AIDS-ONCOLOGY 

RESOURCES 

HANDBOOK 

MAY 2004 

http://cancer.gov/dctd/aids/2004handbook.pdf

DIVISION OF CANCER TREATMENT AND DIAGNOSIS 

NATIONAL CANCER INSTITUTE 

NATIONAL INSTITUTES OF HEALTH

DEPARTMENT OF HEALTH AND HUMAN SERVICES 

BETHESDA, MARYLAND
Contents 

Introduction............................................................................................................ 1 

Organizational Cross-reference............................................................................ 2 

 

NCI Extramural AIDS/AIDS Malignancy Activities 

 Division of Cancer Biology 

 Cancer Etiology Branch ........................................................................... 4 

Division of Cancer Control and Population Sciences................................... 7 

Division of Cancer Treatment and Diagnosis 

Office of the Director ............................................................................... 9 

Cancer Therapy Evaluation Program..................................................... 14 

Developmental Therapeutics Program 

Grants and Contracts Operations Branch ....................................... 17 

Screening Technologies Branch ........................................................ 19 

NCI Intramural AIDS/AIDS Malignancy Activities 

Center for Cancer Research 

Basic Research Laboratory...................................................................... 21 

HIV and AIDS Malignancy Branch ........................................................ 23 

HIV Drug Resistance Program................................................................ 28 

Human Genetics Section........................................................................... 32 

Laboratory of Experimental and Computational Biology .................... 33 

Laboratory of Genomic Diversity............................................................ 35

Laboratory of Medicinal Chemistry ....................................................... 36 

Macromolecular Crystallography Laboratory ...................................... 37 

Division of Cancer Epidemiology and Genetics............................................ 38 

National Institute of Dental and Craniofacial Research .................................... 39 

NCI AIDS/AIDS Malignancy Clinical Trials 

Extramural AIDS-related Malignancy Trials............................................... 41 

Intramural AIDS-related Malignancy Trials................................................ 42 

Intramural AIDS/HIV Trials (non-malignancy) .......................................... 42 

NCI AIDS/AIDS Malignancy Budgets ................................................................. 43 
INTRODUCTION 

The National Cancer (NCI) Institute is committed to enhancing clinical and laboratory research 

opportunities in AIDS malignancies. Our objective is to encourage communication on the breadth and 

depth of research opportunities and facilitate rapid development of tools to pursue crucial research 

questions in this area. The AIDS Oncology Resources Handbook facilitates this objective by providing 

information on the current scope of NCI activities in AIDS malignancy research. The first Handbook was 

presented in 1996 and this version is the annual update. The scope of the Handbook was expanded from 

the original version to include relevant information on activities within other institutes of the National 

Institutes of Health (NIH), including the National Institute of Dental and Craniofacial Research and the 

National Institute of Allergy and Infectious Diseases. 

Web site availability allows broad access of valuable information to the research community at large and 

provides an accessible and comprehensive listing of the array of clinical and laboratory research resources 

that receive NCI AIDS funding. The NCI Intramural AIDS/AIDS Malignancy Activities section provides 

brief synopses of intramural research studies and recent accomplishments. The broad research questions 

and major highlights of the extramural research programs are summarized in the NCI Extramural 

AIDS/AIDS Malignancy Activities section, including a description of the Fogarty International Center 

activities that enhance research and training opportunities in resource-poor countries. The intramural and 

extramural research efforts of the National Institute of Dental and Craniofacial Research can be found in 

the National Institute of Dental and Craniofacial Research section. To facilitate interactions and 

collaborations, a contact person, telephone, email address and related Web site follows each research 

summary. Information on clinical trials and NCI budgets is also included in two separate sections. 

Navigation Tips: Direct links to Web sites appear in underlined blue text. Clicking on either the orange 

titles on the Organizational Cross Reference page, or the page numbers on the Contents page navigates 

the reader directly to those sections. 

Our thanks and appreciation to the many individuals who contributed to this Handbook. We encourage 

readers of this Handbook to let us know how we can make future editions more useful. 

Jodi B. Black. Ph.D. 

Program Director, AIDS Malignancy Program 

Division of Cancer Treatment and Diagnosis 

301-402-6293 

301-496-0826 fax 

blackj@mail.nih.gov 

http://cancer.gov/dctd/aids

Jaime Kenyon, M.P.H. 

Program Specialist 

Division of Cancer Treatment and Diagnosis 

301-496-6711 

301-496-0826 fax 

kenyonj@mail.nih.gov 

http://cancer.gov/dctd/aids

1 
ORGANIZATIONAL CROSS-REFERENCE 

NATIONAL CANCER INSTITUTE (NCI) 

Director – Andrew von Eschenbach, M.D. 

Deputy Director - Alan Rabson, M.D. 

NCI EXTRAMURAL AIDS/AIDS MALIGNANCY ACTIVITIES

 DIVISION OF CANCER BIOLOGY (DCB) 

 Director - Dinah Singer, Ph.D. 

Cancer Etiology Branch (BCB) 

 Chief - Jack Gruber, Ph.D. 

 Program Director, DNA Virus Studies – May Wong, Ph.D. 

 Program Director, AIDS Virus Studies – Betsy Read-Connole, Ph.D. 

Cancer Immunology & Hematology Branch (CIHB) 

 Program Director, Cellular Immunology – Thomas Kevin Howcroft, Ph.D. 

 DIVISION OF CANCER CONTROL & POPULATION SCIENCES (DCCPS) 

Director – Robert Croyle, Ph.D. 

Analytic Epidemiology Research Branch (AERB) 

 Chief - Sandra Melnick, Dr.P.H. 

 Program Director - Vaurice Starks, B.S. 

 DIVISION OF CANCER TREATMENT & DIAGNOSIS (DCTD) 

 Director - James Doroshow, M.D. 

 AIDS Malignancy Program (AMP) 

 Program Director - Jodi Black, Ph.D. 

 Cancer Therapy Evaluation Program (CTEP) 

 Associate Director - Michaele Christian, M.D. 

Clinical Grants & Contracts Branch (CGCB) 

Chief & Program Director - Roy Wu, Ph.D. 

 Developmental Therapeutics Program (DTP) 

 Associate Director – Edward Sausville, M.D. 

Grants & Contracts Operations Branch (GCOB) 

 Chief - Mary Wolpert, Ph.D. Program Director - George Johnson, Ph.D. 

 Screening Technologies Branch (STB) 

 Chief - Robert Shoemaker, Ph.D. 

 Laboratory of Antiviral Drug Mechanisms (LADM) 

 Head – Shizuko Sei, Ph.D. 

 

 

2 
ORGANIZATIONAL CROSS-REFERENCE 

NCI INTRAMURAL AIDS/AIDS MALIGNANCY ACTIVITIES

 CENTER FOR CANCER RESEARCH (CCR) 

 Director - J. Carl Barrett, Ph.D. 

Basic Research Laboratory (BRL) 

 Suresh Arya, Ph.D. 

 David Derse, Ph.D.

 HIV & AIDS Malignancies Branch (HAMB) 

 Chief - Robert Yarchoan, M.D. 

 Director, Pediatric AIDS Clinic - Steven Zeichner, M.D., Ph.D. 

Investigator – Zhi-Ming Zheng, Ph.D. . 

 HIV/AIDS Drug Resistance Program (DRP) 

 Director - John Coffin, M.D. 

Human Genetics Section

Cheryl Ann Winkler, Ph.D. 

Laboratory of Experimental & Computational Biology (LECB) 


 Robert Blumenthal, Ph.D. 


 Dimiter Dimitrov, Ph.D. 

 Laboratory of Genomic Diversity (LGD) 

Mary Carrington, Ph.D. 

Laboratory of Medicinal Chemistry (LMC) 

 Terrence Burke, Jr., Ph.D. Macromolecular Crystallography Laboratory Alexander Wlodawer, Ph.D. 

DIVISION OF CANCER EPIDEMIOLOGY & GENETICS (DCEG) 

Director - Joseph F. Fraumeni, Jr., M.D. 

Viral Epidemiology Branch (VEB) 

Chief - James J. Goedert, M.D. 

HIV-Cancer Coordinator – Charles Rabkin, M.D. 

NATIONAL INSTITUTE OF DENTAL & CRANIOFACIAL RESEARCH (NIDCR) 

Lawrence A. Tabak, D.D.S., Ph.D. 

Division of Basic & Translational Sciences

Infectious Diseases & Immunity Branch 

Chief - Dennis F. Mangan, Ph.D. 

Director, AIDS Program - Mostafa Nokta, M.D., Ph.D. 

Division of Intramural Research

Oral & Pharyngeal Cancer Branch 

Chief - Silvio Gutkind, Ph.D. 

3 
CANCER ETIOLOGY BRANCH 

Division of Cancer Biology

The Cancer Etiology Branch plans, develops, and directs a national extramural research program dealing 

with biological, chemical, and physical agents that are possible etiological factors or co-factors in cancer 

and with the control of these agents and their associated diseases. Specific agents of interest include 

infectious agents such as viruses and bacteria and chemical carcinogens such as polycyclic aromatic 

hydrocarbons and hormones. Investigations include studies of the agents themselves and their properties, 

mechanisms of oncogenesis and carcinogenesis, and interactions of oncogenic microbiological agents 

with their hosts as well as basic studies to identify possible targets for preventive or therapeutic measures. 

Areas of Investigation and Interest 

• Human and animal DNA viruses as etiologic agents in specific cancers and basic studies of the 

molecular mechanisms of malignant transformation. 

• Retroviruses and oncogenes in human and animal cancer, and hepatitis viruses associated with human 

liver cancer. 

• AIDS-associated virology and malignant sequelae: HIV and AIDS; Kaposi’s sarcoma herpesvirus or 

human herpesvirus 8 ((KSHV/HHV8) and Kaposi’s sarcoma; animal models of AIDS-related 

cancers. 

• Chemical carcinogenic agents and their metabolism, identification of tumor initiators and promoters, 

study of mechanism(s) of action, and signal transduction pathways. 

• Metabolism, toxicity, and carcinogenic mechanisms of chemicals and identification of biochemical 

and molecular markers of chemical carcinogenesis. 

• Investigations of the hormone-related biochemistry of cancer and hormonal perturbations in 

malignancy. 

• Studies of the etiologic mechanisms of bacteria and other microbial species associated with human 

cancer. 

• The synthesis and distribution of chemical carcinogens and mutagens as well as experimental tumor 

inhibitors to chemical carcinogenesis investigators. 

Important Study Findings/Highlights 

• The development of genomic instability is a hallmark of human papillomavirus (HPV)-associated 

cervical cancer. HPV-16 E7 has been shown to rapidly induce abnormal centrosome duplication 

resulting in multipolar, abnormal mitoses and aneuploidy. Recent findings demonstrate that both HPV 

E6 and E7 oncoproteins can trigger anaphase bridge formation, which typically develops after 

chromosomal breaks and alterations of chromosomal structure. Furthermore, the expression of both 

high-risk E6 and E7 oncoproteins causes DNA damage. These studies show that HPV 16 E6 and E7 

oncoproteins can independently induce various mitotic abnormalities and trigger the complex 

chromosomal changes that are observed in high-risk HPV-associated cancers. 

• Cervical cancer cells express high-risk HPV E6 and E7 oncoproteins, and repression of HPV gene 

expression causes these cells to cease proliferation and undergo senescence. Repression of the E7 

oncoprotein efficiently triggers Rb-dependent senescence without activating p53 or inducing p21, 

whereas E6 expression triggers p53-dependent senescence and apoptosis without activating the Rb 

pathway. High-level telomerase, cyclin-dependent kinase activity, and c-myc expression require 

continuous expression of both viral oncoproteins. Thus, continuous expression of both E6 and E7 

oncoproteins is required for optimal proliferation of cervical carcinoma cells, and the two viral 

proteins exert distinct effects on cell survival and proliferation. 

• Constitutive STAT activation has been detected in a wide variety of human cancers, including 

Epstein-Barr virus (EBV)-associated tumors, implicating these molecules in tumor formation and 

progression. STAT members 3 and 5 have been found to be constitutively activated in 

nasopharyngeal carcinoma. LMP1, which is essential for EBV-induced transformation of primary B 

cells, has been shown to be primarily responsible for STAT activation that occurs on EBV infection 

4
of epithelial cells. This activation of STAT 3 appears to be mediated through IL-6. STATs may play a 

dual role by regulating EBV latent infection as well as directly contributing to the tumorigenic cell 

phenotype.

• The LMP2A protein of EBV is the only viral protein consistently identified in latently infected B 

cells, suggesting that it plays a key role in viral persistence and in the development of EBV-associated 

malignancies. DNA microarray technology and the transgenic mouse model were both used to study 

changes in gene transcription induced upon LMP2A expression in murine B lymphocytes. LMP2A 

alters the expression of critical transcription factors involved in normal B-cell development. In 

particular, the transcription factors E2A, EBF, and Pax-5 are each down-regulated in bone marrow 

and splenic B cells from LMP2A transgenic mice. The ability of LMP2A to interfere with B-cell 

transcription factor regulation may be important in maintaining EBV latency. 

• Attachment and entry of KSHV/HHV8 particles into host target cells require binding to an 

extracellular receptor followed by endocytosis of the virus particle. The envelope glycoprotein B (gB) 

of KSHV/HHV8 has been identified through in vitro studies to bind to a3β1 integrin molecules on the 

surface of host cells. Initial attachment of gB to the a3β1 integrin occurs through an RDG amino acid 

motif at the amino terminal end of the gB molecule. Attachment of the KSHV/HHV8 particle to the 

integrin molecule induces phosphorylation of focal adhesion kinase (FAK), which then initiates 

endocytosis of the particle into the host cell. 

• Viruses have mastered mechanisms to escape immune surveillance. One mechanism to disrupt the 

initial host response to viral infection employed by KSHV/HHV8 is blocking the induction of 

interferon. The immediate-early protein ORF45 exerts its effect by preventing the phosphorylation of 

the cellular interferon regulatory factor 7 (IRF-7) that must be activated to induce the transcription 

and translation of type-1 interferon genes. Other evasion strategies include the down-regulation of the 

immunomodulatory molecules MHC class 1, B7-2, PE-CAM and ICAM-1 molecules from the cell 

surface of KSHV/HHV8-infected cells. The KSHV/HHV8 K3 protein induces endocytosis of MHC 

class 1 molecules, which prevents CTL-mediated lysis of infected cells. The cell surface molecules 

B7-2 and ICAM-1 are also rapidly removed from the surface of the cell by the HHV8 protein K5. K5 

disrupts normal natural killer cell responses and humoral helper T-cell responses. Recent 

investigations have shown that the down-regulation of MHC I, PE-CAM and ICAM-1 occurs within 

48 hours after de novo infection with KSHV/HHV8 in cultures of primary dermal microvascular 

endothelial cells in cells that express the latent cycle viral protein LANA. 

• The latent KSHV/HHV8 protein LANA uses a signaling pathway (Wnt) to drive cell proliferation in 

infected cell lines through the accumulation of $-catenin. $-catenin enters the nucleus, where it 

associates with LEF/TCF nuclear proteins and induces specific genes involved in cell proliferation. A 

number of different tumor types without presently known viral etiologies have been described that 

use a similar strategy for $-catenin accumulation that leads to cell proliferation. 

May Wong, Ph.D. Elizabeth Read-Connole, Ph.D. 

Program Director, DNA Virus Studies Program Director, AIDS Virus Studies 

Cancer Etiology Branch Cancer Etiology Branch 

301-496-1953 301-496-6085 

wongm@mail.nih.gov bconnole@mail.nih.gov 

http://dcb.nci.nih.gov/branchdetail.cfm?branch=35

 5
CANCER ETIOLOGY BRANCH 

Division of Cancer Biology

Broad Research Questions Currently Under Study 

All aspects of immunology and its relevance to cancer are included in the Cancer Immunology and 

Hematology Branch (CIHB). The CIHB supports three program areas: Cellular Immunology, Molecular 

Immunology and Hematopoiesis and Hematopoietic Malignancies. The Cellular Immunology program 

area supports research on the role of different cells in the immune response to tumors. These include T 

and B lymphocytes, regulatory T cells, macrophages, dendritic cells, natural killer cells, granulocytes the 

role of MHC class I proteins in antigen presentation and the integration of the innate and adaptive 

immune responses. The Molecular Immunology program area, supports research on genes and proteins of 

potential importance in regulating the immune response to transformed cells. This research program 

covers areas such as the B and T lymphocyte ontogeny, lymphocyte activation, the effect of somatic 

mutations on lymphomagenesis, immunodeficiencies, and the use of transgenic animals to address 

complex biological problems. All programs support research on the basic biology of AIDS and 

lymphomas. 

Important Study Findings/Highlights 

Although cell-mediated immune responses to HIV in peripheral blood have been extensively 

characterized, a recently initiated study will assess HIV specific CD8+ T lymphocyte immune responses 

in mucosal tissue in AIDS patients. Preliminary results demonstrate heterogeneity in expression of 

cytotoxic effector molecules among HIV+ CD8+ T lymphocytes from different anatomic compartments. 

Additional structural studies have led investigators to conclude that selective pressure from the host 

immune response generates variant gp120 envelope proteins that enable the virus to persist in the 

presence of vigorous immune response. Another program objective is to gain insight into pathogenic 

mechanisms involved in retrovirus-induced cell death in nervous and immune cells. Recent data using ts1 

(a pathogenic retrovirus with similar tropism compared to HIV) indicate that cytotoxicity is triggered by 

ER stress, resulting in thiol deficiency and subsequent loss of protection against antioxidants (ie. ROS. 

