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Virus Latency, Persistence, and Immune Responses

  • Authors: Jodi Black, PhD
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Target Audience and Goal Statement

This activity is intended for scientists, physicians, and other allied health professionals working in the fields of HIV, hematology, oncology, immunology, infectious diseases, virology, and molecular & cellular biology.

The goal of this activity is to enhance the quality of clinical practice by healthcare professionals involved in the care of individuals with HIV/AIDS by reporting state-of-the-art treatment approaches and clinical strategies for the management of HIV/AIDS.

Upon completion of this activity, participants should be able to:

  1. Describe the malignancies associated with HIV.
  2. Discuss the mechanisms of AIDS-related neoplastic processes.
  3. Outline recent data on the epidemiology and management of the malignancies associated with HIV.


  • Jodi Black, PhD

    Program Director for AIDS-related malignancy clinical trials at the Division of Cancer Treatment and Diagnosis, US National Cancer Institute, Bethesda, Maryland.

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Virus Latency, Persistence, and Immune Responses

Authors: Jodi Black, PhDFaculty and Disclosures


Immune Responses to Human Papillomavirus

Several investigators discussed the role of cellular and humoral immunity in preventing acquisition of human papillomavirus (HPV), or as a means of preventing neoplastic disease.

Laura Koutsky, PhD,[1] from the University of Washington, Seattle, discussed the issues involved in designing prophylactic HPV vaccine trials, including how to define a case, at what age to vaccinate, and what HPV types to target. She presented data from clinical trials testing a vaccine based on the L1 capsid protein of HPV-16, the most common HPV type associated with invasive cervical cancer. The specific aims were to determine the persistence of the HPV-16 antibody response and to estimate vaccine efficacy. A total of 480 women aged 18-25, of whom 75% were HPV-seronegative at baseline, participated in a double-blind, multicenter, placebo-controlled trial. Participants received 3 doses of either HPV LI capsid vaccine or a placebo at 0, 2, and 6 months. Antibody titers at months 7 and 12 were compared in women who were either HPV-seropositive or -seronegative at baseline (Table). The results indicated that peak anti-HPV responses to the LI capsid vaccine were achieved 1 month after the last dose (month 7) and then slowly declined, and that the vaccine yielded a higher anti-HPV-16 geometric mean titer (GMT) at 7 and 12 months than did natural HPV infection.

Table. Anti-HPV-16 GMT in Women Who Were HPV-16-Seropositive or -Seronegative at Baseline

Study arm (n)

Baseline serostatus

Anti-HPV-16 GMT (milliMerck units/mL) (95% confidence interval)

Month 7

Month 12

Placebo (42)


3 (3-3)

4 (3-6)

Placebo (10)


20 (3-152)

25 (5-131)

HPV-16 L1 40 mcg (78)


1976 (1568-2491)

512 (380-690)

HPV-16 L1 40 mcg (26)


2150 (1402-3296)

779 (485-1253)

To examine vaccine efficacy, results were pooled and analyzed from 2 independent phase 1 trials conducted contemporaneously and with similar study designs to the trial described above. In one trial, the women were vaccinated with HPV-11 L1 capsid vaccine, and in the other with HPV-16 L1 capsid vaccine. A total of 195 HPV-16-naive women were enrolled; those vaccinated with HPV-16 (n = 129) were compared with the control group, defined as those vaccinated with HPV-11, plus the placebo groups from both trials (n = 66). Samples were collected for HPV-16 DNA testing at the screening visit, baseline, and months 3, 7, 12, 24, and 36. A case was defined as repeated HPV-16 DNA detection or a single positive HPV-16 DNA test at the last available visit. Of the 66 women vaccinated with HPV-11 or placebo, 9 met the case definition (a 4.3% risk) compared with none of the participants in the HPV-16 vaccine trial, suggesting that immunization with HPV-16 LI capsid vaccine may protect against HPV infection. In addition, HPV-11 vaccine did not protect against infection with HPV-16.

