Products of the major histocompatibility complex and their relationship to the immune response

Correlate the TP53 Mutation and the HRAS Mutation with Immune Signatures in Head and Neck Squamous Cell Cancer

Although immunotherapy has emerged as an effective therapeutic strategy for various cancers including head and neck squamous cell carcinomas (HNSCCs), only a subset of patients can benefit from such therapy. Hence, it is pressing to discover predictive biomarkers for cancer immunotherapy response. TP53 and HRAS mutations frequently occur in HNSCC and correlate with a worse prognosis in HNSCC. We extensively characterized the associations of TP53 mutations and HRAS mutations with HNSCC immunity based on multiple cancer genomics datasets. We compared the enrichment levels of 20 immune signatures between TP53-mutated and TP53-wildtype HNSCCs, and between HRAS-mutated and HRAS-wildtype HNSCCs, and found that TP53 mutations were associated with depressed immune signatures while HRAS mutations were associated with enhanced immune signatures in HNSCC. Moreover, we found multiple p53- and RAS-mediated pathways showing significant correlations with HNSCC immunity. Furthermore, we demonstrated that the association between TP53 mutation and tumor immunity was independent of the human papillomavirus (HPV) infection and smoking status in HNSCC. These data suggest that p53 and RAS may play important roles in regulating HNSCC immunity and that the TP53 and HRAS mutation status could be useful biomarkers for stratifying HNSCC patients responsive to immunotherapy.

TP53 Mutations Promote Immunogenic Activity in Breast Cancer

Background

Although immunotherapy has recently achieved clinical successes in a variety of cancers, thus far there is no immunotherapeutic strategy for breast cancer (BC). Thus, it is important to discover biomarkers for identifying BC patients responsive to immunotherapy. TP53 mutations were often associated with worse clinical outcomes in BC whose triple-negative subtype has a high TP53 mutation rate (approximately 80%). To explore a potentially promising therapeutic option for the TP53-mutated BC subtype, we studied the association between TP53 mutations and immunogenic activity in BC.

Methods

We compared the enrichment levels of 26 immune signatures that indicated activities of diverse immune cells, functions, and pathways between TP53-mutated and TP53-wildtype BCs based on two large-scale BC multiomics datasets. Moreover, we explored the molecular cues associated with the differences in immunogenic activity between TP53-mutated and TP53-wildtype BCs. Furthermore, we performed experimental validation of the findings from bioinformatics analysis.

Results

Bioinformatics analysis showed that almost all analyzed immune signatures showed significantly higher enrichment levels in TP53-mutated BCs than in TP53-wildtype BCs. Moreover, in vitro experiments confirmed that mutant p53 could increase BC immunogenicity. Both computational and experimental results demonstrated that TP53 mutations could promote BC immunogenicity via regulation of the p53-mediated pathways including cell cycle, apoptosis, Wnt, Jak-STAT, NOD-like receptor, and glycolysis. Furthermore, we found that elevated immune activity was likely associated with a better survival prognosis in TP53-mutated BCs, but not necessarily in TP53-wildtype BCs.

Conclusions

TP53 mutations may promote immunogenic activity in BC, suggesting that the TP53 mutation status could be a useful biomarker for stratifying BC patients responsive to immunotherapy.

Correlate tumor mutation burden with immune signatures in human cancers

BACKGROUND

Tumor mutation burden (TMB) has been associated with cancer immunotherapeutic response and cancer prognosis. Although many explorations have revealed that high TMB may yield many neoantigens to incite antitumor immune response, a systematic exploration of the correlation between TMB and immune signatures in different cancer types is lacking.

RESULTS

We classified cancer into the lower-TMB subtype and the higher-TMB subtype for each of 32 cancer types based on their somatic mutation data from the Cancer Genome Atlas (TCGA), and compared the expression levels of immune-related genes and gene-sets between both subtypes of cancers in each cancer type. In some cancer types most of the immune signatures analyzed were upregulated in the lower-TMB subtype, while in some other cancer types the immune signatures were prone to be upregulated in the higher-TMB subtype. However, the regulatory T cells, immune cell infiltrate, tumor-infiltrating lymphocytes, and cytokine signatures tended to be upregulated in the lower-TMB subtype, and the cancer-testis antigen (CTA) and pro-inflammatory signatures were inclined to be upregulated in the higher-TMB subtype. Importantly, high TMB was associated with elevated expression of PD-L1 in diverse prevailing cancers. Furthermore, we found that higher TMB was associated with better survival prognosis in numerous cancer types while was associated with worse prognosis in a few cancer types.

