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Oncoinformatic screening of the gene clusters involved in the HER2-positive breast cancer formation along with the in silico pharmacodynamic profiling of selective long-chain omega-3 fatty acids as the metastatic antagonists

Morshed AKMH, Al Azad S, Mia MAR, Uddin MF, Ema TI, Yeasin RB, et al.

Mol Divers, 2023 Dec;27(6):2651-2672.
PMID: 36445532 DOI: 10.1007/s11030-022-10573-8

The HER2-positive patients occupy ~ 30% of the total breast cancer patients globally where no prevalent drugs are available to mitigate the frequent metastasis clinically except lapatinib and neratinib. This scarcity reinforced researchers' quest for new medications where natural substances are significantly considered. Valuing the aforementioned issues, this research aimed to study the ERBB2-mediated string networks that work behind the HER2-positive breast cancer formation regarding co-expression, gene regulation, GAMA-receptor-signaling pathway, cellular polarization, and signal inhibition. Following the overexpression, promotor methylation, and survivability profiles of ERBB2, the super docking position of HER2 was identified using the quantum tunneling algorithm. Supramolecular docking was conducted to study the target specificity of EPA and DHA fatty acids followed by a comprehensive molecular dynamic simulation (100 ns) to reveal the RMSD, RMSF, Rg, SASA, H-bonds, and MM/GBSA values. Finally, potential drug targets for EPA and DHA in breast cancer were constructed to determine the drug-protein interactions (DPI) at metabolic stages. Considering the values resulting from the combinational models of the oncoinformatic, pharmacodynamic, and metabolic parameters, long-chain omega-3 fatty acids like EPA and DHA can be considered as potential-targeted therapeutics for HER2-positive breast cancer treatment.

Matched MeSH terms: Gene Expression Regulation
Differentiation of osteoblasts: the links between essential transcription factors

Khotib J, Marhaeny HD, Miatmoko A, Budiatin AS, Ardianto C, Rahmadi M, et al.

J Biomol Struct Dyn, 2023 Nov;41(19):10257-10276.
PMID: 36420663 DOI: 10.1080/07391102.2022.2148749

Osteoblasts, cells derived from mesenchymal stem cells (MSCs) in the bone marrow, are cells responsible for bone formation and remodeling. The differentiation of osteoblasts from MSCs is triggered by the expression of specific genes, which are subsequently controlled by pro-osteogenic pathways. Mature osteoblasts then differentiate into osteocytes and are embedded in the bone matrix. Dysregulation of osteoblast function can cause inadequate bone formation, which leads to the development of bone disease. Various key molecules are involved in the regulation of osteoblastogenesis, which are transcription factors. Previous studies have heavily examined the role of factors that control gene expression during osteoblastogenesis, both in vitro and in vivo. However, the systematic relationship of these transcription factors remains unknown. The involvement of ncRNAs in this mechanism, particularly miRNAs, lncRNAs, and circRNAs, has been shown to influence transcriptional factor activity in the regulation of osteoblast differentiation. Here, we discuss nine essential transcription factors involved in osteoblast differentiation, including Runx2, Osx, Dlx5, β-catenin, ATF4, Ihh, Satb2, and Shn3. In addition, we summarize the role of ncRNAs and their relationship to these essential transcription factors in order to improve our understanding of the transcriptional regulation of osteoblast differentiation. Adequate exploration and understanding of the molecular mechanisms of osteoblastogenesis can be a critical strategy in the development of therapies for bone-related diseases.Communicated by Ramaswamy H. Sarma.

Matched MeSH terms: Gene Expression Regulation
Fulltext Genomic characterization, transcriptome analysis, and pathogenicity of the Nipah virus (Indian isolate)

Mohandas S, Shete A, Sarkale P, Kumar A, Mote C, Yadav P

Virulence, 2023 Dec;14(1):2224642.
PMID: 37312405 DOI: 10.1080/21505594.2023.2224642

Nipah virus (NiV) is a high-risk pathogen which can cause fatal infections in humans. The Indian isolate from the 2018 outbreak in the Kerala state of India showed ~ 4% nucleotide and amino acid difference in comparison to the Bangladesh strains of NiV and the substitutions observed were mostly not present in the region of any functional significance except for the phosphoprotein gene. The differential expression of viral genes was observed following infection in Vero (ATCC® CCL-81™) and BHK-21 cells. Intraperitoneal infection in the 10-12-week-old, Syrian hamster model induced dose dependant multisystemic disease characterized by prominent vascular lesions in lungs, brain, kidney and extra vascular lesions in brain and lungs. Congestion, haemorrhages, inflammatory cell infiltration, thrombosis and rarely endothelial syncitial cell formation were seen in the blood vessels. Intranasal infection resulted in respiratory tract infection characterised by pneumonia. The model showed disease characteristics resembling the human NiV infection except that of myocarditis similar to that reported by NiV-Malaysia and NiV-Bangladesh isolates in hamster model. The variation observed in the genome of the Indian isolate at the amino acid levels should be explored further for any functional significance.

