Search results for: lncRNA profiling

Authors: Xiaoping Su, Gabriel G. Malouf

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Introduction: Breast cancer is a heterogeneous disease that can be classified in 4 subgroups using transcriptional profiling. The role of lncRNA expression in human breast cancer biology, prognosis, and molecular classification remains unknown. Methods and results: Using an integrative comprehensive analysis of lncRNA, mRNA and DNA methylation in 900 breast cancer patients from The Cancer Genome Atlas (TCGA) project, we unraveled the molecular portraits of 1,700 expressed lncRNA. Some of those lncRNAs (i.e, HOTAIR) are previously reported and others are novel (i.e, HOTAIRM1, MAPT-AS1). The lncRNA classification correlated well with the PAM50 classification for basal-like, Her-2 enriched and luminal B subgroups, in contrast to the luminal A subgroup which behaved differently. Importantly, estrogen receptor (ESR1) expression was associated with distinct lncRNA networks in lncRNA clusters III and IV. Gene set enrichment analysis for cis- and trans-acting lncRNA showed enrichment for breast cancer signatures driven by breast cancer master regulators. Almost two third of those lncRNA were marked by enhancer chromatin modifications (i.e., H3K27ac), suggesting that lncRNA expression may result in increased activity of neighboring genes. Differential analysis of gene expression profiling data showed that lncRNA HOTAIRM1 was significantly down-regulated in basal-like subtype, and DNA methylation profiling data showed that lncRNA HOTAIRM1 was highly methylated in basal-like subtype. Thus, our integrative analysis of gene expression and DNA methylation strongly suggested that lncRNA HOTAIRM1 should be a tumor suppressor in basal-like subtype. Conclusion and significance: Our study depicts the first lncRNA molecular portrait of breast cancer and shows that lncRNA HOTAIRM1 might be a novel tumor suppressor.

Keywords: lncRNA profiling, breast cancer, HOTAIRM1, tumor suppressor

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Authors: Yael Deutsch, Arieh Gavious

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The threat of aviation terrorism and its potential damage became significant after the 9/11 terror attacks. These attacks have led authorities and leaders to suggest that security personnel should overcome politically correct scruples about profiling and use it openly. However, there is a lack of knowledge about the smart usage of profiling and its advantages. We analyze game models that are suitable to specific real-world scenarios, focusing on profiling as a tool to detect potential violators, such as terrorists and smugglers. We provide analytical and clear answers to difficult questions, and by that help fighting against harmful violation acts.

Keywords: game theory, profiling, security, nash equilibrium

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Authors: Leonard Lipovich, Pattaraporn Thepsuwan, Anton-Scott Goustin, Juan Cai, Donghong Ju, James B. Brown

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Two-thirds of human genes do not encode any known proteins. Aside from long non-coding RNA (lncRNA) genes with recently-discovered functions, the ~40,000 non-protein-coding human genes remain poorly understood, and a role for their transcripts as de-facto unconventional messenger RNAs has not been formally excluded. Ribosome profiling (Riboseq) predicts translational potential, but without independent evidence of proteins from lncRNA open reading frames (ORFs), ribosome binding of lncRNAs does not prove translation. Previously, we mass-spectrometrically documented translation of specific lncRNAs in human K562 and GM12878 cells. We now examined lncRNA translation in human MCF7 cells, integrating strand-specific Illumina RNAseq, Riboseq, and deep mass spectrometry in biological quadruplicates performed at two core facilities (BGI, China; City of Hope, USA). We excluded known-protein matches. UCSC Genome Browser-assisted manual annotation of imperfect (tryptic-digest-peptides)-to-(lncRNA-three-frame-translations) alignments revealed three peptides hypothetically explicable by 'stop-to-nonstop' in-frame replacement of stop codons by amino acids in two ORFs of the lncRNA MMP24-AS1. To search for this phenomenon genomewide, we designed and implemented a novel pipeline, matching tryptic-digest spectra to wildcard-instead-of-stop versions of repeat-masked, six-frame, whole-genome translations. Along with singleton putative stop-to-nonstop events affecting four other lncRNAs, we identified 24 additional peptides with stop-to-nonstop in-frame substitutions from multiple positive-strand MMP24-AS1 ORFs. Only UAG and UGA, never UAA, stop codons were impacted. All MMP24-AS1-matching spectra met the same significance thresholds as high-confidence known-protein signatures. Targeted resequencing of MMP24-AS1 genomic DNA and cDNA from the same samples did not reveal any mutations, polymorphisms, or sequencing-detectable RNA editing. This unprecedented apparent gene-specific violation of the genetic code highlights the importance of matching peptides to whole-genome, not known-genes-only, ORFs in mass-spectrometry workflows, and suggests a new mechanism enhancing the combinatorial complexity of the proteome. Funding: NIH Director’s New Innovator Award 1DP2-CA196375 to LL.

Keywords: genetic code, lncRNA, long non-coding RNA, mass spectrometry, proteogenomics, ribo-seq, ribosome, RNAseq

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Authors: Diana A. Sokolova

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This article is devoted to one of the possibilities for identifying the author of an oral or written text - sociolinguistic profiling. Sociolinguistic profiling is utilized as a forensic linguistics technique to identify individuals through language patterns, particularly in criminal cases. It examines how social factors influence language use. This study aims to showcase the significance of linguistic profiling for attributing authorship in texts and emphasizes the necessity for its continuous enhancement while considering its strengths and weaknesses. The study employs semantic-syntactic, lexical-semantic, linguopragmatic, logical, presupposition, authorization, and content analysis methods to investigate linguistic profiling. The research highlights the relevance of sociolinguistic profiling in authorship attribution and underscores the importance of ongoing refinement of the technique, considering its limitations. This study emphasizes the practical application of linguistic profiling in legal settings and underscores the impact of social factors on language use, contributing to the field of forensic linguistics. Data collection involves collecting oral and written texts from criminal and civil court cases to analyze language patterns for authorship attribution. The collected data is analyzed using various linguistic analysis methods to identify individual characteristics and patterns that can aid in authorship attribution. The study addresses the effectiveness of sociolinguistic profiling in identifying authors of texts and explores the impact of social factors on language use in legal contexts. In spite of advantages challenges in linguistics profiling have spurred debates and controversies in academic circles, legal environments, and the public sphere. So, this research highlights the significance of sociolinguistic profiling in authorship attribution and emphasizes the need for further development of this method, considering its strengths and weaknesses.

