Tissue-specific Biomarkers Research Articles

Long non-coding RNA PCED1B antisense RNA 1 promotes gastric cancer progression via modulating microRNA-215-3p / C-X-C motif chemokine receptor 1 axis

ABSTRACT Long non-coding RNAs (lncRNAs) emerge as vital modulators and tissue-specific biomarkers of multiple cancers, including gastric cancer (GC). Instead, the expression characteristics, biological function and molecular mechanism of lncRNA PCED1B antisense RNA 1 (PCED1B-AS1) in GC await more elaboration. In this study, 48 cases of GC tissues and matched non-cancerous tissues were collected, and PCED1B-AS1, microRNA-215-3p (miR-215-3p) and C-X-C motif chemokine receptor 1 (CXCR1) expression levels were detected by qRT-PCR. Besides, CCK-8, EdU, Transwell and Western blot assays were conducted to assess the impact of PCED1B-AS1 or miR-215-3p on cell growth, migration, invasion and epithelial-mesenchymal transition (EMT). The interaction between genes was verified by bioinformatics analysis, rna immunoprecitipation (RIP) and dual-luciferase reporter gene assays. We demonstrated that, PCED1B-AS1 expression level was raised in GC tissues and cell lines, and increased expression of PCED1B-AS1 was in association with tumor size, TNM stage and lymph node metastasis in GC patients. Additionally, PCED1B-AS1 overexpression promoted GC cells proliferation, migration, invasion and EMT, and miR-215-3p overexpression counteracted the biological effects of PCED1B-AS1. Mechanistically, PCED1B-AS1 specifically inhibited miR-215-3p expressions, thus up-regulating CXCR1 expressions. In conclusion, PCED1B-AS1 accelerates GC progression via adsorbing miR-215-3p and up-regulating CXCR1, indicating that PCED1B-AS1 is a novel therapeutic target for treating GC.

Tissue-Specific Ultra-Short Telomeres in Chronic Obstructive Pulmonary Disease.

PurposeTelomere biology, especially tissue-specific ultra-short telomeres, might provide a strong contribution to our current knowledge in COPD development as well as a predictive marker for prognosis. To test this hypothesis, we investigated telomere lengths in lung tissue and leukocytes in patients diagnosed with COPD.Patients and MethodsThirty-two patients were included in the current study. All patients showed a post-bronchodilator ratio of less than 70% post-bronchodilator predicted value of forced expiratory volume in second (FEV1%), mean 56%; range [19% to 86%]. To be able to investigate ultra-short telomeres, universal single telomere length analysis (U-STELA) was used.ResultsOur results showed a higher level of the ultra-short telomere presence in bronchoalveolar lavage (BAL) cells when compared to leukocytes with statistical significance t(62)=5.771, p<0.00001. The FEV1% was lower in subjects with ultra-short telomeres in BAL (50.6% vs 81.6%: p<0.001) and in ultra-short telomeres in blood leukocytes (37.3% vs 58.5%: p=0.051) when compared to subjects without ultra-short telomeres in leukocytes. Furthermore, the patients who had ultra-short telomeres in BAL samples were significantly older (p=0.014) than patients who did not have ultra-short telomeres. Ultra-short telomeres in BAL (p=0.05) but not in leukocytes (p=0.33) were associated with FEV1% in a regressions model adjusting for age (p<0.0001), ever smoking (p<0.0001) and sex (p=0.71). The patients with ultra-short telomeres were graded higher in the Global Initiative for Chronic Obstructive Lung Disease (GOLD) classification (p=0.006).ConclusionThis study emphasizes the need to investigate the correct tissue to get a representative evaluation of the stage or advancedness of COPD. To our knowledge, this is the first study to show that there is a correlation between the presence of ultra-short telomeres in lung tissue and COPD severity. Our results suggest that ultra-short telomeres are involved in the molecular pathogenesis of COPD and might be used as a tissue-specific predictive biomarker.