Matched MeSH terms: Gene Expression Profiling
Risk assessment of bisphenol analogues towards mortality, heart rate and stress-mediated gene expression in cladocerans Moina micrura

Razak MR, Aris AZ, Yusoff FM, Yusof ZNB, Abidin AAZ, Kim SD, et al.

Environ Geochem Health, 2023 Jun;45(6):3567-3583.
PMID: 36450975 DOI: 10.1007/s10653-022-01442-2

Bisphenol A (BPA) is a well-known endocrine-disrupting compound that causes several toxic effects on human and aquatic organisms. The restriction of BPA in several applications has increased the substituted toxic chemicals such as bisphenol F (BPF) and bisphenol S (BPS). A native tropical freshwater cladoceran, Moina micrura, was used as a bioindicator to assess the adverse effects of bisphenol analogues at molecular, organ, individual and population levels. Bisphenol analogues significantly upregulated the expressions of stress-related genes, which are the haemoglobin and glutathione S-transferase genes, but the sex determination genes such as doublesex and juvenile hormone analogue genes were not significantly different. The results show that bisphenol analogues affect the heart rate and mortality rate of M. micrura. The 48-h lethal concentration (LC50) values based on acute toxicity for BPA, BPF and BPS were 611.6 µg L-1, 632.0 µg L-1 and 819.1 µg L-1, respectively. The order of toxicity based on the LC50 and predictive non-effect concentration values were as follows: BPA > BPF > BPS. Furthermore, the incorporated method combining the responses throughout the organisation levels can comprehensively interpret the toxic effects of bisphenol analogues, thus providing further understanding of the toxicity mechanisms. Moreover, the output of this study produces a comprehensive ecotoxicity assessment, which provides insights for the legislators regarding exposure management and mitigation of bisphenol analogues in riverine ecosystems.

Matched MeSH terms: Gene Expression
Fulltext Impact of Gut Recolonization on Liver Regeneration: Hepatic Matrisome Gene Expression after Partial Hepatectomy in Mice

Amin AR, Hairulhisyam NM, Aqilah RNF, Nur Fariha MM, Mallard BL, Shanahan F, et al.

Int J Mol Sci, 2023 Jun 28;24(13).
PMID: 37445951 DOI: 10.3390/ijms241310774

The hepatic matrisome is involved in the remodeling phase of liver regeneration. As the gut microbiota has been implicated in liver regeneration, we investigated its role in liver regeneration focusing on gene expression of the hepatic matrisome after partial hepatectomy (PHx) in germ-free (GF) mice, and in GF mice reconstituted with normal gut microbiota (XGF). Liver mass restoration, hepatocyte proliferation, and immune response were assessed following 70% PHx. Hepatic matrisome and collagen gene expression were also analyzed. Reduced liver weight/body weight ratio, mitotic count, and hepatocyte proliferative index at 72 h post PHx in GF mice were preceded by reduced expression of cytokine receptor genes Tnfrsf1a and Il6ra, and Hgf gene at 3 h post PHx. In XGF mice, these indices were significantly higher than in GF mice, and similar to that of control mice, indicating normal liver regeneration. Differentially expressed genes (DEGs) of the matrisome were lower in GF compared to XGF mice at both 3 h and 72 h post PHx. GF mice also demonstrated lower collagen expression, with significantly lower expression of Col1a1, Col1a2, Col5a1, and Col6a2 compared to WT mice at 72 h post PHx. In conclusion, enhanced liver regeneration and matrisome expression in XGF mice suggests that interaction of the gut microbiota and matrisome may play a significant role in the regulation of hepatic remodeling during the regenerative process.

Matched MeSH terms: Gene Expression
Fulltext Predicting compressive strength of eco-friendly plastic sand paver blocks using gene expression and artificial intelligence programming

Iftikhar B, Alih SC, Vafaei M, Javed MF, Rehman MF, Abdullaev SS, et al.

