A Query by HIV. I. A query by HIV. II. Recursion

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1 A Query by HIV I. A query by HIV Human immunodeficiency virus (HIV) is a kind of lentivirus (lenti- means "slow") that belongs to the Retroviridae family. HIV is known for slow disease progression. In the last stage of the disease the virus develops acquired immunodeficiency syndrome (AIDS). It typically takes 5 to 10 years since the initial HIV infection to develop the syndrome. AIDS can manifest any kinds of symptoms related to destruction of a component of the immune system called CD4+ T lymphocytes. These symptoms include encephalitis and meningitis in the brain, retinitis in the eyes, pneumocystis pneumonia and tuberculosis in the lungs, esophagitis and chronic diarrhea in the guts, and cancers in different tissues and organs. They are all caused by the loss of CD4+ T lymphocytes, because these T lymphocytes, also called helper T lymphocytes, are essential for both cellular immune response mediated by cytotoxic (CD8+) T lymphocytes and humoral immune response mediated by B lymphocytes and antibodies. It is clear that the immune system finally fails to protect CD4+ T lymphocytes, although the mechanism of the failure is still unclear. However, it is recently suspected that some important part of the whole CD4+ T lymphocyte fraction is already broken in the first several weeks after HIV infection i.e. far earlier than the development of AIDS, and in order to protect this essential part of CD4+ T lymphocytes we would need early treatment with antiretroviral therapies or strong early cellular immune response which could be induced with prophylactic vaccination. So the question here is whether the immune system has potential to protect itself or not. In order to answer it I will discuss here on the design of the T lymphocyte part of the immune system based on the idea of recursion. II. Recursion Recursion is a kind of repeating process in a self-similar way. Recursion can be found in our daily life. For example we can use two mirrors to reflect each other, and then there will be an infinite recursion of the mirrors. Recursive acronym (initialism) can be defined like MIT="MIT Is Tough". A sentence can also be recursive, like the well-known example shown below. 3

2 To understand recursion, we must first understand recursion. In mathematics and computer science recursive function is defined as a function that calls the function itself. f g( f ) Recursive functions include integer sequences expressed in a form of recurrence relation. A typical example is shown below. a n = a n 1 + 1, a 0 = 1 At high schools in Japan we learn how to solve recurrence relations, although in most cases we do not learn why we need to solve them. The reason is clear for computer scientists. In a recurrence relation, recursive call starts before the end of the previous call (i.e. within the previous call). So the calculatiton could consume a lot of memory depending on its depth. For example, if n equals to 1 or 2, then it is quite easy to calculate the results. a 1 = 1+1 a 2 = (1+1)+1 However, if n is huge, then the calculation will require a lot of time and space. a 1,000,000,000 = (((( +1)+1)+1)+1)+1 In this way solving a recurrence relation means to convert it into a more efficient form. This also means that if we have a fast computer equipped with a lot of memory (random access memory: RAM), then we would not need to solve recurrence relations. As already shown, a recurrence relation requires an end condition. Otherwise it will be endless. For example a 0 = 1 is the end condition for a n = a n 1 + 1, the recurrence relation shown in this section. III. The immune system Most immunology textbooks define the immune system as a set of mechanisms that discriminates between self and non-self antigens. However, scientists who propose 4