Studies of B cell proliferation in HIV/AIDS patients indicate varying levels of antigen driven polyclonal 

B cell activation. As long as there are sufficient CD4+ T cells, there is a lower risk of B 

lymphomagenesis. With the decrease in CD4+ T cells in those patients who progress to AIDS, the risk of 

lymphomagenesis increases. 

A complicating factor in AIDS is non-Hodgkins lymphoma (AIDS-NHL) that becomes a significant risk 

when CD4 counts drop below 200mm/3. HIV/AIDS patients demonstrate polyclonal B cell 

activation/proliferation during their infection with concomitant danger of B lymphomagenesis because of 

chronic B cell proliferation and prolonged B cell survival. To prevent malignant B cells from developing, 

apoptotic signals are normally sent through the BCR complex. However, recent evidence has shown that 

mutations in genes coding for the BCR-complex prevent apoptotic signaling with the following 

consequences: (1) prolonged B cell survival, (2) accumulation of mutations, and (3) lymphoma 

development. Current research, in laboratories supported by CIHB, continue to elucidate the genetic 

mutations that lead to B cell malignancies. 

Total Number of Grants and/or Contracts Funded Within CIB

FY2002: 140 with 79 (100% AIDS) and 61 (<100% AIDS) 

Thomas Kevin Howcroft, Ph.D. 301-496-7815 

Program Director howcrofk@mail.nih.gov 

Cancer Immunology and Hematology Branch 

Division of Cancer 

6 
DIVISION OF CANCER CONTROL AND POPULATION SCIENCES 

The Division of Cancer Control and Population Sciences is interested in interdisciplinary studies of the 

molecular epidemiology of pre-neoplastic conditions and cancers among persons infected with, or at high 

risk for, HIV/AIDS. The cancers of primary interest are those associated with concomitant infection with 

viruses conferring latency, including the Epstein-Barr virus (EBV), human herpesvirus 8/Kaposi’s 

sarcoma-associated herpes virus (HHV8/KSHV), human papillomavirus (HPV), and hepatitis B and C. 

Since these infections are apparently necessary, but not sufficient, to cause cancer, both endogenous and 

exogenous cofactors must be involved in the etiology. Epidemiologic variables of interest include host 

susceptibility, age at first acquisition of the oncogenic virus, timing of acquisition of the oncogenic virus 

relative to that of HIV infection, effect of circulating viral load of the oncogenic virus, measurements of 

immune response, and role of lifestyle factors such as tobacco use and diet, and behavioral characteristics. 

Relevant topics also include the progression and clinical course of cancers and pre-neoplastic changes; the 

interplay of the route of acquisition of the DNA virus, particularly HHV8/KSHV, and other cofactors on 

the molecular epidemiology and natural history of oncogenesis; and the role of psychosocial processes in 

infection, disease detection, and progression. 

Important Study Findings / Highlights 

The debate over the effect of highly active antiretroviral therapy (HAART) on cervicovaginal HPV 

infection and cervical intraepithelial neoplasia in HIV-positive women is still ongoing. To date, the data 

suggest that the widespread use of HARRT has not led to a reduction in prevalence of genital HPV 

infections in HIV-positive women. However, data on the effect of HAART on the natural history of CIN 

are mixed. Some studies show no effect of HAART on CIN, whereas other studies show a modest 

positive impact. For example, after adjusting for HPV infection, CD4+ cell levels and cytologic status the 

women in the Women’s Interagency HIV study were more likely to exhibit CIN regression and less likely 

to show progression. The difference in regression rates between women on and off HAART was small 

(36% vs. 30%). It is concluded that HIV positive women should continue to be actively screened and 

treated for CIN whether or not they are on HAART. (Palefsky and colleagues, University o f CaliforniaSan Francisco,CA) 

HPV type 16 is associated with approximately half of all cervical cancers. Although, HPV infection has 

an important role in the development of cervical neoplasm there may be other factors present for the 

infection to progress to a significant lesion. For this reason, a subcohort of 1392 women were selected 

from the on-going Ludwig-McGill HPV natural history epidemiologic study in Brazil to determine 

whether nutritional status may be an important cofactor, affecting both persistence of HPV infection and 

progression to CIN. This study offered the opportunity to conclude that increasing dietary intake of 

lutein/zeaxanthin, β-cryptoxanthin and vitamin C appear to be associated with reduced risks of 

persistence of type-specific HPV infection. In addition, consumption of papaya, a major source of dietary 

carotinoids was associated with reduced risk of persistent infection. (Giuliano and colleagues, University 

of Arizona, AZ) 

It is unknown whether antibodies to HPV capsids, elicited by natural infection are protective. A 

definitive study on the protective role of naturally occurring anti-HPV virus like particle (VLP) antibodies 

to HPV types 16, 18 or 31 was proposed to address this question. The study evaluated 7046 women from 

Costa Rica who had follow-up HPV DNA results five to seven years after recruitment and had serostatus 

measured at baseline. No significant protection from natural infection was observed based on antibody 

detection. This study sets the stage for the introduction of the HPV VLP-based vaccinology. (Burk and 

colleagues, Albert Einstein College of Medicine, NY) 

HPV is sexually transmitted and has been positively associated with the development of several epithelial 

anogenital cancers (cervical, anal, penile and vaginal cancers). Previous epidemiologic studies have also 

found positive associations between the risk of prostate cancer and sexual activity (i.e., age at first 

intercourse and numbers of sexual partners). To evaluate the potential relationship between HPV and 

prostate cancer, a population-based study was conducted in King County Washington on Caucasian and 

 7
African-American men that were between the age of 40 and 64. The data suggest that there was not an 

association between serologic evidence of HPV-16 (OR, 1.05; 95% CI, 0.71 – 1.57) or HPV-18 (OR, 

1.36; 95% CI, 0.69 – 2.69) and the development of prostate cancer. Analysis of the clinical findings also 

revealed no relationship between HPV infection status and Gleason score, stage of disease, or disease 

aggressiveness. (Stanford and colleagues, Fred Hutchinson Cancer Research Center, WA) 

It has been reported that the IL-10 promoter genotype is associated with slower progression to AIDS over 

five years. However, IL-10 is also a B cell stimulatory cytokine that can contribute to B cell 

hyperactivation and/or promote the growth of emerging lymphoma cells. Results of a cross-sectional 

study of IL-10 serum from HIV-infected MACS participants suggest that elevated serum IL-10 or the IL 

10 promoter 592 C/C genotype is associated with the development of AIDS lymphoma. Detectable IL-10 

was five times more likely to be seen in men who went on to develop AIDS-associated lymphoma 

compared to the CD4-matched controls with AIDS but with no malignancies. (Martinez-Maza and 

colleagues, University of California-Los Angeles, CA) 

Total Number of Grants and/or Contracts Funded Within DCCPS 

FY 2003: 47 (AIDS relevant) and 39 (<100% AIDS)

Dr. Sandra L. Melnick Vaurice L. Starks, B.S. 

Chief, Analytic Epidemiology Program Director, Analytic Epidemiology 

Research Branch Research Branch 

301-435-4914 301-402-9375 

sm33k@nih.gov vs38j@nih.gov 

http://epi.grants.cancer.gov/ResPort/infectious.html

8 
OFFICE OF THE DIRECTOR 

Division of Cancer Treatment and Diagnosis 

The AIDS Malignancy Program (AMP), Office of the Director (OD), Division of Cancer Treatment and 

Diagnosis (DCTD) supports pre-clinical and clinical studies for the treatment of cancer in HIV+ and 

immunocompromised patients. The AMP also supports resources for preclinical and translational/ 

interdisciplinary studies including a tissue repository of well characterized specimens collected from 

HIV+ and HIV- patients, natural history cohort studies of HIV+ men and women, and infrastructure at 

institutions that receive significant AIDS funding. In addition, the AMP is working to facilitate research 

on AIDS malignancies in the international arena. 

Broad Research Areas Currently Under Study 

• Identifying hypothesis-driven therapeutic approaches for the treatment of malignancies associated 

with AIDS, including but not limited to non-Hodgkin’s lymphoma, primary central nervous system 

lymphoma, Kaposi’s sarcoma (KS), anogenital dysplasia, and other cancers. The therapeutic 

approaches include, but are not limited to, biologic therapy (e.g., IL-2, IL-12, IFN-alpha, stem-cell 

factor), immune-based therapy (e.g., Mabs directed against B-cell targets, CTLs directed against 

viral-mediated targets, immune system stimulation by IM862, stem-cell transplantation), angiogenesis 

inhibitors (thalidomide, COL-3), and therapeutic vaccines. Cytotoxic chemotherapy in combination 

with immune based or biologic therapies remains an active area of investigation. 

• Identifying the effects of anti-tumor therapy on the underlying HIV infection and impact on the 

immune system. 

• Identifying the effects of anti-HIV therapy on the underlying tumor, the complex issues of drug-drug 

interactions, and overlapping toxicities. 

• Identifying the virologic (HPV, EBV, KSHV, and HTLV-1), immunologic, and molecular markers 

that may be important in the pathogenesis of AIDS malignancies, and defining their potential use as 

therapeutic targets. 

• Identifying the optimum regimen for malignancies associated with AIDS through clinical trials. 

• Developing and providing access to repositories of tumor tissue, relevant biological fluids, and 

controls with associated demographic and clinical outcome information. 

• Identifying unique scientific opportunities in the international arena. 

AIDS Malignancy Consortium (AMC)

The AMC was developed to facilitate the rapid evaluation of hypothesis-driven Phase I, II, and III clinical 

trials that utilize the expertise of both NCI- and National Institute of Allergy and Infectious Diseases 

(NIAID)-sponsored scientists. The AMC consists of 14 Clinical Trials Members and one Data 

Management, Operations, and Statistical Center. They develop and conduct innovative clinical trials 

aimed at improving the treatment and prevention of AIDS-associated cancers and related conditions, and 

identify and develop clinical and laboratory correlates. The AMC has activated a total of 25 clinical trials 

with 5 currently open to patients with AIDS-malignancies (refer to the Clinical Trials section of this 

handbook). Current therapeutic approaches include combination chemotherapy with Mabs directed 

against B-cell targets, compounds that inhibit angiogenesis and restore/improve immune function, 

therapeutic vaccines directed against viral targets (HPV, EBV), and stem cell transplantation. In addition 

to assessing potential anti-tumor activity and drug-drug interactions, the AMC members collaborate with 

investigators outside of the network to develop and utilize laboratory correlates that reveal the 

pathophysiologic basis of drug activity. This includes evaluating the impact of therapy on viral load, 

underlying immune function, and angiogenesis. Additional information about the AMC mission and 

details of trials may be obtained at http://www.amc.uab.edu . 

Important clinical information resulting from completed AMC trials:

• Oral 9-cis-retinoic acid was shown to be an active anti-tumor drug for AIDS-related KS with an 

overall response rate of 37%. 

 9 
• CHOP or a modified dosage of CHOP chemotherapy is an effective and tolerable treatment for NHL 

in HIV+ patients on concurrent HAART. 

• IFN-α2β administered to HIV+ KS patients on protease inhibitors was well tolerated with an overall 

response rate of 39%. 

• Oral COL-3 administered once daily to HIV+ KS patients is well tolerated, with an overall response 

rate of 44% in a phase I trial. A phase 2 trial of COL 3 recently completed accrual and analysis is 

underway. 

• Despite promising phase I and phase II studies, results of a randomized phase III study of IM862 

using a 5 mg QOD dose failed to provide evidence for efficacy. However, HAART was associated 

with a substantial rate of sustained tumor response and this is the largest study to demonstrate the 

efficacy of HAART therapy alone. The unanticipated persistence of the HAART effect on AIDS-KS 

seen here may have contributed to prior estimates of IM862 response. Therapeutic trials for AIDSKS must account for ongoing immune reconstitution in the setting of concurrent HAART that may 

confound estimates of therapeutic activity. 

• Preliminary results of a randomized Phase III trial of CHOP with or without rituximab for patients 

with HIV-associated NHL indicate no response benefit from the addition of rituximab to CHOP. 

However, a high incidence of documented neutropenic infection and death in those receiving 

rituximab raises concern regarding the safety of this approach in this patient population. 

• A phase 1 trial of the stressgen HPV E7-HSP vaccine for the treatment of high grade anal 

intraepithelial neoplasia recently completed accrual and analysis is underway. 

The AIDS and Cancer Specimen Resource (ACSR)

The AMC investigators further contribute toward the research effort in AIDS-associated malignancies by 

collecting and donating specimens to the ACSR, formerly known as the AIDS Malignancy Bank. The 

ACSR consists of three main member institutions, approximately 30 affiliated institutions, and a Central 

Operations and Data Coordinating Center. The ACSR was established to identify and improve access to 

well-characterized tissue, fluids, and associated demographic and clinical data collected from HIV+ and 

HIV- controls, and to encourage and facilitate AIDS-related cancer research. The ACSR contains over 

100,000 specimens collected from cohort studies, clinical trials, and other research, including 

international sources. Samples have been distributed worldwide at no cost to investigators. Specimen 

types made available include tumor and matched control frozen tissues, multi-site autopsy, blood 

cells/serum, frozen/fixed biopsies, AIDS-related lymphomas, KS, lung tissue, and anogenital samples. An 

updated database, application forms, and additional information about the ACSR samples are available at 

http://acsr.ucsf.edu/. 

Partners in AIDS Oncology Research

The AMP partners with other NIH Institutes and Centers to facilitate epidemiology and natural history 

studies, infrastructure, training, and international capacity building for research on cancer in HIV+ 

individuals. 

The AMP supports studies of cancer epidemiology, natural history, and specimen repositories of the 

NIAID-sponsored Multicenter AIDS Cohort Study (MACS) (http://statepi.jhsph.edu/macs/macs.html) 

and the Women’s Interagency HIV Study (WIHS) (https://statepiaps.jhsph.edu/wihs/). The MACS is an 

ongoing multicenter prospective study of the natural and treated histories of HIV-1 infection in 

homosexual and bisexual men, which began in 1984. Important study findings include: 

• In addition to providing samples for the discovery of HHV8 by external investigators, the MACS 

investigators have conducted collaborative studies establishing the seropositivity of HHV8 infection 

with the development of KS (Gao SJ et al. Seroconversion to antibodies against Kaposi's sarcomaassociated herpesvirus-related latent nuclear antigens before the development of Kaposi's sarcoma. 

New England Journal of Medicine 1996;335:233-41). 

10 
• Research on immunopathogenesis of HHV8 infection has provided additional information on the role 

of cytotoxic cell responses in regulating HHV8 infection (Wang QJ et al. CD8+

 cytotoxic T 

lymphocyte responses to lytic proteins of human herpes virus 8 in human immunodeficiency virus 

type 1-infected and -uninfected individuals. Journal of Infectious Diseases 2000;182:928-32). 

• Investigators have relied on MACS samples to investigate the clinical, immunological and virological 

parameters of primary HHV8 infection. Specifically, MACS investigators have shown that the 

development of KS is enhanced in men who acquire incident HHV8 infection after established HIV-1 

infection (Jacobson LP et al. Interaction of human immunodeficiency virus type 1 and human 

herpesvirus type 8 infections on the incidence of Kaposi's sarcoma. Journal of Infectious Diseases 

2000;181:1940-9). 

• Recent studies have shown that DC-SIGN is a primary cell receptor for HHV8. Studies of the host 

genetics related to this viral receptor are being initiated using MACS specimens. 

• With the use of highly active antiretroviral therapy, KS incidence has declined while that of nonHodgkin’s lymphoma did not show a clear decline (Jacobson LP et al. Impact of potent antiretroviral 

therapy on the incidence of Kaposi's sarcoma and non-Hodgkin's lymphomas among HIV-1-infected 

individuals. Multicenter AIDS Cohort Study. Journal of Acquired Immune Deficiency Syndrome 

1999;21 Suppl 1:S34-S41). 

• Elevated expression of immune system activation-associated molecules precedes the clinical 

appearance of AIDS-NHL (Martinez-Maza O et al. Elevated levels of serum sCD23, sCD27, and IgE 

precede the appearance of AIDS-associated non-Hodgkin's lymphoma. In: Guenounou M, ed. HIV 

and Cytokines Agents. Paris: Les Editoins INSERM, 1997:337-40). 

• HIV+ individuals heterozygous for the CCR5-_32 mutation, or those who had a Alow-expressor@ IL10 

promoter genotype, have a reduced risk for the development of AIDS-NHL (Breen EC. Pro- and antiinflammatory cytokines in human immunodeficiency virus infection and acquired immunodeficiency 

syndrome. Pharmacol Ther 2002;95:295-304). 

• The use of HAART prolonged overall survival among HIV-positive men diagnosed with KS and 

NHL even when initiated after the diagnosis of NHL and KS (Tam HK et al. Effect of highly active 

antiretroviral therapy on survival among HIV- infected men with Kaposi sarcoma or non-Hodgkin 

lymphoma. International Journal of Cancer 2002;98:916-22). 

• A recent MACS study has shown an 18-fold increased risk of liver death in individuals coinfected 

with HIV and HBV compared to those only infected with HBV (Thio et al. The Lancet 2002). 

The WIHS is a multicenter prospective study initiated in 1994 and designed to comprehensively 

investigate the natural history of HIV-1 infection in women in the United States. The WIHS has donated 

fresh-frozen tissue from lesional and non-lesions sites of the cervix, vaginal, and vulvar to the ACSR 

since 1999. Important study findings include: 

• Based on results from the analysis of HPV test results from repeated studies in the WIHS and HIV 

Epidemiology Research Study (HERS), a weak association exists between HPV 16 detection and 

CD4 cell strata. HPV 16 may be better at avoiding the effects of immune surveillance, which could 

contribute to HPV 16’s strong association with cervical cancer (Strickler et al. J Natl Cancer Inst 

2003;95:1062-71). 

