Automated single-cell proteomics providing sufficient proteome depth to study complex biology beyond cell type classifications.

The recent technological and computational advances in mass spectrometry-based single-cell proteomics have pushed the boundaries of sensitivity and throughput. However, reproducible quantification of thousands of proteins within a single cell remains challenging. To address some of those limitations, we present a dedicated sample preparation chip, the proteoCHIP EVO 96 that directly interfaces with the Evosep One. This, in combination with the Bruker timsTOF demonstrates double the identifications without manual sample handling and the newest generation timsTOF Ultra identifies up to 4000 with an average of 3500 protein groups per single HEK-293T without a carrier or match-between runs. Our workflow spans 4 orders of magnitude, identifies over 50 E3 ubiquitin-protein ligases, and profiles key regulatory proteins upon small molecule stimulation. This study demonstrates that the proteoCHIP EVO 96-based sample preparation with the timsTOF Ultra provides sufficient proteome depth to study complex biology beyond cell-type classifications.

Impact of Combinatorial Histone Modifications on Acetyllysine Recognition by the ATAD2 and ATAD2B Bromodomains.

The ATPase family AAA+ domain containing 2 (ATAD2) protein and its paralog ATAD2B have a C-terminal bromodomain (BRD) that functions as a reader of acetylated lysine residues on histone proteins. Using a structure-function approach, we investigated the ability of the ATAD2/B BRDs to select acetylated lysine among multiple histone post-translational modifications. The ATAD2B BRD can bind acetylated histone ligands that also contain adjacent methylation or phosphorylation marks, while the presence of these modifications significantly weakened the acetyllysine binding activity of the ATAD2 BRD. Our structural studies provide mechanistic insights into how ATAD2/B BRD-binding pocket residues coordinate the acetyllysine group in the context of adjacent post-translational modifications. Furthermore, we investigated how sequence changes in amino acids of the histone ligands impact the recognition of an adjacent acetyllysine residue. Our study highlights how the interplay between multiple combinations of histone modifications influences the reader activity of the ATAD2/B BRDs, resulting in distinct binding modes.

Nonoperative treatment for anterior cruciate ligament injury in recreational alpine skiers.

PURPOSE: The purpose of this study was to test whether low-grade Lachman test (i.e. Grade 0-1+) and a negative pivot shift at 6-12 weeks post-ACL rupture in recreational alpine skiers can be used to predict good function and normal knee laxity in nonoperated patients at minimum 2 years after the injury. METHODS: Office registry was used to identify 63 recreational alpine skiers treated by the senior author within 6 weeks of a first-time ACL injury between 2003 and 2008. Of these, 34 had early ACL reconstruction but 29 patients were observed and re-evaluated. Office charts and MRI were reviewed. Inclusion criteria for this study were as follows: ACL rupture documented on MRI after the injury, and minimum 2-year follow-up. Exclusion criterion was contralateral knee ligament injury. Of the 29 patients treated nonoperatively, 17 had low-grade Lachman and negative pivot shift tests within 6-12 weeks after the injury and were recommended to continue follow-up without surgery. Of these 17 patients, 6 were lost to follow up, but 11 patients were recalled and evaluated at more than 2 years after the injury. They completed Marx and Tegner activity level and IKDC subjective scores, physical examination of the knee and KT-1000 anterior laxity assessment. RESULTS: Median age at injury was 43 years (range 29-58). Median follow-up was 42 months (range 30-68). Mean IKDC subjective score at latest follow-up was 91.6 ± 6.7. Median Tegner score was 6 (range 6-9) before the injury and 6 (range 4-6) at latest follow-up (p = n.s). Median Marx score was 6 (range 0-16) before the injury and 4 (range 0-12) at latest follow-up (p = 0.03). Ten patients had Lachman Grade 0-1+, and one had Lachman Grade 2+ at latest follow-up. KT-1000 showed mean side-to-side difference of 0.8 ± 1.6 mm, and less than 3 mm difference in the 10 patients with Lachman Grade 0-1+. CONCLUSION: Recreational alpine skiers who sustain ACL injury should be re-evaluated at 6-12 weeks after the injury rather than being operated acutely. If they have negative Lachman and pivot shift tests at that point, they can be treated without surgery since good outcome and normal knee anterior laxity at more than 2 years after the injury is expected. LEVEL OF EVIDENCE: Case series, Level IV.