Receptor-interacting serine/threonine-protein kinase 1 (RIPK1) functions in a variety of cellular pathways related to both cell survival and death. In terms of cell death, RIPK1 plays a role in apoptosis, necroptosis, and PANoptosis Some of the cell survival pathways RIPK1 participates in include NF-κB, Akt, and JNK. [5]
RIPK1 is an enzyme that in humans is encoded by the RIPK1 gene, which is located on chromosome 6. [6] [7] [8] This protein belongs to the Receptor Interacting Protein (RIP) kinases family, which consists of 7 members, RIPK1 being the first member of the family. [9]
RIPK1 protein is composed of 671 amino acids, and has a molecular weight of about 76 kDa. It contains a serine/threonine kinase domain (KD) in the 300 aa N-Terminus, a death domain (DD) in the 112 aa C-Terminus, and a central region between the KD and DD called intermediate domain (ID).
.
Although, RIPK1 has been primarily studied in the context of TNFR signaling, RIPK1 is also activated in response to diverse stimuli. [13]
The kinase domain, while important for necroptotic (programmed necrotic) functions, appears dispensable for pro-survival roles. Kinase activity of RIPK1 is also required for RIPK1-dependent apoptosis in conditions of IAP1/2 depletion, RIPK3 depletion or MLKL depletion. [14] [15] Also, proteolytic processing of RIPK1, through both caspase-dependent and -independent mechanisms, triggers lethality that is dependent on the generation of one or more specific C-terminal cleavage product(s) of RIPk1 upon stress.
It has been shown that cell survival can be regulated through different RIPK1-mediated pathways that ultimately result in the expression of NF-kB, a protein complex known to regulate transcription of DNA and thus, related to survival processes. [16]
The most well-known pathway of NF-kB activation is that mediated by the death receptor TNFR1, which starts as in the necroptosis pathway with the assembly of TRADD, RIPK1, TRAF2 and clAP1 in the lipid rafts of the plasma membrane (complex I is formed). In survival signalling, RIPK1 is then polyubiquitinated, allowing NEMO (Necrosis Factor – kappa – B essential modulator) to bind to the IkB kinase or IKK complex. [17] To activate IKK, TAB2 and TAB3 adaptor proteins recruit TAK1 or MEKK3, which phosphorylate the complex. This results in the phosphorylation of the NF-kB inhibitors by the activated IKK complex, which in turn triggers their polyubiquitination and posterior degradation in the 26S proteasome.
As a result, NF-kB can now migrate to the nucleus where it will control DNA transcription by binding itself to the promoters of specific genes. Some of those genes are thought to have anti-apoptotic properties as well as to promote proteasomal degradation of RIPK1, resulting in a self-regulatory cycle.
While being in complex I, RIPK1 has also been proved to play a role in the activation of MAP (mitogen-activated protein) kinases such as JNK, ERK and p38. In particular, JNK can be found in both cell death and survival pathways, with its role in the cell death process being suppressed by activated NF-kB. [5]
Cell survival signalling can also be mediated by TLR-3 (toll-like receptors) and TLR-4. In here, RIPK1 is recruited to the receptors where it is phosphorylated and polyubiquitinated. This results in the recruit of the IKK complex activating proteins (TAK1, TAB1 and TAB2) so eventually NF-kB can now too migrate to the nucleus. RIPK2 is involved in this TLR-mediated signalling, which suggests that there might be a regulation of cell survival or death (the two possible outcomes) through the mutual interaction between the two RIPK family members. [5] [9]
Upon DNA damage, RIPK1 mediates another NF-kB activation pathway where two simultaneous and exclusive processes occur. A pro-apoptotic complex is created while RIPK1 also mediates the interaction between PIDD, NEMO and IKK subunits that will eventually result in the IKK complex activation after interaction with ATM kinase (a DNA double-strand breaks stimulated protein). The interaction between RIPK1 and PIDD through their death domains is thought to promote cell survival to neutralize this pro-apoptotic complex. [9]