CONCLUSIONS

High TMB may inhibit immune cell infiltrations while promote CTAs expression and inflammatory response in cancer. In many common cancer types, higher TMB may respond favorably to anti-PD-1/PD-L1 immunotherapy. Our data implicate that higher-TMB patients could gain a more favorable prognosis in diverse cancer types if treated with immunotherapy, otherwise would have a poorer prognosis compared to lower-TMB patients.

Immunogenomics Analysis Reveals that TP53 Mutations Inhibit Tumor Immunity in Gastric Cancer

Although immunotherapy continues to demonstrate efficacy in a variety of refractory cancers, currently, no any immunotherapeutic strategy is clinically used for gastric cancer (GC) except its microsatellite instable subtype. Thus, it is important to identify molecular biomarkers for predicting the responders to GC immunotherapy. TP53 mutations frequently occur in GC and are associated with unfavorable clinical outcomes in GC. We performed a comprehensive characterization of the associations between TP53 mutations and immune activities in GC based on two large-scale GC cancer genomics data. We compared expression and enrichment levels of 787 immune-related genes and 23 immune gene-sets among TP53-mutated GCs, TP53‐wildtype GCs, and normal tissue, and explored the correlations between p53-mediated pathways and immune activities in GC. Strikingly, almost all analyzed immune gene-sets were significantly downregulated in enrichment levels in TP53-mutated GCs compared to TP53‐wildtype GCs. These less active immune pathways and cell types in TP53-mutated GCs included 15 immune cell types and function, tumor-infiltrating lymphocytes, regulatory T cells, immune checkpoint, cytokine and cytokine receptor, human leukocyte antigen, pro‐inflammatory, and parainflammation. Moreover, we identified a number of p53-mediated pathways and proteins that were significantly associated with immune activities in GC. Furthermore, we demonstrated that the TP53 mutation itself could result in the depressed immune activities in GC and other cancer types. We revealed that chromosomal instability was an important mechanism for the depressed tumor immunity in TP53-mutated cancers. Finally, we showed that immune cell infiltration and immune activities were likely positively associated with survival prognosis in GC. Our findings suggest that p53 may play an important role in activating tumor immunity in GC and other cancer types and that the TP53 mutation status could be useful in stratifying cancer patients responsive to a certain immunotherapy.

HLA-D-associated 'Ia-like' antigens on human macrophages

Human macrophages procured by culture of adherent peripheral blood mononuclear cells were investigated for reactivity in complement-dependent cytotoxicity tests with antisera having specificity for HLA-D-associated 'Ia-like' B-cell antigens. The antisera were found to be cytotoxic for 30%-70% of the macrophages from donors whose B cells were also reactive, and absorption with B cells also removed macrophage cytotoxicity. A B-cell xenoantiserum was also cytotoxic to macrophages. It is concluded that the HLA-D-associated 'Ia-like' antigens present on B cells are also expressed by macrophages, at least on a subpopulation.

T-cell cytotoxicity in the absence of viral protein synthesis in target cells

Cytotoxic T cells lyse only those virus infected target cells in vitro which express, in addition to the viral antigen(s), those K or D region products of the major histocompatibility complex (MHC) which were present during anti-viral sensitisation in vivo. This 'associative recognition' by cytotoxic T cells could reflect the interaction of two T-cell receptors with specificity for target K or D gene products and independently for the viral antigen, or one receptor with specificity for virally altered K or D region products (see ref. 1 and refs therein). There are various ways that the MHC antigens could be altered, including 'modification from within', where the virus modifies host protein synthesis by interfering with transcription, translation or post-translational glycosylation; or 'modification from without' where enzymic or chemical alteration of cell membrane proteins are induced by virus activity at the cell surface. In this report we show that inactivated Sendai virus or isolated Sendai virus envelopes can serve to modify a cell and make it a specific target for Sendai-immune T-cell killing, thus excluding the possibility of 'modification from within' in this system.

Toxoplasma encephalitis of immunocompetent and nude mice: immunohistochemical characterisation of Toxoplasma antigen, infiltrates and major histocompatibility complex gene products

The experimental infection of immunocompetent and immunodeficient athymic mice with an avirulent encephalitogenic Toxoplasma strain (DX strain) was employed to study the ensuing encephalitic process by use of histological and immunocytochemical methods. In the acute phase of the infection Toxoplasma cysts and tachyzoites were accompanied by an infiltrate composed of macrophages, CD4+ and CD8+ T cells. In the chronic stage a granulomatous encephalitis developed. In contrast to immunocompetent NMRI mice, athymic nude NMRI mice died 3 weeks post-infection because of a generalized toxoplasmosis with predominant involvement of the brain. A salient feature of murine Toxoplasma encephalitis was up-regulation of class I and II major histocompatibility complex (MHC) gene products. Class I antigen was widely expressed on microglial cells and astrocytes. Class II antigen was only expressed on microglial cells despite a considerable astrogliosis. Our results indicate a differential expression of MHC-determined antigens on brain cells in acute and chronic murine Toxoplasma encephalitis.

