Stephen Popper

Stephen Popper
University of California, Berkeley | UCB · Department of Infectious Diseases and Vaccinology

ScD

About

73
Publications
2,855
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2,923
Citations
Citations since 2016
30 Research Items
1011 Citations
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2016201720182019202020212022050100150
2016201720182019202020212022050100150
2016201720182019202020212022050100150

Publications

Publications (73)
Article
Full-text available
There are many outstanding questions about how to control the global COVID-19 pandemic. The information void has been especially stark in the World Health Organization Africa Region, which has low per capita reported cases, low testing rates, low access to therapeutic drugs, and has the longest wait for vaccines. As with all disease, the central ch...
Article
Background Several promising live attenuated virus (LAV) dengue vaccines are in development, but information about innate immune responses and early correlates of protection are lacking. Methods We characterized human genome-wide transcripts in whole blood from 10 volunteers at 11 time-points after immunization with the dengue virus type 3 (DENV-3...
Preprint
Background: Several promising live attenuated virus (LAV) dengue vaccines are in development, but information about innate immune responses and early correlates of protection are lacking. Methods: We characterized human genome-wide transcripts in whole blood from 10 volunteers at 11 time-points after immunization with the dengue virus type 3 (DENV-...
Article
Full-text available
Background To guide treatment of infectious diseases, clinicians need sensitive, specific, and rapid diagnostics. We aim to incorporate complementary methods of microbial sequencing and host-response profiling to improve the diagnosis of patients at risk for acute infections. Methods We enrolled 200 adult patients with systemic inflammatory respon...
Article
Full-text available
[This corrects the article DOI: 10.1371/journal.ppat.1005943.].
Article
Full-text available
Leptospirosis causes significant morbidity and mortality worldwide; however, the role of the host immune response in disease progression and high case fatality (>10–50%) is poorly understood. We conducted a multi-parameter investigation of patients with acute leptospi-rosis to identify mechanisms associated with case fatality. Whole blood transcrip...
Data
Association between acute antibody titer and immunoglobulin transcript fold-change. (XLSX)
Data
Clinical signs and symptoms for patients with leptospirosis. (XLSX)
Data
Determining model fitness for experimental variables associated with death. In order to assess the linearity of features and goodness of model fit (blue lines), we plotted the observed values of variables associated with death (x-axis) as an outcome for confirmed leptospirosis cases versus the predictive probability of death (y-axis) within a 95% c...
Data
Cathelicidin (LL-37) protects hamsters from lethal Leptospira infection. (A) Survival in hamsters pre-treated with 1 mg/kg of cathelicidin (LL-37) (n = 14) was significantly greater than ddH2O-treated controls (n = 14) following lethal challenge with 100 Leptospira (P<0.0001). (B) Bacterial loads (Leptospira genome equivalents per mL of whole blood...
Data
Differentially expressed transcripts in Acute vs Convalescent Survivors (SvC). (XLSX)
Data
All significant Functional GO terms for DE transcripts in Acute vs Convalescence (SvC) and Deceased vs Survivors (DvS). (XLSX)
Data
All significant REACTOME functional pathways for differentially expressed transcripts in Deceased vs Survivors (DvS). (XLSX)
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Statistical modeling of possible risk factors predicting death. (DOCX)
Data
Differential gene expression between acute and convalescence in survivors with leptospirosis. (A) The abundance of these transcripts differs significantly between acute survivors (S) and healthy volunteers (H), but not between convalescent (C) and healthy samples. Rectangles denote transcript clusters with similar expression profiles and functions:...
Data
Differentially expressed transcripts in Deceased vs Survivors (DvS). (XLSX)
Article
Full-text available
Background: The development of a vaccine against dengue faces unique challenges, including the complexity of the immune responses to the four antigenically distinct serotypes. Genome-wide transcriptional profiling provides insight into the pathways and molecular features that underlie responses to immune system stimulation, and may facilitate pred...
