Salivary levels of inflammatory and anti-inflammatory biomarkers in periodontitis patients with and without acute myocardial infarction: implications for cardiovascular risk assessment

Background

Periodontitis is initiated by a dysbiotic activity and furthermore leads to a chronic inflammatory response. The presence of pro-inflammatory markers plays an important role in the inflammatory load. Macrophage inflammatory protein-1 alpha (MIP-1α) and C-reactive protein (CRP) are pro- inflammatory biomarkers that quantify clinical and subclinical inflammation in cardiac ischemia in cardiac inflammation and disease. Adiponectin is an anti-inflammatory marker associated with good health. The susceptibility of periodontitis patients to cardiovascular events needs to be evaluated.

Objective

This study aims to assess the levels of biomarkers in periodontitis patients with and without acute myocardial infarction (AMI) compared to controls.

Material and methods

Pro-inflammatory and anti-inflammatory analytes were examined by collecting unstimulated saliva from three groups (n = 20/each): healthy individuals, individuals with stage III periodontitis, and post-myocardial infarction patients with stage III periodontitis. The samples were collected within 48 h of AMI.

Results

Adiponectin levels were significantly lower in patients with periodontitis with and without AMI compared to controls, while CRP and MIP-1α were significantly higher in patients with periodontitis with and without AMI compared to controls. The highest titers for MIP-1α and CRP were detected among patients with periodontitis with and AMI.

Conclusion

Our study provides possible evidence of the association between periodontitis and salivary analytes that occur in tandem with cardiovascular disease. The lower levels of Adiponectin and higher levels of CRP and MIP-1α in patients with periodontitis indicate that this condition is a potential risk factor for cardiovascular disease. The findings emphasize the importance of early detection and intervention for periodontitis patients to prevent cardiovascular events.

Effectiveness of tranexamic acid in orthognathic surgery: A systematic review of systematic reviews

PURPOSE

This study aimed to review the currently available evidence on the effectiveness of administering tranexamic acid (TXA) to patients undergoing orthognathic surgery.

METHODS

A study protocol was developed in accordance with the Preferred Reporting Guideline for Overviews of Reviews (PRIOR) and registered on the International Prospective Register of Systematic Reviews (PROSPERO) under Registration No. CRD42021232931. Furthermore, the reporting of the present systematic review was performed based on the PRISMA checklist.

RESULTS

The search strategy yielded a total of 50 articles. After reading the abstracts, 28 articles were excluded, and the English full texts of the remaining 22 studies were separately examined for eligibility by two authors; 15 articles were excluded because they did not meet the inclusion criteria. Finally, seven systematic reviews and meta-analysis satisfied the criteria for inclusion and were processed for critical review evaluation.

CONCLUSIONS

Within the limits of the present study and the reviews of the 7 articles included, it is observed that TXA is able to reduce the amount of intraoperative blood loss and the amount of irrigation fluids required. However, it does not influence postoperative levels of hemoglobin or hematocrit, nor does it affect the requirement for blood transfusions. It was interestingly discovered that TXA could increase the quality of the surgical site. These data imply that TXA may be an effective adjuvant in lowering bleeding during orthognathic surgery. As a result, the potential risk of problems related with considerable blood loss may be minimized.

Novel Coronavirus (COVID-19) Knowledge, Attitude, and Practice among Dental Sciences and Internship Students in Ajman University, United Arab Emirates: A Cross-Sectional Study

Background

The aim of this study was to assess the COVID-19-related knowledge, attitudes, and practice among dental students (DS) and internship students at Ajman University (AU).

Methods

A cross-sectional, web-based study was conducted among Ajman dental college students registered in the academic year 2019/2020, about COVID-19 during the first week of April 2020. A questionnaire was developed and distributed to all DS to examine their knowledge and attitudes toward the COVID-19 pandemic. Chi-square (χ²) test was used to investigate the level of association among categorical variables at the significance level of p < 0.05.

Results

Out of 769 students in the dental college, majority (75%) had adequate knowledge of COVID-19, but only 40.6% of the participants projected a positive attitude. A positive behavior was reported by an overwhelming 94.5% of the participants. Participants above 25 years of age had significantly higher (p < 0.001) adequate knowledge (88.2%), positive attitude (56.9%), and positive behavior (100%) compared to those below 25 years of age. Study participants reported social media (71.1%), government websites (63.7%), and family and friends (41.0%) as top three sources of information regarding COVID-19 related information.

Conclusion

The results of this study show that AU dental and internship students have adequate knowledge and positive attitude of the COVID-19 pandemic but the majority are not eager to adopt effective strategies to avoid the spread of COVID-19 (practice). Further education should be offered to encourage efficient infection management practices to protect students, faculty, and other university staff.

Microbiomic and Metabolomic Analyses Unveil the Protective Effect of Saffron in a Mouse Colitis Model

Despite the existence of effective drugs used to treat inflammatory bowel disease (IBD), many patients fail to respond or lose response over time. Further, many drugs can carry serious adverse effects, including increased risk of infections and malignancies. Saffron (Crocus sativus) has been reported to have anti-inflammatory properties. Its protective role in IBD and how the microbiome and metabolome play a role has not been explored extensively. We aimed to establish whether saffron treatment modulates the host microbiome and metabolic profile in experimental colitis. Colitis was induced in C57BL/6 mice with 3% DSS and treated with either saffron in a dose of 20 mg/kg body weight or vehicle through daily gavage. On day 10, stool pellets from mice were collected and analyzed to assess saffron's effect on fecal microbiota and metabolites through 16S rRNA sequencing and untargeted primary metabolite analysis. Saffron treatment maintained gut microbiota homeostasis by counter-selecting pro-inflammatory bacteria and maintained Firmicutes/Bacteroides ratio, which was otherwise disturbed by DSS treatment. Several metabolites (uric acid, cholesterol, 2 hydroxyglutaric acid, allantoic acid, 2 hydroxyhexanoic acid) were altered significantly with saffron treatment in DSS-treated mice, and this might play a role in mediating saffron's colitis-mitigating effects. These data demonstrate saffron's therapeutic potential, and its protective role is modulated by gut microbiota, potentially acting through changes in metabolites.

CellMinerCDB: NCATS Is a Web-Based Portal Integrating Public Cancer Cell Line Databases for Pharmacogenomic Explorations

Major advances have been made in the field of precision medicine for treating cancer. However, many open questions remain that need to be answered to realize the goal of matching every patient with cancer to the most efficacious therapy. To facilitate these efforts, we have developed CellMinerCDB: National Center for Advancing Translational Sciences (NCATS; https://discover.nci.nih.gov/rsconnect/cellminercdb_ncats/), which makes available activity information for 2,675 drugs and compounds, including multiple nononcology drugs and 1,866 drugs and compounds unique to the NCATS. CellMinerCDB: NCATS comprises 183 cancer cell lines, with 72 unique to NCATS, including some from previously understudied tissues of origin. Multiple forms of data from different institutes are integrated, including single and combination drug activity, DNA copy number, methylation and mutation, transcriptome, protein levels, histone acetylation and methylation, metabolites, CRISPR, and miscellaneous signatures. Curation of cell lines and drug names enables cross-database (CDB) analyses. Comparison of the datasets is made possible by the overlap between cell lines and drugs across databases. Multiple univariate and multivariate analysis tools are built-in, including linear regression and LASSO. Examples have been presented here for the clinical topoisomerase I (TOP1) inhibitors topotecan and irinotecan/SN-38. This web application provides both substantial new data and significant pharmacogenomic integration, allowing exploration of interrelationships.

SIGNIFICANCE

CellMinerCDB: NCATS provides activity information for 2,675 drugs in 183 cancer cell lines and analysis tools to facilitate pharmacogenomic research and to identify determinants of response.

BTEX (benzene, toluene, ethylbenzene, and xylene) and risk of cancer - a study from Centers for Disease Control and Prevention's National Health and Nutrition Examination Survey

Introduction/Objective

BTEX (benzene, toluene, ethylbenzene, and xylene) is well know for its toxicity via through environmental, occupational and recreational exposures. However, there is limited literature about the carcinogenic effect of BTEX. Hence, we aim to study the prevalence and association of cancer amongst individuals with exposure of BTEX.

