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Targeted plasma proteomics reveals organ damage signatures of AIDS-related and non-communicable chronic diseases-related deaths in HIV population

ABSTRACT: This project investigates the role of protein biomarkers in differentiating the underlying causes of mortality among people with HIV (PWH). With antiretroviral therapy (ART) significantly reducing deaths from opportunistic infections, noncommunicable chronic diseases (NCDs) have emerged as a leading cause of death in this population. Our study seeks to identify protein signatures that distinguish AIDS-related deaths from those due to NCDs, aiming to enhance early risk prediction and inform targeted interventions.

INSTRUMENT(S): Olink Target 96

ORGANISM(S): Homo Sapiens (human)

TISSUE(S): Blood Plasma

SUBMITTER: Na He

LAB HEAD: Na He

PROVIDER: PAD000008 | Pride | 2025-04-15

REPOSITORIES: pride

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			Action	DRS
	440sample_NPX_CHART_long.npx.csv	Csv
	Validation_Cohort_NPX_long.npx.csv	Csv
	checksum.txt	Txt

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Publications

Targeted plasma proteomics reveals organ damage signatures of AIDS- and noncommunicable disease-related deaths in people with HIV.

Lin Haijiang H He Jiayu J Ren Jiyuan J Chen Xiaoxiao X Wang Tingting T Zhang Haijun H Wang Shanling S Wang Miaochen M Chen Tailin T Duan Song S He Na N

Nature communications 20250424 1

Antiretroviral therapy (ART) is shifting the primary driver of mortality for people with HIV (PWH) from opportunistic infections to noncommunicable diseases (NCDs). Protein biomarkers differentiating both AIDS-related and NCDs-related deaths from PWH may help early and precise risk prediction and intervention. We conduct a nested case-control study where 126 HIV deaths, 162 age-sex-matched HIV survivors and 152 HIV-negative controls are analyzed with 92 protein biomarkers of the Olink Organ Dama ...[more]

PMID: 40274826

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Project description:Proteomics data was measured by using the Olink Explore 1536 panel from baseline plasma sample. The project is also supported by Themistocles L Assimes (Stanford University tassimes@stanford.edu) and Fahim Abbasi (Stanford University, fahim@stanford.edu).

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AIDS-related Kaposi's sarcoma

Project description:Kaposi's Sarcoma (KS) is a proliferation of aberrant vascular structures lined by spindle cells, and is caused by a gammaherpes virus (HHV8/KSHV). Its course is aggravated by co-infection with HIV-1, where the timing of infection with HIV-1 and HHV8 is important for the clinical outcome. METHODS: In order to better understand the pathogenesis of KS, we have analysed tissue from two AIDS-KS lesions, and from normal skin by serial analysis of gene expression (SAGE). Semi-quantitative RT-PCR was then used to validate the results. RESULTS: The expression profile of AIDS-related KS (AIDS-KS) reflects an active process in the skin. Transcripts of HHV8 were found to be very low, and HIV-1 mRNA was not detected by SAGE, although it could be found using RT-PCR. Comparing the expression profile of AIDS-KS tissue with publicly available SAGE libraries suggested that AIDS-KS mRNA levels are most similar to those in an artificially mixed library of endothelial cells and leukocytes, in line with the description of KS lesions as containing spindle cells with endothelial characteristics, and an inflammatory infiltrate. At least 64 transcripts were found to be significantly elevated, and 28 were statistically downregulated in AIDS-KS compared to normal skin. Five of the upregulated mRNAs, including Tie 1 and sialoadhesin/CD169, were confirmed by semi-quantitative PCR to be elevated in additional AIDS-KS biopsies. Antibodies to sialoadhesin/CD169, a known marker of activated macrophages, were shown to specifically label tumour macrophages. CONCLUSION: The expression profile of AIDS-KS showed 64 genes to be significantly upregulated, and 28 genes downregulated, compared with normal skin. One of the genes with increased expression was sialoadhesin (CD169). Antibodies to sialoadhesin/CD169 specifically labelled tumour-associated macrophages, suggesting that macrophages present in AIDS-KS lesions belong to a subset of human CD169+ macrophages. Keywords: other

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Molecular Classification of AIDS-Related Lymphomas

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The tumor virus landscape of AIDS-related lymphomas

Project description:Immunodeficiency dramatically increases susceptibility to cancer as a result of reduced immune surveillance and enhanced opportunities for virus-mediated oncogenesis. While AIDS-related lymphomas (ARLs) are frequently associated with known oncogenic viruses, many cases contain no known transforming virus. To discover novel transforming viruses, we profiled a set of ARL samples using whole transcriptome sequencing. We determined that Epstein-Barr virus (EBV) was the only virus detected in the tumor samples of this cohort, suggesting that if unidentified pathogens exist in this disease, they are present in fewer than 10% of cases or undetectable by our methods. To evaluate the role of EBV in ARL pathogenesis, we analyzed viral gene expression and found highly heterogeneous patterns of viral transcription across samples. We also found significant heterogeneity of viral antigen expression across a large cohort, with many patient samples presenting with restricted type I viral latency, indicating that EBV latency proteins are under increased immunosurveillance in the post-CART era. Furthermore, EBV infection of lymphoma cells in HIV-positive individuals was associated with a distinct host gene expression program. These findings provide insight into the joint host-virus regulatory network of primary ARL tumor samples and expand our understanding of virus-associated oncogenesis. Our findings may also have therapeutic implications, as treatment may be personalized to target specific viral and virus-associated host processes that are only present in a subset of patients.

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Cooking methods affect Advanced Glycation End products and lipid profiles: a randomized cross-over study in healthy subjects

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Project description:Gene expression profiling (GEP) of ARL patient samples was done to determine whether gene expression signatures derived from HIV- lymphomas retained their ability to molecularly classify HIV+ lymphomas. The GEP-based predictors robustly classified ARL tumors, distinguishing molecular Burkitt lymphoma (BL) and diffuse large B-cell lymphoma (DLBCL), as well as activated B-cell-like (ABC) and germinal center B-cell-like (GCB) molecular subtypes of DLBCL. Gene expression profiles were used to identify coordinately regulated gene sets and pathways that differ between HIV+ and HIV- lymphomas of corresponding molecular subtype. Frozen tumor biopsies were obtained from 20 HIV-positive patients with an AIDS-defining lymphoma. Cases were ascertained at the University of Nebraska Medical Center and through the NCI AIDS and Cancer Specimen Resource tumor bank. Sufficient RNA for hybridization to Affymetrix U133 plus 2 arrays was obtained on 17 ARL cases. Details of all 20 HIV-positive patients can be found in the supplementary file below. Third party array data from HIV- lymphomas of corresponding molecular subtype were used for the comparison and molecular classification of the HIV+ cases in this study. The third party HIV- lymphoma samples include the following. [1] HIV- lymphoma, BL cases: 84 samples profiled on the Affymetrix HG U133 Plus 2 array. The data are publicly available on the website companion to Dave et al. NEJM 2006; Volume 354:13-24 (http://llmpp.nih.gov/BL/) and were used 'as is' (ie, not reanalyzed). [2] HIV- lymphoma, DLBCL cases: 200 of the 414 cases in Series GSE10846 (listed in the supplementary file below). These included all R-CHOP treated cases of either ABC or GCB subtype. These data were also used as is. These data were published in Lenz et al. NEJM 2008; Volume 359: 2313-2323.

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