A Bioconductor workflow for processing, evaluating, and interpreting expression proteomics data.

Background: Expression proteomics involves the global evaluation of protein abundances within a system. In turn, differential expression analysis can be used to investigate changes in protein abundance upon perturbation to such a system. Methods: Here, we provide a workflow for the processing, analysis and interpretation of quantitative mass spectrometry-based expression proteomics data. This workflow utilizes open-source R software packages from the Bioconductor project and guides users end-to-end and step-by-step through every stage of the analyses. As a use-case we generated expression proteomics data from HEK293 cells with and without a treatment. Of note, the experiment included cellular proteins labelled using tandem mass tag (TMT) technology and secreted proteins quantified using label-free quantitation (LFQ). Results: The workflow explains the software infrastructure before focusing on data import, pre-processing and quality control. This is done individually for TMT and LFQ datasets. The application of statistical differential expression analysis is demonstrated, followed by interpretation via gene ontology enrichment analysis. Conclusions: A comprehensive workflow for the processing, analysis and interpretation of expression proteomics is presented. The workflow is a valuable resource for the proteomics community and specifically beginners who are at least familiar with R who wish to understand and make data-driven decisions with regards to their analyses.

How does the polymer architecture and position of cationic charges affect cell viability?

Polymer chemistry, composition and molar mass are factors that are known to affect cytotoxicity, however the influence of polymer architecture has not been investigated systematically. In this study the influence of the position of the cationic charges along the polymer chain on cytotoxicity was investigated while keeping constant the other polymer characteristics. Specifically, copolymers of various architectures, based on a cationic pH responsive monomer, 2-(dimethylamino)ethyl methacrylate (DMAEMA) and a non-ionic hydrophilic monomer, oligo(ethylene glycol)methyl ether methacrylate (OEGMA) were engineered and their toxicity towards a panel of cell lines investigated. Of the seven different polymer architectures examined, the block-like structures were less cytotoxic than statistical or gradient/tapered architectures. These findings will assist in developing future vectors for nucleic acid delivery.

Clinical Potential of Nerve Input to Tumors: A Bioelectricity Perspective.

We support the notion that the neural connections of the tumor microenvironment (TME) and the associated 'bioelectricity' play significant role in the pathophysiology of cancer. In several cancers, the nerve input promotes the cancer process. While straightforward surgical denervation of tumors, therefore, could improve prognosis, resulting side effects of such a procedure would be unpredictable and irreversible. On the other hand, tumor innervation can be manipulated effectively for therapeutic purposes by alternative novel approaches broadly termed "electroceuticals." In this perspective, we evaluate the clinical potential of targeting the TME first through manipulation of the nerve input itself and second by application of electric fields directly to the tumor. The former encompasses several different biophysical and biochemical approaches. These include implantable devices, nanoparticles, and electroactive polymers, as well as optogenetics and chemogenetics. As regard bioelectrical manipulation of the tumor itself, the "tumor-treating field" technique, applied to gliomas commonly in combination with chemotherapy, is evaluated. Also, as electroceuticals, drugs acting on ion channels and neurotransmitter receptors are highlighted for completeness. It is concluded, first, that electroceuticals comprise a broad range of biomedical tools. Second, such electroceuticals present significant clinical potential for exploiting the neural component of the TME as a strategy against cancer. Finally, the inherent bioelectric characteristics of tumors themselves are also amenable to complementary approaches. Collectively, these represent an evolving, dynamic field and further progress and applications can be expected to follow both conceptually and technically.

Nerve input to tumours: Pathophysiological consequences of a dynamic relationship.

It is well known that tumours arising in different organs are innervated and that 'perineural invasion' (cancer cells escaping from the tumour by following the nerve trunk) is a negative prognostic factor. More surprisingly, increasing evidence suggests that the nerves can provide active inputs to tumours and there is two-way communication between nerves and cancer cells within the tumour microenvironment. Cells of the immune system also interact with the nerves and cancer cells. Thus, the nerve connections can exert significant control over cancer progression and modulating these (physically or chemically) can affect significantly the cancer process. Nerve inputs to tumours are derived mainly from the sympathetic (adrenergic) and the parasympathetic (cholinergic) systems, which are interactive. An important component of the latter is the vagus nerve, the largest of the cranial nerves. Here, we present a two-part review of the nerve inputs to tumours and their effects on tumorigenesis. First, we review briefly some relevant general issues including ultrastructural aspects, stemness, interactions between neurones and primary tumours, and communication between neurones and metastasizing tumour cells. Ultrastructural characteristics include synaptic vesicles, tumour microtubes and gap junctions enabling formation of cellular networks. Second, we evaluate the pathophysiology of the nerve input to five major carcinomas: cancers of prostate, stomach, colon, lung and pancreas. For each cancer, we present (i) the nerve inputs normally present in the cancer organ and (ii) how these interact and influence the cancer process. The best clinical evidence for the role of nerves in promoting tumorigenesis comes from prostate cancer patients where metastatic progression has been shown to be suppressed significantly in cases of spinal cord injury. The balance of the sympathetic and parasympathetic contributions to early versus late tumorigenesis varies amongst the different cancers. Different branches of the vagus provide functional inputs to several of the carcinomas and, in two-way interaction with the sympathetic nervous system, affect different stages of the cancer process. Overall, the impact of the vagus nerve can be 'direct' or 'indirect'. Directly, the effect of the vagus is primarily to promote tumorigenesis and this is mediated through cholinergic receptor mechanisms. Indirectly, pro- and anti-tumour effects can occur by stimulation or inhibition of the sympathetic nervous system, respectively. Less well understood are the 'indirect' anti-tumour effect of the vagus nerve via immunomodulation/inflammation, and the role of sensory innervation. A frequent occurrence in the nerve-tumour interactions is the presence of positive feedback driven by agents like nerve growth factor. We conclude that the nerve inputs to tumours can actively and dynamically impact upon cancer progression and are open to clinical exploitation.