• A recent study examining serum specimens from the WIHS and HERS showed that HPV 16 

seropositivity was associated with the lifetime number of sex partners (p<0.001) among both HIVinfected and HIV-uninfected women. Approximately 50% of HIV-infected women had serological 

evidence of prior HPV-16 infection, but only approximately 5% had an HPV-16 cervical infection at 

baseline. Despite the higher prevalence of HPV infection in this group, most HIV-infected women 

are able to control HPV-16 replications at the cervix, and reactivation, if it occurs, is not very 

common (Viscidi et al. J Infect Dis 2003;187:194-205). 

• The examination of cervical cancer incidence in WIHS revealed that invasive cervical cancer is 

uncommon in HIV-infected US women participating in a regular prevention program (Massad et al. 

AIDS 2004;18:109-113). 

11 
• A recent study of 503 HIV-infected WIHS participants over six years of follow-up revealed that 

recurrence and incidence of candidiasis are reduced by HAART, and that recurrence is reduced 

independently of CD4 and HIV-1 RNA (Greenspan et al. J Dent Res 2004; 83:145-150). 

• HIV-infected WIHS women were found to have increased incidence rates for KS and non-Hodgkin’s 

lymphoma, but not for invasive cervical cancer when compared to population-based expected rates 

(SEER data). In addition, both HIV-infected and uninfected women had increased incidence rates of 

lung cancer (Hessol et al. 7th International Conference on Malignancies in AIDS and Other 

Immunodeficiencies, Bethesda, MD, April 2003). 

HIV-infected women tend to have lower than expected rates of breast cancer. Further research by WIHS 

investigators indicates that the apparent deficit of breast cancers among women in the WIHS can be 

explained by their overall lower risk, given the distributions in this population of a number of established 

breast cancer risk factors. 

Centers for AIDS Research (CFARs)

The AMP further supports the translation of basic laboratory results to clinical application by cofunding 

the CFAR infrastructure support program along with five other NIH institutes. The CFAR program 

provides administrative and shared research support to synergistically enhance and coordinate highquality AIDS research projects. CFARs accomplish this through core facilities that provide expertise, 

resources, and services not otherwise readily obtained through more traditional funding mechanisms. 

There are 21 sites across the US using the P30 mechanism. Additional information about the CFAR 

program is available at http://www.niaid.nih.gov/research/cfar/ . 

International Research 

Rates of HIV-associated malignancies have increased in developing countries as a result of the HIV 

epidemic, however international collaborations focusing on AIDS-associated malignancies involving USbased investigators and those in developing countries have been limited. This has hampered both the 

training of scientists in developing countries as well as research efforts in this area by US investigators. 

The NCI AMP is helping to strengthen the capacity for research in AIDS-related malignancies in these 

areas by partnering with the Fogarty International Center (FIC) in their AIDS International Training and 

Research Program (AITRP). The purpose of this program is to strengthen the capacity to conduct 

integrated prevention and care research across the full range of conditions and issues that relate to the care 

of adult and pediatric patients with HIV/AIDS, including cancer, in developing countries. The AITRP 

program will increase research training in AIDS associated cancers in those regions with significant 

HIV/AIDS incidence and prevalence and enhance US based research efforts by providing access to 

unique sources of patient populations, resources, and research collaborations. In FY 2003, the NCI cofunded four meritorious cancer relevant competitive supplement applications: 

• The aim of Dr. Detels UCLA AITRP supplemental program is to develop the ability of trainees, 

primarily from Brazil and China, to perform advanced research in cellular and molecular 

epidemiology and pathogenesis relevant to AIDS malignancies associated topics. A secondary aim is 

to enhance the research goals of UCLA-based investigators with NIH-sponsored research projects in 

AIDS malignancies, by providing unique access to population, reagents, or expertise. 

• Dr. Reingold was awarded supplemental funding to his very successful 16 year running AITRP 

program to develop a unique collaboration between the USCF CFAR and the University of California 

Berkeley AITRP to leverage the expertise of both programs for training and research capacity 

building in nine key regions with significant HIV/AIDS prevalence including Zimbabwe, Cambodia, 

Brazil, Uganda, India, Peru, Honduras, Thailand, and Ivory Coast. Members of the expanded team 

include the NCI funded investigators Jeff Martin, Ruth Greenblatt, and Joel Palefsky. 

• Dr. Warren Johnson will conduct training in the Dominican Republic, where there is only a 

rudimentary understanding of the connection between HIV and HPV; no systematic HIV data 

collection or screening has been performed here to correlate HIV with abnormal cytology. The 

investigators plan to build upon the existing gynecologic services in place at Profamilia to determine 

if it’s useful to use abnormal cytology as sentinel evidence to trigger HIV counseling and testing. 

Prospective follow-up will be implemented to evaluate the development of CIN and cancer. 

 12 
• Dr. Woods proposes to expand training activities to China by collaborating with Nankai University in 

Tiajin. The critical increasing STD problem in China has been well documented, however, there is a 

gap in information about the impact of AIDS related malignancies on morbidity and the prevalence 

and incidence of HPV, and KSHV. The objectives of this expanded training program will facilitate 

acquisition of this information to better prepare Chinese health officials. To accomplish this goal, 

trainees will participate in the following coursework: 1) biomedical research rotations to investigate 

the role of HIV, herpesviruses, and papillomavirus in the development of AIDS associated 

malignancies, 2) rotations in clinical management of AIDS and AIDS related malignancies, 3) 

training in epidemiology, behavioral interventions, medical informatics and laboratory techniques, 

and 4) research ethics and regulatory documentation. 

 

Since 1997, the NCI has presented an annual conference on malignancies in AIDS and other 

immunodeficiencies. The objectives of this international conference are to showcase progress and to 

stimulate research across diverse disciplines. In 2004, the AMP sponsored the 8th International 

Conference on Malignancies in AIDS and Other Immunodeficiencies (ICMAOI). 

Total Number of Funded AIDS-related Grants and/or Contracts in Office of the Director, DCTD

FY 2003: 76, 100% AIDS (R01, U01, R21, P01, P30, D43) 

Jodi B. Black, Ph.D. Jaime Kenyon, M.P.H. 

Program Director, AIDS Malignancy Program Program Specialist 

301-402-6293 301-496-6711 

blackj@mail.nih.gov kenyonj@mail.nih.gov 

http://cancer.gov/dctd/aids http://cancer.gov/dctd/aids

13
CLINICAL GRANTS AND CONTRACTS BRANCH 

Cancer Therapy Evaluation Program, Division of Cancer Treatment and Diagnosis 

Broad Research Questions Currently Under Study 

• Database of HIV status of BMT recipients 

• BMT as treatment for AIDS-related malignancies 

• Treatment and prevention of viral and fungal infections 

• Gene therapy to improve BMT outcome and treat HIV disease 

HIV Status of Transplant Recipients 

Dr. Mary Horowitz, principal investigator of a resource cooperative agreement (5U24CA76518-04, 

Medical College of Wisconsin) maintains a database on pretransplant HIV status of allogeneic and 

autologous blood or marrow transplant (BMT) patients and the clinical outcomes of HIV+ BMT patients. 

Eight-one patients out of 45,385 allograft recipients were HIV+. Thirty-three patients out of 22,549 

autologous graft recipients were HIV+. Five HIV+ patients were transplanted for their HIV disease 

alone. 

AIDS-related Malignancies 

HIV+ patients are at increased risk for lymphoma and other malignant diseases. Standard treatment for 

lymphoma includes chemotherapy, monoclonal antibody therapy, and autologous blood or marrow 

transplant (BMT) for patients who relapse. Lymphomas in HIV+ patients tend to be more aggressive and 

thus more difficult to treat than those of HIV- patients. In addition, HIV+ patients may be more sensitive 

to the side effects of chemotherapy. Thus improved treatment for lymphoma in HIV- patients should 

benefit HIV+ patients with lymphoma, but additional improvements will be needed. 

Investigators at the City of Hope Medical Center continue to follow 15 HIV-related lymphoma patients 

(median age, 43 years) who were treated with BMT between March 1998 and May 2001. All patients 

engrafted and the median follow-up for the surviving patients is 24 months. The two year probability of 

overall survival and disease-free survival (DFS) is 79%. This suggests that BMT is well-tolerated in 

patients with HIV-related lymphoma, with no apparent negative effects on the underlying HIV infection. 

It appears that transplant offers the possibility for durable remission and should be considered as an 

alternative to conventional salvage regimens for HIV+ lymphoma patients who relapse. 

Immunotherapy using Rituxan, a monoclonal antibody against the CD 20 protein found on lymphoma 

cells, has emerged as an important new treatment for lymphoma. Investigators at the City of Hope 

Medical Center tested Zevalin (an antibody similar to Rituxan), but with a radioactive element attached 

which can kill lymphoma cells. Eighteen non-HIV-infected patients with follicular lymphoma, diffuse 

large-cell lymphoma or mantle cell lymphoma were treated with Zevalin plus hematopoietic cell 

transplantation (HCT) between May 2000 and December 2004. The treatment was well tolerated. 

Mucositis, neutropenic fever and skin rash were the most common acute toxicities. All patients engrafted; 

the median time to engraft white blood cells was 10 days and 18 days for platelets. One year estimated 

overall survival and disease-free survival are identical at 92%. These data suggest that high dose Zevalin 

can be given safely in combination with high dose chemotherapy and HCT. Zevalin plus BMT did not 

increase transplant related toxicity nor did it delay engraftment. The current Phase II study is continuing. 

A second trial of Zevalin combined with a chemotherapy regimen called BEAM for older patients with 

lymphoma has accrued twelve patents. There have been no transplanted related deaths, two relapses and 

the DFS at 11 months is 79%. 

With funding from NCI’s Quick Trial Program, investigators at Boston University have developed 

another potential new treatment regimen for lymphoma, and other tumors, which develop in Epstein-Barr 

virus (EBV)-infected cells. Unlike cytomegalovirus (CMV), which can be killed by treatment with 

ganciclovir, EBV does not routinely produce thymidine kinase (TK), the enzyme required for 

ganciclovir’s activity. The study drug, butyrate, stimulates TK production. This enzyme then 

metabolizes ganciclovir into a toxic agent, which is incorporated into viral DNA and kills the tumor cells. 

The maximal tolerated dose of butyrate has been identified (1000 mg/kg/dose), with somnolence being 

14 
the dose-limiting side effect. So far, 11/16 patients had a decrease in tumor size after only one cycle of 

treatment. This response, in a patient population with refractory, bulky disease, suggests that this regimen 

may provide a promising new therapy for patients with a usually-fatal malignancy. 

Stem Cell Gene Therapy for AIDS 

The treatment of patients with HIV-related non-Hodgkin's lymphoma (NHL) and Hodgkin's disease (HD) 

is less successful than in the non-HIV setting, in part due to the aggressive character of these lymphomas 

but also due to the underlying HIV infection. High-dose therapy with stem cell transplantation has been 

used with success in the HIV-negative lymphoma setting for high-risk or relapsed disease. However, for 

patients with HIV-NHL and HIV-HD, ultimately the chance for long-term lymphoma-free survival also 

depends on successful control of the HIV infection. Gene therapy approaches may provide the 

opportunity for this long-term control by rendering the transplanted cells resistant to HIV infection. 

Investigators at City of Hope Medical Center are studying BMT in conjunction with gene therapy for the 

treatment of HIV-associated lymphomas. Studies of gene-transduced human cord blood stem cells 

established parameters for proper vector design, demonstrated multi-lineage engraftment of transduced 

cells in mice, and showed that “true” stem cells had been targeted by their growing in secondary 

recipients. They also showed that cells transduced with vectors containing “HIV-resistance” genes 

avoided infection in culture. Studies in the mouse HIV-lymphoma model are underway to verify this 

finding in a whole-animal system. On a parallel track, AAV and Lenti viral vectors are being fitted with 

sequences designed to ensure site-specific insertion and other safety measures. Later this year, 

investigators plan to use AAV-transduced hematopoietic stem cells for transplant of HIV-lymphoma 

patients with anti-sense constructs that convey resistance to infection. 

Anti-fungal Therapy 

Several projects in Dr. Fred Appelbaum’s program project (5P01CA18029-28, Fred Hutchinson Cancer 

Research Center) have AIDS relevancy. In project 5, Dr. Lawrence Corey is studying the T-cell response 

to aspergillus to better understand how to improve post transplant immune responses against this fungus. 

Development of a sensitive assay of T-cell immunity is expected to allow prediction of patients at greatest 

risk of infection. 

The Blood and Marrow Transplant Clinical Trials Network, co-funded by the NCI and National Heart, 

Lung and Blood Institute (NHLBI), is conducting a phase III clinical trial entitled “A Randomized 

Double-blind Trial of Fluconazole vs. Voriconazole for the Prevention of Invasive Fungal Infections in 

Allogeneic Blood and Marrow Transplant Patients.” A total of 600 patients will be accrued (300 to each 

arm) over three years. The primary objective is to compare the fungal-free survival rates between the two 

study arms. The secondary objectives are to compare the frequency of invasive fungal infection, time to 

invasive fungal infection, survival rate, duration of amphotericin B therapy (for possible invasive fungal 

infection), time to neutrophil and platelet engraftment, time to and severity of acute and chronic GVHD, 

and utility of the galactomannan assay in detection of Aspergillus. The relative safety of the two 

antifungal agents will also be assessed through the collection of adverse events and routine laboratory 

monitoring. In addition to determining which of the two drugs is more efficacious, this trial will also 

provide data regarding the predictive value of a clinical assay for Aspergillus (galactomannan assay) 

developed by BioRad Laboratories. 

Anti-viral Therapy 

Individuals infected with human cytomegalovirus (CMV) usually appear asymptomatic unless they 

receive immunosuppressive drugs (for example transplant recipients) or acquire an infection such as HIV, 

which allows reactivation of latent virus. Immunotherapeutic approaches to limit CMV morbidity and 

mortality in BMT, AIDS and other immunocompromised patients are currently under investigation as an 

alternative to antiviral drugs. A safe and effective vaccine to limit disease has been elusive. 

Dr. Don Diamond and colleagues at the City of Hope Medical Center have a multi-faceted approach to 

develop and clinically deliver an efficacious and broadly-reactive vaccine. One strategy is to identify 

several parts of the virus which elicit a vigorous immune response and combine them in one vaccine. 

 15
These investigators have begun a series of clinical trials in BMT patients which will examine the 

advantages of donor immunization versus adoptive immunotherapy. Another approach uses gene therapy 

to induce neutralizing antibodies. 

Investigators at the Fred Hutchinson Cancer Research Center are conducting clinical trials of anti-viral 

drug therapy in BMT patients. A randomized double-blind multicenter trial of valganciclovir vs. placebo 

for the prevention of late CMV infection is underway at seven centers (Fred Hutchinson Cancer Research 

Center, University of Florida, Mayo Clinic, Duke University, Memorial Sloan-Kettering Cancer Center, 

City of Hope National Medical Center, University of Michigan, M.D. Anderson Cancer Center). Eighty 

patients have been randomized with no major problems. Samples are being stored to measure CMVspecific immune responses and ganciclovir resistance. This randomized trial will demonstrate if 

valganciclovir is effective, describe any long-term toxicity, and provide data on the development of drug 

resistance and its impact on CMV-specific immune reconstitution. 

A protocol for a randomized double-blind multicenter trial of valacyclovir vs. placebo has been developed 

to examine whether prevention of subclinical primary CMV with valacyclovir will reduce the post 

transplant development of life-threatening bacterial and fungal infections. This randomized trial of 

valacyclovir in patients at risk for primary CMV infection is aimed at examining the questions of whether 

indirect effects of CMV occur and whether these effects can be prevented by antiviral prophylaxis. 

Total Number of Funded AIDS-related Grants and/or Contracts in CTEP 

FY 2002: 47 grants and cooperative agreements (R01, R21, R37, R42, P01, U01, U24) with 3, 100% 

AIDS relevancy. 

Roy S. Wu, Ph.D. 

Branch Chief and Program Director 

301-496-8866 

wur@ctep.nci.nih.gov 

http://ctep.cancer.gov

16 
GRANTS AND CONTRACTS OPERATIONS BRANCH 

Developmental Therapeutics Program, Division of Cancer Treatment and Diagnosis 

The Grants and Contracts Operations Branch (GCOB) is part of the Developmental Therapeutics Program 

(DTP), Division of Cancer Treatment and Diagnosis. DTP’s mission is to 1) promote preclinical research 

leading to novel discoveries and their translation into effective therapies for cancer and HIV/AIDS and 2) 

support a broad contract-based preclinical drug development program to facilitate the introduction of 

novel therapies into clinical trial. DTP contracts include collections of natural products worldwide, drug 

synthesis, production of laboratory- and clinical-grade drugs and biologics, formulation, and toxicology 

on new agents under consideration for clinical trials. GCOB’s role is to maintain a large portfolio of 

grants and cooperative agreements covering all aspects of preclinical cancer drug discovery and 

development and to coordinate contract competitions that support the drug development activities. 

During 2002 GCOB transferred AIDS preclinical treatment-related R01 grants to the Office of the DCTD 

Director in an effort to consolidate the preclinical and clinical grants in this area in one office. The 

transfer involved all AIDS-related grants except those focused on chemistry and multi-disciplinary studies 

funded through cooperative agreements. 

Contract-Based and Other Assistance to Extramural Investigators

With advice from extramural advisory committees, DTP has created programs to assist the academic 

community with drug discovery activities. In brief, DTP has upgraded its web site at 

http://dtp.nci.nih.gov/ to provide more information on available resources and services, such as access to 

synthetic and natural products repositories, reference reagents, chemical libraries, laboratory animals, cell 

lines, cytotoxicity data on diverse compounds in a 60-cell line panel of cancer cells, AIDS screening data 

in a cell-based assay, screening services in cancer, AIDS, and opportunistic infections, chemical 

structures, molecular target data, analysis tools, such as the COMPARE program, and in vivo antitumor 

data on many marketed and experimental compounds. 