Sci Rep, 2023 Jul 27;13(1):12149.
PMID: 37500697 DOI: 10.1038/s41598-023-39349-2

Plastic sand paver blocks provide a sustainable alternative by using plastic waste and reducing the need for cement. This innovative approach leads to a more sustainable construction sector by promoting environmental preservation. No model or Equation has been devised that can predict the compressive strength of these blocks. This study utilized gene expression programming (GEP) and multi-expression programming (MEP) to develop empirical models to forecast the compressive strength of plastic sand paver blocks (PSPB) comprised of plastic, sand, and fibre in an effort to advance the field. The database contains 135 results for compressive strength with seven input parameters. The R2 values of 0.87 for GEP and 0.91 for MEP for compressive strength reveal a relatively significant relationship between predicted and actual values. MEP outperformed GEP by displaying a higher R2 and lower values for statistical evaluations. In addition, a sensitivity analysis was conducted, which revealed that the sand grain size and percentage of fibres play an essential part in compressive strength. It was estimated that they contributed almost 50% of the total. The outcomes of this research have the potential to promote the reuse of PSPB in the building of green environments, hence boosting environmental protection and economic advantage.

Matched MeSH terms: Gene Expression
Biochemical and gene expression studies reveal the potential of Aspergillus oryzae-fermented broken rice and brewers' rice water extracts as anti-photoageing agents

Jamaluddin A, Mohd Abd Rahman SM, Abd Manan M, Abd Razak DL, Abd Rashid NY, Abd Ghani A, et al.

Cell Mol Biol (Noisy-le-grand), 2023 Nov 15;69(11):9-16.
PMID: 38015547 DOI: 10.14715/cmb/2023.69.11.2

In this study, UVA- and UVB-irradiated human fibroblasts were used to investigate the anti-photoaging efficacy of two aqueous extracts from Aspergillus oryzae-fermented broken rice (FBR) and brewers' rice (FBrR). As UVA and UVB can damage the dermal and epidermal layers, respectively, two UV radiation approaches were utilised: i) direct UVA irradiation on fibroblasts, and ii) UVB-irradiated keratinocytes indirectly co-cultured with fibroblasts to observe their epithelial-mesenchymal interaction during UVB-induced photoaging. The anti-photoaging properties were tested utilising biochemical tests and quantitative polymerase chain reaction (qPCR). The treatment of UV-irradiated human fibroblasts with FBR and FBrR dramatically downregulates MMP-1 and SFE gene expression. Nonetheless, MMP-1 secretion was inhibited by FBR and FBrR, with more substantial decreases in UVB-treated co-cultures, ranging from 0.76- to 1.89-fold relative to the untreated control. In UVA-treated fibroblasts, however, the elastase-inhibiting activity of FBR and FBrR is up to 1.63-fold and 2.13-fold more potent, respectively. In addition, post-UV irradiation treatment with FBR and FBrR was able to repair and enhance collagen formation in UVA-irradiated fibroblasts. Both FBR and FBrR were able to upregulate elastin gene expression in fibroblasts under both culture conditions, especially at 50 µg/mL. The pro-inflammatory cytokines TNF-, IL-1ß, and IL-6 were likewise lowered by FBR and FBrR, which may have contributed to the anti-photoaging effect of the UVB-treated co-culture. These results reveal that FBR and FBrR inhibit photoaging in human fibroblasts under both UV induction conditions. In conclusion, FBR and FBrR may be attractive bio-ingredients for usage in the cosmetic sector as cosmeceuticals.

Matched MeSH terms: Gene Expression
Fulltext An ecological transcriptome approach to capture the molecular and physiological mechanisms of mass flowering in Shorea curtisii

Suhaimi AH, Kobayashi MJ, Satake A, Ng CC, Lee SL, Muhammad N, et al.

