Biomarkers in Genitourinary Cancers, Volume I

project LA/P/0140/2020 of the Associate Laboratory Institute for Health and Bioeconomy - i4HB.Genitourinary cancers are known as significant causes of mortality worldwide. This heterogeneous group includes, among others, the most common cancer in men, prostate cancer, the most common form of kidney cancer, renal cell carcinoma (RCC), and the 10th most common cancer, bladder cancer. These entities present biological diversity with various histological subtypes and a poor prognosis when metastatic. There has been considerable progress in treating patients with genitourinary cancers due to the improved understanding of their pathological mechanisms and the identification of meaningful biomarkers. The treatment progress has led to a fundamental paradigm shift in treatments. For example, our current understanding of the immunogenicity of these tumours has improved tremendously. Thanks to that, today, immunotherapy is a reliable strategy to improve the outcomes of patients with metastatic urothelial carcinoma, renal cell carcinoma, and prostate cancer. However, there is still a critical need to enrich our understanding of additional molecular mechanisms. Along with the mechanisms, there is an urgent requirement to identify novel biomarkers to progress the diagnosis and prognosis of genitourinary cancers and their treatment. Biomarkers have become a significant focus of research, primarily on how they can help predict response to systemic therapy, identify treatment resistance, and avoid toxicities. Biomarkers that reveal the mutated tumour suppressor genes, the altered signalling pathways and the aberrantly expressed molecules help select potentially responsive patients to a given therapy. In this way, biomarkers improve outcomes and reduce costs related to ineffective treatments, and, most importantly, they significantly upsurge patients’ quality of life. This Research Topic named Biomarkers in Genitourinary Cancers includes an interesting and up to date palette of publications from prominent research and clinical groups focused on identifying significant and emerging prognostic and predictive biomarkers. These biomarkers encompass non-coding RNA, serum proteins, gene expression, and glycans, among other entities identified in patients’ cohorts, samples and in the increasing number of public databases.publishersversionpublishe

Dendritic Cells: A Spot on Sialic Acid

This work was supported by the Portuguese Foundation for Science and Technology (FCT) - PTDC/SAU-MII/67561/2006 and CEDOC (Paula A. Videira) and SFRH/BD/61204/2009 (He lio J. Crespo). FCT is co-financed by European Social Fund (ESF) under Human Potential Operation Program (POPH) from National Strategic Reference Framework (NSRF).Glycans decorating cell surface and secreted proteins and lipids occupy the juncture where critical host-host and host-pathogen interactions occur. The role of glycan epitopes in cell-cell and cell-pathogen adhesive events is already well-established, and cell surface glycan structures change rapidly in response to stimulus and inflammatory cues. Despite the wide acceptance that glycans are centrally implicated in immunity, exactly how glycans and their changes contribute to the overall immune response remains poorly defined. Sialic acids are unique sugars that usually occupy the terminal position of the glycan chains and may be modified by external factors, such as pathogens, or upon specific physiological cellular events. At cell surface, sialic acid-modified structures form the key fundamental determinants for a number of receptors with known involvement in cellular adhesiveness and cell trafficking, such as the Selectins and the Siglec families of carbohydrate recognizing receptors. Dendritic cells (DCs) preside over the transition from innate to the adaptive immune repertoires, and no other cell has such relevant role in antigen screening, uptake, and its presentation to lymphocytes, ultimately triggering the adaptive immune response. Interestingly, sialic acid-modified structures are involved in all DC functions, such as antigen uptake, DC migration, and capacity to prime T cell responses. Sialic acid content changes along DC differentiation and activation and, while, not yet fully understood, these changes have important implications in DC functions. This review focuses on the developmental regulation of DC surface sialic acids and how manipulation of DC surface sialic acids can affect immune-critical DC functions by altering antigen endocytosis, pathogen and tumor cell recognition, cell recruitment, and capacity for T cell priming. The existing evidence points to a potential of DC surface sialylation as a therapeutic target to improve and diversify DC-based therapies.publishersversionpublishe

