User talk:Lydia bluestone/sandbox

Kat's comments
I think this is a very good start. Rose's feedback largely echoes the comments I would make: namely, take care to avoid editorializing language, consider the most logical/helpful way to structure your article, and expand your general overview section. Also, take care when formatting your reference section.

I think that some different ways of conveying some of this information would also be helpful. Charts, diagrams, and images can all be useful ways of conveniently showing relationships between gene family members, signaling mechanisms downstream of receptors, etc.

-- Katbartlow (talk) 18:30, 11 March 2016 (UTC)

Hi Lydia,

At this point, I think that all of my major concerns regarding the text of your article have been addressed. This article is now highly-informative and flows very logically. I still think that adding some multimedia images and/or charts would be very helpful, particularly in helping people to understand the relationship between individual KIR genes, the receptors they encode, the length of the tails, and whether the receptors are activating or inhibitory. Including a PDB image of an example structure of a short- or long-tailed KIR might also be a good idea if you can help it.

Great work, and I'm very happy that you chose to post your updated article to Wikipedia -- it represents a major improvement over what was there before.

- Kat — Preceding unsigned comment added by Katbartlow (talk • contribs) 17:02, 18 April 2016 (UTC)

Rose's comments
@lydia bluestone There's a lot of information here, which is definitely good, but it needs to be organized and clarified. Overall, the language can be a bit more neutral (remove linker statements like "interestingly" and "clearly," as well as discussions of individual studies), the grammar in some places should be fixed and simplified, and the citations need to be put into the standard wiki format, but it's a strong start! Specific notes: Introduction: I recommend expanding the general information to include the big points from each of your subcategories, so readers can get a grasp on the overall idea of KIRs without going through each section. Focusing on their role in immunity and disease will also add information about relevance. Gene structure: How many KIRs have been discovered? It says 12, 14, 15 or 17 receptors have been identified, which needs to be explained. Inhibitory receptors: Reorganize the missing self hypothesis description, to make it more clear what's going on, because this is a kind of complicated thing to put into one sentence... Something like "The missing-self hypothesizes that the downregulation of MHC class I molecules in virally infected or transformed cells is recognized by inhibitory KIR receptors, which leads the lysis of unhealthy cells." Go into details about how it does this after the basic description. Role in Natural Killer Cells: First, I think this should be moved up closer to the beginning of the article, perhaps the first specific section, because it's very important for understanding KIRs and why they're important. Second, clarify the information - it might work better to start with a brief statement about what KIRs do in NKs, then define NKs, and then start to go into detail. Genotype and Haplotype Diversity: A chart or table would help explain this more concisely. There's a lot of complicated information here, which is made particularly difficult to read due to the format of KIR gene names. Role in Disease: The last section needs to be edited in terms of grammar, because it gets repetitive in the second half. Rrcopley12 (talk) 20:26, 7 March 2016 (UTC)

Oscar's feedback

= Killer Cell Immunoglobulin-Like Receptor =

Oscar's: ''The page normally starts with an intro section, instead of making it a subsection. So I'd recommend changing the format of this part. Also, adding a little bit more of general introduction would be nice, for example, who discovered or important applications in biotechnology. Be careful with using too many primary sources, remember that Wikipedia's information normally comes from secondary sources ''

Killer cell immunoglobulin-like receptors (KIR) are a family of type I transmembrane glycoproteins expressed on the plasma membrane of natural killer (NK) cells and a minority of T cells. KIR receptors are monomeric and can distinguish between MHC class I allelic variants.

Nomenclature and classification
KIR receptors are named based on the number of their extracellular Ig-like domains (2D or 3D) (What are lg-like domains? or add lg-like domains) and by the length of their cytoplasmic tail (long (L), short (S), or pseudogene (P)). The number following the L, S, or P in the case of a pseudogene, differentiates KIR receptors with the same number of extracellular domains and length of cytoplasmic tail. Finally, the asterisk after this nomenclature indicates allelic variants. (It is difficult to understand, maybe simplying or explaining more this parragraph)

Single substitutions, insertions, or deletions in the genetic material that encodes KIR receptors changes the site of termination for the gene, causing the cytoplasmic tail to be long or short, depending the site of the stop codon. These single nucleotide alterations in the nucleotide sequence fundamentally alter KIR function. With the exception of KIR2DL4, which has both activating and inhibitory capabilities, KIR receptors with long cytoplasmic tails are inhibitory and those with short tails are activating.