PeerJ, 2023;11:e16368.
PMID: 38047035 DOI: 10.7717/peerj.16368

Climatic factors have commonly been attributed as the trigger of general flowering, a unique community-level mass flowering phenomenon involving most dipterocarp species that forms the foundation of Southeast Asian tropical rainforests. This intriguing flowering event is often succeeded by mast fruiting, which provides a temporary yet substantial burst of food resources for animals, particularly frugivores. However, the physiological mechanism that triggers general flowering, particularly in dipterocarp species, is not well understood largely due to its irregular and unpredictable occurrences in the tall and dense forests. To shed light on this mechanism, we employed ecological transcriptomic analyses on an RNA-seq dataset of a general flowering species, Shorea curtisii (Dipterocarpaceae), sequenced from leaves and buds collected at multiple vegetative and flowering phenological stages. We assembled 64,219 unigenes from the transcriptome of which 1,730 and 3,559 were differentially expressed in the leaf and the bud, respectively. Differentially expressed unigene clusters were found to be enriched with homologs of Arabidopsis thaliana genes associated with response to biotic and abiotic stresses, nutrient level, and hormonal treatments. When combined with rainfall data, our transcriptome data reveals that the trees were responding to a brief period of drought prior to the elevated expression of key floral promoters and followed by differential expression of unigenes that indicates physiological changes associated with the transition from vegetative to reproductive stages. Our study is timely for a representative general flowering dipterocarp species that occurs in forests that are under the constant threat of deforestation and climate change as it pinpoints important climate sensitive and flowering-related homologs and offers a glimpse into the cascade of gene expression before and after the onset of floral initiation.

Matched MeSH terms: Gene Expression Profiling
Robustness evaluations of pathway activity inference methods on gene expression data

Hui TX, Kasim S, Aziz IA, Fudzee MFM, Haron NS, Sutikno T, et al.

BMC Bioinformatics, 2024 Jan 12;25(1):23.
PMID: 38216898 DOI: 10.1186/s12859-024-05632-w

BACKGROUND: With the exponential growth of high-throughput technologies, multiple pathway analysis methods have been proposed to estimate pathway activities from gene expression profiles. These pathway activity inference methods can be divided into two main categories: non-Topology-Based (non-TB) and Pathway Topology-Based (PTB) methods. Although some review and survey articles discussed the topic from different aspects, there is a lack of systematic assessment and comparisons on the robustness of these approaches.
RESULTS: Thus, this study presents comprehensive robustness evaluations of seven widely used pathway activity inference methods using six cancer datasets based on two assessments. The first assessment seeks to investigate the robustness of pathway activity in pathway activity inference methods, while the second assessment aims to assess the robustness of risk-active pathways and genes predicted by these methods. The mean reproducibility power and total number of identified informative pathways and genes were evaluated. Based on the first assessment, the mean reproducibility power of pathway activity inference methods generally decreased as the number of pathway selections increased. Entropy-based Directed Random Walk (e-DRW) distinctly outperformed other methods in exhibiting the greatest reproducibility power across all cancer datasets. On the other hand, the second assessment shows that no methods provide satisfactory results across datasets.
CONCLUSION: However, PTB methods generally appear to perform better in producing greater reproducibility power and identifying potential cancer markers compared to non-TB methods.

Matched MeSH terms: Gene Expression
An ensemble of bioinformatics and machine learning approaches to identify shared breast cancer biomarkers among diverse populations

Sultan G, Zubair S

Comput Biol Chem, 2024 Feb;108:107999.
PMID: 38070457 DOI: 10.1016/j.compbiolchem.2023.107999

Breast cancer continues to be a prominent cause for substantial loss of life among women globally. Despite established treatment approaches, the rising prevalence of breast cancer is a concerning trend regardless of geographical location. This highlights the need to identify common key genes and explore their biological significance across diverse populations. Our research centered on establishing a correlation between common key genes identified in breast cancer patients. While previous studies have reported many of the genes independently, our study delved into the unexplored realm of their mutual interactions, that may establish a foundational network contributing to breast cancer development. Machine learning algorithms were employed for sample classification and key gene selection. The best performance model further selected the candidate genes through expression pattern recognition. Subsequently, the genes common in all the breast cancer patients from India, China, Czech Republic, Germany, Malaysia and Saudi Arabia were selected for further study. We found that among ten classifiers, Catboost exhibited superior performance with an average accuracy of 92%. Functional enrichment analysis and pathway analysis revealed that calcium signaling pathway, regulation of actin cytoskeleton pathway and other cancer-associated pathways were highly enriched with our identified genes. Notably, we observed that these genes regulate each other, forming a complex network. Additionally, we identified PALMD gene as a novel potential biomarker for breast cancer progression. Our study revealed key gene modules forming a complex network that were consistently expressed in different populations, affirming their critical role and biological significance in breast cancer. The identified genes hold promise as prospective biomarkers of breast cancer prognosis irrespective of country of origin or ethnicity. Future investigations will expand upon these genes in a larger population and validate their biological functions through in vivo analysis.