It has been observed that RIPK1 may also interact with IGF-1R (insulin-like growth factor 1 receptor) to activate JNK (c-Jun N-terminal Kinases), it may be related to epidermal growth factor receptor signalling and it is largely expressed in glioblastoma cells, suggesting that RIPK1 is indeed involved in cell survival and proliferation processes. [5]
Necroptosis is a programmed form of necrosis which starts with the assembly of the TNF (tumor necrosis factor) ligand to its membrane receptor, the TNFR (tumor necrosis factor receptor). Once activated, the intracellular domain of TNFR starts the recruitment of the adaptor TNFR-1-associated death domain protein TRADD, which recruits RIPK1 and two ubiquitin ligases: TRAF2 and clAP1. This complex is called the TNFR-1 complex I. [18]
Complex-I is then modified by the IAPs (Inhibitor of Apoptosis Proteins) and the LUBAC (Linear Ubiquitination Assembly Complex), which generate linear ubiquitin linkages. The ubiquitination of complex-I leads to the activation of NF-κB, which in turn activates the expression of FLICE-like inhibitory protein FLIP. FLIP then binds to caspase-8, forming a caspase-8 FLIP heterodimer in the cytosol that disrupts the activity of caspase-8 and prevents caspase-8 mediated apoptosis from taking place. [19]
The assembly of complex II-b then starts in the cytosol. This new complex contains the caspase-8 FLIP heterodimer as well as RIPK1 and RIPK3. Caspase inhibition within this complex allows RIPK1 and RIPK3 to autotransphosphorylate each other, forming another complex called the necrosome. [20] The necrosome starts recruiting MLKL (Mixed Lineage Kinase Domain Like protein), which is phosphorylated by RIPK3 and immediately translocates to lipid rafts inside the plasma membrane. This leads to the formation of pores in the membrane, allowing the sodium influx to increase -and consequently the osmotic pressure-, which eventually causes cell membrane rupture. [20]
The apoptotic extrinsic pathway starts with the formation of the TNFR-1 complex-I, which contains TRADD, RIPK1, and two ubiquitin ligases:TRAF2 and clAP1. [21] [18]
Unlike the necroptotic pathway, this pathway doesn't include the inhibition of caspase-8. Thus, in absence of NF-κB function, FLIP is not produced, and therefore active caspase-8 assembles with FADD, RIPK1 and RIPK3 in the cytosol, forming what is known as complex IIa. [20]
Caspase-8 activates Bid, a protein that binds to the mitochondrial membrane, allowing the release of intermembrane mitochondrial molecules such as cytochrome c. Cytochrome c then assembles with Apaf 1 and ATP molecules, forming a complex called apoptosome. The activation of caspase 3 and 9 by the apoptosome starts a proteolitic cascade that eventually leads to the degradation of organelles and proteins, and the fragmentation of the DNA, inducing apoptotic cell death.
PANoptosis is a prominent innate immune, inflammatory, and lytic cell death pathway initiated by innate immune sensors and driven by caspases and receptor-interacting protein kinases (RIPKs) through PANoptosomes. [22] [23] PANoptosomes are multi-protein complexes assembled by germline-encoded pattern-recognition receptor(s) (PRRs) (innate immune sensor(s)) in response to pathogens, including bacterial, viral, and fungal infections, as well as pathogen-associated molecular patterns, damage-associated molecular patterns, cytokines, and homeostatic changes during infections, inflammatory conditions, and cancer. [24] [25] [26] [27] [28] [29] [30] [31] [32] [33] [34] [35] [36] [37] RIPK1 has been identified as a component of multiple PANoptosomes, including the ZBP1-PANoptosome and the AIM2-PANoptosome. Additionally, RIPK1 also drives the formation of the RIPK1-PANoptosome to induce PANoptosis in response to TAK1 inhibition. [38] [39] [40] TAK1 is a central regulator in cell death that prevents spontaneous NLRP3 inflammasome activation and PANoptosis in a RIPK1-dependent manner. [38] [39] [40] Additionally, the Gram-negative bacterium Yersinia produces YopJ, which inhibits TAK1, and Yersinia infection can trigger the activation of the RIPK1-PANoptosome. [40]
Patients with Alzheimer's disease, a neurodegenerative disease characterized by a cognitive deterioration and a behavioural disorder, experience a chronic brain inflammation which leads to the atrophy of several brain regions.