Methods/Case Report

A retrospective cross-sectional study was performed between 2013 and 2018 utilizing the NHANES database. Adult individuals having data on socio-demographic questionnaires and lab findings on exposure to BTEX were included. Prevalence of cancer was identified amongst exposure to BTEX (vs no-BTEX). Univariate (chi-squre test and Mann–Whitney U test) and Multivariate (survey logistic regression) analysis was performed to evaluate the epidemiologic characteristics of individuals exposred to BTEX and association of cancer with BTEX exposure in comparison to no BTEX exposure.The p value of &lt;0.05 considered statistically significant.

Results (if a Case Study enter NA)

124,162 participants were identified with BTEX exposure. Individuals with BTEX exposure were young (40 vs 51 year old), male (91% vs female: 87%), and Mexican American (92% vs Non-Hispanic Black: 89% vs Non-Hispanic White: 89% vs other Hispanic: 87%). Univariate analysis showed higher total prevalence of cancer in BTEX (9.3% vs. 1.3%; p&lt;0.0001) compared to no BTEX. Individuals with BTEX exposure had higher prevalnece of blood cancer (0.47% vs 0.00; p&lt;0.0001), leukemia (0.56% vs 0.00; p&lt;0.001), and lymphoma (1.72% vs 0.39%; p&lt;0.0001) in comparison with no exposure. Multivaritate analysis showed participants with BTEX exposure had 10% higher risk of cancer (aOR: 1.10; 95%CI: 1.10-1.10; p&lt;0.0001) compared to no BTEX exposure. Additionally, exposure to individual components of benzene (aOR: 1.24; 95%CI: 1.24; p&lt;0.0001), ethylbenzene (aOR: 1.08; 95%CI: 1.08-1.08; p&lt;0.0001), and o-xylene (aOR: 1.19; 95%CI: 1.19-1.19; p&lt;0.0001) had higher risk of cancer compared to no exposure participants.

Conclusion

Our study conclude higher risk of cancer among participants with exposure to benzene, ethylbenzene and o-xylene. Future studies are warranted to evaluate the association of various types of cancers in BTEX exposure.

Direct, indirect, post-infection damages induced by coronavirus in the human body: an overview

Background

Severe acute respiratory syndrome Coronavirus-2 invades the cells via ACE2 receptor and damages multiple organs of the human body. Understanding the pathological manifestation is mandatory to endure the rising post-infection sequel reported in patients with or without comorbidities.

Materials and methods

Our descriptive review emphasises the direct, indirect and post-infection damages due to COVID-19. We have performed an electronic database search according to the Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) guidelines with selective inclusion and exclusion criteria.

Results

The included studies substantiated the extensive damages in the multiple organs due to direct and indirect consequences of COVID-19. After an apparent recovery, the prolonged presentation of the symptoms manifests as post-COVID that can be related with persisting viral antigens and dysregulated immune response.

Conclusion

A few of the symptoms of respiratory, cardiovascular, and neuropsychiatric systems that persist or reappear as post-COVID manifestations. Vaccination and preventive programs will effectively reduce the prevalence but, the post-COVID, a multisystem manifestation, will be a significant tribulation to the medical profession. However, the issue can be managed by implementing public health programs, rehabilitation services, and telemedicine virtual supports to raise awareness and reduce panic.

Traumatic Dental Injuries among 12-Year-Old Schoolchildren in the United Arab Emirates

AIMS

This study aimed to evaluate the prevalence of the factors related to traumatic injuries to the permanent incisors of 12-year-old children in the Emirate of Ajman, United Arab Emirates.

METHODS

A sample of 1008 12-year-old children (510 boys and 498 girls) participated in this study. A multi-stage randomized sampling technique was used to select children from public schools for their inclusion in the sample population. An oral examination was completed by a calibrated examiner after receiving training for traumatic dental injury (TDI) to permanent incisor teeth utilizing a modified version of Ellis's classification. Data that were related to sociodemographic factors, TDI causes, and where the TDI took place were recorded using a structured questionnaire.

RESULTS

Of all of the children that were examined, 9.8% of them had experienced dental trauma. The difference in TDI prevalence between boys (15.9%) and girls (3.9%) was statistically significant (p < 0.05). The children whose mothers had low levels of education experienced a higher prevalence of TDI (p = 0.001). The children with incisal overjets that were greater than 5 mm or with inadequate lip coverage tended to have experienced dental injuries (p < 0.01). The main causes of injury to permanent incisors were collision against an object or person (53.5%) and falling (42.4%). Most of the accidents happened at home (58.6%) and school (25.3%). The most prevalent injuries were enamel fractures (58.7%) and enamel-dentine fractures (34.3%).

CONCLUSIONS

This research highlighted many predisposing factors for traumatic dental injuries among children. There is an urgent need to initiate detailed public health policies to decrease the prevalence of dental trauma cases, especially in the identified risk group.

Examining the association between socio-demographic factors, catheter use and antibiotic prescribing in Northern Ireland primary care: a cross-sectional multilevel analysis

Inappropriate use of antibiotics is among the key drivers of antimicrobial resistance (AMR). Antibiotic use in Northern Ireland (NI) is the highest in the UK and approximately 80% is prescribed in primary care. Little information however exists about the patient and prescriber factors driving this. We described the trend in NI primary care total antibiotic prescribing 2010–2019 and conducted a cross-sectional study using a random sample of individuals registered with an NI GP on 1st January 2019. We used multilevel logistic regression to examine how sociodemographic factors and urinary catheter use was associated with the likelihood of being prescribed an antibiotic during 2019, adjusting for clustering at GP practice and GP federation levels. Finite mixture modelling (FMM) was conducted to determine the association between the aforementioned risk factors and quantity of antibiotic prescribed (defined daily doses). The association between age and antibiotic prescription differed by gender. Compared to males 41–50 years, adjusted odds of prescription were higher for males aged 0–10, 11–20 and 51 + years, and females of any age. Catheter use was strongly associated with antibiotic prescription (aOR = 6.82, 95% CI 2.50–18.64). Socioeconomic deprivation and urban/rural settlement were not associated in the multilevel logistic analysis. GP practices and federations accounted for 1.24% and 0.12% of the variation in antibiotic prescribing respectively. FMM showed associations between larger quantities of antibiotics and being older, male and having a catheter. This work described the profile of individuals most likely to receive an antibiotic prescription in NI primary care and identified GP practice as a source of variation; suggesting an opportunity for reduction from effective interventions targeted at both individuals and general practices.

694 IMPROVING OPIATE PRESCRIBING IN OLDER ADULTS WITH HIP FRACTURES TO COMBAT THE IATROGENIC FALLOUT

Background

The number of opioid prescriptions in older patients has increased dramatically and it is recognised that opioids are the fourth most likely drug to cause preventable hospital admissions. The adverse effects of opioids occur more frequently in the geriatric population. Little is known about the impact of postoperative pain in older adults. NICE recommends paracetamol with additional opioids if there is insufficient postoperative pain relief. Multidisciplinary management with early and then daily physiotherapy is critical. We have assessed pre-morbid, immediate and prolonged use of opioids in patients following hip fracture. Local problem Pre-intervention analysis identified 79% (57/72) of all patients being discharged on opiates. At 4-months, 37% (17/46) of those were still using them. This represents 28% (17/61) of all patients.

Methods

Analysis of all patients (excluding poly-trauma) with hip fractures over the age of 60 years admitted to St Mary’s Hospital. Interventions Development of local guideline on analgesia prescribing; particularly focusing senior geriatrician led decision making. Prescribing oxycodone for first 72-hours and initially using nerve block. Avoidance of transdermal preparations and withdrawing stronger opioids prior to discharge. Clear instructions for GP’s on a stop date and need for community review. Patient information leaflet dispensed with all discharge opioid prescriptions.

Results

Post-intervention cycle; 17% (11/63) of patients were taking prescribed opioids prior to admission (similar to the pre-cohort). 52% (33/63) were discharged on opiates, down from 79%. At 4-months, of those discharged on opioids, 30% (9/30) were still using them; lower than in the first cycle (37%). Overall reduction from 28% to 16% of patients on opioids at 4-months.

Conclusion

The use of specific hip fracture analgesia guideline, senior geriatrician decision-making and support to community colleagues can reduce in-patient and community opiate prescribing, and stem the growing problem of opioid addiction, misuse and iatrogenic re-admission.