Data
Genes differentially expressed after TDV vaccination in 30 animals compared to baseline. (XLSX)
Data
Additional modules of IFN-induced gene sets. (XLSX)
Data
Overlap of genes with significant changes in transcript abundance following vaccination and correlated with median neutralizing antibody titers on day 30. (XLSX)
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Blood transcript modules enriched following vaccination (FDR<5%). (XLSX)
Data
Fold-change over time of significant genes in Clusters 1–3 for animals in the placebo (PBS) group following wt DENV challenge. (XLSX)
Data
Correlation between abundance of type I IFN genes and (A) duration of TDV-2 viremia and (B) peak TDV-2 viral load. (PDF)
Data
Baseline-transformed (average of d-11 and d-2) relative transcript abundances (log2) by animal for 595 differentially expressed genes after TDV vaccination. (XLSX)
Data
Correlation of DENV-2 neutralizing antibody titer (PRNT50) on day 30 with (A) duration of viremia; and (B) peak viral load. (PDF)
Data
Supporting information on viruses, animals and study design. (DOCX)
Data
Enriched blood transcript modules from genes ranked by Spearman correlation coefficient r (FDR<5%). (XLSX)
Data
The antiviral/type I IFN response following TDV vaccination. Unsupervised clustering of median expression of 282 genes (379 genes, filtered for reliably measured transcript abundance in 2 out of 3 samples) over time in all vaccinated animals, and median expression by group. Red indicates an increase in transcript abundance, blue indicates a decreas...
Data
Geometric mean neutralizing antibody titer (PRNT50) over time for each treatment group. (PDF)
Article
Full-text available
Type I interferons (IFN-α and IFN-β) are important for protection against many viral infections, whereas type II interferon (IFN-γ) is essential for host defense against some bacterial and parasitic pathogens. Study of IFN responses in human leprosy revealed an inverse correlation between IFN-β and IFN-γ gene expression programs. IFN-γ and its down...
Data
Full-text available
Rank correlation of transcript abundance and platelet levels in dengue patients. Median transcript abundance for each patient group on each of days 3 through day 7 (5 columns per group) is presented. Red indicates more abundant than controls; green indicates less abundant. Gray columns separate each group; the black column represents median value f...
Data
Full-text available
First principal component in the full gene expression data set for dengue patients on fever day 4 and healthy controls. Principal components were derived from the dataset of 10,075 probes used for all analyses, including the data presented in Figure 1. (PDF)
Data
Transcripts that are associated with differences between primary DF and secondary DSS on fever day 3 (FDR<20%). (XLS)
Data
Distribution of PBMC RNA samples by day of fever. DF1 = dengue fever, primary DENV infection; DF2 = dengue fever, secondary DENV infection; DHF = dengue hemorrhagic fever; DSS = dengue shock syndrome. (DOCX)
Data
Full-text available
First principal component in the data. (A) Fever day 3. (B) Fever day 5. H = healthy control; DF1 = dengue fever, primary DENV infection; DF2 = dengue fever, secondary DENV infection; DHF = dengue hemorrhagic fever; DSS = dengue shock syndrome. (PDF)
Data
Comparison of gene expression profiles in response to viral infection. A dengue-response signature was constructed by calculating the median expression across all samples collected between fever day 3 and fever day 7 of genes with differential expression compared to healthy controls (Fig. 4). Studies including one or more comparisons of blood-based...
Article
Full-text available
Dengue is the most prevalent mosquito-borne human illness worldwide. The ability to predict disease severity during the earliest days of the illness is a long-sought, but unachieved goal. We examined human genome-wide transcript abundance patterns in daily peripheral blood mononuclear cell (PBMC) samples from 41 children hospitalized with dengue vi...
Article
Transforming growth factor (TGF)-β is a multifunctional peptide that is important in T-cell activation and cardiovascular remodeling, both of which are important features of Kawasaki disease (KD). We postulated that variation in TGF-β signaling might be important in KD susceptibility and disease outcome. We investigated genetic variation in 15 gene...