Keywords: authorship attribution, detection of identifying, dialect, features, forensic linguistics, social influence, sociolinguistics, unique speech characteristics

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Authors: Adenike Adesanya, Nonthaphat Wong, Xiang-Yun Lan, Shea Ping Yip, Chien-Ling Huang

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Background: The most challenging mutation of the oncokinase BCR-ABL protein T315I, which is commonly known as the “gatekeeper” mutation and is notorious for its strong resistance to almost all tyrosine kinase inhibitors (TKIs), especially imatinib. Therefore, this study aims to identify T315I-dependent downstream microRNA (miRNA) pathways associated with drug resistance in chronic myeloid leukemia (CML) for prognostic and therapeutic purposes. Methods: T315I-carrying K562 cell clones (K562-T315I) were generated by the CRISPR-Cas9 system. Imatinib-treated K562-T315I cells were subjected to small RNA library preparation and next-generation sequencing. Putative lncRNA-miRNA-mRNA networks were analyzed with (i) DESeq2 to extract differentially expressed miRNAs, using Padj value of 0.05 as cut-off, (ii) STarMir to obtain potential miRNA response element (MRE) binding sites of selected miRNAs on lncRNA H19, (iii) miRDB, miRTarbase, and TargetScan to predict mRNA targets of selected miRNAs, (iv) IntaRNA to obtain putative interactions between H19 and the predicted mRNAs, (v) Cytoscape to visualize putative networks, and (vi) several pathway analysis platforms – Enrichr, PANTHER and ShinyGO for pathway enrichment analysis. Moreover, mitochondria isolation and transcript quantification were adopted to determine the new mechanism involved in T315I-mediated resistance of CML treatment. Results: Verification of the CRISPR-mediated mutagenesis with digital droplet PCR detected the mutation abundance of ≥80%. Further validation showed the viability of ≥90% by cell viability assay, and intense phosphorylated CRKL protein band being detected with no observable change for BCR-ABL and c-ABL protein expressions by Western blot. As reported by several investigations into hematological malignancies, we determined a 7-fold increase of H19 expression in K562-T315I cells. After imatinib treatment, a 9-fold increment was observed. DESeq2 revealed 171 miRNAs were differentially expressed K562-T315I, 112 out of these miRNAs were identified to have MRE binding regions on H19, and 26 out of the 112 miRNAs were significantly downregulated. Adopting the seed-sequence analysis of these identified miRNAs, we obtained 167 mRNAs. 6 hub miRNAs (hsa-let-7b-5p, hsa-let-7e-5p, hsa-miR-125a-5p, hsa-miR-129-5p, and hsa-miR-372-3p) and 25 predicted genes were identified after constructing hub miRNA-target gene network. These targets demonstrated putative interactions with H19 lncRNA and were mostly enriched in pathways related to cell proliferation, senescence, gene silencing, and pluripotency of stem cells. Further experimental findings have also shown the up-regulation of mitochondrial transcript and lncRNA MALAT1 contributing to the lncRNA-miRNA-mRNA networks induced by BCR-ABL T315I mutation. Conclusions: Our results have indicated that lncRNA-miRNA regulators play a crucial role not only in leukemogenesis but also in drug resistance, considering the significant dysregulation and interactions in the K562-T315I cell model generated by CRISPR-Cas9. In silico analysis has further shown that lncRNAs H19 and MALAT1 bear several complementary miRNA sites. This implies that they could serve as a sponge, hence sequestering the activity of the target miRNAs.

Keywords: chronic myeloid leukemia, imatinib resistance, lncRNA-miRNA-mRNA, T315I mutation

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Authors: Ioannis P. Panapakidis, Marios N. Moschakis

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With the continuous increment of smart meter installations across the globe, the need for processing of the load data is evident. Clustering-based load profiling is built upon the utilization of unsupervised machine learning tools for the purpose of formulating the typical load curves or load profiles. The most commonly used algorithm in the load profiling literature is the K-means. While the algorithm has been successfully tested in a variety of applications, its drawback is the strong dependence in the initialization phase. This paper proposes a novel modified form of the K-means that addresses the aforementioned problem. Simulation results indicate the superiority of the proposed algorithm compared to the K-means.

Keywords: clustering, load profiling, load modeling, machine learning, energy efficiency and quality

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Authors: Mahdi Daghmhehci Firoozjaei, Minchang Kim, Dima Alhadidi

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In this paper, we present a power profiling model for smart grid consumers based on real time load data acquired smart meters. It profiles consumers’ power consumption behaviour using the dynamic time warping (DTW) clustering algorithm. Due to the invariability of signal warping of this algorithm, time-disordered load data can be profiled and consumption features be extracted. Two load types are defined and the related load patterns are extracted for classifying consumption behaviour by DTW. The classification methodology is discussed in detail. To evaluate the performance of the method, we analyze the time-series load data measured by a smart meter in a real case. The results verify the effectiveness of the proposed profiling method with 90.91% true positive rate for load type clustering in the best case.

Keywords: power profiling, user privacy, dynamic time warping, smart grid

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Authors: Khaled M. Khan, Armstrong Nhlabatsi

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This article attempts to analyse behavioural traits of lone-wolves who struck and killed innocents in six different attacks in Europe in last nine months. The main objective of this study is to develop a profiling template in order to capture commonality of characteristics of these attackers. This study tries to understand the homogeneity of lone-wolves in terms of their social background and state of mind. The commonality among them can possibly be used to build a profiling template that could help detecting vulnerable persons who are prone to be self-radicalised or radicalised by someone else. The result of this study provides us an understanding of their commonality in terms of their state of mind and social characteristics.

