Gene co-expression network reconstruction: a review on computational methods for inferring functional information from plant-based expression data

Abbasali Emamjomeh,Elham Saboori Robat,Javad Zahiri,Mahmood Solouki,Pegah Khosravi 한국식물생명공학회 2017 Plant biotechnology reports Vol.11 No.2

Reconstruction of gene co-expression networks is a powerful tool for better understanding of gene function, biological processes, and complex disease mechanisms. In essence, co-expression network analysis has been widely used for understanding which genes are highly co-expressed through special biological processes or differentially expressed in various conditions. Development of high-throughput experiments has provided a large amount of genomic and transcriptomic data for model and nonmodel organisms. The availability of genome-wide expression data has led to the development of in silico procedures for reconstruction of gene co-expression networks. Gene co-expression networks predict unknown genes’ functions; moreover, it has been successfully applied to understand important biological processes of living organisms such as plants. In this survey, we have reviewed the algorithms, databases, and tools of gene coexpression network reconstruction, which can lead to new landscapes for further research activities. Furthermore, we explain an application of some algorithms, databases, and tools that can significantly boost our current understanding of co-expression networks in Arabidopsis thaliana as a model plant using publicly available data. The presented example shows that using co-expression networks is an efficient way to detect genes, which may involve in various critical biological processes such as defense response.

Shared co-expression networks in frontal cortex of the normal aged brain and schizophrenia

Kim, Sanghyeon,Jo, Yousang,Webster, Maree J.,Lee, Doheon ELSEVIER SCIENCE DIVISION 2019 Schizophrenia Research Vol.204 No.-

<P><B>Abstract</B></P> <P>Previous studies on the brain of people with schizophrenia have identified structural changes and gene expression changes, suggesting that brain aging maybe accelerated in people with schizophrenia. To better characterize gene expression profiles in schizophrenia and in the aged population we constructed co-expression networks using RNA-Seq data from frontal cortex. The first data set analysed was from 62 subjects with schizophrenia and 51 unaffected controls ranging in age from 19 to 63 years. The second separate data set was from normal control individuals ranging in age from 29 to 106 years. In the first data set, we found two co-expression modules significantly associated with schizophrenia. One was a downregulated co-expression module enriched for neuron function related genes and the other was an upregulated immune/inflammation-related module. In the second data set of normal individuals, we found seven co-expression modules significantly correlated with age. A comparison of the co-expression modules from the two data sets revealed a significant consensus in nodes associated with schizophrenia and those associated with normal aging. The results indicate that a co-expression module related to neuronal function is downregulated and an immune/inflammation related co-expression module is upregulated, and associated with cells of the blood vessels, in both schizophrenia and in normal aging. This finding adds further support to the hypothesis that there may be accelerated brain aging in schizophrenia.</P>

An optimized gene expression programming model for forecasting the national CO₂ emissions in 2030 using the metaheuristic algorithms

Hong, Taehoon,Jeong, Kwangbok,Koo, Choongwan Elsevier 2018 APPLIED ENERGY Vol.228 No.-

<P><B>Abstract</B></P> <P>To cope with the approaching POST-2020 scenario, the national CO<SUB>2</SUB> emission in the building sector, which accounts for 25.5% of the total CO<SUB>2</SUB> emissions, should be managed effectively and efficiently. To do this, it is essential to forecast the national CO<SUB>2</SUB> emissions in the building sector by region. As the South Korean government does not currently do this by region, regional characteristics are rarely taken into consideration when managing the national CO<SUB>2</SUB> emissions in the building sector. Towards this end, this study developed an optimized gene expression programming model for forecasting the national CO<SUB>2</SUB> emissions in 2030 using the metaheuristic algorithms. Compared to the forecasting performance of the gene expression programming model, the forecasting performance of the optimized gene expression programming – harmony search optimization model has improved by 7.11, 2.05, and 2.06% in terms of the mean absolute error, root mean square error, and mean absolute percentage error, respectively. Various national CO<SUB>2</SUB> emissions scenarios in the building sector were established in order to better analyze the variation range of the national CO<SUB>2</SUB> emissions in the building sector. Compared to the national CO<SUB>2</SUB> emissions in 2016 (i.e., scenario 1: 41,337 ktCO<SUB>2</SUB>; scenario 2: 45,373 ktCO<SUB>2</SUB>; scenario 3: 46,024 ktCO<SUB>2</SUB>) in multi-family housing complexes, the national CO<SUB>2</SUB> emissions in 2030 (i.e., scenario 1: 37,579 ktCO<SUB>2</SUB>; scenario 2: 37,736 ktCO<SUB>2</SUB>; scenario 3: 37,754 ktCO<SUB>2</SUB>) in multi-family housing complexes are forecasted to increase by 10.00–21.91%. The developed optimized gene expression programming – harmony search optimization model will potentially be able to assist policymakers in central and local governments forecast the national CO<SUB>2</SUB> emissions in 2030. Through this, national CO<SUB>2</SUB> emission management that more closely reflects the characteristics at the regional or national level can be supported.</P> <P><B>Highlights</B></P> <P> <UL> <LI> A model was developed to forecast the national CO<SUB>2</SUB> emissions in 2030. </LI> <LI> Model was developed using gene expression programming and harmony search algorithm. </LI> <LI> The mean absolute percentage error of developed model was estimated to be 2.06%. </LI> <LI> National CO<SUB>2</SUB> emissions in 2030 is increased by 10.0–21.91% than in 2016. </LI> <LI> Developed model can help policy makers forecast the national CO<SUB>2</SUB> emissions. </LI> </UL> </P>

