4 research outputs found
N‑Glycoprotein Analysis Discovers New Up-Regulated Glycoproteins in Colorectal Cancer Tissue
Colorectal
cancer is one of the leading causes of death due to
cancer worldwide. Therefore, the identification of high-specificity
and -sensitivity biomarkers for the early detection of colorectal
cancer is urgently needed. Post-translational modifications, such
as glycosylation, are known to play an important role in cancer progression.
In the present work, we used a quantitative proteomic technique based
on <sup>18</sup>O stable isotope labeling to identify differentially
expressed N-linked glycoproteins in colorectal cancer tissue samples
compared with healthy colorectal tissue from 19 patients undergoing
colorectal cancer surgery. We identified 54 up-regulated glycoproteins
in colorectal cancer samples, therefore potentially involved in the
biological processes of tumorigenesis. In particular, nine of these
(PLOD2, DPEP1, SE1L1, CD82, PAR1, PLOD3, S12A2, LAMP3, OLFM4) were
found to be up-regulated in the great majority of the cohort, and,
interestingly, the association with colorectal cancer of four (PLOD2,
S12A2, PLOD3, CD82) has not been hitherto described
Proteome Speciation by Mass Spectrometry: Characterization of Composite Protein Mixtures in Milk Replacers
The ability of tandem
mass spectrometry to determine the primary
structure of proteolytic peptides can be exploited to trace back the
organisms from which the corresponding proteins were extracted. This
information can be important when food products, such as protein powders,
can be supplemented with lower-quality starting materials. In order
to dissect the origin of proteinaceous material composing a given
unknown mixture, a two-step database search strategy for bottom-up
nanoscale liquid chromatography–tandem mass spectrometry (nanoLC–MS/MS)
data was implemented. A single nanoLC–MS/MS analysis was sufficient
not only to determine the qualitative composition of the mixtures
under examination, but also to assess the relative percent composition
of the various proteomes, if dedicated calibration curves were previously
generated. The approach of two-step database search for qualitative
analysis and proteome total ion current (pTIC) calculation for quantitative
analysis was applied to several binary and ternary mixtures which
mimic the composition of milk replacers typically used in calf feeding
Ionizing radiation drives key regulators of antigen presentation and a global expansion of the immunopeptidome
Little is known about the pathways regulating MHC antigen presentation and the identity of treatment-specific T cell antigens induced by ionizing radiation. For this reason, we investigated the radiation-specific changes in the colorectal tumor cell proteome. We found an increase in DDX58 and ZBP1 protein expression, two nucleic acid sensing molecules likely involved in induction of the dominant interferon response signature observed after genotoxic insult. We further observed treatment-induced changes in key regulators and effector proteins of the antigen processing and presentation machinery. Differential regulation of MHC allele expression was further driving the presentation of a significantly broader MHC-associated peptidome postirradiation, defining a radiation-specific peptide repertoire. Interestingly, treatment-induced peptides originated predominantly from proteins involved in catecholamine synthesis and metabolic pathways. A nuanced relationship between protein expression and antigen presentation was observed where radiation-induced changes in proteins do not correlate with increased presentation of associated peptides. Finally, we detected an increase in the presentation of a tumor-specific neoantigen derived from Mtch1. This study provides new insights into how radiation enhances antigen processing and presentation that could be suitable for the development of combinatorial therapies. Data are available via ProteomeXchange with identifier PXD032003.</p
Differential Cell Adhesion on Mesoporous Silicon Substrates
Porous silicon (PSi) is a promising material in several
biomedical
applications because of its biocompatibility and biodegradability.
Despite the plethora of studies focusing on the interaction of cells
with micrometer and submicro geometrical features, limited information
is available on the response of cells to substrates with a quasi-regular
distribution of nanoscopic pores. Here, the behavior of four different
cell types is analyzed on two mesoporous (MeP) silicon substrates,
with an average pore size of ∼5 (MeP1) and ∼20 nm (MeP2),
respectively. On both MeP substrates, cells are observed to spread
and adhere in a larger number as compared to flat silicon wafers.
At all considered time points, the surface density of the adhering
cells <i>n</i><sub>d</sub> is larger on the PSi substrate
with the smaller average pore size (MeP1). At 60 h, <i>n</i><sub>d</sub> is from ∼1.5 to 5 times larger on MeP1 than on
MeP2 substrates, depending on the cell type. The higher rates of proliferation
are observed for the two neuronal cell types, the mouse neuroblastoma
cells (N2A) and the immortalized human cortical neuronal cells (HCN1A).
It is speculated that the higher adhesion on MeP1 could be attributed
to a preferential matching of the substrate topography with the recently
observed multiscale molecular architecture of focal adhesions. These
results have implications in the rational development of PSi substrates
for supporting cell adhesion and controlling drug release in implants
and scaffolds for tissue engineering applications