In-depth virological and immunological characterization of HIV-1 cure after CCR5Δ32/Δ32 allogeneic hematopoietic stem cell transplantation

nature medicine Brief Communication https://doi.org/10.1038/s41591-023-02213-x In-depth virological and immunological characterization of HIV-1 cure after CCR5Δ32/Δ32 allogeneic hematopoietic stem cell transplantation Received: 5 August 2022 Accepted: 9 January 2023 Published online: xx xx xxxx Check for updates Björn-Erik Ole Jensen 1,24 , Elena Knops 2,3,24, Leon Cords 4,24, Nadine Lübke5,24, Maria Salgado 6,7,23,24, Kathleen Busman-Sahay 8, Jacob D. Estes8, Laura E. P. Huyveneers9, Federico Perdomo-Celis10, Melanie Wittner4,11, Cristina Gálvez6, Christiane Mummert12,20, Caroline Passaes 10, Johanna M. Eberhard 4,11,21, Carsten Münk1, Ilona Hauber13, Joachim Hauber11,13, Eva Heger2,3, Jozefien De Clercq14, Linos Vandekerckhove 14, Silke Bergmann12, Gábor A. Dunay11,13,22, Florian Klein 2,3, Dieter Häussinger 1, Johannes C. Fischer15, Kathrin Nachtkamp16, Joerg Timm 5, Rolf Kaiser2,3, Thomas Harrer12, Tom Luedde 1, Monique Nijhuis 9, Asier Sáez-Cirión 10,25, Julian Schulze zur Wiesch 4,11,25 , Annemarie M. J. Wensing9,17,25, Javier Martinez-Picado 6,7,18,19,25 & Guido Kobbe16,25 Despite scientific evidence originating from two patients published to date that CCR5Δ32/Δ32 hematopoietic stem cell transplantation (HSCT) can cure human immunodeficiency virus type 1 (HIV-1), the knowledge of immunological and virological correlates of cure is limited. Here we characterize a case of long-term HIV-1 remission of a 53-year-old male who was carefully monitored for more than 9 years after allogeneic CCR5Δ32/ Δ32 HSCT performed for acute myeloid leukemia. Despite sporadic traces of HIV-1 DNA detected by droplet digital PCR and in situ hybridization assays in peripheral T cell subsets and tissue-derived samples, repeated ex vivo quantitative and in vivo outgrowth assays in humanized mice did not reveal replication-competent virus. Low levels of immune activation and waning HIV-1-specific humoral and cellular immune responses indicated a lack of ongoing antigen production. Four years after analytical treatment interruption, the absence of a viral rebound and the lack of immunological correlates of HIV-1 antigen persistence are strong evidence for HIV-1 cure after CCR5Δ32/Δ32 HSCT. Human immunodeficiency virus type 1 (HIV-1) persists in the body during antiretroviral therapy (ART) in latently infected CD4+ T cells, but allogeneic hematopoietic stem cell transplantation (HSCT) has been shown to substantially reduce the viral reservoir1,2. However, some A full list of affiliations appears at the end of the paper. Nature Medicine of the reservoir-harboring immune cells are extremely long-lived3, partially resistant to chemotherapy regimens used during HSCT procedures and can cause viral rebound on analytical treatment interruption (ATI)4,5. Notably, both cases of successful HIV-1 cure published e-mail: ; Brief Communication so far—the ‘London patient’ (IciStem no. 36) and the ‘Berlin patient’— received a CCR5Δ32/Δ32 allograft6,7 conferring extended resistance to HIV-1 due to the absence of surface expression of the CCR5 coreceptor. In this study, we provide a detailed longitudinal virological and in-depth immunological analysis of the peripheral blood and tissue compartments of a 53-year-old male patient (IciStem no. 19)8, alive and in good health 117 months after CCR5Δ32/Δ32 allogeneic HSCT and 48 months after ATI. The patient was diagnosed to be HIV-1 clade B positive in January 2008 and presented with a CD4+ T cell count of 964 cells per μl and an HIV-1 plasma viral load of 12,850 copies per ml (Centers for Disease Control and Prevention A1, which was no indication for initiation of ART according to the national guidelines at that time). In October 2010, an ART regimen with tenofovir disoproxil fumarate (TDF), emtricitabine (FTC) and darunavir and ritonavir (DRV/r) was initiated (503 CD4+ T cells per μl and 35,303 HIV-1 copies per ml), resulting in a continuously suppressed plasma viral load (Fig. 1a). In January 2011, the patient was diagnosed with acute myeloid leukemia (AML) M2 according to the French–American–British classification, which carried an inversion of chromosome 16 at p13q22, resulting in the CBFB–MYH11 fusion protein. The patient achieved hematological complete remission after chemotherapy, which included idarubicin, cytarabine, etoposide induction therapy and three high-dose cytarabine (HiDAC) consolidation cycles. To avoid drug–drug interactions, DRV/r was switched to raltegravir in March 2011. In September 2012, the patient experienced an AML relapse but achieved a second complete remission after treatment with the A-HAM chemotherapy regimen (retinoic acid, HiDAC, mitoxantrone) and a second cycle of HiDAC. A systematic search identified a 10/10 HLA-matched (no mismatches in HLA-A, HLA-B, HLA-C, HLA-DR and HLA-DQ loci) unrelated female stem cell donor with a homozygous CCR5Δ32 mutation (Extended Data Table 1). After reduced-intensity conditioning with fludarabine, treosulfan and anti-thymocyte globulin, 8.74 × 106 unmodified CD34+ peripheral blood stem cells per kg of body weight were transplanted in February 2013. Immunosuppressive therapy consisted of cyclosporine and mycophenolate mofetil and was later changed to tacrolimus monotherapy. In June 2013, the patient experienced a second AML relapse. He achieved molecular oncological remission a third time after eight cycles with 5-azacytidine and four donor lymphocyte infusions (DLIs; 1 × 106, 10 × 106 and twice 50 × 106 donor T cells per kg of body weight). Thirty-four days after HSCT, full donor chimerism was established and retained except for a short period during the second relapse at months 3 and 4 after HSCT (Extended Data Fig. 1a). In 2014, elevated liver enzymes caused discussion about possible hepatic graft versus host disease (GvHD), but a liver biopsy in May 2015 was interpreted as drug-induced liver injury. In July 2014, the patient also experienced reactivation of cytomegalovirus (CMV) (duodenal ulcer) and herpes simplex virus 2 (genital ulcers and cerebral vasculitis) and human herpesvirus 8 and Epstein–Barr virus (viremia) but recovered after specific antiviral treatment of the CMV and herpes simplex virus 2 infections. After DLI, mild chronic GvHD of the eyes with bilateral keratoconjunctivitis sicca developed that persists until today. ART was continued throughout and proviral HIV-1 DNA and HIV-1 RNA remained undetectable despite intensified testing in clinical routine assays (Fig. 1a). However, multiple assessments of the HIV-1 viral reservoir in the peripheral blood and lymphoid and gut tissue before and after ATI revealed sporadic HIV-1 DNA traces at several time points, with a higher frequency compared to HIV-1-negative donors and no-template controls (Extended Data Table 2). Although rare, residual HIV-1 DNA and HIV-1 RNA were also detected by in situ hybridization (DNAscope and RNAscope assays) from histological sections of inguinal lymph node tissue from month 51 and some gut biop (...truncated)