I have heard some people claim to have no trouble with eating grains of any kind in Europe when in the U.S. they need to be gluten or even grain free. What are your thoughts on that?

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Gluten

At a prevalence of ~1% of the population, Celiac disease, making specific T cell immune responses to gluten components, still remains relatively rare though even its rates have been increasing since the 1950s. However, in recent years starting from at least 1978 (1), a far larger proportion began to report non-celiac gluten/wheat sensitivity , reaching ~10% in countries ranging from Australia to Italy, Mexico, and the US and UK (2).

Celiac disease can be diagnosed using precise tests. However, with no clear diagnostic, non-celiac gluten/wheat sensitivity is largely self-diagnosed and thus accurate numbers are hard to come by.

That preamble out of the way, a difference in reaction to (wheat) grains when in the US versus when in Europe could be attributed to

• Differences in gluten content of wheats grown in US versus some European countries, or
• Differences in the total gluten present in US versus some European diets, or other diet components (additives, emulsifiers, FODMAP – Wikipedia) difficult to identify separately as the trigger(s).

Differences in gluten content of wheats grown in US versus Europe

Grain gluten differences likely don’t explain recent increases in non-celiac gluten/wheat sensitivity in the US since reports of such sensitivity are increasing the world over including in several European countries (Italy and the UK for example). Though such differences have become a favored explanation in the burgeoning popular media narratives about this increase (3), actual research neither corroborates nor substantiates it (see below from 4, emphasis mine)

‘There are few pertinent papers that address the question of whether or not the protein content of the U.S. wheat crop has increased over time in the 20th century…The hard spring wheats, grown mostly in the Northern Plains, are considered to be highly desirable for bread baking and tend to have protein contents that in general exceed the usual protein contents of winter wheats by about 2 percentage points… The North Dakota Wheat Commission reported13 that, in 2009, the hard red spring wheat crop “ …yielded an average of 13.1 percent (which) was well below the traditional level of more than 14%,” and these protein contents are fairly typical of late 20th century crops for the hard spring wheat region. Various studies have compared the protein contents of wheat varieties from the early part of the 20th century with those of recent varieties.14,15 When grown under comparable conditions, there was no difference in the protein contents. Although nitrogen fertilization can have strong effects on protein content for some wheat varieties,16 the data do not seem to be in accord with the likelihood that recent fertilization protocols have had a strong effect on the protein contents of wheat grown in the United States…

Interpretation of protein data is complicated by occasional major deviations from the more usual range. In 1938, the protein content of spring wheat was exceptionally high (Table 1), averaging close to 19%; these years of exceptionally high protein (or low protein) occur occasionally and are likely to result mainly from environmental factors, rather than nitrogen fertilization or wheat breeding. To maintain a uniformity of quality characteristics from year to year, flour mills usually blend wheat flour that is intended for commercial use by specific customers, for example, bakeries. Very high protein content would usually be unsuitable for direct use, and so high protein wheat flours would usually be blended with lower protein grain to achieve a more normal protein level before reaching the consumer.‘

Differences in total gluten and/or other diet components present in US versus some European diets

Diets have changed dramatically over the course of the 20th century as industrialized mechanization processes were brought to bear in scaling up and streamlining food production. These days, home bread making from scratch is largely a niche hobby and many if not most people purchase commercial breads and other wheat-containing baked goods as a matter of course, not to mention that a great deal of home bread making itself relies on commercially blended products.

Industrial baking and the ingredients it uses are streets removed from home baking, speed and efficiency their hallmarks. Where traditional bread baking uses traditional leavening agents, requires long, slow fermentation, and takes ~16 hours, a cocktail of synthetic ingredients including extra yeast, additives and emulsifiers enables industrial bread making to turn out finished loaves in ~2 hours (3).

• Vital Gluten is a vital part of this sped up process. Usually labeled ‘wheat protein’ (see below from 4),

‘Gluten fractionated from wheat flour by washing starch granules from a dough (sometimes called vital gluten) is often added to food products to achieve improved product characteristics.’

• • Given its capacity to emulsify and to increase cohesiveness, viscosity, elasticity, gelation and foaming (5), vital gluten is today an essential ingredient in industrial baking.
  • Research estimates total US gluten consumption has tripled from ~136 grams per person per year in 1977 to ~408 grams per person per year in 2013 (see below from 4),

‘…it appears that vital gluten consumption has tripled since 1977…Changes in the per capita intake of wheat and gluten might play a role; both increased during the period in question…’

• • Ironically, some consumption pattern changes such as switching to whole wheat products for perceived health reasons may not help but could instead add to this problem of increased hidden gluten consumption (see below from 4),

‘It may be noted that whole wheat products, which are increasing in consumption for health reasons (especially the higher fiber content), often have vital gluten added to them to compensate for the negative effects of the ground whole grain on quality factors, such as loaf volume in breadmaking.’

• Careful, rigorous, double-blind, placebo-controlled crossover trials suggest gluten accounts for only ~17% of non-celiac gluten/wheat sensitivity while the rest can be attributed to fructans, part of FODMAPs, or to nocebo (6, 7). This may be why individuals with self-diagnosed non-celiac gluten/wheat sensitivity switching willy-nilly to a gluten-free diet usually end up hit-or-miss (6, 7).
• Going gluten-free absent proper tests and diagnosis can also back fire (see below from 3),

‘But relying on gluten-free alternatives could be counterproductive. The vast majority of gluten-free creations touted as “tummy friendly” contain the same questionable enzymes and additives that food technologists use in the standard, gluten containing industrial equivalent. In addition, they also rely on hi-tech food manufacturing ingredients to provide their architecture. These include xanthan gum, a strong, glue-like substance also used in the oil industry to thicken drilling mud, hydroxypropyl methyl cellulose, also used in the construction industry for its water-retaining properties in cement, and tapioca starch, a nutritionally depleted, chemically modified starch from the cassava root.’

In sum, differences in total gluten and/or other diet components between US and some European diets could explain why some people react to (wheat) grains when in the US but not when in certain European countries.

Bibliography

1. Ellis, A., and B. D. Linaker. “Non-coeliac gluten sensitivity?.” The Lancet 311.8078 (1978): 1358-1359.

2. Aziz, Imran. “The Global Phenomenon of Self-Reported Wheat Sensitivity.” (2018): 1. The Global Phenomenon of Self-Reported Wheat Sensitivity

3. Not just a fad: the surprising, gut-wrenching truth about gluten

4. Kasarda, Donald D. “Can an increase in celiac disease be attributed to an increase in the gluten content of wheat as a consequence of wheat breeding?.” Journal of agricultural and food chemistry 61.6 (2013): 1155-1159. ActiveView HTML

5. Cabrera-Chávez, F., and AM Calderón de la Barca. “Trends in wheat technology and modification of gluten proteins for dietary treatment of coeliac disease patients.” Journal of cereal science 52.3 (2010): 337-341. http://www.sistemanodalsinaloa.g…

6. Molina-Infante, Javier, and Antonio Carroccio. “Suspected nonceliac gluten sensitivity confirmed in few patients after gluten challenge in double-blind, placebo-controlled trials.” Clinical Gastroenterology and Hepatology 15.3 (2017): 339-348.

7. Skodje, Gry I., et al. “Fructan, rather than gluten, induces symptoms in patients with self-reported non-celiac gluten sensitivity.” Gastroenterology 154.3 (2018): 529-539.

https://www.quora.com/I-have-heard-some-people-claim-to-have-no-trouble-with-eating-grains-of-any-kind-in-Europe-when-in-the-U-S-they-need-to-be-gluten-or-even-grain-free-What-are-your-thoughts-on-that/answer/Tirumalai-Kamala

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Can we redirect the CAR-T cells to kill those MDSC or any cells standing in their way, thereby overcoming the immune suppressive tumor microenvironment of solid tumors?

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CAR (Chimeric Antigen Receptor)-T, Myeloid-derived Suppressor Cell (MDSC)

Is the tumor microenvironment immune suppressive? A common interpretation that could very well be flawed. After all, a wide variety of immune cells, ranging from CAF (Cancer-associated fibroblast), TAM, Tumor-associated macrophage – Wikipedia, TAN (Tumor-associated neutrophils), TIL, Tumor-infiltrating lymphocytes – Wikipedia, to MDSC, Myeloid-derived suppressor cell – Wikipedia, are routinely found within tumors. How could they get in there if tumors suppress immunity?

Rather than non-specifically suppress immunity as steroids do for example, tumors seem to create an immune subversive environment in an attempt to specifically prevent effective anti-tumor immunity.

The fact that tumor-specific TILs are indeed found in tumors implies the immune system does respond to tumor-specific antigens. Such responses are often not effective, the notion being that tumors express and secrete specific molecules that prevent such an outcome. Different interpretations lead to consideration of different treatment approaches.