Analysis of Indoleamine 2-3 Dioxygenase (IDO) and EGFR Co-expression in Breast Cancer Tissue by Immunohistochemistry

Bi, Wei-Wei,Zhang, Wei-Hua,Yin, Gui-Hua,Luo, Hong,Wang, Shou-Qin,Wang, Hongran,Li, Chao,Yan, Wei-Qun,Nie, De-Zhi Asian Pacific Journal of Cancer Prevention 2014 Asian Pacific journal of cancer prevention Vol.15 No.14

Background: To determine the amount of co-expression of IDO and EGFR in breast cancer patients. Materials and Methods:In order to obtain the distribution of co-expression of IDO and EGFR in breast cancer, we tested 110 breast cancer paraffin tissue blocks with immunohistochemical methods. Then we investigated the relationship between the diagnostic and pathologic characteristics (tumor size, lymph node status, histologic grade, the gene expression of ER, PR, HER2, p53, Ki67 and PCNA) with the situation of co-expression of IDO and EGFR by reviewing the medical records of 32 breast cancer patients. Results: Among 110 breast cancers, 32 cases demonstrated IDO and EGFR co-expression (29.1%), IDO and EGFR synchronous co-expression being found in 19.1% and asynchronous in 10.0%. Conclusions: IDO and EGFR were co-expressed in breast cancer, including synchronous and asynchronous co-expression. The results suggest that considering IDO and EGFR as two indicators for breast cancer treatment or prognosis analysis provides a potential option of individual treatment for the portion of breast cancer patients with co-expression of IDO and EGFR.

Aberrant myeloid antigen co-expression is correlated with high percentages of CD34-positive cells among blasts of acute lymphoblastic leukemia patients: an Indian tertiary care center perspective

Rahul Kumar Sharma,Abhishek Purohit,Venkatesan Somasundaram,Pravas Chandra Mishra,Mrinalini Kotru,Ravi Ranjan,Sunil Kumar,Sudha Sazawal,Hara Prasad Pati,Seema Tyagi,Renu Saxena 대한혈액학회 2014 Blood Research Vol.49 No.4

Background Aberrant myeloid antigen (MA) co-expression and high expression of CD34 antigen on the blasts of acute lymphoblastic leukemia (ALL) patients are independently reported to have a role in pathogenesis and prognosis. This study was conducted to determine whether these two parameters are related. Methods A total of 204 cases of ALL were included in an analysis of blast immunophenotypic data. CD34 expression was categorized as low when less than 50% of blasts were CD34-positive (CD34low) and as high when 50% or more were CD34-positive (CD34high). Results Of 204 cases of ALL, 163 and 41 were of B-cell origin (B-ALL) and T-cell origin (T-ALL), respectively. Of all cases, 132 (64.7%) showed co-expression of MA and among these, 101 (76.51%) were CD34high, while the remaining 31 (23.48%) were CD34low. Of 72 cases without MA co-expression, 25 (34.72%) were CD34high and 47 (67.25%) were CD34low. Furthermore, of 163 cases of B-ALL, 111 showed co-expression of MA and 84 of these were CD34high. Of 52 cases of B-ALL without MA expression, 22 were CD34high. Among 41 cases of T-ALL, 21 co-expressed MA, 17 of which were CD34high. Moreover, all 20 cases of T-ALL without co-expression of MA were CD34low. These differences were statistically significant. Conclusion We observed a strong correlation between aberrant MA expression and CD34high expression on the blasts of ALL. We hypothesize that these different patient subsets may represent unique prognostic characteristics.