Identification of differentially methylated HpaII sites by NGS analysis of HpaII-digested libraries

Differentially methylated regions (DMRs) have been widely explored as epigenetic biomarkers. Here, we developed a novel approach combining methylation-sensitive restriction enzyme (MSRE) and next-generation sequencing (NGS) to identify DMRs between chorionic villi (CV) and maternal blood cells (MBC). During NGS library preparation, adapter-ligated genomic DNA of CV and MBC were digested with the MSRE, HpaII, and PCR-amplified. As unmethylated HpaII sites were cleaved, the resulted library should contain only methylated HpaII sites. By sequencing both HpaII-digested CV and MBC libraries, 9 differentially methylated-HpaII sites on chromosome 21 which exhibited more than 50% methylation increase in CV were identified. These DMRs are epigenetic biomarkers to tell the difference between CV and MBC. Our approach will also be applicable to screen various tissue-specific epigenetic biomarkers.

Tumor Tissue-Specific Biomarkers of Colorectal Cancer by Anatomic Location and Stage.

The progress in the discovery and validation of metabolite biomarkers for the detection of colorectal cancer (CRC) has been hampered by the lack of reproducibility between study cohorts. The majority of discovery-phase biomarker studies have used patient blood samples to identify disease-related metabolites, but this pre-validation phase is confounded by non-specific disease influences on the metabolome. We therefore propose that metabolite biomarker discovery would have greater success and higher reproducibility for CRC if the discovery phase was conducted in tumor tissues, to find metabolites that have higher specificity to the metabolic consequences of the disease, that are then validated in blood samples. This would thereby eliminate any non-tumor and/or body response effects to the disease. In this study, we performed comprehensive untargeted metabolomics analyses on normal (adjacent) colon and tumor tissues from CRC patients, revealing tumor tissue-specific biomarkers (n = 39/group). We identified 28 highly discriminatory tumor tissue metabolite biomarkers of CRC by orthogonal partial least-squares discriminant analysis (OPLS-DA) and univariate analyses (VIP > 1.5, p < 0.05). A stepwise selection procedure was used to identify nine metabolites that were the most predictive of CRC with areas under the curve (AUCs) of >0.96, using various models. We further identified five biomarkers that were specific to the anatomic location of tumors in the colon (n = 236). The combination of these five metabolites (S-adenosyl-L-homocysteine, formylmethionine, fucose 1-phosphate, lactate, and phenylalanine) demonstrated high differentiative capability for left- and right-sided colon cancers at stage I by internal cross-validation (AUC = 0.804, 95% confidence interval, CI 0.670–0.940). This study thus revealed nine discriminatory biomarkers of CRC that are now poised for external validation in a future independent cohort of samples. We also discovered a discrete metabolic signature to determine the anatomic location of the tumor at the earliest stage, thus potentially providing clinicians a means to identify individuals that could be triaged for additional screening regimens.

Proteomic analysis in lupus mice identifies Coronin-1A as a potential biomarker for lupus nephritis

BackgroundApproximately 50% of systemic lupus erythematosus (SLE) patients develop nephritis, which is among the most severe and frequent complications of the disease and a leading cause of morbidity and mortality. Despite intensive research, there are still no reliable lupus nephritis (LN) markers in clinical use that can assess renal damage and activity with a high sensitivity and specificity. To this end, the aim of this study was to identify new clinically relevant tissue-specific protein biomarkers and possible underlying molecular mechanisms associated with renal involvement in SLE, using mass spectrometry (MS)-based proteomics.MethodsKidneys were harvested from female triple congenic B6.NZMsle1/sle2/sle3 lupus mice model, and the respective sex- and age-matched C57BL/6 control mice at 12, 24 and 36 weeks of age, representing pre-symptomatic, established and end-stage LN, respectively. Proteins were extracted from kidneys, purified, reduced, alkylated and digested by trypsin. Purified peptides were separated by liquid chromatography and analysed by high-resolution MS. Data were processed by the Progenesis QIp software, and functional annotation analysis was performed using DAVID bioinformatics resources. Immunofluorescence and multiple reaction monitoring (MRM) MS methods were used to confirm prospective biomarkers in SLE mouse strains as well as human serum samples.ResultsProteomic profiling of kidney tissues from SLE and control mice resulted in the identification of more than 3800 unique proteins. Pathway analysis revealed a number of dysregulated molecular pathways that may be mechanistically involved in renal pathology, including phagosome and proximal tubule bicarbonate reclamation pathways. Proteomic analysis supported by human transcriptomic data and pathway analysis revealed Coronin-1A, Ubiquitin-like protein ISG15, and Rho GDP-dissociation inhibitor 2, as potential LN biomarkers. These results were further validated in other SLE mouse strains using MRM-MS. Most importantly, experiments in humans showed that measurement of Coronin-1A in human sera using MRM-MS can segregate LN patients from SLE patients without nephritis with a high sensitivity (100%) and specificity (100%).ConclusionsThese preliminary findings suggest that serum Coronin-1A may serve as a promising non-invasive biomarker for LN and, upon validation in larger cohorts, may be employed in the future as a screening test for renal disease in SLE patients.