• If tumors imposed blanket immune suppression then immunotherapies such as checkpoint inhibitors (monoclonal antibodies that target molecules such as PD-1, PD-L1 or CTLA-4) that lift the brakes off of T cells should work in every single instance and yet that’s not the case since so far they only appear to work in subsets of patients.
  • Anti-PD-1 mAb should block the suppressive effect of MSDC since they are known to express high levels of PD-1.
  • That checkpoint inhibitors don’t work as effectively as envisaged suggests blanket immune suppression within the tumor microenvironment is likely not an accurate interpretation.
• In the CAR T approach, the patient’s own* T cells are harvested, cultured in vitro, genetically engineered to express an antibody-like molecule to specifically target an antigen (protein) expressed on the surface of tumor cells. The process is akin to transforming all sorts of T cells to become tumor-seeking missiles.

Neither approach utilizes the hallmark of T cells, their antigen-specificity.

Theoretically CAR Ts could indeed be engineered to specifically target tumor-infiltrating immune cells thought to impede effective anti-tumor immunity.

MDSC clearly represent important prognostic value in tumors, their presence deemed detrimental in gastric, urogenital, and head and neck cancers but not so in colorectal cancers (1).

• In order for CAR Ts to specifically target MDSC requires a MDSC-specific cell surface protein. The few studies to have examined human tumor-infiltrating MDSC in detail thus far report them to be quite heterogeneous (2, 3), which implies they may not all express the same cell-surface protein. If that turns out be the case, it would represent a formidable technical challenge to the goal of using CAR Ts to target and eliminate MDSCs.
• There are as-yet no validated antibodies that specifically target human MDSC (4). Such an antibody is necessary to construct the CAR part of a CAR T cell.
• High tech approaches such as MDSC-targeting CAR Ts may not even be needed. Mouse model studies have shown that Docetaxel – Wikipedia, a standard cancer chemotherapy drug, can directly deplete mouse MDSCs (5). Unknown whether it can do likewise with human MDSCs.

Some mouse model studies have reported using CAR T’s engineered to target fibroblast activation protein (FAP), which is highly expressed on CAFs (6, 7). Such preliminary studies are proof of concept for such an approach. Do human CAFs also specifically express FAP? Whether such an approach could be practical turns on the answer to such key questions.

* Note that currently biotech and pharma companies are interested in off-the-shelf CAR T cells, i.e., allogeneic rather than derived from the patient’s own T cells, because a personalized approach would be obviously much more expensive.

Bibliography

1. Zhang, Qiong-wen, et al. “Prognostic significance of tumor-associated macrophages in solid tumor: a meta-analysis of the literature.” PloS one 7.12 (2012): e50946. Prognostic Significance of Tumor-Associated Macrophages in Solid Tumor: A Meta-Analysis of the Literature

2. Kotsakis, Athanasios, et al. “Myeloid-derived suppressor cell measurements in fresh and cryopreserved blood samples.” Journal of immunological methods 381.1-2 (2012): 14-22. https://www.ncbi.nlm.nih.gov/pmc…

3. Damuzzo, Vera, et al. “Complexity and challenges in defining myeloid‐derived suppressor cells.” Cytometry Part B: Clinical Cytometry 88.2 (2015): 77-91. Complexity and challenges in defining myeloid‐derived suppressor cells

4. Wang, Guocan, et al. “Targeting YAP-dependent MDSC infiltration impairs tumor progression.” Cancer discovery (2015). http://cancerdiscovery.aacrjourn…

5. Kodumudi, Krithika N., et al. “Blockade of myeloid-derived suppressor cells after induction of lymphopenia improves adoptive T cell therapy in a murine model of melanoma.” The Journal of Immunology (2012): 1200274. Blockade of Myeloid-Derived Suppressor Cells after Induction of Lymphopenia Improves Adoptive T Cell Therapy in a Murine Model of Melanoma

6. Wang, Liang-Chuan S., et al. “Targeting fibroblast activation protein in tumor stroma with chimeric antigen receptor T cells can inhibit tumor growth and augment host immunity without severe toxicity.” Cancer immunology research (2013): http://canimm-0027.http://cancerimmunolres.aacrjournals.org/content/early/2013/11/12/2326-6066.CIR-13-0027.full-text.pdf

7. Lo, Albert, et al. “Tumor-promoting desmoplasia is disrupted by depleting FAP-expressing stromal cells.” Cancer research (2015): canres-3041. http://cancerres.aacrjournals.or…

https://www.quora.com/Can-we-redirect-the-CAR-T-cells-to-kill-those-MDSC-or-any-cells-standing-in-their-way-thereby-overcoming-the-immune-suppressive-tumor-microenvironment-of-solid-tumors/answer/Tirumalai-Kamala

Besides X-linked agammaglobulinemia (which selectively crippled the B cell immunity), are there other genetic defects that affect a very specific part of the immune system?

Tags

PID (primary immunodeficiency), Regulatory T cells

Yes indeed. At present mutations on >120 separate genes are implicated with ~150 different primary immunodeficiencies identified thus far.

Many of these mutations affect multiple cell types but some don’t.

One of the most famous and in my opinion most consequential are mutations in the FOXP3 – Wikipedia gene, which specifically impair Regulatory T cell – Wikipedia. Why so consequential? Because impairment of just this one rather small subset of CD4 T cells causes one of the severest and deadliest immunodeficiencies ever observed, IPEX syndrome – Wikipedia.

This only serves to highlight how extremely critical this T cell subset is for entire immune function. No surprise then that even 17 years after FoxP3 was identified, regulatory T cells continue to mystify and much of what’s known about their function is a mishmash of contradictory observations. At this juncture, immunology can’t make real progress without a proper understanding of regulatory T cell function.

Some other mutations that affect largely one specific aspect of the immune system are,

• Mutations in Elastase – Wikipedia affect neutrophils. Individuals display MDS, Myelodysplastic syndrome – Wikipedia or leukemia.
• Mutations in Granulocyte-macrophage colony-stimulating factor receptor – Wikipedia are reported to affect only alveolar macrophages, leading to Pulmonary alveolar proteinosis – Wikipedia.
• Mutations in NOD2 – Wikipedia that lead to Blau syndrome – Wikipedia are reported to affect monocytes alone. Skin, eye, brain, gut are affected.
• A particular mutation in the NOX2 – Wikipedia gene aka the Macrophage gp91 phox deficiency affects macrophages alone and leads to heightened susceptibility to mycobacteria.
• And of course, BTK mutations that lead to X-linked agammaglobulinemia aren’t the only mutations that selectively cripple B cell function. Other mutations such as μ heavy chain deficiency, λ5 deficiency, Igα deficiency, Igβ deficiency, BLNK deficiency, PI3KR1 deficiency also do so, and there are many other B cell-specific mutations as well.

There are obviously many many more but listing them out one by one would be rather boring. Instead check out the 2015 report from the International Union of Immunological Societies – Wikipedia, which lists the major mutations in 9 large tables: Picard, Capucine, et al. “Primary immunodeficiency diseases: an update on the classification from the International Union of Immunological Societies Expert Committee for Primary Immunodeficiency 2015.” Journal of clinical immunology 35.8 (2015): 696-726. Primary Immunodeficiency Diseases: an Update on the Classification from the International Union of Immunological Societies Expert Committee for Primary Immunodeficiency 2015

https://www.quora.com/Besides-X-linked-agammaglobulinemia-which-selectively-crippled-the-B-cell-immunity-are-there-other-genetic-defects-that-affect-a-very-specific-part-of-the-immune-system/answer/Tirumalai-Kamala

What have we learned about T cell biology from Jurkat cells?

Tags

Jurkat T cell

‘What have we learned about T cell biology from Jurkat cells?‘. A more accurate reformulation would be ‘What have we learned from Jurkat cells that’s applicable to T cell biology and what’s not?”. Unfortunately, the answer isn’t that easy to untangle from archival data.

Much like the tumor cell line HeLa – Wikipedia before it, from the 1980s through the 1990s, Jurkat cells – Wikipedia became a heavyweight tool to understand human T-cell receptor – Wikipedia (TCR) biochemistry (1). Later, Jurkat also became a popular tool to model human T cell infection by HIV. However, very much a Curate’s egg – Wikipedia, Jurkat‘s perceived benefits remained disproportionately the focus during this time while its harms have been considered only much more recently. Meantime, 21st century technological advances have pretty much eliminated reliance on such inherently problematic transformed (tumor) cell lines.

This answer outlines

• A brief history of the Jurkat T cell line, highlighting how the imperatives of prevailing technical limitations drove its past popularity.
• how Jurkat‘s inherent limitations in decoding TCR signaling are predicated on the fact that it is a tumor cell, has mutations and is potentially contaminated, features that cast doubt on the validity of some historical results using it.