Aberrant myeloid antigen co-expression is correlated with high percentages of CD34-positive cells among blasts of acute lymphoblastic leukemia patients: an Indian tertiary care center perspective

Rahul Kumar Sharma,Abhishek Purohit,Venkatesan Somasundaram,Pravas Chandra Mishra,Mrinalini Kotru,Ravi Ranjan,Sunil Kumar,Sudha Sazawal,Hara Prasad Pati,Seema Tyagi,Renu Saxena 대한혈액학회 2014 Blood Research Vol.49 No.4

Background Aberrant myeloid antigen (MA) co-expression and high expression of CD34 antigen on the blasts of acute lymphoblastic leukemia (ALL) patients are independently reported to have a role in pathogenesis and prognosis. This study was conducted to determine whether these two parameters are related. Methods A total of 204 cases of ALL were included in an analysis of blast immunophenotypic data. CD34 expression was categorized as low when less than 50% of blasts were CD34-positive (CD34low) and as high when 50% or more were CD34-positive (CD34high). Results Of 204 cases of ALL, 163 and 41 were of B-cell origin (B-ALL) and T-cell origin (T-ALL), respectively. Of all cases, 132 (64.7%) showed co-expression of MA and among these, 101 (76.51%) were CD34high, while the remaining 31 (23.48%) were CD34low. Of 72 cases without MA co-expression, 25 (34.72%) were CD34high and 47 (67.25%) were CD34low. Furthermore, of 163 cases of B-ALL, 111 showed co-expression of MA and 84 of these were CD34high. Of 52 cases of B-ALL without MA expression, 22 were CD34high. Among 41 cases of T-ALL, 21 co-expressed MA, 17 of which were CD34high. Moreover, all 20 cases of T-ALL without co-expression of MA were CD34low. These differences were statistically significant. Conclusion We observed a strong correlation between aberrant MA expression and CD34high expression on the blasts of ALL. We hypothesize that these different patient subsets may represent unique prognostic characteristics.

Purification of anti‐colorectal cancer monoclonal antibody CO17‐1A from insect cell culture using a French press and sonication

임채연,박세라,이정환,고기성 한국곤충학회 2015 Entomological Research Vol.45 No.2

Monoclonal antibody (mAb) CO17‐1A binds to GA733, which is a tumor‐associated glycoprotein antigen highly expressed on the colorectal cancer cell surface. Thus, mAb CO17‐1A is considered a useful biomolecule for diagnosis and treatment against colorectal cancer. Previously, we established a baculovirus–insect cell expression system for the production of mAb CO17‐1A. In order to use mAb CO17‐1A as a diagnostic and therapeutic tool, however, the antibody must be properly purified from the insect cells. In this study, our aim was to investigate effective purification processes of mAb CO17‐1A expressed in Spodoptera frugiperda (Sf9) insect cells, using a French press and sonication for cell disruption. SDS‐PAGE confirmed that both mAb CO17‐1A and mAb CO17‐1A fused to the KDEL endoplasmic reticulum (ER) retention signal (mAb CO17‐1AK) were expressed clearly in Sf9 insect cells. Western blot analysis showed that detection levels of mAb CO17‐1A and CO17‐1AK were higher when the insect cells were disrupted two times by the French press and then sonicated, compared to only one French press disruption plus sonication. Optical microscopy confirmed that insect cells treated with both the French press and sonication were properly disrupted. Analysis of gene sequence information on mAb CO17‐1A verified that a signal peptide is present but a transmembrane protein does not exist. These results suggest that cell disruption by the French press twice and sonication once is an effective method for improving purification efficiency.

AMPKα, C/EBPβ, CPT1β, GPR43, PPARγ, and SCD Gene Expression in Single- and Co-cultured Bovine Satellite Cells and Intramuscular Preadipocytes Treated with Palmitic, Stearic, Oleic, and Linoleic Acid

Choi, S.H.,Park, S.K.,Johnson, B.J.,Chung, K.Y.,Choi, C.W.,Kim, K. H.,Kim, W.Y.,Smith, S.B. Asian Australasian Association of Animal Productio 2015 Animal Bioscience Vol.28 No.3

We previously demonstrated that bovine subcutaneous preadipocytes promote adipogenic gene expression in muscle satellite cells in a co-culture system. Herein we hypothesize that saturated fatty acids would promote adipogenic/lipogenic gene expression, whereas mono- and polyunsaturated fatty acids would have the opposite effect. Bovine semimembranosus satellite cells (BSC) and intramuscular preadipocytes (IPA) were isolated from crossbred steers and cultured with 10% fetal bovine serum (FBS)/Dulbecco's Modified Eagle Medium (DMEM) and 1% antibiotics during the 3-d proliferation period. After proliferation, cells were treated for 3 d with 3% horse serum/DMEM (BSC) or 5% FBS/DMEM (IPA) with antibiotics. Media also contained $10{\mu}g/mL$ insulin and $10{\mu}g/mL$ pioglitazone. Subsequently, differentiating BSC and IPA were cultured in their respective media with $40{\mu}M$ palmitic, stearic, oleic, or linoleic acid for 4 d. Finally, BSC and IPA were single- or co-cultured for an additional 2 h. All fatty acid treatments increased (p = 0.001) carnitine palmitoyltransferase-1 beta ($CPT1{\beta}$) gene expression, but the increase in $CPT1{\beta}$ gene expression was especially pronounced in IPA incubated with palmitic and stearic acid (6- to 17-fold increases). Oleic and linoleic acid decreased (p = 0.001) stearoyl-CoA desaturase (SCD) gene expression over 80% in both BSC and IPA. Conversely, palmitic and stearic acid increased SCD gene expression three fold in co-cultured in IPA, and stearic acid increased $AMPK{\alpha}$ gene expression in single- and co-cultured BSC and IPA. Consistent with our hypothesis, saturated fatty acids, especially stearic acid, promoted adipogenic and lipogenic gene expression, whereas unsaturated fatty acids decreased expression of those genes associated with fatty acid metabolism.

