development of clinical studies to probe tumour heterogeneity on multiple spatial scales.

bioengineering↗

bioRxiv2018

Genomic landscape and chronological reconstruction of driver events in multiple myeloma

Multiple myeloma (MM) has a heterogeneous genome, evolving through both pre-clinical and post-diagnosis phases. Here, using sequences from 67 MM genomes serially collected from 30 patients together with public datasets, we establish a hierarchy of driver lesions. Point mutations, structural variants and copy number aberrations define at least 7 genomic subgroups of MM, each with distinct sets of co-operating driver mutations. Complex structural events are major drivers of MM, including chromothripsis, chromoplexy and a replication-based mechanism of templated insertions: these typically occur early. Hyperdiploidy also occurs early, with individual chromosomes often gained in more than one chronological epoch of MM evolution, showing a preferred order of acquisition. Positively selected point mutations frequently occur in later phases of disease development, as do structural variants involving MYC. Thus, initiating driver events of MM, drawn from a limited repertoire of structural and numerical chromosomal changes, shape preferred trajectories of subsequent evolution.

cancer biology↗

bioRxiv2017

The evolutionary history of 2,658 cancers

Cancer develops through a process of somatic evolution. Here, we use whole-genome sequencing of 2,778 tumour samples from 2,658 donors to reconstruct the life history, evolution of mutational processes, and driver mutation sequences of 39 cancer types. The early phases of oncogenesis are driven by point mutations in a small set of driver genes, often including biallelic inactivation of tumour suppressors. Early oncogenesis is also characterised by specific copy number gains, such as trisomy 7 in glioblastoma or isochromosome 17q in medulloblastoma. By contrast, increased genomic instability, a nearly four-fold diversification of driver genes, and an acceleration of point mutation processes are features of later stages. Copy-number alterations often occur in mitotic crises leading to simultaneous gains of multiple chromosomal segments. Timing analysis suggests that driver mutations often precede diagnosis by many years, and in some cases decades, providing a window of opportunity for early cancer detection.

cancer biology↗