N-glycoprotein analysis discovers new up-regulated glycoproteins in colorectal cancer tissue

B4GALT1 as a New Biomarker of Idiopathic Pulmonary Fibrosis

Idiopathic pulmonary fibrosis (IPF) is a disease characterized by progressive scarring of the lung that involves the pulmonary interstitium. The disease may rapidly progress, leading to respiratory failure, and the long-term survival is poor. There are no accurate biomarkers available so far. Our aim was to evaluate the expression of the B4GALT1 in patients with IPF. Analysis of B4GALT1 gene expression was performed in silico on two gene sets, retrieved from the Gene Expression Omnibus database. Expression of B4GALT1 was then evaluated, both at the mRNA and protein levels, on lung specimens obtained from lung biopsies of 4 IPF patients, on one IPF-derived human primary cell and on 11 cases of IPF associated with cancer. In silico re-analysis demonstrated that the B4GALT1 gene was overexpressed in patients and human cell cultures with IPF (p = 0.03). Network analysis demonstrated that B4GALT1 upregulation was correlated with genes belonging to the EMT pathway (p = 0.01). The overexpression of B4GALT1 was observed, both at mRNA and protein levels, in lung biopsies of our four IPF patients and in the IPF-derived human primary cell, in other fibrotic non-lung tissues, and in IPF associated with cancer. In conclusion, our results indicate that B4GALT1 is overexpressed in IPF and could represent a novel marker of this disease.

Identification and Validation of a Novel Prognostic Gene Model for Colorectal Cancer

Aims

Colon cancer (CRC), with high morbidity and mortality, is a common and highly malignant cancer, which always has a bad prognosis. So it is urgent to employ a reasonable manner to assess the prognosis of patients. We developed and validated a gene model for predicting CRC risk.

Methods

The Gene Expression Omnibus (GEO) database was used to extract the gene expression profiles of CRC patients (N = 181) from GEO to identify genes that were differentially expressed between CRC patients and controls and then stable signature genes by firstly using both robust likelihood-based modeling with 1000 iterations and random survival forest variable hunting algorithms. Cluster analysis using the longest distance method was drawn out, and Kaplan–Meier (KM) survival analysis was used to compare the clusters. Meanwhile, the risk score was evaluated in three independent datasets including the GEO and Illumina HiSeq sequencing platforms. The corresponding risk index was calculated, and samples were clustered into high- and low-risk groups according to the median. And survival ROC analysis was used to evaluate the prognostic model. Finally, the Gene Set Enrichment Analysis (GSEA) was performed for further functional enrichment analyses.

Results

A 10-gene model was obtained, including 7 negative impact factors (SLC39A14, AACS, ERP29, LAMP3, TMEM106C, TMED2, and SLC25A3) and 3 positive ones (CNPY2, GRB10, and PBK), which related with several important oncogenic pathways (KRAS signaling, TNF-α signaling pathway, and WNT signaling pathway) and several cancer-related cellular processes (epithelial mesenchymal transition and cellular apoptosis). By using colon cancer datasets from The Cancer Genome Atlas (TCGA), the model was validated in KM survival analysis (P ≤ 0.001) and significant analysis with recurrence time (P = 0.0018).

Conclusions

This study firstly developed a stable and effective 10-gene model by using novel combined methods, and CRC patients might be able to use it as a prognostic marker for predicting their survival and monitoring their long-term treatment.

An N-glycoproteomic site-mapping analysis reveals glycoprotein alterations in esophageal squamous cell carcinoma

Background

Aberrant glycosylation has been recognized as a hallmark of cancer and N-glycosylation is one of the main types of glycosylation in eukaryotes. Although N-glycoproteomics has made contributions to the discovery of biomarkers in a variety of cancers, less is known about the abnormal glycosylation signatures in esophageal squamous cell carcinoma (ESCC).

Methods

In this study, we reported the proteomics and N-glycoproteomic site-mapping analysis of eight pairs of ESCC tissues and adjacent normal tissues. With zic-HILIC enrichment, TMT-based isobaric labeling, LC–MS/MS analysis, differentially expressed N-glycosylation was quantitatively characterized. Lectin affinity enrichment combined with western blot was used to validate the potential biomarkers in ESCC.

Results

A series of differentially expressed glycoproteins (e.g., LAMP2, PLOD2) and enriched signaling pathways (e.g., metabolism-related pathway, ECM-receptor interaction, focal adhesion) were identified. Besides that, seven significantly enriched motifs were found from the identified N-glycosylation sites. Three clusters were identified after conducting the dynamic profiling analysis of glycoprotein change during lymph node metastasis progression. Further validation found that the elevated fucosylation level of ITGB1, CD276 contributed to the occurrence and development of ESCC, which might be the potential biomarkers in ESCC.

Conclusion

In summary, we characterized the N-glycosylation and N-glycoprotein alterations associated with ESCC. The typical changes in glycoprotein expression and glycosylation occupancy identified in our study will not only be used as ESCC biomarkers but also improve the understanding of ESCC biology.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12967-022-03489-2.

Proteomics of post-translational modifications in colorectal cancer: Discovery of new biomarkers

Colorectal cancer (CRC) is one of the costliest health problems and ranks second in cancer-related mortality in developed countries. With the aid of proteomics, many protein biomarkers for the diagnosis, prognosis, and precise management of CRC have been identified. Furthermore, some protein biomarkers exhibit structural diversity after modifications. Post-translational modifications (PTMs), most of which are catalyzed by a variety of enzymes, extensively increase protein diversity and are involved in many complex and dynamic cellular processes through the regulation of protein function. Accumulating evidence suggests that abnormal PTM events are associated with a variety of human diseases, such as CRC, thus highlighting the need for studying PTMs to discover both the molecular mechanisms and therapeutic targets of CRC. In this review, we begin with a brief overview of the importance of protein PTMs, discuss the general strategies for proteomic profiling of several key PTMs (including phosphorylation, acetylation, glycosylation, ubiquitination, methylation, and citrullination), shift the emphasis to describing the specific methods used for delineating the global landscapes of each of these PTMs, and summarize the recent applications of these methods to explore the potential roles of the PTMs in CRC. Finally, we discuss the current status of PTM research on CRC and provide future perspectives on how PTM regulation can play an essential role in translational medicine for early diagnosis, prognosis stratification, and therapeutic intervention in CRC.