The correlated expression of COX-2 and keratin 15 in radicular cysts

Background

The expression of cyclooxygenase-2 (COX-2) and Keratin-15 (K15) in radicular cysts (RCs) is poorly understood. Identifying the expression of these two markers may modify the current treatment of RC. The objective of this study was to evaluate the expression of COX-2 and its relationship to K15 expression in the odontogenic epithelial cells of the RC.

Material and Methods

A total of 18 RCs were immunohistochemically analyzed for COX-2 and K15 expression. The cellular inflammatory reaction in the cyst wall was also assessed by measuring the percentage of inflammatory cells to the total number of cells.

Results

COX-2 expression in the odontogenic epithelium of RC was absent in 11.1 % (n=2), mild in 27.8 % (n=5), moderate in 22.2% (n=4) and strong in 38.9% (n=7). Meanwhile, K15 expression was absent in 27.8% (n=5), mild in 16.7% (n=3), moderate in 44.4% (n=8), and strong in 11.1% (n=2) of the cases. The inflammatory infiltrate was mild in 2 cases (11.1%), moderate in 6 cases (33.3%), and high in 10 cases (55.6%). Spearman’s correlation test revealed significant correlation (rho= .533; p= .023) between COX-2 and K15 expression in the odontogenic epithelium of RC. However, no correlation was noted between inflammation and expression of COX-2 (rho= 0.248, p=.321) or K15 (rho= -0.162, p= .520).

Conclusions

There is high and correlated expression of COX-2 and K15 in the odontogenic epithelium of RC. COX-2 could therefore be involved in epithelial cell differentiation of the cyst. Additionally, the expression of K15 in RC may be an indicator of epithelial cell differentiation.

Key words:Cyclooxygenase, COX-2, Keratin-15, K15, Radicular cyst.

Comparison of cellular and differentiation characteristics of mesenchymal stem cells derived from human gingiva and periodontal ligament

Objectives:

Dental tissues possess multipotent stem cells with varying biological properties. The present study was aimed to establish a primary culture of human gingiva-derived mesenchymal stem cells (GMSCs) and periodontal ligament-derived stem cells (PDLSCs) from periodontally healthy subjects and compare their biological characteristics.

Materials and Methods:

Gingival and periodontal ligament (PDL) tissues were collected from extracted premolar teeth of five healthy subjects and primary cultures were established. Basic biological characteristics, such as cell morphology, viability, proliferation capacity, and colony-forming units, and in vitro osteogenic and adipogenic differentiation potential were performed at passage 3 of GMSCs and PDLSCs. This was followed by immuno-phenotyping and flow cytometric analysis for identification of positive mesenchymal stem cell (MSC) markers, such as CD73, CD90, and CD105, and negative markers CD45 and CD34.

Statistical Analysis Used:

One-way analysis of variance (ANOVA).

Results:

Primary cultures of GMSCs and PDLSCs were successfully established. Cells exhibited a fibroblast-like morphology with a homogeneous population at passage 3. Cells derived from both tissues were highly viable (>95%), proliferative, and capable of forming colonies. Both cells did not exhibit any noticeable differences in cellular properties. Immunofluorescence and flow cytometric analyses showed positivity for MSC markers, CD73, CD90, and CD105, and negativity for CD34 and CD45. Furthermore, GMSCs and PDLSCs were capable of differentiating in vitro into osteocytes as evidenced by Alizarin red-S staining, and adipocytes as demonstrated by oil red O staining.

Conclusions:

The results of the present study indicate that both GMSCs and PDLSCs have similar cellular characteristics and mesenchymal differentiation potential. Therefore, they may serve as an equally potent source of stem cells for use in cell-based periodontal therapies.

A brain proteomic signature of incipient Alzheimer's disease in young APOE ε4 carriers identifies novel drug targets

Aptamer-based proteomics revealed differentially abundant proteins in Alzheimer’s disease (AD) brains in the Baltimore Longitudinal Study of Aging and Religious Orders Study (mean age, 89 ± 9 years). A subset of these proteins was also differentially abundant in the brains of young APOE ε4 carriers relative to noncarriers (mean age, 39 ± 6 years). Several of these proteins represent targets of approved and experimental drugs for other indications and were validated using orthogonal methods in independent human brain tissue samples as well as in transgenic AD models. Using cell culture–based phenotypic assays, we showed that drugs targeting the cytokine transducer STAT3 and the Src family tyrosine kinases, YES1 and FYN, rescued molecular phenotypes relevant to AD pathogenesis. Our findings may accelerate the development of effective interventions targeting the earliest molecular triggers of AD.

Tyrosine kinase domain mutations in chronic myelogenous leukemia patients: A single center experience

Introduction:

Despite the impressive responses achieved with tyrosine kinase inhibitor (TKI) therapy, treatment resistance develops in 16–33% of patients of chronic myelogenous leukemia (CML). Of the BCR-ABL1 dependent mechanisms, mutations in the tyrosine kinase domain (TKD) are the commonest cause of resistance.

Material and Methods:

Allele specific oligonucleotide - polymerase chain reaction (ASO-PCR) was done for testing the six common TKD mutations, T315I, G250E, E255K, M244V, M351T, and Y253F.

Results and Conclusion:

TKD mutation study was done on 83 patients. Of these 44 (53%) were positive for one or more mutations. On analyzing specific mutations, E255K was the commonest mutation seen in 24 (29%) cases, followed by T315I in 23(28%) cases. Y253F mutation was not seen in the present study sample. In the present cohort of 83 patients, 29 (35%) cases were positive for single mutation, 12 (14%) had two mutations and 3 (4%) had three mutations.

The gut microbiome in sickle cell disease: Characterization and potential implications

BACKGROUND

Sickle Cell Disease (SCD) is an inherited blood disorder that leads to hemolytic anemia, pain, organ damage and early mortality. It is characterized by polymerized deoxygenated hemoglobin, rigid sickle red blood cells and vaso-occlusive crises (VOC). Recurrent hypoxia-reperfusion injury in the gut of SCD patients could increase tissue injury, permeability, and bacterial translocation. In this context, the gut microbiome, a major player in health and disease, might have significant impact. This study sought to characterize the gut microbiome in SCD.

METHODS

Stool and saliva samples were collected from healthy controls (n = 14) and SCD subjects (n = 14). Stool samples were also collected from humanized SCD murine models including Berk, Townes and corresponding control mice. Amplified 16S rDNA was used for bacterial composition analysis using Next Generation Sequencing (NGS). Pairwise group analyses established differential bacterial groups at many taxonomy levels. Bacterial group abundance and differentials were established using DeSeq software.

RESULTS

A major dysbiosis was observed in SCD patients. The Firmicutes/Bacteroidetes ratio was lower in these patients. The following bacterial families were more abundant in SCD patients: Acetobacteraceae, Acidaminococcaceae, Candidatus Saccharibacteria, Peptostreptococcaceae, Bifidobacteriaceae, Veillonellaceae, Actinomycetaceae, Clostridiales, Bacteroidacbactereae and Fusobacteriaceae. This dysbiosis translated into 420 different operational taxonomic units (OTUs). Townes SCD mice also displayed gut microbiome dysbiosis as seen in human SCD.

CONCLUSION

A major dysbiosis was observed in SCD patients for bacteria that are known strong pro-inflammatory triggers. The Townes mouse showed dysbiosis as well and might serve as a good model to study gut microbiome modulation and its impact on SCD pathophysiology.

Acceptability of Neuroscientific Interventions in Education

Researchers are increasingly applying neuroscience technologies that probe or manipulate the brain to improve educational outcomes. However, their use remains fraught with ethical controversies. Here, we investigate the acceptability of neuroscience applications to educational practice in two groups of young adults: those studying bioscience who will be driving future basic neuroscience research and technology transfer, and those studying education who will be choosing among neuroscience-derived applications for their students. Respondents rated the acceptability of six scenarios describing neuroscience applications to education spanning multiple methodologies, from neuroimaging to neuroactive drugs to brain stimulation. They did so from two perspectives (student, teacher) and for three recipient populations (low-achieving, high-achieving students, students with learning disabilities). Overall, the biosciences students were more favorable to all neuroscience applications than the education students. Scenarios that measured brain activity (i.e., EEG or fMRI) to assess or predict intellectual abilities were deemed more acceptable than manipulations of mental activity by drug use or stimulation techniques, which may violate body integrity. Enhancement up to the norm for low-achieving students and especially students with learning disabilities was more favorably viewed than enhancement beyond the norm for high-achieving students. Finally, respondents rated neuroscientific applications to be less acceptable when adopting the perspective of a teacher than that of a student. Future studies should go beyond the acceptability ratings collected here to delineate the role that concepts of access, equity, authenticity, agency and personal choice play in guiding respondents' reasoning.

