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Cell Biology

10 mitosis genes associated with tamoxifen in breast cancer | OTT – Dove Medical Press

Department of General Surgery, Comprehensive Breast Health Center, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, Peoples Republic of China

Correspondence: Kunwei Shen; Xiaosong ChenShanghai Jiao Tong University School of Medicine, No. 197, Rui Jin Er Road, Shanghai, 200025, Peoples Republic of ChinaTel +86-21-64370045-602102Email [emailprotected]; [emailprotected]

Background: Endocrine therapy is the backbone therapy in estrogen receptor (ER)-positive breast cancer, and tamoxifen resistance is a great challenge for endocrine therapy. Tamoxifen-resistant and sensitive samples from the international public repository, the Gene Expression Omnibus (GEO) database, were used to identify therapeutic biomarkers associated with tamoxifen resistance.Materials and Methods: In this study, integrated analysis was used to identify tamoxifen resistance-associated genes. Differentially expressed genes (DEGs) were identified. Gene ontology and pathway analysis were then analyzed. Weighted correlation network analysis (WGCNA) was performed to find modules correlated with tamoxifen resistance. Proteinprotein interaction (PPI) network was used to find hub genes. Genes of prognostic significance were further validated in another GEO dataset and cohort from Shanghai Ruijin Hospital using RT-PCR.Results: A total of 441 genes were down-regulated and 123 genes were up-regulated in tamoxifen-resistant samples. Those up-regulated genes were mostly enriched in the cell cycle pathway. Then, WGCNA was performed, and the brown module was correlated with tamoxifen resistance. An overlap of 81 genes was identified between differentially expressed genes (DEGs) and genes in the brown module. These genes were also enriched in the cell cycle. Twelve hub genes were identified using PPI network, which were involved in the mitosis phase of the cell cycle. Finally, 10 of these 12 genes were validated to be up-regulated in tamoxifen-resistant patients and were associated with poor prognosis in ER-positive patients.Conclusion: Our study suggested mitosis-related genes are mainly involved in tamoxifen resistance, and high expression of these genes could predict poor prognosis of patients receiving tamoxifen. These genes may be potential targets to improve efficacy of endocrine therapy in breast cancer, and inhibitors targeted these genes could be used in endocrine-resistant patients.

As the most common cancer in the female, breast cancer is a great threat to world health.1 It is the most common cause of cancer death in developing countries and second to lung cancer in more developed countries.2 Breast cancer is a heterogeneous disease. Approximately 70% breast cancers are estrogen receptor (ER)-positive.3 Endocrine therapy is used as the backbone therapy in ER-positive patients by blocking the ER pathway. Tamoxifen, a selective ER modulator, has dual agonistic/antagonistic effects on ER transcription, depending on its effect and location.4 Tamoxifen can cause cell cycle arrest in the G1 phase, inhibiting the proliferation and leading to apoptosis of breast cancer cells.5 In ER-positive patients, recurrence rates were reduced by almost 50% throughout the first 10 years, and the death rate was reduced by 2530% after administration of 5-year tamoxifen.6,7 However, 30% patients who have taken tamoxifen for 5 years will have suffered from recurrence within 15 years. Therefore, finding new therapeutic biomarkers associated with tamoxifen resistance is important to overcome tamoxifen resistance.

Nowadays, gene sequencing has been widely used to identify biomarkers related to tumor biology.8,9 Large-scale sequencing made people have a better understanding of the heterogeneity, pathobiology and mechanism of cancers.3 As tamoxifen-resistant patient samples are difficult to obtain, no large-scale sequencing data about tamoxifen resistance have been systematically analyzed due to the limitation of sample size. However, high-throughput microarray and next-generation sequence datasets have been submitted by research groups to the international public repository, the Gene Expression Omnibus (GEO) database, and data in this database are freely available for integrated analysis.10 In our study, tamoxifen-resistant patients were derived from the GEO database in datasets GSE26971, GSE17705 and GSE45255, and integrated analysis was employed to have a better understanding of the mechanism of tamoxifen resistance.

Analysis of differentially expressed genes has mainly focused on the up-regulation and down-regulation of different genes, ignoring the interaction of different genes. Weighted gene co-expression network analysis (WGCNA) is a systems biology method that can be used to construct correlation networks and find modules of genes highly correlated to clinical traits.11,12 Candidate biomarkers or hub genes related to disease can be identified on the basis of correlation network.

In our study, 44 tamoxifen-resistant and 44 tamoxifen-sensitive patients who were matched with clinicopathological parameters were included. Differentially expressed genes (DEGs) were analyzed after normalization and gene ontology (GO) term enrichment analysis and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis were performed.13,14 Modules correlated to tamoxifen resistance were identified using WGCNA. An interaction of genes in module and DEGs were selected as candidate genes. The proteinprotein interaction (PPI) network was constructed using candidate genes, and hub genes were identified according to the degree in the network.15 Genes with prognostic significance were considered as important genes involved in tamoxifen resistance, and these genes were all involved in mitosis. This study sheds new light on the biological mechanisms of tamoxifen resistance and identifies new targets for tamoxifen-resistant patients.

Microarray datasets GSE26971, GSE17705 and GSE45255 were downloaded from the National Center for Gene Expression Omnibus (GEO) database (https://www.ncbi.nlm.nih.gov/). These microarrays were all generated using an Affymetrix Human Genome U133A microarray (HG-U133A). Dataset GSE6532 generated using the Affymetrix Human Genome U133 Plus 2.0 microarray (HG-U133_Plus_2) was used as a validation dataset. Patients who had taken tamoxifen after resection and suffered from distant metastasis within 2 years were defined as tamoxifen-resistant patients according to the International Consensus Guidelines for Advanced Breast Cancer (ABC). Patients who had no recurrence were defined as tamoxifen-sensitive patients in our study. All paired tamoxifen-sensitive and resistant patients had been administered tamoxifen in our analysis. Then tamoxifen-sensitive patients were 1:1 matched with tamoxifen-resistant patients according to their age, chemotherapy and tumor stage. A total of 17 patients from GSE26971, 19 patients from GSE17705 and 8 patients from GSE45255 were included in the tamoxifen-resistant group.

The getGEOSuppFiles function in the GEOquery package of R was used to identify the raw data, and cel style files were downloaded from the GEO database using the GEOquery package of R. Raw data were converted to expression data using the affy package. Background adjustment and normalization were done using the gcrma package. Batch effect was removed using the combat function in the sva package. DEGs were calculated using the limma package, and statistical significance was defined as adjusted P<0.05 and foldchange 1.5.

Gene ontology (GO) was used to annotate biological processes, molecular functions and cellular components of genes, and Kyoto Encyclopedia of Genes and Genomes (KEGG) was used to annotate the gene pathways. GO functional analysis and KEGG pathway analysis were both performed separately in up-regulated and down-regulated DEGs. The cluster profiler was used to analyze the functional annotation. We also performed enrichment analysis using the DAVID website (https://david.ncifcrf.gov/home.jsp). Adjusted P-value <0.05 was considered as a significant enrichment.

Weighted correlation network analysis (WGCNA) was performed to find modules of highly correlated genes using the WGCNA package. The goodSamplesGenes function in WGCNA package was used to check for missing values, and hierarchical cluster analysis was used to detect outliers, with cut height of 140. After checking data for missing values and identification of outlier microarray samples, an appropriate soft power was selected to meet the requirements of a scale-free network. Genes with a threshold of variation coefficient of expression >0.25 was used to perform WGCNA analysis. One-step network construction was used to construct networks, and modules were identified. Eigengenes were correlated with external traits to identify modules that were significantly associated with the measured clinical traits. A scatterplot of gene significance (GS) vs module membership (MM) in the brown module was plotted to show the correlation of GS and MM.

STRING (http://string-db.org) is a database of known and predicted proteinprotein interactions, and it was used to construct a PPI network. The Cytoscape software and cytoHubba app were then employed to analyze the interactive relationship of the candidate proteins. The cytoHubba app in Cytoscape was used to identify hub genes ranked by degree method to rank the top 20 hub genes.

Ten pairs of matched tamoxifen-resistant and sensitive breast cancer tissues were obtained between January 2009 and December 2011 at the Comprehensive Breast Health Center, Shanghai Ruijin Hospital. As these involved human participants they were reviewed and approved by the independent Ethical Committees of Ruijin Hospital, Shanghai Jiaotong University School of Medicine.

TRIZOL reagent (TaKaRa, Kusatsu, Japan) was used for the isolation of total RNA, and 1000ng RNA was reverse-transcribed into cDNA using Primescript RT Reagent (TaKaRa, Japan). RT-PCR was performed using FastStart Universal SYBR Green Master (Roche, Switzerland) in a real-time PCR instrument (Applied Biosystems, USA), and -actin was used as endogenous control. The primers are listed in Supplementary Table 1.