Keywords: behavioral pattern, terrorism, profiling, commonality

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Authors: Xuyang Song, Jun Yin

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The smart card has been an extremely universal tool in public transit. It collects a large amount of data on buses, urban railway transit, and ferries and provides possibilities for passenger profiling. This paper combines offline analysis of passenger profiling and real-time prediction to propose a method that can accurately predict the destination station in real-time when passengers tag on. Firstly, this article constructs a static database of user travel characteristics after identifying passenger travel patterns based on the Density-Based Spatial Clustering of Applications with Noise (DBSCAN). The dual travel passenger habits are identified: OD travel habits and D station travel habits. Then a rapid real-time prediction algorithm based on Transit Passenger Profiling is proposed, which can predict the destination of in-board passengers. This article combines offline learning with online prediction, providing a technical foundation for real-time passenger flow prediction, monitoring and simulation, and short-term passenger behavior and demand prediction. This technology facilitates the efficient and real-time acquisition of passengers' travel destinations and demand. The last, an actual case was simulated and demonstrated feasibility and efficiency.

Keywords: travel behavior, destination prediction, public transit, passenger profiling

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Authors: Abhaydeep Pandey, Shweta Shukla, Saptamita Goswami, Bhaswati Bandyopadhyay, Vishnampettai Ramachandran, Sudhanshu Vrati, Arup Banerjee

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Background: Long non-coding RNAs (lncRNAs) are the important regulators of gene expression and play important role in viral replication and disease progression. The role of lncRNA genes in the pathogenesis of Dengue virus-mediated pathogenesis is currently unknown. Methods: To gain additional insights, we utilized an unbiased RNA sequencing followed by in silico analysis approach to identify the differentially expressed lncRNA and genes that are associated with dengue disease progression. Further, we focused our study on lncRNAs NEAT1 (Nuclear Paraspeckle Assembly Transcript 1) as it was found to be differentially expressed in PBMC of dengue infected patients. Results: The expression of lncRNAs NEAT1, as compared to dengue infection (DI), was significantly down-regulated as the patients developed the complication. Moreover, pairwise analysis on follow up patients confirmed that suppression of NEAT1 expression was associated with rapid fall in platelet count in dengue infected patients. Severe dengue patients (DS) (n=18; platelet count < 20K) when recovered from infection showing high NEAT1 expression as it observed in healthy donors. By co-expression network analysis and subsequent validation, we revealed that coding gene; IFI27 expression was significantly up-regulated in severe dengue cases and negatively correlated with NEAT1 expression. To discriminate DI from dengue severe, receiver operating characteristic (ROC) curve was calculated. It revealed sensitivity and specificity of 100% (95%CI: 85.69 – 97.22) and area under the curve (AUC) = 0.97 for NEAT1. Conclusions: Altogether, our first observations demonstrate that monitoring NEAT1and IFI27 expression in dengue patients could be useful in understanding dengue virus-induced disease progression and may be involved in pathophysiological processes.

Keywords: dengue, lncRNA, NEAT1, transcriptome

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Authors: Hui Li, Xueying Zhao, Ke Ma, Yu Cao, Fan Yang, Qingwen Xu, Wenbin Liu

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Soil can often link a person or item to a crime scene, which makes it a valuable evidence in forensic casework. Several techniques have been utilized in forensic soil discrimination in previous studies. Because soil contains a vast number of microbiomes, the analyse of soil microbiomes is expected to be a potential way to characterise soil evidence. In this study, we applied massively parallel sequencing (MPS) to soil bacterial profiling on the Ion Torrent Personal Genome Machine (PGM). Soils from different regions were collected repeatedly. V-region 3 and 4 of Bacterial 16S rRNA gene were detected by MPS. Operational taxonomic units (OTU, 97%) were used to analyse soil bacteria. Several bioinformatics methods (PCoA, NMDS, Metastats, LEfse, and Heatmap) were applied in bacterial profiles. Our results demonstrate that MPS can provide a more detailed picture of the soil microbiomes and the composition of soil bacterial components from different region was individualistic. In conclusion, the utility of soil bacterial profiling via MPS of the 16S rRNA gene has potential value in characterising soil evidences and associating them with their place of origin, which can play an important role in forensic science in the future.

Keywords: bacterial profiling, forensic, massively parallel sequencing, soil evidence

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Authors: Doaa Hashad, Amany Elbanna, Abeer Ibrahim, Gihan Khedr

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Background: H19 is one of the long non coding RNAs (LncRNA) that is related to the progression of many diseases including cancers. This work was carried out to study the level of the long non-coding RNA; H119, in plasma of patients with gastric cancer (GC) and to assess its significance in their clinical management. Methods: A total of sixty-two participants were enrolled in the present study. The first group included thirty-two GC patients, while the second group was formed of thirty age and sex matched healthy volunteers serving as a control group. Plasma samples were used to assess H19 gene expression using real time quantitative PCR technique. Results: H19 expression was up-regulated in GC patients with positive correlation to TNM cancer stages. Conclusions: Up-regulation of H19 is closely associated with gastric cancer and correlates well with tumor staging. Convenient, efficient quantification of H19 in plasma using real time PCR technique implements its role as a potential noninvasive prognostic biomarker in gastric cancer, that predicts patient’s outcome and most importantly as a novel target in gastric cancer treatment with better performance achieved on using both CEA and H19 simultaneously.

Keywords: biomarker, gastric, cancer, LncRNA

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Authors: Md. M. Hossain, Regan Roat, Jenica Christopherson, Colette Free, Zhiguang Guo