Cell-mediated immunity plays an important role in controlling viral infections. Wang and colleagues[2] from Albert Einstein College of Medicine, Bronx, New York, presented data on cell-mediated immune responses to the HPV-16 transforming proteins E6 and E7. Peripheral blood lymphocytes were collected from HIV-seronegative women and lymphoproliferative responses (LP) to E6 and E7 peptides were measured. Cervical cells collected from the same women were also tested for the presence of HPV-16 DNA. The investigators found that clearance of HPV-16 infection and regression of cervical intraepithelial neoplasia was associated with cell-mediated immune responses to E6 and E7 in these HIV-negative women. The effect of CD4+ cell counts on LP to mitogens, standard recall antigens (Candida/tetanus), and to E6 and E7 peptides were also examined in HIV-infected women. Of 322 high-risk women, 32.2% were infected with HIV; of these, 81.5% had CD4+ cell counts > 500 cells/mm3 ("high") and 53.6% had high HPV viral loads. Among the overall group of HPV-positive women, 75.3% were also HIV-infected. There were no significant differences in immune response to HPV antigens between HIV-infected women with low or high CD4+ cell counts. HIV-infected women were more likely to exhibit LP to HPV peptides and to clear HPV-16 infection than were HIV-negative women, but had low LP to recall antigens, which correlated with CD4+ cell count. Those who responded to recall antigens were 6-fold more likely to eliminate HPV-16 infection. Of interest, presence of a high HPV-16 viral load correlated with a lower LP to E6 and E7 peptides, raising the question of whether an initial poor immune response resulted in a high viral load, or whether the patient becomes tolerized due to the high viral load. The presenter pointed out that the use of a CD4+ cell count cut point of 500 cells/mm3 to differentiate high and low CD4+ cell counts may have confounded the results, because a level of 500 cells/mm3 may be sufficient to allow measurement of HPV responses but insufficient for measurement of response to recall antigens.

Immunoglobulin Expression in Primary Effusion Lymphoma Cells

Research on the regulation of immunoglobulin gene transcription in primary effusion lymphoma (PEL) cells was presented by DiBartolo and colleagues[3] from the laboratory of Dr. Cesarman at Weill Medical College of Cornell University/New York Presbyterian Hospital, New York, NY. PEL is distinct from other forms of non-Hodgkin's lymphoma in that it is usually found in peritoneal, pleural, and pericardial body cavities and is consistently positive for human herpesvirus type 8 (HHV-8) and sometimes for Epstein-Barr virus (EBV). PEL cells are considerably larger than normal benign lymphocytes and they exhibit cytologic features that bridge large-cell immunoblastic lymphoma and anaplastic large-cell lymphoma. PEL cells exhibit the phenotypic and genotypic characteristics of plasma B cells, an immature B cell that lacks surface immunoglobulin (Ig) expression, but expresses cytoplasmic Ig. However, DiBartolo showed that no cytoplasmic Ig was detectable by immunophenotypic analysis of several PEL cell lines. To elucidate the mechanism of impaired Ig expression, HHV-8-infected PEL cells were examined for defects in expression or activity of 2 transcription factors involved in the transcription regulation machinery of Ig genes in B cells, Oct-2 and Bob-1. Immunohistochemical analysis of PEL cell lines indicated that there was no defect in expression of Bob-1 in these cells. However, results of immunohistochemical, RT-PCR, and immunoblot analysis of the same PEL cells indicated that Oct-2 was expressed poorly or not at all. Thus, defective Ig expression in PEL cells may be attributable to downregulation of Oct-2 expression. The resulting downmodulation of Ig expression may confer virus-infected cells with a long-term survival advantage and may have implications for maintenance of HHV-8 latency. In the future, DiBartolo and colleagues plan to study the consequences of restoring stable Oct-2 expression in these cells.

The Contribution of Cellular Proteins to Viral Episome Maintenance

The ability of EBV, HHV-8, and HPV to maintain their viral DNA in a latent state within host cells is related to the maintenance of pathology associated with these viruses. The latent EBV viral genome replicates only once per cell cycle and maintains a stable copy number, but the mechanisms that regulate the process of replication and maintenance are not well understood. These functions are dependent on the EBV origin of plasmid replication OriP, which consists of 2 regions of repetitive sequence: the family of repeats (FR) and the dyad symmetry region (DS). Episome replication and maintenance is also dependent on the viral-encoded protein EBNA1 binding to OriP.

