Host-symbiont interactions - change labels 'modulation by symbiont of host defense response & children'

[pgaudet]

modulation = evasion evasion = avoidance suppression OK induction >> to be reviewed

[pgaudet]

@SIBVirus @genegodbold @ValWood @mgiglio99 @dsiegele

[mgiglio99]

Hi @pgaudet Is the proposal to change the word "modulation" to "evasion" in all the term labels in the 'modulation by symbiont of host defense response' node?

[genegodbold]

Hey @mgiglio99, I don't think that is correct. "Modulation" should be used in the parental term of which the children would be something like "suppression of..." and "enhancement of..." Example: "Modulation by symbiont of host cell antigen presentation" with the children being "Suppression by..." and "Enhancement by..." (Problem: I know of no symbiont that actually enhances host cell antigen presentation but there are plenty of viral and bacterial sequences that suppress that process.)

The "evasion" term covers a lot of ground relating to innate immune defenses. "Subversion" is probably narrower...maybe?

[pgaudet]

The proposal was to have

• evasion (instead of mitigation)
• • avoidance (instead of evasion)
• • suppression (unchanged)

because it seems like evasion is used in the literature for mechanisms that either 'avoid' host defenses (such as 'evasion by virus of DNA end degradation', 'antigenic variation', as well as for active suppression of host defense responses, for example 'modulation of host cytokine network' (which is currently named 'evasion of host immune response via modulation of host cytokine network' .

This book uses 'evasion' in that general sense: https://www.ncbi.nlm.nih.gov/books/NBK27176/

Thanks, Pascale

[pgaudet]

Also: https://www.sciencedirect.com/topics/agricultural-and-biological-sciences/immune-evasion

Immune Evasion

Immune evasion mechanisms include the promotion of antiapoptotic factors, loss of tumor antigen expression, secretion of local immunosuppressive factors in the tumor microenvironment (e.g., interleukin (IL)-10, transforming growth factor (TGF)-beta, vascular endothelial growth factor (VEGF), indoleamine 2,3-dioxygenase), potentiation of immunosuppressive lymphocytes such as T regulatory cells (Tregs), presence of inhibitory tumor-associated macrophages and myeloid-derived suppressor cells, and the expression of inhibitory molecules that are involved in checkpoint blockade.

[pgaudet]

https://asm.org/Articles/2018/December/Microbial-Ninja-Warriors-Bacterial-Immune-Evasion

Immune evasion strategies are those bacterial pathogens use to avoid or inactivate host defenses and ensure their own survival within a host.

[genegodbold]

I'm fine with using "evasion" as a synonym for "avoidance" and this seems to apply to stealth strategies employed by (say) bacteria that do best when they establish chronic infections, but when the parasite is inactivating/defeating/countering/subverting host defenses enzymatically that is NOT evasion (at least it doesn't seem like evasion to me). I've documented more than 500 examples of these active processes. I'll put in a diagram from our 2022 publication showing a few examples of Streptococcal strategies (https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9119117/). Note that the bacteria is employing nucleases to cut host NETs, proteases to destroy host-produced antimicrobial peptides, proteases to destroy host complement, host antibodies, and host chemokines and membrane-destabilizing enzymes to kill host neutrophils. This doesn't seem like a passive process to me. (Passive is when the parasite enzymatically alters some of its own molecules so they aren't recognized by host pattern recognition receptors.) Evasion applies even less to infections generated by such parasites as Bacillus anthracis and Yersinia pestis. In those cases, the bacterial parasite actively targets host immune cells, destroying or paralyzing them in the infected tissues (lungs and lymph nodes respectively). This is not avoidance, this is war.

[genegodbold]

[genegodbold]

Caption for above picture: Examples of immune subversion by streptococcal effectors. Host phagocytes are debilitated by streptolysin O (SLO) (70), streptolysin S (SLS) (294, 295), and secreted phospholipase A2 (Sla) (296). Neutrophil extracellular traps (NETs) are countered by the Sda1 and SpnA nucleases (264, 265). Antimicrobial peptides are inactivated by the secreted streptococcal inhibitor of complement (Sic) and SpeB proteases (200, 201). M-like proteins bind host factor H and plasminogen/plasmin, which inactivate host complement components to protect the bacterium (297). Sic protects streptococci from phagocytosis by neutrophils, resists the host complement membrane attack complex (MAC) (70), and counters the antibacterial actions of the host secretory leukocyte proteinase inhibitor (SLPI) (200, 201). Host antibodies are destroyed by membrane-associated ZmpC (226) and the secreted IdeS proteases (222) and inactivated by sugar-cleaving EndoS (223). The group B Streptococcus C5a peptidase ScpB is a serine protease and surface invasin (298) that reduces the neutrophil response and bacterial clearance by cutting the chemoattractant C5a (299). The streptococcal complement protector ScpA helps the bacterium resist phagocytosis (183) and also inactivates C5a (300). SpyCEP eliminates the neutrophil chemoattractant IL-8 (230) and other chemokines (225). Note that this figure depicts SoCs found in both group A and group B streptococci for illustrative purposes, but they would not naturally occur together.

[genegodbold]

Dear @pgaudet

Which of these is preferable: Describing a term with reference to another organism a. Mediates deactivation of small GTPase in another organism b. Disrupts tissue structure in another organism c. Mediates cell release from the extracellular matrix in another organism d. Inhibits coagulation in another organism e. Suppresses pro-inflammatory cytokine production in another organism

Describing a term with reference to the host-symbiont relationship a. Mediates deactivation of host small GTPase by symbiont b. Disrupts host tissue structure by symbiont c. Mediates host cell release from extracellular matrix by symbiont d. Symbiont Inhibition of host coagulation e. Symbiont suppression of host pro-inflammatory cytokine production

Right now nearly everything in PathGO is in the first format.

[pgaudet]

Discussion with @genegodbold

probably the most neutral term for the grouping term is 'perturbation'

[genegodbold]

Yes, that sounds best

[mgiglio99]

Sorry for not keeping up on this one lately. Just want to clarify the proposal here - is the plan to change ''modulation by symbiont of host defense response' & children to 'perturbatation by symbiont of host defense response' and children? What ended up being decided with regard to evasion vs. avoidance? Michelle

@dsiegele

[pgaudet]

Hi @mgiglio99

Apologies for the very late response!

is the plan to change ''modulation by symbiont of host defense response' & children to 'perturbatation by symbiont of host defense response' and children?

Yes

What ended up being decided with regard to evasion vs. avoidance?

We're keeping evasion

[pgaudet]

'suppression by virus of host adaptive immune response' 'suppression by virus of host antigen processing and presentation' 'suppression by virus of host complement activation' 'suppression by virus of host innate immune response'

change to 'perturbation'

[pgaudet]

GO:0033660 suppression by symbiont of host resistance gene-dependent defense GO:0052005 suppression by symbiont of host ethylene-mediated defense response GO:0052032 perturbation by symbiont of host inflammatory response GO:0052036 suppression by symbiont of host inflammatory response GO:0052067 disruption of host phagocytosis

change to 'symbiont-mediated xxx'