Over the past decade, the Nomenclature Committee on Cell Death (NCCD) has formulated guidelines for the definition and interpretation of cell death from morphological, biochemical, and functional perspectives. Since the field continues to expand and novel mechanisms that orchestrate multiple cell death pathways are unveiled, we propose an updated classification of cell death subroutines focusing on mechanistic and essential (as opposed to correlative and dispensable) aspects of the process. As we provide molecularly oriented definitions of terms including intrinsic apoptosis, extrinsic apoptosis, mitochondrial permeability transition (MPT)-driven necrosis, necroptosis, ferroptosis, pyroptosis, parthanatos, entotic cell death, NETotic cell death, lysosome-dependent cell death, autophagy-dependent cell death, immunogenic cell death, cellular senescence, and mitotic catastrophe, we discuss the utility of neologisms that refer to highly specialized instances of these processes. The mission of the NCCD is to provide a widely accepted nomenclature on cell death in support of the continued development of the field.

https://biblio.ugent.be/publication/8555786/file/8555788.pdf

Molecular mechanisms of cell death: recommendations of the Nomenclature Committee on Cell Death 2018.

In 2009, the Nomenclature Committee on Cell Death (NCCD) proposed a set of recommendations for the definition of distinct cell death morphologies and for the appropriate use of cell death-related terminology, including 'apoptosis', 'necrosis' and 'mitotic catastrophe'. In view of the substantial progress in the biochemical and genetic exploration of cell death, time has come to switch from morphological to molecular definitions of cell death modalities. Here we propose a functional classification of cell death subroutines that applies to both in vitro and in vivo settings and includes extrinsic apoptosis, caspase-dependent or -independent intrinsic apoptosis, regulated necrosis, autophagic cell death and mitotic catastrophe. Moreover, we discuss the utility of expressions indicating additional cell death modalities. On the basis of the new, revised NCCD classification, cell death subroutines are defined by a series of precise, measurable biochemical features.

/pdf/molecular-definitions-of-cell-death-subroutines-q5g428rlyi.pdf

Molecular definitions of cell death subroutines: recommendations of the Nomenclature Committee on Cell Death 2012

Autophagy is a mechanism by which cellular material is delivered to lysosomes for degradation, leading to the basal turnover of cell components and providing energy and macromolecular precursors. Autophagy has opposing, context-dependent roles in cancer, and interventions to both stimulate and inhibit autophagy have been proposed as cancer therapies. This has led to the therapeutic targeting of autophagy in cancer to be sometimes viewed as controversial. In this Review, we suggest a way forwards for the effective targeting of autophagy by understanding the context-dependent roles of autophagy and by capitalizing on modern approaches to clinical trial design.

/pdf/targeting-autophagy-in-cancer-2pjcn0h04a.pdf

Targeting autophagy in cancer

How does the host sense pathogens? Our present concepts grew directly from longstanding efforts to understand infectious disease: how microbes harm the host, what molecules are sensed and, ultimately, the nature of the receptors that the host uses. The discovery of the host sensors — the Toll-like receptors — was rooted in chemical, biological and genetic analyses that centred on a bacterial poison, termed endotoxin.

Innate immune sensing and its roots: the story of endotoxin

Macroautophagy/autophagy is a conserved transport pathway where targeted structures are sequestered by phagophores, which mature into autophagosomes, and then delivered into lysosomes for degradati...

/pdf/chloroquine-inhibits-autophagic-flux-by-decreasing-29tresuftu.pdf

Chloroquine inhibits autophagic flux by decreasing autophagosome-lysosome fusion.

Principal component analysis was applied to two-dimensional (2-D) gel electrophoresis patterns, obtained in various phases of infection. Untreated controls could be satisfactorily differentiated from patterns after infection on days 3 and 7 whereas day 10 of infection was grouped with the controls. Comparison of host cellular protein patterns could help to classify in vivo developing infection without requiring any so-called immune marker functions. Immunoaffinity separation of infected cells treated with detergent, followed by 2-D electrophoresis of negative as well as positive eluates, did not reveal radiolabeled bacterial protein antigens.

Using two-dimensional gel electrophoresis to study immune response against intracellular bacterial infection.

Francisella tularensis is the causative agent of the potentially lethal disease tularemia. Due to a low infectious dose and ease of airborne transmission, Francisella is classified as a category A biological agent. Despite the possible risk to public health, there is no safe and fully licensed vaccine. A potential vaccine candidate, an attenuated live vaccine strain, does not fulfil the criteria for general use. In this review, we will summarize existing and new candidates for live attenuated and subunit vaccines.

Tularemia vaccines

In this study we examined the protein expression profiles in X-irradiated L929 cells to get insight into how mammalian cells respond to radiation-induced cell damage. L929 cells were irradiated with the dose of 6 Gy and cell lysates were collected at different time intervals (20 min, 12, 24, 36, 48 and 72 h). The extracted proteins were separated by 2-DE and quantified using computerized image analysis. Proteins exhibiting significant abundance alterations when comparing irradiated to unirradiated cells were identified by mass spectrometry. Using the proteomics approach we detected 47 proteins that exhibited a significant radiation-induced increase or decrease in the course of 72 h. From this group of spots 28 proteins were identified by mass spectrometry and of these 24 proteins exhibited minimally 2-fold differences in mean abundance values in comparison to controls. The identified proteins represent diverse sets of proteins participating either in protective and reparative cell responses or in induction of apoptosis and oncogenesis. The results document that proteomics is a useful method for unravelling the molecular mechanisms involved in cell reaction to ionizing radiation.

Proteomic analysis of radiation-induced alterations in L929 cells.

Francisella tularensis, a Gram-negative facultative intracellular bacterium, is a causative agent of zoonotic disease tularemia. It is also listed as a category A potential bioterrorism agent.1 As ...

https://www.tandfonline.com/doi/pdf/10.1080/21505594.2016.1278336

Francisella tularensis type VI secretion system comes of age

In-depth proteome discovery analysis represents new strategy in an effort to identify novel reliable specific protein markers for hypertrophic cardiomyopathy and other life threatening cardiovascular diseases. To systematically identify novel protein biomarkers of cardiovascular diseases with high mortality we employed an isobaric tag for relative and absolute quantitation (iTRAQ) proteome technology to make comparative analysis of plasma samples obtained from patients suffering from non-obstructive hypertrophic cardiomyopathy, stable dilated cardiomyopathy, aortic valve stenosis, chronic stable coronary artery disease and stable arterial hypertension. We found 128 plasma proteins whose abundances were uniquely regulated among the analyzed cardiovascular pathologies. 49 of them have not been described yet. Additionally, application of statistical exploratory analyses of the measured protein profiles indicated the relationship in pathophysiology of the examined cardiovascular pathologies.

/pdf/identification-of-novel-biomarker-candidates-for-5a5yxctf0y.pdf

Jiri Stulik

Papers

Using two-dimensional gel electrophoresis to study immune response against intracellular bacterial infection.

Tularemia vaccines

Proteomic analysis of radiation-induced alterations in L929 cells.

Francisella tularensis type VI secretion system comes of age

Identification of novel biomarker candidates for hypertrophic cardiomyopathy and other cardiovascular diseases leading to heart failure.