The MCF-7 cell line was obtained from the American Type Culture Collection (ATCC, USA) and was cultured in Roswell Park Memorial Institute 1640 (RPMI-1640, Thermo Fisher, USA), supplemented with 10% fetal bovine serum and 100 g/mL penicillin-streptomycin (Hyclone, USA).

We used pLKO.1 (Addgene Plasmid, 10878) to generate lentiviral shRNA plasmids; shRNA plasmids targeting MELK, RACGAP1 and MAD2L1 were constructed. The sequence of shRNAs used were: MELK, 5-GACAUCCUAUCUAGCUGCA-3; MAD2L1, 5-CUACUGAUCUUGAGCUCAU-3; RACGAP1, 5-CAACUAAGCGAGGAGCAAATT-3. Lentivirus was generated by transfection of HEK293T cells with packaging vectors (pMD2.G and psPAX) and transducing vector and concentrated with PEG6000 (Sigma, USA). Forty-eight hours post-infection, puromycin (1 g/mL; 60210ES25, YEASEN) was used to select positively infected cells.

Cells transfected with scramble or shRNA were cultured into 6-well plates with 5000 cells and cultured for 15 days. After seeding cells for 24 hours, tamoxifen with concentration of 2 m/mL was added into every well for 15 days.

The colonies were fixed in 75% absolute ethanol for 10 minutes, washed twice with PBS and stained with Giemsa (Sigma, USA) for 15min, then dried at room temperature. The colonies containing 50 or more cells in each well were counted.

Cells were plated into 96-well in triplicates and then treated with tamoxifen of different concentrations. Cell viability was measured using Cell Titer-Glo 2.0 Assay (G9243, Promega), and data were collected on Synergy H4 Hybrid Reader (BioTek).

The key genes were identified as the intersecting genes of the brown module and DEGs. ER-positive patients treated with tamoxifen in three datasets with disease metastasis survival within five years were divided into two groups according to the medium expression of key genes. KaplanMeier (K-M) plot was plotted using survival package.

The DEGs of tamoxifen-resistant patients were analyzed, and a total of 564 DEGs were identified, including 441 down-regulated genes and 123 up-regulated genes compared to tamoxifen-sensitive patients (Figure 1A). DEGs are also listed in a volcano plot (Figure 1B). In KEGG pathway analysis (Figure 1C), the up-regulated genes are significantly enriched in pathways including cell cycle, cellular senescence and human T-cell leukemia virus 1 infection. The down-regulated genes are mainly enriched in complement and coagulation cascades, PPAR signaling pathway and arachidonic acid metabolism. In GO functional analysis (Figure 1D), these up-regulated genes are mainly enriched in terms including tubulin binding, microtubule binding and ATPase activity. The down-regulated DEGs are enriched in enzyme inhibitor activity and glycosaminoglycan binding.

Figure 1 Differentially expressed genes identified in tamoxifen-resistant and sensitive patients. (A) Heatmap and (B) volcano plot of differentially expressed genes in primary tamoxifen-resistant and sensitive patients. (C) KEGG pathway analysis of up-regulated and down-regulated DEGs. (D) GO functional analysis of up-regulated and down-regulated DEGs.

After excluding outliers, WGCNA analysis was performed to identify key modules correlated with tamoxifen resistance (Supplementary Figure 1). Soft threshold power was set to 6 to ensure a scale-free network (Figure 2). A total of 37 clusters were identified based on the criteria of a cut height = 0.25 and a minimum of 30 genes (Figure 3). To identify modules correlated to tamoxifen resistance, the moduletrait relationship was analyzed, and the brown module with 576 genes was significantly related to tamoxifen resistance (Figure 4A). A scatterplot of module membership and gene significance indicates significant correlation between the brown module and tamoxifen resistance (Figure 4B).

Figure 2 Soft threshold power identified in the weighted gene co-expression network analysis (WGCNA). (A) Analysis of scale-free fit index for various soft threshold powers. (B) Analysis of mean connectivity for various soft threshold powers.

Figure 3 Co-expression network modules for mRNA.

Figure 4 The brown module was identified with tamoxifen resistance. (A) Heatmap of trait correlation with tamoxifen resistance. The brown module was highly correlated with tamoxifen resistance. (B) A scatter plot of module membership in the brown module and gene significance.

To identify genes mostly related to tamoxifen resistance, genes in the brown module and DEGs were overlapped and a total of 81 genes were identified (Figure 5A). To explore the main function of these genes, KEGG pathway analysis was used, and pathways including cell cycle, oocyte meiosis and cellular senescence were enriched in these genes (Figure 5B). KEGG using DAVID was also calculated, and cell cycle was still the top pathway (Supplementary Figure 2). The enrichment analysis was similar to that in up-regulated genes of Figure 1C, indicating that those up-regulated genes in these pathways play an important role in tamoxifen resistance.

Figure 5 Hub genes identified with tamoxifen resistance. (A) Venn plot of DEGs and genes in the brown module. A total of 81 genes overlapped. (B) KEGG pathway analysis of the 81 overlapped genes. (C) Proteinprotein interaction network of the 81 overlapped genes. (D) Proteinprotein interaction network of 21 hub genes. The intensity of red indicates the scores of degrees.

A PPI network was constructed to investigate the interaction between these 81 genes, which consists of 81 nodes and 1941 edges (Figure 5C). To explore hub genes in this network, cytoHubba was used and the top 20 genes were identified according to the degree in the network. AURKA, UBE2C, CCNA2, CDK1, KIF11, RRM2, TOP2A, BUB1B, CCNB2, MELK, BIRC5, NUSAP1, CDC20, KIF20A, KIF4A, MAD2L1, AURKB, DLGAP5, RACGAP1 and KIF23 were the top 20 hub genes (Figure 5D), which were all up-regulated in tamoxifen-resistant patients (Table 1). Survival analysis found that high expression of 12 genes (AURKA, BIRC5, CCNA2, CCNB2, DLGAP5, KIF4A, KIF20A, KIF23, MELK, MAD2L1, RACGAP1, UBE2C) was associated with worse survival when patients were treated with tamoxifen (Figure 6). All these 12 mitotic genes have a prognostic role for ER-positive breast cancer using KaplanMeier plotter website (Supplementary Figures 3 and 4).

Table 1 Top 20 Genes in PPI Network Ranked by Degree Method and Foldchange in DEGs

Figure 6 Survival analysis of 12 significant genes for disease-free survival. (A) K-M plot of AURKA for patients treated with tamoxifen. (B) K-M plot of BIRC5 for patients treated with tamoxifen. (C) K-M plot of CCNA2 for patients treated with tamoxifen. (D) K-M plot of CCNB2 for patients treated with tamoxifen. (E) K-M plot of DLGAP5 for patients treated with tamoxifen. (F) K-M plot of KIF4A for patients treated with tamoxifen. (G) K-M plot of KIF20 for patients treated with tamoxifen. (H) K-M plot of KIF23 for patients treated with tamoxifen. (I) K-M plot of MAD2L1 for patients treated with tamoxifen. (J) K-M plot of MELK for patients treated with tamoxifen. (K) K-M plot of RACGAP1 for patients treated with tamoxifen. (L) K-M plot of UBE2C for patients treated with tamoxifen.

Furthermore, these 12 genes were validated in the GSE6532, and a total of 10 genes were up-regulated in tamoxifen-resistant patients (Figure 7A).

Figure 7 Validation of ten genes in public database and samples from our own database. (A) Validation of significant genes in GSE6532. All genes are statistically significant. (B) Validation of significant genes in 10 pairs of patient samples in Ruijin cohort. (C) Colony formation assay for cells with knockdown of MELK, MAD2L1 and RACGAP1 treated with tamoxifen. (D) Cell viability assay for cells with knockdown of MELK, MAD2L1 and RACGAP1 treated with tamoxifen. *P<0.05.

Ten of these genes (AURKA, CCNA2, CCNB2, DLGAP5, KIF4A, KIF20A, KIF23, MELK, MAD2L1, RACGAP1) were then further validated in 10 paired tamoxifen-resistant and sensitive breast cancer patients from the Ruijin cohort. Tamoxifen-resistant patients were all resisted, and their clinical characteristics were matched. Detailed characteristics for these patients are listed in Supplementary Table 2. RT-PCR results demonstrated that these ten genes were all over-expressed in tamoxifen-resistant patients, and expression of these ten genes in tamoxifen-resistant patients ranges from 2.2- to 4.7-fold that of tamoxifen-sensitive patients (P<0.05, Figure 7B).