Brief History of the Jurkat T cell line

In 1977, a cell line was derived from T cells isolated from a 14 year old boy with Acute lymphoblastic leukemia – Wikipedia (ALL) (2). This cell line was eventually called Jurkat.

Back then, T cells remained very much a mystery, there was little or no consensus on how to maintain them in culture for long periods of time, a basic requirement necessary to dissect their essential properties, especially their biochemistry.

The experimental mouse model, today the backbone of immunology research, was still in its infancy as was molecular biology. Today’s technological mainstays such as gene targeting to create T cell transgenic mice and T cell transgenics with attached reporter genes to facilitate their monitoring were advances decades in the future.

Thus in this vacuum, an immortalized cell line such as Jurkat capable of being maintained in culture in perpetuity became an extremely valuable tool that in hindsight arose at the moment when most needed.

In its early years of use, Jurkat was thus used to delineate a great deal of the signal transduction pathway and molecules triggered by T-cell receptor – Wikipedia (TCR) signaling (1).

Hindsight also suggests a readily available human T cell line made such research far simpler and much cheaper. No need to draft complicated study protocols, get them reviewed and approved by Institutional review board – Wikipedia (IRB) in order to gain permission to bleed people to isolate their T cells in order to study them. Jurkat was thus a convenient tool to study aspects of human TCR biochemistry.

Limitations of Jurkat T cell line

Immortalized cell line versus primary, normal cell. During its early years of use, methods to culture human primary T cells didn’t exist. Even today, primary T cells simply can’t be maintained indefinitely in culture. Their long-term study requires stimulation, expansion, cloning and then immortalization (hybridization [mechanical fusing] with a partner tumor cell).

Yet, being a tumor cell, do results from Jurkat apply to normal human T cells in general? That’s simply unknowable since it’s impossible to know exactly what T cell stage Jurkat represents considering it got established and began to be used back when little was known about T cell development, activation, effector differentiation and memory formation. While papers routinely refer to Jurkat as a Lymphoblast – Wikipedia, at best that’s just a tenuous guess.

Mutations in many key molecules involved in the TCR signaling pathway. Tumor cells replicate uncontrollably, having broken free of biological control. Mutations in cell cycle checkpoints make such liberation possible. During its first two decades of use, how Jurkat‘s mutations might affect its TCR functioning wasn’t a focus. After all, there is an inherent tautology to unraveling signaling defects in cell lines being used to identify signaling pathways in the first place. Signaling pathways need to be comprehensively deciphered first to determine if a particular cell line has a signaling defect or two or however many the case may be.

As T cell biochemistry advanced apace by the late 1990s, some TCR signaling pathways identified using mouse T cells, T cell lines or other human T cell lines didn’t concord with those found in Jurkat. Turns out mutations in Jurkat accounted for such discrepancies.

• Today, signaling of the Phosphoinositide 3-kinase – Wikipedia (PI3K) family is known to be a central feature downstream of TCR signaling. Yet, in the late 1990s-early 2000s, two key molecules that mediate PI3K signaling were found to be missing in Jurkat cells (1). Such a fundamental signaling defect raised questions about the validity of using Jurkat as a tool to understand (human) TCR signaling (1, 3).
• A 2017 analysis uploaded to the preprint server, bioRxiv, comprehensively collates the various defective pathways and key signaling molecules missing in Jurkat (3).
  • In addition to PI3K, it points out Jurkat doesn’t express other molecules such as SHIP1 (INPP5D – Wikipedia), CTLA-4 – Wikipedia and Syk – Wikipedia, all now known to be important components of the TCR signaling pathway.
  • The authors also suggest a potentially ingenious use of such Jurkat defects, namely, to use them in reconstitution experiments to validate functionality of a given molecule in a particular pathway.
• Notwithstanding such grave TCR signaling defects, even today hundreds of papers using Jurkat continue to be published annually.
• Use of Jurkat as a model system to study HIV infection in human T cells yields a similarly confusing story, with many discordances in observations between Jurkat and primary CD4 T cells (4).

Microbial Contamination. A 2008 study reported a batch of Jurkat cells to be contaminated with a retrovirus belonging to the family of Gammaretrovirus – Wikipedia (5). Today this virus is designated as Xenotropic murine leukemia virus-related virus – Wikipedia or XMLV. Note that this study sourced its Jurkat from ATCC (company) – Wikipedia (ATCC), a major global supplier of cell lines. Open questions remain,

• Given ATCC’s Jurkat was found to be contaminated with XMLV in 2008, how many previous published studies on Jurkat used such contaminated cells?
• Are Jurkats stored in other cell bank repositories and maintained by labs around the world similarly infected?
• When did Jurkat become infected? In the 1990s when the XMLV is suspected to have arisen during xenograft studies or later?
• How does this infection influence historical results from Jurkat? Clearly, comparisons of ‘clean’ and ‘contaminated’ Jurkats are needed to figure out if and what effect this has on their TCR signaling.

Bibliography

1. Abraham, Robert T., and Arthur Weiss. “Jurkat T cells and development of the T-cell receptor signalling paradigm.” Nature Reviews Immunology 4.4 (2004): 301-308. https://www.researchgate.net/pro…

2. Schneider, Ulrich, Hans‐Ulrich Schwenk, and Georg Bornkamm. “Characterization of EBV‐genome negative “null” and “T” cell lines derived from children with acute lymphoblastic leukemia and leukemic transformed non‐Hodgkin lymphoma.” International journal of cancer 19.5 (1977): 621-626.

3. Gioia, Louis, et al. “A Genome-wide Survey of Mutations in the Jurkat Cell Line.” bioRxiv (2017): 118117. https://www.biorxiv.org/content/…

4. Markle, Tristan J., Philip Mwimanzi, and Mark A. Brockman. “HIV-1 Nef and T-cell activation: a history of contradictions.” Future virology 8.4 (2013): 391-404. https://www.researchgate.net/pro…

5. Takeuchi, Yasuhiro, Myra O. McClure, and Massimo Pizzato. “Identification of gammaretroviruses constitutively released from cell lines used for human immunodeficiency virus research.” Journal of virology 82.24 (2008): 12585-12588. Identification of Gammaretroviruses Constitutively Released from Cell Lines Used for Human Immunodeficiency Virus Research

https://www.quora.com/What-have-we-learned-about-T-cell-biology-from-Jurkat-cells/answer/Tirumalai-Kamala

Given that adults don’t have a functional thymus, how do T cells reconstitute after a bone marrow transplant?

Tags

Transplant, Transplantation

The Thymus – Wikipedia is where T cell – Wikipedia develop. Progenitor cells from the bone marrow enter the thymus to engage in a complicated developmental process and the ones who make it past various bottlenecks leave the thymus as functional, mature CD4 and CD8 T cells.

In the mouse, the thymus dramatically shrinks with age, a process called Involution (medicine) – Wikipedia that severely curtails its output of new, naive, i.e., antigen-inexperienced, T cells, and for long researchers simply extrapolated from mouse that thymic involution must be similarly consequential in humans as well. Important to remember here that the mouse is the most common experimental model for basic immunological research. Hence the assumption ‘Given that adults don’t have a functional thymus‘.

However, over time, the weight of experimental data informs us that the mouse isn’t simply a mini-human, albeit a four-legged, nocturnal, short-lived (maximum lifespan ~2 years) rodent version but rather a species unto itself whose physiological attributes cannot be directly extrapolated to the human (please do imagine my exaggerated eye roll here that it ever even got to the point that something so self-evident even needed saying). Specifically, extrapolating mouse thymus function to human is quite flawed.

This answer describes

• Key differences between mouse and human thymic function.
• Effects of thymectomy on T cell numbers and function in humans.
• Effects of transplant-related thymus impairment in humans.

Key Differences Between Mouse & Human Thymic Function

That a similar process of fewer new T cells coming out of the thymus with age had similar relevance in humans as it does in the mouse was long assumed. However, it turns out naive T cell maintenance is quite a different process in humans, one that makes it less dependent on the thymus over time.

• Circulating naive T cells in humans self-renew (1), a key difference in kind from naive mouse T cells. Specifically, this groundbreaking study (n=45) showed that the circulating naive T cell pool in elderly humans comprised 10% recent thymic emigrants and 90% self-proliferating (homeostatic proliferation), proportions that were exactly reversed in aged mice. Other studies (2) by other groups including an in silico modeling approach (3) have since corroborated that self-renewal following their emergence from the thymus is a major feature of human naive T cells. Such renewal depends on local levels of IL-7 (Interleukin 7 – Wikipedia) and some other cytokines.
• While short-lived in mice (1), naive T cells are very long lived in humans (4).
• Human thymic output may be already less relevant by the 20s since there is little evidence of increasing turnover of circulating naive T cells between 20 and 70 years of age (5). This implies that already by the 20s, the human thymus has pushed out T cell specificities most biologically relevant for an individual to maintain their immunity during their lifetime.
• Though human thymus begins to involute (reduces its output) early in life, it still remains active until beyond the 60s, only abruptly crashing in the 80s (6). Thus, blunt extrapolation from mouse thymus involution rates to humans is not only inaccurate but also inherently flawed because even the aged human thymus retains measurable capacity to generate new T cells (see below from 7, emphasis mine).