Matched MeSH terms: Gene Expression Profiling
Assessing the efficacy of curcumin-loaded alginate hydrogel on skin wound healing: A gene expression analysis

Zamani S, Salehi M, Ehterami A, Fauzi MB, Abbaszadeh-Goudarzi G

J Biomater Appl, 2024 Apr;38(9):957-974.
PMID: 38453252 DOI: 10.1177/08853282241238581

Skin tissue engineering has gained significant attention as a promising alternative to traditional treatments for skin injuries. In this study, we developed 3D hydrogel-based scaffolds, Alginate, incorporating different concentrations of Curcumin and evaluated their properties, including morphology, swelling behavior, weight loss, as well as hemo- and cytocompatibility. Furthermore, we investigated the therapeutic potential of Alginate hydrogel containing different amounts of Curcumin using an in vitro wound healing model. The prepared hydrogels exhibited remarkable characteristics, SEM showed that the pore size of hydrogels was 134.64 μm with interconnected pores, making it conducive for cellular infiltration and nutrient exchange. Moreover, hydrogels demonstrated excellent biodegradability, losing 63.5% of its weight over 14 days. In addition, the prepared hydrogels had a stable release of curcumin for 3 days. The results also show the hemocompatibility of prepared hydrogels and a low amount of blood clotting. To assess the efficacy of the developed hydrogels, 3T3 fibroblast growth was examined during various incubation times. The results indicated that the inclusion of Curcumin at a concentration of 0.1 mg/mL positively influenced cellular behavior. The animal study showed that Alginate hydrogel containing 0.1 mg/mL curcumin had high wound closure(more than 80%) after 14 days. In addition, it showed up-regulation of essential wound healing genes, including TGFβ1 and VEGF, promoting tissue repair and angiogenesis. Furthermore, the treated group exhibited down-regulation of MMP9 gene expression, indicating a reduction in matrix degradation and inflammation. The observed cellular responses and gene expression changes substantiate the therapeutic efficacy of prepared hydrogels. Consequently, our study showed the healing effect of alginate-based hydrogel containing Curcumin on skin injuries.

Matched MeSH terms: Gene Expression Profiling
Epigenetic regulation of hepatocellular carcinoma progression: MicroRNAs as therapeutic, diagnostic and prognostic factors

Hashemi M, Daneii P, Asadalizadeh M, Tabari K, Matinahmadi A, Bidoki SS, et al.

Int J Biochem Cell Biol, 2024 May;170:106566.
PMID: 38513802 DOI: 10.1016/j.biocel.2024.106566

Hepatocellular carcinoma (HCC), a significant challenge for public healthcare systems in developed Western countries including the USA, Canada, and the UK, is influenced by different risk factors including hepatitis virus infections, alcoholism, and smoking. The disruption in the balance of microRNAs (miRNAs) plays a vital function in tumorigenesis, given their function as regulators in numerous signaling networks. These miRNAs, which are mature and active in the cytoplasm, work by reducing the expression of target genes through their impact on mRNAs. MiRNAs are particularly significant in HCC as they regulate key aspects of the tumor, like proliferation and invasion. Additionally, during treatment phases such as chemotherapy and radiotherapy, the levels of miRNAs are key determinants. Pre-clinical experiments have demonstrated that altered miRNA expression contributes to HCC development, metastasis, drug resistance, and radio-resistance, highlighting related molecular pathways and processes like MMPs, EMT, apoptosis, and autophagy. Furthermore, the regulatory role of miRNAs in HCC extends beyond their immediate function, as they are also influenced by other epigenetic factors like lncRNAs and circular RNAs (circRNAs), as discussed in recent reviews. Applying these discoveries in predicting the prognosis of HCC could mark a significant advancement in the therapy of this disease.

Matched MeSH terms: Gene Expression Regulation, Neoplastic
Transcriptional effects of carbon and nitrogen starvation on Ganoderma boninense, an oil palm phytopathogen

Nagappan J, Ooi SE, Chan KL, Kadri F, Nurazah Z, Halim MAA, et al.