HLA class II molecules on monocytes regulate T cell proliferation through physical interaction in the CD3 activation pathway

HLA class II molecules are involved in the OKT3-induced T cell activation, since monoclonal antibodies (mAb) to monomorphic determinants of class II antigens are able to inhibit T cell proliferation. This effect involves several of the events leading to T cell activation and proliferation, i.e. interleukin (IL) 1, IL 6 and IL2 secretion and IL2 receptor expression. The main target of the inhibition is represented by monocytes, and the interference of anti-class II mAb in the direct interaction of monocytes with T cells is likely to play a relevant role in the inhibition mechanism. To test this hypothesis, we investigated in the present study the effect of anti-class II mAb on the proliferation of T cells stimulated with mAb OKT3 in the presence of paraformaldehyde-treated monocytes. We show that the inhibition of proliferation is specific and dose dependent, and seems to involve particular class II epitopes. Addition of fixed monocytes to inhibited T cell cultures restores proliferation to a moderate extent, only if monocytes are added within the first 12 h of culture, suggesting that class II antigens or spatially related molecules deliver signals concurrently with the mitogenic stimulus. The blocking capability of anti-class II mAb was not restricted to the CD4+ or the CD8+ T cell subsets, suggesting that, under inhibitory conditions, these mAb affect other structures on the T cell surface, relevant to the monocyte-T cell interaction.

An induced fit hypothesis for antigen recognition by T lymphocytes: a role for specific antigen retention structures on antigen-presenting cells

The nature of T lymphocyte recognition of foreign antigens is not known, despite recent advances in elucidating the cellular structures that may be involved in the specific interactions. The central difficulty in this process is that T cells respond to foreign antigen only in the context of major histocompatibility complex (MHC) antigens expressed by another antigen-presenting cell. In addition, T cells that interact with class II MHC antigens do not bind foreign protein antigens in their native form, but seem to recognize only proteolytic peptide fragments as the relevant antigen. The simplest explanation for these observations is that the class II MHC antigens themselves bind antigenic peptides to form the appropriate determinant that interacts with the antigen-specific T cell receptor. However, to date no such antigenic complex has been found with MHC antigens despite rigorous attempts at their demonstration. One alternative explanation described here is that there is no preexisting foreign antigen-MHC antigen complex prior to interaction with T cells, and it is the T cells that cause the two moieties to become associated for recognition by a single antigen-specific T cell receptor. Central to this mechanism is that foreign antigenic peptides must be associated with specific antigen retention structures (SARS) expressed by antigen-presenting cells which retain and protect the peptide on the cell surface. These SARS, upon interaction with T cell membrane moieties, would subsequently associate with MHC antigens. A hypothesis to describe this mechanism is developed to account for published observations of antigen processing by antigen-presenting cells and T cell antigen recognition, and makes several predictions that are experimentally testable. This mechanism is also generally applicable to other cellular interactions in which soluble peptide mediators may become associated with surface components of one cell type, and this newly formed complex is in turn recognized by a receptor on a second cell type to deliver functional signals.

The identification of a tissue-restricted plasma membrane marker in Xenopus laevis embryos by using a monoclonal antibody

A library of monoclonal antibodies raised against partially purified membrane fractions from Xenopus laevis oocytes has been produced. One of these antibodies has been cloned and characterized in detail. It was found to be specific for a membrane-bound antigen of apparent Mr, 55,000. The distribution of the antigen has been studied by indirect immunofluorescence on sections of X. laevis embryos and has been found to be highly specific for some ectodermal and endodermal tissues. It was not present on mesodermal tissues.

