Search results for: biomarker

Authors: Iulianna Taritsa, Kuldeep Neote, Eric Fossel

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Lysosome-induced immunogenic cell death (LIICD) is a powerful mechanism of targeting cancer cells that kills circulating malignant cells and primes the host’s immune cells against future remission. Current immunotherapies for cancer are limited in preventing recurrence – a gap that can be bridged by training the immune system to recognize cancer neoantigens. Lysosomal leakage can be induced therapeutically to traffic antigens from dying cells to dendritic cells, which can later present those tumorigenic antigens to T cells. Previous research has shown that oxidative agents administered in the tumor microenvironment can initiate LIICD. We generated a fusion protein between an oxidative agent known as xanthine oxidase (XO) and a mini-antibody specific for EGFR/HER2-sensitive breast tumor cells. The anti-EGFR single domain antibody fragment is uniquely sourced from llama, which is functional without the presence of a light chain. These llama micro-antibodies have been shown to be better able to penetrate tissues and have improved physicochemical stability as compared to traditional monoclonal antibodies. We demonstrate that the fusion protein created is stable and can induce early markers of immunogenic cell death in an in vitro human breast cancer cell line (SkBr3). Specifically, we measured overall cell death, as well as surface-expressed calreticulin, extracellular ATP release, and HMGB1 production. These markers are consensus indicators of ICD. Flow cytometry, luminescence assays, and ELISA were used respectively to quantify biomarker levels between treated versus untreated cells. We also included a positive control group of SkBr3 cells dosed with doxorubicin (a known inducer of LIICD) and a negative control dosed with cisplatin (a known inducer of cell death, but not of the immunogenic variety). We looked at each marker at various time points after cancer cells were treated with the XO/antibody fusion protein, doxorubicin, and cisplatin. Upregulated biomarkers after treatment with the fusion protein indicate an immunogenic response. We thus show the potential for this fusion protein to induce an anticancer effect paired with an adaptive immune response against EGFR/HER2+ cells. Our research in human cell lines here provides evidence for the success of the same therapeutic method for patients and serves as the gateway to developing a new treatment approach against breast cancer.

Keywords: apoptosis, breast cancer, immunogenic cell death, lysosome

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Authors: Ciprian Briciu-Burghina, Brendan Heery, Dermot Brabazon, Fiona Regan

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Good quality bathing water is a highly desirable natural resource which can provide major economic, social, and environmental benefits. Both in Ireland and Europe, such water bodies are managed under the European Directive for the management of bathing water quality (BWD). The BWD aims mainly: (i) to improve health protection for bathers by introducing stricter standards for faecal pollution assessment (E. coli, enterococci), (ii) to establish a more pro-active approach to the assessment of possible pollution risks and the management of bathing waters, and (iii) to increase public involvement and dissemination of information to the general public. Standard methods for E. coli and enterococci quantification rely on cultivation of the target organism which requires long incubation periods (from 18h to a few days). This is not ideal when immediate action is required for risk mitigation. Municipalities that oversee the bathing water quality and deploy appropriate signage have to wait for laboratory results. During this time, bathers can be exposed to pollution events and health risks. Although forecasting tools exist, they are site specific and as consequence extensive historical data is required to be effective. Another approach for early detection of faecal pollution is the use of marker enzymes. β-glucuronidase (GUS) is a widely accepted biomarker for E. coli detection in microbiological water quality control. GUS assay is particularly attractive as they are rapid, less than 4 h, easy to perform and they do not require specialised training. A method for on-site detection of GUS from environmental samples in less than 75 min was previously demonstrated. In this study, the capability of ColiSense as an early warning system for faecal pollution in freshwater is assessed. The system successfully detected GUS activity in all of the 45 freshwater samples tested. GUS activity was found to correlate linearly with E. coli (r2=0.53, N=45, p < 0.001) and enterococci (r2=0.66, N=45, p < 0.001) Although GUS is a marker for E. coli, a better correlation was obtained for enterococci. For this study water samples were collected from 5 rivers in the Dublin area over 1 month. This suggests a high diversity of pollution sources (agricultural, industrial, etc) as well as point and diffuse pollution sources were captured in the sample size. Such variety in the source of E. coli can account for different GUS activities/culturable cell and different ratios of viable but not culturable to viable culturable bacteria. A previously developed protocol for the recovery and detection of E. coli was coupled with a miniaturised fluorometer (ColiSense) and the system was assessed for the rapid detection FIB in freshwater samples. Further work will be carried out to evaluate the system’s performance on seawater samples.

Keywords: faecal pollution, β-glucuronidase (GUS), bathing water, E. coli

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Authors: Abdullah S. Alghamdi, Khaled Alghamdi, Richard O. Jenkins, Parvez I. Haris

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Background: Unhealthy diet is one of the modifiable risk factors for developing type 2 diabetes mellitus (T2DM). Improvement in diet can be beneficial for countering diabetes. For example, HbA1c, an important biomarker for diabetes, can be reduced by 1.1% through only alteration in diet. Ramadan fasting has been reported to provide positive health benefits. However, optimal benefits are not achieved, often due to poor dietary habits and lifestyle. There is a need to better understand the dietary habits of people fasting during Ramadan, so that necessary improvements can be made to develop this form of fasting as a non-pharmacological strategy for management and prevention of T2DM. Aim: This study aimed to assess the dietary patterns of Saudi adult patients with T2DM over three different periods (before, during, and after Ramadan) and relate this to HbA1c levels. Methods: This study recruited 82 Saudi with T2DM, who chose to fast during Ramadan, from the Endocrine and Diabetic Centre of Al Iman General Hospital, Riyadh, Saudi Arabia. Ethical approvals for the study were obtained from De Montfort University and Saudi Ministry of Health. Dietary patterns were assessed by a self-administered questionnaire in each period. This assessment included the diet type and frequency. Blood samples were collected in each period for determination of HbA1c. Results: The number of meals per day for the participants significantly decreased during Ramadan (P < 0.001). The consumption of fruit and vegetables significantly increased during Ramadan (P = 0.017). However, the consumption of sugary drinks significantly increased during and after Ramadan (P = 0.005). Approximately 60% of the patients indicated that they ate sugary foods at least once per week. The consumption of bread and rice was reported to be at least two times per week. The consumption of rice significantly reduced during Ramadan (P = 0.002). The mean HbA1c significantly varied between periods (P = 0.001), with lowest level during Ramadan compared to before and after Ramadan. The increase in the consumption of fruits and vegetables had a medium effect size on the reduction in HbA1c during Ramadan. There was a variance of 7.7% in the mean difference in HbA1c levels between groups (who changed their fruit and vegetable consumption) which can be accounted for by the increase in the consumption of fruits and vegetables. Likewise, 9.3% of the variance in the mean HbA1c difference between the groups was accounted for by a decrease in the consumption of rice. Conclusion: The increase in the frequency of fruit and vegetables intake, and especially the reduction in the frequency of rice consumption, during Ramadan produce beneficial effects in reducing HbA1c level. Therefore, further improving the dietary habits of patients with T2DM, such as reducing their sugary drinks intake, may help them to obtain greater benefits from Ramadan fasting in the management of their diabetes. It is recommended that dietary guidance is provided to the public to maximise health benefits through Ramadan fasting.

Keywords: Diabetes, Diet, Fasting, HbA1c, Ramadan

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Authors: Alaa G. M. Osman, Abd-El –Baset M. Abd El Reheem, Khaled Y. Abouelfadl, Usama M. Mahmoud, Mohsen A. Moustafa

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This study aimed to explore new sites of biomarker research and to establish the use of blood parameters in wild fish populations. Four hundred and twenty fish samples were collected from six sites along the whole course of the river Nile, Egypt. The mean values of erythrocytes, thrombocytes, hemoglobin concentration, hematocrit value, and mean corpuscular volume were significantly lower in the blood of Nile tilapia and African catfish collected from downstream (contaminated) compared to upstream sites. In contrast, mean corpuscular hemoglobin and mean corpuscular hemoglobin concentration in the peripheral blood of both fish species significantly increased from upstream to downstream river Nile. The leukocytes count was significantly decreased in contaminated sites compared to upstream area. Hematological variables in the peripheral blood of Oreochromis niloticus niloticus and Clarias gariepinus exhibited significant (p<0.05) correlation with nearly all the detected chemical and physical parameters along the Nile course. In the present study, lower cellular and nuclear areas and cellular and nuclear shape factor were recorded in the erythrocytes of fish collected from downstream compared to those caught from upstream sites. This was confirmed by higher immature ratios of red cells in the blood of fish sampled from downstream river Nile. Karyorrhetic and enucleated erythrocytes were significantly correlated with physiochemical parameters in water samples collected from the same sites is being higher in the blood of fish collected from downstream sites. To see if there was any correlation between fish altered physiological fitness and environmental stress, we measured serum biochemical variables namely; total protein, cholesterol, triglycerides, calcium, chlorides, alkaline phosphatase activity (ALP), aspartate aminotransferase (AST), alanine aminotransferase (ALT), uric acid activity, creatinine, and serum glucose. The level of all the selected biochemical variables in the blood of O. niloticus niloticus and C. gariepinus were recorded to be significantly higher (p<0.05) in downstream sites. According to the present results, nearly all the detected haematological and blood biochemical variables are suitable indicators of contaminant exposure in O. niloticus niloticus and C. gariepinus. Also the detected erythrocytes malformations in blood collected from Nile tilapia and African catfish were proven to be suitable for bio-monitoring aquatic pollution. The results revealed species-specific differences in sensitivities, suggesting that Nile tilapia may serve as a more sensitive test species compared to African catfish.