Exploration of the typical features of tubulovillous adenoma using in-depth quantitative proteomics analysis

This present study aimed to explore the typical protein features of tubulovillous adenoma (TVA) using proteomic and bioinformatic analyses. Tandem mass tag (TMT)-based quantitative proteomic analyses were conducted on normal mucosa, tubular adenoma, TVA and adenocarcinoma tissues. We identified 5,665 proteins categorized into seven clusters based on Pearson’s correlation analysis. The bioinfomatic analysis showed mitochondrial and metabolism-related events were typical characteristics of TVA and mitochondrial-, ribosome- and matrisome-related biological processes may contribute to carcinogenesis. PLOD3 was identified as a key protein associated with the malignant potential of TVA and promoted the viability of adenoma organoids. The Cancer Genome Atlas (TCGA) analysis revealed PLOD3 as a risk factor for disease-free and overall survival. Furthermore, the PLOD3 expression correlated negatively with the abundance of B cells, CD8 + T cells, CD4 + T cells, neutrophils, macrophages and myeloid dendritic cells. In conclusion, enhanced metabolic and mitochondrial reprogramming are typical features of TVA, and PLOD3 might be related to the “immune desert” phenotype and contribute to TVA tumorigenesis and colorectal cancer development.

PLODs are overexpressed in ovarian cancer and are associated with gap junctions via connexin 43

Procollagen-lysine, 2-oxoglutarate 5-dioxygenases (PLODs) play important roles in cancer progression, but their role in ovarian cancer remains elusive. In silico analysis of expression of PLODs in ovarian cancer was performed with reproduction of The Cancer Genome Atlas dataset. PLOD-enriched pathways and related gene(s) were validated by immunohistochemistry (IHC) in 80 ovarian cancer tissue blocks and in vivo xenograft murine models. PLODs (PLOD-1, -2, and -3) were overexpressed in ovarian cancer tissue. Overexpression of individual PLODs showed mutual exclusivity. Each of the three PLODs was differentially expressed between normal and cancer tissue of the ovary. PLOD1 was not prognostic, whereas lower PLOD2 and higher PLOD3 expression were associated with worsened prognosis, respectively. Cases with PLOD overexpression showed enrichment in gap junctions. GJA1 (connexin 43) was significantly overexpressed in cases with PLOD overexpression. IHC in tissue showed the strongest positive correlation between PLOD3 and connexin 43 expression, followed by PLOD2. As per Harmonizome, we selected SKOV3 and CAOV3 cell lines based on constitutive high PLOD1 and PLOD2/PLOD3 expression, respectively for in vitro and in vivo modeling. Only knockdown of PLOD3 was significantly associated with decreased GJA1 expression level in both cell lines. IHC in murine xenograft tumors also showed significantly lower connexin 43 in PLOD3-KD SKOV3 tumors. We conclude that PLODs are generally overexpressed in ovarian cancer and each PLOD may be functionally non-redundant. Association between PLOD3 and gap junctions warrants further investigation.

The matrix in cancer

The extracellular matrix is a fundamental, core component of all tissues and organs, and is essential for the existence of multicellular organisms. From the earliest stages of organism development until death, it regulates and fine-tunes every cellular process in the body. In cancer, the extracellular matrix is altered at the biochemical, biomechanical, architectural and topographical levels, and recent years have seen an exponential increase in the study and recognition of the importance of the matrix in solid tumours. Coupled with the advancement of new technologies to study various elements of the matrix and cell-matrix interactions, we are also beginning to see the deployment of matrix-centric, stromal targeting cancer therapies. This Review touches on many of the facets of matrix biology in solid cancers, including breast, pancreatic and lung cancer, with the aim of highlighting some of the emerging interactions of the matrix and influences that the matrix has on tumour onset, progression and metastatic dissemination, before summarizing the ongoing work in the field aimed at developing therapies to co-target the matrix in cancer and cancer metastasis.

Glycoproteomic Analysis of Human Urinary Exosomes

Exosomes represent a class of secreted biological vesicles, which have recently gained attention due to their function as intertissue and interorganism transporters of genetic materials, small molecules, lipids, and proteins. Although the protein constituents of these exosomes are often glycosylated, a large-scale characterization of the glycoproteome has not yet been completed. This study identified 3144 unique glycosylation events belonging to 378 glycoproteins and 604 unique protein sites of glycosylation. With these data, we investigated the level of glycan microheterogeneity within the urinary exosomes, finding on average 5.9 glycans per site. The glycan family abundance on individual proteins showed subtle differences, providing an additional level of molecular characterization compared to the unmodified proteome. Finally, we show protein site-specific changes in regard to the common urinary glycoprotein, uromodulin. While uromodulin is an individual case, these same site-specific analyses provide a way forward for developing diagnostic glycoprotein biomarkers with urine as a noninvasive biological fluid. This study represents an important first step in understanding the functional urinary glycoproteome.

