Longitudinal Large-Scale Semiquantitative Proteomic Data Stability Across Multiple Instrument Platforms.

With the rapid developments in mass spectrometry (MS)-based proteomics methods, label-free semiquantitative proteomics has become an increasingly popular tool for profiling global protein abundances in an unbiased manner. However, the reproducibility of these data across time and LC-MS platforms is not well characterized. Here, we evaluate the performance of three LC-MS platforms (Orbitrap Elite, Q Exactive HF, and Orbitrap Fusion) in label-free semiquantitative analysis of cell surface proteins over a six-year period. Sucrose gradient ultracentrifugation was used for surfaceome enrichment, following gel separation for in-depth protein identification. With our established workflow, we consistently detected and reproducibly quantified >2300 putative cell surface proteins in a human acute myeloid leukemia (AML) cell line on all three platforms. To our knowledge this is the first study reporting highly reproducible semiquantitative proteomic data collection of biological replicates across multiple years and LC-MS platforms. These data provide experimental justification for semiquantitative proteomic study designs that are executed over multiyear time intervals and on different platforms. Multiyear and multiplatform experimental designs will likely enable larger scale proteomic studies and facilitate longitudinal proteomic studies by investigators lacking access to high throughput MS facilities. Data are available via ProteomeXchange with identifier PXD022721.

Biochemical and functional characterization of mutant KRAS epitopes validates this oncoprotein for immunological targeting.

Activating RAS missense mutations are among the most prevalent genomic alterations observed in human cancers and drive oncogenesis in the three most lethal tumor types. Emerging evidence suggests mutant KRAS (mKRAS) may be targeted immunologically, but mKRAS epitopes remain poorly defined. Here we employ a multi-omics approach to characterize HLA class I-restricted mKRAS epitopes. We provide proteomic evidence of mKRAS epitope processing and presentation by high prevalence HLA class I alleles. Select epitopes are immunogenic enabling mKRAS-specific TCRαß isolation. TCR transfer to primary CD8+ T cells confers cytotoxicity against mKRAS tumor cell lines independent of histologic origin, and the kinetics of lytic activity correlates with mKRAS peptide-HLA class I complex abundance. Adoptive transfer of mKRAS-TCR engineered CD8+ T cells leads to tumor eradication in a xenograft model of metastatic lung cancer. This study validates mKRAS peptides as bona fide epitopes facilitating the development of immune therapies targeting this oncoprotein.

Outcomes following surgical versus endovascular treatment of spinal dural arteriovenous fistula: a systematic review and meta-analysis.

Although surgical resection is associated with a complete cure in most cases of spinal dural arteriovenous fistulas (SDAVF), there has been an increasing trend towards embolisation. We performed a systematic review and meta-analysis comparing surgical resection with endovascular treatment in terms of success of treatment, rate of recurrence and complications. A literature search was conducted using Preferred Reporting Items for Systematic Reviews and Meta-Analyses guidelines. Strength of evidence was assessed using the Grading of Recommendations Assessment, Development and Evaluation Working Group system. Surgical outcomes such as initial treatment failure, late recurrence, neurological improvement and complications were compared between the two approaches. We included 57 studies with 2029 patients, of which 32 studies with 1341 patients directly compared surgery (n=590) and embolisation (n=751). Surgery was found to be associated with significantly lower odds of initial treatment failure (OR: 0.15, 95% CI 0.09 to 0.24, I2 0%, p<0.001) and late recurrence (OR 0.18, 95% CI 0.09 to 0.39, I2 0%, p<0.001). The odds of neurological improvement following surgery were also significantly higher compared with embolisation alone (OR: 2.73, CI:1.67 to 4.48, I2 :49.5%, p<0.001). No difference in complication rates was observed between the two approaches (OR 1.78, 95% CI 0.97 to 3.26, I2 0%, p=0.063). Onyx was associated with significantly higher odds of initial failure/late recurrence as compared with n-butyl 2-cyanoacrylate (OR: 3.87, CI: 1.73 to 8.68, I2 :0%, p<0.001). Surgery may be associated with superior outcomes for SDAVFs in comparison to endovascular occlusion. Newer embolisation agents like Onyx have not conferred a significant improvement in occlusion rate.