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Long noncoding RNA (lncRNA) mediated post-transcriptional gene regulation, and their epigenetic landscapes have been shown to be involved in many human diseases. However, their regulation in diabetes through governing islet’s β-cell function and survival needs to be elucidated. Due to the technical and ethical constraints, it is difficult to study their role in β-cell function and survival in human under in vivo condition. In this study, humanized mice have been developed through transplanting human pancreatic islet under the kidney capsule of NOD.SCID mice and induced β-cell death leading to diabetes condition to study lncRNA mediated regulation. For this, human islets from 3 donors (3000 IEQ, purity > 80%) were transplanted under the kidney capsule of STZ induced diabetic NOD.scid mice. After at least 2 weeks of normoglycecemia, lymphocytes from diabetic NOD mice were adoptively transferred and islet grafts were collected once blood glucose reached > 200 mg/dl. RNA from human donor islets, islet grafts from humanized mice with either adoptive lymphocyte transfer (ALT) or PBS control (CTL) were ribodepleted; barcoded fragment libraries were constructed and sequenced on the Ion Proton sequencer. lncRNA expression in isolated human islets, islet grafts from humanized mice with and without induced β-cell death and their regulation in human islets function in vitro under glucose challenge, cytokine mediated inflammation and induced apoptotic condition were investigated. Out of 3155 detected lncRNAs, 299 that highly expressed in islets were found to be significantly downregulated and 224 upregulated in ALT compared to CTL. Most of these are found to be collocated within 5 kb upstream and 1 kb downstream of 788 up- and 624 down-regulated mRNAs. Genomic Regions Enrichment of Annotations Analysis revealed deregulated and collocated genes are related to pancreas endocrine development; insulin synthesis, processing, and secretion; pancreatitis and diabetes. Many of them, that found to be located within enhancer domains for islet specific gene activity, are associated to the deregulation of known islet/βcell specific transcription factors and genes that are important for β-cell differentiation, identity, and function. RNA sequencing analysis revealed aberrant lncRNA expression which is associated to the deregulated mRNAs in β-cell function as well as in molecular pathways related to diabetes. A distinct set of candidate lncRNA isoforms were identified as highly enriched and specific to human islets, which are deregulated in human islets from donors with different BMIs and with type 2 diabetes. These RNAs show an interesting regulation in cultured human islets under glucose stimulation and with induced β-cell death by cytokines. Aberrant expression of these lncRNAs was detected in the exosomes from the media of islets cultured with cytokines. Results of this study suggest that the islet specific lncRNAs are deregulated in human islet with β-cell death, hence important in diabetes. These lncRNAs might be important for human β-cell function and survival thus could be used as biomarkers and novel therapeutic targets for diabetes.

Keywords: β-cell, humanized mouse, pancreatic islet, LncRNAs

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Authors: X. Cervantes-López, C. Arriaga-Canon, L. Contreras Espinosa

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The goal of this study is to validate the overexpression of the lncRNA GATA3-AS1 associated with resistance to neoadjuvant chemotherapy of female patients with locally advanced mammary adenocarcinoma of luminal B subtype This study involved a cohort of one hundred thirty-seven samples for which total RNA was isolated from formalin fixed paraffin embedded (FFPE) tissue. Samples were cut using a Microtome Hyrax M25 Zeiss and RNA was isolated using the RNeasy FFPE kit and a deparaffinization solution, the next step consisted in the analysis of RNA concentration and quality, then 18 µg of RNA was treated with DNase I, and cDNA was synthesized from 50 ng total RNA, finally real-time PCR was performed with SYBR Green/ROX qPCR Master Mix in order to determined relative gene expression using RPS28 as a housekeeping gene to normalize in a fold calculation ΔCt. As a result, we validated by real-time PCR that the overexpression of the lncRNA GATA3-AS1 is associated with resistance to neoadjuvant chemotherapy in locally advanced breast cancer patients of luminal B subtype.

Keywords: breast cancer, biomarkers, genomics, neoadjuvant chemotherapy, lncRNAS

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Authors: Tania Vasquez Mata, Luis A. Herrera, Cristian Arriaga Canon

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Background: Locally advanced breast cancer of the luminal B phenotype, poses challenges due to its variable response to neoadjuvant chemotherapy. A predictive biomarker is needed to identify patients who will not respond to treatment, allowing for alternative therapies. This study aims to validate the use of the lncRNA GATA3-AS1, as a predictive biomarker using RNA in situ hybridization. Research aim: The aim of this study is to determine if GATA3-AS1 can serve as a biomarker for resistance to neoadjuvant chemotherapy in patients with locally advanced luminal B breast cancer. Methodology: The study utilizes RNA in situ hybridization with predesigned probes for GATA3-AS1 on Formalin-Fixed Paraffin-Embedded tissue sections. The samples underwent pretreatment and protease treatment to enable probe penetration. Chromogenic detection and signal evaluation were performed using specific criteria. Findings: Patients who did not respond to neoadjuvant chemotherapy showed a 3+ score for GATA3-AS1, while those who had a complete response had a 1+ score. Theoretical importance: This study demonstrates the potential clinical utility of GATA3-AS1 as a biomarker for resistance to neoadjuvant chemotherapy. Identifying non-responders early on can help avoid unnecessary treatment and explore alternative therapy options. Data collection and analysis procedures: Tissue samples from patients with locally advanced luminal B breast cancer were collected and processed using RNA in situ hybridization. Signal evaluation was conducted under a microscope, and scoring was based on specific criteria. Questions addressed: Can GATA3-AS1 serve as a predictive biomarker for neoadjuvant chemotherapy response in locally advanced luminal B breast cancer? Conclusion: The lncRNA GATA3-AS1 can be used as a biomarker for resistance to neoadjuvant chemotherapy in patients with locally advanced luminal B breast cancer. Its identification through RNA in situ hybridization of tissue obtained from the initial biopsy can aid in treatment decision-making.

Keywords: biomarkers, breast neoplasms, genetics, neoadjuvant therapy, tumor

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Authors: Farahnaz Amini, Woo Yun Kin, Lazwani Kolandaiveloo