Corneal allograft rejection. The role of the major histocompatibility complex

The greater success of corneal transplantation compared to other organ transplants has led to the concept that the cornea is a site of "immunological privilege." Corneal cells possess the antigens of the major histocompatibility complex responsible for allograft rejection in other tissues (i.e., HLA antigens). The avascularity of the cornea accounts for the relative protection of the donor cornea from the immunological surveillance of the recipient. As the roles and functions of the major histocompatibility complex are unravelled, the mechanisms responsible for host sensitization, lymphocyte activation and allograft rejection are becoming better understood. In particular, the HLA-DR antigen in humans is believed to play an integral part in allograft rejection. Langerhans cells in human corneal epithelium have been shown to bear this antigen. Evidence suggests that these cells or similar HLA-DR-bearing cells in the cornea play a major role in corneal allograft rejection. In light of these advances in transplantation immunobiology, new methods of suppressing and possibly preventing allograft rejection in corneal transplantation are presented.

Changes in the expression of HLA and beta 2-microglobulin by cultured lymphoid cells

Changes in the expression of HLA and beta 2-microglobulin (beta 2-m) antigens by cultured human lymphoid cell lines were investigated. HLA expression was assayed by indirect trace binding radioimmunoassay (RIA) with monoclonal antibodies and by determining sensitivity to complement-dependent lysis by alloantisera. Lymphoid cells in culture were found to undergo changes in the expression of HLA and beta 2-m antigens characterized by decreased membrane expression of these antigens at high cell densities or after a prolonged period of cultivation. The decreased expression of HLA and beta 2-m antigens apparently is due neither to a masking phenomenon nor to a lack of nutrients or an accumulation of metabolites in the culture media but is perhaps mediated by a cell-to-cell contact mechanism. Human interferon was found to enhance the expression of HLA and beta 2-m, apparently overriding the effects on major histocompatibility complex (MHC) expression induced by cell density.

HLA-linked control of susceptibility to tuberculoid leprosy and association with HLA-DR types

In an attempt to confirm an HLA-linked effect on the course of Mycobacterium leprae infection observed in families from Surinam (South America), we conducted a similar family study in an endemic area in India. We observed a significant (P less than .05) excess of identical HLA-GLO haplotypes only from healthy parents among siblings affected with tuberculoid leprosy. Compared with healthy controls, unrelated patients with tuberculoid leprosy (n = 15) showed a significant heterogeneity at the HLA-DR locus (P less than .05). This heterogeneity was caused by an increased frequency of HLA-DRw2 (.93 versus .53, P less than .05), particularly of DRw2 homozygotes (.53 versus .11, P less than .005), and a decreased frequency of HLA-DRw6 (.07 versus .58, P less than .005). We observed a significant (P = .03) preferential segregation of DRw2 from DRw2 heterozygous parents not affected with tuberculoid leprosy to children with the tuberculoid type of the disease. These data confirm an HLA-linked control of susceptibility to tuberculoid leprosy only, and suggest a recessive inheritance of this trait for which HLA-Drw2 appears to be a genetic marker.

Genetic control of survival in epidemics

Descendants of Dutch colonists, who emigrated to Surinam in the last century and survived epidemics of typhoid and yellow fever with a total mortality of about 60%, were tested for twenty-six polymorphisms. The gene frequencies were compared with those of a large Dutch control sample. An analysis of drift indicated that the variations in gene frequencies observed for C3, Gm, HLA-B, and GLO were unlikely to be due to drift. Therefore these data might indicate selection through genetic control of survival in these epidemics.

beta 2-Microglobulin: methods and clinical applications

beta 2-Microglobulin is a low molecular weight protein that is found in most biological fluids. It was originally isolated from urine of cadmium-poisoned patients. Its amino acid sequence was established and shown to be structurally related to immunoglobulin constant domains. With the aid of antibodies specific against beta 2-microglobulin, the protein was detected on the membranes of all nucleated cells, normal and neoplastic. Measuring the quantity of beta 2-microglobulin showed that high levels are present in patients with renal tubular deficiencies and several other pathological conditions including neoplastic diseases. Extremely high levels were detected in seminal fluid and colostrum. Despite the structural relationship to immunoglobulins, no immunological relationship was demonstrated with these proteins using antibodies specific for beta 2-microglobulin. However, such antibodies are cytotoxic to all cells carrying beta 2-microglobulin on their surfaces. The discovery that beta 2-microglobulin is an integral part of the histocompatibility antigens of human and murine origin stimulated further research and interest in this molecule. Several groups of investigators have shown that beta 2-microglobulin is the low molecular weight chain and is noncovalently bound to a high molecular weight chain which carries the histocompatibility antigens. The structure of the histocompatibility antigens of lymphocytes (HLA) was shown by immunochemical as well as biological methods, and it is now well accepted. The antibodies against beta 2-microglobulin are extremely useful in the isolation of the histocompatibility antigens for sequence studies. Furthermore, the antibody to beta 2-microglobulin revealed that other structures may be bound to beta 2-microglobulin such as phytohemoagglutimin (PHA) receptors, mixed lymphocyte culture (MLC) antigens, etc. Murine thymus leukemia (TL) antigen also contains beta 2-microglobulin as an integral part of its structure; other tumor antigens may have a similar structure. Through all these studies, beta 2-microglobulin emerged as the best known membrane protein that can serve as a model for study of the arrangement and the function of the cell membrane.