AMPKα, C/EBPβ, CPT1β, GPR43, PPARγ, and SCD Gene Expression in Single- and Co-cultured Bovine Satellite Cells and Intramuscular Preadipocytes Treated with Palmitic, Stearic, Oleic, and Linoleic Acid

S. H. Choi,박성권,B.J. Johnson,K.Y. Chung,C.W. Choi,김경훈,W.Y. Kim,S.B. Smith 아세아·태평양축산학회 2015 Animal Bioscience Vol.28 No.3

We previously demonstrated that bovine subcutaneous preadipocytes promote adipogenic gene expression in muscle satellite cells in a co-culture system. Herein we hypothesize that saturated fatty acids would promote adipogenic/lipogenic gene expression, whereas mono- and polyunsaturated fatty acids would have the opposite effect. Bovine semimembranosus satellite cells (BSC) and intramuscular preadipocytes (IPA) were isolated from crossbred steers and cultured with 10% fetal bovine serum (FBS)/ Dulbecco’s Modified Eagle Medium (DMEM) and 1% antibiotics during the 3-d proliferation period. After proliferation, cells were treated for 3 d with 3% horse serum/DMEM (BSC) or 5% FBS/DMEM (IPA) with antibiotics. Media also contained 10 μg/mL insulin and 10 μg/mL pioglitazone. Subsequently, differentiating BSC and IPA were cultured in their respective media with 40 μM palmitic, stearic, oleic, or linoleic acid for 4 d. Finally, BSC and IPA were single- or co-cultured for an additional 2 h. All fatty acid treatments increased (p = 0.001) carnitine palmitoyltransferase-1 beta (CPT1β) gene expression, but the increase in CPT1β gene expression was especially pronounced in IPA incubated with palmitic and stearic acid (6- to 17- fold increases). Oleic and linoleic acid decreased (p = 0.001) stearoyl-CoA desaturase (SCD) gene expression over 80% in both BSC and IPA. Conversely, palmitic and stearic acid increased SCD gene expression three fold in co-cultured in IPA, and stearic acid increased AMPKα gene expression in single- and co-cultured BSC and IPA. Consistent with our hypothesis, saturated fatty acids, especially stearic acid, promoted adipogenic and lipogenic gene expression, whereas unsaturated fatty acids decreased expression of those genes associated with fatty acid metabolism.

In vitro wound healing: Inhibition activity of insect-derived mAb CO17-1A in human colorectal cancer cell migration

Park Se Ra,Ko Kisung,Lim Sohee,Cha So Yeon,정현주,Park Soon Ju,Myung Soon‐Chul,Kim Mi Kyung 한국곤충학회 2020 Entomological Research Vol.50 No.4

The monoclonal antibody (mAb) CO17-1A specifically binds to the tumor associated cell surface glycoprotein GA733 in colorectal cancer cells. Thus, mAb CO17-1A has the potential to act as an immune therapeutic protein against colorectal cancer. Recently, it was shown that the baculovirus insect cell expression system produces anti-colorectal cancer mAb CO17-1A. In this study, the colorectal cancer antibody mAb CO17-1A fused to the endoplasmic reticulum (ER) retention signal sequence (KDEL), and the (mAb CO17-1AK) was expressed in Spodoptera frugiperda Sf9 insect cells. The yield, cell cytotoxicity, and in vitro anti-tumor activity of mAb CO17-1AK were verified. Western blotting was performed to confirm that both heavy and light chains of mAb CO17-1A were expressed in Sf9 insect cells. The insect-derived mAb (mAbI ) CO17-1A was purified using a protein G affinity column. An in vitro wound healing assay was conducted to determine the inhibition activity of mAb CO17-1A during tumor cell migration, showing that mAbI CO17-1AK was effective as mammalian-derived mAb CO17-1A (mAbM CO17-1A). These results suggest that the insect cell expression system can produce and properly assemble mAbs that inhibit tumor cell migration.