Knockdown of PLOD3 suppresses the malignant progression of renal cell carcinoma via reducing TWIST1 expression

Procollagen-lysine, 2-oxoglutarate 5-dioxygenase (PLOD3), also known as lysyl hydroxylase 3 (LH3) has been demonstrated to be overexpressed in several kinds of cancers and facilitate cell migration. Currently, we aimed to reveal the role of PLOD3 in renal cell carcinoma (RCC) progression, and explore whether TWIST1 (Twist family bHLH transcription factor 1) is involved in this process. Fifty-eight paired RCC tissues and normal tissues were collected and subjected to qPCR and immunohistochemistry (IHC) technology to detect the expression levels of PLOD3. The clinical value of PLOD3 in predicting RCC progression was then explored. Cell-Counting Kit-8 (CCK-8), wound healing, transwell chambers and tumor-bearing experiments were applied to monitor cell proliferation, migration, invasion and tumorigenesis. Protein levels were determined by using western blotting technology to assess cell apoptosis and epithelial to mesenchymal transition (EMT). PLOD3 expression was enhanced in RCC tissues and cells, which predicted higher T (tumor), N (lymph node) and M (metastasis) stages, histological grade and TNM (tumor, lymph node, metastasis) stage. PLOD3 downregulation in RCC A498 cells obviously inhibited cell proliferation, migration, invasion, EMT and tumorigenesis and increased cell apoptosis. PLOD3 overexpression led to opposite results in RCC A704 cells. PLOD3 downregulation reduced the expression levels of TWIST1, β-catenin and p-AKT. In addition, TWIST1 overexpression rescued the repressions of cell proliferation, migration, invasion, EMT and the activation of β-catenin and AKT signaling in addition to apoptosis promotion induced by PLOD3 downregulation. Collectively, this study illustrated that PLOD3 knockdown suppressed RCC malignance via inhibiting TWIST1-mediated activation of β-catenin and AKT signaling.

Variation in Blood and Colorectal Epithelia's Key Trace Elements Along with Expression of Mismatch Repair Proteins from Localized and Metastatic Colorectal Cancer Patients

Colorectal cancer (CRC) is an increasingly common medical issue affecting millions worldwide, and contribution of the body's trace elements to CRC is arguable. The concentrations and buffered status of selenium, iron, copper, zinc, and phosphorus in blood and large intestinal tissues of CRC patients are, respectively, variable and vital for cell physiology. The aim of this study was to assess selenium, iron, copper, zinc, and phosphorus variations in blood and colorectal epithelia along with examining the expression of mismatch repair proteins in CRC patients with/without metastasis for potential diagnosis/therapy. Concentrations of selenium, iron, copper, zinc, and phosphorus in blood of healthy versus CRC patients and colorectal epithelia (adenocarcinomatous versus non-adenocarcinomatous/control) were measured in 40 CRC patients (55.87 ± 11.9 years old) with/without metastasis before surgery using ICP-OES. Mismatch repair (MMR) protein expression was analyzed through histopathological/immunohistochemistry assays, which was sparse in 5 CRC patient's colorectal tissues (12%). Compared with healthy individuals, blood and colorectal tissue's levels of phosphorus, copper, and iron were significantly higher in the CRC patients, and more pronounced in metastatic CRC patients; conversely, blood and colorectal tissue's selenium levels were significantly lower in metastatic patients. Unlike blood zinc, cancerous colorectal tissue's zinc concentration was significantly lower in CRC patients compared to healthy control cohorts. There was no significant difference on the measured elements in samples from CRC patients with MMR^- compared to CRC patients with MMR⁺. Receiver operating characteristic analysis revealed a correlation of blood iron, zinc, copper, and phosphorus to CRC, and inappropriately low levels of blood and colorectal selenium correlated with exacerbated metastasis. Altered levels of selenium, iron, copper, zinc, and phosphorus in vivo may impact the pathogenesis and detection of CRC, and their diagnostic/therapeutic potential in CRC would be revealing.

PLOD2 promotes aerobic glycolysis and cell progression in colorectal cancer by upregulating HK2

The purpose of this study was to characterize the expression of procollagen-lysine, 2-oxoglutarate 5-dioxygenase 2 (PLOD2), a membrane-bound homodimeric enzyme that specifically hydroxylates lysine in the telopeptide of procollagens, and assess the clinical significance of PLOD2 in colorectal cancer (CRC). Our results show that PLOD2 is highly expressed in CRC tumor tissues and cell lines, both at the mRNA and protein levels. Next, we found that PLOD2 was positively correlated with tumor grade (P = 0.001), T stage (P = 0.001), N stage (P < 0.001), and an advanced TNM stage (P < 0.001). Knockdown of PLOD2 attenuated CRC cell proliferation, migration, and invasiveness, in vitro. Our analysis of the mechanism behind the effects of PLOD2 suggests that PLOD2 affected glycolysis by regulating the expression of hexokinase 2 (HK2). HK2 reverses the inhibitory effects of PLOD2 knockdown in CRC. Furthermore, the data suggest that PLOD2 regulates the expression of HK2 via the STAT3 signaling pathway. Survival analysis revealed that high expression levels of PLOD2 (HR = 3.800, P < 0.001) and HK2 expression (HR = 10.222, P < 0.001) correlated with the overall survival rate. After analyzing their expression and correlation, PLOD2 positively correlated with HK2 (r = 0.590, P < 0.001). Our findings have revealed that PLOD2 is a novel regulatory factor in glucose metabolism, exerted via controlling HK2 expression in CRC cells, suggesting PLOD2 as a promising therapeutic target for CRC treatment.

N-GlycositeAtlas: a database resource for mass spectrometry-based human N-linked glycoprotein and glycosylation site mapping

BACKGROUND

N-linked glycoprotein is a highly interesting class of proteins for clinical and biological research. The large-scale characterization of N-linked glycoproteins accomplished by mass spectrometry-based glycoproteomics has provided valuable insights into the interdependence of glycoprotein structure and protein function. However, these studies focused mainly on the analysis of specific sample type, and lack the integration of glycoproteomic data from different tissues, body fluids or cell types.