‘As an individual ages, the thymus involutes and the output of new T cells falls significantly [38–40]. In 1985, Steinman et al elegantly demonstrated that thymic function gradually starts decreasing from year one of life [38,39]. The observation of dual components of the human thymus, the true thymic epithelial space, in which thymopoiesis occurs, and the non-epithelial non thymopoietic perivascular space [38,39], was critical to the current understanding of thymic atrophy. The expansion of the perivascular space (adipocytes, peripheral lymphocytes, stroma) with age results in a shift in the ratio of true thymic epithelial space to perivascular space. The thymic epithelial space shrinks to less than 10% of the total thymus tissue by 70 years of age. When extrapolated, Steinman’s data suggest that the thymus would cease to produce new T cells at approximately 105 years of age (Figure 1) [41]…We and others have also demonstrated that while the thymopoietic area of the human thymus decreases with age, the thymopoietic potential per cell, as measured by sjTRECs [47] or by TCR ligation-mediated polymerase chain reaction [3], remains constant at least until approximately 50 years of age [43,45,47–50].’

Such data help understand what had long remained a conundrum, why the naive human T cell population only shrank modestly with age (8, 9, 10, 11), a reduction not in line with the much more rapid pace and extent of thymic involution. Since circulating naive human T cells appear to both hang around longer and be capable of proliferating (homeostatic proliferation) to maintain themselves, in practical terms, this means with age, human T cell repertoire depends less on a functioning thymus, relying instead on maintaining what’s already emerged from the thymus, a difference in kind from the mouse that makes the human T cell system more resilient to withstand damage to the T cell generating capabilities of the thymus. Repertoire refers to the antigen specificities of individual T cell TCRs (T-cell receptor – Wikipedia), with a broader diversity reflecting better anticipatory preparedness. After all, being prepared to specifically engage with antigens not previously encountered is the calling card of the Adaptive immune system – Wikipedia.

• Homeostatic proliferation is more important for CD4 rather than CD8 T cell maintenance (12), which may be why even the very old have a measurable naive CD4 T cell pool (11) and why impact of aging is greater for human CD8 T cells.
• None of this negates the importance of the thymus in introducing T cells with new specificities, i.e., T cells with TCRs capable of recognizing new antigens (epitopes). After all homeostatic proliferation can only maintain, not expand, the existing T cell repertoire, a function that’s the sole purview of the thymus. To quote from 1 (emphasis mine),

‘Although these data show that in terms of naive T cell numbers created per day, peripheral T cell proliferation by far exceeds thymic output in human adults, the thymus may still have an essential role – if only because new T cell specificities can only be created by the thymus.’

Effects of Thymectomy on T cell Numbers & Function in Humans

At 1 in 100 newborns, congenital heart disease is among the most common of birth defects (13). Over the past 30 years, having become safer and thus routine, open-heart surgery is increasingly used to correct these defects. However, this also often requires complete or partial thymectomy (thymus removal) since the thymus blocks surgical access to the heart and large vessels, especially in newborns. Researching immune function in such thymectomized individuals in turn provides valuable information on the consequences of such thymectomy.

• One study (14) on neonatally thymectomized children examined impact in either the short- (within 1 to 5 years, n=17 and 19 healthy controls) or longer-term (at least 10 years later, n=26 and 11 healthy controls) and found it drastically affects T cell diversity (measured as range of TCRs) in the short-term but that the thymus at such a young age is capable of some degree of regeneration since diversity is restored in later life.
• Another study (15) found rates of autoimmunity and allergy among the neonatally thymectomized (n=7) to be similar to healthy controls (n=7).
• Though both degree (partial versus total) (16) and age (17) at thymectomy influence outcome on T cell number and function, they don’t affect general health on the whole apart from a tendency for exaggerated responses to cytomegalovirus (CMV) (18). How to explain this? One plausible explanation could be that thymectomy provides impetus for increased plasma IL-7 levels (19), which in turn could support T cell homeostatic proliferation (20, 21).
• >20 years post-thymectomy, patients infected with CMV had fewer circulating naive T cells and reduced TCR diversity (18) and delayed primary antibody response to tick-borne encephalitis vaccination (22, 23).

Since routine neonatal open-heart surgery and its attendant thymectomy are at 30 years or so of recent vintage, lifelong impact on immunity and health is still work in progress. However, these and other studies suggest impact is individual, hard to predict and highly influenced by chronic infections, especially CMV.

Effects of Transplant-related Thymus Function or Impairment in Humans

Preparing the body for transplant (transplant conditioning regimens) entails the kinds of preparatory treatments (irradiation, chemotherapy, steroids) that severely damage the thymus, impairing its capacity to push out new T cells.

• Adequate thymic recovery was observed after autologous stem cell transplant
  • Even in those with severe autoimmune diseases (n=10, age range 16 to 49 years old, n=21 controls, age range 20 to 55 years old) (24).
  • In Multiple Sclerosis (MS) patients (n=7, age range 28 to 53) (25).
• Adequate thymic recovery was observed after heterologous kidney transplant (n=48 patients, 39 controls) (26).
• One study (27) of 32 adult breast cancer patients treated with autologous peripheral blood stem cell transplant (age range 30 to 69) found thymic recovery to be strictly a function of age, with measurable thymus enlargement (sign of recovery) post-transplant in
  • 4 of 5 of those 30 to 39 years old
  • 6 of 13 in those 40 to 49 years old.
  • Only 2 of 14 in those >50 years old.

Given its capacity for some regeneration as well as its ability to continue to push out new T cells even later in life, albeit at markedly lower rates, no surprise that the human thymus can bounce back after neonatal thymectomy as well as from transplant-related damage. Degree of recovery is also unsurprisingly a function of age and environment. As well, unlike their mouse counterparts, human naive T cell capacity for self-propagation helps maintain them even into old age.

Bibliography

1. den Braber, Ineke, et al. “Maintenance of peripheral naive T cells is sustained by thymus output in mice but not humans.” Immunity 36.2 (2012): 288-297. https://ac.els-cdn.com/S10747613…

2. Thome, Joseph JC, et al. “Longterm maintenance of human naive T cells through in situ homeostasis in lymphoid tissue sites.” Science immunology 1.6 (2016). https://www.ncbi.nlm.nih.gov/pmc…

3. Johnson, Philip LF, et al. “Peripheral selection rather than thymic involution explains sudden contraction in naive CD4 T-cell diversity with age.” Proceedings of the National Academy of Sciences 109.52 (2012): 21432-21437. http://www.pnas.org/content/109/…

4. Vrisekoop, Nienke, et al. “Sparse production but preferential incorporation of recently produced naive T cells in the human peripheral pool.” Proceedings of the National Academy of Sciences 105.16 (2008): 6115-6120. http://www.pnas.org/content/105/…

5. Naylor, Keith, et al. “The influence of age on T cell generation and TCR diversity.” The Journal of Immunology 174.11 (2005): 7446-7452. https://www.researchgate.net/pro…

6. Czesnikiewicz-Guzik, Marta, et al. “T cell subset-specific susceptibility to aging.” Clinical Immunology 127.1 (2008): 107-118. https://www.researchgate.net/pro…

7. Gruver, A. L., L. L. Hudson, and G. D. Sempowski. “Immunosenescence of ageing.” The Journal of pathology 211.2 (2007): 144-156. http://onlinelibrary.wiley.com/d…

8. Bertho, Jean-Marc, et al. “Phenotypic and immunohistological analyses of the human adult thymus: evidence for an active thymus during adult life.” Cellular immunology 179.1 (1997): 30-40.

9. Douek, Daniel C., et al. “Changes in thymic function with age and during the treatment of HIV infection.” Nature 396.6712 (1998): 690.