Rapid Access to Intervention Development (RAID), an assistance program, is helping extramural 

academic investigators develop promising agents for the treatment of cancer and AIDS-associated 

malignancies. RAID accepts applications from the extramural community twice per year. Applications are 

peer-reviewed by academic investigators, and DTP contract resources are used to complete tasks, such as 

large animal toxicology studies. 

NCI and NIAID created a special assistance mechanism, NIH Inter-Institute Program for the 

Development of AIDS-Related Therapeutics, to assist the HIV/AIDS research community by reducing 

barriers to the discovery and development of new products to clinical trial. In contrast to the RAID 

program, this program offers assistance to investigators from either academia or small businesses, and 

will support discovery as well as development activities. This program accepts applications from the 

extramural community twice each year. The applications are peer-reviewed, and successful applicants 

receive requested services that are supported by NCI and NIAID contracts. For example, production of 

clinical-grade material can be arranged through this mechanism at no charge to the applicant. 

In addition to providing more research services, DTP has re-engineered its drug discovery programs in 

both cancer and HIV/AIDS to emphasize molecular targets, especially those that represent particular 

vulnerabilities or are important in disease pathogenesis. More information on these new directions in 

cancer drug discovery can be found in the NCI ByPass Budget request to Congress. In the future, more 

imaging agents or measurements of biomarkers are expected to be used in clinical trials to evaluate both 

“target” and “off-target” effects of new agents and to stratify patients. Increased knowledge about cancer 

and other diseases has contributed an abundance of new targets for drug action. This information, coupled 

with the use of new technologies, provides the underpinnings of a new era in drug discovery. To assist 

investigators in these endeavors, GCOB supports several funding opportunities that can be found at the 

DTP web site. The initiatives, which focus on potential targets for therapeutic intervention, use a variety 

of funding mechanisms. Once funding actions are complete, abstracts for each award are posted on the 

DTP web site at http://dtp.nci.nih.gov/branches/gcob/gcob_web9.html to foster collaborations and 

communication about potential drug targets, which may have application to more than one disease. 

17
Grant Initiatives 

GCOB sponsors a number of initiatives that can be used effectively by investigators in the HIV/AIDS 

malignancy community as well as others. Most new initiatives involve cooperation and collaboration 

with other areas of NIH. GCOB is cooperating with the NCI Office of Cancer Complementary and 

Alternative Medicine, National Center for Complementary and Alternative Medicine, National Institute of 

Nursing Research, and the National Institute of Dental and Craniofacial Research to invite research grant 

applications for basic and clinical complementary cancer research in PA-04-053: Developmental Projects 

in Complementary Approaches to Cancer Care. GCOB is representing NCI in a new initiative with the 

National Institute of Diabetes and Digestive and Kidney Diseases and the National Institute of Allergy 

and Infectious Diseases on PA-04-031: Development of Assays for High Throughput Drug Screening. 

The purpose of this PA is to encourage the development of high throughput small molecule screening for 

use in both research and drug discovery programs by funding the development of innovative assays that 

may be adapted for automated screening. The assays could be used to identify new tools for basic 

research and promising new avenues for therapeutics development. 

Public-Private Partnerships are being encouraged by NIH in several Roadmap initiatives as a way to deal 

with complex issues such as speeding progress toward better treatments 

(http://www.nihroadmap.nih.gov/). Since 1983 GCOB has supported multidisciplinary or team science 

through the National Cooperative Drug Discovery Group (NCDDG) program, which involves 

partnerships between academia, industry and government to create new anticancer therapies. On January 

16, 2004, GCOB issued a Request for Applications to continue the NCDDG program, and especially 

solicited applications for AIDS-related malignancies. Applications are due May 19, 2004 and awards are 

planned for 2005. During 2003 DTP competed the Academic Public Private Partnership Program (AP4), 

a new partnership arrangement that will require funding from both government and industrial sources. 

However, the principal investigator must be from an academic institution. Planning grants for this new 

endeavor are undergoing review, with award anticipated in 2004. GCOB also is co-funding several 

International Cooperative Biodiversity Groups (ICBGs) to address issues of biodiversity conservation, 

economic growth, and human health through discovery of therapeutic agents for cancer, infectious 

diseases including HIV/AIDS, mental disorders, and diseases of primary concern to developing countries, 

such as parasitic diseases and tuberculosis. New awards were made during 2003. The ICBG program is a 

unique interagency initiative led by the Fogarty International Center with support from several institutes 

of the NIH, including NCI, as well as the National Science Foundation and the United States Department 

of Agriculture. 

Mary K. Wolpert, Ph.D. George S. Johnson, Ph.D. 

Chief, Grants and Contracts Operations Branch Program Director 

301-496-8783 301-496-8783 

wolpertm@exchange.nih.gov johnsong@exchange.nih.gov 

http://dtp.nci.gov/branches/gcob/gcob_index.html 

18
SCREENING TECHNOLOGIES BRANCH

Developmental Therapeutics Program, Division of Cancer Treatment and Diagnosis 

Research sponsored by the Branch is directed towards the discovery and development of new agents with 

the potential for treatment of patients with cancer, AIDS, and opportunistic infections. Various drug 

screening models are employed to identify and characterize novel therapeutic agents from synthetic 

chemical and natural product libraries. 

In recent years, AIDS-related efforts have focused primarily on the identification of anti-HIV-1 agents 

using a cell-based primary screen. Current anti-HIV-1 research is directed towards the characterization 

and exploitation of molecular targets unique to this virus. New initiatives in the areas of AIDS associated 

malignancies and opportunistic infections are currently being formulated. The rapidly expanding research 

literature regarding viral involvement in AIDS-associated malignancies suggests novel molecular targets 

for drug discovery that may be addressed through screening or molecular modeling and drug design. 

Important Study Findings/Highlights 

Many structural classes of anti-HIV compounds previously unrecognized as antiviral agents have been 

discovered using the cell-based screen. Detailed preclinical studies addressing formulation, 

pharmacokinetics, and toxicology have been pursued for promising compounds. The cell-based screen 

was instrumental in the discovery of two Food and Drug Administration approved drugs, 3TC and the 

carbovir prodrug Ziagen. Based on recommendations of external Scientific Review Committees, the NCI 

has discontinued use of the cell-based model for large-scale drug screening. The National Institute of 

Allergy and Infectious Diseases (NIAID) also offers screening and mechanistic follow-up as a service to 

the research community (http://www.niaid.nih.gov/daids/PDATguide/HIVThera.htm). 

The NIH Inter-Institute Program for the Development of AIDS-Related Therapeutics

(http://dtp.nci.nih.gov/docs/dart/dart.html) was introduced in January 2001 to make the drug discovery 

and development resources of the NCI and NIAID available to the extramural research community in a 

coordinated way was introduced. This Program receives applications twice per year that are peerreviewed. Successful applicants receive access to NIH resources intended to support investigator 

development of therapeutic concepts towards clinical trial. Details regarding approved projects from the 

first five cycles of review are available at the bottom of the webpage listed above. Among other IIP 

projects, the Branch has concluded a research project in natural product drug discovery for cancer and 

AIDS which was enabled by a successful application to the Inter-Institute Program. More recently, 

several peer-approved projects involving drug screening/discovery are in the early stages of 

implementation, and in one case may add valuable mechanistic information concerning historical NCI 

AIDS screening data. 

Ongoing efforts include: development of high throughput screening (HTS) methods which would allow 

rapid screening of chemical libraries, the development of multidrug resistant HIV which is compatible 

with HTS and may provide relevant drug development leads for the future. Progress has been marked in 

the development of a HTS assay for human herpesvirus 8 (HHV-8) polymerase (Dorjsuren et al. Protein 

Expr Purif 29(1):42-50;2003). Preliminary work of screening the NCI diversity set chemical library using 

in vitro translated HHV-8 polymerase in collaboration with Dr. R. Ricciardi (U. Penn) has been 

completed. Future plans involve the screening of larger chemical libraries. A CRADA with Phytobiotech 

Inc. has been implemented in which the company will provide novel plant-derived natural products for 

screening of new drug leads for cancer and AIDS related screens. 

Robert H. Shoemaker, Ph.D. 

Chief, Screening Technologies Branch 

301-846-6845 

rs17e@nih.gov 

http://dtp.nci.nih.gov/

19
LABORATORY OF ANTIVIRAL DRUG MECHANISMS 

Screening Technologies Branch, Developmental Therapeutics Program, Division of Cancer 

Treatment and Diagnosis 

The Laboratory of Antiviral Drug Mechanisms (LADM) concentrates on three areas of research: 1) 

identification of novel molecular targets, 2) development of high-throughput screening (HTS) assays, and 

3) discovery of novel therapeutics, which are relevant to AIDS and AIDS-associated malignancies. One 

of our main focuses has been to facilitate the discovery of novel inhibitors of human herpesvirus 8 

(HHV8), a causative agent for Kaposi’s sarcoma and a subset of AIDS-associated lymphoma, through 

molecular target-based screening and secondary characterization assays. Using a microplate-based HHV8 

polymerase (Pol) and processivity factor (PPF) DNA synthesis assay (HHV8 Pol/PPF assay), established 

in collaboration with Dr. Robert Ricciardi of the University of Pennsylvania, we completed the screening 

of the NCI Diversity Set and identified 28 hit compounds with greater than 50% inhibition. The 

inhibitory activities of 23 of 26 hit compounds available for further investigation were confirmed by the 

recombinant enzyme-based assay with the IC50 concentrations ranging from 0.23 ± 0.04 (mean ± SD) to 

15.78 ± 1.26 μM. Automation of HHV8 POL/PPF assay is currently being pursued to promote future 

HTS campaigns. We also uncovered anti-HHV8 activity of a new thymidine analog, nmethanocarbathymidine (N-MCT), using HHV8-infected BCBL-1 cell-based assay. We found that IC50 

of N-MCT was up to 10-fold lower than cidofovir, one of the most potent HHV8 Pol inhibitors identified 

to date. Mechanistic characterization of N-MCT anti-HHV8 activity is ongoing in collaboration with Dr. 

Victor Marquez, NCI and Dr. Riad Agbaria, Ben-Gurion Univ. of the Negev. One of the newer HHV8 

molecular targets pursued in our laboratory is latency-associated nuclear antigen (LANA). LANA tethers 

HHV8 DNA to host chromosomes, playing a key role in the maintenance of episomal HHV8 in host cells. 

LANA-binding element of viral DNA has been mapped to specific sites within the terminal repeat (TR) of 

HHV8 genome by Dr. Rolf Renne of the Case Western Reserve University. Small molecules that disrupt 

or interfere with the LANA-DNA binding may hinder or suppress the critical functions of LANA. In 

collaboration with Dr. Renne, we are currently trying to establish LANA-DNA binding inhibition assay 

using fluorescence polarization-based methodology toward the development of anti-LANA drug 

screening assay. 

The LADM also contributes to many facets of anti-HIV therapeutics development. The lab screens 

compounds submitted by intramural and extramural investigators for anti-HIV activities, using 

conventional cell-based assays. Selected compounds are further evaluated for their ability to inhibit 

replication of various HIV isolates in primary and laboratory-established cell line-based assays, 

specifically designed to elucidate distinct molecular targeting sites: virus attachment, fusion, reverse 

transcriptase, integrase, protease (PR), nucleocapsid protein, virus assembly, and budding. Information 

obtained from the mechanistic characterization assays determines if given compounds are to be pursued 

for further development. Another ongoing effort is the development of a cell-based HTS assay, using 

specific HIV-1 strains known to be resistant to many conventional inhibitors of reverse transcriptase (RT) 

and PR (anti-MDR-HIV screen), in order to find anti-HIV agents that act through novel mechanisms other 

than inhibition of viral RT or PR. We have identified suitable MDR strains that are highly resistant to 

multiple RT or PR inhibitors while maintaining high degree of replication fitness. Optimization of antiMDR-HIV for HTS is actively pursued at this time. In summary, the LADM conducts an array of 

virological studies with a major focus on the discovery of novel molecular targets and development of 

new therapeutic agents for AIDS and AIDS-associated malignancies. 

Shizuko Sei, M.D. 

Head, Laboratory of Antiviral Drug Mechanisms 

NCI-FCRDC 

301-846-1780 

sei@dtpax2.ncifcrf.gov 

http://spheroid.ncifcrf.gov/stb/staff/sei/sei.cfm

http://spheroid.ncifcrf.gov/STB/stb_index.cfm

 20
BASIC RESEARCH LABORATORY 

Center for Cancer Research 

Lentiviral Vectors for Gene Therapy and Functional Genomics 

While a source of great misery, lentiviruses can be modified and channeled toward usefulness as vectors 

for gene transfer in gene therapy, functional genomics, and animal model transgenesis. Because of their 

unique properties, they are ideally suited for gene transfer into non dividing cells, including stem cells. 

They are also vehicles of choice for siRNA delivery for gene function validation and for molecular targetdirected therapy. The lentiviral vectors may well be the only means available to create transgenic animals 

of species other than the mouse, barring heroic efforts. For full exploitation of their translational potential, 

three inter related issues must be addressed - regulation, targeting, and safety. 

Lentiviral vector regulation 

To achieve the goal of acquiring the ability to regulate vector expression in vivo from outside and at will, 

we hypothesize that molecule(s) exist, or can be made to exist, that modulate all biological functions. As 

proof of principle, we have chosen to target the transcriptional apparatus of the lentiviral vectors, focusing 

on the viral LTR promoter, to search for such a drug-like molecule. In parallel, we are also targeting 

cellular hTERT promoter, as a control for the viral promoter. We have undertaken high throughput 

screening of chemical and natural products libraries in a cell-based assay. Genetically modified cell 

clones for the cell-based assay were created that carried a cassette of the promoter (viral LTR and cellular 

hTERT) linked to the indicator GFP gene for read out, and puromycin-resistance gene for cell selection. 

The clones met the following criteria: low basal activity of the promoters, responsiveness to known 

modulatory signals (Tat for LTR promoter and c-Myc for hTERT promoter), stable maintenance of the 

transgene cassette, and deficient MDR activity of the cell itself. Once screening of the ‘diversity set’ part 

of the chemical library is completed to validate the assay and set the parameters of the search, a campaign 

to screen thousands of compounds will be mounted. The current results suggest that fine mapping of the 

determinants and more defined exchanges will yield vectors with the desired characteristics. 

Lentiviral vector safety 

The major concern of safety is the generation of replication competent recombinants during vector 

production, or in patients who may be infected with HIV. We hypothesize that lentiviruses HIV-1 and 

HIV-2 are functionally homologous but are divergent enough in sequence that the chimera derived from 

them will have minimized the chance of recombination during vector production. Similar argument holds 

that the vectors derived mainly from HIV-2 will be safer for gene therapy of HIV-1 infected individuals 

and conversely, HIV-1 derived vectors better for HIV-2 infected individuals. The exercise here is to 

design chimeric vectors with enhanced safety but with no loss of efficiency of gene transfer. Utilizing the 

knowledge of the determinants of encapsidation and transduction, we have created chimeric vectors with 

judicious exchange of genes and regulatory elements between HIV-1 and HIV-2. 

Vector validation 

An integral part of the research effort is to validate vectors with model genes and promoters. We have 

chosen induction of cell death of a neoplastic cell as a model. With the idea that two hits are better than 

one, our objective is to promote apoptosis by delivering Bax transgene and suppress cell survival by 

delivering Bcl2 siRNA. The challenge of creating high titer lentiviral vectors with cytotoxic transgenes, 

such as Bax, was initially under appreciated. One solution to this problem was to use a regulated 

promoter, preferably a eukaryotic promoter with relevance to cancer. Ideally there will be a promoter that 

is, or can be, down regulated in the producer cell line and is, or can be, up regulated in the target cell. We 

are using cancer cell-selective hTERT promoter as a prototype. The search for drug-like molecules to up 

or down regulate hTERT promoter noted above is tied to this idea. Whether this will be sufficient to 

produce high titer Bax transgene and Bcl2 shRNA vectors remains to be determined. 

Suresh K. Arya, Ph.D. 301-496-8783 or 301-846-1857 

Senior Investigator, Basic Research Laboratory, CCR aryas@exchange.nih.gov 

Program Director, Developmental Therapeutics Program http://ccr.cancer.gov/labs/lab.asp?labid=38

21
BASIC RESEARCH LABORATORY 

Center for Cancer Research 

HTLV-1 Molecular Biology and Pathobiology 

We previously constructed an infectious molecular clone of human T-cell leukemia virus type 1 (HTLV1) and developed cell culture systems to examine virus entry, replication and particle maturation. 

Recombinant HTLV-1 vectors have now been made to study individual steps in the virus infectious cycle. 

These vectors have been used to determine the basis for the very low infectivity of HTLV-1 compared to 

other retroviruses. We found that a major block to efficient HTLV-1 infection occurs at a post-entry step. 