To validate the function of these genes in tamoxifen resistance, MELK, RACGAP1 and MAD2L1 were knocked down in MCF-7 cells because function of these genes in tamoxifen resistance was not reported while other genes were reported. As shown in colony formation assay and cell viability assay, knocking down these genes sensitized cells to tamoxifen compared with control (Figure 7C and D). This validated the robustness of our analysis.

In our study, we collected data from the GEO database, and an integrated analysis was used to identify genes associated with tamoxifen resistance in ER-positive breast cancer patients. Analysis of differentially expressed genes ignores correlation between different genes. In our study, we combined WGCNA with DEGs to identify differentially expressed genes with high correlation. The interaction of different proteins is an important mechanism to regulate cell biology. So, PPI network identified hub genes which were mostly engaged in tamoxifen resistance.

A total of 564 DEGs were identified, including 441 down-regulated genes and 123 up-regulated genes. The up-regulated genes were enriched in the cell cycle pathway, which is the most common pathway studied in tamoxifen resistance. The brown module with 576 genes was identified using WGCNA. An overlap of genes between DEGs and the brown module was also enriched in the cell cycle. A total of 10 mitosis genes with prognostic significance were identified as hub genes associated with tamoxifen resistance and were validated in the public database and in our cohort samples.

Studies of tamoxifen resistance mainly focus on acquired resistance due to limitation of sample size for tamoxifen resistance.16,17 According to the ESMO International Consensus Guidelines for Advanced Breast Cancer (ABC), acquired resistance was defined as patients who relapse while on adjuvant endocrine therapy (ET) but after the first 2 years, or relapse within 12 months of completing adjuvant ET, or have progression disease (PD) 6 months after initiating ET for ABC, while on ET. In our study, primary tamoxifen-resistant patients were studied using data from the public repository, and the mitosis phase of the cell cycle was identified as the main pathway. The most well-known mechanism of tamoxifen resistance is the mutation of ESR1.18 And recently, CDK4/6 inhibitors were combined with endocrine therapy to overcome endocrine resistance.19,20 In MONALEESA-7, 26.3% pre- and perimenopausal patients received tamoxifen. Patients receiving tamoxifen and ribociclib had longer median progression-free survival of 22.1 months (95% CI 16.624.7) than patients in the placebo group who had progression-free survival of 11.0 months (9.116.4) (HR 0.59, 95% CI 0.390.88). In our analysis, we illustrated the role of cell cycle-related genes in tamoxifen resistance, and these genes may serve as targets to overcome tamoxifen resistance. Except genes regulating G1/S transition like CCNE2 (Figure 5C), hub genes were all involved in mitosis. CCNE2 is a regulatory subunit of cyclin-dependent kinase 2. It interacts with CDK2 and forms a catalytically active kinase complex.21 This complex phosphorylates histone H1 and Rb and promotes the transition of G1/S. It has been reported that cell cycle and mitosis genes were involved in tamoxifen insensitivity and suppression of these genes could re-inhibit growth.22,23 Our study further indicated that therapy targeting mitosis is a potential strategy in overcoming tamoxifen resistance. As endocrine therapy is a standard adjuvant therapy of ER-positive breast cancer patients and there was no dataset with patients both receiving and not receiving tamoxifen, we cannot evaluate the interaction of genes regarding prognosis and efficacy to tamoxifen. When we assessed the prognostic role of these mitotic genes in ER breast cancers, high expression of these genes indicated poor survival for ER breast cancers though the treatment information was unknown.

AURKA, Aurora kinase A, controls many processes of the G2/M transition.2426 AURKA was identified as a marker for endocrine resistance in early estrogen receptor-positive breast cancer, and knockdown of AURKA made tamoxifen-resistant cells re-sensitized to tamoxifen treatment.27 CCNA2 is highly expressed from S phase to early mitosis and binds to CDK1 during the transition from G2 to M phase.28 It was overexpressed in tamoxifen-resistant cells. CCNB2 levels gradually increase during S and G2 phase and peak at mitosis.29,30 It was reported that ER-positive patients who have high expression of CCNA2 or CCNB2 have inferior survival.31,32 KIF4A, KIF20A and KIF23 are all mitotic kinesins and have a highly conserved motor domain involving ATP-binding and microtubule-binding sequences.33 They all promote the proliferation of breast cancers, and treatment with tamoxifen reduced the expression of these three proteins. Knockout of KIF4A re-sensitized cancer cells to tamoxifen.34 Maternal embryonic leucine zipper kinase (MELK) is a member of both the sucrose-non-fermenting (snf)1 and the AMP-activated protein kinase (AMPK) families.35 It has been reported that MELK is overexpressed in many cancers, and high expression of this gene correlated with a poor survival.35,36 MAD2L1 is a key protein in mediating spindle checkpoint activation.37,38 The disks large-associated protein 5 (DLGAP5), a microtubule-associated protein, is responsible for stabilizing and correct formation of microtubules, and the bipolar arrays of dynamic microtubules are critical in forming the mitotic spindle. It is overexpressed in many cancers and indicates a poor prognosis in these cancers.3941 Rac GTPase-activating protein 1 (RACGAP1) links the mitotic spindle to the plasma membrane to secure the final cut during cytokinesis in animal cells. RACGAP1 was identified as an oncogene in many cancers.42,43 The role of MAD2L1, DLGAP5 and RACGAP1 in tamoxifen resistance was validated in our study, and knockdown of these genes sensitizes breast cancer to tamoxifen.

In conclusion, this present study provides evidence that mitosis genes contributed to tamoxifen resistance. We concluded that ten mitosis genes showed high expression in tamoxifen-resistant patients and lead to poor analysis in patients receiving tamoxifen and in ER-positive breast cancer patients. Knockdown of three genes (MAD2L1, DLGAP5, RACGAP1) makes cells more sensitive to tamoxifen. Our results indicates that mitosis is an important biological process of tamoxifen resistance, and mitotic genes may serve as potential targets to overcome tamoxifen resistance.

ER, estrogen receptor ; GEO, Gene Expression Omnibus; DEGs, differentially expressed genes; WGCNA, weighted correlation network analysis; PPI, proteinprotein interaction; GO, gene ontology; KEGG, Kyoto Encyclopedia of Genes and Genomes; HG-U133A, human genome U133A microarray; GS, gene significance; MM, module membership; K-M, KaplanMeier; AURKA, Aurora kinase A; MELK, maternal embryonic leucine zipper kinase; AMPK, AMP-activated protein kinase; DLGAP5, disks large-associated protein 5; RACGAP1, Rac GTPase-activating protein 1.

The investigations involving human participants were reviewed and approved by the independent Ethical Committees of Ruijin Hospital, Shanghai Jiaotong University School of Medicine and all subjects gave written informed consent. The ethics number for our analysis is 2020-309. This study was conducted in accordance with the Declaration of Helsinki.

XS participated in all experimental work and drafted the paper. XC and KS designed the article. SD, ZW and SL collected the data. All authors made substantial contributions to conception and design, acquisition of data, or analysis and interpretation of data; took part in drafting the article or revising it critically for important intellectual content; agreed to submit to the current journal; gave final approval of the version to be published; and agree to be accountable for all aspects of the work.

The authors appreciate the financial supported by the National Natural Science Foundation of China (Grant Number: 81772797), Shanghai Municipal Education Commission-Gaofeng Clinical Medicine Grant Support (20172007); Ruijin Hospital, Shanghai Jiao Tong University School of Medicine-Guangci Excellent Youth Training Program (GCQN-2017-A18). All these financial sponsors had no role in the study design, collection, analysis or interpretation of data.

The authors report no conflicts of interest in this work.