Keywords: biomarkers, water pollution, blood parameters, river nile, african catfish, nile tilapia

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Authors: Franck kem Acho

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This is a chronic metabolic disorder which is a fast-growing global problem with a huge social, health, and economic consequences. It is estimated that in 2010 there were globally 285 million people (approximately 6.4% of the adult population) suffering from this disease. This number is estimated to increase to 430 million in the absence of better control or cure. An ageing population and obesity are two main reasons for the increase. Diabetes mellitus is a chronic heterogeneous metabolic disorder with a complex pathogenesis. It is characterized by elevated blood glucose levels or hyperglycemia, which results from abnormalities in either insulin secretion or insulin action or both. Hyperglycemia manifests in various forms with a varied presentation and results in carbohydrate, fat, and protein metabolic dysfunctions. Long-term hyperglycemia often leads to various microvascular and macrovascular diabetic complications, which are mainly responsible for diabetes-associated morbidity and mortality. Hyperglycemia serves as the primary biomarker for the diagnosis of diabetes as well. Furthermore, it has been shown that almost 50% of the putative diabetics are not diagnosed until 10 years after onset of the disease, hence the real prevalence of global diabetes must be astronomically high. This study was conducted in a locality to access the level of knowledge, awareness and risk factors associated with people leaving with diabetes mellitus. A month before the screening was to be conducted, a health screening in some selected churches and on the local community radio as well as on relevant WhatsApp groups were advertised. A general health talk was delivered by the head of the screening unit to all attendees who were all educated on the procedure to be carried out with benefits and any possible discomforts after which the attendee’s consent was obtained. Evaluation of the participants for any leads to the diabetes selected for the screening was done by taking adequate history and physical examinations such as excessive thirst, increased urination, tiredness, hunger, unexplained weight loss, feeling irritable or having other mood changes, having blurry vision, having slow-healing sores, getting a lot of infections, such as gum, skin and vaginal infections. Out of the 94 participants the finding show that 78 were females and 16 were males, 70.21% of participants with diabetes were between the ages of 60-69yrs.The study found that only 10.63% of respondents declared a good level of knowledge of diabetes. Out of 3 symptoms of diabetes analyzed in this study, high blood sugar (58.5%) and chronic fatigue (36.17%) were the most recognized. Out of 4 diabetes risk factors analyzed in this study, obesity (21.27%) and unhealthy diet (60.63%) were the most recognized diabetes risk factors, while only 10.6% of respondents indicated tobacco use. The diabetic foot was the most recognized diabetes complication (50.57%), but some the participants indicated vision problems (30.8%),or cardiovascular diseases (20.21%) as diabetes complications.

Keywords: diabetes mellitus, non comunicable disease, general health talk, hyperglycemia

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Authors: C. Villamizar, M. Serrato

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In the pursuit of athletic performance, the role of physical training which is determined by a number of charges or taxes on physiological stress and musculoskeletal systems of the human body generated by the intensity and duration is fundamental. Given the physical demands of these activities both training and competitive must take into account the optimal relationship with a straining process recovery post favoring the process of overcompensation which aims to facilitate the return and rising energy potential and protein synthesis also of different tissues. Allowing muscle function returns to baseline or pre-exercise states. If this recovery process is not performed or is not allowed in a proper way, will result in an increased state of fatigue. Active recovery, is one of the strategies implemented in the sport for a return to pre-exercise physiological states. However, there are some adverse assumptions regarding the negative effects, as is the possibility of increasing the degradation of muscle glycogen and thus delaying the synthesis thereof. For them, it is necessary to investigate what would be the effects generated application made at different times after the effort. The aim of this study was to determine the effects of active recovery post effort made at three different times: immediately, at 12 and 24 hours on biochemical markers creatine kinase in youth soccer player’s categories. A randomized controlled trial with allocation to three groups was performed: A. active recovery immediately after the effort; B. active recovery performed at 12 hours after the effort; C. active recovery made at 24 hours after the effort. This study included 27 subjects belonging to a Colombian soccer team of the second division. Vital signs, weight, height, BMI, the percentage of muscle mass, fat mass percentage, personal medical history, and family were valued. The velocity, explosive force and Creatin Kinase (CK) in blood were tested before and after interventions. SAFT 90 protocol (Soccer Field specific Aerobic Test) was applied to participants for generating fatigue. CK samples were taken one hour before the application of the fatigue test, one hour after the fatigue protocol and 48 of the initial CK sample. Mean age was 18.5 ± 1.1 years old. Improvements in jumping and speed recovery the 3 groups (p < 0.05), but no statistically significant differences between groups was observed after recuperation. In all participants, there was a significant increment of CK when applied SAFT 90 in all the groups (median 103.1-111.1). The CK measurement after 48 hours reflects a recovery in all groups, however the group C, a decline below baseline levels of -55.5 (-96.3 /-20.4) which is a significant find. Other research has shown that CK does not return quickly to their baseline, but our study shows that active recovery favors the clearance of CK and also to perform recovery 24 hours after the effort generates higher clearance of this biomarker.

Keywords: active recuperation, creatine phosphokinase, post training, young soccer players

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Authors: Elena Maria Scalisi

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Currently, photodegradation by nanoparticles (NPs) is a common solution for wastewater treatment. Nanoparticles are efficient for removing organic and inorganic pollutants, heavy metals from wastewater and killing microorganisms through environmentally friendly. In this context, the major representative of photocatalytic technology for industrial wastewater treatment are TiO₂ nanoparticles (TiO₂-NPs). TiO₂-NPs have a strong catalytic activity that depends to their physicochemical properties. Thanks to their small size (between 1-100 nm), nanoparticles occupy less volume, then their surface area increases. The increase in the surface-to-volume ratio results in the increase of the particle surface energy, which improve their reactivity potential. However, these unique properties represent risks to the ecosystems and organisms when unintentionally TiO₂-NPs are release into the environment and absorbed by living organisms. Several studies confirm that there is a high level of interest concerning the safety of TiO₂-NPs in the aquatic environment, furthermore, ecotoxicological tools are useful to correctly evaluate their toxicity. In the current study, we aimed to characterize potential toxic effects of TiO₂-NP suspension to zebrafish during embryo-larval stages to evaluate parameters such as survival rates, malformation, hatching, the overall length of the larvae heartbeat, and biochemical biomarkers that reflect the acute toxicity and sublethal effects of TiO₂-NPs. Zebrafish embryos were exposed to titanium dioxide nanoparticles (TiO₂-NPs at 1mg/L, 2mg/L, and 4mg/L) from fertilization to the free swimming stage (144hpf). Every day, we recorded the toxicological endpoints, moreover, immunohistochemical analysis has been performed at the end of the exposure. In particular, we have evaluate the expression of the following biomarkers: Heat Shock Protein 70 (HSP70), Poly ADP-Ribose Polymerase-1 (PARP-1), Metallothioneins (MTs). Our results have shown that hatch ability, survival, and malformation rate were not affected by TiO₂ NPs at these exposure levels. However, TiO₂-NPs caused an increase of heartbeat and reduction of body length; at the same time, TiO₂-NPs have inducted the production of ROS and the expression of oxidative stress biomarkers HSP70 and PARP-1. Hight positivity for PARP-1 at all concentration tested was observed. As regards MT, positivity was found in the expression of this biomarker in the whole body of the embryo, with the exception of the end of the tail. Metallothioneins (MT) are biomarkers widely used in environmental monitoring programs for aquatic creatures. At the light of our results i.e. no death until the end of the experiment (144hpf), no malformation and expression of the biomarkers mentioned, it is evident that zebrafish larvae with their natural detoxification pathways are able to resist the presence of toxic substances and then they can tolerate the presence of metal concentrations. However, an excessive oxidative state can compromise cell function, therefore the uncontrolled release of nanoparticles into the environment is severe and must be constantly monitored.

