Whole blood RNA signatures in leprosy patients identify reversal reactions before clinical onset: a prospective, multicenter study
SCIENTIFIC REPORTS
Authors: Tio-Coma, Maria; van Hooij, Anouk; Bobosha, Kidist; van der Ploeg-van Schip, Jolien J.; Banu, Sayera; Khadge, Saraswoti; Thapa, Pratibha; Kunwar, Chhatra B.; Goulart, Isabela M.; Bekele, Yonas; Hagge, Deanna A.; Moraes, Milton O.; Teles, Rosane M. B.; Pinheiro, Roberta Olmo; van Zwet, Erik W.; Goeman, Jelle J.; Aseffa, Abraham; Haks, Marielle C.; Ottenhoff, Tom H. M.; Modlin, Robert L.; Geluk, Annemieke
Abstract
Early diagnosis of leprosy is challenging, particularly its inflammatory reactions, the major cause of irreversible neuropathy in leprosy. Current diagnostics cannot identify which patients are at risk of developing reactions. This study assessed blood RNA expression levels as potential biomarkers for leprosy. Prospective cohorts of newly diagnosed leprosy patients, including reactions, and healthy controls were recruited in Bangladesh, Brazil, Ethiopia and Nepal. RNA expression in 1,090 whole blood samples was determined for 103 target genes for innate and adaptive immune profiling by dual color Reverse-Transcription Multiplex Ligation-dependent Probe Amplification (dcRT-MLPA) followed by cluster analysis. We identified transcriptomic biomarkers associated with leprosy disease, different leprosy phenotypes as well as high exposure to Mycobacterium leprae which respectively allow improved diagnosis and classification of leprosy patients and detection of infection. Importantly, a transcriptomic signature of risk for reversal reactions consisting of five genes (CCL2, CD8A, IL2, IL15 and MARCO) was identified based on cross-sectional comparison of RNA expression. In addition, intra-individual longitudinal analyses of leprosy patients before, during and after treatment of reversal reactions, indicated that several IFN-induced genes increased significantly at onset of reaction whereas IL15 decreased. This multi-site study, situated in four leprosy endemic areas, demonstrates the potential of host transcriptomic biomarkers as correlates of risk for leprosy. Importantly, a prospective five-gene signature for reversal reactions could predict reversal reactions at least 2 weeks before onset. Thus, transcriptomic biomarkers provide promise for early detection of these acute inflammatory episodes and thereby help prevent permanent neuropathy and disability in leprosy patients.
Efficient Tumor Clearance and Diversified Immunity through Neoepitope Vaccines and Combinatorial Immunotherapy
CANCER IMMUNOLOGY RESEARCH
Authors: Lee, Karin L.; Benz, Stephen C.; Hicks, Kristin C.; Nguyen, Andrew; Gameiro, Sofia R.; Palena, Claudia; Sanborn, John Z.; Su, Zhen; Ordentlich, Peter; Rohlin, Lars; Lee, John H.; Rabizadeh, Shahrooz; Soon-Shiong, Patrick; Niazi, Kayvan; Schlom, Jeffrey; Hamilton, Duane H.
Abstract
Progressive tumor growth is associated with deficits in the immunity generated against tumor antigens. Vaccines targeting tumor neoepitopes have the potential to address qualitative defects; however, additional mechanisms of immune failure may underlie tumor progression. In such cases, patients would benefit from additional immune-oncology agents targeting potential mechanisms of immune failure. This study explores the identification of neoepitopes in the MC38 colon carcinoma model by comparison of tumor to normal DNA and tumor RNA sequencing technology, as well as neoepitope delivery by both peptide-and adenovirus-based vaccination strategies. To improve antitumor efficacies, we combined the vaccine with a group of rationally selected immune-oncology agents. We utilized an IL15 superagonist to enhance the development of antigen-specific immunity initiated by the neoepitope vaccine, PD-L1 blockade to reduce tumor immunosuppression, and a tumor-targeted IL12 molecule to facilitate T-cell function within the tumor microenvironment. Analysis of tumor-infiltrating leukocytes demonstrated this multifaceted treatment regimen was required to promote the influx of CD8(+) T cells and enhance the expression of transcripts relating to T-cell activation/ effector function. Tumor-targeted IL12 resulted in a marked increase in clonality of T-cell repertoire infiltrating the tumor, which when sculpted with the addition of either a peptide or adenoviral neoepitope vaccine promoted efficient tumor clearance. In addition, the neoepitope vaccine induced the spread of immunity to neoepitopes expressed by the tumor but not contained within the vaccine. These results demonstrate the importance of combining neoepitope- targeting vaccines with a multifaceted treatment regimen to generate effective antitumor immunity.