METHODS

In this study, we collected the human glycosite-containing peptides identified through their de-glycosylated forms by mass spectrometry from over 100 publications and unpublished datasets generated from our laboratory. A database resource termed N-GlycositeAtlas was created and further used for the distribution analyses of glycoproteins among different human cells, tissues and body fluids. Finally, a web interface of N-GlycositeAtlas was created to maximize the utility and value of the database.

RESULTS

The N-GlycositeAtlas database contains more than 30,000 glycosite-containing peptides (representing > 14,000 N-glycosylation sites) from more than 7200 N-glycoproteins from different biological sources including human-derived tissues, body fluids and cell lines from over 100 studies.

CONCLUSIONS

The entire human N-glycoproteome database as well as 22 sub-databases associated with individual tissues or body fluids can be downloaded from the N-GlycositeAtlas website at http://nglycositeatlas.biomarkercenter.org.

Procollagen-lysine, 2-oxoglutarate 5-dioxygenases 1, 2, and 3 are potential prognostic indicators in patients with clear cell renal cell carcinoma

Intratumoral fibrosis is a frequent histologic finding in highly vascularized clear cell renal cell carcinoma (ccRCC). Here, we investigated the expression of a family of collagen-modifying enzymes, procollagen-lysine, 2-oxoglutarate 5-dioxygenases 1, 2, and 3 (PLOD1/2/3), in ccRCC tissues and assessed the prognostic value of wild-type and genetically mutated PLOD1/2/3 for ccRCC patients. Normal kidney and ccRCC mRNA and protein expression datasets were obtained from Oncomine, The Cancer Genome Atlas, and Human Protein Atlas databases. Associations between PLOD1/2/3 expression, clinicopathological variables, and patient survival were evaluated using Cox regression and Kaplan–Meier analyses. PLOD1/2/3 mRNA and protein expression levels were significantly elevated in ccRCC tissues compared with normal kidney. Increased PLOD1/2/3 mRNA expression was significantly associated with advanced tumor stage, high pathological grade, and shorter progression-free and overall survival (all p<0.01). Genetic mutation of PLOD1/2/3 was present in ~3% of ccRCC patients and was associated with significantly poorer prognosis compared with expression of wild-type PLOD1/2/3 (p<0.001). This study thus identifies tumor expression of wild-type or mutated PLOD1/2/3 mRNA as a potential predictive biomarker for ccRCC patients and sheds light on the underlying molecular pathogenesis of ccRCC.

Mapping human N-linked glycoproteins and glycosylation sites using mass spectrometry

N-linked glycoprotein is a highly interesting class of proteins for clinical and biological research. Over the last decade, large-scale profiling of N-linked glycoproteins and glycosylation sites from biological and clinical samples has been achieved through mass spectrometry-based glycoproteomic approaches. In this paper, we reviewed the human glycoproteomic profiles that have been reported in more than 80 individual studies, and mainly focused on the N-glycoproteins and glycosylation sites identified through their deglycosylated forms of glycosite-containing peptides. According to our analyses, more than 30,000 glycosite-containing peptides and 7,000 human glycoproteins have been identified from five different body fluids, twelve human tissues (or related cell lines), and four special cell types. As the glycoproteomic data is still missing for many organs and tissues, a systematical glycoproteomic analysis of various human tissues and body fluids using a uniform platform is still needed for an integrated map of human N-glycoproteomes.

PLOD3 suppression exerts an anti-tumor effect on human lung cancer cells by modulating the PKC-delta signaling pathway

Current lung cancer treatments are far from satisfactory; thus, finding novel treatment targets is crucial. We recently identified procollagen-lysine, 2-oxoglutarate 5-dioxygenase 3 (PLOD3), which is involved in fibrosis and tissue remodeling as a radioresistance-related protein in lung cancer cells; however, its mechanism is unclear. In this study, we designed human PLOD3-specific short interfering (si)RNAs and tested their effects on tumor growth inhibition in vitro and in vivo. PLOD3 knockdown overcame chemoresistance and decreased radioresistance by inducing caspase-3-dependent apoptosis in lung cancer cells. Furthermore, PLOD3 interacted with PKCδ to activate caspase-2,4-dependent apoptosis through ER-stress-induced IRE1α activation and the downstream unfolded-protein response pathway. In a mouse xenograft model, PLOD3 knockdown promoted radiation-induced tumor growth inhibition, without side effects. Moreover, lung cancer patients with high PLOD3 expression showed poorer prognosis than those with low PLOD3 expression upon radiotherapy, suggesting that PLOD3 promotes tumor growth. Therefore, PLOD3 siRNA suppresses radioresistance and chemoresistance by inducing apoptosis and renders PLOD3 as a candidate lung cancer biomarker. PLOD3 gene therapy might enhance the efficacy of radiotherapy or chemotherapy in lung cancer patients.

PLOD3 promotes lung metastasis via regulation of STAT3

Procollagen-lysine, 2-oxoglutarate 5-dioxygenase (PLOD3), a membrane-bound homodimeric enzyme, hydroxylates lysyl residues in collagen-like peptides; however, its role in lung cancer is unknown. This study aimed to investigate the role of PLOD3 as a pro-metastatic factor and to elucidate the underlying mechanism. First, we experimentally confirmed the release of PLOD3 in circulation in animal models, rendering it a potential serum biomarker for lung cancer in humans. Thereafter, we investigated the effects of PLOD3 overexpression and downregulation on cancer cell invasion and migration in vitro and in vivo, using human lung cancer cell lines and a mouse tumor xenograft model, respectively. Further, PLOD3 levels were determined in lung tissue samples from lung cancer patients. Functional analyses revealed that PLOD3 interacts with STAT3, thereby expressing matrix metalloproteinases (MMP-2 and MMP-9) and with urokinase plasminogen activator (uPA) to enhance tumor metastasis. PLOD3 and the STAT3 pathway were significantly correlated in the metastatic foci of lung cancer patients; PLOD3–STAT3 levels were highly correlated with a poor prognosis. These results indicate that PLOD3 promotes lung cancer metastasis in a RAS-MAP kinase pathway-independent manner. Therefore, secreted PLOD3 serves as a potent inducer of lung cancer metastasis and a potential therapeutic target to enhance survival in lung cancer.