Long noncoding RNA SLC30A10 promotes colorectal tumor proliferation and migration via miR-21c/APC axis.

Colorectal cancer is a common malignancy and a common cause of tumor-related death. Long non-coding RNAs (lncRNAs) have become an important regulatory factor and tissue specific biomarker for a variety of cancers, including colorectal cancer. Recent evidence indicates that the novel lncRNA SLC30A10 plays an important role in tumor progression and metastasis. However, its role and molecular mechanisms in colorectal cancer are unclear. SLC30A10 expression was detected in 12 colorectal cancer and adjacent normal tissues by quantitative reverse transcription PCR. Insights into the underlying mechanisms of competitive endogenous RNAs (ceRNAs) were determined by transwell assay, CCK8 assay, and luciferase assay. SLC30A10 was down-regulated in colorectal cancer tissues and cell lines, and its low expression was positively correlated with colorectal cancer progression and metastasis. Functionally, SLC30A10 depletion promotes cell proliferation and migration in colorectal cancer cells, while SLC30A10 overexpression has the opposite effect. Bioinformatics prediction and luciferase assay indicated that miR-21c is a direct target of SLC30A10, which plays the role of ceRNA in regulating colorectal cancer metastasis. In addition, miR-21c specifically targets APC gene. Our findings suggest that reduced expression of SLC30A10 is associated with aggressive tumor phenotypes and poor patient outcomes in colorectal cancer. SLC30A10 inhibits colorectal cancer progression and metastasis by acting as a ceRNA for miR-21c to regulate APC expression, suggesting that SLC30A10 may serve as a potential prognostic biomarker and anti-metastatic therapeutic target for colorectal cancer.

Identification of miRNA signatures associated with radiation-induced late lung injury in mice.

Acute radiation exposure of the thorax can lead to late serious, and even life-threatening, pulmonary and cardiac damage. Sporadic in nature, late complications tend to be difficult to predict, which prompted this investigation into identifying non-invasive, tissue-specific biomarkers for the early detection of late radiation injury. Levels of circulating microRNA (miRNA) were measured in C3H and C57Bl/6 mice after whole thorax irradiation at doses yielding approximately 70% mortality in 120 or 180 days, respectively (LD70/120 or 180). Within the first two weeks after exposure, weight gain slowed compared to sham treated mice along with a temporary drop in white blood cell counts. 52% of C3H (33 of 64) and 72% of C57Bl/6 (46 of 64) irradiated mice died due to late radiation injury. Lung and heart damage, as assessed by computed tomography (CT) and histology at 150 (C3H mice) and 180 (C57Bl/6 mice) days, correlated well with the appearance of a local, miRNA signature in the lung and heart tissue of irradiated animals, consistent with inherent differences in the C3H and C57Bl/6 strains in their propensity for developing radiation-induced pneumonitis or fibrosis, respectively. Radiation-induced changes in the circulating miRNA profile were most prominent within the first 30 days after exposure and included miRNA known to regulate inflammation and fibrosis. Importantly, early changes in plasma miRNA expression predicted survival with reasonable accuracy (88–92%). The miRNA signature that predicted survival in C3H mice, including miR-34a-5p, -100-5p, and -150-5p, were associated with pro-inflammatory NF-κB-mediated signaling pathways, whereas the signature identified in C57Bl/6 mice (miR-34b-3p, -96-5p, and -802-5p) was associated with TGF-β/SMAD signaling. This study supports the hypothesis that plasma miRNA profiles could be used to identify individuals at high risk of organ-specific late radiation damage, with applications for radiation oncology clinical practice or in the context of a radiological incident.