10. Jamieson, Beth D., et al. “Generation of functional thymocytes in the human adult.” Immunity 10.5 (1999): 569-575. http://www.cell.com/immunity/pdf…

11. Wertheimer, Anne M., et al. “Aging and cytomegalovirus infection differentially and jointly affect distinct circulating T cell subsets in humans.” The Journal of Immunology 192.5 (2014): 2143-2155. http://www.jimmunol.org/content/…

12. Goronzy, Jörg J., et al. “Naive T cell maintenance and function in human aging.” The Journal of Immunology 194.9 (2015): 4073-4080. http://www.jimmunol.org/content/…

13. Hoffman, Julien IE, and Samuel Kaplan. “The incidence of congenital heart disease.” Journal of the American college of cardiology 39.12 (2002): 1890-1900. https://ac.els-cdn.com/S07351097…

14. Van Den Broek, Theo, et al. “Neonatal thymectomy reveals differentiation and plasticity within human naive T cells.” The Journal of clinical investigation 126.3 (2016): 1126. https://www.ncbi.nlm.nih.gov/pmc…

15. Silva, Susana L., et al. “Autoimmunity and allergy control in adults submitted to complete thymectomy early in infancy.” PloS one 12.7 (2017): e0180385. http://journals.plos.org/plosone…

16. Halnon, Nancy J., et al. “Thymic function and impaired maintenance of peripheral T cell populations in children with congenital heart disease and surgical thymectomy.” Pediatric research 57.1 (2005): 42-48. https://www.researchgate.net/pro…

17. Prelog, Martina, et al. “Thymectomy in early childhood: significant alterations of the CD4+ CD45RA+ CD62L+ T cell compartment in later life.” Clinical immunology 130.2 (2009): 123-132. http://www.musiklexikon.ac.at:80…

18. Sauce, Delphine, et al. “Evidence of premature immune aging in patients thymectomized during early childhood.” The Journal of clinical investigation 119.10 (2009): 3070. Evidence of premature immune aging in patients thymectomized during early childhood

19. Mancebo, E., et al. “Longitudinal analysis of immune function in the first 3 years of life in thymectomized neonates during cardiac surgery.” Clinical & Experimental Immunology 154.3 (2008): 375-383. http://onlinelibrary.wiley.com/d…

20. Fry, Terry J., and Crystal L. Mackall. “The many faces of IL-7: from lymphopoiesis to peripheral T cell maintenance.” The Journal of Immunology 174.11 (2005): 6571-6576. http://www.jimmunol.org/content/…

21. Silva, Susana L., et al. “Human naive regulatory T-cells feature high steady-state turnover and are maintained by IL-7.” Oncotarget 7.11 (2016): 12163. https://pdfs.semanticscholar.org…

22. Prelog, Martina, et al. “Diminished response to tick-borne encephalitis vaccination in thymectomized children.” Vaccine 26.5 (2008): 595-600.

23. Zlamy, Manuela, et al. “Antibody dynamics after tick-borne encephalitis and measles–mumps–rubella vaccination in children post early thymectomy.” Vaccine 28.51 (2010): 8053-8060.

24. Thiel, Andreas, et al. “Direct assessment of thymic reactivation after autologous stem cell transplantation.” Acta haematologica 119.1 (2008): 22-27.

25. Muraro, Paolo A., et al. “Thymic output generates a new and diverse TCR repertoire after autologous stem cell transplantation in multiple sclerosis patients.” Journal of Experimental Medicine 201.5 (2005): 805-816. http://jem.rupress.org/content/j…

26. Nickel, Peter, et al. “CD31+ Naïve Th Cells Are Stable during Six Months Following Kidney Transplantation: Implications for Post‐transplant Thymic Function.” American journal of transplantation 5.7 (2005): 1764-1771. http://onlinelibrary.wiley.com/d…

27. Hakim, Frances T., et al. “Age-dependent incidence, time course, and consequences of thymic renewal in adults.” Journal of Clinical Investigation 115.4 (2005): 930. http://content-assets.jci.org/ma…

https://www.quora.com/Given-that-adults-dont-have-a-functional-thymus-how-do-T-cells-reconstitute-after-a-bone-marrow-transplant/answer/Tirumalai-Kamala

In what ways can antibodies serve as immunogens in the body?

Question appears to ask whether a person’s own antibodies could serve as immunogens to their own immune system so that’s what this answer addresses. An Immunogen – Wikipedia is any substance capable of eliciting an immune response, i.e., target of an immune response. Though immunogen and Antigen – Wikipedia are often interchangeably used terms, key difference between the two is the final outcome. While both antigen and immunogen can bind an immune receptor, typically immunogen is used for something known to trigger an immune response.

Essential building blocks of life, proteins are far and away the singular focus of the human immune system, especially of the adaptive immune system, which consists of T and B cells. Antibodies are protein molecules so of course, they could be targets of immune responses, except there are inbuilt processes that serve as safeguards to minimize, not eliminate, such likelihood. Why minimize but not eliminate the likelihood antibodies could themselves be immunogens?

T cells are the master architects of human adaptive immune responses. B cells typically need T cell help to make antibodies, even antibodies against other antibodies. T cell help for B cells is usually called cognate, meaning the T cell ‘sees’ a portion of the same antigen as the B cell.

Antibodies, just like other protein molecules can be internalized by antigen presenting cells such as dendritic cells, macrophages and monocytes, get digested and their peptides presented to T cells within MHC molecules. However, normally, T cells with receptors specific for most of the peptide pieces generated from digesting antibody molecules would be already deleted during their development in the thymus by a process called Central tolerance – Wikipedia, the key mechanism that ensures our immune system doesn’t constantly attack our own cells, tissues and organs.

Central tolerance though is and never could be complete, no, not even in the healthiest of humans, for the simple reason that not everything that can be expressed by the body (called the periphery by immunologists, as opposed to the thymus where Central Tolerance occurs) is or could be expressed and/or presented by the thymus. This is especially the case for one particular portion of antibodies namely a part within its variable portion.

Antibodies have essentially two parts that help them perform their various functions (which immunologists call effector functions).

• The antigen-binding part is the antibody’s variable portion, variable as in being the product of Somatic recombination – Wikipedia, a unique B (also T) cell capability responsible for the enormous diversity in antibody binding specificities. Somatic hypermutation – Wikipedia further endows antibodies with unique hypermutated regions, which immunologists call Complementarity-determining region – Wikipedia (CDR3), that enable each one to bind more specifically and with higher affinity to its target.
• The antibody’s constant part, its Fc, is unique to each antibody isotype (Isotype (immunology) – Wikipedia or antibody class) with each isotype binding to different Fc receptor – Wikipedia (FcR). Antibody’s Fc binding to cell-surface FcR enables antibodies to mediate phagocytosis, complement-dependent killing, Antibody-dependent cell-mediated cytotoxicity – Wikipedia (ADCC), as well as cytokine secretion from antibody-bound cells.

Peptides derived from an antibody’s hypermutated region, its CDR3, could not only be antigens but could theoretically also serve as immunogens for T cells. However, this normally rarely happens even in autoimmunity because T cell generation is a Stochastic – Wikipedia process and frequency of T cells with receptors capable of binding peptides derived from any one antibody’s CDR3 are too few to get a full-fledged immune response going.

OTOH, ordinarily an antibody’s constant portion, its FcR, is far less likely to be an immunogen. T cells whose receptors could bind FcR-derived peptides would be deleted during their development in the thymus by the process of Central Tolerance. Thus, antibody’s Fc portion could usually become targets of body’s own immune response only when normal tolerance mechanisms break down, as happens in autoimmunity. This is because as long as they belong to the same isotype (antibody class), a whole bunch of antibodies specific for different antigens would still have the same Fc portion. Thus, provided there is a problem with Central Tolerance, this increases the likelihood of sufficient T cells whose receptors could ‘see’ Fc-derived peptides to initiate and sustain an anti-antibody response.

https://www.quora.com/In-what-ways-can-antibodies-serve-as-immunogens-in-the-body/answer/Tirumalai-Kamala

What are the risks and benefits of using cell therapy that “turbocharges” the immune system to fight cancer?

Tags

CAR (Chimeric Antigen Receptor)-T

CAR-T cells and checkpoint inhibitors are currently the two major approaches to ‘turbocharge’ the immune system to fight cancer. While current generation of CAR-Ts have been found to work fairly well for blood cancers, especially B cell – Wikipedia cancers, I’ve argued elsewhere (1) this could well be because such approaches piggy-back on evolutionarily conserved mechanisms for T cell-B cell interactions which are the backbone of proper Adaptive immune system – Wikipedia function. However, such results haven’t yet been achieved for solid tumors where such approaches remain largely non-tumor specific, a major liability since it leaves open the possibility of fulminant tissue pathology and even autoimmunity.

In that respect, these two approaches aren’t necessarily an improvement on current cancer therapy mainstays, radiation and chemotherapy, both of which come with the well-known price tag of considerable collateral tissue damage. For example, CAR-Ts are increasingly hitting roadblocks in the form of life-threatening complications and even deaths in clinical trials and that too for other blood not even solid tissue cancers, so much so that leading cancer immunotherapy biotech, Juno Therapeutics – Wikipedia, recently mothballed its lead CAR-T therapy, for ALL (Acute lymphoblastic leukemia – Wikipedia) (2).

As-yet unattained, singular promise of Cancer immunotherapy – Wikipedia is potential to specifically target tumors, using tumor antigen-specific approaches. Major obstacles in achieving this goal remain

1. Identifying and validating tumor-specific antigens for various cancers.
2. Identifying, isolating and in vitro expanding tumor antigen-specific T cells, both CD4 and CD8.
3. Confirming tumor antigen-specificity of such T cells.