Mol Biol Rep, 2024 Jan 25;51(1):212.
PMID: 38273212 DOI: 10.1007/s11033-023-09054-4

BACKGROUND: Ganoderma boninense is a phytopathogen of oil palm, causing basal and upper stem rot diseases.
METHODS: The genome sequence was used as a reference to study gene expression during growth in a starved carbon (C) and nitrogen (N) environment with minimal sugar and sawdust as initial energy sources. This study was conducted to mimic possible limitations of the C-N nutrient sources during the growth of G. boninense in oil palm plantations.
RESULTS: Genome sequencing of an isolate collected from a palm tree in West Malaysia generated an assembly of 67.12 Mb encoding 19,851 predicted genes. Transcriptomic analysis from a time course experiment during growth in this starvation media identified differentially expressed genes (DEGs) that were found to be associated with 29 metabolic pathways. During the active growth phase, 26 DEGs were related to four pathways, including secondary metabolite biosynthesis, carbohydrate metabolism, glycan metabolism and mycotoxin biosynthesis. G. boninense genes involved in the carbohydrate metabolism pathway that contribute to the degradation of plant cell walls were up-regulated. Interestingly, several genes associated with the mycotoxin biosynthesis pathway were identified as playing a possible role in pathogen-host interaction. In addition, metabolomics analysis revealed six metabolites, maltose, xylobiose, glucooligosaccharide, glycylproline, dimethylfumaric acid and arabitol that were up-regulated on Day2 of the time course experiment.
CONCLUSIONS: This study provides information on genes expressed by G. boninense in metabolic pathways that may play a role in the initial infection of the host.

Matched MeSH terms: Gene Expression Profiling
Fulltext To Establish a Nomogram Prediction of Prostate Cancer Based on Pyroptosis-Related Genes that Affect the Immune Microenvironment

Ji C, Shrestha S, Jumuddin FA

Asian Pac J Cancer Prev, 2024 Jul 01;25(7):2319-2327.
PMID: 39068564 DOI: 10.31557/APJCP.2024.25.7.2319

BACKGROUND: Prostate cancer is the most common tumor in men worldwide with a poor prognosis. In recent years, studies have revealed that pyroptosis can affect the tumor immune microenvironment. However, the relationship between the immune microenvironment regulated by pyroptosis-related genes and the prognosis of prostate cancer is still unclear.
METHODS: Thirty-three cell death-associated genes were selected from a literature review. The "DESeq2" R package was used to identify differentially expressed cell death-associated genes between normal prostate tissue (GTEx) and prostate cancer tissue (TCGA) samples. Biological functional enrichment analysis of differentially expressed cell death genes was performed using R statistical software packages, such as "clusterProfiler," "org.Hs.eg.db," "enrichplot," "ggplot2," and "GOplot." Univariate Cox and LASSO Cox regression analyses were conducted to identify prognostic genes associated with the immune microenvironment using the "survival" package. Finally, a predictive model was established based on Gleason score, T stage, and cell death-associated genes.odel was established based on Gleason score, T stage, and cell death-associated genes.
RESULTS: Seventeen differentially expressed genes related to pyroptosis were screened out. Based on these differentially expressed genes, biological function enrichment analysis showed that they were related to pyroptosis of prostate cells. Based on univariate Cox and (LASSO) Cox regression analysis, four pyroptosis-related genes (CASP3, PLCG1, GSDMB, GPX4) were determined to be related to the prognosis of prostate cancer, and the immune correlation analysis of the four pyroptosis-related genes was performed. The expression of CASP3, PLCG1 and GSDMB was positively correlated with the proportion of immune cells, and the expression of GPX4 was negatively correlated with the proportion of immune cells. A predictive nomogram was established by combining Gleason score, T and pyroptosis genes. The nomogram was accompanied by a calibration curve and used to predict 1 -, 2 -, and 5-year survival in PAAD patients.
CONCLUSION: Cell death-associated genes (CASP3, PLCG1, GSDMB, GPX4) play crucial roles in modulating the immune microenvironment and can be used to predict the prognosis of prostate cancer.