Structure
Oscar's:'' The page may have too many subsections. I would suggest to create a main category that could include several subcategories.. for example here: I added Structure, and inside Structure I can include Gene and Protein structure as subcategories ''

Gene structure
Oscar's: ''I think it is a good description. Perhaps adding a image about the gene locus would be cool.''

The KIR gene cluster has approximately 150 kb and is located in the leukocyte receptor complex (LRC) on human chromosome 19q13.4 (Radaev and Sun 2003; Parham 2004; Bashirova et al. 2006; Rajalingam 2012).

The human killer cell immunoglobulin-like receptors superfamily (which share 35-50% sequence identity and the same fold as KIR) includes immunoglobulin-like transcripts (ILT, also known as leukocyte immunoglobulin-like receptors (LIRs)), leukocyte-associated Ig-like receptors (LAIR), paired Ig-like receptors (PIR), and gp49 (Radaev and Sun 2003). Moreover, 12, 14, 15 or 17 KIR receptors have been identified to date, which share more than 90% sequence identity (Yawata et al. 2002=17; Radaev and Sun 2003=12; Parham 2004=15; Rajalingam 2012=14). There was a single ancestral gene from which all extant KIR receptor genes arose via duplications, recombinations, and mutations (Bashirova et al. 2006). (Oscar's: I would recommend using the Wikipedia citation format that consists of numbers that reference the citations at the end of the page. I find repeating the papers name very distracting)

KIR genes all have 9 exons, which are strongly correlated with KIR receptor protein domains (leader, D0, D1, and D2, stem, transmembrane, and cytosolic domains) (Bashirova et al. 2006). Furthermore, the promoter regions of the KIR genes share greater than 90% sequence identity, which indicates that there is similar transcriptional regulation of KIR genes (Bashirova et al. 2006).

Protein structure
NK cell receptors bind directly to the major histocompatibility complex class I molecules on the surface of target cells (Raulet et al. 2001). Human killer cell immunoglobulin-like receptors recognize the α1 and α2 domains of class I human leukocyte antigens (HLA-A, -B, and –C), which are the human versions of MHCs (Rajalingam 2012). Position 44 in the D1 domain of KIR receptors and position 80 in HLA-C are important for the specificity of KIR-HLA binding (Bashirova et al. 2006).

Receptor type
Oscar's: ''I would recommend something similar to the above said. In this way it would be easier for the readers to find what they are looking for ''

Activating receptors
Activating receptors recognize ligands that indicate host cell aberration, including induced-self antigens (which are markers of infected self cells and include MICA, MICB, and ULBP, all of which are related to MCH class 1 molecules), altered-self antigens (MHC class I antigens laden with foreign peptide), and/or non-self (pathogen encoded molecules) (Bashirova et al. 2006; Rajalingam 2012). The binding of activating KIR receptors to these molecules causes the activation of signaling pathways that cause NK cells to lyse virally infected or transformed cells (Rajalingam 2012). Much less is known about activating receptors compared to inhibitory receptors. Interestingly, a significant proportion of the human population lacks activating KIR receptors on the surface of their NK cells as a result of truncated variants of KIR2DS4 and 2DL4, which are not expressed on the cell surface, in individuals who are heterozygous for the KIR group A haplotype (Bashirova et al. 2006). This suggests that a lack of activating KIR receptors is not incredibly detrimental, likely because there are other families of activating NK cell surface receptors that bind MHC class I molecules that are probably expressed in individuals with this phenotype. Because little is known about the function of activating KIR receptors, however, it is possible that there is an important function of activating KIR receptors of which we are not yet aware (Bashirova et al. 2006).

Activating receptors do not have the immunoreceptor tyrosine-base inhibition motif (ITIM) characteristic of inhibitory receptors, and instead contain a positively charged lysine or arginine residue in their transmembrane domain (with the exception of KIR2B4) that helps to bind DAP12, an adaptor molecule containing a negatively charged residue as well as immunoreceptor tyrosine-based activation motifs (ITAM) (Radaev and Sun 2003; Rajalingam 2012). Activating KIR receptors include KIR2DS, KIR2DL, and KIR3DS (Raulet et al. 2001).

Activating receptors have lower affinity for their ligands than do inhibitory receptors (Raulet et al. 2001). Although the purpose of this difference in affinity is uncertain, it is possible that the cytolysis of target cells occurs preferentially under conditions in which the expression of stimulating MHC class I molecules on target cells is high, which may occur during viral infection (Raulet et al. 2001). This difference, which is also present in Ly49, the murine homolog to KIR, also tips the balance towards self-tolerance (Bashirova et al. 2006).