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Availability of different genetic tests after completion of Human Genome Project increases the physicians’ responsibility to keep themselves update on the potential implementation of these genetic tests in their daily practice. However, due to numbers of barriers, still many of physicians are not either aware of these tests or are not willing to offer or refer their patients for genetic tests. This study was conducted an anonymous, cross-sectional, mailed-based survey to develop a primary data of Malaysian physicians’ level of knowledge and perception of gene profiling. Questionnaire had 29 questions. Total scores on selected questions were used to assess the level of knowledge. The highest possible score was 11. Descriptive statistics, one way ANOVA and chi-squared test was used for statistical analysis. Sixty three completed questionnaires was returned by 27 general practitioners (GPs) and 36 medical specialists. Responders’ age range from 24 to 55 years old (mean 30.2 ± 6.4). About 40% of the participants rated themselves as having poor level of knowledge in genetics in general whilst 60% believed that they have fair level of knowledge. However, almost half (46%) of the respondents felt that they were not knowledgeable about available genetic tests. A majority (94%) of the responders were not aware of any lab or company which is offering gene profiling services in Malaysia. Only 4% of participants were aware of using gene profiling for detection of dosage of some drugs. Respondents perceived greater utility of gene profiling for breast cancer (38%) compared to the colorectal familial cancer (3%). The score of knowledge ranged from 2 to 8 (mean 4.38 ± 1.67). Non-significant differences between score of knowledge of GPs and specialists were observed, with score of 4.19 and 4.58 respectively. There was no significant association between any demographic factors and level of knowledge. However, those who graduated between years 2001 to 2005 had higher level of knowledge. Overall, 83% of participants showed relatively high level of perception on value of gene profiling to detect patient’s risk of disease. However, low perception was observed for both statements of using gene profiling for general population in order to alter their lifestyle (25%) as well as having the full sequence of a patient genome for the purpose of determining a patient’s best match for treatment (18%). The lack of clinical guidelines, limited provider knowledge and awareness, lack of time and resources to educate patients, lack of evidence-based clinical information and cost of tests were the most barriers of ordering gene profiling mentioned by physicians. In conclusion Malaysian physicians who participate in this study had mediocre level of knowledge and awareness in gene profiling. The low exposure to the genetic questions and problems might be a key predictor of lack of awareness and knowledge on available genetic tests. Educational and training workshop might be useful in helping Malaysian physicians incorporate genetic profiling into practice for eligible patients.

Keywords: gene profiling, knowledge, Malaysia, physician

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Authors: Marcus Smith

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DNA profiling has made a valuable contribution to criminal investigations over the past thirty years. Direct matching DNA profiles from a crime scene and suspect, or between a suspect and a database remain of great importance to crimes such as murder, assault, and property theft. As scientific and technological advancement continues, a wide range of new DNA profiling applications has been developed. The application of new techniques involves an interesting balancing act between admitting probative evidence in a criminal trial, evaluating its degree of relevance and validity, and limiting its prejudicial impact. The impact of new DNA profiling applications that have significant implications for law enforcement and the legal system can be evaluated through a review of relevant case law, legislation and the latest empirical evidence from jurisdictions around the world including the United States, United Kingdom, and Australia. There are benefits in further examining the implications of these new developments, including how the criminal law can best be adapted to ensure that new technology is used to enhance criminal investigation and prosecution while ensuring it is applied in a measured way that respects individual rights and maintains principles of fairness enshrined in the legal system.

Keywords: criminal procedure, forensic evidence, DNA profiling, familial searching, phenotyping

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Authors: Chengcao Sun, Shujun Li, Cuili Yang, Yongyong Xi, Liang Wang, Feng Zhang, Dejia Li

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Recently, the long non-coding RNA (lncRNA) NEAT1 has been identified as an oncogenic gene in multiple cancer types and elevated expression of NEAT1 was tightly linked to tumorigenesis and cancer progression. However, the molecular basis for this observation has not been characterized in progression of non-small cell lung cancer (NSCLC). In our studies, we identified NEAT1 was highly expressed in NSCLC patients and was a novel regulator of NSCLC progression. Patients whose tumors had high NEAT1 expression had a shorter overall survival than patients whose tumors had low NEAT1 expression. Further, NEAT1 significantly accelerates NSCLC cell growth and metastasis in vitro and tumor growth in vivo. Additionally, by using bioinformatics study and RNA pull down combined with luciferase reporter assays, we demonstrated that NEAT1 functioned as a competing endogenous RNA (ceRNA) for has-miR-377-3p, antagonized its functions and led to the de-repression of its endogenous targets E2F3, which was a core oncogene in promoting NSCLC progression. Taken together, these observations imply that the NEAT1 modulated the expression of E2F3 gene by acting as a competing endogenous RNA, which may build up the missing link between the regulatory miRNA network and NSCLC progression.

Keywords: long non-coding RNA NEAT1, hsa-miRNA-377-3p, E2F3, non-small cell lung cancer, tumorigenesis

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Authors: Aniya Everette

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In June of 1971, President Richard Nixon made his first public declaration regarding the “War on Drugs,” deeming it America’s number one public enemy. Since then, the drug war has been a divisive topic in the US. Black and brown children have been unfairly targeted and imprisoned at alarming rates as a result of this policy, which has had a negative effect on them. Black and Latino youth have faced significant obstacles that have impacted their educational opportunities, employment prospects, and general quality of life due to harsh mandatory sentences, aggressive policing tactics, and racial profiling.

Keywords: war, drugs, crime, racial profiling

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Authors: Ricardo Alberto Chiong Zevallos, Eduardo Moraes Rego Reis

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Pancreatic adenocarcinoma (PDAC) patients have a less than 10% 5-year survival rate. PDAC has no defined diagnostic and prognostic biomarkers. Gemcitabine is the first-line drug in PDAC and several other cancers. Long non-coding RNAs (lncRNAs) contribute to the tumorigenesis and are potential biomarkers for PDAC. Although lncRNAs aren’t translated into proteins, they have important functions. LncRNAs can decoy or recruit proteins from the epigenetic machinery, act as microRNA sponges, participate in protein translocation through different cellular compartments, and even promote chemoresistance. The chromatin remodeling enzyme EZH2 is a histone methyltransferase that catalyzes the methylation of histone 3 at lysine 27, silencing local expression. EZH2 is ambivalent, it can also activate gene expression independently of its histone methyltransferase activity. EZH2 is overexpressed in several cancers and interacts with lncRNAs, being recruited to a specific locus. EZH2 can be recruited to activate an oncogene or silence a tumor suppressor. The lncRNAs misregulation in cancer can result in the differential recruitment of EZH2 and in a distinct epigenetic landscape, promoting chemoresistance. The relevance of the EZH2-lncRNAs interaction to chemoresistant PDAC was assessed by Real Time quantitative PCR (RT-qPCR) and RNA Immunoprecipitation (RIP) experiments with naïve and gemcitabine-resistant PDAC cells. The expression of several lncRNAs and EZH2 gene targets was evaluated contrasting naïve and resistant cells. Selection of candidate genes was made by bioinformatic analysis and literature curation. Indeed, the resistant cell line showed higher expression of chemoresistant-associated lncRNAs and protein coding genes. RIP detected lncRNAs interacting with EZH2 with varying intensity levels in the cell lines. During RIP, the nuclear fraction of the cells was incubated with an antibody for EZH2 and with magnetic beads. The RNA precipitated with the beads-antibody-EZH2 complex was isolated and reverse transcribed. The presence of candidate lncRNAs was detected by RT-qPCR, and the enrichment was calculated relative to INPUT (total lysate control sample collected before RIP). The enrichment levels varied across the several lncRNAs and cell lines. The EZH2-lncRNA interaction might be responsible for the regulation of chemoresistance-associated genes in multiple cancers. The relevance of the lncRNA-EZH2 interaction to PDAC was assessed by siRNA knockdown of a lncRNA, followed by the analysis of the EZH2 target expression by RT-qPCR. The chromatin immunoprecipitation (ChIP) of EZH2 and H3K27me3 followed by RT-qPCR with primers for EZH2 targets also assess the specificity of the EZH2 recruitment by the lncRNA. This is the first report of the interaction of EZH2 and lncRNAs HOTTIP and PVT1 in chemoresistant PDAC. HOTTIP and PVT1 were described as promoting chemoresistance in several cancers, but the role of EZH2 is not clarified. For the first time, the lncRNA LINC01133 was detected in a chemoresistant cancer. The interaction of EZH2 with LINC02577, LINC00920, LINC00941, and LINC01559 have never been reported in any context. The novel lncRNAs-EZH2 interactions regulate chemoresistant-associated genes in PDAC and might be relevant to other cancers. Therapies targeting EZH2 alone weren’t successful, and a combinatorial approach also targeting the lncRNAs interacting with it might be key to overcome chemoresistance in several cancers.

