TAM kinases as regulators of cell death

Receptor Tyrosine Kinases are critical regulators of signal transduction that support cell survival, proliferation, and differentiation. Dysregulation of normal Receptor Tyrosine Kinase function by mutation or other activity-altering event can be oncogenic or can impact the transformed malignant cell so it becomes particularly resistant to stress challenge, have increased proliferation, become evasive to immune surveillance, and may be more prone to metastasis of the tumor to other organ sites. The TAM family of Receptor Tyrosine Kinases (TYRO3, AXL, MERTK) is emerging as important components of malignant cell survival in many cancers. The TAM kinases are important regulators of cellular homeostasis and proper cell differentiation in normal cells as receptors for their ligands GAS6 and Protein S. They also are critical to immune and inflammatory processes. In malignant cells, the TAM kinases can act as ligand independent co-receptors to mutant Receptor Tyrosine Kinases and in some cases (e.g. FLT3-ITD mutant) are required for their function. They also have a role in immune checkpoint surveillance. At the time of this review, the Covid-19 pandemic poses a global threat to world health. TAM kinases play an important role in host response to many viruses and it is suggested the TAM kinases may be important in aspects of Covid-19 biology. This review will cover the TAM kinases and their role in these processes.     

MicroRNAs as regulators of cell death mechanisms in amyotrophic lateral sclerosis

Amyotrophic lateral sclerosis (ALS) is a progressive neurodegenerative disorder affecting upper and lower motor neurons (MNs), resulting in paralysis and precocious death from respiratory failure. Although the causes of ALS are incompletely understood, the role of alterations in RNA metabolism seems central. MicroRNAs (miRNAs) are noncoding RNAs implicated in the regulation of gene expression of many relevant physiological processes, including cell death. The recent model of programmed cell death (PCD) encompasses different mechanisms, from apoptosis to regulated necrosis (RN), in particular necroptosis. Both apoptosis and necroptosis play a significant role in the progressive death of MNs in ALS. In this review, we present key research related to miRNAs that modulate apoptosis and RN pathways in ALS. We also discuss whether these miRNAs represent potential targets for therapeutic development in patients.     

Mutational analysis of the interacting cell death regulators CED-9 and CED-4

The genes ced-3, ced-4 and ced-9 are central components in the cell death pathway of the nematode C. elegans. Ced-9, which functions to inhibit cell death, is homologous to the Bcl-2 family of mammalian anti-apoptotic genes. The ced-3 gene encodes a protein homologous to the caspases, a family of cysteine proteases involved in the execution of programmed cell death. It has recently been demonstrated that CED-4, an inducer of apoptosis for which no mammalian equivalent has been reported, can interact with CED-9 and Bcl-x(L). Here we confirm that CED-9 and CED-4 interact and using a series of deletion mutants, demonstrate that only short N-terminal deletions are tolerated in each molecule without loss-of-interaction. Two loss-of-function point mutations in different regions of CED-4 also lead to a significant loss of interaction suggesting further that the relevant interaction domains are not short linear sequences, but rather, are formed by more complex structural determinants in each molecule. Furthermore, we demonstrate that CED-4 not only interacts with Bcl-x(L) but also with its homologue, Bcl-2, and that the unstructured loop region present in Bcl-x(L) and Bcl-2 can regulate the CED-4 interaction. Lastly, we show that a BH3 peptide that can inhibit Bcl-2 family interactions also inhibits the interaction between Bcl-x(L) and CED-4.     

