Biology subjects

Paes Leme, A.

Publications and source records attributed to Paes Leme, A..

4 recordsLinked to original sources

bioRxiv2026

Single-cell proteomics maps circulating monocyte dynamics in advanced head and neck squamous cell carcinoma

It remains unclear whether metastatic progression in head and neck squamous cell carcinoma (HNSCC) is accompanied by functional remodeling of circulating immune cells at the proteome level. To address this question, we applied single-cell proteomics (SCP) to cryopreserved peripheral blood mononuclear cells (PBMCs) from three patients with HNSCC representing distinct stages of metastatic progression and two healthy donors. Proteomic analysis of 619 individual PBMCs resolved major immune cell populations, with up to 1,638 proteins quantified per cell. Trajectory inference, clustering, and differential abundance analyses revealed proteomic remodeling associated with disease progression, with the most pronounced changes occurring within a monocyte cluster composed exclusively of cells from patients with nodal metastasis. This population showed increased abundance of interferon-related proteins, HLA molecules, and myeloid immunoregulatory signatures, consistent with an activated, interferon-associated monocyte state. In parallel, lymphocytes showed reduced coordinated abundance of proteins associated with activation, cytotoxicity, and degranulation, consistent with altered cytotoxic effector programs across disease stages. Overall, these findings reveal distinct proteomic states in circulating monocytes and lymphocytes associated with HNSCC progression and identify selective remodeling of the monocyte compartment in nodal metastatic disease.

cancer biology↗

bioRxiv2025

Single-cell proteomics workflow for characterizing heterogeneous cell populations in saliva and tear fluid

Single-cell proteomics (SCP) has advanced considerably but still is largely limited to homogeneous populations and distant from clinical applicability. We present an SCP workflow for assessing the cellular heterogeneity in saliva and tear fluid. Initially, benchmarks were established using a standard HeLa digestion curve, resulting in more than 5,463 protein groups (PGs) at 50 pg. For single HeLa cells, the workflow was improved to minimize contamination and increase quantitative performance, reaching a maximum of 3,785 PGs per single cell. Following, SCP was benchmarked across heterogenous populations of saliva and tear fluid, collected from 10 healthy individuals. By improving cell isolation, contamination control, and DIA-based search and quantitation, single cells from saliva (n=110) and tear fluid (n=149), with average diameters of 8 and 11 {micro}m, respectively, yielded a maximum of 700 PGs per single cell. Downstream analysis indicated overrepresented protein functions, distinct cluster markers and twenty-three validated therapeutic targets identified from single-cell data. Taken together, this study demonstrates the robustness of our SCP workflow applied to biofluids, driving the discovery of biomarkers and therapeutic targets in complex microenvironments.

molecular biology↗

bioRxiv2022

Comprehensive glycoprofiling of oral tumours associates N-glycosylation with lymph node metastasis and patient survival

While altered protein glycosylation is regarded a trait of oral squamous cell carcinoma (OSCC), its heterogeneous glycoproteome and dynamics with disease progression remain unmapped. To this end, we here employ an integrated multi-omics approach comprising unbiased and quantitative glycomics and glycoproteomics applied to a valuable cohort of resected tumour tissues from OSCC patients with (n = 19) and without (n = 12) lymph node metastasis. While all tumour tissues displayed uniform N-glycome profiles suggesting relatively stable global N-glycosylation during lymph node metastasis, glycoproteomics and advanced correlation analysis notably uncovered altered site-specific N-glycosylation and previously unknown associations with several key clinicopathological features. Importantly, focused analyses of the multi-omics data unveiled two N-glycans and three N-glycopeptides that were closely associated with patient survival. This study provides novel insight into the complex OSCC tissue N-glycoproteome forming an important resource to further explore the underpinning disease mechanisms and uncover new prognostic glyco-markers for OSCC. TeaserDeep survey of the dynamic landscape of complex sugars in oral tumours paves a way for new prognostic disease markers.

cancer biology↗

bioRxiv2022

Different biological effects of exposure to far-UVC (222 nm) and near-UVC (254 nm) irradiation

Ultraviolet C (UVC) light has long been used as a sterilizing agent, primarily through devices that emit at 254 nm. Depending on the dose and duration of exposure, UV 254 nm can cause erythema and photokeratitis and potentially cause skin cancer since it directly modifies nitrogenated nucleic acid bases. Filtered KrCl excimer lamps (emitting mainly at 222 nm) have emerged as safer germicidal tools and have even been proposed as devices to sterilize surgical wounds. All the studies that showed the safety of 222 nm analyzed cell number and viability, erythema generation, epidermal thickening, the formation of genetic lesions such as cyclobutane pyrimidine dimers (CPDs) and pyrimidine-(6-4)-pyrimidone photoproducts (6-4PPs) and cancer-inducing potential. Although nucleic acids can absorb and be modified by both UV 254 nm and UV 222 nm equally, compared to UV 254 nm, UV 222 nm is more intensely absorbed by proteins (especially aromatic side chains), causing photooxidation and cross-linking. Here, in addition to analyzing DNA lesion formation, for the first time, we evaluated changes in the proteome and cellular pathways, reactive oxygen species formation, and metalloproteinase (MMP) levels and activity in full-thickness in vitro reconstructed human skin (RHS) exposed to UV 222 nm. We also performed the longest (40 days) in vivo study of UV 222 nm exposure in the HRS/J mouse model at the occupational threshold limit value (TLV) for indirect exposure (25 mJ/cm2) and evaluated overall skin morphology, cellular pathological alterations, CPD and 6-4PP formation and MMP-9 activity. Our study showed that processes related to reactive oxygen species and inflammatory responses were more altered by UV 254 nm than by UV 222 nm. Our chronic in vivo exposure assay using the TLV confirmed that UV 222 nm causes minor damage to the skin. However, alterations in pathways related to skin regeneration raise concerns about direct exposure to UV 222 nm.

cell biology↗