Immunoglobulin A antibodies to oxidized collagen type II as a potential biomarker for the stratification of spondyloarthritis from rheumatoid arthritis

Objectives The discovery of diseased tissue-specific neoantigens offers the opportunity to develop important disease tissue-specific biomarkers that can help in the prediction, diagnosis, and stratification of diseases. This opportunity is specifically significant for autoimmune diseases where diagnostic biomarkers are not available. Inflammatory autoimmune diseases are commonly associated with local generation of large amounts of reactive oxidants. We have previously identified oxidative post-translationally modified (oxPTM) tissue-specific neoantigens in rheumatoid arthritis (RA) and type 1 diabetes that elicit an immune response. In the current study, we studied the presence and clinical significance of antibodies to oxPTM collagen type II (CII) in patients with spondyloarthritis (SpA). Method Levels of antibodies specific to native CII and oxPTM-CII were assessed by enzyme-linked immunosorbent assay. Results Immunoglobulin G (IgG) binding to oxPTM-CII was observed in 52%, 83%, and 28% of serum samples from patients with axial spondyloarthritis (axSpA), RA, and psoriatic arthritis (PsA), respectively. Importantly, while strong IgA anti-oxPTM-CII responses were detected in axSpA and PsA patients, with 47% and 84% respective binders, no IgA anti-oxPTM-CII was detected in RA patients. IgA anti-oxPTM-CII reactivity in axSpA patients treated with biologics was higher and more frequent, with 85% binders compared to 9% binders in patients treated with synthetic disease-modifying anti-rheumatic drugs. Conclusion Our data imply that SpA and PsA are associated with the presence of antibodies to oxPTM-CII, suggesting that there may be a humoral component that may distinguish patients with SpA from RA. Our approach could be adapted to other diseases, particularly to inflammatory autoimmune diseases.

Identification of cadaveric liver tissues using thanatotranscriptome biomarkers

Thanatotranscriptome studies involve the examination of mRNA transcript abundance and gene expression patterns in the internal organs of deceased humans. Postmortem gene expression is indicative of the cellular status of a corpse at the time of death, a portion of which may represent a cascade of molecular events occasioned by death. Specific gene biomarkers identify perceptible transcriptional changes induced by stochastic responses to the cessation of biological functions. Transcriptome analyses of postmortem mRNA from a tissue fragment may determine unique molecular identifiers for specific organs and demonstrate unique patterns of gene expression that can provide essential contextual anatomical information. We evaluated the impact of targeted transcriptome analysis using RNA sequencing to reveal global changes in postmortem gene expression in liver tissues from 27 Italian and United States corpses: 3.5-hour-old to 37-day-old. We found that our single blind study using eight liver tissue-specific gene biomarkers (e.g. AMBP and AHSG) is highly specific, with autopsy-derived organ samples correctly identified as tissues originating from postmortem livers. The results demonstrate that 98–100% of sequencing reads were mapped to these liver biomarkers. Our findings indicate that gene expression signatures of mRNA exposed up to 37 days of autolysis, can be used to validate the putative identity of tissue fragments.

Syncytiotrophoblast extracellular microvesicle profiles in maternal circulation for noninvasive diagnosis of preeclampsia