Keywords: nanoparticles, embryo zebrafish, HSP70, PARP-1

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Authors: Seema Dhariwal, Kiran Maan, Ruchi Baghel, Apoorva Sharma, Poonam Rana

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Introduction: Traumatic brain injury (TBI) is defined as the temporary or permanent alteration in brain function and pathology caused by an external mechanical force. It represents the leading cause of mortality and morbidity among children and youth individuals. Various models of TBI in rodents have been developed in the laboratory to mimic the scenario of injury. Blast overpressure injury is common among civilians and military personnel, followed by accidents or explosive devices. In addition to this, the lateral Controlled cortical impact (CCI) model mimics the blunt, penetrating injury. Method: In the present study, we have developed two different mild TBI models using blast and CCI injury. In the blast model, helium gas was used to create an overpressure of 130 kPa (±5) via a shock tube, and CCI injury was induced with an impact depth of 1.5mm to create diffusive and focal injury, respectively. C57BL/6J male mice (10-12 weeks) were divided into three groups: (1) control, (2) Blast treated, (3) CCI treated, and were exposed to different injury models. Serum was collected on Day1 and day7, followed by biphasic extraction using MTBE/Methanol/Water. Prepared samples were separated on Charged Surface Hybrid (CSH) C18 column and acquired on UHPLC-Q-TOF-MS using ESI probe with inhouse optimized parameters and method. MS peak list was generated using Markerview TM. Data were normalized, Pareto-scaled, and log-transformed, followed by multivariate and univariate analysis in metaboanalyst. Result and discussion: Untargeted profiling of lipids generated extensive data features, which were annotated through LIPID MAPS® based on their m/z and were further confirmed based on their fragment pattern by LipidBlast. There is the final annotation of 269 features in the positive and 182 features in the negative mode of ionization. PCA and PLS-DA score plots showed clear segregation of injury groups to controls. Among various lipids in mild blast and CCI, five lipids (Glycerophospholipids {PC 30:2, PE O-33:3, PG 28:3;O3 and PS 36:1 } and fatty acyl { FA 21:3;O2}) were significantly altered in both injury groups at Day 1 and Day 7, and also had VIP score >1. Pathway analysis by Biopan has also shown hampered synthesis of Glycerolipids and Glycerophospholipiods, which coincides with earlier reports. It could be a direct result of alteration in the Acetylcholine signaling pathway in response to TBI. Understanding the role of a specific class of lipid metabolism, regulation and transport could be beneficial to TBI research since it could provide new targets and determine the best therapeutic intervention. This study demonstrates the potential lipid biomarkers which can be used for injury severity diagnosis and identification irrespective of injury type (diffusive or focal).

Keywords: LipidBlast, lipidomic biomarker, LIPID MAPS®, TBI

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Authors: Caroline Lavratti, Pedro Dal Lago, Gustavo Reinaldo, Gilson Dorneles, Andreia Bard, Laira Fuhr, Daniela Pochmann, Alessandra Peres, Luciane Wagner, Viviane Elsner

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Approximately 1% of the world's population is affected by schizophrenia (SZ), a chronic and debilitating neurodevelopmental disorder. Among possible factors, reduced levels of Brain-derived neurotrophic factor (BDNF) has been recognized in physiopathogenesis and course of SZ. In this context, peripheral BDNF levels have been used as a biomarker in several clinical studies, since this neurotrophin is able to cross the blood-brain barrier in a bi-directional manner and seems to present a strong correlation with the central nervous system fluid levels. The patients with SZ usually adopts a sedentary lifestyle, which has been partly associated with the increase in obesity incidence rates, metabolic syndrome, type 2 diabetes and coronary heart disease. On the other hand, exercise, a non-invasive and low cost intervention, has been considered an important additional therapeutic option for this population, promoting benefits to physical and mental health. To our knowledge, few studies have been pointed out that the positive effects of exercise in SZ patients are mediated, at least in part, to enhanced levels of BDNF after training. However, these studies are focused on evaluating the effect of single bouts of exercise of chronic interventions, data concerning the short- and long-term exercise outcomes on BDNF are scarce. Therefore, this study aimed to evaluate the effect of a concurrent exercise protocol (CEP) on plasma BDNF levels of SZ patients in different time-points. Material and Methods: This study was approved by the Research Ethics Committee of the Centro Universitário Metodista do IPA (no 1.243.680/2015). The participants (n=15) were subbmited to the CEP during 90 days, 3 times a week for 60 minutes each session. In order to evaluate the short and long-term effects of exercise, blood samples were collected pre, 30, 60 and 90 days after the intervention began. Plasma BDNF levels were determined with the ELISA method, from Sigma-Aldrich commercial kit (catalog number RAB0026) according to manufacturer's instructions. Results: A remarkable increase on plasma BDNF levels at 90 days after training compared to baseline (p=0.006) and 30 days (p=0.007) values were observed. Conclusion: Our data are in agreement with several studies that show significant enhancement on BDNF levels in response to different exercise protocols in SZ individuals. We might suggest that BDNF upregulation after training in SZ patients acts in a dose-dependent manner, being more pronounced in response to chronic exposure. Acknowledgments: This work was supported by Fundação de Amparo à Pesquisa do Estado do Rio Grande do Sul (FAPERGS)/Brazil.

Keywords: exercise, BDNF, schizophrenia, time-points

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Authors: Mustafa M. Donma, Orkide Donma

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Zinc is a vital element required for growth and development. This fact makes zinc important, particularly for children. It maintains normal cellular structure and functions. This essential element appears to have protective effects against coronary artery disease and cardiomyopathy. Higher serum zinc levels are associated with lower risk of cardiovascular diseases (CVDs). There is a significant association between low serum zinc levels and heart failure. Zinc may be a potential biomarker of cardiovascular health. High sensitive cardiac troponin T (hs-cTnT) and cardiac myosin binding protein C (cMyBP-C) are new generation markers used for prediagnosis, diagnosis, and prognosis of CVDs. The aim of this study is to determine zinc as well as new generation cardiac markers profiles in children with normal body mass index (N-BMI), obese (OB), morbid obese (MO) children, and children with metabolic syndrome (MetS) findings. The association among them will also be investigated. Four study groups were constituted. The study protocol was approved by the institutional Ethics Committee of Tekirdag Namik Kemal University. Parents of the participants filled informed consent forms to participate in the study. Group 1 is composed of 44 children with N-BMI. Group 2 and Group 3 comprised 43 OB and 45 MO children, respectively. Forty-five MO children with MetS findings were included in Group 4. World Health Organization age- and sex-adjusted BMI percentile tables were used to constitute groups. These values were 15-85, 95-99, and above 99 for N-BMI, OB, and MO, respectively. Criteria for MetS findings were determined. Routine biochemical analyses, including zinc, were performed. High sensitive-cTnT and cMyBP-C concentrations were measured by kits based on enzyme-linked immunosorbent assay principle. Appropriate statistical tests within the scope of SPSS were used for the evaluation of the study data. p<0.05 was accepted as statistically significant. Four groups were matched for age and gender. Decreased zinc concentrations were measured in Groups 2, 3, and 4 compared to Group 1. Groups did not differ from one another in terms of hs-cTnT. There were statistically significant differences between cMyBP-C levels of MetS group and N-BMI as well as OB groups. There was an increasing trend going from N-BMI group to MetS group. There were statistically significant negative correlations between zinc and hs-cTnT as well as cMyBP-C concentrations in MetS group. In conclusion, inverse correlations detected between zinc and new generation cardiac markers (hs-TnT and cMyBP-C) have pointed out that decreased levels of this physiologically essential trace element accompany increased levels of hs-cTnT as well as cMyBP-C in children with MetS. This finding emphasizes that both zinc and these new generation cardiac markers may be evaluated as biomarkers of cardiovascular health during severe childhood obesity precipitated with MetS findings and also suggested as the messengers of the future risk in the adulthood periods of children with MetS.