Abstract 2413: POLE gene mutations in African Americans colorectal cancer

Background: Most focus in genetic instability in colon carcinogenic transformation was on DNA Mismatch Repair (MMR) genes alterations as they relate to the microsatellite instability phenotype. However, POLE gene mutations can also be instrumental in triggering genetic instability, at even higher magnitude of genome mutation rate.

Aim: To assess POLE gene mutations in African Americans with colorectal cancer (CRC).

Methods: Data from Whole exome sequencing of 12 CRC African American tumors was searched to scan POLE gene mutations. All detected mutations were checked in tumors and matched normal. The detected mutations were validated in a second set of samples that were sequenced using POLE gene targeted sequencing. Detected and validated mutations were checked in available databases such as COSMIC and dbSNP to determine novel mutations in our population that is at high risk of aggressive CRC.

Results: Six out of 12 patients (50%) displayed mutations in POLE gene. There were 41 detected mutations, 11 are novel mutations and 15 are amino-acid changing. Nine of these were non-synonymous and predicted to have deleterious effects. All these mutations were validated using targeted sequencing. In comparison to DNA MMR, POLE gene has four folds more mutations than MSH2gne (10 mutations and MSH6 (11 mutations and two fold more than MSH3 gene (20 mutations) in the same set of 12 cancer/matched normals. The POLE mutations heterozygous/homozygous status was overall similar in normal and matched normal. However, most of the mutations were homozygous.

Conclusion: POLE gene mutations are increasingly recognized as another important element in genetic instability. Our data shows that mutations affecting this gene are likely more significant than those affecting DNA MMR genes. Moreover, POLE mutations might be more consequential, especially those affecting its exonuclease domain of polymerase epsilon, proofreading catalytic subunit. Microsatellite-stable, hypermutated CRCs might need to be explored for POLE gene mutations to track the origin of high mutation rates.

Citation Format: Hassan Brim, Babak Shokrani, Hamed Azimi, Sudhir Varma, Edward Lee, Hassan Ashktorab. POLE gene mutations in African Americans colorectal cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2021; 2021 Apr 10-15 and May 17-21. Philadelphia (PA): AACR; Cancer Res 2021;81(13_Suppl):Abstract nr 2413.

Abstract 212: Sarcoma-CellMiner: An extensive resource for patient-derived sarcoma cell line epigenetics, genomics and pharmacology

Sarcomas represent a heterogeneous group of cancers with many histological subtypes. Their prognosis remains poor and treatment is mainly based on palliative chemotherapy at metastatic stage. Tumor genome sequencing failed to identify recurrent somatic drivers while several oncogenic gene fusion-translocations have been identified in specific sarcoma subtypes. Because of the rarity and heterogeneity of sarcomas, only few sarcoma patients are enrolled in clinicals trials according their subtype. Increased translational research according subtypes of sarcoma patients is needed to improve patient management. To characterize the differences between subgroups and build translational hypotheses, we built a novel resource, Sarcoma-Cellminer, which integrates drug sensitivity and genomic data from 112 patient-derived sarcoma cell lines. These data will be available from a web-based tool (https://discover.nci.nih.gov/SclcCellMinerCDB/) derived from our CellMiner cross-database web application (https://discover.nci.nih.gov/cellminercdb). Among the 112 cell lines, 65 are bone sarcomas (including 38 Ewing sarcomas and 22 osteosarcomas), 45 are soft tissue sarcomas (including 21 rhabdomyosarcomas). Transcriptome (RNAseq and microarray), copy number, microRNA, genome-wide methylation, and drug sensitivity data are included and made publicly available. We also generated new genomic data including copy number and methylation (850 k) for 79 cell lines from the NCI in addition to the 42 cell lines from Broad Institute (CCLE) and the 40 cell lines from the MGH-Sanger (GDSC). We created the “SCLC-Global” expression set by regrouping all datasets by Z-score normalization, which enables cross-database analyses of gene expression and molecular pathways. Hierarchical clustering based on expression and methylation data identifies subtypes of sarcomas. Histone genes stand out suggesting that epigenetic regulation of canonical histones is a feature of sarcoma genesis. Sarcoma-CellMiner includes drug sensitivity data for over 500 different drugs tested in the NCI, CCLE and GDSC databases. They show two subgroups of Ewing sarcomas: one sensitive to PARP inhibitors and one resistant. Similarly, profile of response to dasatinib is different when comparing alveolar and embryonal rhabdomyosarcomas. Sarcoma-CellMiner is a powerful tool demonstrating the value of patient-derived cancer cell line databases. It provides hypothesis-driven rationale for using omics, especially transcriptome and epigenetic data to better understand sarcoma heterogeneity and select personalized treatments for clinical trials.

Citation Format: Camille Tlemsani, Lorinc Pongor, Javed Khan, Fathi Elloumi, Sudhir Varma, Augustin Luna, Vinodh Rajapakse, Kurt Kohn, Julia Krushkal, Mirit Aladjem, Beverly Teicher, Paul Meltzer, William Reinhold, Christine Heske, Yves Pommier. Sarcoma-CellMiner: An extensive resource for patient-derived sarcoma cell line epigenetics, genomics and pharmacology [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2021; 2021 Apr 10-15 and May 17-21. Philadelphia (PA): AACR; Cancer Res 2021;81(13_Suppl):Abstract nr 212.

Bile acid synthesis, modulation, and dementia: A metabolomic, transcriptomic, and pharmacoepidemiologic study

BACKGROUND

While Alzheimer disease (AD) and vascular dementia (VaD) may be accelerated by hypercholesterolemia, the mechanisms underlying this association are unclear. We tested whether dysregulation of cholesterol catabolism, through its conversion to primary bile acids (BAs), was associated with dementia pathogenesis.

METHODS AND FINDINGS

We used a 3-step study design to examine the role of the primary BAs, cholic acid (CA), and chenodeoxycholic acid (CDCA) as well as their principal biosynthetic precursor, 7α-hydroxycholesterol (7α-OHC), in dementia. In Step 1, we tested whether serum markers of cholesterol catabolism were associated with brain amyloid accumulation, white matter lesions (WMLs), and brain atrophy. In Step 2, we tested whether exposure to bile acid sequestrants (BAS) was associated with risk of dementia. In Step 3, we examined plausible mechanisms underlying these findings by testing whether brain levels of primary BAs and gene expression of their principal receptors are altered in AD. Step 1: We assayed serum concentrations CA, CDCA, and 7α-OHC and used linear regression and mixed effects models to test their associations with brain amyloid accumulation (N = 141), WMLs, and brain atrophy (N = 134) in the Baltimore Longitudinal Study of Aging (BLSA). The BLSA is an ongoing, community-based cohort study that began in 1958. Participants in the BLSA neuroimaging sample were approximately 46% male with a mean age of 76 years; longitudinal analyses included an average of 2.5 follow-up magnetic resonance imaging (MRI) visits. We used the Alzheimer's Disease Neuroimaging Initiative (ADNI) (N = 1,666) to validate longitudinal neuroimaging results in BLSA. ADNI is an ongoing, community-based cohort study that began in 2003. Participants were approximately 55% male with a mean age of 74 years; longitudinal analyses included an average of 5.2 follow-up MRI visits. Lower serum concentrations of 7α-OHC, CA, and CDCA were associated with higher brain amyloid deposition (p = 0.041), faster WML accumulation (p = 0.050), and faster brain atrophy mainly (false discovery rate [FDR] p = <0.001-0.013) in males in BLSA. In ADNI, we found a modest sex-specific effect indicating that lower serum concentrations of CA and CDCA were associated with faster brain atrophy (FDR p = 0.049) in males.Step 2: In the Clinical Practice Research Datalink (CPRD) dataset, covering >4 million registrants from general practice clinics in the United Kingdom, we tested whether patients using BAS (BAS users; 3,208 with ≥2 prescriptions), which reduce circulating BAs and increase cholesterol catabolism, had altered dementia risk compared to those on non-statin lipid-modifying therapies (LMT users; 23,483 with ≥2 prescriptions). Patients in the study (BAS/LMT) were approximately 34%/38% male and with a mean age of 65/68 years; follow-up time was 4.7/5.7 years. We found that BAS use was not significantly associated with risk of all-cause dementia (hazard ratio (HR) = 1.03, 95% confidence interval (CI) = 0.72-1.46, p = 0.88) or its subtypes. We found a significant difference between the risk of VaD in males compared to females (p = 0.040) and a significant dose-response relationship between BAS use and risk of VaD (p-trend = 0.045) in males.Step 3: We assayed brain tissue concentrations of CA and CDCA comparing AD and control (CON) samples in the BLSA autopsy cohort (N = 29). Participants in the BLSA autopsy cohort (AD/CON) were approximately 50%/77% male with a mean age of 87/82 years. We analyzed single-cell RNA sequencing (scRNA-Seq) data to compare brain BA receptor gene expression between AD and CON samples from the Religious Orders Study and Memory and Aging Project (ROSMAP) cohort (N = 46). ROSMAP is an ongoing, community-based cohort study that began in 1994. Participants (AD/CON) were approximately 56%/36% male with a mean age of 85/85 years. In BLSA, we found that CA and CDCA were detectable in postmortem brain tissue samples and were marginally higher in AD samples compared to CON. In ROSMAP, we found sex-specific differences in altered neuronal gene expression of BA receptors in AD. Study limitations include the small sample sizes in the BLSA cohort and likely inaccuracies in the clinical diagnosis of dementia subtypes in primary care settings.