Inhibitory receptors
Inhibitory receptors recognize self-MHC class I molecules on target self cells, causing the activation of signaling pathways that stop the cytolytic function of NK cells (Rajalingam 2012). Self-MHC class I molecules are always expressed under normal circumstance (Bashirova et al. 2006). According to the missing-self hypothesis, inhibitory KIR receptors recognize the downregulation of expression of MHC class I molecules in virally-infected or transformed self cells, leading these receptors to stop sending the inhibition signal and thus to the lysis of these unhealthy cells (Bashirova et al. 2006; Rajalingam 2012). Because natural killer cells target virally infected host cells and tumor cells, inhibitory KIR receptors are important in facilitating self-tolerance (Parham 2004).

KIR inhibitory receptors signal through their immunoreceptor tyrosine-based inhibitory motif (ITIM) in their cytoplasmic domain. When inhibitory KIR receptors bind to a ligand, their ITIMs are tyrosine phosphorylated and protein tyrosine phosphatases, including SHP-1, are recruited. Inhibition occurs early in the activation signaling pathway, likely through the interference of the pathway by these phosphatases (Raulet et al. 2001; Bashirova et al. 2006).

Role in natural killer cells
Oscar's: ''Instead of the tittle: Role in..., I would recommend using a simple word like Function or Mechanism. Many Wikipedia pages have this simple-named categories. You could also take advantage and include the Role of T-cells part too into one category''

Natural killer (NK) cells are a type of lymphocyte cell involved in the innate immune system’s response to viral infection and tumor transformation of host cells (Bashirova et al. 2006; Rajalingam 2012). Natural killer cell cytolysis of target cells and cytokine production is controlled by a balance of inhibitory and activating signals, which are facilitated by NK cell receptors (Boyington and Sun 2001; Radaev and Sun 2003; Bashirova et al. 2006). NK cell inhibitory receptors are part of either the immunoglobulin-like (IgSF) superfamily or the C-type lectin-like receptor (CTLR) superfamily (Radaev and Sun 2003; Bashirova et al. 2006). Members of the IgSF family include the human killer cell immunoglobulin-like receptor (KIR) and the Immunoglobulin-like transcripts (ILT) (Radaev and Sun 2003). CTLR inhibitory receptors include the CD94/NKG2A and the murine Ly49, which is probably analogous to the human KIR (Raulet et al. 2001; Radaev and Sun 2003).

Because NK cell targets self cells, they have an intricate mechanism by which they differentiate self and nonself cells (Bashirova et al. 2006).

Like T cells, NK cells have many qualities characteristic of the adaptive immune system, including the production of “memory” cells that persist following encounter with antigens and the ability to create a secondary recall response (Rajalingam 2012). Unlike T cells, NK cell receptors are germline encoded, and therefore do not require somatic gene rearrangements (Rajalingam 2012).

Role in T cells
KIR and CD94 (CTLR) receptors are expressed by 5% of peripheral blood T cells (Raulet et al. 2001).

Expression
Activating and inhibitory KIR receptors are expressed on NK cells in patchy, variegated combinations, leading to distinct NK cells (Rajalingam 2012). The IgSF and CTLR superfamily inhibitory receptors expressed on the surface of NK cells are each expressed on a subset of NK cells in such a way that not all classes of inhibitory NK cell receptors are expressed on each NK cell, but there is some overlap (Raulet et al. 2001). This creates unique repertories of NK cells, increasing the specificity with which NK cells recognize virally-infected and transformed self-cells (Raulet et al. 2001). Expression of KIR receptors is determined primarily by genetic factors, but recent studies have found that epigenetic mechanisms also play a role in KIR receptor expression (Rajalingam 2012). Activating and inhibitory KIR receptors that recognize the same class I MHC molecule are mostly not expressed by the same NK cell (Raulet et al. 2001). This pattern of expression is beneficial in that target cells that lack inhibitory MHC molecules but express activating MHC molecules are extremely sensitive to cytolysis (Raulet et al. 2001).

