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The biggest obstacle to understanding how HIV causes immune damage is the complexity of the human immune system, a vast collection of different cells and tissues that typically work together in concert to protect against disease. HIV infects CD4 T cells — a central coordinator of the immune response — and causes a gradual depletion of these cells from both the peripheral blood and lymphoid tissue, along with a spreading dysfunction among the remaining CD4 T cell population. The precise mechanisms governing the loss and dysfunction of CD4 T cells, particularly the relative contributions of direct and indirect effects of HIV replication, continue to be hotly disputed among scientists. These disputes persist because immunologists do not fully understand how the huge pool of CD4 T cells in humans (numbering in the billions) is generated and maintained under normal conditions. It is known, however, that a majority of CD4 T cells reside not in the circulating blood but in lymphoid tissue throughout the body, including the gut.

Over the past few years, there has been renewed interest in studying the potential impact of HIV infection on CD4 T cells in the gut in the hopes of answering outstanding questions about HIV pathogenesis. Some researchers, particularly a group at the National Institutes of Health Vaccine Research Center (VRC) led by Daniel Douek, have generated data suggesting HIV causes a rapid, severe depletion of CD4 T cells from the gut-associated lymphoid tissue (GALT), leading to the theory that this depletion sets the stage for the eventual development of severe immunodeficiency and AIDS. In its most dramatic formulation, this theory holds that people lose half their memory CD4 T cells within weeks of becoming infected. (Douek’s research group has very recently published data suggesting that this loss of CD4 T cells actually allows commensal “friendly” bacteria [which normally aid digestion] to leak from the gut into the circulation, and this causes the systemic immune activation that is associated with HIV infection [see Update: Leaking LPS].)

However, not all researchers accept the CD4 catastrophe theory; several have published alternative interpretations of the data and argue that the importance of gut CD4 T cell depletion has been overstated. Among this camp of researchers are Zvi Grossman, Martin Meier Schellersheim, Bill Paul, and Louis Picker who argue that the CD4 T cells lost from the GALT are highly activated short-lived effector CD4 T cells and not the long-lived memory CD4 T cells that are essential for protection against opportunistic infections. They point out that long-lived (also known as “central”) memory CD4 T cells are eroded far more slowly over the course of disease. This point of view has recently been dramatically bolstered by the revelation that sooty mangabeys infected with SIV, a monkey form of HIV, show a similar gut “depletion” of CD4 T cells, despite the fact that they almost never progress to immunodeficiency.

Australian immunologists Anthony Kelleher and John Zaunders have also argued that the GALT data are less clear-cut than it may at first appear, citing studies that appear inconsistent with Douek’s hypothesis and echoing the notion that effector CD4 T cells appear most depleted and that the impact on memory CD4 T cells is far less clear.

As it stands, only additional research can resolve these differences of opinion. But as the debates continue, it’s helpful to review the data and take a look at how theories about the importance of GALT originated.

The Intestinal Terrain

The surface area of the human intestine, which is lined with folds and creases, villi and crypts, is almost inconceivably enormous — larger than a football field, were it all flattened out. The gut begins with the small intestine, which has three parts: the duodenum, jejunum and ileum. This is followed by the large intestine, also subdivided into three parts: the caecum, colon and rectum. The entire intestinal tract contains lymphoid cells scattered throughout the intestinal epithelium (the cellular layer that makes up the surface of the intestine) and lamina propria (a thin layer of tissue beneath the epithelium containing capillaries and a lymph vessel).

There is also an additional layer of complexity: the GALT includes distinct immunological areas known as inductive and effector sites. As the name implies, inductive sites are where immune responses are initiated. It is here that antigen-presenting cells activate CD4 T cells, CD8 T cells and B cells. Effector sites are where these cells migrate subsequent to activation. The balance between inductive and effector sites varies somewhat in different locations in the intestine: in humans, the jejunum and the region of the ileum closest to it (the proximal ileum) possess relatively little inductive lymphoid tissue whereas the terminal ileum (closer to the colon) and colon contain both inductive and effector sites.

Early Studies in HIV

Scientific papers describing alterations in T cell subsets in the gut of HIV-infected individuals began appearing in the late 1980s. The common theme that emerged from this research was that the percentage of CD4 T cells was severely decreased while the percentage of CD8 T cells was elevated. Notably, results were similar regardless of the route of transmission.

A 1995 study that compared samples taken simultaneously from the duodenum and peripheral blood found that the decrease in the proportion of CD4 T cells in the duodenum was consistently more profound than that seen in the blood, even in people with asymptomatic infection. Further details emerged from a 1997 study by Donald Kotler’s group which evaluated the extent of CD4 T cell depletion in the inductive versus effector sites of the rectal mucosa. These researchers found that the extent of depletion in the inductive sites was limited and more closely mirrored the peripheral blood; in contrast, CD4 T cells were dramatically reduced in the effector sites of the lamina propria. A logical hypothesis suggested by these data was that HIV’s preference for replicating in activated CD4 T cells made effector sites in the GALT a particularly hospitable environment for the virus.

Depletion Theories Take Hold

In 2004, two studies were published simultaneously in the Journal of Experimental Medicine. One study, from Daniel Douek’s laboratory, evaluated 14 people with HIV along with seven controls. The second study was conducted by Martin Markowitz’s research group at the Aaron Diamond AIDS Research Center (ADARC) in New York and involved 27 people with HIV and 10 uninfected controls.

The Markowitz study compared inductive and effector sites and reported that the former showed no absolute CD4 T cell depletion. At the effector sites, CD4 T cell depletion was more severe, with a mean CD4/CD8 ratio of 0.4 in the setting of HIV infection compared to 1.3 in HIV-negative controls.