Steps 1 and 2 are extremely technologically challenging in basic immunological research itself so likely even more so in human immunology. As technological capabilities to a) identify tumor-specific antigens, and b) manipulate human T cells in vitro improve, chances of achieving a theoretical no-pain-all-gain goal could improve. Only such an approach would optimally harness the unique antigen-specific capacity of the adaptive immune system to specifically target and eliminate tumors without damaging normal tissues. A 2015 review (3) by Ton Schumacher and Robert D. Schreiber – Wikipedia is one of the most comprehensive in contextualizing the scope and potential of such as-yet unrealized tumor antigen-specific immunotherapy.

However, such an approach would likely still remain rather labor-intensive and artisanal since it’d remain individualized, personalized if you will. For one, mutations within tumors are increasingly recognized to be very idiosyncratic, varying not only from one patient to another but also from one part of a tumor to another. For another, as we already know from transplantation, T cell capacity for Graft-versus-host disease – Wikipedia necessitates autologous T cell infusions for cancer Rx (Autotransplantation – Wikipedia).

Bibliography

1. Tirumalai Kamala’s answer to Why is CAR T not very effective on solid tumors?

2. Xconomy, Alex Lash, March 1, 2017. After Trial Deaths, Juno Pivots and Scraps Lead CAR-T Therapy | Xconomy

3. Schumacher, Ton N., and Robert D. Schreiber. “Neoantigens in cancer immunotherapy.” Science 348.6230 (2015): 69-74. http://pmpathway.wustl.edu/files…

https://www.quora.com/What-are-the-risks-and-benefits-of-using-cell-therapy-that-turbocharges-the-immune-system-to-fight-cancer/answer/Tirumalai-Kamala

How do T-cells recognize foreign MHC molecules?

Tags

alloreactivity

Question details: How do T-cells recognize foreign MHC molecules (and get activated thereafter), when the T-cells are positively selected in the thymus to recognize only own MHC (and foreign peptide, and get activated thereafter)?

T cell development occurs in the Thymus – Wikipedia. T cells bind pMHC (peptides bound to Major histocompatibility complex – Wikipedia (MHC)). In fact they can bind peptides presented both by MHC expressed by cells in the Thymus – Wikipedia of the body in which they develop, MHC restriction – Wikipedia, as well as by MHC expressed in genetically non-identical transplants, for e.g. during Allotransplantation – Wikipedia (1) *. The latter phenomenon is called alloreactivity.

As-Yet Unresolved Conundrums About T cell Development

The remarkable feature about the repertoire of B and T cells bearing unique B-cell receptor – Wikipedia (BCRs) and TCRs is they’re generated blind, i.e., in the absence of foreknowledge of antigens and antigen-derived peptides a person may encounter and need to respond to through their lifetime. T cell repertoire refers to the diversity of clonotypic T cells expressing unique TCRs, clonotypic meaning when a given T cell divides it creates a multitude of T cells bearing that same unique somatically generated TCR (Somatic recombination – Wikipedia).

T cells aren’t ‘positively selected in the thymus to recognize only own MHC (and foreign peptide)‘. To understand how that’s not even possible, consider someone who gets infected with flu. Thymic selection of T cells that ‘recognize only own MHC and foreign peptide‘ implies that to even have flu-specific T cells in the first place, the thymus should express flu antigens to positively select T cells expressing flu-specific TCRs, and so on ad nauseam for every one of the millions of peptides derived from the multitude of different kinds of entities a body might encounter and need to prevail over in the course of a lifetime. Crux is the thymus needs to select myriad T cell specificities during thymic T cell development even though the body can’t predict what antigen-derived peptides and antigens it would encounter in future. After all, the human adaptive immune system does have T (and B) cells that can specifically recognize and bind any number and variety of them. A conundrum indeed in that mature T cells bind specifically to both peptides (the norm in any immune response) and MHC molecules (the case in ‘direct’ response to allogeneic transplants) that they “couldn’t” have encountered during their development in the thymus.

• How are TCR specificities selected during T cell development, as in the nature of the selecting thymic peptides. Cross-reactivity – Wikipedia is implicit in this process since clearly flu-derived peptides cannot have selected for a flu-specific T cell and so on.
• Alloreactvity only adds to the conundrum since T cells also appear capable of binding MHC molecules they’ve obviously never previously encountered as happens with genetically mismatched transplants.

MHC Restriction Of T cells

Two principal models explain MHC restriction of T cells (2, 3, 4, 5, 6, 7).

• One suggests the CD4 – Wikipedia and CD8 – Wikipedia co-receptors impose it during thymic development. These coreceptors are associated with the unique T cell Kinase – Wikipedia, Lck – Wikipedia and the idea is only those developing T cells, i.e., Thymocyte – Wikipedia, that succeed in binding MHC II or I with CD4 or CD8, respectively, could generate the full complement of signaling necessary within themselves to make it past this do or die bottleneck.
• The other postulates germline-encoded CDRs (Complementarity-determining region – Wikipedia), CDR1 and 2 within the TCR, need to bind distinct pockets within the MHC.

Though not mutually exclusive, these models make different predictions. For the first one it doesn’t matter whether the T cell repertoire contains TCRs that bind pMHC or not while the second one requires TCRs biased to bind MHC, regardless of its class (I or II) or allele.

T cells That Make It Through Thymic Development Appear Wired to Bind MHC

Back in 1971, Niels Kaj Jerne – Wikipedia hypothesized ‘parallel evolution’ (8) of MHC and the then-undiscovered T-cell receptor – Wikipedia (TCR). After all, how else to explain alloreactivity other than by coevolution of TCR and MHC (9)?

As a recent illustrative example, a clever in vitro cellular model from 2016 demonstrates that TCRs may indeed be hard-wired to bind MHC (10; see figure below from 11).

This 2016 study thus concurs with many previous experimental (mostly mouse and some human) studies that found some Germline – Wikipedia amino acid residues on TCR alpha and beta chains to be crucial for binding MHC (4, 12, 13, 14, 15).

Cumulative data thus allows to infer that T cell development in the thymus may be mainly to ensure that only T cells with a ‘functional’ TCR get through developmental bottlenecks to be released into the ‘periphery’, i.e., a TCR capable of binding pMHC and delivering a modicum of signals downstream into the T cell, just enough, not too much nor too little, a la Goldilocks.

How To Explain T cell Alloreactivity (Ability of T cells to bind and respond to MHCs other than those that selected them in the thymus)

TCRs clearly bind both MHC molecules and the peptides they present. Two prevalent models to explain alloreactivity largely differ in which is more important, recognition of the peptides that allo MHC present, peptide-centric model, or the MHC molecules themselves, MHC-centric model (see figure below from (1).

Structural and some functional data from different experimental studies (16, 17, 18, 19) support either model.

One mouse TCR (17) was found to assume different conformations to accommodate binding to selecting versus novel MHC and in that study interfering with TCR’s ability to engage the peptide had little effect, i.e., support for the MHC-centric model. One mouse TCR was found to assume different conformations to accommodate binding to different peptides (16), i.e., support for the peptide-centric model. Meantime studies with human TCRs and HLA class I (18, 19) also support the MHC-centric model. Rather than one or the other, both approaches likely play their part in physiology.

* Note this answer deliberately avoids using ‘self’ and ‘non-self’/‘foreign’, mainstay words in immunology that obfuscate rather than clarify. In the age of Human microbiota – Wikipedia they’re also obviously unsuitable.

Bibliography

1. Boardman, Dominic A., et al. “What Is Direct Allorecognition?.” Current Transplantation Reports (2016): 1-9. What Is Direct Allorecognition?

2. Feng, Dan, et al. “Structural evidence for a germline-encoded T cell receptor–major histocompatibility complex interaction’codon’.” Nature immunology 8.9 (2007): 975-983. https://www.researchgate.net/pro…

3. Dai, Shaodong, et al. “Crossreactive T Cells spotlight the germline rules for αβ T cell-receptor interactions with MHC molecules.” Immunity 28.3 (2008): 324-334. http://www.cell.com/immunity/pdf…

4. Garcia, K. Christopher, et al. “The molecular basis of TCR germline bias for MHC is surprisingly simple.” Nature immunology 10.2 (2009): 143-147. https://www.ncbi.nlm.nih.gov/pmc…

5. Garcia, K. Christopher. “Reconciling views on T cell receptor germline bias for MHC.” Trends in immunology 33.9 (2012): 429-436. https://www.ncbi.nlm.nih.gov/pmc…

6. Yin, Lei, et al. “T cells and their eons‐old obsession with MHC.” Immunological reviews 250.1 (2012): 49-60. https://www.ncbi.nlm.nih.gov/pmc…

7. Van Laethem, François, Anastasia N. Tikhonova, and Alfred Singer. “MHC restriction is imposed on a diverse T cell receptor repertoire by CD4 and CD8 co-receptors during thymic selection.” Trends in immunology 33.9 (2012): 437-441. https://www.ncbi.nlm.nih.gov/pmc…

8. Jerne, Niels Kaj. “The somatic generation of immune recognition.” European journal of immunology 1.1 (1971): 1-9. http://onlinelibrary.wiley.com/d…

9. Felix, Nathan J., and Paul M. Allen. “Specificity of T-cell alloreactivity.” Nature Reviews Immunology 7.12 (2007): 942-953.