We are currently asking whether the mode of transmission of the virus (as cell-free virus particles versus 

cell-to-cell contacts) influences infection efficiency. The recombinant HTLV-1 vector system also 

provides the first rapid and sensitive means to examine HTLV-1 susceptibility to antiviral agents. We 

found that HTLV-1 replication was inhibited by the reverse transcriptase (RT) inhibitors AZT, 3TC, d4T, 

tenofovir and abacavir. We have begun to define the catalytically active form of HTLV-1 RT that is 

produced from a polyprotein precursor by the viral protease. This work will establish the subunit 

composition of the active enzyme, prerequisite to expressing the recombinant protein for structural and 

functional analyses. We are also examining viral and cellular proteins that cooperate in the process of 

virus assembly and release. We have shown that a peptide motif in the matrix protein of the virus core 

particle interacts with components of the cellular endosomal sorting pathway. The interaction of the viral 

late assembly domain with Nedd4 protein was found to be essential for virus budding from the plasma 

membrane. The diseases associated with HTLV-1 infection are often accompanied by immunological 

abnormalities that could be related to the activation of specific genes in the HTLV-1 infected T cell. In 

the course of examining cytokine gene expression in T cells, we found that the Th2 cytokine, IL-13, was 

over-expressed in HTLV-1 chronically infected cell lines. Moreover, examination of CD4+ T cells from 

HTLV-1 infected patients revealed a correlation between the levels of expression of IL-13 and viral Tax 

protein. We are currently examining the mechanism of activation of the human IL-13 promoter by the 

viral trans-regulatory protein, Tax. 

David D. Derse, Ph.D. 

Senior Investigator 

301-846-5611 

derse@ncifcrf.gov 

http://www.nci.nih.gov/intra/llb/derse.htm

 22
HIV AND AIDS MALIGNANCY BRANCH 

Center for Cancer Research 

Development of Novel Therapies for HIV Infection and Related Malignancies

The HIV and AIDS Malignancy Branch (HAMB) was established in 1996 to conduct translational clinical 

and laboratory research aimed at the development of novel therapies for HIV infection and AIDS-related 

malignancies. HAMB also conducts laboratory research focused on an understanding of these diseases. 

More detailed information about clinical trials can be found at http://ccr.cancer.gov/trials/. Also, the 

research of other investigators in the Branch can be found separately in this Handbook. 

Research of Dr. Robert Yarchoan 

During the past year, Drs. Richard Little and Robert Yarchoan have been conducting several clinical trials 

to evaluate novel therapies for Kaposi's sarcoma (KS). We are also studying the cytokine and antiangiogenesis agent IL-12, and preliminary results indicate that it has activity. We are following this 

observation up with a study of liposomal doxorubicin plus IL-12 in patients with advanced KS. In 

addition, we have initiated a protocol to study amonoclonal anti-VEGF antibody (bevacizumab) in 

patients with KS. In collaboration with Dr. Wyndham Wilson of the Medicine Branch in the Center for 

Cancer Research, we have been exploring the possible role of infusional therapy with etopside, 

prednisone, vincristine, cyclophosphamide, and doxorubicin (EPOCH) followed by IL-12 in AIDSassociated lymphomas. We are now extending this to study the use of short-course EPOCH plus 

rituximab. Finally, we are currently planning a clinical trial to investigate the natural history and targeted 

virolytic therapy in multicentric Castleman’s disease (MCD). 

We are exploring the area of therapeutic vaccination for patients with HIV infection and are planning a 

therapeutic trial of a peptide vaccine directed at reverse transcriptase. The long-term virological and 

immunological effects of protease-containing anti-HIV therapy in children with HIV infection is also 

being studied. Preliminary results suggest that some children have long-term increases in their naïve CD4 

cells in spite of a transient or minimal anti-HIV response. 

In the laboratory, Drs. David A. Davis, Robert Yarchoan, and colleagues have investigated the role of 

conserved cysteines at positions 67 and 95 on the activity of HIV protease. We have found that 

glutathiolation of Cys 95 abolishes HIV protease activity, while glutathiolation of Cys 67 can enhance 

activity. In addition, we have found that a cellular protein called thioltransferase can deglutathiolate 

cysteines of HIV-1 protease and that this protein is taken up in secreted virions. HIV virions with 

mutations of Cys 95 and Cys 67 have been generated, and we are studying the effects that these mutations 

have on the fitness of HIV under various conditions. We are studying the regulatory activity of similar 

cysteines in the protease of other retroviruses. We are also studying mutations at position 95 that can 

occur in patients on long-term protease inhibitor therapy and several novel inhibitors of HIV protease that 

act at the dimer interface. Finally, we are attempting to design novel protease inhibitors that work by 

binding to the dimer interface. 

We recently made the observation that hypoxia can activate lytic replication of Kaposi’s sarcoma 

herpesvirus (KSHV), also known as human herpesvirus 8 (HHV-8) in latently infected cell lines. We are 

exploring the mechanism for this effect and in particular are trying to dissect the molecular mechanisms 

by which KSHV responds to hypoxia. We have preliminary results showing that the virus contains 

several hypoxia response elements (HRE) that can respond to hypoxia inducible factor (HIF). We are 

focusing additional efforts on analyzing the upregulation of ORF34 and related genes by hypoxia. We are 

also studying Epstein-Barr virus for a similar response to hypoxia. 

Robert Yarchoan, M.D. 

Chief, HIV and AIDS Malignancy Branch 

301-496-0328 

ry1n@nih.gov 

http://www-dcs.nci.nih.gov/branches/aidstrials/

http://ccr.cancer.gov/staff/staff.asp?staffid=339

23
HIV AND AIDS MALIGNANCY BRANCH

Center for Cancer Research 

Pediatric HIV/AIDS Clinical Research 

The pediatric HIV clinical research program in the HIV and AIDS Malignancy Branch (HAMB) is a 

multidisciplinary effort that takes a comprehensive approach to investigating HIV treatment and its 

infectious, malignant, neurologic, and psychosocial complications. Antiretroviral and immunologic 

approaches are being investigated in both children and adolescents. Current protocols are aimed at 

several scientific goals: 1) The examination of the long term effects of highly active antiviral therapy 

(HAART), particularly HAART regimens containing a protease inhibitor, and the ability of such 

regimens to produce long term immune reconstitution in pediatric patients, 2) The development of new 

therapies for pediatric HIV patients, particularly therapies for patients who have failed prior antiretroviral 

therapies and are in need of “salvage” regimens. One current protocol uses a new antiretroviral agent, 

tenofovir. Studies of this agent, will not only obtain the pharmacokinetic and toxicity/tolerability data 

needed to use the agent safely and effectively in children, but will also use the drug to obtain information 

about viral evolution, the potential for immune reconstitution in the heavily treated pediatric HIV patient, 

models that may help predict the response to therapy, and how to treat pediatric HIV patients who have 

failed several prior therapeutic regimens and are in need of “salvage therapy”, and 3) Studies aimed at 

optimizing currently available treatment, including studies that combine viral resistance testing with 

pharmacokinetic measures and antiretroviral drug dose adjustments in a “therapeutic drug monitoring” 

strategy that aims to customize antiretroviral drug doses to the resistance pattern of an individual patient’s 

virus and the pharmacokinetic characteristics of that individual patient. 

Longitudinal studies of neurocognitive function, brain imaging, and immune measures in children 

receiving antiretroviral therapy are being conducted in addition to investigation of the pathophysiology of 

HIV encephalopathy. Psychosocial studies include investigation of issues surrounding disclosure of the 

diagnosis, the prevalence of psychiatric disorders in long-term survivors, and rates of adherence to 

treatment and factors which influence adherence among pediatric patients with HIV infection. 

HIV/AIDS-related work accounts for 100% of this project. 

Steven Zeichner, M.D. 

Investigator 

301-402-3637 

zeichner@nih.gov 

http://ccr.cancer.gov/Staff/Staff.asp?StaffID=348

24 
HIV AND AIDS MALIGNANCY BRANCH 

Center for Cancer Research 

HIV and Herpesvirus Molecular Virology and Pathogenesis 

Our group is principally concerned with the molecular biology of HIV and herpesvirus pathogenesis, 

particularly the pathogenesis of pediatric HIV disease. The course of HIV disease in pediatric patients 

differs substantially from the course of disease in adults. We are therefore particularly interested in trying 

to understand the involvement of host cell factors in HIV replication and the effect of HIV infection on 

the host cell. In order to better understand the involvement of the host cell in the processes of viral 

replication we are characterizing the cellular genes differentially expressed during HIV replication using 

microarray technology and are attempting to assign responsibility for the differential expression of the 

cellular genes to particular phases of the viral replication cycle and to individual HIV viral gene products. 

We are also interested in understanding how the host cell may be involved in the maintenance of HIV 

latent infections. In other projects, we are working to understand the viral replication and pathogenesis 

strategies of Kaposi’s sarcoma-associated herpesvirus (KSHV). KSHV is the agent that causes Kaposi’s 

sarcoma, certain primary effusion lymphomas, and some types of multicentric Castleman’s disease. To 

better understand replication cycle of KSHV and the pathogenesis of the cancers caused by the virus we 

have developed microarrays containing the complete genome of KSHV. We have used these materials to 

produce a comprehensive description of the viral transcription program that is seen during KSHV 

replication, and are now doing additional experiments to dissect the viral gene expression program using 

inhibitors that block viral replication at known points in the viral life cycle. We are making several cell 

lines that inducibly express KSHV genes to determine their effects on KSHV replication and the viral 

gene expression program. We expect that these studies will provide new insights into how the expression 

of particular KSHV genes controls the viral lytic replication cycle and helps maintain viral latency, and 

how the expression of certain KSHV genes leads to malignant transformation and influences the 

pathogenesis of the cancers caused by KSHV. Additional studies explore the viral gene expression 

patterns in the KSHV-related cancers and try to link the biological features of the tumors with particular 

patterns of viral gene expression. About 90% of the work is AIDS-related (about 30% of the work is also 

related to cancer). 

Steven L. Zeichner, M.D., Ph.D. 

Investigator 

301-402-3637 

zeichner@nih.gov 

http://ccr.cancer.gov/Staff/Staff.asp?StaffID=348

 25
HIV AND AIDS MALIGNANCY BRANCH

Center for Cancer Research 

RNA Splicing Regulation of Tumorigenic DNA Viruses

Pre-mRNA splicing is one of the most important steps in the control of gene expression. This essential 

step involves intron removal from a primary transcript and exon ligation to form a real message. In many 

cases, the mechanisms that regulate RNA splicing remain poorly understood. Infection with DNA tumor 

viruses such as cervical cancer-associated human papillomaviruses (HPVs) and Kaposi's 

sarcoma-associated herpesvirus (KSHV), also known as human herpesvirus 8, is common in AIDS 

patients. HPVs and KSHV have several critical genes undergoing regulation by RNA splicing at the 

post-transcriptional level. Our research focus is to understand the mechanisms that control viral RNA 

splicing and to look for new tools and molecular targets for antiviral and anticancer therapy at the RNA 

level. Present studies in our laboratory focus on 1) identification of viral cis elements that are involved in 

the regulation of the RNA splicing of viral structural and nonstructural genes including viral oncogenes in 

high- and low-risk HPVs and KSHV, 2) characterization of cellular splicing factors and viral proteins 

involved in processing of RNA splicing, and 3) development of RNA interference as a new tool for 

antiviral and anticancer therapy. 

Regulation of Papillomavirus RNA Splicing

We have been utilizing high-risk HPV 16 and 18 E6 and E7 RNA transcripts as a first step to approach 

our goal. The E6 and E7 genes of HPV 16 and 18 are two major viral oncogenes and are expressed in 

almost every cancer cell of cervical carcinoma. E6 and E7 proteins inactivate cellular tumor suppressor 

proteins p53 and pRb, respectively, and play key roles in the induction of human cervical cancer. 

However, expression of E6 and E7 is complicated by their transcription as a bi-cistronic mRNA and 

alternative splicing of their primary transcripts from which a large portion of E6 has been removed 

through using two alternative 3' splice sites within E6 coding regions. These alternatively spliced RNA 

species are termed E6*I and E6*II and form the majority of early viral transcripts both in cervical tumors 

and in tumor-derived cell lines. Ironically, transcripts for unspliced, full-length E6 are in extremely low 

abundance and sometimes difficult to detect in many tumors or tumor-derived cell lines. We have 

demonstrated that splicing of HPV 16 E6-E7 pre-mRNA is cap dependent and can be restrained by 

distance of the cap-proximal intron from RNA 5' cap. Based on this observation and using a special 

strategy to limit 16E6E7 RNA splicing, we have identified three nuclear localization signals (NLS) for the 

first time in HPV16 E6E7 that drive the protein to accumulate in the nucleus. When inserted into 

corresponding regions of low-risk HPV6 E6, the three NLSs sequences described for 16E6 were active in 

converting the normally cytoplasmic HPV6 E6 into a nuclear protein. We are also focusing on the 

characterization of cellular splicing factors and viral proteins involved in the E6-E7 RNA splicing. 

Another approach in our laboratory is to determine how cellular splicing factors are involved in viral 

RNA splicing. We are using a bovine papillomavirus type 1 (BPV-1, a prototype virus in the 

papillomavirus family) late pre-mRNA as our model to address this question because this pre-mRNA has 

two alternative 3' splice sites (3'ss). Switching from one 3'ss to another in the splicing of this transcript 

relates to keratinocyte differentiation and involves viral cis elements interacting with cellular splicing 

factors. We have established a series of cell lines with stable transfection of BPV-1 late genes. These cell 

lines have a cellular splicing factor ASF/SF2 under the control of a tetracycline (tet)-repressible promoter. 

Using these cell lines, we have demonstrated that the splicing factor ASF/SF2 is required for usage of the 

proximal 3'ss, depletion of ASF/SF2 from the cells leads to use of the distal 3'ss. Activation of the 

ASF/SF2-depleted cells does not restore ASF/SF2 expression, but restores selection of the proximal 3'ss 

through activation of other splicing factor expression and PI3K/Akt pathway. Currently, we are focusing 

on the characterization of transcription and polyadenylation coupling with this feature of the splicing and 

what cellular splicing factor devotes to regulation of the distal 3'ss. 

Regulation of KSHV RNA Transcription and Splicing

KSHV is a newly identified human gamma herpes virus strongly associated with the development of 

Kaposi’s sarcoma, body cavity-based B-cell lymphoma, and Castleman's disease. Currently, our lab is 

26
focusing on the KSHV K8 and K8.1 which are two juxtaposed, but unrelated genes positioned from nt 

74850 to nt 76695 of the virus genome. However, both genes share a single poly (A) site at nt 76714. The 

K8 gene consists of four exons and three introns, which are alternatively spliced during the viral gene 

expression. The K8.1, although sharing the exon 4 with K8, utilizes the intron 3 of K8 as its own coding 

region, which is also alternatively spliced to the exon 4. It has been proposed that a K8.1 pre-mRNA uses 

the K8 intron 3 as its coding region exon 1 and the K8 exon 4 as its exon 2, although neither the K8.1 

promoter nor the 5' ends of their primary transcripts have been definitely identified. Alternative splicing 

of KSHV K8 and K8.1 pre-mRNAs each produces three different isoforms (", $, and() of the mRNAs. 

We have mapped the 5' end of the K8.1 RNA in butyrate-induced KSHV-positive JSC-1 cells to nt 75901 

in KSHV genome, 14 nts upstream of the first AUG of the K8.1 at nt 75915. A K8.1 late promoter has 

been identified immediately upstream of the K8.1 transcription start site, and its activity has been 

associated with viral DNA replication. Our current focus is to understand how viral DNA replication 

controls late promoter activity and its contributions to K8.1 transcription initiation and K8.1 RNA 

processing in the KSHV life cycle and B cell differentiation. In addition, works are in progress on the 

characterization of a KSHV protein that affects both viral and cellular RNA shuttling through cell nuclear 

membranes. 

References: 

1. Shuang Tang and Zhi-Ming Zheng. Kaposi’s sarcoma-associated herpesvirus K8 exon 3 contains 

three 5' splice sites and harbors a K8.1 transcription start site. J. Biol. Chem. 277: 14547-14556, 

2002. 

2. Xuefeng Liu, Akila Mayeda, Mingfang Tao and Zhi-Ming Zheng. Exonic splicing enhancerdependent selection of the bovine papillomavirus type 1 nucleotide 3225 3' splice site can be rescued 

in a cell lacking splicing factor ASF/SF2 through activation of the phosphatidylinositol 3-kinase/Akt 

pathway. J. Virol. 77: 2105-2115, 2003. 

3. Mingfang Tao, Michael Krulak, Shuhua Xia, Elliot Androphy, and Zhi-Ming Zheng, Signals that 

dictate nuclear localization of human papillomavirus type 16 oncoprotein E6 in living cells. J. Virol. 

77: 13232-13247, 2003. 

4. Shuang Tang, Koji Yamanegi, and Zhi-Ming Zheng. Requirement of a 12-base-pair TATT-containing 

sequence and viral lytic DNA replication in activation of the Kaposi’s sarcoma-associated herpesvirus 

K8.1 late promoter. J. Virol. 78: 2609-14, 2004. 

5. Zhi-Ming Zheng, Mingfang Tao, Koji Yamanegi, Sohrab Bodaghi, and Wei Xiao. Splicing of a capproximal human papillomavirus 16 E6E7 intron promotes E7 expression, but can be restrained by 

distance of the intron from its RNA 5’ cap. J. Mol. Boil. In press, 2004 

Zhi-Ming Zheng, M.D., Ph.D. 

Investigator 

301-594-1382 

zhengt@exchange.nih.gov 

http://ccr.cancer.gov/staff/staff.asp?staffid=349

27
HIV DRUG RESISTANCE PROGRAM 

Center for Cancer Research 

The recent application of therapies using combinations of antiviral drugs has shown that virus growth in 

HIV-infected people can be brought to a halt and, in many individuals, provide considerable and longlasting improvement in their condition. These therapies have helped large numbers of people live 

relatively normal lives despite their HIV infection. Most importantly, they prove the concept that antiviral 

drugs can give long-term relief to patients with HIV infection, but fall far short of providing a long-term 

solution. 