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35. Hiwatashi K, Ueno S, Sakoda M, et al. Expression of maternal embryonic leucine zipper kinase (MELK) correlates to malignant potentials in hepatocellular carcinoma. Anticancer Res. 2016;36(10):51835188. doi:10.21873/anticanres.11088

36. Wang Y, Lee YM, Baitsch L, et al. MELK is an oncogenic kinase essential for mitotic progression in basal-like breast cancer cells. eLife. 2014;3:e01763. doi:10.7554/eLife.01763

37. Chen X, Cheung ST, So S, et al. Gene expression patterns in human liver cancers. Mol Biol Cell. 2002;13(6):19291939. doi:10.1091/mbc.02-02-0023

38. Garber ME, Troyanskaya OG, Schluens K, et al. Diversity of gene expression in adenocarcinoma of the lung. Proc Natl Acad Sci U S A. 2001;98(24):1378413789. doi:10.1073/pnas.241500798

39. Fragoso MC, Almeida MQ, Mazzuco TL, et al. Combined expression of BUB1B, DLGAP5, and PINK1 as predictors of poor outcome in adrenocortical tumors: validation in a Brazilian cohort of adult and pediatric patients. Eur J Endocrinol. 2012;166(1):6167. doi:10.1530/EJE-11-0806

40. Schneider MA, Christopoulos P, Muley T, et al. AURKA, DLGAP5, TPX2, KIF11 and CKAP5: five specific mitosis-associated genes correlate with poor prognosis for non-small cell lung cancer patients. Int J Oncol. 2017;50(2):365372. doi:10.3892/ijo.2017.3834

41. Weinberger P, Ponny SR, Xu H, et al. Cell cycle M-phase genes are highly upregulated in anaplastic thyroid carcinoma. Thyroid. 2017;27(2):236252. doi:10.1089/thy.2016.0285

42. Lawson CD, Der CJ. Filling GAPs in our knowledge: ARHGAP11A and RACGAP1 act as oncogenes in basal-like breast cancers. Small GTPases. 2018;9(4):290296. doi:10.1080/21541248.2016.1220350

43. Saigusa S, Tanaka K, Mohri Y, et al. Clinical significance of RacGAP1 expression at the invasive front of gastric cancer. Gastric Cancer. 2015;18(1):8492. doi:10.1007/s10120-014-0355-1

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10 mitosis genes associated with tamoxifen in breast cancer | OTT - Dove Medical Press

Cell Biology

Scientists Use DNA To Trace the Origins of Giant Viruses – SciTechDaily

Scientists investigate the evolution of Mimivirus, one of the worlds largest viruses, through how they replicate DNA. Credit: Indian Institute of Technology Bombay

Researchers from the Indian Institute of Technology Bombay shed light on the origins of Mimivirus and other giant viruses, helping us better understand a group of unique biological forms that shaped life on Earth. In their latest study published in Molecular Biology and Evolution, the researchers show that giant viruses may have come from a complex single-cell ancestor, keeping DNA replication machinery but shedding genes that code for other vital processes like metabolism.

2003 was a big year for virologists. The first giant virus was discovered in this year, which shook the virology scene, revising what was thought to be an established understanding of this elusive group and expanding the virus world from simple, small agents to forms that are as complex as some bacteria. Because of their link to disease and the difficulties in defining themthey are biological entities but do not fit comfortably in the existing tree of life viruses incite the curiosity of many people.

Scientists have long been interested in how viruses evolved, especially when it comes to giant viruses that can produce new viruses with very little help from the hostin contrast to most small viruses, which utilize the hosts machinery to replicate.

Even though giant viruses are not what most people would think of when it comes to viruses, they are actually very common in oceans and other water bodies. They infect single-celled aquatic organisms and have major effects on the latters population. In fact, Dr. Kiran Kondabagil, molecular virologist at the Indian Institute of Technology (IIT) Bombay, suggests, Because these single-celled organisms greatly influence the carbon turnover in the ocean, the viruses have an important role in our worlds ecology. So, it is just as important to study them and their evolution, as it is to study the disease-causing viruses.

Scientists investigate the evolution of Mimivirus, one of the worlds largest viruses, through how they replicate DNA. Researchers from the Indian Institute of Technology Bombay shed light on the origins of Mimivirus and other giant viruses, helping us better understand a group of unique biological forms that shaped life on earth. Credit: Indian Institute of Technology Bombay

In a recent study, the findings of which have been published in Molecular Biology and Evolution, Dr. Kondabagil and co-researcher Dr. Supriya Patil performed a series of analyses on major genes and proteins involved in the DNA replication machinery of Mimivirus, the first group of giant viruses to be identified. They aimed to determine which of two major suggestions regarding Mimivirus evolutionthe reduction and the virus-first hypotheses were more supported by their results. The reduction hypothesis suggests that the giant viruses emerged from unicellular organisms and shed genes over time; the virus-first hypothesis suggests that they were around before single-celled organisms and gained genes, instead.

Dr. Kondabagil and Dr. Patil created phylogenetic trees with replication proteins and found that those from Mimivirus were more closely related to eukaryotes than to bacteria or small viruses. Additionally, they used a technique called multidimensional scaling to determine how similar the Mimiviral proteins are. A greater similarity would indicate that the proteins coevolved, which means that they are linked together in a larger protein complex with coordinated function. And indeed, their findings showed greater similarity. Finally, the researchers showed that genes related to DNA replication are similar to and fall under purifying selection, which is natural selection that removes harmful gene variants, constraining the genes and preventing their sequences from varying. Such a phenomenon typically occurs when the genes are involved in essential functions (like DNA replication) in an organism.

Taken together, these results imply that Mimiviral DNA replication machinery is ancient and evolved over a long period of time. This narrows us down to the reduction hypothesis, which suggests that the DNA replication machinery already existed in a unicellular ancestor, and the giant viruses were formed after getting rid of other structures in the ancestor, leaving only replication-related parts of the genome.

Our findings are very exciting because they inform how life on earth has evolved, Dr. Kondabagil says. Because these giant viruses probably predate the diversification of the unicellular ancestor into bacteria, archaea, and eukaryotes, they should have had major influence on the subsequent evolutionary trajectory of eukaryotes, which are their hosts.

In terms of applications beyond this contribution to basic scientific knowledge, Dr. Kondabagil feels that their work could lay the groundwork for translational research into technology like genetic engineering and nanotechnology. He says, An increased understanding of the mechanisms by which viruses copy themselves and self-assemble means we could potentially modify these viruses to replicate genes we want or create nanobots based on how the viruses function. The possibilities are far-reaching!

Reference: Coevolutionary and Phylogenetic Analysis of Mimiviral Replication Machinery Suggest the Cellular Origin of Mimiviruses by Supriya Patil and Kiran Kondabagil, 11 February 2021, Molecular Biology and Evolution.DOI: 10.1093/molbev/msab003

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Scientists Use DNA To Trace the Origins of Giant Viruses - SciTechDaily

Cell Biology

Purdue researcher working to harness power of sea slugs – Purdue Agricultural Communications

These were high-risk, high-reward proposals, Widhalm said. Not only can we learn a lot about basic cell biology, but there are opportunities to put that knowledge to use in so many ways.

POTENTIAL USES

Transferring the sea slugs ability to retain chloroplasts in their cells to other organisms or synthetic cells has the potential to usher in a giant leap for synthetic biology, with the lessons learned being applicable to so many other areas.

Photosynthesis requires light and carbon dioxide. If photosynthesis could be introduced as a trait packaged and delivered via organellar transfer, designer cells could be engineered to pull carbon dioxide from the atmosphere and impact climate change.

Mitochondrial diseases affect a cells ability to produce energy. Understanding how to insert organelles without damaging the host cell could allow for new clinical treatments for repairing or replacing defective organelles in those suffering from hard-to-treat illnesses.

Drug development might also be improved. Yeast and microbial cells often need sugars to consume during the process of creating new molecules. Eliminating the need for fixed carbon input could improve the sustainability and cost efficiency of engineering valuable products.

Widhalm and his graduate students have spent the last year working with a single aquarium setup and attempting to successfully rear sea slugs through their life cycles in captivity. Theyve now gotten the creatures to reproduce and the offspring to feed on cultured algae and metamorphose into green adults.

Now, Widhalm has obtained funding to develop a more elaborate aquarium system with multiple areas for culturing algae, holding slugs at different stages of their lives and monitoring water chemistry.

With support from a 2020 Showalter Research Trust award, Widhalms team is focused on answering questions about sea slug cell biology. In addition to their team award from Research Corporation, Widhalm, Landry and Weng were also recently funded by The Gordon and Betty Moore Foundation to develop tools for studying sea slug genes. Through a Center for Plant Biology seed grant, Widhalm is also working with collaborator Jennifer Wisecaver, assistant professor of biochemistry, to sequence the Elysia clarki genome.

We can learn so much about whether the slugs modify the chloroplasts in any way before taking them in and how they control chloroplast function, Widhalm said. Its early in the work, but with our new setup and the tools we are developing with our collaborators, we expect to learn a lot about this awesome evolutionary phenomenon.

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Purdue researcher working to harness power of sea slugs - Purdue Agricultural Communications

Cell Biology

Botany: 3 things you need to know about getting this degree – Study International News

Plant science, like plant biology or phytology, is more commonly known as botany. Its a branch within biology that studies plants. This includes their structure, properties and biochemical processes. This herb field of study also focuses on plant diseases and interactions with the environment which provides a foundation for applied sciences like agriculture, horticulture and forestry.

According to the US of Bureau Labour Statistics, the positions for soil and plant scientists are set to increase at a rate of eight to 10% which would add 6,700 jobs by 2022. With the progression of the clean energy economy, the field of botany lies on the cutting edge and is also a great profession for nature enthusiasts.