10. Parrish, Heather L., et al. “Functional evidence for TCR-intrinsic specificity for MHCII.” Proceedings of the National Academy of Sciences 113.11 (2016): 3000-3005. http://www.pnas.org/content/113/…

11. Krovi, Sai Harsha, and Laurent Gapin. “Revealing the TCR bias for MHC molecules.” Proceedings of the National Academy of Sciences 113.11 (2016): 2809-2811. http://www.pnas.org/content/113/…

12. Huseby, Eric S., et al. “How the T cell repertoire becomes peptide and MHC specific.” Cell 122.2 (2005): 247-260. http://www.cell.com/cell/pdf/S00…

13. Marrack, Philippa, et al. “Evolutionarily conserved amino acids in TCR V regions and MHC control their interaction.” Annual review of immunology 26 (2008): 171. https://www.ncbi.nlm.nih.gov/pmc…

14. Scott-Browne, James P., et al. “Germline-encoded amino acids in the αβ T cell receptor control thymic selection.” Nature 458.7241 (2009): 1043. https://www.ncbi.nlm.nih.gov/pmc…

15. Adams, Jarrett J., et al. “Structural interplay between germline interactions and adaptive recognition determines the bandwidth of TCR-peptide-MHC cross-reactivity.” Nature immunology 17.1 (2016): 87-94. https://www.ncbi.nlm.nih.gov/pmc…

16. Reiser, Jean-Baptiste, et al. “Crystal structure of a T cell receptor bound to an allogeneic MHC molecule.” Nature immunology 1.4 (2000): 291-297. https://www.researchgate.net/pro…

17. Colf, Leremy A., et al. “How a single T cell receptor recognizes both self and foreign MHC.” Cell 129.1 (2007): 135-146. https://www.researchgate.net/pro…

18. Archbold, Julia K., et al. “Alloreactivity between disparate cognate and allogeneic pMHC-I complexes is the result of highly focused, peptide-dependent structural mimicry.” Journal of Biological Chemistry 281.45 (2006): 34324-34332. Alloreactivity between Disparate Cognate and Allogeneic pMHC-I Complexes Is the Result of Highly Focused, Peptide-dependent Structural Mimicry

19. Macdonald, Whitney A., et al. “T cell allorecognition via molecular mimicry.” Immunity 31.6 (2009): 897-908. https://www.researchgate.net/pro…

https://www.quora.com/How-do-T-cells-recognize-foreign-MHC-molecules/answer/Tirumalai-Kamala

How is it possible that a T Cell Receptor (TCR) recognises as few as 1-3 residues of the MHC-associated peptide?

Tags

Complementarity-determining region (CDR)3, Immunodominance, pMHC (peptide bound to MHC molecule), somatic gene rearrangement, VDJ recombination

Question details: In Basic Immunology, 5th Edition, it was mentioned that “each TCR recognizes as few as one to three residues of the MHC-associated peptide”. How is that possible while retaining specificity to the antigen? It seems to me that any single amino acid could be common to more than 1 peptide.

Short answer: Structural constraints on how many amino acid residues TCRs can bind on short peptide sequences include

• Several of the peptide’s amino acid residues are already engaged in binding firmly to an MHC (Major histocompatibility complex) molecule creating the pMHC (peptide bound to MHC molecule).
• At the same time the TCR also needs to bind some amino acid residues of the MHC molecule itself.

Different parts of the TCR bind peptide and MHC. The unique process of somatic nucleotide insertions and deletions makes the TCR’s Complementarity-determining region (CDR)3 region hypervariable and thus quite flexible and effective in binding a few conserved residues on a MHC-bound peptide. This feature also makes TCRs cross-reactive, i.e., capable of binding >1 unique pMHC.

Longer answer on theoretical basis for why it should be so and some data on how TCRs actually bind peptides

The adaptive immune system is predicated on the notion of anticipatory defense. CD4 and CD8 T cells express the alphabeta TCR, composed of two protein chains, alpha and beta. Each undergoes somatic gene rearrangement, specifically V(D)J recombination, i.e., nucleotide insertions and deletions at the V(D) J junctions in the Complementarity-determining region (CDR)3 regions of each chain of the TCR. This means each human body iterates from scratch its adaptive defense armamentarium, something that a 2015 immune parameter analysis of 210 healthy monozygotic twin pairs only confirms (1).

At first glance, this seems reasonable enough. After all, TCRs on CD4 and CD8 T cells have evolved to recognize and bind not whole protein molecules, ‘antigens’, but rather presented by MHC molecules, tiny pieces thereof, ‘peptides’, 12- to 20-mer (12-20 amino acids in length) in the case of CD4s, and 8- to 14-mer in the case of CD8s.

On second glance, this imposes a heavy burden on such a recognition system. Zooming in from larger structures to much smaller ones means the number of peptides presented to T cells by MHC class I and II molecules should be very large. Why should? Zooming in to such magnification simply exponentially increases the number of targets, i.e., peptides. If MHC molecules didn’t present as diverse of a peptide pool as possible from within a cell, missed pathogen-derived peptides become missed opportunities weakening the anticipatory potential of the adaptive immune system.

Given that TCRs bind short peptide sequences presented by MHC molecules, how could recognition be based on other than a handful of amino acid residues? Much of the rest of the peptide binds the MHC molecule. Peptide binding to MHC is itself a critical filtering event of great consequence in adaptive immunity. Antigen processing generates many peptides of varying lengths during protein digestion but only a handful succeed in making it past several bottlenecks to successfully and tightly bind MHC in such a way that they get presented on the cell surface, a feature called Immunodominance.

Why Most T cell Receptors (TCRs) Need To Be Inherently Cross-Reactive, Capable Of Binding >1 pMHC Complex

T cell receptors (TCRs) bind bits of both MHC and peptide. TCRs are hypothesized to have been evolutionarily selected to recognize and bind MHC. Thus, considering just the TCR engagement with the peptide cuts off too small a slice of the pie since outcome, TCR-mediated biochemical activation of T cells, depends on other critical factors,

• How the peptide is bound within the MHC, which in turn determines which of its amino acid residues are available to make contact with the TCR and how optimally that could happen.
• How the peptide is bound within the MHC also determines how optimally key anchor residues of the MHC molecule itself are available to bind the TCR.
• How optimally can T cell co-receptors CD3 (immunology), CD4 (for CD4+ T cells)/CD8 (for CD8+ T cells) bind MHC at the same time.

Corollary of the fact that TCRs recognize and bind peptides presented by MHC molecules is the need for correspondingly large repertoire of specific T cells, one specific enough to recognize and bind each peptide processed and presented by each MHC molecule. However, if each TCR bound only one specific peptide, a logical extension of the Clonal selection theory (2, 3), each individual would theoretically need >10^15 T cells. Why? Because the 20 amino acid alphabet predicates the possible number of peptides that could bind to MHC molecules to be in the range of 10^15 (4). But 10^15 monospecific T cells necessary for optimal anticipatory defense entails a body weight of >500kgs (4), clearly and simply a physical impossibility, something that Don Mason already demonstrated in 1998 with his absurd mouse cartoon (see below from 5).

Given the constraint that there can only be far fewer T cells with unique TCRs compared to the potential diversity of possible unique pMHC complexes, no surprise TCRs tend to be cross-reactive, i.e., capable of binding >1 pMHC complex. An elegant 2014 experimental study found each of 5 different mouse and human TCRs even capable of binding >100 different peptides presented by one MHC molecule (6). Thus far crystal structures of ~120+ TCR- pMHC complexes have been published. One of the most striking observations of such crystal structures is the tremendous flexibility in how TCRs bind to pMHC (7). Rather than binding unique peptides, a given TCR can bind many but TCR binding’s supposed to be very specific. Cross-reactivity is antithetical to specificity. Can the two be reconciled? Yes, by the fact that the common thread linking cross-reactive peptides that bind a given TCR is the presence of conserved motifs, i.e., one, two, three or more conserved residues at specific TCR-binding positions (see quote, emphasis mine, and figure below from 6).