Type-2 histone deacetylases as new regulators of elicitor-induced cell death in plants

? Plant resistance to pathogen attack is often associated with a localized programmed cell death called hypersensitive response (HR). How this cell death is controlled remains largely unknown. ? Upon treatment with cryptogein, an elicitor of tobacco defence and cell death, we identified NtHD2a and NtHD2b, two redundant isoforms of type-2 nuclear histone deacetylases (HDACs). These HDACs are phosphorylated after a few minutes' treatment, and their rate of mRNAs are rapidly and strongly reduced, leading to a 40-fold decrease after 10 h of treatment. ? By using HDAC inhibitors, RNAi- and overexpression-based approaches, we showed that HDACs, and especially NtHD2a/b, act as inhibitors of cryptogein-induced cell death. Moreover, in NtHD2a/b-silenced plants, infiltration with cryptogein led to HR-like symptoms in distal leaves. ? Taken together, these results show for the first time that type-2 HDACs, which are specific to plants, act as negative regulators of elicitor-induced cell death in tobacco (Nicotiana tabacum), suggesting that the HR is controlled by post-translational modifications including (de)acetylation of nuclear proteins.     

World of small RNAs: from ribozymes to siRNA and miRNA

RNAs, besides bridging genetic information to proteins, the major determinants of bio-structures and functions, serve as active regulators of gene expression. Initiated nearly 20 years ago with ribozymes (the small RNAs with catalytic activity providing fine tuning of gene expression and function, used as molecular scissors and tools for gene discovery), an era of more complex and coordinated gene regulation by small RNAs, siRNA, and miRNA has recently started. Simple nucleotide complementarity results in highly ordered and regulated events, such as assembly of RNA and proteins, resulting in gene silencing either by mRNA degradation or suppression of translation. This article reviews our contributions to the understanding of structure, the function of small RNAs, their use in biotechnology, and the understanding of phenotypes such as apoptosis, metastasis, and differentiation.     

Multiple mediators of plant programmed cell death: interplay of conserved cell death mechanisms and plant-specific regulators

Programmed cell death (PCD) is a process aimed at the removal of redundant, misplaced, or damaged cells and it is essential to the development and maintenance of multicellular organisms. In contrast to the relatively well-described cell death pathway in animals, often referred to as apoptosis, mechanisms and regulation of plant PCD are still ill-defined. Several morphological and biochemical similarities between apoptosis and plant PCD have been described, including DNA laddering, caspase-like proteolytic activity, and cytochrome c release from mitochondria. Reactive oxygen species (ROS) have emerged as important signals in the activation of plant PCD. In addition, several plant hormones may exert their respective effects on plant PCD through the regulation of ROS accumulation. The possible plant PCD regulators discussed in this review are integrated in a model that combines plant-specific regulators with mechanisms functionally conserved between animals and plants.     

Akt and Bcl-x_L are independent regulators of the mitochondrial cell death pathways

Akt and Bcl-xL both promote resistance to apoptosis. A comparison of Akt- and Bcl-xL-dependent cell survival was undertaken. Expression of constitutively active Akt allows cells to survive for prolonged periods in the absence of growth factors. This survival correlates with the expression level of activated Akt and is comparable in magnitude to the protection provided by the anti-apoptotic gene Bcl-xL. Although both genes prevent cell death, Akt-protected cells can be distinguished from Bcl-xL-protected cells on the basis of increased glucose transporter expression, glycolytic activity, mitochondrial potential, and cell size. In addition, Akt-expressing cells require high levels of extracellular nutrients to support cell survival. In     

Oxidative nerve cell death in Alzheimer's disease and stroke: antioxidants as neuroprotective compounds