Preeclampsia is the most common placental pathology in pregnant females, with increased morbidity and mortality incurred on the mother and the fetus. There is a need for improved biomarkers for diagnosis and monitoring of this condition. Placental syncytiotrophoblasts at the maternal-fetal interface release nanoparticles, including extracellular microvesicles, into the maternal blood during pregnancy. Syncytiotrophoblast extracellular microvesicles (STEVs) are being studied for their diagnostic potential and for their potential physiologic role in preeclampsia. We hypothesized that STEV profiles in maternal circulation would be altered under conditions of preeclampsia compared to normal pregnancy. Extracellular vesicles (EVs) released by BeWo cells in vitro showed high expression of syncytin-1, but no plac1 expression, demonstrating that trophoblast cell EVs express syncytin-1 on their surface. Placental alkaline phosphatase also showed high expression on BeWo EVs, but due to concern for cross reactivity to highly prevalent isoforms of intestinal and bone alkaline phosphatase, we utilized syncytin-1 as a marker for STEVs. In vivo, syncytin-1 protein expression was confirmed in maternal plasma EVs from Control and Preeclampsia subjects by Western blot, and overall, lower expression was noted in samples from patients with preeclampsia (n = 8). By nanoparticle analysis, EV profiles from Control and Preeclampsia groups showed similar total plasma EV quantities (p = 0.313) and size distribution (p = 0.415), but STEV quantitative signal, marked by syncytin-1 specific EVs, was significantly decreased in the Preeclampsia group (p = 2.8 × 10−11). Receiver operating characteristic curve demonstrated that STEV signal threshold cut-off of <0.316 was 95.2% sensitive and 95.6% specific for diagnosis of preeclampsia in this cohort (area under curve = 0.975 ± 0.020). In conclusion, we report that the syncytin-1 expressing EV profiles in maternal plasma might serve as a placental tissue specific biomarker for preeclampsia.

Bioinformatic Identification of a Breast Tissue-Specific Gene Expression Profile

The clinical significance of cancer biomarkers is undoubtedly, especially for those with tissue specificity. To date, there are not any widely-accepted breast tissue-specific biomarkers. The revolutionized development of gene analysis techniques has generated a vast amount of data on human transcriptomics and proteomics, allowing us to search for breast tissue-specific biomarkers in a systematic way. In this study, by integrating and investigating the standardized raw RNA-Seq data of near 50,000 human genes across 88 human tissues from the GTEx, the Illumina Body Map, and the RIKEN FANTOM5 project, we identified that only 96 genes in human genome were potential breast tissue-specific biomarkers, with the majority of these genes were poorly understood at the current stage. Moreover, by further analyzing the TCGA project, the GEPIA database, the Ensemble Genome Browser, and the Kaplan-Meier Plotter database, we demonstrated that two breast-specific genes, ANKRD30A and LINC00993 that we previously identified to be considerably down-regulated in TNBC, may play important roles in breast cancer because of their breast cancer specificity, distinct expression patterns in breast cancer subtypes, and effectiveness for prognostic predictions. In summary, we present a potential breast tissue-specific gene expression profile, an updated strategy for the search of tissue-specific biomarkers, and reasons for performing further researches on these promising biomarkers in breast cancer. Funding Statement: This study is supported by the China Scholarship Council (CSC). Declaration of Interests: The authors have declared no conflicts of interest related to the present manuscript. Ethics Approval Statement: Not required.

Serum uromodulin is inversely associated with the metabolic syndrome in the KORA F4 study.

ObjectiveMetabolic syndrome and obesity are risk factors for chronic kidney disease. However, early kidney alterations may escape diagnosis in these conditions due to glomerular hyperfiltration. Uromodulin, a glycoprotein exclusively synthesized in tubular cells of the thick ascending limb of Henle's loop, is a novel tissue-specific biomarker for kidney function. In contrast to the commonly used markers creatinine and cystatin C, serum uromodulin does not primarily depend on glomerular filtration. We hypothesized that serum uromodulin is a marker for metabolic syndrome and related components.DesignThe analyses included 1088 participants of the population-based KORA F4 study aged 62–81 years. Metabolic syndrome was present in 554 participants. After a mean follow-up time of 6.5 years, 621 participants were reevaluated, of which 92 had developed incident metabolic syndrome.MethodsThe association of serum uromodulin with metabolic syndrome and its components were assessed using multivariable logistic regression models.ResultsSerum uromodulin was inversely associated with metabolic syndrome after adjustment for sex, age, estimated glomerular filtration rate, physical activity, smoking, alcohol consumption and high-sensitivity C-reactive protein (OR 0.65; 95% CI 0.56–0.76 per standard deviation uromodulin; P < 0.001). Serum uromodulin was inversely associated with all single components of metabolic syndrome. However, serum uromodulin was not associated with new-onset metabolic syndrome after the follow-up period of 6.5 ± 0.3 years (OR 1.18; 95% CI 0.86–1.60).ConclusionsSerum uromodulin is independently associated with prevalent, but not with incident metabolic syndrome. Low serum uromodulin may indicate a decreased renal reserve in the metabolic syndrome.