Keywords: epigenetics, chemoresistance, long non-coding RNAs, pancreatic cancer, histone modification

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Authors: Yi-Lin Chen, Sheng-Jou Hung, Tsunglin Liu

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Adaptive immune system recognizes a wide range of antigens via expressing a large number of structurally distinct T cell and B cell receptor genes. The distinct receptor genes arise from complex rearrangements called V(D)J recombination, and constitute the immune repertoire. A common method of profiling immune repertoire is via amplifying recombined receptor genes using multiple primers and high-throughput sequencing. This multiplex-PCR approach is efficient; however, the resulting repertoire can be distorted because of primer bias. To eliminate primer bias, 5’ RACE is an alternative amplification approach. However, the application of RACE approach is limited by its low efficiency (i.e., the majority of data are non-regular receptor sequences, e.g., containing intronic segments) and lack of the convenient tool for analysis. We propose a computational tool that can correctly identify non-regular receptor sequences in RACE data via aligning receptor sequences against the whole gene instead of only the exon regions as done in all other tools. Using our tool, the remaining regular data allow for an accurate profiling of immune repertoire. In addition, a RACE approach is improved to yield a higher fraction of regular T-cell receptor sequences. Finally, we quantify the degree of primer bias of a multiplex-PCR approach via comparing it to the RACE approach. The results reveal significant differences in frequency of VJ combination by the two approaches. Together, we provide a new experimental and computation pipeline for an unbiased profiling of immune repertoire. As immune repertoire profiling has many applications, e.g., tracing bacterial and viral infection, detection of T cell lymphoma and minimal residual disease, monitoring cancer immunotherapy, etc., our work should benefit scientists who are interested in the applications.

Keywords: immune repertoire, T-cell receptor, 5' RACE, high-throughput sequencing, sequence alignment

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Authors: Amanina Iymia Jeffree, Reena Thriumani, Mohammad Iqbal Omar, Ammar Zakaria, Yumi Zuhanis Has-Yun Hashim, Ali Yeon Md Shakaff

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Metabolite profiling is a strategy to be approached in the pattern recognition method focused on three types of cancer cell line that driving the most to death specifically lung, breast, and colon cancer. The purpose of this study was to discriminate the VOCs pattern among cancerous and control group based on metabolite profiling. The sampling was executed utilizing the cell culture technique. All culture flasks were incubated till 72 hours and data collection started after 24 hours. Every running sample took 24 minutes to be completed accordingly. The comparative metabolite patterns were identified by the implementation of headspace-solid phase micro-extraction (HS-SPME) sampling coupled with gas chromatography-mass spectrometry (GCMS). The optimizations of the main experimental variables such as oven temperature and time were evaluated by response surface methodology (RSM) to get the optimal condition. Volatiles were acknowledged through the National Institute of Standards and Technology (NIST) mass spectral database and retention time libraries. To improve the reliability of significance, it is of crucial importance to eliminate background noise which data from 3rd minutes to 17th minutes were selected for statistical analysis. Targeted metabolites, of which were annotated as known compounds with the peak area greater than 0.5 percent were highlighted and subsequently treated statistically. Volatiles produced contain hundreds to thousands of compounds; therefore, it will be optimized by chemometric analysis, such as principal component analysis (PCA) as a preliminary analysis before subjected to a pattern classifier for identification of VOC samples. The volatile organic compound profiling has shown to be significantly distinguished among cancerous and control group based on metabolite profiling.

Keywords: in vitro cancer cell line, metabolite profiling, pattern recognition, volatile organic compounds

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Authors: Aadita Chaudhury

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Since at least the early 2000s, DNA profiling has achieved a preeminent status in forensic investigations into criminal acts. While the criminal justice system has a long history of using forensic evidence and testing them through establish technoscientific means, the primacy of DNA in establishing 'truth' or reconstructing a series of events is unparalleled in the history of forensic science. This paper seeks to elucidate the ways in which DNA profiling has become the most authoritative instrument of 'truth' in criminal investigations, and how it is used in the legal process to ascertain culpability, create the notion of infallible evidence, and advance the search for justice. It is argued that DNA profiling has created a paradigm shift in how the legal system and the general public understands crime and culpability, but not without limitations. There are indications that even trace amounts of DNA evidence can point to causal links in a criminal investigation, however, there still remains many rooms to create confusion and doubt from empirical evidence within the narrative of crimes. Many of the shortcomings of DNA-based forensic investigations are explored and evaluated with regards to claims of the authority of biological evidence and implications for the public understanding of the elusive concepts of truth and justice in the present era. Public misinformation about the forensic analysis processes could produce doubt or faith in the judgements rooted in them, depending on other variables presented at the trial. A positivist understanding of forensic science that is shared by the majority of the population does not take into consideration that DNA evidence is far from definitive, and can be used to support any theories of culpability, to create doubt and to deflect blame.