The problem facing all the strategies is the development of resistance in the virus due to the appearance of 

specific mutations. In an effort to avoid resistance, drugs have to be given at high—somewhat toxic—

doses, in expensive combinations, and on exacting and difficult-to-follow schedules. Even then, the 

therapy often fails, and resistant virus appears. There is, therefore, a desperate need to understand how the 

virus develops resistance to drugs, and to use this understanding to develop more effective strategies for 

treating HIV infection. 

The goal of the HIV Drug Resistance Program (DRP) is to establish a focused basic science research 

effort that addresses this need and builds on the existing strength of HIV and retrovirus research within 

the NCI. Specific goals include the following: (1) to extend our understanding of the structure and 

biochemistry of known and potential drug targets in HIV replication, as well as their mechanism of 

resistance to antiviral drugs; (2) to use this information to develop new strategies of inhibition of virus 

replication; (3) to improve our knowledge of the interaction of HIV with its human host, both in the single 

cell and the whole organism; (4) to understand the mechanisms by which virus variants arise during single 

infections and propagate in the infected patient; (5) to develop and test novel therapeutic strategies based 

on the improved knowledge obtained; and (6) to promote the exchange of information relevant to the 

problem of drug-resistant virus among researchers in all relevant disciplines. 

The DRP includes eight principal investigators in two laboratories, as well as a patient-based research unit 

in the Clinical Center and a Virology Core Facility. 

The Retroviral Replication Laboratory (RRL) focuses on obtaining a detailed understanding of important 

events in the virus life cycle, from initial interactions between virus and host cell, through reverse 

transcription, and to mechanisms of virus assembly and release. Whole-organism studies, including the 

development of important animal models and the use of retroviral vectors, are included in the work of the 

RRL. The RRL includes the Vector Design and Replication Section, under the direction of Dr. Stephen H. 

Hughes, the Retrovirus Assembly Section, directed by Dr. Alan Rein, the Model Development Section, 

led by Dr. Vineet N. KewalRamani, and two sections that joined the Laboratory in 2003, the Virus-Cell 

Interaction Section, under the direction of Dr. Eric O. Freed, and the Retrovirus Gene Expression Section, 

directed by Dr. David Derse. 

Dr. Hughes and the members of his section are studying several aspects of retroviruses. Their efforts are 

intended to provide a better understanding of retroviral replication. There are two major projects. In the 

first project, the goal is to design improved retroviral vectors, which are modified viruses that can be used 

to deliver foreign genes. The second project is intended to better understand the structure and function of 

the reverse transcriptase (RT) of HIV-1. RT is a major target for anti-HIV drugs; mutations in RT can 

lead to drug resistance. A better understanding of HIV-1 RT and of the mechanisms that underlie drug 

resistance could lead to the development of better anti-HIV drugs and drug therapies. 

Research in the Retrovirus Assembly Section is directed toward a fundamental understanding of the 

retroviral life cycle, with a special emphasis on the molecular mechanisms involved in retrovirus particle 

assembly and maturation. The current research of Dr. Rein’s lab involves protein-protein interactions, 

protein-nucleic acid interactions, and nucleic acid-nucleic acid interactions. Their experiments combine 

the power of molecular analysis of defined systems in vitro with the careful study of retroviral replication 

in living cells. It is hoped that the insights gained from their basic research will result in the development 

of new antiviral strategies. 

The research focus of Dr. KewalRamani’s lab begins with obtaining an understanding of the specific 

interactions between HIV viral components and human proteins. This process will define which host 

factors are required for a productive infection. An immediate objective of these studies is to provide new 

 28
targets for the development of novel drug therapies. Using what is learned from these molecular studies, 

they are attempting to develop small animal models to study the interaction of HIV with the host’s 

immune system. 

Dr. Freed’s research program focuses on a variety of key aspects of HIV-1 assembly and release. Of 

particular interest are the interplay between viral and host factors in the targeting of assembly to the 

plasma membrane, the role of lipid rafts in membrane association and virus assembly, and the mechanism 

by which the viral envelope glycoproteins are incorporated into virions. Recent studies have been aimed 

at defining the cellular pathways and host factors involved in the budding of retrovirus particles from the 

plasma membrane and identifying inhibitors of virus budding. 

The research efforts of Dr. Derse’s lab are directed toward understanding the molecular genetics of HIV-1 

and human T cell leukemia virus (HTLV-1). The latter is associated with adult T cell leukemia and 

degenerative neurologic diseases. Although HTLV-1 is only distantly related to HIV-1, both viruses 

evade the immune system and are slow to cause disease. The premise that virus-encoded regulatory 

factors and elements largely determine pathological consequences of infection, such as tissue tropism, 

disease spectrum, latency, and cytopathology, has motivated Dr. Derse and the members of his lab to 

identify and characterize the complex regulatory circuits that modulate virus gene expression and alter 

host cell metabolism. Analyses of HIV-1 and HTLV-1 genetics combined with comparative analyses of 

distant relatives of the human viruses have provided novel insights into the regulatory strategies and 

pathogenic mechanisms of these agents. 

Collectively, the interests of the five sections of the RRL are relatively broad. We believe that having a 

broad range of research interests is beneficial; if intellectual or experimental issues arise in one of the 

sections that are outside the expertise of that section, other members of the Laboratory usually can help 

provide the necessary expertise. We also believe that sharing ideas within the Laboratory makes the 

intellectual environment of the laboratory better for everyone and, in particular, that this approach 

provides better training for the postdoctoral fellows. All of them should have the opportunity to 

understand retroviruses in a broad sense, and be exposed to a wide range of experimental approaches so 

that they will be able to take the most effective experimental approach when confronted with a problem. 

The Resistance Mechanisms Laboratory (RML) focuses principally on the biochemistry and biology of 

RT, its interaction with templates and substrates, and its role during replication in mutation and 

recombination. The RML consists of three sections: RT Biochemistry Section, under the direction of Dr. 

Stuart Le Grice, Viral Recombination Section, under Dr. Wei-Shau Hu and Viral Mutation Section, under 

Dr. Vinay Pathak. 

Despite a constantly expanding spectrum of highly potent and selective antiviral agents, the rapid 

acquisition of drug resistance continually confounds therapeutic strategies designed to combat HIV 

infection. Two properties of the virus-coded RT can be considered central to this problem—namely, an 

elevated rate at which inappropriate nucleotides are incorporated into the growing DNA chain, and the 

lack of an efficient proofreading mechanism. The capacity of the replication machinery to exploit 

information from both RNA genomes packaged into the virus, i.e., recombination, has the further 

consequence of increasing genetic diversity by an assortment of mutations. Therefore, multiple drug 

resistance can result from recombination between strains originally resistant to a single drug. The RML 

combines the disciplines of biochemistry with molecular, cellular, and structural biology to better 

understand these events at the molecular level, with the ultimate goal of applying the knowledge gained to 

future antiviral strategies. 

Both the DNA polymerase and RNase H functions of RT from HIV-1 and related lentiviruses are under 

investigation as therapeutic targets in the RT Biochemistry Section. Despite an absolute requirement for 

virus-coded RNase H for replication, there have been few reports on agents targeted to this function. The 

development of model systems accurately mimicking specialized RNase H-mediated events (e.g., 

polypurine tract selection and excision from nascent DNA and tRNA primer release prior to secondstrand transfer) and mutants specifically impaired in these steps provide important mechanistic 

information on this C-terminal RT domain. This knowledge is currently being applied to develop highthroughput “smart” screening strategies. Novel mutations in the primer grip of the DNA polymerase 

domain that lead to increased fidelity have been identified and are under investigation. 

 29
The projects of the RT Biochemistry Section are complemented by those of the Viral Recombination 

Section, which investigates the molecular mechanisms of recombination, RNA packaging and virus 

assembly, and interactions between distinct retroviruses. Evidence shows that recombinant viruses can be 

generated through packaging of heterologous viral RNA genomes, i.e., of avian and murine origin, into a 

single virion. The implications and limitations of these events are under investigation. Packaging of the 

viral genome is dependent on interactions between the Gag polyprotein with a packaging signal in the 

viral RNA. Experiments are underway to define the cis- and trans-acting elements involved in the 

specificity of viral RNA packaging. 

The theme of recombination is extended to the Viral Mutation Section, which makes use of in vivo

systems with recombinant retroviruses to understand the mechanisms that generate variation in retroviral 

populations. In vitro assays have identified structural determinants important for fidelity and RT template 

switching, which include the active-site YXDD motif, the dNTP-binding site and thumb subdomain of the 

DNA polymerase catalytic center, and, surprisingly, the C-terminal RNase H domain. The latter 

observations indicate important “communication” between the DNA polymerase and RNase H catalytic 

centers of RT. The in vivo approach of the Viral Mutation Section provides an excellent complement to 

the structure/function studies conducted in vitro by the RT Biochemistry Section. 

The clinical arm of the DRP is the Host-Virus Interaction Unit (HVIU). The HVIU has the goal of using 

patient-based studies to elucidate mechanisms underlying the evolution of resistance in vivo, the dynamics 

of infection under treatment, the role of resistance mutations in subsequent treatment efficacy and failure, 

and the development of novel strategies to counter evolution of resistance in patients. Currently, the 

HVIU consists of the In Vivo Biology research group, under the direction of Dr. Frank Maldarelli, and the 

Virology Core, under the direction of Dr. Sarah Palmer. Dr. John Coffin serves as acting leader of the 

HVIU. 

The primary research focus of the In Vivo Biology group is to study the population genetics, evolution, 

and dynamics of HIV infection in patients, particularly the development of and possible ways to 

overcome resistance. In collaboration with the NIAID/CCMD AIDS clinic and the NCI HIV AIDS 

Malignancy Branch, Dr. Maldarelli develops and secures IRB approval for clinical trials, and implements 

them using the support of these groups. At present, there are three active protocols, corresponding to the 

three ongoing projects: HIV Expression in Patients with Viral Loads Suppressed on HAART (Protocol 

02-I-0232), Genetic Analysis of HIV Prior to Initiation of Highly Active Antiretroviral Therapy (Protocol 

00-I-0110), and An Assessment of the Relationship Between Antiretroviral Drug Genotype/Phenotype 

(IC50) and Antiretroviral Activity in HIV-Infected, Drug-Experienced Patients with Suboptimal 

Suppression of Plasma Viral Load (Protocol 01-I-0004). 

The Virology Core conducts analyses of HIV samples from clinical and basic studies on HIV, which will 

provide new and important information on viral dynamics, genetics, and evolution both in vitro and in 

vivo. Dr. Palmer and the Virology Core staff have been working closely with Dr. Maldarelli, in 

consultation with Dr. John Mellors of the University of Pittsburgh, to develop methods for obtaining very 

large numbers of sequences from virus circulating in plasma and for measuring virus load with much 

greater sensitivity than can be reliably attained with currently available tests. As part of this work, the 

Virology Core is conducting in vitro drug resistance selection assays, genotypic and phenotypic analyses, 

and a range of other techniques such as polymerase chain reaction (PCR), site-directed mutagenesis, viral 

load monitoring, and viral enzyme analysis. 

The DRP has established numerous collaborations with other NIH and extramural researchers to develop 

new screens for novel targets (such as RNase H and integrase) and to analyze compounds for resistance 

profiles. An important part of these projects will be to develop an understanding of how these new targets 

behave under selection pressure, to estimate fitness decreases due to resistance mutations, and to predict 

what the effect of drug therapy might be when specific antiviral compounds are administered to patients. 

John Coffin, Ph.D. 

Director, HIV Drug Resistance Program 

301-846-5943 

jcoffin@ncifcrf.gov 

http://www.retrovirus.info

30
HIV DRUG RESISTANCE PROGRAM 

Center for Cancer Research 

Regulation of Retrovirus RNA Splicing and Transport 

Infectious transmission of retroviruses can be divided into two phases: 1) the assembly and release of 

virions from the infected cell and 2) virion entry and replication in the target cell. For human T-cell 

leukemia virus type 1 (HTLV-1), the molecular mechanisms underlying the individual steps in these 

processes are not well defined. Recent experimental evidence supports a model in which HTLV-1 can be 

transmitted directly between T lymphocytes that have formed a stable cell-cell synapse. The model 

suggests that infection may be coordinately regulated with formation of the cell-cell junction. However, 

the integration of cellular and viral pathways has not been defined. Our goal is to elucidate the 

components and pathways of HTLV-1 transmission and replication in the conceptual framework of this 

model. We are examining the mechanisms of HTLV-1 infection and replication with cell-free and cellassociated virus particles produced from viral vectors. We are characterizing HTLV-1 replication 

enzymes and analyzing reverse transcription in infected cells. We are also determining the mechanisms 

that HTLV-1 has evolved to evade cellular defense mechanisms that restrict the replication of other 

retroviruses. We are also studying the mechanisms and pathways of virion assembly and release. An 

important part of these studies are experiments aimed at defining the interactions between virus proteins 

and cellular membrane proteins that direct the virion to the site of cell-cell contact, where HTLV-1 is 

transmitted to the target cell. Although the basic mechanisms for transmission and replication are 

conserved among retroviruses, variations on common themes are likely to reveal important insights into 

the strategies that different viruses use for propagation and persistence in vivo. In this respect, it is useful 

to compare HTLV-1 and HIV-1; both are T-cell-tropic retroviruses whose distinct biological properties 

may be traced back to divergent strategies for escaping host-mediated immune and cellular defense 

mechanisms. 

David D. Derse, Ph.D. 

Chief, Retrovirus Gene Expression Section 

Retroviral Replication Laboratory 

HIV Drug Resistance Program 

301-846-5611 

derse@ncifcrf.gov 

http://www.nci.nih.gov/intra/llb/derse.htm

31
HUMAN GENETICS SECTION 

Center for Cancer Research 

Although not well-appreciated, pathogens are associated with a number of human malignancies. These 

include cancers with limited geographic distribution as well as common cancers with global impact: 

gastric cancer (helicobacter pylori); bladder cancer (Schistosoma haemtobium); adult T cell 

leukemia/lymphoma (Human T-cell leukemia virus (HTLV)-1); hairy cell leukemia (HTLV-2); 

hepatocellular carcinoma (Hepatitis B virus (HBV)); Kaposi’s sarcoma [Human herpes virus-8, human 

immunodeficiency virus (HIV)-1]; nasal pharyngeal carcinoma and Burkitt’s lymphoma [Epstein Barr 

virus (EBV)]; anogenital and cervical carcinoma (Human papilloma virus, HIV-1); and lymphomas (HIV1). Pathogen infections are notable for the diversity of host responses to infection, rate of progression and 

disease outcome. Our laboratory has focused on differential responses to viral pathogens due, in part, to 

naturally occurring genetic variation among people. We are using a combination of epidemiology, 

molecular genetics, and population genetics to identify and characterize host genes that may be operative 

in resistance or increased susceptibility to infection by HIV-1, the hepatitis B and C viruses (HBV and 

HCV) and EBV. We are also investigating the role of host genetic variation in the development of EBV 

persistant infection leading to nasal pharyngeal carcinoma in a cross-sectional case-control study of Han 

Chinese with chronic EBV infection and nasal pharyngeal carcinoma. 

Although twin and family studies and epidemiological evidence in humans support the hypothesis that 

there is a strong genetic component to infectious disease susceptibilities, it is very difficult to identify and 

map these genes by conventional family studies. Our group is utilizing the extensive human genome map 

in combination with the methods of population genetic theory to identify, map, and characterize five 

classes of genetic loci: (1) those that restrict infection by a viral pathogen following exposure; (2) those 

that modulate or control the immune response; (3) those that influence outcome to infection; (4) those that 

influence the temporal course of infection (fast versus slow progression); and (5) those that contribute to 

resistance to drug therapies. 

Considerable progress has been made on this project. The laboratory has developed cell lines for 

renewable DNA for over 10,000 persons enrolled in prospective cohorts for HIV-1, HBV, HVC and in a 

nasopharyngeal carcinoma (NPC) case-control study. We have identified and characterized SNP 

organization and haplotype structure for: 1) The APOBEC3G (CEM15) gene, an RNA editing enzyme 

that introduces G->C hypermutation in retroviruses including HIV-1∆vif (deleted for the vif accessory 

gene); we identified a codon changing variant that may be associated with accelerated progression to 

AIDS and 2) the MCP-1 MCP-3 – Eotaxin chemokine gene cluster. We have identified a single haplotype 

associated with resistance to infection by HIV-1. We have also confirmed that genetic variants in MIP1A 

are strongly associated with more rapid progression to AIDS. These studies provide proof of principle 

that chemokines and cytokines may be potential targets for drug development. To date more than 12 host 

genetic factors that are involved with viral cell entry, innate resistance or acquired immune response have 

been shown to effect HIV-1 infection or progression to AIDS. 

In an effort to identify genes associated with NPC, one of the most common cancers in South China and 

Southeast Asia, we have organized case-control study of 366 NPC cases, 218 IgA antibodies positive to 

EBV capsid antigen (EBV/IgA/VCA) cases (IgA+), and 419 spouses with EBV/IgA/VCA negative (IgA-

). EBV-associated NPC is caused by the interaction between genetic susceptibility and environmental 

factors. A recently reported genome-wide linkage analysis of familial NPC implicated a susceptibility 

locus on short arm of chromosome 4. We have completed genotyping 34 microsatellite markers in the 

region to confirm the family study and to identify NPC candidate genes for further analysis. 

Cheryl Ann Winkler, Ph.D. 