Keywords: cardiac myosin binding protein-C, cardiovascular diseases, children, high sensitive cardiac troponin T, obesity

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Authors: Almudena Espin Perez, Tyler Risom, Carl Pelz, Isabel English, Robert M. Angelo, Rosalie Sears, Andrew J. Gentles

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Pancreatic ductal adenocarcinoma (PDAC) is one of the most deadly malignancies. The role of the tumor microenvironment (TME) is gaining significant attention in cancer research. Despite ongoing efforts, the nature of the interactions between tumors, immune cells, and stromal cells remains poorly understood. The cell-intrinsic properties that govern cell lineage plasticity in PDAC and extrinsic influences of immune populations require technically challenging approaches due to the inherently heterogeneous nature of PDAC. Understanding the cell lineage plasticity of PDAC will improve the development of novel strategies that could be translated to the clinic. Members of the team have demonstrated that the acquisition of ductal to neuroendocrine lineage plasticity in PDAC confers therapeutic resistance and is a biomarker of poor outcomes in patients. Our approach combines computational methods for deconvolving bulk transcriptomic cancer data using CIBERSORTx and high-throughput single-cell imaging using Multiplexed Ion Beam Imaging (MIBI) to study lineage plasticity in PDAC and its relationship to the infiltrating immune system. The CIBERSORTx algorithm uses signature matrices from immune cells and stroma from sorted and single-cell data in order to 1) infer the fractions of different immune cell types and stromal cells in bulked gene expression data and 2) impute a representative transcriptome profile for each cell type. We studied a unique set of 300 genomically well-characterized primary PDAC samples with rich clinical annotation. We deconvolved the PDAC transcriptome profiles using CIBERSORTx, leveraging publicly available single-cell RNA-seq data from normal pancreatic tissue and PDAC to estimate cell type proportions in PDAC, and digitally reconstruct cell-specific transcriptional profiles from our study dataset. We built signature matrices and optimized by simulations and comparison to ground truth data. We identified cell-type-specific transcriptional programs that contribute to cancer cell lineage plasticity, especially in the ductal compartment. We also studied cell differentiation hierarchies using CytoTRACE and predict cell lineage trajectories for acinar and ductal cells that we believe are pinpointing relevant information on PDAC progression. Collaborators (Angelo lab, Stanford University) has led the development of the Multiplexed Ion Beam Imaging (MIBI) platform for spatial proteomics. We will use in the very near future MIBI from tissue microarray of 40 PDAC samples to understand the spatial relationship between cancer cell lineage plasticity and stromal cells focused on infiltrating immune cells, using the relevant markers of PDAC plasticity identified from the RNA-seq analysis.

Keywords: deconvolution, imaging, microenvironment, PDAC

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Authors: Chien-Ho Lin, Ho-Ching Yang, Barbara Knowlton, Shin-Leh Huang, Ming-Chang Chiang

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Practicing motor tasks arranged in an interleaved order (interleaved practice, or IP) generally leads to better learning than practicing tasks in a repetitive order (repetitive practice, or RP), an example of how desirable difficulty during practice benefits learning. Greater difficulty during practice, e.g. IP, is associated with greater brain activity measured by higher blood-oxygen-level dependent (BOLD) signal in functional magnetic resonance imaging (fMRI) in the sensorimotor areas of the brain. In this study resting-state fMRI was applied to investigate whether increase in resting-state brain connectivity immediately after practice predicts the benefit of desirable difficulty to motor learning. 26 healthy adults (11M/15F, age = 23.3±1.3 years) practiced two sets of three sequences arranged in a repetitive or an interleaved order over 2 days, followed by a retention test on Day 5 to evaluate learning. On each practice day, fMRI data were acquired in a resting state after practice. The resting-state fMRI data was decomposed using a group-level spatial independent component analysis (ICA), yielding 9 independent components (IC) matched to the precuneus network, primary visual networks (two ICs, denoted by I and II respectively), sensorimotor networks (two ICs, denoted by I and II respectively), the right and the left frontoparietal networks, occipito-temporal network, and the frontal network. A weighted resting-state functional connectivity (wRSFC) was then defined to incorporate information from within- and between-network brain connectivity. The within-network functional connectivity between a voxel and an IC was gauged by a z-score derived from the Fisher transformation of the IC map. The between-network connectivity was derived from the cross-correlation of time courses across all possible pairs of ICs, leading to a symmetric nc x nc matrix of cross-correlation coefficients, denoted by C = (pᵢⱼ). Here pᵢⱼ is the extremum of cross-correlation between ICs i and j; nc = 9 is the number of ICs. This component-wise cross-correlation matrix C was then projected to the voxel space, with the weights for each voxel set to the z-score that represents the above within-network functional connectivity. The wRSFC map incorporates the global characteristics of brain networks measured by the between-network connectivity, and the spatial information contained in the IC maps measured by the within-network connectivity. Pearson correlation analysis revealed that greater IP-minus-RP difference in wRSFC was positively correlated with the RP-minus-IP difference in the response time on Day 5, particularly in brain regions crucial for motor learning, such as the right dorsolateral prefrontal cortex (DLPFC), and the right premotor and supplementary motor cortices. This indicates that enhanced resting brain connectivity during the early phase of memory consolidation is associated with enhanced learning following interleaved practice, and as such wRSFC could be applied as a biomarker that measures the beneficial effects of desirable difficulty on motor sequence learning.

Keywords: desirable difficulty, functional magnetic resonance imaging, independent component analysis, resting-state networks

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Authors: Frederick Huie, Lauren Fusfeld, William Burchenal, Scott Howell, Alyssa McVey, Thomas F. Goss

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Alzheimer’s Disease (AD) is a degenerative brain disease characterized by memory loss and cognitive decline that presents a substantial economic burden for patients and health insurers in the US. This study evaluates the payer budget impact of the DISCERN™ test in the diagnosis and management of patients with symptoms of dementia evaluated for AD. DISCERN™ comprises three assays that assess critical factors related to AD that regulate memory, formation of synaptic connections among neurons, and levels of amyloid plaques and neurofibrillary tangles in the brain and can provide a quicker, more accurate diagnosis than tests in the current diagnostic pathway (CDP). An Excel-based model with a three-year horizon was developed to assess the budget impact of DISCERN™ compared with CDP in a Medicare Advantage plan with 1M beneficiaries. Model parameters were identified through a literature review and were verified through consultation with clinicians experienced in diagnosis and management of AD. The model assesses direct medical costs/savings for patients based on the following categories: •Diagnosis: costs of diagnosis using DISCERN™ and CDP. •False Negative (FN) diagnosis: incremental cost of care avoidable with a correct AD diagnosis and appropriately directed medication. •True Positive (TP) diagnosis: AD medication costs; cost from a later TP diagnosis with the CDP versus DISCERN™ in the year of diagnosis, and savings from the delay in AD progression due to appropriate AD medication in patients who are correctly diagnosed after a FN diagnosis.•False Positive (FP) diagnosis: cost of AD medication for patients who do not have AD. A one-way sensitivity analysis was conducted to assess the effect of varying key clinical and cost parameters ±10%. An additional scenario analysis was developed to evaluate the impact of individual inputs. In the base scenario, DISCERN™ is estimated to decrease costs by $4.75M over three years, equating to approximately $63.11 saved per test per year for a cohort followed over three years. While the diagnosis cost is higher with DISCERN™ than with CDP modalities, this cost is offset by the higher overall costs associated with CDP due to the longer time needed to receive a TP diagnosis and the larger number of patients who receive a FN diagnosis and progress more rapidly than if they had received appropriate AD medication. The sensitivity analysis shows that the three parameters with the greatest impact on savings are: reduced sensitivity of DISCERN™, improved sensitivity of the CDP, and a reduction in the percentage of disease progression that is avoided with appropriate AD medication. A scenario analysis in which DISCERN™ reduces the utilization for patients of computed tomography from 21% in the base case to 16%, magnetic resonance imaging from 37% to 27% and cerebrospinal fluid biomarker testing, positive emission tomography, electroencephalograms, and polysomnography testing from 4%, 5%, 10%, and 8%, respectively, in the base case to 0%, results in an overall three-year net savings of $14.5M. DISCERN™ improves the rate of accurate, definitive diagnosis of AD earlier in the disease and may generate savings for Medicare Advantage plans.

Keywords: Alzheimer’s disease, budget, dementia, diagnosis.

Procedia PDF Downloads 114

Authors: Raj Chandran, Saul Datwyler, Jaime Marino, Daniel West, Karla Grasso, Adam Buss, Hina Syed, Zina Al Sahouri, Jennifer Yen, Krista Caudle, Beth McQuiston

Abstract:

The Alinity i TBI test is Therapeutic Goods Administration (TGA) registered and is a panel of in vitro diagnostic chemiluminescent microparticle immunoassays for the measurement of glial fibrillary acidic protein (GFAP) and ubiquitin C-terminal hydrolase L1 (UCH-L1) in plasma and serum. The Alinity i TBI performance was evaluated in a multi-center pivotal study to demonstrate the capability to assist in determining the need for a CT scan of the head in adult subjects (age 18+) presenting with suspected mild TBI (traumatic brain injury) with a Glasgow Coma Scale score of 13 to 15. TBI has been recognized as an important cause of death and disability and is a growing public health problem. An estimated 69 million people globally experience a TBI annually1. Blood-based biomarkers such as glial fibrillary acidic protein (GFAP) and ubiquitin C-terminal hydrolase L1 (UCH-L1) have shown utility to predict acute traumatic intracranial injury on head CT scans after TBI. A pivotal study using prospectively collected archived (frozen) plasma specimens was conducted to establish the clinical performance of the TBI test on the Alinity i system. The specimens were originally collected in a prospective, multi-center clinical study. Testing of the specimens was performed at three clinical sites in the United States. Performance characteristics such as detection limits, imprecision, linearity, measuring interval, expected values, and interferences were established following Clinical and Laboratory Standards Institute (CLSI) guidance. Of the 1899 mild TBI subjects, 120 had positive head CT scan results; 116 of the 120 specimens had a positive TBI interpretation (Sensitivity 96.7%; 95% CI: 91.7%, 98.7%). Of the 1779 subjects with negative CT scan results, 713 had a negative TBI interpretation (Specificity 40.1%; 95% CI: 37.8, 42.4). The negative predictive value (NPV) of the test was 99.4% (713/717, 95% CI: 98.6%, 99.8%). The analytical measuring interval (AMI) extends from the limit of quantitation (LoQ) to the upper LoQ and is determined by the range that demonstrates acceptable performance for linearity, imprecision, and bias. The AMI is 6.1 to 42,000 pg/mL for GFAP and 26.3 to 25,000 pg/mL for UCH-L1. Overall, within-laboratory imprecision (20 day) ranged from 3.7 to 5.9% CV for GFAP and 3.0 to 6.0% CV for UCH-L1, when including lot and instrument variances. The Alinity i TBI clinical performance results demonstrated high sensitivity and high NPV, supporting the utility to assist in determining the need for a head CT scan in subjects presenting to the emergency department with suspected mild TBI. The GFAP and UCH-L1 assays show robust analytical performance across a broad concentration range of GFAP and UCH-L1 and may serve as a valuable tool to help evaluate TBI patients across the spectrum of mild to severe injury.