A sign of this inflammation is an increased number of microglia, a type of glial cells located in the brain and the spinal cord. RIPK1 is known to appear in larger quantities in brains from those affected with AD. [41] This enzyme regulates not only necroptosis, but cell inflammation as well, and as a result it is involved in the regulation of microglial functions, specially those associated with the appearance and development of neurodegenerative diseases such as AD. [41]
Amyotrophic Lateral Sclerosis (ALS) is characterized by the degeneration of motor neurons which leads to the progressive loss of mobility. Consequently, patients are unable to do any physical activity due to the atrophy of their muscles. [42]
The optineurin gene (OPTN) and its mutation are known to be involved in ALS. When the organism loses OPTN, the dysmyelination of axons and its degeneration start. The degeneration of the axons is produced by several components from the Central Nervous System (CNS) including RIPK1 and another enzyme from the Receptor Interacting Protein kinases family, RIPK3, as well as other proteins such as MLKL. [43]
Once RIPK1, RIPK3 and MLKL have contributed to the dysmyelination and the consequent degeneration of axons, the nerve impulse can't to go from one neuron to another due to the lack of myelin, which leads to the consequent mobility problems as the nerve impulse does not arrive to its final destination. [44]
RIPK1 plays a role in the activation of multiple sclerosis and its progression driving neuroinflammatory signaling in microglia And astrocytes. SAR443820 is an investigational RIPK1 inhibitor that may be useful in the management of multiple sclerosis. [45]
An autoinflammatory disease characterised by recurrent fevers and lymphadenopathy has been associated with mutations in this gene. [46]
CRIA syndrome (Cleavage-resistant RIPK1-induced autoinflammatory syndrome) is a disorder caused by specific mutations of the RIPK1 gene. Symptoms include "fevers, swollen lymph nodes, severe abdominal pain, gastrointestinal problems, headaches and, in some cases, abnormally enlarged spleen and liver". [47]
RIPK1 has been shown to interact with:
Tumor necrosis factor (TNF), formerly known as TNF-α, is a chemical messenger produced by the immune system that induces inflammation. TNF is produced primarily by activated macrophages, and induces inflammation by binding to its receptors on other cells. It is a member of the tumor necrosis factor superfamily, a family of transmembrane proteins that are cytokines, chemical messengers of the immune system. Excessive production of TNF plays a critical role in several inflammatory diseases, and TNF-blocking drugs are often employed to treat these diseases.
The p75 neurotrophin receptor (p75NTR) was first identified in 1973 as the low-affinity nerve growth factor receptor (LNGFR) before discovery that p75NTR bound other neurotrophins equally well as nerve growth factor. p75NTR is a neurotrophic factor receptor. Neurotrophic factor receptors bind Neurotrophins including Nerve growth factor, Neurotrophin-3, Brain-derived neurotrophic factor, and Neurotrophin-4. All neurotrophins bind to p75NTR. This also includes the immature pro-neurotrophin forms. Neurotrophic factor receptors, including p75NTR, are responsible for ensuring a proper density to target ratio of developing neurons, refining broader maps in development into precise connections. p75NTR is involved in pathways that promote neuronal survival and neuronal death.
FAS-associated death domain protein, also called MORT1, is encoded by the FADD gene on the 11q13.3 region of chromosome 11 in humans.
TRAF6 is a TRAF human protein.
TNF receptor-associated factor 2 is a protein that in humans is encoded by the TRAF2 gene.
Tumor necrosis factor receptor type 1-associated DEATH domain protein is a protein that in humans is encoded by the TRADD gene.
IKK-β also known as inhibitor of nuclear factor kappa-B kinase subunit beta is a protein that in humans is encoded by the IKBKB gene.
