HIV persistence during combination antiretroviral therapy (ART) is the principal challenge preventing viral eradication. We and others reported that HIV infected cells undergo clonal expansion during ART, and we reported that clones of infected cells are present in tissues and in a neoplasm. The tissue distribution of infected cells and their roles in HIV persistence are not well understood. To determine the distribution of clones of infected cells during ART, we analyzed tissues obtained from individuals who underwent autopsy after expiring with comorbid neoplasms.
Participants (N=2) underwent autopsy after therapy for primary effusion lymphoma (PEL) or metastatic adenocarcinoma; both were on effective ART with HIV RNA < 50 c/ml. Tissue samples (lung, mediastinal lymph node, spleen, testes, liver, and neoplastic tissue, including individual metastases) were obtained during autopsy; nucleic acid was extracted and levels of HIV and total cellular DNA were quantified by qPCR as previously described. HIV integration sites were determined for one individual with PEL [for whom single genome sequencing (SGS) have been reported]. For the individual with adenocarcinoma, HIV pro-pol SGS were obtained.
Levels of HIV DNA were diverse (range 30-700 copies/106 cells), highest in lymphoid tissue. In the individual with PEL, 391 integration sites were obtained from lymph node, lung, spleen, and testes; 72 sites (18.4%) were from cell clones. Clones were detected within individual tissues, but were also present across tissues, in both local (lung and draining lymph node), and distant tissues (lung, spleen, testes); infected cells were present in the effusion. HIV was integrated in many host genes, including STAT5B, which has been associated with clonal expansion and persistence of infected cells. In the individual with adenocarcinoma, 183 SGS were recovered; HIV was genetically highly diverse, but identical sequences were present, these were possible cell clones. Identical sequences were present within and across tissues. Individual metastases all contained HIV infected cells.
Populations of clonally expanded HIV infected cells are widely, but not uniformly, distributed in individuals with neoplasms, showing that cells from some of the largest infected clones are widely distributed in different tissues. Tumors contain infected cells and analyzing neoplasms contributes to understanding their role in the immune response during ART.