Article
Full-text available
Interferons are key modulators of the immune system, and are central to the control of many diseases. The response of immune cells to stimuli in complex populations is the product of direct and indirect effects, and of homotypic and heterotypic cell interactions. Dissecting the global transcriptional profiles of immune cell populations may provide...
Article
Full-text available
We used microarrays and transcriptional profiling of peripheral blood to investigate the host response of 29 individuals who contracted typhoid fever in the Mekong Delta region of Vietnam. Samples were taken over a nine month period encompassing acute disease, convalescence, and recovery. We found that typhoid fever induced a distinct and highly re...
Article
Full-text available
Acute Kawasaki disease (KD) is difficult to distinguish from other illnesses that involve acute rash or fever, in part because the etiologic agent(s) and pathophysiology remain poorly characterized. As a result, diagnosis and critical therapies may be delayed. We used DNA microarrays to identify possible diagnostic features of KD. We compared gene...
Article
Full-text available
We employed DNA microarray technology to investigate the host response to Streptococcus pneumoniae in a mouse model of asymptomatic carriage. Over a period of six weeks, we profiled transcript abundance and complexity in the Nasal Associated Lymphoid Tissue (NALT) to identify genes whose expression differed between pneumococcal-colonized and uncolo...
Data
Gene List resulting from SAM analysis. List of gene symbols and description as well as the microarray oligo ID for genes whose expression consistently differed between infected and mock-infected mice over the entire time course.
Data
Gene List resulting from Variation analysis. List of gene symbols and description as well as the microarray oligo ID for genes whose expression varied most between infected and mock-infected mice over the entire time course.
Conference Paper
Background: Dengue virus (DENV) infection in humans ranges in severity from mild febrile illness and classic dengue fever (DF) to the severe and potentially fatal dengue hemorrhagic fever (DHF) and dengue shock syndrome (DSS). Much remains unknown about its molecular pathophysiology. Methods: We conducted a dengue clinical study in a hospital in Ma...
Data
Seven RNA samples from different KD patients were amplified, labeled, and hybridized to cDNA microarrays on two separate occasions. The set of 601 array elements that were present in both the final dataset for cohort 1 (Figure 1) and cohort 2 (Figure 4) were used to center and organize each of the two sets of seven samples. The two datasets were th...
Data
A spreadsheet containing a list of the genes in clusters 1 and 2 in Figure 1 (cohort 1). Gene symbol, gene name, and gene cluster are listed for each gene.
Data
Detailed information on the quantitative RT-PCR methods used in this study.
Data
A spreadsheet containing the list of genes identified as having person-specific patterns of expression (see Figure 3).
Data
A list of the genes whose expression was correlated with clinical parameters in cohort 2. Gene symbol, gene name, and gene cluster (see Figure 4) are listed for each gene.
Article
Full-text available
Kawasaki disease (KD) is an acute self-limited vasculitis and the leading cause of acquired heart disease in children in developed countries. No etiologic agent(s) has been identified, and the processes that mediate formation of coronary artery aneurysms and abatement of fever following treatment with intravenous immunoglobulin (IVIG) remain poorly...
Article
The Tat protein of human immunodeficiency virus (HIV) is essential for viral replication and has extracellular pathogenic activity. We sought to determine whether the anti-Tat antibody response was predictive of disease progression in 144 HIV type 2 (HIV-2)–infected subjects observed longitudinally between 1985 and 2003. Sixty-eight percent of the...
Article
Full-text available
DNA microarray-based gene transcript-profiling of the responses of primates to infection has begun to yield new insights into host-pathogen interactions; this approach, however, remains plagued by challenges and complexities that have yet to be adequately addressed. The rapidly changing nature over time of acute infectious diseases in a host, and t...
Conference Paper
In Vietnam, malaria illness is typically caused by either falciparum or vivax infection. Though both infections can present with similar clinical features, mortality is predominantly associated with falciparum infection. There is limited information about molecular differences in the host response associated with infection by these parasites. We ex...
