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A shot to missing protein from an aneuploidy cell line

ABSTRACT: With fast development of proteomic technology, the scale of missing proteins (MPs) has being continuously shrunk, approximately 1,470 MPs not explored yet. Discovery of MPs, on the other hand, is appearing more difficult. In some aneuploid cells, the abundance changes are proportional to the additional chromosome(s), while several MPs were found within them. Herein, we hypothesize that a stable aneuploid cell line with the increased chromosomes was a useful material that assists MP exploration. Ker-CT cell line with trisomy at chromosome 5 and 20 was selected. With a combination strategy of RNA-Seq and LC-M/MS, a total of 22,178 transcripts and 8,846 proteins were identified in Ker-CT. Although the transcripts corresponding to 31 and 32 MP genes located at chromosome 5 and 20 were detected, none of MPs was found in Ker-CT. Surprisingly, 3 MPs containing at least two unique non-nest peptides of length ≥9 amino acid were identified in Ker-CT, whose genes are located in chromosome 3 and 10. Furthermore, the 3 MPs were verified using the method of parallel reaction monitoring (PRM).

INSTRUMENT(S): Q Exactive HF

ORGANISM(S): Homo Sapiens (human)

TISSUE(S): Cell Culture

SUBMITTER: Bu fanyu

LAB HEAD: Liu Si Qi

PROVIDER: PXD028647 | Pride | 2021-11-25

REPOSITORIES: Pride

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Project description:Tissue macrophages (MPs) develop distinctive functions due to unique transcriptional programs driven by local environmental ques. In the intestine, it is known that MPs are heterogeneous cells that differentiate from blood monocytes and embryonic precursors, and are essential for homeostasis with the vast microbiome through their ability to kill invading microbes, clear apoptotic cells, and produce regulatory cytokines. However, the full extent of MP heterogeneity, their developmental relationships, and how the intestinal microbiota affects MP generation is not known. Here, we performed single cell RNA sequencing of colonic myeloid cells from specific pathogen free (SPF) and germ free (GF) C57BL/6 mice and found extensive heterogeneity of colon MP, with at least six different identifiable populations, with less heterogeneity of dendritic cells (DCs). Unsupervised modeling of developmental pathways combined with inference of gene regulatory networks suggested two major trajectories from common CCR2+ precursors resulting in CD11c+CD9+MMRintCD121b+ and CD11c-CD9intMMRhiCD121b- MP populations with unique transcription factors activities to coordinate downstream target molecules. The generation of both mature populations of colon MPs was impaired in germ-free mice, which coincided with the appearance of a dominant unique population of MPs, whereas the generation of DC populations in GF mice were unaffected or increased. Furthermore, the two major MP populations were clearly distinct from other populations regarding their gene expression profile, localization within the lamina propria, and ability to phagocytose macromolecules from the blood. These data uncover the diversity of intestinal myeloid cell populations, highlight the importance of microbiota on the unique developmental as well as anatomical and functional fates of colon MPs. We anticipate that these findings will form the basis for future studies on how tissue myeloid cell development is influenced either directly or indirectly by signals from endogenous microbiota in the intestine, as well as other tissues.

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A shot to missing protein from an aneuploidy cell line

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