Douek’s research group also noted that a decline in CD4 T cell percentage does not necessarily equate with an absolute CD4 T cell decline and took pains to home in on CCR5-expressing memory CD4 T cells, which made up a dramatically smaller proportion of memory CD4 T cells in the GALT of HIV-infected study participants compared to controls.

Included in this report was a photograph from the ileum of an individual with acute infection, showing a complete absence of lymphoid tissue. This photo was subsequently shown by Douek during a plenary session of the 2005 Conference on Retroviruses and Opportunistic Infections (CROI 2005) (where he also offered his speculation regarding the role of commensal bacteria in causing immune activation in people with HIV); this single photo became emblematic of the guts-theory of HIV pathogenesis, which was widely reported by journalists at the conference.

Since CROI 2006, there have been three published reviews which reflect the divergent perspectives on the importance of the GALT in HIV pathogenesis outlined in the introduction to this article. Jason Brenchley, David Price and Daniel Douek from the VRC offered “HIV Disease: Fallout from a Mucosal Catastrophe?” in Nature Immunology. Despite the title’s question mark, this piece strongly defends the notion that the GALT is central to HIV pathogenesis in language that drifts toward excessive certainty (one section begins: “Now that we have established that it is the virus in the acute phase of the disease rather than immune activation in the chronic phase that is responsible for the bulk of CD4 T cell depletion …”). In essence, the review suggests that HIV wreaks an almost instantaneous blitzkrieg in the GALT, people lose half their memory CD4 T cells within a matter of weeks, and, to top it off, commensal bacteria leak out of the gut and cause immune activation.

Partly in response to the review by Brenchley and colleagues, Zvi Grossman, Martin Meier-Schellersheim, William Paul and Louis Picker published “Pathogenesis of HIV Infection: What the Virus Spares is as Important as What it Destroys” in Nature Medicine shortly afterward. They mention the mangabey data, and present their case that the virus spares, at least initially, the long-lived naïve and central memory CD4 T cells which are crucial to immune protection. They note that these long-lived CD4 T cells can regenerate the short-lived effector CD4 T cells that seem most affected by HIV initially. The authors also argue that immune activation could be sufficient to account for the gradual erosion of long-lived CD4 T cell populations. Although the precise nature of the antigens driving immune activation remain obscure (particularly the contributions of HIV-derived versus other antigens), these researchers contend that it’s unlikely that commensal bacteria play a major role (again citing the mangabey GALT data). The paper is considerably more circumspect than the VRC’s offering, and ultimately stresses that ignorance regarding the mechanisms governing T cell homeostasis under normal conditions is perhaps the most significant barrier to a full understanding of HIV pathogenesis.

The only researchers pondering the role of nascent HIV-specific CD4 T cell responses in all this, the Australians Anthony Kelleher and John Zaunders, were relegated to a lowlier journal called Current HIV/AIDS Reports where they authored “Decimated or Missing in Action: CD4+ T Cells as Targets and Effectors in the Pathogenesis of Primary HIV Infection.” The review echoes the points made by Grossman and colleagues regarding the uncertain impact of early GALT CD4 T cell depletion on the long-lived memory CD4 T cell pool. However, the crux of the paper is that, somewhere amidst the many immunological and virological events that have been described during acute HIV infection, a primary HIV-specific CD4 T cell response is occurring. A primary response involves the recruitment and activation of naïve CD4 T cells specific for HIV antigens and their subsequent proliferation and development (or maturation) into HIV-specific memory CD4 T cells. While HIV-specific memory CD4 T cell can be detected within a few weeks of acute HIV infection, they typically lack the ability to perform the full spectrum of functions normally associated with memory CD4 T cells and are also more likely to be infected with HIV than CD4 T cells of other specificities. Kelleher and Zaunders argue that a better understanding of this early disruption of the first generation of HIV-specific memory CD4 T cells may provide crucial insights into both disease pathogenesis and correlates of immunological control of HIV replication.

Forging Ahead

The pursuit of science is not immune to fads and fashions, and many theories of HIV pathogenesis have briefly caught the imaginations of researchers, only to be undermined by the emergence of new data and consigned to the scientific scrapheap. Although sooty mangabeys appear to be pointing the GALT theory in the same direction, it is premature to conclude that its fate is sealed. The GALT contains a significant number of the body’s T cells, and elucidating HIV’s effects in this important immunological milieu will remain critically important, even if some of the initial data turns out to have been over-interpreted. The debates regarding these studies serve as a reminder that gaining an understanding of HIV pathogenesis requires grappling with the effects of the virus not just in the blood, but in the key immunological thoroughfares of the human body.


  1. Brenchley JM, Douek DC, et al. CD4+ T cell depletion during all stages of HIV disease occurs predominantly in the gastrointestinal tract. J Exp Med. 2004 Sep 20; 200(6):749-59.
  2. Mehandru S, Markowitz M, et al. Primary HIV-1 infection is associated with preferential depletion of CD4+ T lymphocytes from effector sites in the gastrointestinal tract. J Exp Med. 2004 Sep 20;200(6):761-70.
  3. Brenchley JM, Price DA, Douek DC. HIV disease: fallout from a mucosal catastrophe? Nat Immunol. 2006 Mar;7(3):235-9.
  4. 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 Mar;12(3):289-95.
  5. Kelleher AD, Zaunders JJ. Decimated or missing in action: CD4+ T cells as targets and effectors in the pathogenesis of primary HIV infection. Curr HIV/AIDS Rep. 2006 Feb;3(1):5-12.
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