Dendritic Cells: A Spot on Sialic Acid

Glycans decorating cell surface and secreted proteins and lipids occupy the juncture where critical host–host and host-pathogen interactions occur. The role of glycan epitopes in cell–cell and cell-pathogen adhesive events is already well-established, and cell surface glycan structures change rapidly in response to stimulus and inflammatory cues. Despite the wide acceptance that glycans are centrally implicated in immunity, exactly how glycans and their changes contribute to the overall immune response remains poorly defined. Sialic acids are unique sugars that usually occupy the terminal position of the glycan chains and may be modified by external factors, such as pathogens, or upon specific physiological cellular events. At cell surface, sialic acid-modified structures form the key fundamental determinants for a number of receptors with known involvement in cellular adhesiveness and cell trafficking, such as the Selectins and the Siglec families of carbohydrate recognizing receptors. Dendritic cells (DCs) preside over the transition from innate to the adaptive immune repertoires, and no other cell has such relevant role in antigen screening, uptake, and its presentation to lymphocytes, ultimately triggering the adaptive immune response. Interestingly, sialic acid-modified structures are involved in all DC functions, such as antigen uptake, DC migration, and capacity to prime T cell responses. Sialic acid content changes along DC differentiation and activation and, while, not yet fully understood, these changes have important implications in DC functions. This review focuses on the developmental regulation of DC surface sialic acids and how manipulation of DC surface sialic acids can affect immune-critical DC functions by altering antigen endocytosis, pathogen and tumor cell recognition, cell recruitment, and capacity for T cell priming. The existing evidence points to a potential of DC surface sialylation as a therapeutic target to improve and diversify DC-based therapies

Carcinoembryonic antigen is a sialyl Lewis x/a carrier and an E‑selectin ligand in non‑small cell lung cancer

LPCC/Pfizer 2011. Tagus TANK award 2018 (grant no. 1/2018). SFRH/BD/100970/2014 SFRH/BPD/108686/2015The formation of distant metastasis resulting from vascular dissemination is one of the leading causes of mortality in non-small cell lung cancer (NSCLC). This metastatic dissemination initiates with the adhesion of circulating cancer cells to the endothelium. The minimal requirement for the binding of leukocytes to endothelial E-selectins and subsequent transmigration is the epitope of the fucosylated glycan, sialyl Lewis x (sLex), attached to specific cell surface glycoproteins. sLex and its isomer sialyl Lewis a (sLea) have been described in NSCLC, but their functional role in cancer cell adhesion to endothelium is still poorly understood. In this study, it was hypothesised that, similarly to leukocytes, sLe glycans play a role in NSCLC cell adhesion to E-selectins. To assess this, paired tumour and normal lung tissue samples from 18 NSCLC patients were analyzed. Immunoblotting and immunohistochemistry assays demonstrated that tumour tissues exhibited significantly stronger reactivity with anti‑sLex/sLea antibody and E-selectin chimera than normal tissues (2.2- and 1.8-fold higher, respectively), as well as a higher immunoreactive score. High sLex/sLea expression was associated with bone metastasis. The overall α1,3-fucosyltransferase (FUT) activity was increased in tumour tissues, along with the mRNA levels of FUT3, FUT6 and FUT7, whereas FUT4 mRNA expression was decreased. The expression of E-selectin ligands exhibited a weak but significant correlation with the FUT3/FUT4 and FUT7/FUT4 ratios. Additionally, carcinoembryonic antigen (CEA) was identified in only 8 of the 18 tumour tissues; CEA-positive tissues exhibited significantly increased sLex/sLea expression. Tumour tissue areas expressing CEA also expressed sLex/sLea and showed reactivity to E-selectin. Blot rolling assays further demonstrated that CEA immunoprecipitates exhibited sustained adhesive interactions with E-selectin-expressing cells, suggesting CEA acts as a functional protein scaffold for E-selectin ligands in NSCLC. In conclusion, this work provides the first demonstration that sLex/sLea are increased in primary NSCLC due to increased α1,3-FUT activity. sLex/sLea is carried by CEA and confers the ability for NSCLC cells to bind E-selectins, and is potentially associated with bone metastasis. This study contributes to identifying potential future diagnostic/prognostic biomarkers and therapeutic targets for lung cancer.preprintpublishe

Toxicity and structure-activity relationship (SAR) of α, β-dehydroamino acids against human cancer cell lines

A library of N-protected dehydroamino acids, namely dehydroalanine, dehydroaminobutyric acid and dehydrophenylalanine derivatives, was screened in three human cancer cell lines [(lung (A549), gastric (AGS) and neuroblastoma (SH-SY5Y)] in order to characterize their toxicological profile and identify new molecules with potential anticancer activity. Results showed N-protected dehydrophenylalanine and dehydroaminobutyric acid derivatives have no or low toxicity for all tested cell lines. The N-protected dehydroalanines exhibit significant toxic effects and the AGS and SH-SY5Y cells were significantly more vulnerable than A549 cells. Four α,β- dehydroalanine derivatives, with IC50 < 62.5 μM, were selected to investigate the pathways by which these compounds promote cell death. All compounds, at their IC50 concentrations, were able to induce apoptosis in both AGS and SH-SY5Y cell lines. In both cell lines, loss of mitochondrial membrane potential (ΔΨm) was found and caspase activity was increased, namely endoplasmic reticulum-resident caspase-4 in AGS cells and caspase-3/7 in SH-SY5Y cells. When evaluated in a non-cancer cell line, the molecules displayed no to low toxicity, thus suggesting some degree of selectivity for cancer cells. The results indicate that α,β-dehydroalanine derivatives can be considered a future resource of compounds able to work as anticancer drugs.This work received financial support from National Funds (FCT/MEC) through Project UID/QUI/50006/2013, co-financed by European Union (FEDER under the Partnership Agreement PT2020); and from Norte Portugal Regional Operational Programme (NORTE 2020), under the PORTUGAL 2020 Partnership Agreement, through the European Regional Development Fund (ERDF) (project NORTE-01-0145-FEDER 000024).info:eu-repo/semantics/publishedVersio

