Yu, G. Y. | bioRxiv Science

bioRxiv2022

Increasing the sensitivity, recovery, and integrality of spatially resolved proteomics by LCM-MTA

Conventional proteomic approaches neglect tissue heterogeneity and spatial localization information. Laser capture microdissection (LCM) can isolate specific cell populations or histological areas from heterogeneous tissue specimens while preserving spatial localization information. Formalin-fixed paraffin-embedded (FFPE) is currently a standardized method for long-term stable preservation of clinical tissue specimens. However, spatially resolved proteomics (SRP) studies of FFPE tissues by combined LCM and mass spectrometry (MS)-based proteomics face challenges, such as formalin-induced protein crosslinking limits protein extraction and digestion, protein loss during sample preparation, and the detectability of MS for trace tissues. Therefore, it is necessary to specifically develop SRP sample preparation methods and MS methods suitable for trace FFPE tissues. Here, we provide an SRP method suitable for trace FFPE tissues produced by LCM, termed LCM-Magnetic Trace Analysis (LCM-MTA), which can significantly increase the sensitivity, recovery, and integrality of SRP. The starting material has been reduced to about 15 cells, which resolution is comparable to existing spatially resolved transcriptome (SRT). We also apply our LCM-MTA into SRP studies on clinical colorectal cancer (CRC) tissues and accurately distinguish the functional differences of different cell types. In conclusion, LCM-MTA is a convenient, universal, and scalable method for SRP of trace FFPE tissues, which can be widely used in clinical and non-clinical research fields.

systems biology↗

bioRxiv2019

Cannibalism as a feeding strategy for mantis shrimp Oratosquilla oratoria (De Haan, 1844) in the Tianjin coastal zone of Bohai Bay

A representative semi-enclosed bay of China, Bohai Bay has experienced severe interference in recent decades and is under threat from rapid human development. Although the mantis shrimp Oratosquilla oratoria plays an important role in the ecosystem and fishery, its feeding ecology and the impact of habitat changes on its feeding habits are poorly known. In this study, we sought to identify the prey consumed by O. oratoria through the separation of stomach contents and to describe its trophic ecology during maturation, from March to July, in the Tianjin coastal zone of Bohai Bay. A total of 594 specimens were collected and 347 (58.59%) stomachs were found to have food remains. More than half of the O. oratoria individuals had poor feeding activity, and the degree of feeding activity of females was higher than that of males, but there was no significant difference in the visual fullness index and the fullness weight index (FWI) between sexes for each month. And the feeding activities of O. oratoria were consistent over the study months. A total of 207 prey items yielded 231 readable sequences and 24 different taxa were identified. Prey detected in O. oratoria consisted mainly of crustaceans, which accounted for 71.86 % of the clones detected; 16.02% corresponded to fishes, 8.23% corresponded to mollusks and the remaining 3.90% corresponded to other marine organisms. Cannibalism (occured frequently, 69.08%) in this study was noticeably higher than that seen in previous studies and confirmed that cannibalism may be a significant feeding strategy in the mantis shrimp O. oratoria in the Tianjin coastal zone of Bohai Bay. The ecological environment in Bohai Bay has been affected by anthropogenic activities and the macrofaunal biodiversity and abundance have noticeably declined, which might make the food scarce for the mantis shrimp O. oratoria. Then, the starvation obviously increased cannibalistic tendencies.

molecular biology↗