Death receptor 4 (DR4), also known as TRAIL receptor 1 (TRAILR1) and tumor necrosis factor receptor superfamily member 10A (TNFRSF10A), is a cell surface receptor of the TNF-receptor superfamily that binds TRAIL and mediates apoptosis.
TNF receptor-associated factor 1 is a protein that in humans is encoded by the TRAF1 gene.
TNF receptor-associated factor (TRAF3) is a protein that in humans is encoded by the TRAF3 gene.
Death receptor 5 (DR5), also known as TRAIL receptor 2 (TRAILR2) and tumor necrosis factor receptor superfamily member 10B (TNFRSF10B), is a cell surface receptor of the TNF-receptor superfamily that binds TRAIL and mediates apoptosis.
Receptor-interacting serine/threonine-protein kinase 2 is an enzyme that in humans is encoded by the RIPK2 gene.
Mitogen-activated protein kinase kinase kinase 14 (MAP3K14), also known as NF-kappa-B-inducing kinase (NIK), is a MAP kinase kinase kinase enzyme that in humans is encoded by the MAP3K14 gene.
Receptor-interacting serine/threonine-protein kinase 3 is an enzyme that is encoded by the RIPK3 gene in humans.
Z-DNA-binding protein 1, also known as DNA-dependent activator of IFN-regulatory factors (DAI) and DLM-1, is a protein that in humans is encoded by the ZBP1 gene.
The death domain (DD) is a protein interaction module composed of a bundle of six alpha-helices. DD is a subclass of protein motif known as the death fold and is related in sequence and structure to the death effector domain (DED) and the caspase recruitment domain (CARD), which work in similar pathways and show similar interaction properties. DD bind each other forming oligomers. Mammals have numerous and diverse DD-containing proteins. Within these proteins, the DD domains can be found in combination with other domains, including: CARDs, DEDs, ankyrin repeats, caspase-like folds, kinase domains, leucine zippers, leucine-rich repeats (LRR), TIR domains, and ZU5 domains.
NLRC5, short for NOD-like receptor family CARD domain containing 5, is an intracellular protein that plays a role in the immune system. NLRC5 is a pattern recognition receptor implicated in innate immunity to viruses potentially by regulating interferon activity. It also acts as an innate immune sensor to drive inflammatory cell death, PANoptosis. In humans, the NLRC5 protein is encoded by the NLRC5 gene. It has also been called NOD27, NOD4, and CLR16.1.
Necroptosis is a programmed form of necrosis, or inflammatory cell death. Conventionally, necrosis is associated with unprogrammed cell death resulting from cellular damage or infiltration by pathogens, in contrast to orderly, programmed cell death via apoptosis. The discovery of necroptosis showed that cells can execute necrosis in a programmed fashion and that apoptosis is not always the preferred form of cell death. Furthermore, the immunogenic nature of necroptosis favors its participation in certain circumstances, such as aiding in defence against pathogens by the immune system. Necroptosis is well defined as a viral defense mechanism, allowing the cell to undergo "cellular suicide" in a caspase-independent fashion in the presence of viral caspase inhibitors to restrict virus replication. In addition to being a response to disease, necroptosis has also been characterized as a component of inflammatory diseases such as Crohn's disease, pancreatitis, and myocardial infarction.
Vishva Mitra Dixit is a Kenyan-American physician who is currently Vice President and Senior Fellow of Physiological Chemistry and Research Biology at Genentech.
PANoptosis is a prominent innate immune, inflammatory, and lytic cell death pathway initiated by innate immune sensors and driven by caspases and receptor-interacting protein kinases (RIPKs) through multiprotein PANoptosome complexes. The assembly of the PANoptosome cell death complex occurs in response to germline-encoded pattern-recognition receptors (PRRs) sensing pathogens, including bacterial, viral, and fungal infections, as well as pathogen-associated molecular patterns, damage-associated molecular patterns, and cytokines that are released during infections, inflammatory conditions, and cancer. Several PANoptosome complexes, such as the ZBP1-, AIM2-, RIPK1-, and NLRC5- and NLRP12-PANoptosomes, have been characterized so far.