HLA antigens in persistent palmoplantar pustulosis and its relationship to psoriasis

HLA typing was performed on 93 patients with persistent palmoplantar pustulosis. The incidence of either HLA B13 or BW17 was not significantly increased as compared to controls. In addition the frequency of BW35 was no different from controls. However, the present results document a significantly increased frequency (38.7%) of B8. Taken together these data are good evidence that palmoplantar pustulosis is a genetically distinct disease entity from psoriasis vulgaris, despite the increased incidence of psoriasis in the condition.

Familial lichen planus. Another disease or a distinct people?

When lichen planus strikes families, a very rare happening, it is likely to afflict younger members, to erupt more acutely, extensively, and gravely, attacking also nails and mucous membranes, and to recur. Ten patients with familial lichen planus, two each from five distinct Caucasian families, the parents of whom were unrelated by birth, were found to be carrying HLA-B7 statistically more frequently than in the normal population or in those with the characteristic forms of lichen planus. We hint that their genotype might have rendered them susceptible to a pathogen that precipitated their disease.

Self and non-sense: an organism-centered approach to immunology

This paper provides a conceptual framework to accommodate important recent developments in immunology (genetic determination, cellular interactions, suppression). The basic idea is to look at the immune system as a closed network of interactions which self-determines its ongoing pattern of stability and its capacities of interaction with its environment. Thus, all immune events are understood as a form of self-recognition, and whatever falls outside this domain, shaped by genetics and ontogeny, is simply nonsensical. This paradigm, stemming from the ideas of Jerne, represents almost a logical inversion of the Burnetian idea of self-discrimination. A detailed discussion of the immunological evidence that substantiates this view is presented, together with some new concepts (eigenbehavior, cognitive domains). Although the paper is addressed to biologists and immunologists, we make extensive use of system-theoretic notions in a non-mathematical form (recursion, nets and trees, self-organization).

In vitro immune responsiveness to vaccinia virus and HLA

Because several lines of evidence suggest that HLA products might have an important function in the immune response to infectious agents, we studied the possible relation between immune response to vaccinia virus and HLA phenotype in 79 soldiers who received a primary vaccination. A low in vitro response to vaccinia virus was associated with HLA-Cw3 both in 49 subjects tested three to four weeks after vaccination (P less than 0.001) and in the remaining 30 subjects tested five to 11 weeks after vaccination (P = 0.035). Responses to unrelated antigens and phytohemagglutinin of lymphocytes tested before, three to four weeks and five to 11 weeks after vaccination indicated that this association was specific for vaccinia virus and suggested that differences in immune response to vaccinia were reflected in temporarily altered immune responsiveness to unrelated antigens. Our results indicate that HLA-Cw3 or an HLA product associated with Cw3 is involved in the cellular immune response to vaccinia virus.

Different B lymphocyte alloantigens associated with multiple sclerosis in Arabs and North Europeans

The frequencies of HLA and B-lymphocyte alloantigens were investigated in 32 Arab patients with clinically definite or early probable multiple sclerosis (M.S.) and compared with those found in 43 healthy Arab controls. A significant association was found between M.S. and the B-lymphocyte alloantigen, BT 102; this contrasts with previous findings of an association between the B-lymphocyte alloantigen BT 101 and M.S. in North Europeans. It is suggested that this difference is due to the involvement of different environmental agents, possibly viruses, in the pathogenesis of M.S. in these populations.

Genetic markers and cancer epidemiology

The study of potential associations between genetic markers and various cancers has a long history in cancer epidemiology. Such investigations are subject to serious problems of statistical significance and the choice of appropriate control populations. A promising future for the use of human population genetics in cancer epidemiology may be in the investigation of genetic markers (such as the HL-A complex) which code for proteins of potential immunological or physiological importance in susceptibility or resistance to cancer. The cerumen gentic marker has played a central part in a hypothesis formulated in our laboratory for the etiology of breast cancer. A second new development in this field is likely to be the investigation of genetic markers in families with high incidence of cancer. Such families permit the simultaneous study of genetic hypotheses of cancer inheritance and the association of marker genotypes with cancer through segregation and linkage analysis.