Biology subjects

Coelho, P.

Publications and source records attributed to Coelho, P..

6 recordsLinked to original sources

bioRxiv2026

The Single Cell Proteomic blueprint, navigating instrumentation platforms, software tools and high-load libraries in neutrophils, RKO and A549 cells

Mass spectrometry-based single cell proteomics (SCP) is rapidly emerging as a powerful approach for biological research, with applications extending beyond in-vitro cancer cell lines. Recent advances make it possible to apply SCP to ex-vivo human cells from tissues such as the brain and pancreas, as well as to technically challenging immune populations such as neutrophils. However, these analyses remain more challenging and typically result in reduced proteomic coverage. To support the development of robust workflows for SCP data acquisition and analysis, we systematically evaluated multiple DIA search engines, search engine settings, the inclusion of high-load library samples in single-cell search spaces, the impact of contaminants, and the quantitative properties of identified proteins. These comparisons were performed across two major instrumentation platforms, Orbitrap Astral and timsTOF SCP, and across A549, RKO cells and neutrophils, three cell types differing in size and protein content. Our work here provides guidelines on the software parameters to use for SCP, instrument specific results and cell dependent optimizations of high-load libraries, as well as novel evaluation of the quantitative properties of proteins for single cell and low input proteomics.

biochemistry↗

bioRxiv2025

Does ecological restoration align prokaryotic community structure with natural references across European coastal wetlands?

AbstractCoastal wetlands are crucial for biodiversity and act as critical buffers for carbon sequestration and atmospheric greenhouse gases (GHG) concentrations, yet their degradation often turns them into GHG sources. Restoration is widely implemented to recover these services, but it remains unclear whether interventions successfully reestablish the microbial functional diversity underpinning biogeochemical cycles. We tested the hypothesis that restoration aligns prokaryotic community structure with natural references, analyzing, a European gradient of coastal wetlands, comparing well-preserved, altered, and restored sites in water and sediment. Using 16SrRNA-metabarcoding and IndVal-Analysis, we characterized community assembly identifying diagnostic functional consortia. Results revealed a marked difference in water and sediment recovery after restoration. Bacterioplankton communities rapidly converge to natural references, while sediment microbiome displayed significant "ecological memory". Restored wetlands show sediment communities structurally distinct from well-preserved, retaining alteration-associated guilds decades. Results support the initial hypothesis: restoration processes in coastal wetlands can re-establish communities and metabolisms resembling well-preserved conditions in the water in the short term, while sediments retain microbial communities and metabolisms inherited from altered conditions for a long time. Future strategies must integrate active sediment interventions using molecular bioindicators to validate not only the landscape appearance, but the effective reactivation of ecosystem processes and microbiota-related services.

ecology↗

bioRxiv2025

Single cell proteomic analysis defines discrete neutrophil functional states in human glioblastoma

Neutrophils are vital innate immune cells shown to infiltrate glioblastomas, however we currently lack the molecular understanding of their functional states within the tumour niche. Given that neutrophils are known to display a prominent discordance between mRNA and protein abundance, we developed ultra-sensitive mini-bulk and single cell proteomic (SCP) workflows to study the heterogeneity of peripheral blood and tumour associated neutrophils (TAN) from patients with glioblastoma. Mini-bulk analysis enabled a deeper protein coverage of circulating immature, mature and TAN populations, defining signatures of maturity and demonstrating that TANs resemble mature circulating neutrophils. Analysis of the SCP data resulted in the detection of >1,100 proteins from a single TAN providing a detailed characterization of neutrophil subsets in glioblastoma. Our approach shows evidence of pathogenic and anti-tumorigenic clusters and discovers cell states invisible to scRNAseq, opening new opportunities to selectively target pro-tumoural neutrophil states.

immunology↗

bioRxiv2024

Rapid evolution of Klebsiella pneumoniae biofilms in vitro delineates adaptive changes selected during infection

Biofilm formation facilitates infection by the opportunistic pathogen Klebsiella pneumoniae, primarily through indwelling medical devices. Here, we address how K. pneumoniae can increase its biofilm capacity by experimental evolution of surface-attached biofilms to mimic catheter-associated infections. We observed rapid convergent evolution that altered or abolished capsule, modified the fimbrial adhesin MrkD, or increased production of fimbriae and cellulose via upregulated c-di-GMP-dependent pathways. However, evolutionary trajectories and resulting phenotypes showed strain differences, illustrating the importance of genetic background on biofilm adaptation. Multiple biofilm aspects, such as early attachment, biofilm topology, surface preference, and extracellular matrix composition, were affected in a mutation-specific manner. Acute virulence was linked to the underlying genetic change rather than the overall biofilm capacity. Single mutations conferring hypermucoidy and c-di-GMP-related changes extensively overlapped with previously identified adaptive changes in UTI and wound isolates, confirming biofilm as an important selective trait in vivo.

microbiology↗

bioRxiv2023

A Machine Learning One-Class Logistic Regression Model to Predict Stemness in Single Cell Transcriptomics and Spatial Omics Datasets

Cell annotation is a crucial methodological component to interpreting single cell and spatial omics data. These approaches are often biased and manually curated. Here we harness an existing stemness model for assessing oncogenic states to transform its application to single cell and spatial omic datasets. This one-class logistic regression machine learning algorithm is used to extract transcriptomic or proteomic features from non-transformed stem cells to identify dedifferentiated cell states. We found this method identifies single cell states in metastatic tumor cell populations without the requirement of cell annotation. Finally these stemness indices are applicable across a variety of spatial transcriptomic and proteomic technologies for the identification of oncogenic cell types in the tumor microenvironment. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=162 SRC="FIGDIR/small/539461v1_ufig1.gif" ALT="Figure 1"> View larger version (37K): org.highwire.dtl.DTLVardef@f2973forg.highwire.dtl.DTLVardef@a7aa9corg.highwire.dtl.DTLVardef@1b1ea27org.highwire.dtl.DTLVardef@183b4a5_HPS_FORMAT_FIGEXP M_FIG C_FIG

genomics↗

bioRxiv2022

Hypoxia shapes the immune landscape in lung injury promoting inflammation persistence

Acute Respiratory Distress Syndrome (ARDS), an often-fatal complication of pulmonary or systemic inflammation, has no cure. Hypoxemia is a defining feature, yet its impact on inflammation is often neglected. Patients with ARDS are monocytopenic early in the onset of the disease. Endotoxin or Streptococcus pneumoniae acute lung injury (ALI) in the context of hypoxia replicates this finding, through hypoxia-driven suppression of type I interferon signalling. This results in failed lung monocyte-derived interstitial macrophages (IM) niche expansion and unchecked neutrophilic inflammation. Administration of colony stimulating factor 1 (CSF1) rescues the monocytopenia, alters the circulating classical monocyte phenotype in hypoxic endotoxin-driven ALI and enables lung IM population expansion, thus limiting lung injury in endotoxin- and virally-induced hypoxic ALI. Hypoxia directly alters immune dynamics to the detriment of the host and manipulation of this aberrant response offers new therapeutic strategies for ARDS.

cell biology↗