What can you work as? One job in popular demand is a plant ecologist. They help conserve endangered species and natural areas. For instance, the Rafflesia flower (the largest on the planet) that has pungent odors of decomposing flesh can be found in the forests of Borneo and Sumatra. Its also on the brink of extinction and the only way to save it, is to preserve its natural habitat. Below we take a look at the whatnots of getting a degree in botany and what jobs you can expect from it:

You must demonstrate a broad general education especially in literacy and numeracy with a minimum of a 4 in your GCSE or IGCSE. Practical skills are a must in science education and therefore youll need to pass any science A-Level taken. Usually, this includes grades AAA-ABB (two in biology), chemistry, physics and maths.

Britains Royal Botanic Gardens warned on May 10 about the threats facing the worlds plant kingdom in the first global report of its kind aimed at drawing attention to often-overlooked species. Source: Daniel Leal-Olivas/AFP

If youre submitting your International Baccalaureate, a minimum of 36-33 points is needed (including two higher level science subjects). To add to that, you must show your English Language proficiency in your GCSE/IGCSE grades or an IELTS (or equivalent) with no less than 6.5.

The undergraduate programmes in botany focuses on the growth, development, and productivity of plants. Youll be learning how to apply concepts from a wide range of biological subjects to plant science. This includes genetics, molecular biology, biochemistry and cell biology.

Depending on what institution you choose, the majority that offer this course usually have a combination of seminars and interactive events. To further add, youll most likely be getting hands-on experience in field studies where you can properly study plant environments.

A picture shows containers of Chanel creams made from camellia flowers at the Chanel fashion house camellia farm in Gaujac. Chanel uses camellias to create cosmetic products, notably creams, for the exceptional moisturising properties it can produce.Source: Gaizka Iroz/AFP

An obvious job would land you the role of a botanist whose average pay a year sums up to US$78,552. Your role would have you studying the many aspects of plants and conducting experiments to enhance the yield, disease resistance, drought resistance or the nutritional value of crops.

A biological scientist studies the living organisms and their relationship to the environment through basic and applied research. You could be doing this and earning an average of US$52,601 a year.

What about landscape design? This would be you making practical and alternative spaces that are beneficial for our health, wellbeing, and most of all protecting the environment. This could make you up to US$55,000 a year.

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Botany: 3 things you need to know about getting this degree - Study International News

Cell Biology

Michael Andreeff, M.D., Ph.D to Join the Scientific Advisory Board of Brooklyn ImmunoTherapeutics, Inc. – Business Wire

BROOKLYN, N.Y.--(BUSINESS WIRE)--Brooklyn ImmunoTherapeutics, Inc. (NYSE American: BTX) ("Brooklyn"), a biopharmaceutical company focused on exploring the role that cytokine and gene editing/cell therapy can have in treating patients with cancer and blood disorders, today announced the appointment of Michael Andreeff, M.D., Ph.D. to Brooklyns Scientific Advisory Board, effective May 21, 2021.

Dr. Andreeff currently serves as a Professor of Medicine at MD Anderson Cancer Center where he holds the Paul and Mary Haas Chair in Genetics and is the Chief of Molecular Hematology and Therapy. Dr. Andreeff received his M.D. and Ph.D. from the University of Heidelberg, Germany, and additional training at Memorial Sloan Kettering Cancer Center (MSKCC). Dr. Andreff has been a pioneer in flow cytometry since 1971, when he established the first flow cytometry laboratory at the University of Heidelberg and organized the first European flow cytometry conference. In 1977 he joined MSKCC, became head of the Leukemia Cell Biology and Hematopathology flow cytometry laboratory, and organized the first Clinical Cytometry Conference in 1986. Since 1990 he has been Professor of Medicine at MD Anderson Cancer Center. He has published over 700 peer-reviewed papers, 5 books and 75 book chapters.

Dr. Andreeff brings a tremendous amount of experience in developing treatments for leukemia and I am thrilled to welcome him to Brooklyns Scientific Advisory Board, said Howard J. Federoff, M.D., Ph.D., Chief Executive Officer and President of Brooklyn. He is an established leader in analyzing the interactions between leukemia stem cells and their microenvironment. He has also laid the foundation for using mesenchymal stem cells in cancer therapy. Dr. Andreeffs expertise will be crucial as we continue to advance our work in the gene editing and cell therapy space.

Having worked extensively in the leukemia space, I am eager to join the Brooklyn team and contribute to their efforts to develop impactful oncology therapies, said Dr. Andreeff. With the recent license with Factor Bioscience Limited and Novellus Therapeutics Limiteds gene editing technology, Brooklyn has tremendous potential as a leader in cancer therapy with a diverse pipeline of products. I am excited to be a part of this team.

About Brooklyn ImmunoTherapeutics

Brooklyn is exploring the role that cytokine-based therapy can have in treating patients with cancer, both as a single agent and in combination with other anti-cancer therapies. The company is also exploring opportunities to advance oncology, blood disorder, and monogenic disease therapies using leading edge gene editing/cell therapy technology through the newly acquired license from Factor Bioscience and Novellus Therapeutics.

Brooklyns most advanced program is studying the safety and efficacy of IRX-2 in patients with head and neck cancer. In a Phase 2A clinical trial in head and neck cancer, IRX-2 demonstrated an overall survival benefit. Additional studies are either underway or planned in other solid tumor cancer indications.

For more information about Brooklyn and its clinical programs, please visit http://www.BrooklynITx.com.

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Michael Andreeff, M.D., Ph.D to Join the Scientific Advisory Board of Brooklyn ImmunoTherapeutics, Inc. - Business Wire

Cell Biology

This One Thing Can Seriously Increase Your Chances of Diabetes | Eat This Not That – Eat This, Not That

Approximately ten percent of Americans, 34 million, suffer from diabetes, per the Centers for Disease Control and Prevention. Type 2 is the most common, accounting for 90-95 percent of cases. There are multiple risk factors, some preventable and others not. However, one of them can increase your chances of developing by a whopping six timesand it might be within your control. Read on to find out what it isand to ensure your health and the health of others, don't miss these Sure Signs You Had COVID And Should Tell Your Doctor.

Jonathan Bogan, MD, Yale Medicine endocrinologist specializing in diabetes and weight management as well as associate professor of medicine and cell biology, Yale School of Medicine, explains that diabetes is a disease that results in altered metabolism, including excessive amounts of glucose (sugar) in the bloodstream. "This can lead to problems with the eyes, kidneys, heart, nerves, circulation, and other organs," he says.

The biggest risk factor for type 2 diabetes, per Dr. Bogan? Obesity. According to a 2020 study, obesity increases your risk of developing type 2 diabetes by a whopping six timesregardless of genetic predisposition to the disease. Those who were overweight had a 2.4 times increased risk.

In most cases, obesity is preventable. And, it can also be remedied. "The results suggest that type 2 diabetes prevention by weight management and healthy lifestyle is critical across all genetic risk groups. Furthermore, we found that the effect of obesity on type 2 diabetes risk is dominant over other risk factors, highlighting the importance of weight management in type 2 diabetes prevention," the study concluded. Dr. Bogan also endorses diet and exercise to help maintain a healthy weight.

RELATED: The #1 Cause of Diabetes, According to Science

According to the CDC, "people who have obesity, compared to those with a healthy weight, are at increased risk for many serious diseases and health conditions." They are more likely to die from all-causes of death, more likely to have high blood pressure, high LDL and low HDL cholesterol, or high levels of triglycerides (Dyslipidemia), coronary heart disease, stroke, gallbladder disease, osteoarthritis (a breakdown of cartilage and bone within a joint), sleep apnea and breathing problems, many types of cancer, mental illness, body pain, and in general, a lower quality of life.

RELATED: 9 Everyday Habits That Might Lead to Dementia, Say Experts

Scientists at The Irish Longitudinal Study on Aging (TILDA) at Trinity College Dublin recently discovered that being overweight or obese can also significantly reduce blood flow to the brain, a term called "cerebral hypoperfusion." The new study pointed out that it is considered an early mechanism in vascular dementia and Alzheimer's disease. And to get through life at your healthiest, don't miss: This Supplement Can Raise Your Cancer Risk, Experts Say.

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This One Thing Can Seriously Increase Your Chances of Diabetes | Eat This Not That - Eat This, Not That

Cell Biology

Newly Discovered Glycosylated RNA Is All Over Cells: Study – The Scientist

The emergence of nucleic acids and that of proteins have sometimes been called the first and second evolution revolutions, as they made life as we know it possible. Some experts argue that glycosylationthe addition of glycans to other biopolymersshould be considered the third, because it allowed cells to build countless molecular forms from the same DNA blueprints. Its long been believed that only proteins and lipids receive these carbohydrate constructs, but a May 17 paper in Cellthat builds upon a 2019 bioRxiv preprint posits that RNAs can be glycosylated, too, and these sugar-coated nucleic acids seem to localize to cell membranes.