Principal Investigator 

301-846-5747 

winkler@ncifcrf.gov 

http://ccr.cancer.gov/staff/staff.asp?staffid=643

 

32
LABORATORY OF EXPERIMENTAL AND COMPUTATIONAL BIOLOGY 

Center for Cancer Research

Anti-HIV Activity of the Chemopreventive Drug, N-(4-hydroxyphenyl) Retinamide (4-HPR) 

Studies of ceramide metabolism and function in a wide range of biological processes have revealed a role 

for this lipid in regulating key biologic responses. N-(4-hydroxyphenyl) retinamide (4-HPR, fenretinide) 

has been reported to cause large increases of ceramide levels in tumor cell lines and induce cell death with 

minimal toxicity to normal lymphocytes, fibroblasts and myeloid progenitors. The compound is under 

investigation in clinical trials as a cancer preventive and therapeutic agent. Our research on the role of 

sphingolipids in HIV entry has led to the hypothesis that modulation of ceramide levels in target cells 

affects their susceptibility to HIV infection by rearranging HIV receptors. Ceramide levels were 

determined following incorporation of [3

H] sphingosine for 48 hours in the presence of the appropriate 

agent. Infectivity assays were performed using a HeLa-derived indicator cell line TZM-bl, CD4+ 

lymphocytes and monocytes. We observed a dose-dependent inhibition by 4-HPR of infection of TZM-bl 

cells by a broad range of HIV-1 isolates at low μM concentrations with an IC50 less than 1μM for most 

isolates tested. Near complete inhibition was seen at 1 μM, a dose that enhanced ceramide levels by 50-

100%, yet was non-toxic to the cells. Treating cells with other pharmacological agents that cause 

enhanced ceramide levels, or with sphingomyelinase, or exogenous addition of long chain ceramide also 

resulted in inhibition of HIV-1 infection. Enhancing ceramide levels in CD4+ lymphocytes had no effect 

on susceptibility to HIV-1 infection. By contrast treatment of human monocytes with 4-HPR or 

sphingomyelinase reduced infectivity to less than 10% of control without toxicity. Our data suggest that 

the drug may be exceedingly suitable as a combined chemopreventive and anti HIV therapeutic agent. 

Robert Blumenthal, Ph.D. 

Chief, Section on Membrane Structure and Function 

301-846-1446 

blumen@helix.nih.gov 

http://ccr.cancer.gov/staff/staff.asp?staffid=603

 33
LABORATORY OF EXPERIMENTAL AND COMPUTATIONAL BIOLOGY 

Center for Cancer Research 

Potent Cross-Reactive HIV-1 Neutralizing Human Monoclonal Antibodies 

Major achievements include the identification and characterization of several potent broadly HIVneutralizing human monoclonal antibodies that may have potential as therapeutics and help in the design 

of vaccines. Among those the scFv m9 exhibits the most potent and broad neutralizing activity especially 

for clade B and C isolates – it neutralized with high potency (on average IC50 of 1 ug/ml) almost all 

(90%) of tested 20 clade C isolates and 15 clade B isolates. Some of the results are described in the 

publications listed below 

References: 

1. Dimitrov DS. Virus entry: molecular mechanisms and biomedical applications. Nature Reviews, 

Microbiology 2: 109-122, 2004. 

2. Zhang M-Y, Shu Y, Rudolph D, Prabakaran P, Labrijn AF, Zwick MB, Lal RB, Dimitrov, DS 

Improved breadth and potency of an HIV-1-neutralizing human single-chain antibody by random 

mutagenesis and sequential antigen panning. J. Mol. Biol. 335: 209-219, 2004. 

3. Zhang M-Y, Shu Y, Phogat S, Xiao X, Cham F, Bouma P, Choudhary A, Feng Y-R, Sanz I, Rybak S, 

Broder CC, Quinnan GV Jr., Evans T., Dimitrov DS Broadly cross-reactive HIV neutralizing human 

monoclonal antibody Fab selected by sequential antigen panning of a phage display library J. 

Immunol. Meth. 283: 17-25, 2003. 

4. Xiao X, Phogat S, Shu Y, Phogat A, Chow YH, Wei OL, Goldstein H, Broder CC, Dimitrov DS. 

Purified complexes of HIV-1 envelope glycoproteins with CD4 and CCR5 (CXCR4): production, 

characterization and immunogenicity. Vaccine 21(27-28): 4275-4284, 2003. 

5. Labrijn AF, Poignard P, Raja A, Zwick MB, Delgado K, Franti M, Binley J, Vivona V, Grundner C, 

Huang CC, Venturi M, Petropoulos CJ, Wrin T, Dimitrov DS, Robinson J, Kwong PD, Wyatt RT, 

Sodroski J, Burton DR. Access of antibody molecules to the conserved coreceptor binding site on 

glycoprotein gp120 is sterically restricted on primary human immunodeficiency virus type 1. J. Virol. 

77(19): 10557-10565, 2003. 

6. Bouma P, Leavitt M, Zhang PF, Sidorov IA, Dimitrov DS, Quinnan GV Jr. Multiple Interactions 

across the Surface of the gp120 Core Structure Determine the Global Neutralization Resistance 

Phenotype of Human Immunodeficiency Virus Type 1. J. Virol. 77(14): 8061-8071, 2003. 

7. Leavitt M, Park EJ, Sidorov IA, Dimitrov DS, Quinnan GV Jr. Concordant modulation of 

neutralization resistance and high infectivity of the primary HIV-1 MN strain and definition of a 

potential gp41 binding site in gp120. J. Virol. 77(1): 560-570, 2003. 

Dimiter S. Dimitrov, Ph.D., Sc.D. 

Senior Investigator 

301-846-1352 

dimitrov@ncifcrf.gov 

http://ccr.cancer.gov/Staff/Staff.asp?profileid=5749

34
LABORATORY OF GENOMIC DIVERSITY

Center for Cancer Research (Contract) 

We and others have identified a human homologue of CD209, which we termed L-SIGN (CD209L1), 

corresponding to a partial sequence described previously. Like CD209, CD209L1 captures HIV-1 through 

gp120 binding and enhances HIV-1 infection of T cells in vitro, but it is specifically expressed on liver 

sinusoidal cells and on vascular-associated cells in the lymph node rather than on DCs. Thus, we 

proposed that CD209L1 might facilitate interactions between liver sinusoidal endothelium and trafficking 

lymphocytes, as well as function in the pathogenesis of HIV-1 in a DC-independent manner. The 

identification of two CD209 family homologues in humans raised the possibility that additional members 

of this gene family might exist in rhesus monkeys and other nonhuman primates. We found that all Old 

World monkeys (OWM) and apes tested have orthologues of human CD209, and although CD209L1 is 

present in apes, it is missing in OWM. Further, we discovered a third family member in rhesus monkey, 

CD209L2, which is also present in OWM and all apes except for humans. Thus, the CD209 gene family 

has undergone recent evolutionary processes involving duplications and deletions, which may result in 

differential expression and function across primate species.

Reference: 

Bashirova AA, Wu L, Cheng J, Martin TD, Martin MP, Benveniste RE, Lifson JD, KewalRamani VN, 

Hughes A, and Carrington M: Novel member of the CD209 (DC-SIGN) gene family in primates. J Virol.

77:217-227, 2003. 

Mary Carrington, Ph.D. 

NCI-Frederick 

301-846-1390 

carringt@ncifcrf.gov 

http://ccr.cancer.gov/staff/staff.asp?staffid=639

35 
LABORATORY OF MEDICINAL CHEMISTRY 

Center for Cancer Research 

Inhibitors of HIV Integrase as Potential AIDS Therapeutics 

The reliance of current AIDS treatments on combination regimes directed at just two enzymes, HIV 

reverse transcriptase and HIV protease, has lead to a loss of therapeutic effectiveness through 

development of resistance. HIV integrase (IN) is a third enzyme required for HIV reproduction that 

represents an attractive target for new AIDS-directed antivirals. Accordingly, one focus of our research is 

the design and synthesis of IN inhibitors as potential anti-AIDS drugs. Currently, our efforts are directed 

toward two aspects of inhibitor development. In one project novel "azide" functionality, which we 

recently showed enhances cellular efficacy of "diketo-aryl" (DKA)-based IN inhibitors, is being 

examined for its potential utility in other IN-directed platforms. In a second project, the use of IN-directed 

"affinity acylators" is being undertaken to study the molecular basis IN•inhibitor interactions. This work 

seeks to develop small molecules that specifically bind and trans-acylate amino acid side chains at sites of 

inhibitor binding to the IN protein. Such covalent modification could effectively tag and identify the sites 

of inhibitor binding as well as potentially inactivate or modify enzyme activity. 

Terrence R. Burke, Jr., Ph.D. 

Laboratory of Medicinal Chemistry 

301-846-5906 

tburke@helix.nih.gov 

http://ccr.cancer.gov/staff/staff.asp?staffid=736

36 
MACROMOLECULAR CRYSTALLOGRAPHY LABORATORY 

Center for Cancer Research 

Protein Structure Section

We are using high-resolution X-ray diffraction to study the relationship between protein structure and 

function. Over the past years, our work has focused on four distinct areas: 

I. Enzymes with Anticancer Properties 

We have been investigating crystal structures of several members of the family of L-asparaginases, some 

of which are used clinically as drugs directed against childhood lymphoblastic leukemia. While the 

mechanism of anticancer activity of these enzymes is not yet clear, we have concentrated on the studies of 

their enzymatic properties. We investigated a number of mutants of Escherichia coli L-asparaginase and 

many complexes of the Erwinia chrysanthemi enzyme with substrates and products, leading to the 

elucidation of the enzymatic mechanism. The structure of the latter enzyme, solved at 1 Å resolution, 

represents the largest protein investigated at the atomic level. Another enzyme with potential therapeutic 

properties is Onconase, a cytotoxic ribonuclease isolated from frog eggs. We have been involved in 

reengineering this enzyme in order to make it applicable to human cancer therapy and to restore its 

activity in the absence of posttranslational modifications. The structure of the eosinophil-derived 

neurotoxin, another related antitumor ribonuclease, has also been evaluated by us at atomic resolution. 

II. Cytokines and Cytokine Receptors 

Our section has been investigating the crystal structures of several cytokines and has made progress in 

preparing their receptor complexes. We have established that a helical cytokine, interleukin-10 (IL-10), is 

a domain-swapped dimer in which each compact half is composed of fragments of two identical 

molecules. The structure of a related cytokine encoded in the genome of Epstein-Barr virus has now been 

determined, providing the first glimpse of the molecular architecture of an agent used by the virus to 

control the host's immune system. We have solved the crystal structure of IL-19 and are studying the 

complexes with its receptors. 

III. Retroviral Enzymes 

Enzymes encoded by retroviruses such as HIV are prime targets for designing effective drug therapies. 

We have been studying the structure of native and drug-resistant HIV-1 protease (PR) complexed with 

inhibitors, with the aim of tracing the molecular basis of the resistance phenomenon. We have also 

determined the structures of related enzymes from feline immunodeficiency virus (FIV) and equine 

infectious anemia virus (EIAV). The latter PRs are poorly inhibited by most inhibitors of HIV-1 PR, 

including those in clinical use, although they are capable of cleaving HIV-1-derived sequences. To study 

the mechanism of drug resistance, we solved the structures of HIV-1, FIV, and EIAV PRs complexed 

with an identical inhibitor, while the studies of an inactive mutant of FIV PR with a substrate helped in 

delineating the catalytic mechanism. Another retroviral enzyme under investigation in our laboratory is 

integrase. We have solved the structure of the catalytic domain of avian sarcoma virus integrase in the 

presence and absence of divalent cations to atomic resolution and are attempting cocrystallization of 

complexes with different substrates and with monoclonal antibodies. 

IV. Proteases and RNA-Processing Enzymes 

Our Section has been investigating the structures of a number of different proteases. In particular, we 

have discovered that the Pseudomonas serine-carboxyl protease (sedolisin) is a novel serine protease with 

a unique catalytic triad. The structures of a number of complexes of this enzyme, many of them solved at 

atomic resolution, have been helpful in the analysis of the mechanism of action of this family. Another 

related enzyme, kumamolisin-As, is a thermostable collagenase. We solved crystal structures of its free 

and inhibited forms, as well as of an active-site mutant. We have also solved crystal structures of the 

catalytic and substrate-recognition domains of an E. coli protease Lon, finding that this is a unique 

enzyme among serine proteases. Among the RNA-processing enzymes, we have solved the structure of 

RNA cyclase and of native and semi-reduced cyclic nucleotide phosphodiesterase from Arabidopsis 

thaliana. 

Alexander Wlodawer, Ph.D. 301-846-5036 

Chief, Macromolecular Crystallography Laboratory wlodawer@ncifcrf.gov 

Chief, Protein Structure Section http://mcl1.ncifcrf.gov/wlodawer.html

37
DIVISION OF CANCER EPIDEMIOLOGY AND GENETICS

The Viral Epidemiology Branch (VEB) has used a variety of approaches to define the nature and 

magnitude of malignancies associated with HIV-1 and other chronic infections, including analyses of 

population-based data, prospective cohort studies, and laboratory investigations. We are currently 

conducting a limited follow-up of 2,480 subjects with CDC-defined AIDS (i.e., <200 CD4+ T-cells/ul) 

recruited in 1998-99. Analyses of this cohort have identified alcohol drinking as a risk factor for antibody 

reactivity to human herpesvirus 8 (HHV-8), the Kaposi's sarcoma (KS)-associated herpesvirus. Among 

HHV-8 seropositives, alcohol was additionally associated with increased risk of KS. Similarly, cigarette 

smoking was protective both against HHV-8 antibody as well as against KS risk among HHV-8 

seropositives. Alcohol and cigarettes each appear to have consistent effects at multiple stages of KS 

etiology, and further studies are planned to identify the underlying mechanisms. Nested case-control 

studies of incident cancers are planned, utilizing the detailed clinical and interview data and banked blood 

specimens (plasma and cryopreserved lymphocytes) collected at enrollment. We are currently planning an 

intensive laboratory investigation of non-Hodgkin's lymphoma (NHL)-associated mutations in these 

lymphocyte samples and their potential relationship to risk of NHL. Findings will be compared for HIVrelated and unrelated NHL. Our two previous cohort studies of HIV-infected hemophilia patients have 

been incorporated into a larger cohort that includes HIV-uninfecteds, whose prospective followup for 

cancer has recently been initiated. These cohorts will be applied to studies of potential risk factors for 

AIDS-related malignancy, including genetic polymorphisms and/or altered baseline levels of cytokines 

and other immune factors, chromosomal translocations, EBV and HHV-8 viral loads, antibody titers, and 

cell mediated immunity, and environmental exposures and medications. We are continuing our studies of 

EBV infection and immune response as a causative factor in AIDS-related lymphoma, with 

determinations of viral load, cell-mediated immunity, antibody reactivity, and other immune system 

parameters. These studies also include examination of host genetic variation in B-cell-stimulatory 

cytokines. In collaboration with the Occupational Epidemiology Branch, we are continuing our 

investigations of cytokine polymorphisms as risk factors for gastric cancer. In a collaboration with the 

Veterans' Administration, we are investigating a cohort of liver disease patients originally recruited in the 

1970s, for which we are assessing effects of baseline hepatitis C viremia and subsequent infection with 

HIV. 

Z01CP05781-03 VEB Principal Investigator: Charles S. Rabkin, M.D., M.Sc. 

October 1, 2002 to September 30, 2003 Other VEB/NCI Personnel: RJ Biggar, JJ Goedert, EA Engles 

Title of Project: HIV and AIDS Cancers Cooperating Units: Laboratory of Genetics, CCR, NCI 

References: 

1. Engels EA, Biggar RJ, Marshall VA, Walters MA, Gamache CJ, Whitby D, Goedert JJ. Detection 

and quantification of Kaposi's sarcoma-associated herpesvirus to predict AIDS-associated Kaposi's 

sarcoma. AIDS. 2003;17:1847-51. 

2. Mbulaiteye SM, Parkin DM, Rabkin CS. Epidemiology of AIDS-related malignancies an 

international perspective. Hematol Oncol Clin North Am. 2003;17:673-96. 

3. Engels EA, Pittaluga S, Whitby D, Rabkin C, Aoki Y, Jaffe ES, Goedert JJ. Immunoblastic 

lymphoma in persons with AIDS-associated Kaposi's sarcoma: a role for Kaposi's sarcoma-associated 

herpesvirus. Mod Pathol. 2003;16:424-9. 

4. Mbulaiteye SM, Biggar RJ, Goedert JJ, Engels EA. Immune deficiency and risk for malignancy 

among persons with AIDS. J Acquir Immune Defic Syndr. 2003;32:527-33. 

5. Goedert JJ, Vitale F, Lauria C, Serraino D, Tamburini M, Montella M, Messina A, Brown EE, Rezza 

G, Gafa L, Romano N; Classical Kaposi's Sarcoma Working Group. Risk factors for classical 

Kaposi's sarcoma. J Natl Cancer Inst. 2002;94:1712-8. 

6. Eltom MA, Jemal A, Mbulaiteye SM, Devesa SS, Biggar RJ. Trends in Kaposi's sarcoma and nonHodgkin's lymphoma incidence in the United States from 1973 through 1998. J Natl Cancer Inst. 

2002;94:1204-10. 

Charles Rabkin, M.D., M.Sc. 301-435-4731 

HIV-Cancer Coordinator rabkinc@mail.nih.gov 

Viral Epidemiology Branch http://dceg.cancer.gov/people/RabkinCharles.html

 38
NATIONAL INSTITUTE OF DENTAL AND CRANOFACIAL RESEARCH 

Broad Research Questions Currently Under Study 

Oral cancer remains a major cause of cancer mortality, with a five-year survival rate of less than 50% in 

patients diagnosed with oral cancer. Oral tumors, both benign and malignant, are early complications of 

the immunodeficiency caused by HIV infection/AIDS. A NIDCR goal is to support outstanding research 

that will lead to the early detection, prevention, and treatment of oral cancers in HIV infected/AIDS 

patients. To this end, NIDCR is currently supporting extramural as well as intramural research on this 

topic. 