CONCLUSIONS

We combined targeted metabolomics in serum and amyloid positron emission tomography (PET) and MRI of the brain with pharmacoepidemiologic analysis to implicate dysregulation of cholesterol catabolism in dementia pathogenesis. We observed that lower serum BA concentration mainly in males is associated with neuroimaging markers of dementia, and pharmacological lowering of BA levels may be associated with higher risk of VaD in males. We hypothesize that dysregulation of BA signaling pathways in the brain may represent a plausible biologic mechanism underlying these results. Together, our observations suggest a novel mechanism relating abnormalities in cholesterol catabolism to risk of dementia.

115 Multi-Disciplinary Simulation Training on Delirium

Introduction

Delirium is still perceived as a “geriatric medicine competency”, despite its high prevalence across most specialties. Collective multi-disciplinary team performance in implementation of multi-component interventions is key. Simulation training incorporates the complex interplay of non-technical factors, specifically, role recognition and empowerment, inter-personal skills and teamwork that are pivotal in delivering effective delirium care.

Methods

Funding was approved by Health Education England. 2 pilot teaching sessions were arranged in the simulation ward. 3 scenarios were developed, each requiring a facilitator, an actor and three participants- a foundation-year doctor, a nurse/healthcare assistant and a therapist. Scenario 1 dealt with a patient with hypoactive delirium with focus on identification and multidisciplinary optimisation. Scenario 2 challenged participants with management of an agitated patient. Scenario 3 involved discharging a patient with resolving delirium and a reluctant relative, with emphasis on mental capacity assessment. Communication, patient risk assessment and challenging perceived role barriers were global themes. Participant feedback was captured using unstructured interviews and pre- and post-session 5-point Likert confidence scale in various learning outcomes.

Results

16 participants were included- 4 foundation year doctors, 3 therapists, 2 healthcare assistants and 7 nurses. There was an average improvement in Likert confidence scales in all measured learning outcomes. All participants would recommend the course to their colleagues (average Likert scale 4.9). Qualitative feedback appraised the course for demonstration of de-escalation communication strategies, the application of mental capacity and recognition of early discharge planning.

Conclusion

Simulation training targeted at multi-disciplinary groups is an effective way to deliver teaching on delirium. It contextualises synergistic operation of different skills and personal accountability in influencing patient management. The challenge to its potential remains its adoption as mandatory training for various disciplines involved in care of older adults and its implementation at a wider-scale, to assure cost effectiveness.

CellMiner Cross-Database (CellMinerCDB) version 1.2: Exploration of patient-derived cancer cell line pharmacogenomics

CellMiner Cross-Database (CellMinerCDB, discover.nci.nih.gov/cellminercdb) allows integration and analysis of molecular and pharmacological data within and across cancer cell line datasets from the National Cancer Institute (NCI), Broad Institute, Sanger/MGH and MD Anderson Cancer Center (MDACC). We present CellMinerCDB 1.2 with updates to datasets from NCI-60, Broad Cancer Cell Line Encyclopedia and Sanger/MGH, and the addition of new datasets, including NCI-ALMANAC drug combination, MDACC Cell Line Project proteomic, NCI-SCLC DNA copy number and methylation data, and Broad methylation, genetic dependency and metabolomic datasets. CellMinerCDB (v1.2) includes several improvements over the previously published version: (i) new and updated datasets; (ii) support for pattern comparisons and multivariate analyses across data sources; (iii) updated annotations with drug mechanism of action information and biologically relevant multigene signatures; (iv) analysis speedups via caching; (v) a new dataset download feature; (vi) improved visualization of subsets of multiple tissue types; (vii) breakdown of univariate associations by tissue type; and (viii) enhanced help information. The curation and common annotations (e.g. tissues of origin and identifiers) provided here across pharmacogenomic datasets increase the utility of the individual datasets to address multiple researcher question types, including data reproducibility, biomarker discovery and multivariate analysis of drug activity.

Bile Acids in Dementia: Brain Amyloid, White Matter Lesions, and Atrophy

While Alzheimer’s disease (AD) and vascular dementia (VaD) may be accelerated by hypercholesterolemia, the mechanisms underlying this association is unclear. Using a novel, 3-step study design we examined the role of cholesterol catabolism in dementia by testing whether 1) the synthesis of the primary cholesterol breakdown products (bile acids (BA)) were associated with neuroimaging markers of dementia; 2) pharmacological modulation of BAs alters dementia risk; and 3) brain BA concentrations and gene expression were associated with AD. We found that higher serum concentrations of BAs are associated with lower brain amyloid deposition, slower WML accumulation, and slower brain atrophy in males. Opposite effects were observed in females. Modulation of BA levels alters risk of incident VaD in males. Altered brain BA signaling at the metabolite and gene expression levels occurs in AD. Dysregulation of peripheral cholesterol catabolism and BA synthesis may impact dementia pathogenesis through signaling pathways in the brain.

Targeting abnormal metabolism in Alzheimer's disease: The Drug Repurposing for Effective Alzheimer's Medicines (DREAM) study

Drug discovery for disease-modifying therapies for Alzheimer's disease and related dementias (ADRD) based on the traditional paradigm of experimental animal models has been disappointing. We describe the rationale and design of the Drug Repurposing for Effective Alzheimer's Medicines (DREAM) study, an innovative multidisciplinary alternative to traditional drug discovery. First, we use a systems biology perspective in the "hypothesis generation" phase to identify metabolic abnormalities that may either precede or interact with the accumulation of ADRD neuropathology, accelerating the expression of clinical symptoms of the disease. Second, in the "hypothesis refinement" phase we propose use of large patient cohorts to test whether drugs approved for other indications that also target metabolic drivers of ADRD pathogenesis might alter the trajectory of the disease. We emphasize key challenges in population-based pharmacoepidemiologic studies aimed at quantifying the association between medication use and ADRD onset and outline robust causal inference principles to safeguard against common pitfalls. Candidate ADRD treatments emerging from this approach will hold promise as plausible disease-modifying therapies for evaluation in randomized controlled trials.

SCLC-CellMiner: A Resource for Small Cell Lung Cancer Cell Line Genomics and Pharmacology Based on Genomic Signatures

CellMiner-SCLC (https://discover.nci.nih.gov/SclcCellMinerCDB/) integrates drug sensitivity and genomic data, including high-resolution methylome and transcriptome from 118 patient-derived small cell lung cancer (SCLC) cell lines, providing a resource for research into this "recalcitrant cancer." We demonstrate the reproducibility and stability of data from multiple sources and validate the SCLC consensus nomenclature on the basis of expression of master transcription factors NEUROD1, ASCL1, POU2F3, and YAP1. Our analyses reveal transcription networks linking SCLC subtypes with MYC and its paralogs and the NOTCH and HIPPO pathways. SCLC subsets express specific surface markers, providing potential opportunities for antibody-based targeted therapies. YAP1-driven SCLCs are notable for differential expression of the NOTCH pathway, epithelial-mesenchymal transition (EMT), and antigen-presenting machinery (APM) genes and sensitivity to mTOR and AKT inhibitors. These analyses provide insights into SCLC biology and a framework for future investigations into subtype-specific SCLC vulnerabilities.