Keywords: DNA profiling, epistemology of forensic science, philosophy of forensic science, sociology of scientific knowledge

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Authors: Abdulaziz Fageeh

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In the bustling digital landscape of Saudi Arabia, a chilling wave of cybercrime has swept across the nation. Among the most nefarious acts are financial blackmail schemes, perpetrated by anonymous actors lurking within the shadows of social media platforms. This chilling reality necessitates the utilization of forensic linguistic techniques to unravel the identities of these virtual villains. This research delves into the complex world of authorship profiling, investigating the effectiveness of various linguistic features in identifying the perpetrators of malicious messages within the Saudi social media environment. By meticulously analyzing patterns of language, vocabulary choice, and stylistic nuances, the study endeavors to uncover the hidden characteristics of the individuals responsible for these heinous acts. Through this linguistic detective work, the research aims to provide valuable insights to investigators and policymakers in the ongoing battle against cybercrime and to shed light on the evolution of malicious online behavior within the Saudi context.

Keywords: authorship profiling, arabic linguistics, saudi social media, cybercrime, financial blackmail, linguistic features, forensic linguistics, online threats

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Authors: L. Agneni, F. Carta, C. Micheletta, V. Tersigni

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The development of a qualitative method to profile jobseekers is needed to improve the quality of the Public Employment Services (PES) in Italy. This is why the National Agency for Active Labour Market Policies (ANPAL) decided to introduce a Qualitative Profiling Service in the context of the activities carried out by local employment offices’ operators. The qualitative profiling service provides information and data regarding the jobseeker’s personal transition status, through a semi-structured questionnaire administered to PES clients during the guidance interview. The questionnaire responses allow PES staff to identify, for each client, proper activities and policy measures to support jobseekers in their reintegration into the labour market. Data and information gathered by the qualitative profiling tool are the following: frequency, modalities and motivations for clients to apply to local employment offices; clients’ expectations and skills; difficulties that they have faced during the previous working experiences; strategies, actions undertaken and activated channels for job search. These data are used to assess jobseekers’ personal and career characteristics and to measure their employability level (qualitative profiling index), in order to develop and deliver tailor-made action programmes for each client. This paper illustrates the use of the above-mentioned qualitative profiling service on the national territory and provides an overview of the main findings of the survey: concerning the difficulties that unemployed people face in finding a job and their perception of different aspects related to the transition in the labour market. The survey involved over 10.000 jobseekers registered with the PES. Most of them are beneficiaries of the “citizens' income”, a specific active labour policy and social inclusion measure. Furthermore, data analysis allows classifying jobseekers into a specific group of clients with similar features and behaviours, on the basis of socio-demographic variables, customers' expectations, needs and required skills for the profession for which they seek employment. Finally, the survey collects PES staff opinions and comments concerning clients’ difficulties in finding a new job and also their strengths. This is a starting point for PESs’ operators to define adequate strategies to facilitate jobseekers’ access or reintegration into the labour market.

Keywords: labour market transition, public employment services, qualitative profiling, vocational guidance

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Authors: Bi Xiao Fang, Tan Bao Zhen

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Soft skills, core competencies, and generic competencies are exchangeable terminologies often used to represent a similar concept. In the Singapore context, such skills are currently being referred to as Critical Core Skills (CCS). In 2019, SkillsFuture Singapore (SSG) reviewed the Generic Skills and Competencies (GSC) framework that was first introduced in 2016, culminating in the development of the Critical Core Skills (CCS) framework comprising 16 soft skills classified into three clusters. The CCS framework is part of the Skills Framework, and whose stated purpose is to create a common skills language for individuals, employers and training providers. It is also developed with the objectives of building deep skills for a lean workforce, enhance business competitiveness and support employment and employability. This further helps to facilitate skills recognition and support the design of training programs for skills and career development. According to SSG, every job role requires a set of technical skills and a set of Critical Core Skills to perform well at work, whereby technical skills refer to skills required to perform key tasks of the job. There has been an increasing emphasis on soft skills for the future of work. A recent study involving approximately 80 organizations across 28 sectors in Singapore revealed that more enterprises are beginning to recognize that soft skills support their employees’ performance and business competitiveness. Though CCS is of high importance for the development of the workforce’s employability, there is little attention paid to the CCS use and profiling across occupations. A better understanding of how CCS is distributed across the economy will thus significantly enhance SSG’s career guidance services as well as training providers’ services to graduates and workers and guide organizations in their hiring for soft skills. This CCS profiling study sought to understand how CCS is demanded in different occupations. To achieve its research objectives, this study adopted a quantitative method to measure CCS use across different occupations in the Singaporean workforce. Based on the CCS framework developed by SSG, the research team adopted a formative approach to developing the CCS profiling tool to measure the importance of and self-efficacy in the use of CCS among the Singaporean workforce. Drawing on the survey results from 2500 participants, this study managed to profile them into seven occupation groups based on the different patterns of importance and confidence levels of the use of CCS. Each occupation group is labeled according to the most salient and demanded CCS. In the meantime, the CCS in each occupation group, which may need some further strengthening, were also identified. The profiling of CCS use has significant implications for different stakeholders, e.g., employers could leverage the profiling results to hire the staff with the soft skills demanded by the job.

Keywords: employability, skills profiling, skills measurement, soft skills

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Authors: Elbert S. Moyon, Edsel Matt O. Morales, Jaymer M. Jayoma, Kent C. Espejon, Jayson C. Dollete, Mark Phil B. Pacot

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This research paper focuses on the potential of using Web-GIS technology in prioritizing farm-to-market road projects by the Philippines’ Department of Agriculture (DA). The study aimed to explore the benefits of Web-GIS in addressing the limitations faced by the DA in terms of Farm to Market Road profiling and project prioritization, which include a lack of access to updated data, limited spatial analysis capabilities, and difficulties in sharing information between stakeholders. The research methodology involves a comprehensive literature review and a case study of a Web-GIS application developed for the DA, which was used to profile and prioritize farm-to-market road projects in the Philippines. The results showed that the Web-GIS technology provides the DA with an effective tool for analyzing and visualizing data, which can help in profiling and prioritizing road projects based on various criteria such as economic, social, and environmental impacts. The study also showed that Web-GIS technology could help in reducing the time and effort required for road project prioritization and improve communication between stakeholders.