Anna-Marie Fairhurst, who studies autoimmunity at the Agency for Science, Technology and Research in Singapore, describes the study as exciting. Obviously, its the first time ever that weve seen this with RNA, she says, adding that the diversity of methods used to demonstrate the presence of glycoRNAs makes the findings especially robust.

What really intrigues her are the parts present in the 2021 Cellpaper that arent in the 2019 preprintin particular, that glycoRNAs appear to predominantly end up on the cells outer membrane. There, they can attach to two kinds of sialic acid-binding immunoglobulin-type lectins (Siglecs)a family of immune receptors implicated in several diseases, including systemic lupus erythematosus (SLE). All of this suggests glycoRNAs may play a role in immune signaling. Its a really exciting era of science, Fairhurst says.

Ryan Flynn, the first author on the new paper and an RNA biologist at Harvard University and Boston Childrens Hospital, says he made the startling discovery of glycoRNAs while working in chemical biologist Carolyn Bertozzis lab at Stanford University. Bertozzi says she was skeptical at first but came around after thinking about how her own assumptions might be shaping her views. We bring to every experiment all this unconscious bias, she explains, and once she re-examined her own, she found no reason to think glycoRNAs shouldnt exist. These are ancient molecules, she says. Theres no reason to just presume that they wouldnt have found a way to connect and to create new biology.

These are ancient molecules . . . Theres no reason to just presume that they wouldnt have found a way to connect and to create new biology.

Carolyn Bertozzi, Stanford University

As it happens, Flynn did set out to overturn glycosylation dogma when he joined Bertozzis lab as a postdoc in 2017although it didnt happen the way he expected. At first, he explains, he had his eye on a quirky cytosolic protein glycosylation pathway because hed noticed that one of its key enzymes has an RNA-binding domain. If theres a glycosylation enzyme with the potential to bind RNA, and its functioning in the cytosol where RNAs tend to be, he reasoned, it could be sticking sugars to RNAs, too.

To search for the existence of these structures, it was really important that I had access to things that were not dependent on high temperatures, and not dependent on metals that might otherwise degrade the RNA, he says, and thats exactly what Bertozzis lab had to offer. Shes a pioneer in the field of bioorthogonal chemistry, which aims to develop chemical methods for tracking biomolecules in their native environments. Her lab was brimming with reagents that label specific kinds of glycans without harming other molecules or setting off side-reactions.

Flynn set to work adding these glycan-labeling compounds to HeLa cells and then isolating RNA from them to see if any glycan signal remained after hed removed all proteins and lipids. He says he thought he might see a signal when he labeled the kind of glycans used in that cytosolic glycosylation pathway.

However, months of experiments failed to support that hypothesis.

Instead, something strange kept happening with what was supposed to be a negative control: cells treated with ManNAz, an azide-labeled precursor for sialoglycans, a group of glycans known for their role as modifiers of secretory and cell surface proteins and lipids. Once the cells were given the chance to incorporate ManNAz, they were lysed with TRIzol, which breaks apart cellular components without damaging RNAs, and any surviving proteins were chopped up with proteases. The idea was that thered be no azide signal at the end, as sialoglycans are attached to proteins and lipids in the endoplasmic reticulum and Golgi, where RNAs have no business being. I was like, theres no way that a reagent that labels sialoglycans is going to end up labeling an RNA, even a glycoRNA, Bertozzi says, but those experiments consistently gave Flynn positive signals.

So, the team dug further. Not only did the glycoRNAs the team found contain this specific subgroup of glycans, they appeared to largely consist of YRNAs, a family of small, highly conserved noncoding RNAs whose cellular functions remain unclear, although previous studies have suggested they may play a role in oncogenesis and autoimmunity. The specificity of both the glycans and the type of RNAs involved strongly point to their being attached to one another with an enzyme, says Bertozzi.

Furthermore, once the researchers started looking for them, they found these glycoRNAs in numerous established cell lines, including cancer-derived ones such as HeLa and T-ALL 4118 cells, as well as stem cellderived CHO and H9 cells. They were even able to detect glycoRNAs in liver and spleen cells extracted from live mice that received intraperitoneal injections of ManNAz, suggesting that glycoRNAs are everywhere.

By 2019, the team members felt they had enough supportive data to submit their findings, so they put the preprint version up on bioRxiv. It made a splash in the scientific community, but without peer review, some remained skeptical. Now, after even more experiments and a rigorous review process, the team says its data have become even more compelling.

They clearly have isolated a covalent RNA-glycan conjugate, says Laura Kiessling, a chemical biology researcher who studies carbohydrates at MIT and was not involved in the study. However, big questions remain, including what these glycoRNAs do and how they form. For instance, its unclear exactly how the RNAs and glycans are physically connected to one another, she notes, and without that information, shes not quite convinced that the binding happens enzymatically.

Flynn and Bertozzi suggest that the RNAs are glycosylated much in the same way proteins are, and that it even requires some of the same proteins. As noted in the original preprint, when they inhibited key enzymes involved in glycosylation, glycoRNAs disappeared in a dose-dependent manner. Similarly, cell lines engineered to have errors in protein glycosylation produced very little glycoRNA. But for RNAs to be glycosylated by the same pathway as proteins would be weird, Kiessling says, noting that multiple glycosylation steps only proceed after a check for proper protein folding. Its hard for me to imagine exactly how that would occur with RNA.

The researchers were even able to detect glycoRNAs in liver and spleen cells extracted from live mice, suggesting that glycoRNAs are everywhere.

Fairhurst says she also wants to know more about the synthesis pathway. She has lots of other questions, too, which she says is a good sign. A really good, exciting paper leaves a lot more questions than it does answers, she notes.

While the 2019 preprint raised many of these questions, some are unique to the new data presented in the Cell version. Perhaps the biggest addition to the work was the discovery of where these glycoRNAs spend their timestuck on the outsides of cells, explains Flynn. The team demonstrated this by briefly exposing some ManNAz-labeled HeLa cells toan enzyme that can cleave sialic acid glycans from the cell surface. If the glycoRNAs were on the outside, they would be cut off, and the total amount of glycoRNAs remaining would drop. And thats exactly what they found: the glycoRNA signal started to decrease after as little as 20 minutes of incubation with the sialidase and was reduced by more than 50 percent after an hour, which the team suggests means that more than half of a cells glycoRNAs are stuck on its outer membrane.

The researchers further probed the hypothesis of extracellular localization by labeling living cells with an antibody that binds to double-stranded RNA. About one-fifth of a culture of HeLa cells were positive for antibody staining, and the label was sensitive to RNase treatment, further supporting the idea that glycoRNAs are indeed present on the outer cell membrane. That opens up a lot of ideas, and a lot of possibilities, functionally and mechanistically, for what they could be doing, says Flynn.

One of those possibilities is that glycoRNAs are involved in cell-to-cell signaling, especially in an immune context, as thats a known function of membrane glycolipids and glycoproteins. Bertozzi had already been investigating the ligands of Siglecs, a group of sugar-binding receptors that modulate immune reactions, so the team decided to see if any of them bound to glycoRNAs. They first treated HeLa cells with different Siglecs to show that the receptors bound normally, then treated the cells with RNase. Lo and behold, the binding of Siglec-11 and Siglec-14 dropped precipitously, suggesting that their ligands were cleaved from the surface by the RNA-cutting enzyme.

Bertozzi says the experiment indicated glycoRNAs are ligands for Siglec-11 and Siglec-14, and if so, theyd be the first identified for Siglec-11.

As a receptor family, [Siglecs have] kind of been ignored, notes Fairhurst, so the fact that these glycoRNAs can interact with them is very exciting, she says. My immediate desire is to see whether they are associated with diseases, particularly in SLE, she adds.

Lan Lin, an RNA biologist at the University of Pennsylvania and the Childrens Hospital of Philadelphia, says she found the 2019 preprint so interesting that she applied for and received a pilot grant from the Frontiers in Congenital Disorders of Glycosylation (CDG) Consortium to study the roles glycoRNAs may play in CDG, a group of rare congenital conditions arising from mutations in protein glycosylation pathways. Because RNA glycosylation may be related to protein glycosylation, she tells The Scientist, it was only rational or reasonable for [my colleagues and I] to hypothesize that . . . some of these patients might have differences in the glycoRNA in their system, and therefore, CDG conditions could be used to examine the potential functions of glycoRNAs.