Correction: Dysregulation of multiple metabolic networks related to brain transmethylation and polyamine pathways in Alzheimer disease: A targeted metabolomic and transcriptomic study

[This corrects the article DOI: 10.1371/journal.pmed.1003012.].

Candidate biomarker assessment for pharmacological response

Using the information from our CellMiner (https://discover.nci.nih.gov/cellminer/) and CellMinerCDB (https://discover.nci.nih.gov/cellminercdb/) web-based applications, we identified 3978 molecular events with significant links to pharmacological response for genes that are either targets, biomarkers, or have established causal linkage to drugs. Molecular events included DNA copy number, methylation and mutation; and transcript; and whole or phospho-protein expression for the NCI-60 human cancer cell lines. While all forms of molecular data were informative in some (gene-drug) pairings, the type of significantly linked molecular events was found to vary widely by drug. Some forms of molecular data were found to have more frequent significant correlation than others. Leading were phosphoproteins as measured by antibody (31%), followed by transcript as measured by microarray (16%), and total protein levels as measured by mass spectrometry or antibody (14%). All other measurements ranged between 5 and 11%. Data reliability was underscored by concordant results when using differing drugs with the same targets, as well as different measurements of the same molecular parameter. The significance of correlations of the various molecular parameters to the pharmacological responses provides functional indication of those parameters that are biologically relevant for each gene-drug pairing, as well as comparisons between measurement types.

Epigenome-wide DNA methylation analysis of small cell lung cancer cell lines suggests potential chemotherapy targets

BACKGROUND

Small cell lung cancer (SCLC) is an aggressive neuroendocrine lung cancer. SCLC progression and treatment resistance involve epigenetic processes. However, links between SCLC DNA methylation and drug response remain unclear. We performed an epigenome-wide study of 66 human SCLC cell lines using the Illumina Infinium MethylationEPIC BeadChip array. Correlations of SCLC DNA methylation and gene expression with in vitro response to 526 antitumor agents were examined.

RESULTS

We found multiple significant correlations between DNA methylation and chemosensitivity. A potentially important association was observed for TREX1, which encodes the 3' exonuclease I that serves as a STING antagonist in the regulation of a cytosolic DNA-sensing pathway. Increased methylation and low expression of TREX1 were associated with the sensitivity to Aurora kinase inhibitors AZD-1152, SCH-1473759, SNS-314, and TAK-901; the CDK inhibitor R-547; the Vertex ATR inhibitor Cpd 45; and the mitotic spindle disruptor vinorelbine. Compared with cell lines of other cancer types, TREX1 had low mRNA expression and increased upstream region methylation in SCLC, suggesting a possible relationship with SCLC sensitivity to Aurora kinase inhibitors. We also identified multiple additional correlations indicative of potential mechanisms of chemosensitivity. Methylation of the 3'UTR of CEP350 and MLPH, involved in centrosome machinery and microtubule tracking, respectively, was associated with response to Aurora kinase inhibitors and other agents. EPAS1 methylation was associated with response to Aurora kinase inhibitors, a PLK-1 inhibitor and a Bcl-2 inhibitor. KDM1A methylation was associated with PLK-1 inhibitors and a KSP inhibitor. Increased promoter methylation of SLFN11 was correlated with resistance to DNA damaging agents, as a result of low or no SLFN11 expression. The 5' UTR of the epigenetic modifier EZH2 was associated with response to Aurora kinase inhibitors and a FGFR inhibitor. Methylation and expression of YAP1 were correlated with response to an mTOR inhibitor. Among non-neuroendocrine markers, EPHA2 was associated with response to Aurora kinase inhibitors and a PLK-1 inhibitor and CD151 with Bcl-2 inhibitors.

CONCLUSIONS

Multiple associations indicate potential epigenetic mechanisms affecting SCLC response to chemotherapy and suggest targets for combination therapies. While many correlations were not specific to SCLC lineages, several lineage markers were associated with specific agents.

Determination of distinctive hypomethylated genes in African American colorectal neoplastic lesions

BACKGROUND

Few studies have analyzed progressive demethylation in the path to cancer. This is of utmost importance, especially in populations such as African Americans, who display aggressive tumors at diagnosis, and for whom markers of early neoplastic transformation are needed. Here, we determined hypomethylated targets in the path to colorectal cancer (CRC) using Reduced Representation Bisulfite Sequencing (RRBS).

METHODS

DNA was extracted from fresh frozen tissues of patients with different colon lesions (normal, tubular adenoma, tubulovillous adenoma, and five cancers). RRBS was performed on these DNA extracts to identify hypomethylated gene targets. Alignment, mapping, and methylation analyses were performed. Pathways affected by the hypomethylated gene targets were determined using Ingenuity Pathway Analysis (IPA).

RESULTS

Pairwise analyses of samples led to the identification of the following novel hypomethylated genes: ELMO3 (Engulfment and cell motility 3), SLC6A2 (Solute carrier family 6 member 2), SYNM (Synemin), and HMX2 (Homeobox 2). The ELMO3 promoter was significantly hypomethylated at five CpG sites, SYNM at two CpG sites, SLC6A2 at one CpG site, and the HMX2 gene at one CpG site. IPA placed these genes within important carcinogenic pathways.

CONCLUSIONS

This work provides insight into the role of hypomethylation in colon carcinogenesis in African Americans. The identified targets affected many important pathways, as demonstrated through IPA. These targets might serve as biomarkers for early diagnosis and potential targets for therapy.

Serum progranulin/tumor necrosis factor-α ratio as independent predictor of systolic blood pressure in overweight hypertensive patients: a cross-sectional study

Background

Vascular inflammation plays a key role in the progression of hypertension. Progranulin (PGRN), an anti-inflammatory growth factor, mediated inhibition of tumor necrosis factor-α (TNF-α), a pleiotropic cytokine, activity has been well-established. Despite the role of chronic low-grade inflammation in hypertension, serum levels of PGRN and PGRN/TNF-α ratio and, their association with systolic and diastolic blood pressure has not been determined in hypertensive patients till now. This study aims to find and correlate the serum levels of pro-inflammatory cytokine (TNF-α), anti-inflammatory growth factor (PGRN), and PGRN/TNF-α ratio with the blood pressure in systolic-diastolic hypertension (SDH) and isolated systolic hypertension (ISH) patients.

Results

A cross-sectional study was conducted on SDH patients (mean age, 52.95 ± 12.6 years; male/female (M/F) number = 15/10) and ISH patients (mean age, 55.80 ± 9.40 years; M/F number = 12/13) (n = 25 each). Twenty-five age and body mass index (BMI)-matched healthy subjects (mean age, 56.00 ± 8.55 years; male/female number = 11/14) were considered as control. All patients and healthy subjects were overweight (BMI, 25–30 kg/m²). Overnight fasting blood samples of subjects were taken and levels of PGRN and TNF-α were measured using ELISA diagnostic kits. PGRN and TNF-α levels were found significantly high, whereas PGRN/TNF ratio was found very low, in SDH and ISH patients as compared to healthy subjects. Reduced PGRN/TNF-α ratio and pulse pressure were found as independent predictors of SBP both in SDH and ISH patients.

Conclusions

Findings of elevated PGRN levels in response to raised TNF-α levels depict the counter regulation by PGRN to neutralize TNF-α. Findings of reduced PGRN/TNF ratio, and it being an independent predictor of SBP, ascertain the key role of imbalance in pro- and anti-inflammatory environment in hypertension. Thus, it strengthens the cross-link between the concept of immunity–adiposity–inflammation–blood pressure¸ a vicious network. Further, this cross-link of SBP and progranulin must be explored in longitudinal studies. New researches should be focused not only on impact of pro-inflammatory environment rather to find on a balance between pro- and anti-inflammatory status, so that new target sites could be explored for therapeutic management of hypertension.