Many neurodegenerative disorders and syndromes are associated with an excessive generation of reactive oxygen species (ROS) and oxidative stress. The pathways to nerve cell death induced by diverse potential neurotoxins such as peptides, excitatory amino acids, cytokines or synthetic drugs commonly share oxidative downstream processes, which can cause either an acute oxidative destruction or activate secondary events leading to apoptosis. The pathophysiological role of ROS has been intensively studied in in vitro and in vivo models of chronic neurodegenerative diseases such as Alzheimer's disease (AD) and of syndromes associated with rapid nerve cell loss as occuring in stroke. In AD, oxidative neuronal cell dysfunction and cell death caused by protofibrils and aggregates of the AD-associated amyloid beta protein (Abeta) may causally contribute to pathogenesis and progression. ROS and reactive nitrogen species also take part in the complex cascade of events and the detrimental effects occuring during ischemia and reperfusion in stroke. Direct antioxidants such as chain-breaking free radical scavengers can prevent oxidative nerve cell death. Although there is ample experimental evidence demonstrating neuroprotective activities of direct antioxidants in vitro, the clinical evidence for antioxidant compounds to act as protective drugs is relatively scarce. Here, the neuroprotective potential of antioxidant phenolic structures including alpha-tocopherol (vitamin E) and 17beta-estradiol (estrogen) in vitro is summarized. In addition, the antioxidant and cytoprotective activities of lipophilic tyrosine- and tryptophan-containing structures are discussed. Finally, an outlook is given on the neuroprotective potential of aromatic amines and imines, which may comprise novel lead structures for antioxidant drug design.     

Caspases as regulators of apoptosis and other cell functions

This review covers current knowledge on the involvement in apoptosis of a new family of endopeptidases denoted as caspases. Their structure, specific substrates, and inhibitors are considered. The recent classification of cysteine proteases of the caspase family based on their structural and functional features is presented. The biological significance of caspases not related to their proapoptotic effect is discussed.     

c-Myc-deficient B lymphocytes are resistant to spontaneous and induced cell death

C-myc gene is a member of the myc family of proto-oncogenes involved in proliferation, differentiation, and apoptosis. Overexpression of c-myc in fibroblasts causes apoptosis under low serum conditions in a process that requires the interaction of CD95 and CD95L on the surface. We have previously reported an in vivo conditional model to inactivate the c-myc gene in B lymphocytes. Here, we show that c-Myc-deficient primary B lymphocytes are resistant to different apoptotic stimuli. Nonactivated c-Myc-deficient B cells are resistant to spontaneous cell death. Upon activation, c-Myc-deficient B lymphocytes express normal surface levels of activation markers, and show resistance to staurosporine and CD95-induced cell death.     

Quantitative proteomic analysis and functional studies reveal that nucleophosmin is involved in cell death in glioblastoma cell line transfected with siRNA

Previously, we reported that nucleophosmin (NPM) was increased in glioblastoma multiforme (GBM). NPM is a phosphoprotein related to apoptosis, ribosome biogenesis, mitosis, and DNA repair, but details about its function remain unclear. We treated U87MG and A172 cells with small interference RNA (siRNA) and obtained a reduction of 80% in NPM1 expression. Knockdown at the protein level was evident after the 4th day and was maintained until the 7th day of transfection that was investigated by quantitative proteomic analysis using isobaric tags. The comparison of proteomic analysis of NPM1-siRNA against controls allowed the identification of 14 proteins, two proteins showed increase and 12 presented a reduction of expression levels. Gene ontology assigned most of the hypoexpressed proteins to apoptosis regulation, including GRP78. NPM1 silencing did not impair cell proliferation until the 7th day after transfection, but sensitized U87MG cells to temozolomide (TMZ), culminating with an increase in cell death and provoking at a later period a reduction of colony formation. In a large data set of GBM patients, both GRP78 and NPM1 genes were upregulated and presented a tendency to shorter overall survival time. In conclusion, NPM proved to participate in the apoptotic process, sensitizing TMZ-treated U87MG and A172 cells to cell death, and in association with upregulation of GRP78 may be helpful as a predictive factor of poor prognosis in GBM patients.     

The Bcl-2 family of proteins: regulators of cell death and survival

The Bcl-2 protein inhibits apoptosis induced by a variety of signals, in a range of cell types and in diverse organisms, and it is implicated in both normal development and oncogenesis. Despite this central role, the mechanism of action of Bcl-2 is not yet clear. Recent studies have uncovered a number of Bcl-2-related gene products that regulate apoptosis either negatively or positively, and Bcl-2 forms heterodimers with at least one of these proteins, Bax. This article discusses the role of the Bcl-2 family of proteins in the light of these findings.