Proteogenomic identification of Hepatitis B virus (HBV) genotype-specific HLA-I restricted peptides from HBV-positive patient liver tissues.

The presentation of virus-derived peptides by HLA class I molecules on the surface of an infected cell and the recognition of these HLA-peptide complexes by, and subsequent activation of, CD8+ cytotoxic T cells provides an important mechanism for immune protection against viruses. Recent advances in proteogenomics have allowed researchers to discover a growing number of unique HLA-restricted viral peptides, resulting in a rapidly expanding repertoire of targets for immunotherapeutics (i.e. bispecific antibodies, engineered T-cell receptors (TCRs), chimeric antigen receptor T-cells (CAR-Ts)) to infected tissues. However, genomic variability between viral strains, such as Hepatitis-B virus (HBV), in combination with differences in patient HLA alleles, make it difficult to develop therapeutics against these targets. To address this challenge, we developed a novel proteogenomics approach for generating patient-specific databases that enable the identification of viral peptides based on the viral transcriptomes sequenced from individual patient liver samples. We also utilized DNA sequencing of patient samples to identify HLA genotypes and assist in target selection. Liver samples from 48 HBV infected patients, primarily from Asia, were examined to reconstruct patient-specific HBV genomes, identify regions within the human chromosomes targeted by HBV integrations and obtain a comprehensive view of HBV peptide epitopes using our HLA class-I (HLA-I) immunopeptidomics discovery platform. Two previously reported HLA associated HBV-derived peptides, HLA-A02 binder FLLTRILTI (S194-202) from the large surface antigen and HLA-A11 binder STLPETTVVRR (C141-151) from the capsid protein were validated by our discovery platform, but both were detected at very low frequencies. In addition, we identified and validated, using heavy peptide analogues, novel strain-specific HBV-HLA associated peptides, such as GSLPQEHIVQK (P606-616) and variants. Overall, our novel approach can guide the development of bispecific antibody, TCR-T, or CAR-T based therapeutics for the treatment of HBV-related HCC and inform vaccine development.

Homozygous ALS-linked FUS P525L mutations cell- autonomously perturb transcriptome profile and chemoreceptor signaling in human iPSC microglia.

Amyotrophic lateral sclerosis is a fatal disease pathologically typified by motor and cortical neurodegeneration as well as microgliosis. The FUS P525L mutation is highly penetrant and causes ALS cases with earlier disease onset and more aggressive progression. To date, how P525L mutations may affect microglia during ALS pathogenesis had not been explored. In this study, we engineered isogenic control and P525L mutant FUS in independent human iPSC lines and differentiated them into microglia-like cells. We report that the P525L mutation causes FUS protein to mislocalize from the nucleus to cytoplasm. Homozygous P525L mutations perturb the transcriptome profile in which many differentially expressed genes are associated with microglial functions. Specifically, the dysregulation of several chemoreceptor genes leads to altered chemoreceptor-activated calcium signaling. However, other microglial functions such as phagocytosis and cytokine release are not significantly affected. Our study underscores the cell-autonomous effects of the ALS-linked FUS P525L mutation in a human microglia model.

The monoclonal antibody combination REGEN-COV protects against SARS-CoV-2 mutational escape in preclinical and human studies.

Monoclonal antibodies against SARS-CoV-2 are a clinically validated therapeutic option against COVID-19. Because rapidly emerging virus mutants are becoming the next major concern in the fight against the global pandemic, it is imperative that these therapeutic treatments provide coverage against circulating variants and do not contribute to development of treatment-induced emergent resistance. To this end, we investigated the sequence diversity of the spike protein and monitored emergence of virus variants in SARS-COV-2 isolates found in COVID-19 patients treated with the two-antibody combination REGEN-COV, as well as in preclinical in vitro studies using single, dual, or triple antibody combinations, and in hamster in vivo studies using REGEN-COV or single monoclonal antibody treatments. Our study demonstrates that the combination of non-competing antibodies in REGEN-COV provides protection against all current SARS-CoV-2 variants of concern/interest and also protects against emergence of new variants and their potential seeding into the population in a clinical setting.

Tibial Stems in Revision Total Knee Arthroplasty: Is There an Anatomic Conflict?

Tibial stems are frequently used in revision total knee arthroplasty (TKA). We investigated the effect of tibial stems on final component alignment and tray position. Thirty 3D reconstructed cadaveric tibial models were classified according to canal bow angle. After virtual implantation of 120 mm and 200 mm stemmed tibial components, deviation from native mechanical axis was measured. Tibial alignment valgus malposition of up to three degrees occurred and most pronounced with 120 mm stems. Canal alignment using 200 mm stems deviated tray position medially and posteriorly. Mild to moderate valgus bowing of the tibial canal is not uncommon (57% in our series) possibly leading to valgus malalignment. Anatomic conflict between the tibial mechanical axis and intramedullary canal can exist, with alignment and tray placement implications.

Changes in blood ion levels after removal of metal-on-metal hip replacements: 16 patients followed for 0-12 months.

BACKGROUND AND PURPOSE: In patients with metal-on-metal (MoM) hip prostheses, pain and joint effusions may be associated with elevated blood levels of cobalt and chromium ions. Since little is known about the kinetics of metal ion clearance from the body and the rate of resolution of elevated blood ion levels, we examined the time course of cobalt and chromium ion levels after revision of MoM hip replacements. PATIENTS AND METHODS: We included 16 patients (13 female) who underwent revision of a painful MoM hip (large diameter, modern bearing) without fracture or infection, and who had a minimum of 4 blood metal ion measurements over an average period of 6.1 (0-12) months after revision. RESULTS: Average blood ion concentrations at the time of revision were 22 ppb for chromium and 43 ppb for cobalt. The change in ion levels after revision surgery varied extensively between patients. In many cases, over the second and third months after revision surgery ion levels decreased to 50% of the values measured at revision. Decay of chromium levels occurred more slowly than decay of cobalt levels, with a 9% lag in return to normal levels. The rate of decay of both metals followed second-order (exponential) kinetics more closely than first-order (linear) kinetics. INTERPRETATION: The elimination of cobalt and chromium from the blood of patients who have undergone revision of painful MoM hip arthroplasties follows an exponential decay curve with a half-life of approximately 50 days. Elevated blood levels of cobalt and chromium ions can persist for at least 1 year after revision, especially in patients with high levels of exposure.