Dr Niklas Gebauer is a Novogene customer who recently published a study in Blood Advances entitled “Integrative genomic and transcriptomic analysis of PBL identifies disruption of key regulatory pathways”, a paper that uncovered a number of novel mutations involved in the oncogenesis of plasmablastic lymphoma (PBL). We recently spoke with Niklas to gain some insight into the process of the research, its goal, and any future plans his team currently have for the findings of the present study.
Niklas studied medicine at the University of Lübeck while completing his doctoral thesis in pathology in parallel to his studies. His original plan was to focus his medical expertise on haematological diseases as he had always wanted to be an oncologist, but thanks to a mentor at Lübeck who went above and beyond and always taught him more than was necessary, he changed his focus to molecular pathology. After a year in the lab however, Niklas began to miss treating and interacting with patients. This sent him back to the clinic for internal rotations and he ultimately ended up back at his original goal of haematology and oncology.
During his time in the pathology lab, he spent a lot of time analysing the molecular underpinnings of aggressive lymphomas, as the University Medical Centre Schleswig-Holstein in Lübeck has a large reference centre of lymphomas for clinical trials, where a lot of rare subtypes can be found. One such lymphoma is PBL, a subtype of aggressive B-cell non-Hodgkin lymphoma. It is extremely difficult to treat, as most sufferers are immunosuppressed, either due to old age, organ transplantation, or HIV infection. In a very successful attempt at keeping cooperation between the clinic and the lab alive, Niklas set up a study involving analysis of samples from the archive of the reference centre for haematopathology at Lübeck.
In their recent publication, Niklas and his team chose 70 patient samples from the biobank registry, with 40 of those used for molecular studies and 33 used for genetic sequencing after quality control. Although a small patient cohort, this was still a very large sample size for such a rare phenomenon. Studies are underway by other research groups in Germany and the US with larger patient cohorts, and efforts are currently being made to consolidate and integrate all data sets available on PBL for a comprehensive view of the disease.
The study identified key mutational drivers involved in the oncogenesis of PBL in both HIV positive and HIV negative patients. Previous studies had done similar, but by using whole exome sequencing (WES) and other very targeted sequencing strategies. This paper was the first to report on the mutational landscape and transcriptional profile of PBL on a global scale. This wider approach also highlighted the difference in oncogenesis pathways between HIV+ and HIV- patients, but the similarity in ultimate disease progression and prognosis, contrary to previous studies. This discovery was also enabled by the access to the reference centre archive, which held samples from HIV- PBL patients that were referred to the centre for confirmation, because, as rare as PBL is, it is even rarer in patients without a HIV infection.
DNA sequencing data uncovered this difference in oncogenesis route to be due to activating mutations of oncogenes such as STAT3 in HIV+ patients, and mutational inactivation of tumour suppressor genes such as p53 in HIV- patients. Also found in HIV- patients, but in 2 cases only, was an NTRK mutation. Recently FDA-approved NTRK inhibitors are only permitted as treatment when an NTRK fusion gene is present, which was not found in this study, however it has recently been shown that the NTRK mutation found in this study results in the same signalling alteration as an NTRK fusion gene. With this mutation found in only 2 cases, there is currently limited evidence for this specific variant, and even with a deleterious CAT score, there remains a lack of functional evidence that these drugs could be used to treat PBL in these patients. Many potential therapeutic targets were identified in the study, such as the general accumulation of IL-6/JAK/STAT activation, however functional analysis is needed before any extrapolations can be made.
Other alterations found were involved in the nuclear factor kB (NFkB) signalling pathway. The mutations found were not those to be expected based on a diffuse B-cell lymphoma (DCBL) background, but a combination of mutations in the pathway itself and its interactome. These observations still require functional analysis for confirmation. Many of the alterations to the NFkB pathway were epigenetic changes. Niklas and his team are currently gaining experience in Reduced Representation Bisulfite Sequencing (RRBS) in the context of another disease, and pending the outcome of those experiments, may return to examine the epigenetic landscape of PBL in the future.
Another shortfall of previous studies was that they were influenced by looking for mutations expected in other types of B-cell lymphoma (BCL), but by taking this wider approach without bias, Niklas and his team were able to identify the expected mutational overlaps of PBL with other BCLs, but, in case of activating RAS mutations, also with multiple myeloma (MM), suggesting that the mutational landscape of PBL falls somewhere between these two entities. This hypothesis, previously supported by the morphological and immunohistochemical profile of PBL and its similarities with both MM and DLBCL, has already been applied to current treatment strategies for PBL, with the use of agents like Bortezimib and lenalidomide in the clinic and preliminary investigations of combined treatment approaches have yielded encouraging results. Bortezomib is a proteasome inhibitor while lenalidomide primarily works as a modulator of the immune system. Both agents have been approved for the treatment of MM, either in combination with each other and dexamethasone or combined with a chemotherapeutic backbone. Current approaches in PBL pair bortezomib and lenalidomide with a DLBCL-type chemotherapy (CHO(E)P) that has been used to treat aggressive lymphomas for over 40 years. DNA sequencing did, however, uncover an additional variety of druggable vulnerabilities in PBL, that may further complement the therapeutic landscape for this rare and aggressive disease in the future. PBL currently only has one HIV+ cell line for research purposes, however Niklas and his team are working with a HIV- patient to try and establish a HIV- cell line.
Novogene were delighted to offer our services to this extremely worthwhile research. “The turnaround time was excellent, much faster than expected, and the data quality was really high, especially given the low quality of the extracted material you had to deal with” said Niklas when we interviewed him about this recent paper. The data produced was passed back to Lübeck to their bioinformatics pipeline designed by the Systems Biology Department.
This project was a really excellent example of industry-clinical collaboration and Niklas and his team were a pleasure to work with. Novogene would like to wish them the best of luck with all their future endeavours and hope to be involved in many more exciting projects to come!
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