Effect of the Biofield Energy Treated Test Formulation on Tissue Specific Biomarkers in Various Human Cells

Effect of the Biofield Energy Treated Test Formulation on Tissue Specific Biomarkers in Various Human Cells

Immunotherapy clinical trials suggest predictive immune-related biomarkers are tissue specific.

e14206 Background: RNA-based immune landscape signatures (RILS) portray the breadth of immune and stromal cell activity in the tumor microenvironment (TME). Their predictive and prognostic capability for patients with solid tumors and treated with various therapies has been reported. Methods: Single and multi-variable survival analysis, multi-variable linear models, publicly available data on clinical trials NCT00796445, NCT01621490, NCT02108652. Results: Using publicly available data, RILS were compared to each other and to tumor mutational burden (TMB) to determine their relative ability to identify responders/non-responders and estimate patient survival in a series of immunotherapy clinical trials. These immunotherapy trials include patients treated with a PD1 inhibitor, PD-L1 inhibitor or MAGE-A3 tumor antigen combined with immunostimulant (MAGE-A3). Although no single RILS/TMB biomarker emerged as a clear indicator of immunotherapy response and survival for all cases, there were certain immune-related signatures that recurred as significant (p &lt; .05) or had near-significance (p &lt; .10) related to a specific cancer or therapy. Immune signatures for T cell trafficking, ratios of PD1 to PD-L1 expression, cytotoxic lymphocytes and B cells were consistently predictive and prognostic in melanoma patients treated with the PD1 inhibitor, nivolumab or MAGE-A3. However, while these same signatures were not predictive/prognostic in bladder and kidney/ureter cancer patients treated with the PD-L1 inhibitor, atezolizumab, biomarkers significantly associated with outcome included TMB, TGFB1, and the ratio of T cell trafficking to M2 tumor associated macrophage activity. Since TMB and various immune signatures generally worked better together than individually in predicting outcome, there is potential for utilization of a combination of biomarkers and immune signatures in the design of effective immunotherapy clinical trials. Conclusions: In summary, our results suggest effective immunotherapy trials may require tissue-specific biomarker development. Further, a combination of immune signatures and biomarkers such as TMB shows markedly increased utility compared to single factor such as TMB, PD-1 or PD-L1 expression alone.

Serum uromodulin and Roux-en-Y gastric bypass: improvement of a marker reflecting nephron mass

BackgroundEarly diagnosis of kidney disease in obese patients and in such patients with type 2 diabetes (T2D) can significantly improve treatment outcome. Serum uromodulin (sUMOD) may be a sensitive parameter for early detection of nephropathy. ObjectivesTo analyze sUMOD and traditional markers of kidney function in a cohort study of patients with and without obesity or T2D undergoing metabolic surgery compared with blood donors. SettingUniversity of Heidelberg, Germany. MethodsPatients with obesity (body mass index >35 kg/m2) without T2D (n = 10) and T2D (n = 10) and patients with nonsevere obesity (body mass index, 25–35 kg/m2) and insulin-dependent T2D (n = 16) undergoing Roux-en-Y gastric bypass (RYGB) were enrolled. The control group consisted of 190 blood donors. sUMOD was compared with established renal markers. ResultsUsing sUMOD, impaired kidney function at baseline was present in both groups with T2D and in none of the patients with obesity without T2D. This impairment was not detectable through traditional markers. Significant improvement of sUMOD was shown in patients with obesity and T2D 12 months postoperatively (from 130.0 ± 77.5 to 239.5 ± 179.0 ng/mL; P = .004) and in patients with nonsevere obesity and T2D 6 months after RYGB (from 140.6 ± 78.0 to 298.7 ± 154.0 ng/mL; P = .017). In patients with obesity without T2D, sUMOD remained stable (P = .375). ConclusionssUMOD may serve as a tissue-specific biomarker in incipient diabetic nephropathy. Improvement of sUMOD after RYGB seems to profoundly restore the structural integrity of nephrons in these patients at risk for diabetic nephropathy.