Blind estimation and correction of microarray batch effect

Microarray batch effect (BE) has been the primary bottleneck for large-scale integration of data from multiple experiments. Current BE correction methods either need known batch identities (ComBat) or have the potential to overcorrect, by removing true but unknown biological differences (Surrogate Variable Analysis SVA). It is well known that experimental conditions such as array or reagent batches, PCR amplification or ozone levels can affect the measured expression levels; often the direction of perturbation of the measured expression is the same in different datasets. However, there are no BE correction algorithms that attempt to estimate the individual effects of technical differences and use them to correct expression data. In this manuscript, we show that a set of signatures, each of which is a vector the length of the number of probes, calculated on a reference set of microarray samples can predict much of the batch effect in other validation sets. We present a rationale of selecting a reference set of samples designed to estimate technical differences without removing biological differences. Putting both together, we introduce the Batch Effect Signature Correction (BESC) algorithm that uses the BES calculated on the reference set to efficiently predict and remove BE. Using two independent validation sets, we show that BESC is capable of removing batch effect without removing unknown but true biological differences. Much of the variations due to batch effect is shared between different microarray datasets. That shared information can be used to predict signatures (i.e. directions of perturbation) due to batch effect in new datasets. The correction can be precomputed without using the samples to be corrected (blind), done on each sample individually (single sample) and corrects only known technical effects without removing known or unknown biological differences (conservative). Those three characteristics make it ideal for high-throughput correction of samples for a microarray data repository. We also compare the performance of BESC to three other batch correction methods: SVA, Removing Unwanted Variation (RUV) and Hidden Covariates with Prior (HCP). An R Package besc implementing the algorithm is available from http://explainbio.com.

National survey of UK Dermatologists demonstrates significant variation in how to obtain consent for dermatological procedures

Consent must be undertaken prior to any dermatological procedure; however, in doing this, the clinician needs to ensure consent is valid and satisfies the principles of determining material risk. We aimed to assess variations in obtaining consent in the UK and understanding of material risk through a nationally distributed survey to members of the British Society for Dermatological Surgery and British Association of Dermatologists. Of 165 responses, we found that written consent was being obtained for all procedures in 73.9% of cases and typically at the time of procedure in the operating room/theatre (78.8%). Fifty-seven per cent of respondents were not familiar with the term 'material risk' and almost one-third were not aware of the Montgomery vs. Lanarkshire ruling, which replaced the Bolam test in 2015. We would encourage readers to be aware of these changes to consent law in the UK and how it might affect their approach to obtaining consent.

Abstract B013: Associations of epigenome-wide DNA methylation patterns with chemosensitivity and chemoresistance of small cell lung cancer cell lines

Small cell lung cancer (SCLC), an aggressive neuroendocrine type of lung cancer, rapidly acquires resistance to treatment. SCLC progression, lineage differentiation, and resistance to therapy have been suggested to involve epigenetic processes. To date, epigenetic links connecting SCLC DNA methylation patterns to drug response and the ways in which these links are mediated by gene expression remain unclear. In order to understand how DNA methylation may affect SCLC response to chemotherapy, we performed an epigenome-wide association study of 66 SCLC cell lines. We used Illumina Infinium MethylationEPIC BeadChip to measure methylation of 866,091 probes. We examined how methylation of probes and gene regions was associated with SCLC in vitro response to 526 antitumor agents. We also identified associations of epigenetic variation with drug response which may be mediated by regulation of gene expression. A potentially important strong association was observed for TREX1, which encodes the 3’ exonuclease I (DNase III) that is involved in resolution of chromatin bridges and has a potential role in chromothripsis. Increased methylation and low expression of TREX1 were associated with SCLC cell line sensitivity to multiple Aurora kinase inhibitors AZD-1152, SCH-1473759, SNS-314, and TAK-901, as well as to the CDK inhibitor R-547, Vertex ATR inhibitor Cpd 45, and the mitotic spindle disruptor vinorelbine. TREX1 upregulation has been previously associated with resistance of other cancers to DNA damaging agents and with DNA repair or DNA degradation after drug exposure. In our analysis, when compared to other cancer categories, TREX1 in SCLC cell lines had low mRNA expression and increased DNA methylation upstream of its transcription start site, which may provide a possible molecular mechanism for SCLC sensitivity to Aurora kinase inhibitors. CEP350 and MLPH, which are involved in centrosome machinery and microtubule tracking, were associated with several Aurora kinase inhibitors and other agents. Among other examples, EPAS1 (HIF2A) was associated with several Aurora kinase inhibitors, the PLK1 inhibitor GSK-461364, and the Bcl-2 inhibitor ABT-737. Methylation of KDM1A, encoding the histone modifier lysine demethylase 1A (LSD1), was associated with PLK1 inhibitors and the KSP inhibitor SB-743921. IGFBP5, which is expressed in the tuft cell-like SCLC subtype, was associated with the mTOR inhibitor INK-128. Upstream regions of MDM2 and DLL3, a Notch pathway regulator overexpressed in ASCL1-high SCLC tumors, were associated with Bcl-2 inhibitors. Methylation and expression of YAP1, a SCLC lineage driver regulating the Hippo pathway, were correlated with the MTOR inhibitor rapamycin. Among non-neuroendocrine lineage markers, EPHA2 was associated with Aurora kinase inhibitors and a PLK1 inhibitor, and CD151 with Bcl-2 inhibitors. Increased methylation upstream of SLFN11 was correlated with resistance to DNA damaging agents, which is likely mediated by SLFN11 expression. The 5’ UTR region of the epigenetic modifier EZH2 was associated with Aurora kinase inhibitors and the FGFR inhibitor BGJ-398. These and multiple other associations identified in this study provide a novel understanding of epigenetic mechanisms which may modulate SCLC response to chemotherapy, and suggest potential molecular targets for combination therapies. This research was supported in part with federal funds from the National Cancer Institute, NIH, under contract HHSN261200800001E.

Citation Format: Julia Krushkal, Thomas Silvers, Dmitriy Sonkin, Suleyman Vural, John Connelly, Sudhir Varma, Paul S. Meltzer, William C. Reinhold, Annamaria Rapisarda, David Evans, Yves Pommier, Beverly A. Teicher. Associations of epigenome-wide DNA methylation patterns with chemosensitivity and chemoresistance of small cell lung cancer cell lines [abstract]. In: Proceedings of the AACR-NCI-EORTC International Conference on Molecular Targets and Cancer Therapeutics; 2019 Oct 26-30; Boston, MA. Philadelphia (PA): AACR; Mol Cancer Ther 2019;18(12 Suppl):Abstract nr B013. doi:10.1158/1535-7163.TARG-19-B013

Mandibular Gonial Angle Measurement as a Predictor of Gender-A Digital Panoramic Study

Objective:

The present study is intended for properly assessing, comparing, and evaluating the contemporary measurements of gonial angle using digital panoramic radiography. In addition, this research evaluates the importance of mandibular gonial angle in gender determination.

Materials and Methods:

Technically, this is a retrospective cross-sectional study, where the study sample was composed of 590 (295 males and 295 females) patients undergoing digital panoramic radiography in the College of Dentistry in University of Science & Technology of Fujairah, Fujairah, UAE . These patients had been prescribed panoramic radiographs based on different factors. As a generally adopted procedure, bilateral gonial angle measurements were carried out, results were recorded, and their predictability as a determinant of gender was assessed. ANOVA and t-test procedures were utilized for statistical analysis of the collected data.

Results:

The analysis of the present study confirmed a statistically significant difference between the right and left sides of the gonial angle in both genders. Further, the mean comparison exposed a variation between males and females, based on gonial angle values; females have a statistically significant higher mean angle values than males. Based on the analysis, the present study concludes that this difference between males and females from both sides suggests that the gonial angle helps in sex identification.

Conclusion:

It has been concluded that gender significantly influences the gonial region and has great potential to be used as a forensic tool in gender determination. Digital panoramic radiography is a good study tool and it can be used to determine the morphology of the mandible.

Quantitative Proteome Landscape of the NCI-60 Cancer Cell Lines

Here we describe a proteomic data resource for the NCI-60 cell lines generated by pressure cycling technology and SWATH mass spectrometry. We developed the DIA-expert software to curate and visualize the SWATH data, leading to reproducible detection of over 3,100 SwissProt proteotypic proteins and systematic quantification of pathway activities. Stoichiometric relationships of interacting proteins for DNA replication, repair, the chromatin remodeling NuRD complex, β-catenin, RNA metabolism, and prefoldins are more evident than that at the mRNA level. The data are available in CellMiner (discover.nci.nih.gov/cellminercdb and discover.nci.nih.gov/cellminer), allowing casual users to test hypotheses and perform integrative, cross-database analyses of multi-omic drug response correlations for over 20,000 drugs. We demonstrate the value of proteome data in predicting drug response for over 240 clinically relevant chemotherapeutic and targeted therapies. In summary, we present a novel proteome resource for the NCI-60, together with relevant software tools, and demonstrate the benefit of proteome analyses.