So far, she says, her team hasnt detected any consistent differences in glycoRNAs between the cells of healthy controls and CDG patients. She says that may be because differences are more qualitative than quantitative, such as alterations to the sugars themselves or the subset of RNAs that are glycosylated. Alternatively, she notes, the new data in the 2021 Cell paper may provide an explanation: the membrane localization of glycoRNAs wasnt in the preprint, so maybe we are looking in the wrong place, she muses.

Its also possible that new methods are needed to detect glycoRNA differences between cells. She points out that a major limitation of the study is that the ManNAz labeling method cant readily be applied to preserved human tissue samples or blood samples.

Fairhurst says shed like to see more work in primary cell cultures rather than immortalized ones, especially leukocyte subtypes, where one might expect pronounced differences if the RNAs have a role in immunity. For example, she says shed like to see whether, in people with conditions like SLE, different cell types have fewer or more glycoRNAs, though obviously, those experiments are really challenging.

Seeing these big milestones is amazing

Anna-Marie Fairhurst, Agency for Science, Technology and Research in Singapore

Still, she says, seeing these big milestones is amazing.

Kiessling says she thinks glycoRNAs could be really important in the field of glycobiology. Her lab focuses on how carbohydrate-binding proteins can read glycans on the surfaces of cells, she explains, so these glycoRNAs could be a new kind of information to read. Lin points out that the findings are especially impactful for RNA researchers, as they suggest a whole new kind of post-transcriptional modification in need of investigation. Because glycoRNA sits at the intersection of glycobiology, immunology, and RNA biology, says Bertozzi, Ryans discovery has brought together these disparate worlds.

Flynn and Bertozzi say theyre hoping to start answering some of the many questions that remain, including how the glycans attach to RNAs and how and where that happens. The most exciting part, they say, will be the investigations into what glycoRNAs do.

R. Flynn et al., Small RNAs are modified with N-glycans and displayed on the surface of living cells,Cell, doi:10.1016/j.cell.2021.04.023, 2021.

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Newly Discovered Glycosylated RNA Is All Over Cells: Study - The Scientist

Cell Biology

Bit.bios cell revolution looks to transform dementia treatments and grow organs to order – Express

The Cambridge University spinout combines coding and biology for its breakthrough Opti-ox technology that precisely reprograms stem cells, the type that are embryos for all the others, to make any cell required at scale.

Everything that Bit.bio does is geared towards sustainability, improving the planet and the lives of people, says chief executive and co-founder Dr Mark Kotter, both a stem cell biologist and a trained complex spine neurosurgeon.

Human cells, from blood and skin samples for example, are excellent for drug development and their mass production in pure batches overcomes the traditional bottlenecks of availability, reliability and cost.

We are a new type of synthetic biology company where it is mammalian cells rather than bugs like E.coli that are engineered to create new solutions. We bridge the gap with a scalable consistent source, explains Dr Kotter as Bit.bio prepares to increase output to two billion cells a day.

Thar source material opens the doors for research, development, licensing and therapies and, as well as accelerating drug discovery, it can reduce the 1.5 billion average amount spent on a drugs innovation and the need for animal testing.

Stems cells have transcription factors (proteins) that identify their particular type and silence any new activations. Bit.bio is overcoming that and creating new identities by cracking the code of human cells from the inside, says Dr Kotter.

The companys first challenge has been to figure out what the programs are that you want to engineer into a cell to give you the desired type, he explains.

We are developing new models with the London Institute for Mathematical Sciences to analyse the complex biological data.

The second challenge is understanding exactly where in a cells DNA to engineer in the programs and also to engineer in more than one successfully.

Silicon Valley and the life sciences sector showed their enthusiasm for the businesss prospects with a 30 million first funding raise last year.

Bit.bio has so far commercialised two products, the first brain and muscle cells mass produced from a single model. These are ready for experiments in a third of the time normally expected.

Fifteen more products will be coming through over the next three years with cancers on the schedule and the growth of organs forecast to arrive within the next decade.

Attracting leading lights in the stem cell sector such as Dr Roger Pedersen and clinical immune-oncologist Dr Ramy Ibrahim, expansion in the US is a next major step along with Bit.bios transition into a clinical company producing its own therapies.

The UK workforce has grown 50 per cent and will reach 150 by the end of the year.

But what will it take to keep Bit.bio headquartered in the UK? We want to see a bolder, long term investment mindset away from quick wins, declares Dr Kotter.

We also want to see better access to talent and help tocreate physical spaces where we can grow a global HQ.

The company is however extremely excited about Breakthrough, the 375 million UK scheme launching this summer that encourages UK venture capital to co-invest with government in high-growth, innovative firms to transform industries, develop new medicines and support the move to a net zero economy.

We are on a moonshot mission to facilitate things that are affordable for everyone that were previously in the realm of science fiction, adds Dr Kotter. Ultimately our technology will help decode the operating system of life.

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Bit.bios cell revolution looks to transform dementia treatments and grow organs to order - Express

Cell Biology

Maryland Today | The Mettle Behind the Medal – Maryland Today

They interned across campus, around the country and on the other side of the globe. They founded nonprofits, volunteered at hospitals and schools, conducted groundbreaking research, and even played violin in the universitys Gamer Symphony Orchestra.

These are the six Terps considered for the University Medal, the highest honor given to an undergraduate by UMD, awarded at each spring commencement to the graduate or graduates who best personify academic distinction, extraordinary character and extracurricular contributions to the university and the larger community.

This years medalist is Sherry Fan, who is graduating with a 4.0 GPA and a dual degree in biological sciences and nutritional science.

Read on for more about her accomplishments as well as this years five finalists:

A published researcher, devoted volunteer to fighting hunger and poverty, and burgeoning artist in communicating complex science, Fan stood out even in a class of high-achieving Honors College students because of her intellect and enthusiasm.

In my 42 years teaching at the UMD, I have never taught an undergraduate student with a stronger academic record, said Todd J. Cooke, research professor in the Department of Cell Biology and Molecular Genetics and founding director of the Integrated Life Sciences Program in the Honors College.

The daughter of an immigrant from rural China, Fan grew up in Montgomery County, Md., hearing his stories about not having enough food or fresh watera motivation to seek ways to help those in dire need. She became a National Merit Scholarship finalist and earned a Banneker/Key Scholarship at the University of Maryland, where she joined the Food Recovery Network to reduce campus food waste and served meals at homeless shelters in Washington, D.C., as a member of UMD Tzu Ching.

I wanted to be able to give back to communities who were facing similar insecurities, she said. It was a personal issue to me.

Fan worked for three years with Professor Wenxia Song on uncovering the cellular relationship between obesity, chronic inflammation and insulin resistance, and spent two summers interning at the University of Maryland School of Medicine, studying a cancer-promoting protein that could help with new treatments and analyzing potential genetic markers for aortic aneurysms. Fan will be a co-author on an upcoming paper in the peer-reviewed journal PLOS ONE.

Beyond the lab, she led service trips to Kentucky and made coloring books for patients at the Childrens Inn at the National institutes of Healtha talent that also landed one of her drawings with an article in Virology.

After graduation, Fan will pursue a dual M.D./Ph.D. at Cornell University and hopes to eventually work at an academic medical center to integrate service, research, art and teaching.

Ive grown a lot as a student but also as a human being during my time at UMD, she said. I was really able to step outside my own bubble.

Elizabeth ChildsElizabeth Childs has been fascinated by human-robot interaction (HRI) since she was a kid watching Pokemon on TV.

She spent her time at UMD advancing complex research in that area while participating in the Honors Colleges Entrepreneurship and Innovation program and majoring in mechanical engineering as a Banneker/Key Scholar, with a 3.98 GPA.

Among her work, Childs explored virtual reality applications in the Geometric Algorithms for Modeling, Motion, and Animation Lab, shortened 3D-printing post-production time in the Bioinspired Advanced Manufacturing Lab and studied modular robotics for explosive ordinance disposal in Cambodia. Her first-author, peer-reviewed paper on 3D printing processes was published in the IEEE Journal of Microelectromechanical Systems.

Meanwhile, Childs was a teaching fellow in a thermodynamics course for five semesters, participated in the Quality Enhancement Systems and Teams (QUEST) honors program, competed in TerpTank with a business model to provide affordable meals to college students, and taught ACT/SAT prep in Chicago through the Alternative Breaks Program.

She was awarded a Knight-Hennessy Scholarship to Stanford University, where she will pursue a doctorate studying HRI, augmented reality and haptics (technologies stimulating touch and motion).

I am so excited to see what the future holds for Elizabeth, said Catherine Hamel, Keystone Instructor in engineering who teaches the thermodynamics course. I know that she will be on the forefront of developing technologies that will better our society.