Roles of PLODs in Collagen Synthesis and Cancer Progression

Collagen is the major component of extracellular matrix. Collagen cross-link and deposition depend on lysyl hydroxylation, which is catalyzed by procollagen-lysine, 2-oxoglutarate 5-dioxygenase (PLOD). Aberrant lysyl hydroxylation and collagen cross-link contributes to the progression of many collagen-related diseases, such as fibrosis and cancer. Three lysyl hydroxylases (LH1, LH2, and LH3) are identified, encoded by PLOD1, PLOD2, and PLOD3 genes. Expression of PLODs is regulated by multiple cytokines, transcription factors and microRNAs. Dysregulation of PLODs promotes cancer progression and metastasis, suggesting that targeting PLODs is potential strategy for cancer treatment. Here, we summarize the recent progress in the investigation of function and regulation of PLODs in normal tissue development and disease progression, especially in cancer.

Probing the colorectal cancer proteome for biomarkers: Current status and perspectives

Colorectal cancer (CRC) is one of the most prevalent malignancies worldwide. Biomarkers that can facilitate better clinical management of CRC are in high demand to improve patient outcome and to reduce mortality. In this regard, proteomic analysis holds a promising prospect in the hunt of novel biomarkers for CRC and in understanding the mechanisms underlying tumorigenesis. This review aims to provide an overview of the current progress of proteomic research, focusing on discovery and validation of diagnostic biomarkers for CRC. We will summarize the contributions of proteomic strategies to recent discoveries of protein biomarkers for CRC and also briefly discuss the potential and challenges of different proteomic approaches in biomarker discovery and translational applications.

Lectin Microarray Combined with Mass Spectrometry Identifies Haptoglobin-Related Protein (HPR) as a Potential Serologic Biomarker for Separating Nonbacterial Pneumonia from Bacterial Pneumonia in Childhood

PURPOSE

Etiological diagnosis of pediatric patients with community-acquired pneumonia is difficult. For therapy, one of the major problems is the difficulty in separating bacterial pneumonia which would benefit from antibiotics from nonbacterial pneumonia. Therefore, to identify potential biomarkers for distinguishing nonbacterial pneumonia from bacterial pneumonia are sought .

EXPERIMENTAL DESIGN

Lectin microarray containing 91 lectins is used to screen serums from pediatric patients with pneumonia. Lectin-based pull-down assay combined with LC-MS/MS is used to identify the potential biomarkers.

RESULTS

SNA-I, a lectin binding preferentially to α2-6 linked sialic acid residues, shows higher binding signals (near 42 kDa) in the mycoplasma pneumonia group, when compared with the other groups. A total of 18 proteins are identified with LC-MS/MS. By western blot analysis, the authors confirm that the expression of haptoglobin-related protein (HPR) is elevated in pediatric patients with pneumonia compared with normal children (p < 0.001). Furthermore, HPR is higher in the mycoplasma pneumonia group (p < 0.01) and the viral pneumonia group (p < 0.05), when compared with the bacterial pneumonia group.

CONCLUSIONS AND CLINICAL RELEVANCE

These results indicate that HPR is a potential serologic biomarker which can differentiate between bacterial pneumonia and nonbacterial pneumonia. Detection of serum HPR might be useful for clinical diagnosis.

Hypoxia-induced PLOD2 promotes proliferation, migration and invasion via PI3K/Akt signaling in glioma

Gliomas are the most common form of malignant primary brain tumors with poor 5-year survival rate. Dysregulation of procollagen-lysine, 2-oxoglutarate 5-dioxygenase 2 (PLOD2) was observed in gliomas, but the specific role and molecular mechanism of PLOD2 in glioma have not been reported yet. In this study, PLOD2 was found to be frequently up-regulated in glioma and could serve as an independent prognostic marker to identify patients with poor clinical outcome. Knockdown of PLOD2 inhibited proliferation, migration and invasion of glioma cells in vitro and in vivo. Mechanistically, inhibition of PLOD2 inactivated PI3K/AKT signaling pathway and thus regulated the expression of its downstream epithelial–mesenchymal transition (EMT)-associated regulators, including E-cadherin, vimentin, N-cadherin, β-catenin, snail and slug in glioma cells. Moreover, PLOD2 could be induced by hypoxia-inducible factor-1α (HIF-1α) via hypoxia, thereby promoting hypoxia-induced EMT in glioma cells. Our data suggests that PLOD2 may be a potential therapeutic target for patients with glioma.

Overexpression of PLOD3 promotes tumor progression and poor prognosis in gliomas

High-grade gliomas are the most threatening brain tumors due to aggressive proliferation and poor prognosis. Thus, utilizing genetic glioma biomarkers to forecast prognosis and guide clinical management is crucial. Procollagen-lysine, 2-oxoglutarate 5-dioxygenase 3 (PLOD3) modulates cancer progression and metastasis. However, its detailed function in cancer remains largely uninvestigated. PLOD3 expression was evaluated with real-time PCR in glioblastoma (GBM) cell lines and by Gene Expression Omnibus dataset analysis and immunohistochemistry of glioma tissues. We investigated the clinical use of PLOD3 for determining glioma prognosis. The biological roles of PLOD3 in proliferation, migration and invasion of GBM cells were studied both in vitro with wound-healing and transwell assays and in vivo using an orthotopic xenograft mouse model. Hypoxia and western blotting were applied to discover the molecular mechanisms underlying PLOD3 functions. PLOD3 mRNA and protein expression were upregulated in glioma tissues compared to normal brain tissues. PLOD3 overexpression was correlated with negative survival in glioma patients. PLOD3 silencing suppressed cell proliferation and induced G1 phase arrest through p53-independent regulation of the p21 pathway. Inhibition of PLOD3 in glioma cells decreased VEGF expression, migration and invasion by downregulating mesenchymal markers, including Snail and Twist. Notably, knockdown of PLOD3 inhibited HIF-1α accumulation via the ERK signaling pathway under hypoxia. Taken together, these discoveries reveal that PLOD3 is a potential therapeutic target in human gliomas.