Keywords: GIS, web application, farm-to-market road, FMR prioritization, Django, GeoServer

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Authors: Nicole Ramlachan, Samuel Mark West

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Lung cancer is the leading cause of cancer-associated deaths in North America, with the vast majority being non-small cell lung cancer (NSCLC), with a five-year survival rate of only 24%. Non-invasive discovery of biomarkers associated with early-diagnosis of NSCLC can enable precision oncology efforts using liquid biopsy-based multiomics profiling of plasma. Although tissue biopsies are currently the gold standard for tumor profiling, this method presents many limitations since these are invasive, risky, and sometimes hard to obtain as well as only giving a limited tumor profile. Blood-based tests provides a less-invasive, more robust approach to interrogate both tumor- and non-tumor-derived signals. We intend to examine 30 stage III-IV NSCLC patients pre-surgery and collect plasma samples.Cell-free DNA (cfDNA) will be extracted from plasma, and next-generation sequencing (NGS) performed. Through the analysis of tumor-specific alterations, including single nucleotide variants (SNVs), insertions, deletions, copy number variations (CNVs), and methylation alterations, we intend to identify tumor-derived DNA—ctDNA among the total pool of cfDNA. This would generate data to be used as an accurate form of cancer genotyping for diagnostic purposes. Using liquid biopsies offer opportunities to improve the surveillance of cancer patients during treatment and would supplement current diagnosis and tumor profiling strategies previously not readily available in Trinidad and Tobago. It would be useful and advantageous to use this in diagnosis and tumour profiling as well as to monitor cancer patients, providing early information regarding disease evolution and treatment efficacy, and reorient treatment strategies in, timethereby improving clinical oncology outcomes.

Keywords: genomics, multiomics, clinical genetics, genotyping, oncology, diagnostics

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Authors: A. Maciejak, M. Kiliszek, G. Opolski, D. Tulacz, A. Segiet, K. Matlak, S. Dobrzycki, G. Sygitowicz, B. Burzynska, M. Gora

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Introduction and aims: Acute myocardial infarction (AMI) is one of the most severe cardiovascular diseases affecting millions of patients each year worldwide. An early and accurate diagnosis of AMI is essential for optimal treatment. Therefore, new approaches that can complement and improve current strategies for AMI diagnosis are urgently needed. Recent studies have revealed the presence of stable circulating myocardial-derived microRNAs (miRNAs) in human peripheral blood, suggesting that such miRNAs could serve as potential biomarkers of infarction. The present study aimed to identify differentially expressed circulating miRNAs in ST-segment elevation myocardial infarction (STEMI) patients. Materials and methods: miRNA expression profile analysis was performed using Exiqon Serum/Plasma Focus microRNA PCR panel in plasma samples of n=16 patients on the first day of AMI (admission) and in samples from the same patients collected six months after AMI. Selected miRNAs were validated by RT-qPCR using serum samples from an independent set of n=14 AMI patients. Results: The profiling study identified 46 species of plasma miRNAs that were differentially expressed (p < 0.05) on admission compared to six months after AMI. The validation in the independent group of patients confirmed that miR-133b and miR-22-5p were significantly up-regulated upon AMI. Conclusions: Our results suggest that miRNA expression profiling provides better understanding of the changes that occur in the acute phase of MI in the myocardium and could be useful in determination of the potential role of extracellular miRNAs as paracrine signaling molecules. miR-22-5p represents a novel promising biomarker for the diagnosis of acute myocardial infarction.

Keywords: acute myocardial infarction, circulating microRNAs, microRNA expression profiling, miR-22-5p

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Authors: Mónica P. Cala, Juan S. Carreño, Roland J.W. Meesters

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Recently, collection of biological fluids on special filter papers has become a popular micro-sampling technique. Especially, the dried blood spot (DBS) micro-sampling technique has gained much attention and is momently applied in various life sciences reserach areas. As a result of this popularity, DBS are not only intensively competing with the venous blood sampling method but are at this moment widely applied in numerous bioanalytical assays. In particular, in the screening of inherited metabolic diseases, pharmacokinetic modeling and in therapeutic drug monitoring. Recently, microsampling techniques were also introduced in “omics” areas, whereunder metabolomics. For a metabolic profiling study we applied micro-sampling of biological fluids (blood and plasma) from healthy controls and from women with breast cancer. From blood samples, dried blood and plasma samples were prepared by spotting 8uL sample onto pre-cutted 5-mm paper disks followed by drying of the disks for 100 minutes. Dried disks were then extracted by 100 uL of methanol. From liquid blood and plasma samples 40 uL were deproteinized with methanol followed by centrifugation and collection of supernatants. Supernatants and extracts were evaporated until dryness by nitrogen gas and residues derivated by O-methyxyamine and MSTFA. As internal standard C17:0-methylester in heptane (10 ppm) was used. Deconvolution and alignment of and full scan (m/z 50-500) MS data were done by AMDIS and SpectConnect (http://spectconnect.mit.edu) software, respectively. Statistical Data analysis was done by Principal Component Analysis (PCA) using R software. The results obtained from our preliminary study indicate that the use of dried blood/plasma on paper disks could be a powerful new tool in metabolic profiling. Many of the metabolites observed in plasma (liquid/dried) were also positively identified in whole blood samples (liquid/dried). Whole blood could be a potential substitute matrix for plasma in Metabolomic profiling studies as well also micro-sampling techniques for the collection of samples in clinical studies. It was concluded that the separation of the different sample methodologies (liquid vs. dried) as observed by PCA was due to different sample treatment protocols applied. More experiments need to be done to confirm obtained observations as well also a more rigorous validation .of these micro-sampling techniques is needed. The novelty of our approach can be found in the application of different biological fluid micro-sampling techniques for metabolic profiling.

Keywords: biofluids, breast cancer, metabolic profiling, micro-sampling

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