Matched MeSH terms: Gene Expression Regulation, Neoplastic
Fulltext RNA-seq data of Ganoderma boninense at axenic culture condition and under in planta pathogen-oil palm (Elaeis guineensis Jacq.) interaction

Wong MY, Govender NT, Ong CS

BMC Res Notes, 2019 Sep 24;12(1):631.
PMID: 31551084 DOI: 10.1186/s13104-019-4652-y

OBJECTIVE: Basal stem rot disease causes severe economic losses to oil palm production in South-east Asia and little is known on the pathogenicity of the pathogen, the basidiomyceteous Ganoderma boninense. Our data presented here aims to identify both the house-keeping and pathogenicity genes of G. boninense using Illumina sequencing reads.
DESCRIPTION: The hemibiotroph G. boninense establishes via root contact during early stage of colonization and subsequently kills the host tissue as the disease progresses. Information on the pathogenicity factors/genes that causes BSR remain poorly understood. In addition, the molecular expressions corresponding to G. boninense growth and pathogenicity are not reported. Here, six transcriptome datasets of G. boninense from two contrasting conditions (three biological replicates per condition) are presented. The first datasets, collected from a 7-day-old axenic condition provide an insight onto genes responsible for sustenance, growth and development of G. boninense while datasets of the infecting G. boninense collected from oil palm-G. boninense pathosystem (in planta condition) at 1 month post-inoculation offer a comprehensive avenue to understand G. boninense pathogenesis and infection especially in regard to molecular mechanisms and pathways. Raw sequences deposited in Sequence Read Archive (SRA) are available at NCBI SRA portal with PRJNA514399, bioproject ID.

Matched MeSH terms: Gene Expression Regulation, Bacterial*; Gene Expression Profiling/methods*; Gene Expression Profiling/statistics & numerical data
Metabolomics and its role in understanding cellular responses in plants

Bhalla R, Narasimhan K, Swarup S

Plant Cell Rep, 2005 Dec;24(10):562-71.
PMID: 16220342

A natural shift is taking place in the approaches being adopted by plant scientists in response to the accessibility of systems-based technology platforms. Metabolomics is one such field, which involves a comprehensive non-biased analysis of metabolites in a given cell at a specific time. This review briefly introduces the emerging field and a range of analytical techniques that are most useful in metabolomics when combined with computational approaches in data analyses. Using cases from Arabidopsis and other selected plant systems, this review highlights how information can be integrated from metabolomics and other functional genomics platforms to obtain a global picture of plant cellular responses. We discuss how metabolomics is enabling large-scale and parallel interrogation of cell states under different stages of development and defined environmental conditions to uncover novel interactions among various pathways. Finally, we discuss selected applications of metabolomics.

Matched MeSH terms: Gene Expression Regulation, Plant/genetics; Gene Expression Profiling/methods; Gene Expression Profiling/trends*
Fulltext Flexible model-based clustering of mixed binary and continuous data: application to genetic regulation and cancer

Zainul Abidin FN, Westhead DR

Nucleic Acids Res, 2017 04 20;45(7):e53.
PMID: 27994031 DOI: 10.1093/nar/gkw1270

Clustering is used widely in 'omics' studies and is often tackled with standard methods, e.g. hierarchical clustering. However, the increasing need for integration of multiple data sets leads to a requirement for clustering methods applicable to mixed data types, where the straightforward application of standard methods is not necessarily the best approach. A particularly common problem involves clustering entities characterized by a mixture of binary data (e.g. presence/absence of mutations, binding, motifs and epigenetic marks) and continuous data (e.g. gene expression, protein abundance, metabolite levels). Here, we present a generic method based on a probabilistic model for clustering this type of data, and illustrate its application to genetic regulation and the clustering of cancer samples. We show that the resulting clusters lead to useful hypotheses: in the case of genetic regulation these concern regulation of groups of genes by specific sets of transcription factors and in the case of cancer samples combinations of gene mutations are related to patterns of gene expression. The clusters have potential mechanistic significance and in the latter case are significantly linked to survival. The method is available as a stand-alone software package (GNU General Public Licence) from http://github.com/BioToolsLeeds/FlexiCoClusteringPackage.git.

Matched MeSH terms: Gene Expression Regulation, Fungal; Gene Expression Regulation, Neoplastic*; Gene Expression Profiling/methods*
Relative quantification of human β‑defensins gene expression in pterygium and normal conjunctiva samples

Abubakar SA, Isa MM, Omar N, Tan SW

Mol Med Rep, 2020 Dec;22(6):4931-4937.
PMID: 33174018 DOI: 10.3892/mmr.2020.11560