Jackson DevadasBiological sciences major Jackson Devadas spent his four years at Maryland examining how social contexts play a role in health, particularly the mental well-being of LGBTQ students and students of color.

A Presidents Scholar and member of the Honors Colleges Design, Cultures and Creativity program, he minored in statistics and conducted multiple research projects in the Sexual Orientation and Gender Identity lab, leading to a role in several published papers.

He is driven by a desire for equity and justice, eager to learn and expand his areas of expertise, and thrives in a community-based, interdisciplinary learning environment, said American studies Professor Jason Farman, director of the Design, Cultures and Creativity program.

Devadas was student director of the Ed Snider Center for Enterprise and Markets and held leadership positions with the LGBTQ+ Students and Allies in Public Health, the Pride Alliance, the Honors College Student Advisory Board and as Honors Ambassador.

He hopes to pursue a masters degree in public health and doctorate in sociomedical sciences, focusing on mental illness within vulnerable communities, with the goal of becoming an educator.

Meron HaileLooking back toher familys movefrom Ethiopia to the U.S. in 2007, Meron Haile most remembers her parents focus on education as the key to independence.

She took that to heart, winning a Banneker/Key scholarship to Maryland, where she participated in the Honors Colleges Integrated Life Sciences program, majored in biological sciences on the pre-med track, minored in global poverty and earned a 4.0 GPA.

Haile conducted research in a campus lab on oxycodone addiction, held internships at the National Institutes of Health and the Walter Reed Army Institute of Research, and served as a medical assistant at local hospitals and medical practices.

On campus, shes been active in organizations that support immigrant and other underserved groups, including the Global Poverty Student Advisory Board, United Against Inequities in Disease (USAID), Terps for Change and CASA-Mi Esposito, where she helped immigrant youths learn English and tutored in other classes. Shes also been a teaching assistant for three years.

Marcia Shofner, senior lecturer in the Department of Entomology who teaches the Principles of Ecology & Evolution course, called Haile one of the most consistent, reliable and creative assistants shed ever worked with. I will miss her after she graduates, but she will be an amazing physician to whom I would love to take my family.

Kyeisha LaurenceOnly a few weeks into her freshman year at UMD, Kyeisha Laurence saw Hurricane Irma ravage her native St. Maarten. With the support of her new community in the Honors Colleges Gemstone program, she led a collection drive to send clothes and other supplies there.

That set the tone for Laurences time at Maryland, where she was a Banneker/Key Scholar and earned a 3.97 GPA while pursuing a biological sciences major and minor in French studies.

In Gemstone, she led a research team focused on finding a novel therapeutic agent to treat allergies. She also interned as a UM Scholar at the University of Maryland School of Medicine.

Laurence served as a member of the College of Computer, Mathematical, and Natural Sciences Diversity and Inclusion Advisory Council, president of the Charles R. Drew Pre-Health Society, a cabinet member for the Caribbean Student Association, and a supplemental instructor for the Academic Achievement Programs.

She plans to spend a year conducting clinical research at the National Institute of Health, then pursue M.D. and M.P.H. degrees for a career in improving health care for low-income and underrepresented minority communities.

Maryland has enabled me to follow my passions by supporting and providing me with a community of people who uplift, motivate and push me to be my very best, she said.

Veeraj ShahAs co-founder and CEO of ChatHealth, Veeraj Shah initially planned to promote health care services to Terps via a chatbot. Now he has ambitions to reduce preventable diseases globally.

He dived into the opportunities at Maryland, where he combined his work in the Integrated Life Sciences Honors College program with research in the School of Public Health (SPH). He took advantage of expertise and funding through the School of Public Policy and its Do Good Institute and he co-founded his first company, Vitalize App, with the support of the Robert H. Smith School of Business Dingman Center for Entrepreneurship.

Shah interned in the Office of the U.S. Surgeon General, was a fellow of the National Institutes of Health (NIH) and led UMDs chapter of Public Health Beyond Borders, among many other experiences. He contributed to 10 academic publications.

Dushanka V. Kleinman, principal associate dean and professor in SPH and a former NIH administrator, called Shah the most productive and universally outstanding undergraduate student I have encountered.

He earned a 3.98 GPA and dual degrees in biological sciences along with health policy and technology, a major he developed. He also completed 10 masters and doctoral courses in health services research and biostatistics.

As one of 24 recipients nationwide of the Gates-Cambridge Scholarship, he will head to Cambridge University to pursue a doctorate in public health and primary care, then a medical degree at Icahn School of Medicine at Mount Sinai.

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Maryland Today | The Mettle Behind the Medal - Maryland Today

Cell Biology

3D Cell Culture Market 2021 Trends, Covid-19 Impact Analysis, Supply Demand Scenario and Growth Prospects Survey till 2027 investigated in the latest…

Global 3D Cell Culture Market is valued approximately at USD 892 million in 2019 and is anticipated to grow with a healthy growth rate of more than 15.7% over the forecast period 2020-2027. A 3D cell culture is an in-vitro technique wherein the cells can grow in controlled simulated or artificially created environment, outside of a living organism. This environment has similar architecture and functioning of the native tissue. 3D cell culture technique helps biological cells to differentiate, proliferate, and migrate by interacting with their surroundings in all three dimensions. This technique has varied applications in the fields of stem cell therapies, regenerative medicine, drug screening, cancer research and cell biology. The extracellular matrix in this technique enables cell-cell communication by direct contact, by secreting cytokines and trophic factors.

The growing prevalence of chronic diseases rise in demand in organ transplantation, tissue regeneration, and regenerative medicine are the few factors responsible for growth of the market over the forecast period. The rising number of organ donors due to the favourable government initiatives & growing number of deceased donors is creating a lucrative opportunity for the growth of market over the forecast years. For instance: in 1994, India government framed Transplantation of Human Organ Act to enable a proper system for removal, storage and transplantation of human organ and framed budget of approx. USD 19.95 million to promote organ donation from deceased person. Similarly, In October 1982, a federal agency, Health Resources and Services Administration (HRSA) was established in United States. The agency monitors the transplantation system of organ in the economy and provides the safest and most equitable system for allocation, transplantation, and distribution of donated organs. Thus, such factors escalate the number of organ donors across the globe, creating a lucrative thrust to the market growth. Whereas, lack of infrastructure for 3d cell-based research and high cost of cell biology research is the major factor restraining the growth of global 3D Cell Culture market during the forecast period.

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The regional analysis of global 3D Cell Culture market is considered for the key regions such as Asia Pacific, North America, Europe, Latin America and Rest of the World. North America is the leading/significant region across the world owing to the increasing incidence of cancer and the presence of a well-established pharmaceutical & biotechnology industry. Whereas, Asia-Pacific is also anticipated to exhibit highest growth rate / CAGR over the forecast period 2020-2027.

Major market player included in this report are:Thermo Fisher ScientificCorning IncorporatedMerck KGaALonza GroupReprocell3D Biotek LLCEmulate, Inc.CN Bio Innovations LimitedHamilton CompanyInsphero AG

The objective of the study is to define market sizes of different segments & countries in recent years and to forecast the values to the coming eight years. The report is designed to incorporate both qualitative and quantitative aspects of the industry within each of the regions and countries involved in the study. Furthermore, the report also caters the detailed information about the crucial aspects such as driving factors & challenges which will define the future growth of the market. Additionally, the report shall also incorporate available opportunities in micro markets for stakeholders to invest along with the detailed analysis of competitive landscape and product offerings of key players. The detailed segments and sub-segment of the market are explained below:

by Product:Scaffold-based 3D Cell CulturesScaffold-free 3D Cell CulturesMicrofluidics-based 3D Cell CulturesMagnetic & Bioprinted 3D Cell Cultures

by Application:Cancer & Stem Cell ResearchDrug Discovery & Toxicology TestingTissue Engineering & Regenerative Medicine

By End-User:Pharmaceutical & Biotechnology CompaniesResearch InstitutesCosmetics IndustryOthers

By Region:North AmericaU.S.CanadaEuropeUKGermanyFranceSpainItalyROE

Asia PacificChinaIndiaJapanAustraliaSouth KoreaRoAPACLatin AmericaBrazilMexicoRest of the World

Furthermore, years considered for the study are as follows:

Historical year 2017, 2018Base year 2019Forecast period 2020 to 2027

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Target Audience of the Global 3D Cell Culture Market in Market Study:

Key Consulting Companies & AdvisorsLarge, medium-sized, and small enterprisesVenture capitalistsValue-Added Resellers (VARs)Third-party knowledge providersInvestment bankersInvestors

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3D Cell Culture Market 2021 Trends, Covid-19 Impact Analysis, Supply Demand Scenario and Growth Prospects Survey till 2027 investigated in the latest...