Feasibility of Cell-Free DNA Collection and Clonal Immunoglobulin Sequencing in South African Patients With HIV-Associated Lymphoma

Abstract

PURPOSE Diagnosis of AIDS lymphoma in low-resource settings, like South Africa, is often delayed, leaving patients with limited treatment options. In tuberculosis (TB) endemic regions, overlapping signs and symptoms often lead to diagnostic delays. Assessment of plasma cell-free DNA (cfDNA) by next-generation sequencing (NGS) may expedite the diagnosis of lymphoma but requires high-quality cfDNA. METHODS People living with HIV with newly diagnosed aggressive B-cell lymphoma and those with newly diagnosed TB seeking care at Chris Hani Baragwanath Academic Hospital and its surrounding clinics, in Soweto, South Africa, were enrolled in this study. Each participant provided a whole blood specimen collected in cell-stabilizing tubes. Quantity and quality of plasma cfDNA were assessed. NGS of the immunoglobulin heavy chain was performed. RESULTS Nine HIV+ patients with untreated lymphoma and eight HIV+ patients with TB, but without lymphoma, were enrolled. All cfDNA quantity and quality metrics were similar between the two groups, except that cfDNA accounted for a larger fraction of recovered plasma DNA in patients with lymphoma. The concentration of cfDNA in plasma also trended higher in patients with lymphoma. NGS of immunoglobulin heavy chain showed robust amplification of DNA, with large amplicons (> 250 bp) being more readily detected in patients with lymphoma. Clonal sequences were detected in five of nine patients with lymphoma, and none of the patients with TB. CONCLUSION This proof-of-principle study demonstrates that whole blood collected for cfDNA in a low-resource setting is suitable for sophisticated sequencing analyses, including clonal immunoglobulin NGS. The detection of clonal sequences in more than half of patients with lymphoma shows promise as a diagnostic marker that may be explored in future studies.

Significance of lymph node fine needle aspiration for the diagnosis of HIV-associated lymphoma in a low-resource setting

“…We note that with the incorporation of GeneXpert technology, TB diagnosis has been greatly facilitated [8]. Molecular characterization of FNA specimens might similarly assist with lymphoma diagnosis [30,31]. Exactly how and when this testing should be incorporated into the diagnostic paradigm will require further evaluation but the present study highlights the extent of the opportunity in low-resource settings where pathology infrastructure is limiting.…”

Focused investigations to expedite cancer diagnosis among patients with lymphadenopathy in a tuberculosis and HIV-endemic region

“…In these cases, we recommend specialist consultation at a tertiary institute where specialized tests such as flow cytometry of FNAs or bone marrow biopsies can be used for diagnosis or specialized surgical services are available to access nodes in difficult sites. Improved molecular tests and biomarkers from peripheral blood or urine are urgently needed in TB-endemic areas, and exciting advances in the use of cell-free DNA or liquid biopsy may improve diagnosis in these patients [24].…”

Cancer and HIV: The Molecular Mechanisms of the Deadly Duo

“…Importantly, these efforts have taken into account cultural and socioeconomic factors, providing a holistic understanding that shapes prevention and treatment strategies with cultural sensitivity [104]. African researchers have also tackled challenges specific to the continent, offering innovative solutions applicable on a global scale [105,106]. Moreover, collaborations between African researchers and the international scientific community have fostered a rich exchange of ideas and knowledge, enhancing research capacity within Africa and strengthening its ability to address the distinct healthcare challenges posed by HIV-associated cancers.…”