Article
Full-text available
Malaria is a global problem, and there is a critical need for further understanding of the disease process. When malarial parasites invade and develop within the bloodstream, they stimulate a profound host response whose main clinical sign is fever. To explore this response, we measured host gene expression in whole blood from Kenyan children hospi...
Conference Paper
Kawasaki disease (KD) is the most common cause of acquired heart disease in children in the United States. The epidemiology of the disease suggests an infectious agent, but the absence of a defined etiology complicates efforts to achieve a diagnosis as well as to identify risk factors associated with development of coronary artery lesions, or lack...
Article
Full-text available
Human immunodeficiency virus type 2 (HIV-2), the second human retrovirus known to cause AIDS, is endemic to West Africa but is infrequently found outside this region. We present a case series of 10 HIV-2—infected individuals treated in the United States. Physicians applied the principles of highly active antiretroviral therapy (HAART), normally use...
Conference Paper
Kawasaki disease (KD) is the most common cause of acquired heart disease in children in the United States. The epidemiology of the disease suggests an infectious agent, but the absence of a defined etiology has complicated diagnosis, treatment, and attempts to understand the KD-associated cellular events that lead to damage of the coronary arteries...
Article
Full-text available
The nature and extent of interindividual and temporal variation in gene expression patterns in specific cells and tissues is an important and relatively unexplored issue in human biology. We surveyed variation in gene expression patterns in peripheral blood from 75 healthy volunteers by using cDNA microarrays. Characterization of the variation in g...
Article
Human immunodeficiency virus type 2 (HIV-2) progression to disease is significantly slower than that of human immunodeficiency virus type 1 (HIV-1). Genetic determinants for susceptibility to disease progression were hypothesized to play a more significant role in this infection compared with HIV-1. We sought to identify common human lymphocyte ant...
Article
Twelve HIV-1-infected, nine HIV-2-infected patients and eight HIV-negative subjects were given a 40IU booster dose of tetanus toxoid (TT). Blood was collected on days 0, 7 and 30 after immunization. Changes in HIV-1 or HIV-2 RNA load were evaluated by nested PCR. TT-IgG antibody levels were quantified by ELISA. CD4 cell counts as well as activation...
Article
Evaluation of immune mechanisms responsible for control of viral replication is critical to understanding HIV-2 attenuated biological characteristics in pathogenesis and transmission. Evaluation of the cellular immune response is often based on labor-intensive techniques that limit the scope of most studies performed. A simple and rapid anthrax tox...
Article
Twelve HIV-1-infected, nine HIV-2-infected patients and eight HIV-negative subjects were given a 40IU booster dose of tetanus toxoid (TT). Blood was collected on days 0, 7 and 30 after immunization. Changes in HIV-1 or HIV-2 RNA load were evaluated by nested PCR. TT-IgG antibody levels were quantified by ELISA. CD4 cell counts as well as activation...
Article
Levels of virus in the plasma are closely related to the pathogenicity of human immunodeficiency virus type 1 (HIV-1). HIV-2 is much less pathogenic than HIV-1, and infection with HIV-2 leads to significantly lower plasma viral load. To identify the source of this difference, we measured both viral RNA and proviral DNA in matched samples from 34 HI...
Article
Full-text available
Human immunodeficiency virus type 2 (HIV-2) is less pathogenic than HIV type 1 (HIV-1), but the mechanisms underlying this difference have not been defined. We developed an internally controlled quantitative reverse transcriptase-polymerase chain reaction to measure HIV-2 viral load and determined levels of plasma virus in a cohort of registered co...
Article
To explore and compare the relations between proviral DNA load and CD4+ lymphocyte counts in both HIV-2 monotypic and HIV dual infection. In Dakar, Senegal, where the HIV-1 and HIV-2 epidemics overlap, serum and peripheral blood mononuclear cell (PBMC) DNA samples were collected from registered female sex workers and hospitalized patients. Sera wer...