Identification of a potential tissue-specific biomarker cathepsin L-like gene from the planarian Dugesia japonica: Molecular cloning, characterization, and expression in response to heavy metal exposure

Heavy metal pollution is a global health issue affecting people worldwide, and the exploration of sensitive biomarkers to assess the toxicity of heavy metals is an important work for researchers. Cathepsin L, role as a tissue-specific biomarker to assess the biological effects of environmental pollutants, has not received much attention. In this work, the full-length cDNA of cathepsin L gene from the planarian Dugesia japonica (designated DjCatL) was cloned by rapid amplification of cDNA ends (RACE) technique. The cDNA sequence of DjCatL is 1161 bp, which encodes a protein of 346 amino acids with a molecular weight of 39.03 kDa. Sequence analysis revealed that DjCatL contains highly conserved ERF/WNIN, GNFD, and GCXGG motifs, which are the features of the cathepsin L protein family. Whole-mount in situ hybridization (WISH) results revealed that the transcripts of DjCatL are specifically distributed in the intestinal system, suggesting that this gene is related to food digestion in planarians. Both quantitative polymerase chain reaction (qPCR) and WISH results revealed that the transcriptional levels of DjCatL are inhibited significantly by heavy metal (Cd2+, Hg2+, and Cu2+) exposure in a dose-dependent manner. Therefore, we proposed that cathepsin L can be used as a tissue-specific biomarker to assess the heavy metal pollution in the aquatic environment.

Tissue-Specific Biomarker Responses in the Blue Mussel Mytilus spp. Exposed to a Mixture of Microplastics at Environmentally Relevant Concentrations

The impact of a microplastic (MP) mixture composed of polyethylene (PE) andpolypropylene (PP) plastic particles, prepared from commercially available products,was evaluated in blue mussels Mytilus spp. exposed to three environmentally relevantconcentrations: 0.008 μg L−1 (low), 10 μg L−1 (medium), and 100 μg L−1 (high).Organisms were exposed for 10 days followed by 10 days of depuration in clean seawaterunder controlled laboratory conditions. The evaluation of MP effects on mussel clearancerate, tissue structure, antioxidant defenses, immune and digestive parameters, and DNAintegrity were investigated while the identification of plastic particles in mussel tissues(gills, digestive gland, and remaining tissues), and biodeposits (feces and pseudofaeces)was performed using infrared microscopy (μFT-IR). Results showed the presence of MPsonly in the digestive gland of mussels exposed to the highest tested concentration ofMPs with a mean of 0.75 particle/mussel (after the 10 days of exposure). In biodeposits,PE and PP particles were detected following exposure to all tested concentrationsconfirming the ingestion of MPs by the organisms. A differential response of antioxidantenzyme activities between digestive gland and gills was observed. Significant increasesin superoxide dismutase (SOD) and catalase (CAT) activities were measured in thedigestive gland of mussels exposed to the low (0.008 μg L−1) and medium (10 μg L−1)concentrations ofMPs and in the gills frommussels exposed to the highest concentration(100 μg L−1) of MPs that could be indicative of a change in the redox balance. Moreover,an increase in acid phosphatase activity was measured in hemolymph of musselsexposed to 0.008 and 10 μg L−1concentrations. No significant difference was observedin the clearance rate, and histopathological parameters between control and exposedmussels. This study brings new insights on the potential sublethal impacts of MPs atenvironmentally relevant concentrations in marine bivalves.

Characterization of tissue-specific biomarkers with the expression of circRNAs in forensically relevant body fluids.