‘TCR cross-reactivity is not achieved by each receptor recognizing a large number of unrelated peptide epitopes but rather through greater tolerance for substitutions to peptide residues outside of the TCR interface, differences in residues that contact the MHC, and relatively conservative changes to the residues that contact the TCR CDR loops. The segregation of TCR recognition and MHC binding allows for TCRs to simultaneously accommodate needs for specificity and cross-reactivity.’

Thus, this example shows that even though peptides like 2A and MCC are very different in their sequences, both successfully bind the same TCR 2B4 because the process of somatic nucleotide insertions and deletions makes the region that primarily makes contact with a peptide, the TCR’s CDR3 region, hypervariable. This endows TCRs with the capacity to be quite flexible in accommodating different peptide sequences and also be able to bind firmly by contacting only a handful of conserved residues on any given MHC-bound peptide.

Human epidemiological studies reveal the implications of T cell recognition being the way it is. A relatively obscure set of data epitomize not only the extent of T cell cross-reactivity but also suggest that such functionality enables a vast, connected immunoprotective landscape against disparate entities ranging from bacteria to virus to cancer.

~85% of malignant melanocytes express an antigen called HERV-K-MEL (8, 9, 10), product of a pseudo-gene incorporated in the HERV-K env gene. HERV (Human Endogenous retrovirus) in turn are endogenous retroviruses incorporated into the human genome over millions of years. Acquired between 3 and 6 million years back, HERV-K are the latest family (11), making them the only HERVs still capable of replicating in the human population within the last few million years. HERV-K appears to be involved in several stages of melanoma formation (12, 13, 14).

Spontaneous melanoma regressions have occasionally been reported in the literature, suggesting effective anti-melanoma immune responses occur in nature. But what are the coordinates of such immunity? Taking a leaf out of William Coley and his Coley’s toxins, the European Organization for Research and Treatment of Cancer (EORTC) established the Febrile Infections and Melanoma (FEBIM) working group, tasked to explore how prior infectious diseases and vaccines influenced melanoma risk.

Their studies thus far suggest the Tuberculosis (TB) BCG vaccine, the Vaccinia vaccine against small pox and the 17D Yellow fever vaccine provide some degree of protection against melanoma (15, 16, 17).

What could possibly link such disparate characters as BCG, Vaccinia, Yellow fever and Melanoma and what connects this story to TCRs and peptides? Turns out each of these really disparate agents, a bacterium and two unrelated viruses, express peptides with high sequence homology to the melanoma HERV-K-MEL peptide (see below from 18).

BCG, vaccinia and yellow fever vaccines are of course expected to induce specific immune responses against themselves. However, given they express proteins with high sequence homology, vaccine-specific cytotoxic CD8+ and helper CD4+ T cells would also include those cross-reactive to melanoma HERV-K-MEL peptide. This could prevent melanoma development in those vaccinees who retain robust memory immune responses against this cross-reactive peptide.

Such phenomena may underlie the observation that certain live vaccines like BCG and measles can protect against unrelated pathogens and even reduce rates of all-cause mortality (19, 20). And as more microbiota-immunity interactions get mined, such examples that at present seem unanticipated will become more commonplace.

Bibliography

1. Brodin, Petter, et al. “Variation in the human immune system is largely driven by non-heritable influences.” Cell 160.1 (2015): 37-47.

2. Jerne, Niels K. “The natural-selection theory of antibody formation.” Proceedings of the National Academy of Sciences 41.11 (1955): 849-857. http://www.pnas.org/content/41/1…

3. Jerne, Niels Kaj. “The somatic generation of immune recognition.” European journal of immunology 1.1 (1971): 1-9.

4. Sewell, Andrew K. “Why must T cells be cross-reactive?.” Nature Reviews Immunology 12.9 (2012): 669-677. http://www.tcells.org/scientific…

5. Mason, Don. “A very high level of crossreactivity is an essential feature of the T-cell receptor.” Immunology today 19.9 (1998): 395-404.

6. Birnbaum, Michael E., et al. “Deconstructing the peptide-MHC specificity of T cell recognition.” Cell 157.5 (2014): 1073-1087. http://www.cell.com/cell/pdf/S00…

7. Rudolph, Markus G., Robyn L. Stanfield, and Ian A. Wilson. “How TCRs bind MHCs, peptides, and coreceptors.” Annu. Rev. Immunol. 24 (2006): 419-466. http://nfs.unipv.it/nfs/minf/dis…

8. Kölmel, K. F., O. Gefeller, and B. Haferkamp. “Febrile infections and malignant melanoma: results of a case-control study.” Melanoma research 2.3 (1992): 207-212

9. Schiavetti, Francesca, et al. “A human endogenous retroviral sequence encoding an antigen recognized on melanoma by cytolytic T lymphocytes.” Cancer research 62.19 (2002): 5510-5516. https://www.researchgate.net/pro…

10. Grange, John M., et al. “Can prior vaccinations against certain infections confer protection against developing melanoma?.” Medical Journal of Australia 191.9 (2009): 478. http://citeseerx.ist.psu.edu/vie…

11. Sverdlov, Eugene D. “Retroviruses and primate evolution.” Bioessays 22.2 (2000): 161-171.

12. Muster, Thomas, et al. “An endogenous retrovirus derived from human melanoma cells.” Cancer research 63.24 (2003): 8735-8741. https://www.researchgate.net/pro…

13. Serafino, A., et al. “The activation of human endogenous retrovirus K (HERV-K) is implicated in melanoma cell malignant transformation.” Experimental cell research 315.5 (2009): 849-862. https://www.researchgate.net/pro…

14. Singh, Sarita, et al. “The role of human endogenous retroviruses in melanoma.” British Journal of Dermatology 161.6 (2009): 1225-1231.

15. Grange, John M., Bernd Krone, and John L. Stanford. “Immunotherapy for malignant melanoma–tracing Ariadne’s thread through the labyrinth.” European Journal of Cancer 45.13 (2009): 2266-2273.

16. Krone, Bernd, et al. “Protection against melanoma by vaccination with Bacille Calmette-Guerin (BCG) and/or vaccinia: an epidemiology-based hypothesis on the nature of a melanoma risk factor and its immunological control.” European Journal of Cancer 41.1 (2005): 104-117.

17. Mastrangelo, G., et al. “Does yellow fever 17D vaccine protect against melanoma?.” Vaccine 27.4 (2009): 588-591.

18. Cegolon, Luca, et al. “Human endogenous retroviruses and cancer prevention: evidence and prospects.” BMC cancer 13.1 (2013): 1. http://bmccancer.biomedcentral.c…

19. Goodridge, Helen S., et al. “Harnessing the beneficial heterologous effects of vaccination.” Nature Reviews Immunology (2016).

20. Muraille, Eric. “The Unspecific Side of Acquired Immunity Against Infectious Disease: Causes and Consequences.” Frontiers in microbiology 6 (2015). https://www.ncbi.nlm.nih.gov/pmc…

https://www.quora.com/How-is-it-possible-that-a-T-Cell-Receptor-TCR-recognises-as-few-as-1-3-residues-of-the-MHC-associated-peptide/answer/Tirumalai-Kamala

Why is chimeric antigen receptor better than just injecting anti-CD19 antibodies? Since our natural killer cells can kill the cells attached with antibodies via antibody-dependent cell-mediated cytotoxicity.

Tags

Antibody-dependent cell-mediated cytotoxicity (ADCC), CD19, Chimeric antigen receptor (CAR), NK (natural killer) cell

Selectively getting rid of B cells is the therapeutic goal with many Leukemia and Lymphoma. It stands to reason that anti-CD19 antibodies would target B cell, which ~ exclusively and specifically express the CD19 molecule. In turn, anti-CD19 antibody-bound B cells are the target of Natural killer cell-mediated Antibody-dependent cell-mediated cytotoxicity, i.e., how antibodies that specifically bind to B cells could be used to get rid of them in B cell malignancies.

In practical terms, the success of such an antibody-mediated approach depends on the antibody’s Biological half-life within the body. Since much of the injected Antibody is simply eliminated, not all of the injected bolus is going to be therapeutically useful. This is why such Rx approaches typically require multiple shots.

On the other hand, Chimeric antigen receptor (CAR) essentially endows a T cell with additional Monoclonal antibody -like functionality. Here, such antibody-like specificity is ‘grafted’ onto the T cell by genetically engineering it to express a CAR that specifically binds the CD19 molecule expressed on the surface of B cells.

Even if, much like injected antibodies, some or many of such genetically engineered CAR-T cells are simply eliminated from the body shortly after injection, cells can replicate but molecules like antibodies can’t. Essentially CAR-T cells can a) replicate in the body to make more copies of themselves, and b) thus stick around longer. Thus, the CAR-T cell approach to target malignant B cells is more effective because it uses a replication-capable cell compared to antibodies which can’t replicate.

https://www.quora.com/Why-is-chimeric-antigen-receptor-better-than-just-injecting-anti-CD19-antibodies/answer/Tirumalai-Kamala