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High-quality NCI-60 proteotypes created using pressure cycling technology and SWATH-MS

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Proteotypes improve drug response prediction in multi-omics regression analysis

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∼3000 measured proteins allow investigation into protein complex stoichiometry

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CellMinerCDB (discover.nci.nih.gov/cellminercdb) portal allows dataset exploration

A novel assay to screen siRNA libraries identifies protein kinases required for chromosome transmission

One of the hallmarks of cancer is chromosome instability (CIN), which leads to aneuploidy, translocations, and other chromosome aberrations. However, in the vast majority of human tumors the molecular basis of CIN remains unknown, partly because not all genes controlling chromosome transmission have yet been identified. To address this question, we developed an experimental high-throughput imaging (HTI) siRNA assay that allows the identification of novel CIN genes. Our method uses a human artificial chromosome (HAC) expressing the GFP transgene. When this assay was applied to screen an siRNA library of protein kinases, we identified PINK1, TRIO, IRAK1, PNCK, and TAOK1 as potential novel genes whose knockdown induces various mitotic abnormalities and results in chromosome loss. The HAC-based assay can be applied for screening different siRNA libraries (cell cycle regulation, DNA damage response, epigenetics, and transcription factors) to identify additional genes involved in CIN. Identification of the complete spectrum of CIN genes will reveal new insights into mechanisms of chromosome segregation and may expedite the development of novel therapeutic strategies to target the CIN phenotype in cancer cells.

RNA Sequencing of the NCI-60: Integration into CellMiner and CellMiner CDB

CellMiner (http://discover.nci.nih.gov/cellminer) and CellMinerCDB (https://discover.nci.nih.gov/cellminercdb/) are web-based applications for mining publicly available genomic, molecular, and pharmacologic datasets of human cancer cell lines including the NCI-60, Cancer Cell Line Encyclopedia, Genomics of Drug Sensitivity in Cancer, Cancer Therapeutics Response Portal, NCI/DTP small cell lung cancer, and NCI Almanac cell line sets. Here, we introduce our RNA sequencing (RNA-seq) data for the NCI-60 and their access and integration with the other databases. Correlation to transcript microarray expression levels for identical genes and identical cell lines across CellMinerCDB demonstrates the high quality of these new RNA-seq data. We provide composite and isoform transcript expression data and demonstrate diversity in isoform composition for individual cancer- and pharmacologically relevant genes, including HRAS, PTEN, EGFR, RAD51, ALKBH2, BRCA1, ERBB2, TP53, FGFR2, and CTNND1. We reveal cell-specific differences in the overall levels of isoforms and show their linkage to expression of RNA processing and splicing genes as well as resultant alterations in cancer and pharmacologic gene sets. Gene-drug pairings linked by pathways or functions show specific correlations to isoforms compared with composite gene expression, including ALKBH2-benzaldehyde, AKT3-vandetanib, BCR-imatinib, CDK1 and 20-palbociclib, CASP1-imexon, and FGFR3-pazopanib. Loss of MUC1 20 amino acid variable number tandem repeats, which is used to elicit immune response, and the presence of the androgen receptor AR-V4 and -V7 isoforms in all NCI-60 tissue of origin types demonstrate translational relevance. In summary, we introduce RNA-seq data to our CellMiner and CellMinerCDB web applications, allowing their exploration for both research and translational purposes. SIGNIFICANCE: The current study provides RNA sequencing data for the NCI-60 cell lines made accessible through both CellMiner and CellMinerCDB and is an important pharmacogenomics resource for the field.

Driver genes exome sequencing reveals distinct variants in African Americans with colorectal neoplasia

BACKGROUND

Colorectal cancer (CRC) is the third leading cause of cancer-related deaths in the United States. African Americans are disproportionately affected by CRC. Our hypothesis is that driver genes with known and novel mutations have an impact on CRC outcome in this population. Therefore, we investigated the variants' profiles in a panel of 15 CRC genes.

PATIENTS & METHODS

Colorectal specimens (n=140) were analyzed by targeted exome sequencing using an Ion Torrent platform. Detected variants were validated in 36 samples by Illumina sequencing. The novel status of the validated variants was determined by comparison to publicly available databases. Annotated using ANNOVAR and in-silico functional analysis of these variants were performed to determine likely pathogenic variants.

RESULTS

Overall, 121 known and novel variants were validated: APC (27%), AMER1 (3%), ARID1 (7%), MSH3 (12%), MSH6 (10%), BRAF (4%), KRAS (6%), FBXW7 (4%), PIK3CA (6%), SMAD4 (5%), SOX9 (2%), TCF7L2 (2%), TGFBR2 (5%), TP53 (7%). From these validated variants, 12% were novel in 8 genes (AMER1, APC, ARID1A, BRAF, MSH6, PIK3CA, SMAD4, and TCF7L2). Of the validated variants, 23% were non-synonymous, 14% were stopgains, 24% were synonymous and 39% were intronic variants.

CONCLUSION

We here report the specifics of variants' profiles of African Americans with colorectal lesions. Validated variants showed that Tumor Suppressor Genes (TSGs) APC and ARID1 and DNA Mismatch repair (MMR) genes MSH3 and MSH6 are the genes with the highest numbers of validated variants. Oncogenes KRAS and PIK3CA are also altered and likely participate in the increased proliferative potential of the mutated colonic epithelial cells in this population.

A Clinical Study on the Circadian Rhythm of Salivary Cortisol on Aggressive Periodontitis and Its Correlation with Clinical Parameters using Electrochemiluminescence Immunoassay Method

AIM

Periodontal pathologies are gaining importance as there is a clear indication of bi-way control on general homeostasis of an individual. The study of HPA axis in various diseases has proved that there is evident vulnerability existing for any organism when the Cortisol diurnal rhythm is altered. The aim was to compare the diurnal rhythm of salivary cortisol in aggressive periodontitis with control patients. This study also compared various parameters like body mass index (BMI), waist circumference, Hamilton anxiety scale, OHI-S, clinical attachment loss in aggressive periodontitis.

MATERIALS AND METHODS

30 control patients were compared against 30 aggressive periodontitis patients in Salivary cortisol diurnal rhythm. It was estimated using the electrochemiluminescence (ECL) method on a 3 point analysis-Soon after waking up, 30 minutes after waking up, 1 hour before sleep to see the diurnal variation in aggressive periodontitis patients. The samples were transferred to CABRI labs to be frozen to -20°C. The analysis was done using Cobas e-411 autoanalyzer by Roche, USA.

RESULTS

The average cortisol in aggressive patients was found to be higher compared to control patients and was found to be statistically significant with a p value of 0.012. Control group is moderately skewed left (negative skewness graph) while the aggressive p periodontitis patients showed moderately skewed right (+ve skewness graph).

CONCLUSION

The cortisol awakening response seen in control patients is not observed in aggressive periodontitis. Instead of giving a surge, the cortisol showed a dip in the first 30 minutes followed by a gradual increase in aggressive periodontitis instead of decline as observed in normal patients.

CLINICAL SIGNIFICANCE

The study will focus on the importance of cortisol circadian rhythm on periodontal health allowing the microorganism to create an environment of dysbiosis.

Incidence of sleep problems and their mediating role on depression and anxious preoccupation in patients with resected, non-advanced cancer: data from NEOcoping study

BACKGROUND

Our study analyzes the incidence of sleep problems and their mediating role on depression and anxious preoccupation in patients with resected, non-advanced cancer.

METHODS

A multi-institutional, prospective, observational study was conducted with 750 participants of 14 hospitals in Spain. Participants' socio-demographic and clinical characteristics were collected using a standardized self-report form and using EORTC QoL-QLQ-C30, BSI, Mini-MAC questionnaires.

RESULTS

In women, sleep problems, depression and anxious preoccupation were observed in 65, 41 and 21%, respectively. In men, sleep problems, depression and anxious preoccupation were reported in 51, 29 and 61%, respectively. More sleep problems, depression and anxious preoccupation were found among women than males. Depression was a significant predictor of anxious preoccupation. In males, sleep problems partially mediated this association. This was not confirmed in women.

CONCLUSION

Our findings point toward the importance of developing interventions that decrease depression and sleep problems in cancer.