Messenger RNA (mRNA) markers have been extensively investigated for the identification of forensically relevant body fluids and tissues based on their expression profiles among cell types. As products of the backsplicing of pre-mRNAs, circular RNAs (circRNAs) share exonic sequences with their linear counterparts. The inclusion of circRNAs in mRNA profiling is shown to facilitate the detection of biomarkers in the identification of body fluids. In this study, we identified the expression of circRNAs of 14 out of 45 biomarkers from five body fluid types using outward-facing primer sets and revealed the ratio of circular to total transcripts of biomarkers by RNase R treatment. Furthermore, our results of qPCR analysis show that the inclusion of circRNAs in the detection of biomarkers, including HBA and ALAS2 for blood; MMP7 and MMP10 for menstrual blood; HTN3 for saliva; SPINK5, SERPINB3, ESR1, and CYP2B7P1 for vaginal secretions; TGM4, KLK3, and PRM2 for semen; and SLC22A6 and MIOX for urine, does not impair the specificity of these biomarkers. Additionally, a high copy number of targets from linear transcripts could be employed to increase the detection sensitivity of TGM4 and KLK3 with a low expression level of circRNAs in urine samples. Altogether, these results will help with the development of robust multiplex assays for body fluid identification.

Tissue-specific transcriptional biomarkers in medicinal plants: Application of large-scale meta-analysis and computational systems biology

Biosynthesis of secondary metabolites in plant is a complex process, regulated by many genes and influenced by several factors. In recent years, the next-generation sequencing (NGS) technology and advanced statistical analysis such as meta-analysis and computational systems biology have provided novel opportunities to overcome biological complexity. Here, we performed a meta-analysis on publicly available transcriptome datasets of twelve economically significant medicinal plants to identify differentially expressed genes (DEGs) between shoot and root tissues and to find the key molecular features which may be effective in the biosynthesis of secondary metabolites. Meta-analysis identified a total of 880 genes with differential expression between two tissues. Functional enrichment and KEGG pathway analysis indicated that the functions of those DEGs are highly associated with the developmental process, starch metabolic process, response to stimulus, porphyrin and chlorophyll metabolism, biosynthesis of secondary metabolites and phenylalanine metabolism. In addition, systems biology analysis of the DEGs was applied to find protein–protein interaction network and discovery of significant modules. The detected modules were associated with hormone signal transduction, transcription repressor activity, response to light stimulus and epigenetic processes. Finally, analysis was extended to search for putative miRNAs that are associated with DEGs. A total of 31 miRNAs were detected which belonged to 16 conserved families. The present study provides a comprehensive view to better understand the tissue-specific expression of genes and mechanisms involved in secondary metabolites synthesis and may provide candidate genes for future researches to improve yield of secondary metabolites.

Identification of tissue-specific tumor biomarker using different optimization algorithms.

Identification of differentially expressed genes, i.e., genes whose transcript abundance level differs across different biological or physiological conditions, was indeed a challenging task. However, the inception of transcriptome sequencing (RNA-seq) technology revolutionized the simultaneous measurement of the transcript abundance levels for thousands of genes. In this paper, such next-generation sequencing (NGS) data is used to identify biomarker signatures for several of the most common cancer types (bladder, colon, kidney, brain, liver, lung, prostate, skin, and thyroid) METHODS: Here, the problem is mapped into the comparison of optimization algorithms for selecting a set of genes that lead to the highest classification accuracy of a two-class classification task between healthy and tumor samples. As the optimization algorithms Artificial Bee Colony (ABC), Ant Colony Optimization, Differential Evolution, and Particle Swarm Optimization are chosen for this experiment. A standard statistical method called DESeq2 is used to select differentially expressed genes before being feed to the optimization algorithms. Classification of healthy and tumor samples is done by support vector machine RESULTS: Cancer-specific validation yields remarkably good results in terms of accuracy. Highest classification accuracy is achieved by the ABC algorithm for Brain lower grade glioma data is 99.10%. This validation is well supported by a statistical test, gene ontology enrichment analysis, and KEGG pathway enrichment analysis for each cancer biomarker signature CONCLUSION: The current study identified robust genes as biomarker signatures and these identified biomarkers might be helpful to accurately identify tumors of unknown origin.