Keywords: biomarker, diagnostic, neurology, TBI

Procedia PDF Downloads 34

Authors: Berengere Vire, Nicolas Salvetat, Yoann Lannay, Guillaume Marcellin, Siem Van Der Laan, Franck Molina, Dinah Weissmann

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Predicting suicidal behaviors is one of the most complex challenges of daily psychiatric practices. Today, suicide risk prediction using biological tools is not validated and is only based on subjective clinical reports of the at-risk individual. Therefore, there is a great need to identify biomarkers that would allow early identification of individuals at risk of suicide. Alterations of adenosine-to-inosine (A-to-I) RNA editing of neurotransmitter receptors and other proteins have been shown to be involved in etiology of different psychiatric disorders and linked to suicidal behavior. RNA editing is a co- or post-transcriptional process leading to a site-specific alteration in RNA sequences. It plays an important role in the epi transcriptomic regulation of RNA metabolism. On postmortem human brain tissue (prefrontal cortex) of depressed suicide victims, Alcediag found specific alterations of RNA editing activity on the mRNA coding for the serotonin 2C receptor (5-HT2cR). Additionally, an increase in expression levels of ADARs, the RNA editing enzymes, and modifications of RNA editing profiles of prime targets, such as phosphodiesterase 8A (PDE8A) mRNA, have also been observed. Interestingly, the PDE8A gene is located on chromosome 15q25.3, a genomic region that has recurrently been associated with the early-onset major depressive disorder (MDD). In the current study, we examined whether modifications in RNA editing profile of prime targets allow identifying disease-relevant blood biomarkers and evaluating suicide risk in patients. To address this question, we performed a clinical study to identify an RNA editing signature in blood of depressed patients with and without the history of suicide attempts. Patient’s samples were drawn in PAXgene tubes and analyzed on Alcediag’s proprietary RNA editing platform using next generation sequencing technology. In addition, gene expression analysis by quantitative PCR was performed. We generated a multivariate algorithm comprising various selected biomarkers to detect patients with a high risk to attempt suicide. We evaluated the diagnostic performance using the relative proportion of PDE8A mRNA editing at different sites and/or isoforms as well as the expression of PDE8A and the ADARs. The significance of these biomarkers for suicidality was evaluated using the area under the receiver-operating characteristic curve (AUC). The generated algorithm comprising the biomarkers was found to have strong diagnostic performances with high specificity and sensitivity. In conclusion, we developed tools to measure disease-specific biomarkers in blood samples of patients for identifying individuals at the greatest risk for future suicide attempts. This technology not only fosters patient management but is also suitable to predict the risk of drug-induced psychiatric side effects such as iatrogenic increase of suicidal ideas/behaviors.

Keywords: blood biomarker, next-generation-sequencing, RNA editing, suicide

Procedia PDF Downloads 230

Authors: Colin S. Chen, Chien-Jung Tien, Hsin-Jan Huang

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For weathering studies, the change of chemical constituents by biodegradation effect in diesel-contaminated soils are important factors to be considered, especially when there is a prolonged period of weathering processes. The objective was to evaluate biodegradation effects onto hydrocarbon fingerprinting and distribution patterns of diesel fuels, fuel source screening and differentiation, source-specific marker compounds, and diagnostic ratios of diesel fuel constituents by laboratory and field studies. Biodegradation processes of diesel contaminated soils were evaluated by experiments lasting for 15 and 12 months, respectively. The degradation of diesel fuel in top soils was affected by organic carbon content and biomass of microorganisms in soils. Higher depletion of total petroleum hydrocarbon (TPH), n-alkanes, and polynuclear aromatic hydrocarbons (PAHs) and their alkyl homologues was observed in soils containing higher organic carbon content and biomass. Decreased ratio of selected isoprenoids (i.e., pristane (Pr) and phytane (Ph)) including n-C17/pristane and n-C18/phytane was observed. The ratio of pristane/phytane was remained consistent for a longer period of time. At the end of the experimental period, a decrease of pristane/phytane was observed. Biomarker compounds of bicyclic sesquiterpanes (BS) were less susceptible to the effects of biodegradation. The ratios of characteristic factors such as C15 sesquiterpane/ 8β(H)-drimane (BS3/BS5), C15 sesquiterpane/ 8β(H)-drimane (BS4/BS5), 8β(H)-drimane/8β(H)-homodrimane (BS5/BS10), and C15 sesquiterpane/8β(H)-homodrimane (BS3/BS10) could be adopted for source identification of diesel fuels in top soil. However, for biodegradation processes lasted for six months but shorter than nine months, only BS3/BS5 and BS3/BS10 could be distinguished in two diesel fuels. In subsoil experiments (contaminated soil located 50 cm below), the ratios of characteristic factors including BS3/BS5, BS4/BS5, and BS5/BS10 were valid for source identification of two diesel fuels for nine month biodegradation. At the early stage of contamination, biomass of soil decreased significantly. However, 6 and 7 dominant species were found in soils in top soil experiments, respectively. With less oxygen and nutrients in subsoil, less biomass of microorganisms was observed in subsoils. Only 2 and 4 diesel-degrading species of microorganisms were identified in two soils, respectively. Parameters of double ratio such as fluorene/C1-fluorene: C2-phenanthrene/C3-phenanthrene (C0F/C1F:C2P/C3P) in both top and subsoil, C2-naphthalene/C2-phenanthrene: C1-phenanthrene/C3-phenanthrene (C2N/C2P:C1P/C3P), and C1-phenanthrene/C1-fluorene: C3-naphthalene/C3-phenanthrene (C1P/C1F:C3N/C3P) in subsoil could serve as forensic indicators in diesel contaminated sites. BS3/BS10:BS4/BS5 could be used in 6 to 9 months of biodegradation processes. Results of principal component analysis (PCA) indicated that source identification of diesel fuels in top soil could only be perofrmed for weathering process less than 6 months. For subsoil, identification can be conducted for weathering process less than 9 months. Ratio of isoprenoids (pristane and phytane) and PAHs might be affected by biodegradation in spilled sites. The ratios of bicyclic sesquiterpanes could serve as forensic indicators in diesel-contaminated soils. Finally, source identification was attemped for samples collected from different fuel contaminated sites by using the unique pattern of sesquiterpanes. It was anticipated that the information generated from this study would be adopted by decision makers to evaluate the liability of cleanup in diesel contaminated sites.

Keywords: biodegradation, diagnostic ratio, diesel fuel, environmental forensics

Procedia PDF Downloads 190

Authors: Banafsheh Nikmehr, Mohsen Bahrami, Yueqiang Song, Anuradha Koduru, Ayse K. Vuruskan, Hongkun Lu, Mallory Pitts, Tolga B. Mesen, Tamer M. Yalcinkaya

Abstract:

The number of people who receive in vitro fertilization (IVF) treatment has increased on a startling trajectory over the past two decades. Despite advances in this field, particularly the introduction of intracytoplasmic sperm injection (ICSI) and the preimplantation genetic screening (PGS), the IVF success remains low. A major factor contributing to IVF failure is embryonic aneuploidy (abnormal chromosome content), which often results in miscarriage and birth defects. Although PGS is often used as the standard diagnostic tool to identify aneuploid embryos, it is an invasive approach that could affect the embryo development, and yet inaccessible to many patients due its high costs. As such, there is a clear need for a non-invasive cost-effective approach to identify euploid embryos for single embryo transfer (SET). The reported differences between morphokinetic behaviors of aneuploid and euploid embryos has shown promise to address this need. However, current literature is inconclusive and further research is urgently needed to translate current findings into clinical diagnostics. In this ongoing study, we found significant differences between morphokinetic behaviors of euploid and aneuploid embryos that provides important insights and reaffirms the promise of such behaviors for developing non-invasive methodologies. Methodology—A total of 242 embryos (euploid: 149, aneuploid: 93) from 74 patients who underwent IVF treatment in Carolinas Fertility Clinics in Winston-Salem, NC, were analyzed. All embryos were incubated in an EmbryoScope incubator. The patients were randomly selected from January 2019 to June 2021 with most patients having both euploid and aneuploid embryos. All embryos reached the blastocyst stage and had known PGS outcomes. The ploidy assessment was done by a third-party testing laboratory on day 5-7 embryo biopsies. The morphokinetic variables of each embryo were measured by the EmbryoViewer software (Uniesense FertiliTech) on time-lapse images using 7 focal depths. We compared the time to: pronuclei fading (tPNf), division to 2,3,…,9 cells (t2, t3,…,t9), start of embryo compaction (tSC), Morula formation (tM), start of blastocyst formation (tSC), blastocyst formation (tB), and blastocyst expansion (tEB), as well as intervals between them (e.g., c23 = t3 – t2). We used a mixed regression method for our statistical analyses to account for the correlation between multiple embryos per patient. Major Findings— The average age of the patients was 35.04 yrs. The average patient age associated with euploid and aneuploid embryos was not different (P = 0.6454). We found a significant difference in c45 = t5-t4 (P = 0.0298). Our results indicated this interval on average lasts significantly longer for aneuploid embryos - c45(aneuploid) = 11.93hr vs c45(euploid) = 7.97hr. In a separate analysis limited to embryos from the same patients (patients = 47, total embryos=200, euploid=112, aneuploid=88), we obtained the same results (P = 0.0316). The statistical power for this analysis exceeded 87%. No other variable was different between the two groups. Conclusion— Our results demonstrate the importance of morphokinetic variables as potential biomarkers that could aid in non-invasively characterizing euploid and aneuploid embryos. We seek to study a larger population of embryos and incorporate the embryo quality in future studies.

Keywords: IVF, embryo, euploidy, aneuploidy, morphokinteic

Procedia PDF Downloads 59

Authors: Saule Balmagambetova, Zhenisgul Tlegenova, Saule Madinova

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Cardiotoxicity associated with anticancer treatment, now defined as cancer therapy-related cardiac dysfunction (CTRCD), accompanies cancer patients and negatively impacts their survivorship. Currently, a cardio-oncological service is being created in Kazakhstan based on the provisions of the European Society of Cardio-oncology (ESC) Guidelines. In the frames of a pilot project, a cohort study on CTRCD conditions was initiated at the Aktobe Cancer center. One hundred twenty-eight newly diagnosed breast cancer patients started on doxorubicin and/or trastuzumab were recruited. Echocardiography with global longitudinal strain (GLS) assessment, biomarkers panel (cardiac troponin (cTnI), brain natriuretic peptide (BNP), myeloperoxidase (MPO), galectin-3 (Gal-3), D-dimers, C-reactive protein (CRP)), and other tests were performed at baseline and every three months. Patients were stratified by the cardiovascular risks according to the ESC recommendations and allocated into the risk groups during the pre-treatment visit. Of them, 10 (7.8%) patients were assigned to the high-risk group, 48 (37.5%) to the medium-risk group, and 70 (54.7%) to the low-risk group, respectively. High-risk patients have been receiving their cardioprotective treatment from the outset. Patients were also divided by treatment - in the anthracycline-based 83 (64.8%), in trastuzumab- only 13 (10.2%), and in the mixed anthracycline/trastuzumab group 32 individuals (25%), respectively. Mild symptomatic CTRCD was revealed and treated in 2 (1.6%) participants, and a mild asymptomatic variant in 26 (20.5%). Mild asymptomatic conditions are defined as left ventricular ejection fraction (LVEF) ≥50% and further relative reduction in GLS by >15% from baseline and/or a further rise in cardiac biomarkers. The listed biomarkers were assessed longitudinally in repeated-measures linear regression models during 12 months of observation. The associations between changes in biomarkers and CTRCD and between changes in biomarkers and LVEF were evaluated. Analysis by risk groups revealed statistically significant differences in baseline LVEF scores (p 0.001), BNP (p 0.0075), and Gal-3 (p 0.0073). Treatment groups found no statistically significant differences at baseline. After 12 months of follow-up, only LVEF values showed a statistically significant difference by risk groups (p 0.0011). When assessing the temporal changes in the studied parameters for all treatment groups, there were statistically significant changes from visit to visit for LVEF (p 0.003); GLS (p 0.0001); BNP (p<0.00001); MPO (p<0.0001); and Gal-3 (p<0.0001). No moderate or strong correlations were found between the biomarkers values and LVEF, between biomarkers and GLS. Between the biomarkers themselves, a moderate, close to strong correlation was established between cTnI and D-dimer (r 0.65, p<0.05). The dose-dependent effect of anthracyclines has been confirmed: the summary dose has a moderate negative impact on GLS values: -r 0.31 for all treatment groups (p<0.05). The present study found myeloperoxidase as a promising biomarker of cardiac dysfunction in the mixed anthracycline/trastuzumab treatment group. The hazard of CTRCD increased by 24% (HR 1.21; 95% CI 1.01;1.73) per doubling in baseline MPO value (p 0.041). Increases in BNP were also associated with CTRCD (HR per doubling, 1.22; 95% CI 1.12;1.69). No cases of chemotherapy discontinuation due to cardiotoxic complications have been recorded. Further observations are needed to gain insight into the ability of biomarkers to predict CTRCD onset.

Keywords: breast cancer, chemotherapy, cardiotoxicity, Kazakhstan

Procedia PDF Downloads 55

Authors: Sachin Mulmi Shrestha, Xin Fang, Hui Ye, Lihua Ren, Qinghua Ji, Ruihua Shi

Abstract:

Background: Esophageal squamous cell carcinoma (ESCC) is a tumor arising from esophageal epithelial cells and is one of the major disease subtype in Asian countries, including China. Esophageal cancer is the 7th highest incidence based on the 2020 data of GLOBOCAN. The pathogenesis of cancer is still not well understood as many molecular and genetic basis of esophageal carcinogenesis has yet to be clearly elucidated. Circular RNAs are RNA molecules that are formed by back-splicing covalently joined 3′- and 5′-endsrather than canonical splicing, and recent data suggest circular RNAs could sponge miRNAs and are enriched with functional miRNA binding sites. Hence, we studied the mechanism of circular RNA, its biological function, and the relationship between microRNA in the carcinogenesis of ESCC. Methods: 4 pairs of normal and esophageal cancer tissues were collected in Zhongda hospital, affiliated to Southeast University, and high-throughput RNA sequencing was done. The result revealed that circ_0032746 was upregulated, and thus we selected circ_0032746 for further study. The backsplice junction of circRNA was validated by sanger sequence, and stability was determined by RNASE R assay. The binding site of circRNA and microRNA was predicted by circinteractome,mirandaand RNAhybrid database. Furthermore, circRNA was silenced by siRNA and then by lentivirus. The regulatory axis of circ0032746/miR4270 was validated by shRNA, mimic, and inhibitor transfection. Then, in vitro experiments were performed to assess the role of circ0032746 on proliferation (CCK-8 assay and colon formation assay), migration and invasion (Transewell assay), and apoptosis of ESCC. Results: The upregulated circ0032746 was validated in 9 pairs of tissues and 5 types of cell lines by qPCR, which showed high expression and was statistically significant (P<0.005) ). Upregulated circ0032746 was silenced by shRNA, which showed significant knockdown in KYSE 30 and TE-1 cell lines expression compared to control. Nuclear and cytoplasmic mRNA fraction experiment displayed the cytoplasmic location of circ0032746. The sponging of miR4270 was validated by co-transfection of sh-circ0032746 and mimic or inhibitor. Transfection with mimic showed the decreased expression of circ_0032746, whereas inhibitor inhibited the result. In vitro experiments showed that silencing of circ_0032746 inhibited the proliferation, migration, and invasion compared to the negative control group. The apoptosis was seen higher in a knockdown group than in the control group. Furthermore, 11 common mircoRNA target mRNAs were predicted by Targetscan, MirTarbase, and miRanda database, which may further play role in the pathogenesis. Conclusion: Our results showed that novel circ_0032746 is upregulated in ESCC and plays role in itsoncogenicity. Silencing of circ_0032746 inhibits the proliferation and migration of ESCC whereas increases the apoptosis of cancer cells. Hence, circ0032746 acts as an oncogene in ESCC by sponging with miR4270 and could be a potential biomarker in the diagnosis of ESCC in the future.