Although initial expression of inhibitory and activating receptors on NK cells appears to be stochastic, there is an education process based on MHC class I alleles expressed by the host that determines the final repertoire of NK receptor expression (Raulet et al. 2001; Rajalingam 2012). This process of education is not well understood (Raulet et al. 2001). Different receptor genes are expressed primarily independently of other receptor genes (based on the product rule), which substantiates the idea that initial expression of receptors is stochastic (Raulet et al. 2001). Receptors are not expressed entirely independently of each other, however, which supports the idea that there is an education process that reduces the amount of randomness associated with receptor expression. Further, once an NK receptor gene is activated in a cell, its expression is maintained for many cell generations (Raulet et al. 2001; Rajalingam 2012). It appears that some proportion of NK cells are developmentally immature and therefore lack inhibitory receptors, making them hyporesponsive to target cells (Rajalingam 2012). In the human fetal liver, KIR and CD49 receptors are already expressed by NK cells, indicating that at least some KIR receptors are present in fetal NK cells, although more studies are needed to substantiate this idea (Raulet et al. 2001). Although the induction of NK receptor expression is not fully understood, one study found that human progenitor cells cultured in vitro with cytokines developed into NK cells, and many of these cells expressed CD94/NKG2A receptors, a CTLR receptor (Raulet et al. 2001). Moreover, there was little to no KIR receptor expression in these cells, so additional signals are clearly required for KIR induction (Raulet et al. 2001).

The balance between effective defense and self-tolerance is important to the functioning of NK cells. It is thought that NK cell self-tolerance is regulated by the educational process of receptor expression described above, although the exact mechanism is not known (Raulet et al. 2001). The “at least one” hypothesis is an attractive, though not yet fully substantiated, hypothesis that tries to explain the way in which self-tolerance is regulated in the education process. This hypothesis posits that the NK cell repertoire is regulated so that at least one inhibitory receptor (either of the IgSF or CTLR superfamily) is present on every NK cell, which would ensure self-tolerance (Raulet et al. 2001). Effective defense, interestingly, requires an opposing pattern of receptor expression. The co-expression of many MHC-specific receptors by NK cells is disfavored, likely because cells that co-express receptors are less able to attack virally infected or transformed cells that have down-regulated or lost one MHC molecule compared to NK cells that co-express receptors to a lesser degree (Raulet et al. 2001). Minimization of co-expression, therefore, is important for mounting an effective defense by maximizing the sensitivity of response (Raulet et al. 2001).

Allelic Diversity
All but two KIR receptors (KIR2DP1 and KIR3DL3) have multiple alleles, with KIR3DL2 and KIR3DL1 having the most variations (12 and 11, respectively) (Yawata et al. 2002). In total, as of 2012 there were 614 known KIR nucleotide sequences, which encode 321 distinct KIR proteins (Rajalingam 2012). Further, inhibitory receptors are more polymorphic than activating receptors (Rajalingam 2012). The great majority (69%) of substitutions in the KIR DNA sequence are nonsynonymous, and 31% are synonymous (Yawata et al. 2002). As a result, the ratio of nonsynonymous to synonymous substitutions (dN/dS) is greater than one for every KIR and every KIR domain, indicating that positive selection is occurring (Yawata et al. 2002). Further, the 5` exons, which encode the leader peptide and the Ig-like domains, have a larger proportion of nonsynonymous substitutions than do the 3` exons, which encode the stem, transmembrane region, and the cytoplasmic tail (Yawata et al. 2002). This indicates that stronger selection is occurring on the 5` exons, which in the translated protein makes up the extracellular part of the KIR that binds to the MHC (Yawata et al. 2002). There is, therefore, evidence of strong selection on the KIR ligand binding sites, which is consistent with the high specificity of the KIR ligand binding site, as well as the rapid evolution of class I MHC molecules and viruses (Yawata et al. 2002; Rajalingam 2012).

Genotype and haplotype diversity
Human genomes differ in their amount of KIR genes, in their proportion of inhibitory versus activating genes, and in the allelic variations of each gene (Parham 2004; Yawata et al. 2002). As a result of these polygenic and polymorphic variations, less than 2% of unrelated individuals have the same KIR genotype, and ethnic populations have broadly different KIR genotype frequencies (Parham 2004). This incredible diversity likely reflects the pressure from rapidly evolving viruses (Rajalingam 2012). 30 distinct haplotypes have been classified, all of which can be broadly characterized by group A and group B haplotypes (Rajalingam 2012). Group A haplotype has a fixed set of genes, which are KIR3DL3-2L3-2DP1-2DL1-3DP1-2DL4-3DL1-2DS4-3DL2 (Bashirova et al. 2006; Rajalingam 2012). Group B haplotypes encompass all other haplotypes, and therefore have a variable set of genes, including several genes absent from group A, which are KIR2DS1, 2DS2, 2DS3, 2DS5, 2DL2, 2DL5, and 3DS1 (Bashirova et al. 2006; Rajalingam 2012). Because group B has both gene and allelic diversity (compared to just allelic diversity in group A), group B is even more diverse than group A (Bashirova et al. 2006). Four KIR genes (2DL4, 3DL2, 3DL3, AND 3DP1) are present in nearly all KIR haplotypes and as a result are known as framework genes (Bashirova et al. 2006; Rajalingam 2012). Inheritance of maternal and paternal haplotypes results in further diversity of individual KIR genotype (Rajalingam 2012).