Current studies are developing non-human primate models for Kaposi’s sarcoma (KS) in oral cavity, and 

are using both animal, human, and in vitro models to study the oral biology of herpesviruses (e.g., HHV8) associated with KS, oral immune responses to HHV-8, viral lysis of KS, as well as the natural history 

and transmission of HHV-8 in the oral cavity. 

Epstein Barr Virus (EBV) and human papillomaviruses (HPV) persistently infect the oral cavity and are 

shed into surrounding tissues/saliva as a result of the immunosuppression in AIDS patients. Several 

projects are examining these viruses with regard to the host immune responses, reactivation and oral 

cancer. Other studies are focusing on viral genetic stability and host genetic susceptibility to these viral 

infections. 

Oral hairy leukoplakia (OHL) is a benign epithelial hyperplasia of the lingual squamous epithelium in 

AIDS patients. The lesions are associated with reactivation of latent EBV infection. Studies are now 

underway to better understand the pathogenesis, detection, and treatment of OHL in these patients. 

Finally, the prevalence of oral tumors is changing in the context of new therapies for AIDS. Studies are 

underway to evaluate the biological changes associated with therapy in order to further improve 

treatments and reduce treatment failures. Similarly, research is being supported to reduce oral cancer by 

strengthening the specific host immune responses. 

Important Study Findings/Highlights 

In patients with AIDS, women have a lower prevalence of OHL and oral KS than men. 

The incidence of AIDS-related non-Hodgkin’s lymphomas was not affected by the introduction of highly 

active antiretroviral therapy (HAART). Among those, plasmablastic lymphoma is a relatively new entity 

that is considered to be a diffuse, large B-cell lymphoma with a unique immunophenotype and a 

predilection for the oral cavity. The lymphoma cells stain strongly with plasma-cell-reacting antibodies 

VS38c/B-B4 and lack the CD20 and CD45 surface markers. The lymphoma appears to be associated with 

EBV and not HHV-8 infection, as most tumor cells express EBV-encoded RNA. Recognition of 

plasmablastic lymphoma is important because it represents an HIV-associated malignancy that 

predominantly involves the oral cavity, may mimic KS, and has a poor prognosis. 

The changes in the pattern of oral disease associated with HAART was assessed over the past nine years 

in a San Francisco clinic. The data show a significant decrease in oral candidiasis, OHL, and KS over 

time, but no change in the occurrence of aphthous ulcers. There was an increase in salivary-gland disease 

and a striking increase in warts: three-fold for patients on antiretroviral therapy and six-fold for those on 

HAART (p = .01). This pattern of oral disease in a referral clinic suggests that an increase in oral warts 

could be occurring as a complication of HAART. 

An intimate association between Kaposi's sarcoma-associated herpesvirus (HHV-8) and KS exists. It has 

been shown that HHV-8 encodes and expresses a large number of proteins with oncogenic potential. Such 

proteins include the latency-associated nuclear antigen (LANA), which can interfere with transcription of 

p53, and viral G protein-coupled receptor (GPCR), which induces angioproliferation. Intramural 

researchers at NIDCR have shown that HHV-8-GPCR, when overexpressed in tissue culture cells, 

enhanced the expression and secretion of vascular endothelial growth factor through regulation of 

different intracellular signaling pathways. The results provide further evidence of the signal 

transduction pathways activated by HHV-8-GPCR and support the key role these receptors play in 

promoting the survival of viral-infected cells. Moreover, the findings also emphasize the importance of 

this G protein-coupled receptor in the development of HHV-8-related neoplasias. 

39
Scientists at the NIDCR have recently developed an in vivo high throughput endothelial specific retroviral 

gene transfer system, and use it to specifically express candidate HHV-8 oncogenes in mouse endothelial 

cells. Among the many HHV-8 genes tested, only one gene, the HHV-8-GPCR, was able to promote the 

development of visible dermal and internal vascular tumors that strikingly resemble human KS lesions. 

Furthermore, they provided evidence that HHV-8-GPCR can initiate Kaposi’s sarcomagenesis, and that 

cells expressing this gene can further promote the cancerous growth of cells expressing other HHV-8 

genes, such as those expressed during the latent phase of HHV-8 infection. These findings further support 

a critical role for HHV-8-GPCR in initiating KS tumor development, and suggest that this receptor may 

represent a suitable target for anti-KS drug development. Cancer Cell. 2003 Jan;3(1):23-36

Investigators at the University of Michigan Dental School report that vascular endothelial growth factor, a 

potent mediator of angiogenesis that functions as a survival factor for endothelial cells, up-regulates Bcl-2 

gene expression. Using a mouse model of tumor vascularized with human blood vessels, they showed 

that up-regulation of IL-8 levels and Bcl-2 expression in endothelial cells in the tumor microvessels 

enhances intratumoral microvascular survival and density and accelerates growth of oral squamous cell 

carcinoma or KS. 

A study of health-care providers found that, compared with dentists, medical clinicians fail to recognize 

25–60% of the HIV-related oral abnormalities, including tumors, and often describe the lesions 

inaccurately. Good teamwork between health care providers and more awareness of oral complications of 

AIDS-related lesions is warranted. 

HIV-infected adolescents develop the same types of oral lesions, including tumors, as are seen in HIVinfected adults. The prevalence of these lesions, however, was lower in teens than in adults. 

HIV-infected subjects with OHL displayed significantly higher levels of salivary IL-1 alpha and IFNgamma compared with the HIV-infected individuals with no oral disease, and a higher level of IFNgamma than from the healthy control subjects. These findings may be diagnostic as well as indicative of 

pathogenesis. 

The prevalence of oral lesions was assessed in a five-center subset of the Women’s Interagency HIV 

Study (WIHS) and correlated with other features of HIV disease. Oral candidiasis and OHL were 

confirmed as being common features of HIV infection in women and appear to be associated with HIV 

viral load, immunosuppression, and various other behaviorally determined variables. 

Researchers at the University of North Carolina found a novel state of EBV infection with concurrent 

expression of replicative and transforming proteins. It is probable that both replicative and latent proteins 

contribute to OHL development and induce many of the histologic features of OHL, such as acanthosis 

and hyperproliferation. In contrast to other permissive herpesvirus infections, expression of EBVtransforming proteins within the permissively infected OHL tissue enables epithelial cell survival and 

may enhance viral replication. 

OHL is characterized by high-level replication of EBV and multiple EBV strains. Although multiple EBV 

strains were found in both the OHL and peripheral blood specimens, 13 of 16 (81%) patients showed 

evidence of strain identity for at least one strain and analysis of two patients suggested that EBV strains 

from OHL could infect the blood leukocytes. These data are consistent with active trafficking of EBV 

between the oral and blood compartments. 

Total Number of Funded AIDS-Related Grants and/or Contracts 

FY2002: 36 projects funded on this topic. 

Dennis F. Mangan, Ph.D. 301-594-2421 

Chief, Infectious Diseases and Immunity Branch dennis.mangan@nih.gov 

Division of Basic and Translational Sciences http://www.nidcr.nih.gov/research/dbts/immunology.asp

Mostafa Nokta, M.D., Ph.D. 301-594-7985 

Director, AIDS Program mostafa.nokta@nih.gov 

Division of Basic and Translational Sciences http://www.nidcr.nih.gov/research/dbts/aids.asp

J. Silvio Gutkind, Ph.D. 301-496-6259 

Chief, Oral and Pharyngeal Cancer Branch sg39v@nih.gov 

Division of Intramural Research http://wwwdir.nidcr.nih.gov/dirweb/opcb/sgutkind.asp

 40
Extramural AIDS-related Malignancy Trials (Active)

PROTOCOL 

NUMBER 

SOURCE TITLE PRINCIPAL 

INVESTIGATOR 

AMC 020 AIDS Malignancy 

Consortium 

Pilot Study of the Safety & Feasibility of Autologous Peripheral 

Blood Stem Cell Transplantation for Patients With Relapsed AIDSrelated Lymphoma

D. Scadden 

scadden.david@mg

h.harvard.edu 

AMC 032 AIDS Malignancy 

Consortium 

Phase II Infrared Coagulator for Treatment of High Grade 

Squamous Intraepithelial Neoplasia of the Anal Canal in HIVinfected Individuals 

E. Stier 

stiere@mwkcc.org 

AMC 033 AIDS Malignancy 

Consortium 

Phase II Trial of Induction Therapy With EPOCH Chemotherapy & 

Maintenance Therapy With Combivir/Interferon for HTLV-1 

Associated T-cell Non-Hodgkin's Lymphoma

L. Ratner 

Lratner@imgate.wu

stl.edu 

AMC 034 AIDS Malignancy 

Consortium 

Randomized Phase II Trial of EPOCH Chemotherapy & Rituximab 

for HIV-associated Non-Hodgkin's Lymphoma

J. Sparano 

sparano@jimmy.ha

rvard.edu 

AMC 035 AIDS Malignancy 

Consortium 

Phase I Study of Stressgen 00101 for High-grade Anal 

Intraepithelial Neoplasia

J. Palefsky 

joelp@medicine.uc

sf.edu 

AMC 036 AIDS Malignancy 

Consortium 

Phase II Trial of Halofuginone in Patients With HIV-related 

Kaposi’s Sarcoma

S. Krown 

krowns@mskcc.org 

AMC 037 AIDS Malignancy 

Consortium 

Zevalin Radioimmunotherapy for Patients With Post Transplant 

Lymphoproliferative Disease Following Solid Organ 

Transplantation 

D. Scadden 

scadden.david@mg

h.harvard.edu 

AMC 038 AIDS Malignancy 

Consortium 

A Pilot Trial of Valproic Acid in Patients With Kaposi’s Sarcoma R. Ambinder 

rambinder@jhmi.edu 

AMC 039 AIDS Malignancy 

Consortium 

Ultra-sensitive Infra-red Thermographic Analysis of Kaposi’s 

Sarcoma Skin Lesions 

C. Martins 

crmartin@jhmi.edu 

CWRU029828J, NCIG02-2126 Case Western 

University 

Phase II Study of Lomustine/Etopside/Cyclophosphamide/ 

Procarbazine (CECP) in Patients With AIDS-related Stage IIB-IV

Hodgkin’s Disease

S. Remick 

scr@cwru.edu 

BUMC-3756 

NCI-V00-1609 

Boston University Phase I Study of Arginine Butyrate & Ganciclovir in Patients With 

Epstein Barr Virus-Induced Malignancies or 

Lymphoproliferative Disorders

D. Faller 

dfaller@bu.edu 

41 
Intramural AIDS-related Malignancy Trials (Active)

PROTOCOL 

NUMBER 

SOURCE TITLE PRINCIPAL 

INVESTIGATOR 

00-C-0193 HAMB, CCR, 

NCI 

A Study of the Effects of Potent Anti-HIV Therapy on Parameters 

Hypothesized to be Related to the Pathogenesis of Kaposi’s 

Sarcoma in HIV-Infected Individuals 

R. Yarchoan 

ry1n@nih.gov 

01-C-0030, 

NCI-2890 

MOCRU, CCR, 

NCI 

Short-course EPOCH-Rituximab for Untreated CD-20+ HIVassociated LymphomasW. Wilson 

wilsonw@mail.nih.

gov 

01-C-0038 HAMB, CCR, 

NCI 

Collection of Blood, Bone Marrow, Tumor or Tissue Samples 

From Patients with HIV Infection, KSHV Infection, Viral-related 

Pre-malignant Lesions, &/or Cancer

R. Yarchoan 

ry1n@nih.gov 

01-C-0067 HAMB, CCR, 

NCI 

A Phase II Study Liposomal Doxorubicin & IL-12 in AIDSassociated Kaposi’s Sarcoma Followed by Chronic 

Administration of IL-12 

R. Little 

rl48e@nih.gov 

01-C-0158 HAMB, CCR, 

NCI 

Protocol to Assess Vascularity in Kaposi’s Sarcoma Lesions 

Utilizing Non-invasive Imaging Techniques 

R. Yarchoan 

ry1n@nih.gov 

03-C-0110 HAMB, CCR, 

NCI 

Phase II Study of Intravenous Recombinant Humanized AntiVascular Endothelial Cell Growth Factor Antibody (Bevacizumab) 

in Classical (HIV-negative) & in AIDS-associated Kaposi’s 

Sarcoma

R. Yarchoan 

ry1n@nih.gov 

Intramural AIDS/HIV Trials (Non-malignancy, Active)

PROTOCOL 

NUMBER 

SOURCE TITLE PRINCIPAL 

INVESTIGATOR 

OH99-CNO18 HAMB, CCR, 

NCI 

Collection of Samples for Studies Concerning the Pathogenesis & 

Immunology of Viral Diseases 

S. Zeichner 

zeichnes@mail.nih.gov 

99-C-0134 HAMB, CCR, 

NCI 

A Long-term Observational Study of Immunologic Reconstitution 

in HIV-1 Infected Children Who Are Receiving Combination 

Protease Inhibitor & Reverse Transcriptase Inhibitors 

S. Zeichner 

zeichnes@mail.nih.gov 

01-C-0025 HAMB, CCR, 

NCI 

A Phase I Study of Capravine (AG-1549), a Novel Nonnucleoside Reverse Transcriptase Inhibitor in Children with HIV1 Infection S. Zeichner 

zeichnes@mail.nih.gov 

01-C-0038 HAMB, CCR, 

NCI 

Collection of Blood, Bone Marrow, Tumor or Tissue Samples 

From Patients with HIV Infection, KSHV Infection, Viral-related 

Pre-malignant Lesions, &/or Cancer 

R. Yarchoan 

ry1n@nih.gov 

02-C-0006 HAMB, CCR, 

NCI 

A Phase I Study of Tenofir Disproxil Fumarate (PMPA Prodrug), 

a Novel Nucleotide Analog Reverse Transcriptase Inhibitor, in 

Children with HIV Infection 

S. Zeichner 

zeichnes@mail.nih.gov 

02-C-0150 HAMB, CCR, 

NCI 

Therapeutic Drug Monitoring & Viral Resistance Testing in the 

Treatment of HIV-infected Children 

S. Zeichner 

zeichnes@mail.nih.gov 

03-C-0084 HAMB, CCR, 

NCI 

Collection of Blood Samples from Pediatric Patients HIV 

Infection & Their Family Members 

S. Zeichner 

zeichnes@mail.nih.gov 

03-C-0169 HAMB, CCR, 

NCI 

Psychological & Environmental Factors Associated With 

Medication Adherence in Children & Adolescents with HIV 

Infection 

L. Wood 

woodl@mail.nih.gov 

04-C-0106 HAMB, CCR, 

NCI 

Proton Magnetic Resonance Spectroscopy & Neuropsychological 

Functioning in Children With HIV: A Pilot Study 

S. Zeichner 

zeichnes@mail.nih.gov 

Further information on NCI Clinical Trials can be obtained at http://cancer.gov/clinicaltrials/

42
Funding for AIDS Related Malignancies 

Fiscal Year 1999 - 2003 

(dollars in thousands) 

FY 2003 Actuals 

Mechanism 

AIDS 

Related 

Malignancies 

% of Total 

AIDS 

Related 

Malignancies 

Total 

AIDS 

% of Total 

AIDS 

Grants....................... 60,260 54.19% 114,457 44.99% 

Contracts....................... 7,775 6.99% 41,000 16.12% 

Intramural....................... 30,506 27.43% 92,485 36.35% 

RMS....................... 12,663 11.39% 15,500 6.09% 

Total - 111,204 100.00% 263,442 103.56% 

FY 2002 Actuals 

Mechanism 

AIDS 

Related 

Malignancies 

% of Total 

AIDS 

Related 

Malignancies 

Total 

AIDS 

% of Total 

AIDS 

Grants....................... 75,431 60.79% 106,904 42.02% 

Contracts....................... 8,213 6.62% 40,878 16.07% 

Intramural....................... 26,517 21.37% 91,288 35.88% 

RMS....................... 13,925 11.22% 15,326 6.02% 

Total - 124,086 100.00% 254,396 100.00% 

FY 2001 Actuals 

Mechanism 

AIDS 

Related 

Malignancies 

% of Total 

AIDS 

Related 

Malignancies 

Total 

AIDS 

% of Total 

AIDS 

Grants....................... 84,457 69.92% 106,172 41.48% 

Contracts....................... 5,995 4.96% 56,807 22.19% 

Intramural....................... 19,865 16.45% 80,031 31.27% 

RMS....................... 10,477 8.67% 12,950 5.06% 

Total - 120,794 100.00% 255,960 100.00% 

FY 2000 Actuals 

Mechanism 

AIDS 

Related 

Malignancies 

% of Total 

AIDS 

Related 

Malignancies 

Total 

AIDS 

% of Total 

AIDS 

Grants....................... 61,774 62.61% 100,415 41.13% 

Contracts....................... 9,002 9.12% 49,958 20.46% 

Intramural....................... 18,089 18.33% 82,072 33.62% 

RMS....................... 9,795 9.93% 11,700 4.79% 

Total - 98,660 100.00% 244,145 100.00% 

43
FY 1999 Actuals 

Mechanism 

AIDS 

Related 

Malignancies 

% of Total 

AIDS 

Related 

Malignancies 

Total 

AIDS 

% of Total 

AIDS 

Grants....................... 64,972 70.06% 122,858 51.36% 

Contracts....................... 10,072 10.86% 36,191 15.13% 

Intramural....................... 11,210 12.09% 68,591 28.68% 

RMS....................... 6,483 6.99% 11,550 4.83% 

Total - 92,737 100.00% 239,190 100.00% 

44