Keywords: circRNA, esophageal squamous cell carcinoma, microRNA, upregulated

Procedia PDF Downloads 81

Authors: Miroslava Cuperlovic-Culf, Lipu Wang, Ketty Boyle, Nadine Makley, Ian Burton, Anissa Belkaid, Mohamed Touaibia, Marc E. Surrette

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Metabolic changes are one of the major factors in the development of a variety of diseases in various species. Metabolism of agricultural plants is altered the following infection with pathogens sometimes contributing to resistance. At the same time, pathogens use metabolites for infection and progression. In humans, metabolism is a hallmark of cancer development for example. Quantified metabolomics data combined with other omics or clinical data and analyzed using various unsupervised and supervised methods can lead to better diagnosis and prognosis. It can also provide information about resistance as well as contribute knowledge of compounds significant for disease progression or prevention. In this work, different methods for metabolomics quantification and analysis from Nuclear Magnetic Resonance (NMR) measurements that are used for investigation of disease development in wheat and human cells will be presented. One-dimensional 1H NMR spectra are used extensively for metabolic profiling due to their high reliability, wide range of applicability, speed, trivial sample preparation and low cost. This presentation will describe a new method for metabolite quantification from NMR data that combines alignment of spectra of standards to sample spectra followed by multivariate linear regression optimization of spectra of assigned metabolites to samples’ spectra. Several different alignment methods were tested and multivariate linear regression result has been compared with other quantification methods. Quantified metabolomics data can be analyzed in the variety of ways and we will present different clustering methods used for phenotype determination, network analysis providing knowledge about the relationships between metabolites through metabolic network as well as biomarker selection providing novel markers. These analysis methods have been utilized for the investigation of fusarium head blight resistance in wheat cultivars as well as analysis of the effect of estrogen receptor and carbonic anhydrase activation and inhibition on breast cancer cell metabolism. Metabolic changes in spikelet’s of wheat cultivars FL62R1, Stettler, MuchMore and Sumai3 following fusarium graminearum infection were explored. Extensive 1D 1H and 2D NMR measurements provided information for detailed metabolite assignment and quantification leading to possible metabolic markers discriminating resistance level in wheat subtypes. Quantification data is compared to results obtained using other published methods. Fusarium infection induced metabolic changes in different wheat varieties are discussed in the context of metabolic network and resistance. Quantitative metabolomics has been used for the investigation of the effect of targeted enzyme inhibition in cancer. In this work, the effect of 17 β -estradiol and ferulic acid on metabolism of ER+ breast cancer cells has been compared to their effect on ER- control cells. The effect of the inhibitors of carbonic anhydrase on the observed metabolic changes resulting from ER activation has also been determined. Metabolic profiles were studied using 1D and 2D metabolomic NMR experiments, combined with the identification and quantification of metabolites, and the annotation of the results is provided in the context of biochemical pathways.

Keywords: metabolic biomarkers, metabolic network, metabolomics, multivariate linear regression, NMR quantification, quantified metabolomics, spectral alignment

Procedia PDF Downloads 315

Authors: Nurkhairul Bariyah Baharun, Afzan Adam, Reena Rahayu Md Zin

Abstract:

Tumor microenvironment (TME) in breast cancer is mainly composed of cancer cells, immune cells, and stromal cells. The interaction between cancer cells and their microenvironment plays an important role in tumor development, progression, and treatment response. The TME in breast cancer includes tumor-infiltrating lymphocytes (TILs) that are implicated in killing tumor cells. TILs can be found in tumor stroma (sTILs) and within the tumor (iTILs). TILs in triple negative breast cancer (TNBC) have been demonstrated to have prognostic and potentially predictive value. The international Immune-Oncology Biomarker Working Group (TIL-WG) had developed a guideline focus on the assessment of sTILs using hematoxylin and eosin (H&E)-stained slides. According to the guideline, the pathologists use “eye balling” method on the H&E stained- slide for sTILs assessment. This method has low precision, poor interobserver reproducibility, and is time-consuming for a comprehensive evaluation, besides only counted sTILs in their assessment. The TIL-WG has therefore recommended that any algorithm for computational assessment of TILs utilizing the guidelines provided to overcome the limitations of manual assessment, thus providing highly accurate and reliable TILs detection and classification for reproducible and quantitative measurement. This study is carried out to develop a TNBC digital whole slide image (WSI) dataset from H&E-stained slides and IHC (CD4+ and CD8+) stained slides. TNBC cases were retrieved from the database of the Department of Pathology, Hospital Canselor Tuanku Muhriz (HCTM). TNBC cases diagnosed between the year 2010 and 2021 with no history of other cancer and available block tissue were included in the study (n=58). Tissue blocks were sectioned approximately 4 µm for H&E and IHC stain. The H&E staining was performed according to a well-established protocol. Indirect IHC stain was also performed on the tissue sections using protocol from Diagnostic BioSystems PolyVue™ Plus Kit, USA. The slides were stained with rabbit monoclonal, CD8 antibody (SP16) and Rabbit monoclonal, CD4 antibody (EP204). The selected and quality-checked slides were then scanned using a high-resolution whole slide scanner (Pannoramic DESK II DW- slide scanner) to digitalize the tissue image with a pixel resolution of 20x magnification. A manual TILs (sTILs and iTILs) assessment was then carried out by the appointed pathologist (2 pathologists) for manual TILs scoring from the digital WSIs following the guideline developed by TIL-WG 2014, and the result displayed as the percentage of sTILs and iTILs per mm² stromal and tumour area on the tissue. Following this, we aimed to develop an automated digital image scoring framework that incorporates key elements of manual guidelines (including both sTILs and iTILs) using manually annotated data for robust and objective quantification of TILs in TNBC. From the study, we have developed a digital dataset of TNBC H&E and IHC (CD4+ and CD8+) stained slides. We hope that an automated based scoring method can provide quantitative and interpretable TILs scoring, which correlates with the manual pathologist-derived sTILs and iTILs scoring and thus has potential prognostic implications.

Keywords: automated quantification, digital pathology, triple negative breast cancer, tumour infiltrating lymphocytes

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Authors: M. Skibinska, A. Rajewska-Rager, M. Dmitrzak-Weglarz, N. Lepczynska, P. Sibilski, P. Kapelski, J. Pawlak, J. Twarowska-Hauser

Abstract:

Introduction: Neurotrophic factors have been implicated in neuropsychiatric disorders. Brain-Derived Neurotrophic Factor (BDNF) influences neuron differentiation in development as well as synaptic plasticity and neuron survival in adulthood. BDNF is widely studied in mood disorders and has been proposed as a biomarker for depression. BDNF is synthesized as precursor protein – proBDNF. Both forms are biologically active and exert opposite effects on neurons. Aim: The aim of the study was to examine the serum levels of BDNF and proBDNF in unipolar and bipolar young patients below 24 years old during hypo/manic, depressive episodes and in remission compared to healthy control group. Methods: In a prospective 2 years follow-up study, we investigated alterations in levels of BDNF and proBDNF in 79 patients (23 males, mean age 19.08, SD 3.3 and 56 females, mean age 18.39, SD 3.28) diagnosed with mood disorders: unipolar and bipolar disorder compared with 35 healthy control subjects (7 males, mean age 20.43, SD 4.23 and 28 females, mean age 21.25, SD 2.11). Clinical characteristics including mood, comorbidity, family history, and treatment, were evaluated during control visits and clinical symptoms were rated using the Hamilton Depression Rating Scale and Young Mania Rating Scale. Serum BDNF and proBDNF concentrations were determined by Enzyme-Linked Immunosorbent Assays (ELISA) method. Serum BDNF and proBDNF levels were analysed with covariates: sex, age, age > 18 and < 18 years old, family history of affective disorders, drug-free vs. medicated status. Normality of the data was tested using Shapiro-Wilk test. Levene’s test was used to calculate homogeneity of variance. Non-parametric Tests: Mann-Whitney U test, Kruskal-Wallis ANOVA, Friedman’s ANOVA, Wilcoxon signed rank test, Spearman correlation coefficient were applied in analyses The statistical significance level was set at p < 0.05. Results: BDNF and proBDNF serum levels did not differ between patients at baseline and controls as well as comparing patients in acute episode of depression/hypo/mania at baseline and euthymia (at month 3 or 6). Comparing BDNF and proBDNF levels between patients in euthymia and control group no differences have been found. Increased BDNF level in women compared to men at baseline (p=0.01) have been observed. BDNF level at baseline was negatively correlated with depression and mania occurence at 24 month (p=0.04). BDNF level at 12 month was negatively correlated with depression and mania occurence at 12 month (p=0.01). Correlation of BDNF level with sex have been detected (p=0.01). proBDNF levels at month 3, 6 and 12 negatively correlated with disease status (p=0.02, p=0.008, p=0.009, respectively). No other correlations of BDNF and proBDNF levels with clinical and demographical variables have been detected. Discussion: Our results did not show any differences in BDNF and proBDNF levels between depression, mania, euthymia, and controls. Imbalance in BDNF/proBDNF signalling may be involved in pathogenesis of mood disorders. Further studies on larger groups are recommended. Grant was founded by National Science Center in Poland no 2011/03/D/NZ5/06146.