Group A only has one activating KIR receptor, whereas Group B contains many activating KIR receptors, and as a result group-B haplotype carriers have a stronger response to virally infected and transformed cells (Rajalingam 2012). Interestingly, as a result of the huge migrations peoples indigenous to India, Australia, and the Americas made from Africa, activating KIR receptors became advantageous to these populations, and as a result these populations acquired activating KIR receptors (Rajalingam 2012).

A study of the genotypes of 989 individuals representing eight distinct populations found 111 distinct KIR genotypes. Individuals with the most frequent genotype, which comprised 27% of the individuals studied, are homozygous for the group A haplotype (Yawata et al. 2002). The remaining 110 KIR genotypes found in this study are either group A and group B heterozygotes or group B homozygotes (who are indistinguishable from heterozygotes by genotype alone). 41% (46) of the genotypes identified were found in only one individual, and 90% of individuals had the same 40 genotypes (Yawata et al. 2002). Clearly, there is extensive diversity in human KIR genotypes, which allows for rapid evolution in response to rapidly evolving viruses.

Role in disease
Genotypes that are inhibitory KIR receptor dominant are likely susceptible to infection and reproductive disorders but protective against autoimmune diseases, whereas activating KIR receptor dominant genotypes are likely susceptible to autoimmunity but protective against viral infection and cancer (Bashirova et al. 2006; Rajalingam 2012). The relationship between inhibitory vs stimulatory KIR genotype dominance, however, is more complicated than this because diseases are so diverse and have so many different causes, and immune activation or de-activation may not be protective or harmful at every stage of disease (Bashirova et al. 2006). KIR2DS2 or 2DS1, which are activating receptors, are strongly correlated with most autoimmune diseases, which is logical because activating receptors induce signaling pathways that lead to cytolysis of target cells (Bashirova et al. 2006; Rajalingam 2012). Interestingly, another activating receptor, KIR3DS1, is protective to hepatitis-C virus infection, is associated with slowing down of AIDs progression, and is associated with cervical cancer, which is associated with a distinct strain of HPV (Bashirova et al. 2006; Rajalingam 2012). It is likely that KIR3DS1 is associated with cervical cancer despite its stimulatory nature because cervical tumors generally associate with localized inflammation (Bashirova et al. 2006).

References== == Yawata, M., Yawata, N., and Abi-Rached, L. 2002. Variation within the human killer cell immunoglobulin-like receptor (KIR) gene family. Immunology 22(5&6): 463-482.

Raulet, D.H., Vance, R.E., and McMahon, C.W. 2001. Regulation of the natural killer cell receptor repertoire. Immunology 19: 291-330.

Bashirova, A.A., Martin, M.P., McVicar, D.W., and Carrington, M. 2006. The killer immunoglobulin-like receptor gene cluster: tuning the genome for defense. Genomics and Human Genetics 7: 277-300.

Rajalingam, R. 2012. Overview of the killer cell immunoglobulin-like receptor system. Immunogenetics: Methods and Applications in Clinical Practice 882: 391-414.

Radaev, S., and Sun, P.D. 2003. Structure and function of natural killer cell surface receptors. Annual Review of Biophysics and Biomolecular Structure 32: 93-114.

Parham, P. 2005. Immunogenetics of killer cell immunoglobulin-like receptors. Molecular Immunology 42: 459-462.

Boyington, J.C., and Sun, P.D. 2001. A structural perspective on MHC class I recognition by killer cell immunoglobulin-like receptors. Molecular Immunology 38: 1007-1021.

I want a puppy
Puppies are adorableLydia bluestone (talk) 16:43, 18 January 2016 (UTC)
 * I agreeLydia bluestone (talk) 16:46, 18 January 2016 (UTC)