3 alternative theories including the danger theory have been debating the self/non-self paradigm 1. The idea shown in this article is close but not identical to the danger theory. It is also important to keep in mind the possible design of life presented by Erwin Schrödinger 2. According to his idea our bodies are designed so that they will be maintained in steady states in decades. Viruses have deoxyribonucleic acid (DNA) or ribo nucleic acid (RNA) as their genomes. After a virus infects a host cell, the viral genome provides information about proteins that are not coded by the genome of the cell. According to the information virus-infected cells produce unexpected proteins. This could result in unexpected cell functions including virus particle production, cell death and cell proliferation. The unexpected cell proliferation could lead to neoplasm (cancers) although cancers can also be caused by DNA mutations, deletions, and recombination of the cell genome without viral infections. In this way expression of unexpected information can threat integrity of our bodies. However, there is a mechanism called cellular immunity that consists of white blood cells called T lymphocytes or T cells. T cells are designed to detect abnormal cells expressing unexpected and potentially risky proteins (functions) in order to maintain integrity of our bodies. The mechanism of the detection is as follows. (1) All the cells in our bodies synthesize proteins, but part of these proteins is processed into small fragments consisting of 8-10 amino acids (called peptides) and transferred to and put on the cell surfaces so that T lymphocytes can detect unexpected proteins. (2) T cells circulate in our bodies to test all the presented proteins synthesized in the cells referring to their "unexpected protein database". So this is basically an interaction between every single cell and a T cell. All the cells in our bodies express molecules to interact with a set of T cells called cytotoxic T cells or CD8+ T cells. These molecules are called major histocompatibility complexes (MHC) class I. An MHC molecule has a groove to contain an 8-10 amino acid sequence (peptide). There are several different MHC molecules encoded in our genome, and each MHC molecule has a groove with a different shape so that it can hold peptides of different shapes. In this way millions of peptides derived from proteins expressed and processed in every single cell in our bodies are presented on MHC molecules to be assessed by CD8+ T cells. CD8+ T cells are specialized white blood cells to assess all the cells in our bodies presenting peptides on MHC molecules expressed on cell surfaces. Every single T cell recognizes only a single unexpected peptide by its shape, and the number of total T cells in a human body is estimated as about Therefore if we assume that 10 4 T cells recognize the same unexpected peptide, this means that the whole T cell database contains data for 10 7 different unexpected peptides, which might be large enough for detection of many pathogens and cancers (Table 1) 3. 5

4 weight n o T cells/epitope latency before AIDS Human 50,000 g 10,000 ~ 100,000 5 ~ 10 years Monkey 5,000 g 1,000 ~ 10,000 1 ~ 5 years Mouse 25 g 10 ~ 100??? Table 1. Estimated number of unstimulated (naïve) T cells per epitope per capita. *AIDS is caused in monkeys by simian immunodeficiency virus (SIV) infection instead of HIV infection. **There is no immunodeficiency virus so far which infects mice. It is interesting to imagine what happens if an HIV-like immunodeficiency virus infects mice. T cells express molecules called T cell receptors (TCR) that interact with MHC molecules bearing peptides. A TCR molecule also has a groove to test peptides. If the shape of a peptide on an MHC molecule matches the TCR groove, then the peptide will be recognized as unexpected and potentially risky, and the CD8+ T cell bearing the TCR initiates immune response in order to kill the cell expressing the peptide. Every T cell expresses only a single TCR clone. This is why every T cell recognizes only a single unexpected peptide. In this way the T cell immune system detects cells producing unexpected proteins due to expression of unexpected genes, and kills those cells in order to maintain integrity of our bodies. In addition, it is interesting to know that there is a different set of T cells called helper T cells or CD4+ T cells (Table 2). CD4+ T cells interact with limited types of cells expressing different types of MHC molecules called MHC class II molecules. Majority of these cells belong to the immune system and are called antigen-presenting cells. Activated T cells can also express MHC class II molecules. MHC class II is important in initiation and amplification of T cell response by interacting with CD4+ T cells. However, it is also assumed that CD4+ T cells might be also detecting unexpected proteins expressed in cells that belongs to the immune system. This can be regarded as part of a mechanism of the immune system for protecting the immune system itself. 6

5 nickname evolutionarily interact with HIV infectivity CD4+ T cells helper advanced MHC class II yes (expressed in immune cells) CD8+ T cells cytotoxic (killer) primitive MHC class I (expressed in all cells) no Table 2. Known characteristics of CD4+ and CD8+ T cells. HIV attacks HIVspecific CD4+ T cells which will otherwise help HIV-specific CD8+ T-cell function. IV. HIV infection HIV infects CD4+ T cells, but it usually depletes CD4+ T cells slowly. Thus HIV infection lasts for several years and results in AIDS. Total CD4+ T cell count in peripheral blood is regarded as the best marker for disease progression. However, HIV infection is different from typical acute infection already in the early phase as described in Figure 1. The reason for the failure of the immune system to control HIV replication in the early phase is not well understood, although it might be partly because HIV does not evenly attack all CD4+ T cells 4. Figure 1. The immune system fails to control HIV replication in the early phase of infection. This leads to persistent HIV infection. HIV needs interaction with molecules expressed on the cell surface. These molecules are called receptors. CD4+ is a molecule expressed on the surface of CD4+ T cells and is known as the main receptor for HIV. There is another molecule called CCR5 that is used 7