Recent insights into the mechanism of EBV viral DNA episome replication in dividing host cells were discussed. John Yates, PhD,[4,5] from Roswell Park Cancer Institute, Buffalo, New York, presented data showing that ORC and MCM, 2 cellular protein complexes that are involved in replication of host chromosomes and in regulating DNA replication to only once per cell cycle, may participate in regulation of latent EBV genome replication. By using chromosome immunoprecipitation assays, Dr. Yates showed that antibodies against MCM and ORC pulled down the DS subunit of OriP, suggesting that they load at or near DS. He also showed that EBNA1 is involved in recruiting ORC to DS or the vicinity. Thus, for EBV episome replication, OriP uses the same cellular initiation factors that regulate chromosomal replication.

Deng and colleagues[6] from the Wistar Institute in Philadelphia, Pennsylvania, also presented data on the molecular mechanisms involved in EBV plasmid episome maintenance and replication during latency. To identify the cellular factors that interact with DS at OriP, they used a biochemistry strategy to detect cell proteins interacting with EBNA1.[7] Affinity chromatography was performed using the DS element of OriP and EBNA1-transduced HeLa cell extracts. A series of polypeptides that specifically associated with EBNA1 at DS were isolated, including Telomeric Repeat Factor 2 (TRF-2), the TRF-2-interacting protein hRap1, and Tankyrase, a telomere-associated poly-ADP ribose polymerase (PARP). These proteins are known to have functions associated with telomere length maintenance. Of interest, the TRF-2 bound cooperatively with EBNA1 to the 3 nonamer sites within DS (TTAGGGTTA), which resembles telomeric repeats. The investigators suggested that this set of proteins might modulate plasmid replication efficiency and maintenance in response to the cellular microenvironment.

Data presented last year at the 5th International AIDS Malignancy conference showed that latent HPV, EBV and HHV-8 episomes used similar mechanisms of tethering to host chromosomes during cell division to ensure segregation of viral DNA into daughter cells.[8,9] Tethering is mediated via specific virus/host cell protein-protein interactions. The HHV-8 LANA protein has been shown to play a key role in tethering the latent genome to chromosomes.[10] At this year's conference, Krithivas and colleagues[11] from the Sidney Kimmel Comprehensive Cancer Center at the Johns Hopkins School of Medicine in Baltimore, Maryland, presented data showing that the N-terminal and C-terminal regions of LANA can independently interact with host chromosomes in the absence of viral DNA. To identify the cellular proteins mediating viral DNA tethering, proteins known to interact with histone deacetylase complexes were examined. The N-terminus of LANA reacted with the methyl CpG binding protein MeCP2, a chromosome-associated protein, at amino acids 1-15. The C-terminus was shown to interact with the histone-associated protein DEK at amino acids 986-1042 (Figure). Mutations in either of these regions abrogated targeting of the N or C terminal regions to chromosomes. These results suggest a novel mechanism of targeting LANA to chromosomes via multiple contact points. However, these interactions need to be examined in the context of the whole protein.

Figure. LANA chromosome tethering domains.

A Viral Interferon Regulatory Factor Homolog

HHV-8 encodes 4 interferon regulatory factor (IRF) homologs. IRFs are transcription factors involved in interferon signal transduction. They are involved in mediating antiviral responses, transformation susceptibility, apoptosis and cell proliferation, B-cell differentiation, and induction of cellular immune responses. Mori and colleagues,[12] from several German institutions, are studying the expression pattern and function of the vIRF known as K10.5, Lana 2, or vIRF3. Conflicting results have previously been reported regarding whether K10.5 is expressed during the lytic or latent cycle of viral replication.[13,14] Mori and colleagues presented data showing that K10.5 is constitutively expressed during latency, and levels of gene transcripts were not affected by agents that induce the lytic cycle of viral replication. Experiments designed to identify the functional domains of K10.5 showed that the gene encodes a strong acidic transactivation domain between amino acids 220 and 260. The ability of this domain to transactivate a variety of different interferon inducible and noninducible promoters was tested. They found that K10.5 induced the promoter of the interferon consensus sequence binding protein (ICSBP) about 5-fold. Since ICSBP represses expression of those genes induced by interferon-alfa, Mori suggested that K10.5 could upregulate ICSBP in cells with insufficient levels to downregulate interferon-alfa-mediated signal transduction.