Identification of metabolism-associated genes and pathways involved in different stages of clear cell renal cell carcinoma

The lack of early diagnostic markers and novel therapeutic targets for clear cell renal cell carcinoma (ccRCC) negatively affects patient prognosis. Cancer metabolism is an attractive area for the understanding of the molecular mechanism of carcinogenesis. The present study attempted to identify metabolic changes from the view of the expression of metabolism-associated genes between control samples and those of ccRCC at different disease stages. Data concerning ccRCC gene expression obtained by RNA-sequencing was obtained from The Cancer Genome Atlas and data on metabolism-associated genes were extracted using the Recon2 model. Following analysis of differential gene expression, multiple differentially expressed metabolic genes at each tumor-node-metastasis disease stage were identified, compared with control non-disease samples: Metabolic genes (305) were differentially expressed in stage I disease, 323 in stage II disease, 355 in stage III disease and 363 in stage IV disease. Following enrichment analysis for differential metabolic genes, 22 metabolic pathways were identified to be dysregulated in multiple stages of ccRCC. Abnormalities in hormone, vitamin, glucose and lipid metabolism were present in the early stages of the disease, with dysregulation to reactive oxygen species detoxification and amino acid metabolism pathways occurring with advanced disease stages, particularly to valine, leucine, and isoleucine metabolism, which was substantially dysregulated in stage IV disease. The xenobiotic metabolism pathway, associated with multiple cytochrome P450 family genes, was dysregulated in each stage of the disease. This pathway is worthy of substantial attention since it may aid understanding of drug resistance in ccRCC. The results of the present study offer information to aid further research into early diagnostic biomarkers and therapeutic targets of ccRCC.

Vitamin D3 regulates LAMP3 expression in monocyte derived dendritic cells

The family of lysosome-associated membrane proteins (LAMPs) encompassing LAMP1, LAMP2 and DC-LAMP (LAMP3) are the major constituents of the glycoconjugates coat present on the inside of the lysosomal membrane. LAMP3 is highly expressed only in certain cell types and during the differentiation stages. Its expression is linked the maturation of dendritic cells, inflammation, poor prognosis of certain tumors, and the locus where it is encoded was identified as a risk factor for Parkinson's disease (PD). Here, we investigated the capacity of Vitamin D3 to modulate the expression of LAMP3 during the dendritic cells differentiation and maturation. Our results demonstrated that the Vitamin D3 reduce the LAMP3 mRNA/protein expression during the dendritic cells differentiation and maturation, via NFκB pathways. Furthermore, we demonstrated that the Vitamin D3 was able to modulate the expression of LAMP3 likewise to in vitro tolerogenic dendritic cells. In summary, these data showed that the decrease of LAMP3 expression by Vitamin D3could enhance the tolerogenic characteristic of dendritic cells.

Radiotherapy diagnostic biomarkers in radioresistant human H460 lung cancer stem-like cells

Tumor cell radioresistance is a major contributor to radiotherapy failure, highlighting the importance of identifying predictive biomarkers for radioresistance. In this work, we established a radioresistant H460 (RR-H460) cell line from parental radiosensitive H460 lung cancer cells by exposure to fractionated radiation. The radiation-resistant, anti-apoptotic phenotype of RR-H460 cell lines was confirmed by their enhanced clonogenic survival and increased expression of the radioresistance genes Hsp90 and Her-3. RR-H460 cells displayed characteristics of cancer stem-like cells (CSCs), including induction of the surface marker CD44 and stem cell markers Nanog, Oct4, and Sox2. RR-H460 cells also exhibited sphere formation and malignant behavior, further supporting a CSC phenotype. Using proteomic analyses, we identified 8 proteins that were up-regulated in RR-H460 CSC lines and therefore potentially involved in radioresistance and CSC-related biological processes. Notably, 4 of these—PAI-2, NOMO2, KLC4, and PLOD3—have not been previously linked to radioresistance. Depletion of these individual genes sensitized RR-H460 cells to radiotoxicity and additively enhancing radiation-induced apoptosis. Our findings suggest the possibility of integrating molecular targeted therapy with radiotherapy as a strategy for resolving the radioresistance of lung tumors.

Association of N-Linked Glycoprotein Acetyls and Colorectal Cancer Incidence and Mortality

Background

Acute phase proteins highlight the dynamic interaction between inflammation and oncogenesis. GlycA, a novel nuclear magnetic resonance (NMR) inflammatory marker that identifies primarily circulating N-acetyl glycan groups attached to acute phase proteins, may be a future CRC risk biomarker.

Methods

We examined the association between GlycA and incident CRC and mortality in two prospective cohorts (N = 34,320); Discovery cohort: 27,495 participants from Women's Health Study (WHS); Replication cohort: 6,784 participants from Multi-Ethnic Study of Atherosclerosis (MESA). Multivariable Cox models were adjusted for clinical risk factors and compared GlycA to acute phase proteins (high-sensitivity C-reactive protein [hsCRP], fibrinogen, and soluble intercellular adhesion molecule-1 [sICAM-1]).