6 by major strains of HIV as a co-receptor. CCR5 is expressed in CD4+ T cells that have been stimulated by antigens. Therefore HIV prefers T cells that have been activated by peptide stimulation and express CCR5. Such T cells are called memory T cells. HIV has its own genome as RNA. HIV genome RNA encodes proteins important for HIV particle formation and persistent infection, and HIV-infected cells produce proteins that are "unexpected" for the immune system. Therefore peptides derived from HIV proteins are presented on MHC molecules and detected by T cells that recognizes those peptides. Such T cells are called HIV-specific T cells. HIV-specific T cells express CCR5 after detection of HIV peptides and therefore HIV can also infect them. Taken together, HIV prefers activated HIV-specific CD4+ T cells 5. It is interesting to notice that while most T cells are protecting organs like intestine, lungs, liver, brain, HIV-specific T cells are trying to protect T cells. However, I assume here that protecting T cells themselves is more difficult than protecting other organs, because after HIV-specific CD4+ T cells are activated by detecting HIV-infected cells, they become susceptible to HIV infection (Figure 2). In this way HIV-specific CD4+ T cells can be repeatedly activated, infected and destroyed. If this is true, then HIV-specific memory CD4+ T cells will need to expand forever, which is similar to a recursive process lacking an end condition. Figure 2. HIV-specific CD4+ T cells try to protect T cells but they are targeted by HIV. 8

7 So in the end of the section I would point out that immune surveys could be regarded as a recursive process as shown in the following example written in a programming language called Lisp 6. (defun T.detect? (organ)...) (defun T.proliferate (organ)...) (defun T.kill (organ)...) (defun T.survey (organ) (when (T.detect? organ) ;; yes (T.proliferate organ) (T.kill organ) (T.survey organ))) When the process is executed, the result may differ according to the targeted "organ". If the target is "lung", then the process exits normally. However, if the target is "T", the process could be endless because the function T.proliferate() can be nullified by HIV infection and killing of proliferated T cells. (T.survey "lung") -> (T.survey "lung") -> O.K. (T.survey "T") -> (T.survey "T") ->> (T.survey "T") ->>> (T.survey "T")... If the recursive process is repeated so many times, then there could be a risk for total depletion of HIV-specific CD4+ T-cell early in the infection. Selective depletion of HIV-specific CD4+ T cells might not be repaired because it is different from repairing in other tissues. For example, lung epithelia can be easily repaired after viral infection because epithelial cells around the lesion are functionally identical to the lost epithelial cells. On the other hand, after HIV-specific CD4+ T-cell depletion the remaining T cells are expressing different TCRs and thus functionally different from the lost CD4+ T-cell populations. 9

8 V. Conclusion The immune system must protect itself, while other organs are protected by the immune system. This could be regarded as vulnerability or a security hole hard corded in our body. Indeed, HIV seems to attack the vulnerability. Control of HIV infection is extremely difficult at this moment because of the estimated limitation in the function of the immune system described in this article. However, this also suggests that protection or recovery of HIV-specific CD4+ T cells will solve the problem and I believe that researchers are finding methods to achieve the goal. Acknowledgements I thank Prof. Tetsuro Matano (AIDS Research Center, National Institute of Infectious Diseases, Japan; The Institute of Medical Science, The University of Tokyo, Japan) for discussions. References 1. Matzinger P. The danger model: a renewed sense of self. Science. 2002; 296: Schrödinger E. What is life? - The physical aspect of the living cell. Cambridge University Press, Moon JJ, Chu HH, Pepper M, McSorley SJ, Jameson SC, Kedl RM, Jenkins MK. Naïve CD4(+) T cell frequency varies for different epitopes and predicts repertoire diversity and response magnitude. Immunity. 2007; 27: Grossman Z, Meier-Schellersheim M, Paul WE, Picker LJ. Pathogenesis of HIV infection: what the virus spares is as important as what it destroys. Nat Med. 2006; 12: Douek DC, Brenchley JM, Betts MR, Ambrozak DR, Hill BJ, Okamoto Y, Casazza JP, Kuruppu J, Kunstman K, Wolinsky S, Grossman Z, Dybul M, Oxenius A, Price DA, Connors M, Koup RA. HIV preferentially infects HIV-specific CD4+ T cells. Nature. 2002; 417: McCarthy J. Recursive functions of symbolic expressions and their computation by machine, part I. Communications of the ACM. 1960; 3: Tetsuo TSUKAMOTO CEA/Fontenay-aux-Roses 10