The human ocular surface produces highly conserved cationic peptides. Human β‑defensins (HBDs) serve an important role in innate and adaptive immunity. They are primarily expressed in epithelial cells in response to infection and provide the first line of defence against invading microbes. Defensin β1 (DEFB1) is constitutively expressed and regulated by inflammatory mediators including interferon‑γ, lipopolysaccharide and peptidoglycans. DEFB4A is locally induced in response to microbial infection while DEFB109 is induced via Toll‑like receptor 2. The present study examined the expression of the HBD DEFB1, DEFB4A and DEFB109 genes in pterygium. The pterygium tissues and normal conjunctiva samples were obtained from 18 patients undergoing pterygium surgery. The reverse transcription‑quantitative polymerase chain reaction method was employed to determine the expression of DEFB1, DEFB4A and DEFB109 genes. The results revealed that the expression of DEFB1 and DEFB4A was significantly higher and upregulated in pterygium samples when compared with normal conjunctiva samples from each patient (P<0.05), while the expression of DEFB109 was observed to be lower in pterygium samples when compared with normal samples from the same patient. Previous studies have revealed that DEFB1 and DEFB4A genes are present in low concentrations inside the human eye, and they are upregulated during the maturation of keratinocytes, suggesting a possible role in cell differentiation. The DEFB109 gene is present in higher concentrations inside the human eye, though it is newly discovered. It has also been reported that DEFB1 may be involved in carcinogenesis epithelial tumours. Collectively, the current data suggests that HBDs may serve a crucial role in the pathogenesis and development of pterygia, and thus may be considered as novel molecular targets in understanding pterygia development.

Matched MeSH terms: Gene Expression Regulation/genetics; Gene Expression/genetics; Gene Expression Profiling/methods
Fulltext A hybrid distance measure for clustering expressed sequence tags originating from the same gene family

Ng KH, Ho CK, Phon-Amnuaisuk S

PLoS One, 2012;7(10):e47216.
PMID: 23071763 DOI: 10.1371/journal.pone.0047216

Clustering is a key step in the processing of Expressed Sequence Tags (ESTs). The primary goal of clustering is to put ESTs from the same transcript of a single gene into a unique cluster. Recent EST clustering algorithms mostly adopt the alignment-free distance measures, where they tend to yield acceptable clustering accuracies with reasonable computational time. Despite the fact that these clustering methods work satisfactorily on a majority of the EST datasets, they have a common weakness. They are prone to deliver unsatisfactory clustering results when dealing with ESTs from the genes derived from the same family. The root cause is the distance measures applied on them are not sensitive enough to separate these closely related genes.

Matched MeSH terms: Gene Expression Profiling/methods*
Gene expression profiling and cancer-related pathways in type I endometrial carcinoma

Saghir FS, Rose IM, Dali AZ, Shamsuddin Z, Jamal AR, Mokhtar NM

Int. J. Gynecol. Cancer, 2010 Jul;20(5):724-31.
PMID: 20973258

INTRODUCTION: Malignant transformation of type I endometrium involves alteration in gene expression with subsequent uncontrolled proliferation of altered cells.
OBJECTIVE: The main objective of the present study was to identify the cancer-related genes and gene pathways in the endometrium of healthy and cancer patients.
MATERIALS AND METHODS: Thirty endometrial tissues from healthy and type I EC patients were subjected to total RNA isolation. The RNA samples with good integrity number were hybridized to a new version of Affymetrix Human Genome GeneChip 1.0 ST array. We analyzed the results using the GeneSpring 9.0 GX and the Pathway Studio 6.1 software. For validation assay, quantitative real-time polymerase chain reaction was used to analyze 4 selected genes in normal and EC tissue.
RESULTS: Of the 28,869 genes profiled, we identified 621 differentially expressed genes (2-fold) in the normal tissue and the tumor. Among these genes, 146 were up-regulated and 476 were down-regulated in the tumor as compared with the normal tissue (P < 0.001). Up-regulated genes included the v-erb-a erythroblastic leukemia viral oncogene homolog 3 (ErbB3), ErbB4, E74-like factor 3 (ELF3), and chemokine ligand 17 (CXCL17). The down-regulated genes included signal transducer and activator transcription 5B (STAT5b), transforming growth factor A receptor III (TGFA3), caveolin 1 (CAV1), and protein kinase C alpha (PKCA). The gene set enrichment analysis showed 10 significant gene sets with related genes (P < 0.05). The quantitative polymerase chain reaction of 4 selected genes using similar RNA confirmed the microarray results (P < 0.05).
CONCLUSIONS: Identification of molecular pathways with their genes related to type I EC contribute to the understanding of pathophysiology of this cancer, probably leading to identifying potential biomarkers of the cancer.

Matched MeSH terms: Gene Expression Profiling*

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