Results

In WHS (median follow-up 19 years, 337 cases, 103 deaths), adjusted HRs (95% CIs) per SD increment of GlycA for CRC incidence and mortality were 1.19 (1.06–1.35; p = 0.004) and 1.24 (1.00–1.55; p = 0.05), respectively. We replicated findings in MESA (median follow-up 11 years, 70 cases, 23 deaths); HRs (95% CIs) per SD of GlycA for CRC incidence and mortality were 1.32 (1.06–1.65; p = 0.01) and 1.54 (1.06–2.23; p = 0.02), respectively, adjusting for age, sex, and race. Pooled analysis, adjusted HR (95% CI) per SD of GlycA for CRC incidence and mortality was 1.26 (1.15–1.39; p = 1 x 10⁻⁶). Other acute phase proteins (hsCRP, fibrinogen, and sICAM-1) had weaker or no association with CRC incidence, while only fibrinogen and GlycA were associated with CRC mortality.

Conclusions

The clinical utility of GlycA to personalize CRC therapies or prevention warrants further study.

Trial Registration

ClinicalTrials.gov: WHS NCT00000479, MESA NCT00005487

Single incision laparoscopic cholecystectomy in geriatric patients

BACKGROUND

Laparoscopy is a surgical approach recommended for the treatment of gall bladder disease. It is recommended also in geriatric patients. Recently Single Incision Laparoscopic Cholecystectomy (SILC) has been proposed to minimize surgical trauma, recovery and hospitalization time. However, the results and advantages of SILC in the geriatric population have received minimal attention. This case series review is focused on the results of SILC in the geriatric population.

METHODS

The records of 355 patients who had undergone SILC were reviewed. This report identifies, in the entire cohort, 40 patients aged 65 years or older at the time of surgery who will be the object of this study (geriatric series). Clinical outcomes and results were evaluated. Moreover, post-operative pain of the geriatric cohort was compared to that of the entire series.

RESULTS

SILC was successfully completed for 347 out of 355 patients of the entire series, with no mortality reported. In total SILC was converted to standard laparoscopy in 10 patients (2.2%) but never to open procedure. No significant difference was found between the total cohort and the geriatric series in terms of median time of operation (61.20 min vs 68.38 min). Post-operative pain was significantly lower in geriatric patients.

CONCLUSION

SILC is an effective and safe procedure for the treatment of gallbladder disease of elderly, also in terms of post-operative pain and it represents an alternative to the standard laparoscopic approach on a routine basis.

Silencing of ST6Gal I enhances colorectal cancer metastasis by down-regulating KAI1 via exosome-mediated exportation and thereby rescues integrin signaling

Aberrant sialylation has long been correlated with human cancer. Increased ST6 Gal I (β-galactoside α 2, 6 sialyltransferase) and consequently higher levels of cell-surface α 2, 6 sialylation has been associated with human colorectal cancer (CRC) metastasis. We have extensive circumstantial data that sialylation is connected to cancer metastasis, but we do not understand in detail how sialylation can switch on/off multiple steps in cancer metastasis. To investigate the molecular mechanism underlying the ST6Gal I-mediated metastasis of CRC, we silenced the ST6Gal I gene in a metastatic SW620 CRC cell line (SW620-shST6Gal I) and examined the metastatic behavior of the cells. We found that various hallmarks of metastatic ability were considerably enhanced in ST6Gal 1-depleted SW620 clones, as assessed both in vitro and in vivo . In particular, the metastasis suppressor, KAI1, was down-regulated in ST6Gal I-deficient SW620 clones. This reflected the increased exosome-mediated exportation of KAI1, and was associated with a decrease in the KAI1-mediated inhibition of integrin. These findings indicate that gene silencing of ST6Gal I could enhance metastasis of CRC by down-regulating KAI1 activity and rescuing its negative effects on integrin signaling.

Multivisceral resection for occlusive colorectal cancer: Is it justified?

BACKGROUND

The only possibility of curative surgery in primary T4, locally advanced, adherent colorectal carcinoma (LAACRC) or recurrent disease with infiltration of adjacent organs is the en bloc resection of the invaded structures to achieve clear surgical margins (R0). The role of extended resections for occlusive LAACRC remains unclear. We report on our experience on Multivisceral resections (MVR) for LAACRC patients between 2003 and 2012.

METHODS

Twenty-two patients, who were treated with MVR with curative purpose for non-metastatic disease were recruited. General epidemiologic data, clinical findings, surgical treatment and/or multimodal therapy, histo-pathological examination and follow-up were collected. In addition post-operative complications were classified. Patients with occlusive LAACRC (n = 6) were compared to patients with uncomplicated presentation (n = 16) defined according to the UICC classification.

RESULTS

No statistically significant differences were observed between the two groups, in terms of median age, gender and localization of tumors. R0 resection was performed in 14 (87.5%) patients with uncomplicated tumors and in all patients with occlusive LAACRC. R1 resection was performed in 2/16 (12.5%) patients with uncomplicated disease. No peri-operative mortality was reported in patients of both groups. In the group of uncomplicated tumors, 11 patients (68.7%) were classified as pathological (p)T4 and 5 patients (31.2%) were classified pT3 whereas in the group of occlusive LAACRC the majority of patients were classified as pT4 (83.3%). Lymph node involvement occurred in 9 patients (56.2%) of the fist group and in two patients (33.3%) of the second group, respectively. The 3-year survival rates in all patients with both uncomplicated and occlusive diseases were 58.4% and 33.3%, respectively. The 3-years survival of patients with locally advanced adherent rectal cancer was significantly lower than the observed survival of patients with colon cancer (p < 0.0001).

CONCLUSION

MVR offers cure (R0 resections) in uncomplicated and obstructive LAACRC with three years survival in 40% of patients. Patients affected by rectal cancer with occlusive disease showed significantly decreased survival in comparison with those affected by colon cancer.