Sialyl LewisX/A and Cytokeratin Crosstalk in Triple Negative Breast Cancer

project LA/P/0140/2020 of the Associate Laboratory Institute for Health and Bioeconomy—i4HB. Publisher Copyright: © 2023 by the authors.Triple-negative breast cancer (TNBC) encompasses multiple entities and is generally highly aggressive and metastatic. We aimed to determine the clinical and biological relevance of Sialyl-Lewis X and A (sLeX/A)—a fucosylated glycan involved in metastasis—in TNBC. Here, we studied tissues from 50 TNBC patients, transcripts from a TNBC dataset from The Cancer Genome Atlas (TCGA) database, and a primary breast cancer cell line. All 50 TNBC tissue samples analysed expressed sLeX/A. Patients with high expression of sLeX/A had 3 years less disease-free survival than patients with lower expression. In tissue, sLeX/A negatively correlated with cytokeratins 5/6 (CK5/6, which was corroborated by the inverse correlation between fucosyltransferases and CK5/6 genes. Our observations were confirmed in vitro when inhibition of sLeX/A remarkably increased expression of CK5/6, followed by a decreased proliferation and invasion capacity. Among the reported glycoproteins bearing sLeX/A and based on the STRING tool, α6 integrin showed the highest interaction score with CK5/6. This is the first report on the sLeX/A expression in TNBC, highlighting its association with lower disease-free survival and its inverse crosstalk with CK5/6 with α6 integrin as a mediator. All in all, sLeX/A is critical for TNBC malignancy and a potential prognosis biomarker and therapeutic target.publishersversionpublishe

Application of hyperthermia for cancer treatment: Synthesis and characterization of magnetic nanoparticles and their internalization on tumor cell lines

FEDER funds through the COMPETE 2020 Program under the project number POCI-01-0145-FEDER-007688. This work was also funded by the Scientific merit prize Santander-Totta - Lisbon New University - "Antibody engineering for breast cancer therapy" 2013. Catarina I. P. Chaparro also acknowledges the financial support from Liga Portuguesa Contra o Cancro (LPCC)/Pfizer 2017.Truncated sialylated O-glycans, such as cell-surface carbohydrate antigen sialyl-Tn (STn) are overexpressed by several cancer types, but not by the respective normal tissues. STn expression is associated with oncogenesis and metastatic ability of cancer cells, with reduced overall survival and lack of response to chemotherapy. Advances in nanomedicine have resulted in rapid development of biocompatible superparamagnetic iron oxide nanoparticles (SPIONs) with considerable potential in cancer treatment. Therefore, in this study SPIONs coated with oleic acid (OA) or dimercaptosuccinic acid (DMSA) were developed and characterized for internalization in two breast cancer cell lines: cell line expressing the STn antigen and the corresponding control. SPIONs with an average diameter of 8 nm showed superparamagnetic behavior and high potential to be used as magnetic hyperthermia agents. OA and DMSA coating provided high stability of SPIONs in physiological conditions while not changing their main properties. NPs internalization studies showed a higher accumulation of DMSA coated NPs in the breast cancer MDA-MB-231 WT cell line. In MDA-MB-231 cell line expressing STn both coated NPs showed a similar accumulation. Therefore, STn antigen can act as a receptor capable of detecting and covalently bind to the molecules present on NPs surface and induce their cellular uptake by endocytosis.publishersversionpublishe

the web-based case study of the Immunology and Congenital Disorders of Glycosylation questionnaire (ImmunoCDGQ)