  1. Koutsky LA. HPV VLP vaccines and prevention of HPV 16 infection and oncogenesis. Program and abstracts of the 6th International Conference on Malignancies in AIDS and Other Immunodeficiencies; April 22-24, 2002; Bethesda, Maryland. Abstract S21.
  2. Wang Y, Negassa A, Klein RS, et al. Lymphoproliferative cellular immune responses to HPV 16 E6 and E7 peptides in HIV-infected women are independent of CD4 counts, but are associated with clearance of HPV infection. Program and abstracts of the 6th International Conference on Malignancies in AIDS and Other Immunodeficiencies; April 22-24, 2002; Bethesda, Maryland. Abstract 24.
  3. DiBartolo D, Hyjek E, Keller S, et al. Defective Oct transcription factor expression/activity may explain impaired immunoglobulin (Ig) expression in KSHV-infected primary effusion lymphoma (PEL) cells. Program and abstracts of the 6th International Conference on Malignancies in AIDS and Other Immunodeficiencies; April 22-24, 2002; Bethesda, Maryland. Abstract 26.
  4. Yates JL, Chaudhuri B, Xu H. Human DNA replication initiation factors and maintenance of the EBV episome during latent infection. Program and abstracts of the 6th International Conference on Malignancies in AIDS and Other Immunodeficiencies; April 22-24, 2002; Bethesda, Maryland. Abstract S22.
  5. Chaudhuri B, Xu H, Todorov I, Dutta A, Yates JL. Human DNA replication initiation factors, ORC and MCM, associate with oriP of Epstein-Barr virus. Proc Natl Acad Sci U S A. 2001;98:10085-10089.
  6. Deng Z, Lezina L, Chen CJ, Shtivelband S, So W, Lieberman PM. Telomeric proteins regulate episomal maintenance of Epstein-Barr virus origin of plasmid replication. Mol Cell. 2002;9:493-503.
  7. Deng Z, Lezina L, Chen CJ, Shtivelband S, So W, Lieberman PM. Telomeric proteins regulate Epstein-Barr virus plasmid maintenance of EBV. Program and abstracts of the 6th International Conference on Malignancies in AIDS and Other Immunodeficiencies; April 22-24, 2002; Bethesda, Maryland. Abstract 28.
  8. McBride AA, Bastien N, Zzheng PS, Penrose K. Regulation of the papillomavirus lifecycle by the E2 regulatory proteins. Program and abstracts of the 5th International AIDS Malignancy Conference; April 23-25, 2002; Bethesda, Maryland. Abstract S20.
  9. Kapoor P, Wu H, Shire K, Ceccrelli D, Frappier L. The segregation mechanism of latent Epstein-Barr virus genomes. Program and abstracts of the 5th International AIDS Malignancy Conference; April 23-25, 2002; Bethesda, Maryland. Abstract S21.
  10. Ballestas ME, Chatis PA, Kaye KM. Efficient persistence of extrachromosomal KSHV DNA mediated by latency-associated nuclear antigen. Science. 1999;284:641-644.
  11. Krithivas A, Young D, Fujimoro M, Weidner M, Hayward SD. The Kaposi's sarcoma-associated herpesvirus (KSHV/HHV8) latency-associated nuclear antigen (LANA) is targeted to chromosomes by two chromosome-associated proteins through both LANA N- and C-terminal interactions. Program and abstracts of the 6th International Conference on Malignancies in AIDS and Other Immunodeficiencies; April 22-24, 2002; Bethesda, Maryland. Abstract 29.
  12. Mori Y, Schellhorn T, Stürzl M, Kremmer E, Fleckenstein B, Neipel F. A KSHV encoded interferon regulatory factor expressed in latency. Program and abstracts of the 6th International Conference on Malignancies in AIDS and Other Immunodeficiencies; April 22-24, 2002; Bethesda, Maryland. Abstract S23.
  13. Rivas C, Thlick AE, Parravicini C, Moore PS, Chang Y. Kaposi's sarcoma-associated herpesvirus LANA2 is a B-cell-specific latent viral protein that inhibits p53. J Virol. 2001;75:429-438.
  14. Lubyova B, Pitha PM. Characterization of a novel human herpesvirus 8-encoded protein, vIRF-3, that shows homology to viral and cellular interferon regulatory factors. J Virol. 2000;74:8194-8201.