The impact of BMI on early colorectal neoplastic lesions and the role of endoscopic diagnosis:. An Italian observational study

INTRODUCTION

CRC often arises from polyps: an early detection and resection are effective in decreasing both incidence and mortality rate. Relation between risk factors, adenomas and CRC have been showed, but there is little evidence for overweight association with preneoplastic lesions. This study analyzed the correlation between body mass index (BMI) and primitive site of polyps.

METHODS

We performed a retrospective study, in a period between January 2010 and October 2014. Subjects aged 50 years and older who underwent their first-time screening colonoscopy were included. Reports regarding characteristic of the polyps were collected.

RESULTS

142 patients were enrolled and they were divided into two groups: group I - patients with left sided colonic polyps, and group II - patients who right sided colonic polyps. The ANOVA test-one way, documents a difference between the BMI and the colon localization of polyps.

CONCLUSIONS

Patients with overweight had a higher risk to develop lesions in the left colon compared to patients with normal weight. Despite the fact that Italian epidemiological studies have found a prevalence of polyps of 44-53% in rectal-sigmoid segment, 32-36% in transverse segment and of 14-20% in right segment, we showed an incidence of 26.05% for right sided polyps, which maybe related with the eating habits of the territory.

Lectin-based protein microarray analysis of differences in serum alpha-2-macroglobulin glycosylation between patients with colorectal cancer and persons without cancer

Glycosylation is co- and posttranslational modifications affecting proteins. The glycopattern changes are associated with changes in biological function and are involved in many diseases including cancer. We present the lectin-based protein microarray method enabling determination of differences in protein glycosylation. The method involves isolation of targeted protein from samples by immunoprecipitation, spotting of protein from multiple samples into arrays on a microarray slide, incubation with set of biotinylated lectins, the reaction with fluorescent conjugate of streptavidin, and detection of fluorescent intensities by microarray scanner. Lectin-based protein microarray was applied in investigation of differences in alpha-2-macroglobulin (α2M) glycosylation isolated from sera samples of healthy persons and patients with colorectal cancer (CC). From 14 lectins used in analysis, statistically significant differences (Student's t-test, P < 0.05) between two groups of samples (persons without cancer and CC patients) were found for 5 of them. α2M molecules isolated from sera of CC patients have higher content of α2,6 sialic acid, N-acetylglucosamine and mannose residues, and tri-/tetraantennary complex type high-mannose N-glycans. A novel lectin-based protein microarray developed and described can serve as a suitable analytical technique for sensitive, simple, fast, and high-throughput determination of differences in protein glycosylation isolated from serum or other samples.

Dose-dependent effect of 2-deoxy-D-glucose on glycoprotein mannosylation in cancer cells

High glucose consumption due to Warburg effect is one of the metabolic hallmarks of cancer. Consequently, glucose antimetabolites, such as 2-deoxy-glucose (2DG), can induce substantial growth inhibition of cancer cells. However, the inhibition of metabolic pathways is not the sole effect of 2DG on cancer cells. As mannose-mimetic molecule, 2DG is believed to interfere with normal glycosylation of proteins in cells. Here, we address how 2DG influences protein glycosylation in cancer cells and discuss possible implications of the consequences of this influence. In detail, six colorectal cancer cell lines were examined for alterations of protein glycosylation by measuring monosaccharide incorporation into cellular glycoproteins and cell surface glycosylation by lectin FACS. A significant increase in mannose incorporation was observed on treatment with 2DG (1 mM for 48 h), which was also reflected by an increased binding of the mannose-binding lectin Concanavalin A in FACS analysis. This phenomenon, which could be reversed by external addition of mannose, was not caused by 2DG-mediated mannosidase inhibition, as shown by pulse-chase experiments, arguing in favor of the hypothesis that 2DG directly influenced the incorporation of mannose. Increased mannose content was generally observed in cellular glycoproteins, including glycoproteins isolated from the plasma membrane fraction. Our results indicate that 2DG at low doses, which have only a limited metabolism-related effect on glycosylation, induces a strong increase in mannose incorporation into cellular glycoproteins. On the other hand, higher 2DG concentrations (10 and 20 mM) led to a significant decrease of absolute mannose incorporation accompanied by a dramatically reduced protein synthesis rate. 2DG-induced alterations of glycosylation may represent a novel mechanism potentially explaining the varied effects of 2DG on cancer cells. Moreover, 2DG treatment may open a path toward novel diagnostic and cancer therapeutic approaches, which specifically target altered glycoantigen structures induced by 2DG.

Lysyl hydroxylase 2 induces a collagen cross-link switch in tumor stroma

Epithelial tumor metastasis is preceded by an accumulation of collagen cross-links that heighten stromal stiffness and stimulate the invasive properties of tumor cells. However, the biochemical nature of collagen cross-links in cancer is still unclear. Here, we postulated that epithelial tumorigenesis is accompanied by changes in the biochemical type of collagen cross-links. Utilizing resected human lung cancer tissues and a p21CIP1/WAF1-deficient, K-rasG12D-expressing murine metastatic lung cancer model, we showed that, relative to normal lung tissues, tumor stroma contains higher levels of hydroxylysine aldehyde-derived collagen cross-links (HLCCs) and lower levels of lysine aldehyde-derived cross-links (LCCs), which are the predominant types of collagen cross-links in skeletal tissues and soft tissues, respectively. Gain- and loss-of-function studies in tumor cells showed that lysyl hydroxylase 2 (LH2), which hydroxylates telopeptidyl lysine residues on collagen, shifted the tumor stroma toward a high-HLCC, low-LCC state, increased tumor stiffness, and enhanced tumor cell invasion and metastasis. Together, our data indicate that LH2 enhances the metastatic properties of tumor cells and functions as a regulatory switch that controls the relative abundance of biochemically distinct types of collagen cross-links in the tumor stroma.