Funding Information: This work is financed by national funds from FCT—Fundação para a Ciência e a Tecnologia, I.P., in the scope of the project UIDP/04378/2020 and UIDB/04378/2020 of the Research Unit on Applied Molecular Biosciences—UCIBIO and the project LA/P/0140/2020 of the Associate Laboratory Institute for Health and Bioeconomy—i4HB. R.F. (SFRH/BD/124326/2016) and C.P. (SFRH/BD/138647/2018) acknowledge the funding from the Fundação para a Ciência e Tecnologia (FCT), Portugal. S.B. was supported by CDG & Allies-PPAIN funding (6th Liliana Scientific Scholarship). Publisher Copyright: © 2022, The Author(s).BACKGROUND: Congenital Disorders of Glycosylation (CDG) are a complex family of rare metabolic diseases. Robust clinical data collection faces many hurdles, preventing full CDG biological and clinical comprehension. Web-based platforms offer privileged opportunities for biomedical data gathering, and participant recruitment, particularly in rare diseases. The immunology and CDG electronic (e-) questionnaire (ImmunoCDGQ) explores this paradigm, proposing a people-centric framework to advance health research and participant empowerment. OBJECTIVE: The objectives of this study were to: (1) Describe and characterize the ImmunoCDGQ development, engagement, recruitment, participation, and result dissemination strategies; (2) To critically compare this framework with published literature and making recommendations. METHODS: An international, multistakeholder people-centric approach was initiated to develop and distribute the ImmunoCDGQ, a multi-lingual e-questionnaire able to collect immune-related data directly from patients and family caregivers. An adapted version was produced and distributed among the general "healthy" population (ImmunoHealthyQ), serving as the control group. Literature screening was performed to identify and analyze comparable studies. RESULTS: The ImmunoCDGQ attained high participation and inclusion rates (94.6%, 209 out of 221). Comparatively to the control, CDG participants also showed higher and more variable questionnaire completion times as well as increased English version representativeness. Additionally, 20% of the CDG group (42 out of 209) chose not to complete the entire questionnaire in one go. Conditional logic structuring guided participant data provision and accurate data analysis assignment. Multi-channel recruitment created sustained engagement with Facebook emerging as the most followed social media outlet. Still, most included ImmunoCDGQ questionnaires (50.7%, 106 out of 209) were submitted within the first month of the project's launch. Literature search and analysis showed that most e-questionnaire-based studies in rare diseases are author-built (56.8%, 25 out of 44), simultaneously addressing medical and health-related quality of life (HRQoL) and/or information needs (79.5%, 35 out of 44). Also, over 68% of the studies adopt multi-platform recruitment (30 out of 44) actively supported by patient organizations (52.3%, 23 out of 44). CONCLUSIONS: The ImmunoCDGQ, its methodology and the CDG Community served as models for health research, hence paving a successful and reproducible road to people-centricity in biomedical research.publishersversionpublishe

Computational Approaches Drive Developments in Immune-Oncology Therapies for PD-1/PD-L1 Immune Checkpoint Inhibitors

Funding Information: This research was funded by Fundação para a Ciência e Tecnologia (FCT) Portugal, grant number UIDB/50006/2020 (LAQV-REQUIMTE), UIDP/04378/2020 and UIDB/04378/2020 (UCIBIO) and LA/P/0140/2020 (i4HB), the European Commission GLYCOTwinning (GA 101079417), the EJPRD ProDGNE (EJPRD/0001/2020 EU 825575) and SI I&DT, DCMatters (AVISO Nº 17/SI/2019) REF 47212. F.P. gratefully acknowledges FCT for an Assistant Research Position (CEECIND/01649/2021). Publisher Copyright: © 2023 by the authors.Computational approaches in immune-oncology therapies focus on using data-driven methods to identify potential immune targets and develop novel drug candidates. In particular, the search for PD-1/PD-L1 immune checkpoint inhibitors (ICIs) has enlivened the field, leveraging the use of cheminformatics and bioinformatics tools to analyze large datasets of molecules, gene expression and protein–protein interactions. Up to now, there is still an unmet clinical need for improved ICIs and reliable predictive biomarkers. In this review, we highlight the computational methodologies applied to discovering and developing PD-1/PD-L1 ICIs for improved cancer immunotherapies with a greater focus in the last five years. The use of computer-aided drug design structure- and ligand-based virtual screening processes, molecular docking, homology modeling and molecular dynamics simulations methodologies essential for successful drug discovery campaigns focusing on antibodies, peptides or small-molecule ICIs are addressed. A list of recent databases and web tools used in the context of cancer and immunotherapy has been compilated and made available, namely regarding a general scope, cancer and immunology. In summary, computational approaches have become valuable tools for discovering and developing ICIs. Despite significant progress, there is still a need for improved ICIs and biomarkers, and recent databases and web tools have been compiled to aid in this pursuit.publishersversionpublishe