Keywords: bipolar disorder, Brain-Derived Neurotrophic Factor (BDNF), proBDNF, unipolar depression

Procedia PDF Downloads 215

Authors: Joseph M. Rich, Vinay A. Duddalwar, Assad A. Oberai

Abstract:

Prostate adenocarcinoma is the most common cancer in males, with osseous metastases as the commonest site of metastatic prostate carcinoma (mPC). Treatment monitoring is based on the evaluation and characterization of lesions on multiple imaging studies, including Computed Tomography (CT). Monitoring of the osseous disease burden, including follow-up of lesions and identification and characterization of new lesions, is a laborious task for radiologists. Deep learning algorithms are increasingly used to perform tasks such as identification and segmentation for osseous metastatic disease and provide accurate information regarding metastatic burden. Here, nnUNet was used to produce a model which can segment CT scan images of prostate adenocarcinoma vertebral bone metastatic lesions. nnUNet is an open-source Python package that adds optimizations to deep learning-based UNet architecture but has not been extensively combined with transfer learning techniques due to the absence of a readily available functionality of this method. The IRB-approved study data set includes imaging studies from patients with mPC who were enrolled in clinical trials at the University of Southern California (USC) Health Science Campus and Los Angeles County (LAC)/USC medical center. Manual segmentation of metastatic lesions was completed by an expert radiologist Dr. Vinay Duddalwar (20+ years in radiology and oncologic imaging), to serve as ground truths for the automated segmentation. Despite nnUNet’s success on some medical segmentation tasks, it only produced an average Dice Similarity Coefficient (DSC) of 0.31 on the USC dataset. DSC results fell in a bimodal distribution, with most scores falling either over 0.66 (reasonably accurate) or at 0 (no lesion detected). Applying more aggressive data augmentation techniques dropped the DSC to 0.15, and reducing the number of epochs reduced the DSC to below 0.1. Datasets have been identified for transfer learning, which involve balancing between size and similarity of the dataset. Identified datasets include the Pancreas data from the Medical Segmentation Decathlon, Pelvic Reference Data, and CT volumes with multiple organ segmentations (CT-ORG). Some of the challenges of producing an accurate model from the USC dataset include small dataset size (115 images), 2D data (as nnUNet generally performs better on 3D data), and the limited amount of public data capturing annotated CT images of bone lesions. Optimizations and improvements will be made by applying transfer learning and generative methods, including incorporating generative adversarial networks and diffusion models in order to augment the dataset. Performance with different libraries, including MONAI and custom architectures with Pytorch, will be compared. In the future, molecular correlations will be tracked with radiologic features for the purpose of multimodal composite biomarker identification. Once validated, these models will be incorporated into evaluation workflows to optimize radiologist evaluation. Our work demonstrates the challenges of applying automated image segmentation to small medical datasets and lays a foundation for techniques to improve performance. As machine learning models become increasingly incorporated into the workflow of radiologists, these findings will help improve the speed and accuracy of vertebral metastatic lesions detection.

Keywords: deep learning, image segmentation, medicine, nnUNet, prostate carcinoma, radiomics

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Authors: Camille Perréard, Yoann Ladner, Fanny D'Orlyé, Stéphanie Descroix, Vélan Taniga, Anne Varenne, Cédric Guyon, Michael. Tatoulian, Frédéric Kanoufi, Cyrine Slim, Sophie Griveau, Fethi Bedioui

Abstract:

The development of micro total analysis systems is of major interest for contaminant and biomarker analysis. As a lab-on-chip integrates all steps of an analysis procedure in a single device, analysis can be performed in an automated format with reduced time and cost, while maintaining performances comparable to those of conventional chromatographic systems. Moreover, these miniaturized systems are either compatible with field work or glovebox manipulations. This work is aimed at developing an analytical microsystem for trace and ultra trace quantitation in complex matrices. The strategy consists in the integration of a sample pretreatment step within the lab-on-chip by a confinement zone where selective ligands are immobilized for target extraction and preconcentration. Aptamers were chosen as selective ligands, because of their high affinity for all types of targets (from small ions to viruses and cells) and their ease of synthesis and functionalization. This integrated target extraction and concentration step will be followed in the microdevice by an electrokinetic separation step and an on-line detection. Polymers consisting of cyclic olefin copolymer (COC) or fluoropolymer (Dyneon THV) were selected as they are easy to mold, transparent in UV-visible and have high resistance towards solvents and extreme pH conditions. However, because of their low chemical reactivity, surface treatments are necessary. For the design of this miniaturized diagnostics, we aimed at modifying the microfluidic system at two scales : (1) on the entire surface of the microsystem to control the surface hydrophobicity (so as to avoid any sample wall adsorption) and the fluid flows during electrokinetic separation, or (2) locally so as to immobilize selective ligands (aptamers) on restricted areas for target extraction and preconcentration. We developed different novel strategies for the surface functionalization of COC and Dyneon, based on plasma, chemical and /or electrochemical approaches. In a first approach, a plasma-induced immobilization of brominated derivatives was performed on the entire surface. Further substitution of the bromine by an azide functional group led to covalent immobilization of ligands through “click” chemistry reaction between azides and terminal alkynes. COC and Dyneon materials were characterized at each step of the surface functionalization procedure by various complementary techniques to evaluate the quality and homogeneity of the functionalization (contact angle, XPS, ATR). With the objective of local (micrometric scale) aptamer immobilization, we developed an original electrochemical strategy on engraved Dyneon THV microchannel. Through local electrochemical carbonization followed by adsorption of azide-bearing diazonium moieties and covalent linkage of alkyne-bearing aptamers through click chemistry reaction, typical dimensions of immobilization zones reached the 50 µm range. Other functionalization strategies, such as sol-gel encapsulation of aptamers, are currently investigated and may also be suitable for the development of the analytical microdevice. The development of these functionalization strategies is the first crucial step in the design of the entire microdevice. These strategies allow the grafting of a large number of molecules for the development of new analytical tools in various domains like environment or healthcare.

Keywords: alkyne-azide click chemistry (CuAAC), electrochemical modification, microsystem, plasma bromination, surface functionalization, thermoplastic polymers

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Authors: Subhash Nerella, Ziyuan Guan, Azra Bihorac, Parisa Rashidi

Abstract:

Intensive care units (ICUs) provide care to critically ill patients in severe and life-threatening conditions. However, patient monitoring in the ICU is limited by the time and resource constraints imposed on healthcare providers. Many critical care indices such as mobility are still manually assessed, which can be subjective, prone to human errors, and lack granularity. Other important aspects, such as environmental factors, are not monitored at all. For example, critically ill patients often experience circadian disruptions due to the absence of effective environmental “timekeepers” such as the light/dark cycle and the systemic effect of acute illness on chronobiologic markers. Although the occurrence of delirium is associated with circadian disruption risk factors, these factors are not routinely monitored in the ICU. Hence, there is a critical unmet need to develop systems for precise and real-time assessment through novel enabling technologies. We have developed the mobility and circadian disruption quantification system (Mobi-DiQ) by augmenting biomarker and clinical data with pervasive sensing data to generate mobility and circadian cues related to mobility, nightly disruptions, and light and noise exposure. We hypothesize that Mobi-DiQ can provide accurate mobility and circadian cues that correlate with bedside clinical mobility assessments and circadian biomarkers, ultimately important for delirium risk assessment and prevention. The collected multimodal dataset consists of depth images, Electromyography (EMG) data, patient extremity movement captured by accelerometers, ambient light levels, Sound Pressure Level (SPL), and indoor air quality measured by volatile organic compounds, and the equivalent CO₂ concentration. For delirium risk assessment, the system recognizes mobility cues (axial body movement features and body key points) and circadian cues, including nightly disruptions, ambient SPL, and light intensity, as well as other environmental factors such as indoor air quality. The Mobi-DiQ system consists of three major components: the pervasive sensing system, a data storage and analysis server, and a data annotation system. For data collection, six local pervasive sensing systems were deployed, including a local computer and sensors. A video recording tool with graphical user interface (GUI) developed in python was used to capture depth image frames for analyzing patient mobility. All sensor data is encrypted, then automatically uploaded to the Mobi-DiQ server through a secured VPN connection. Several data pipelines are developed to automate the data transfer, curation, and data preparation for annotation and model training. The data curation and post-processing are performed on the server. A custom secure annotation tool with GUI was developed to annotate depth activity data. The annotation tool is linked to the MongoDB database to record the data annotation and to provide summarization. Docker containers are also utilized to manage services and pipelines running on the server in an isolated manner. The processed clinical data and annotations are used to train and develop real-time pervasive sensing systems to augment clinical decision-making and promote targeted interventions. In the future, we intend to evaluate our system as a clinical implementation trial, as well as to refine and validate it by using other data sources, including neurological data obtained through continuous electroencephalography (EEG).

Keywords: deep learning, delirium, healthcare, pervasive sensing

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