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Stemness gene expression profile of human adipose derived stem cells in long-term culture

Zaman WS, Makpol S, Santhapan S, Chua KH

Med J Malaysia, 2008 Jul;63 Suppl A:61-2.
PMID: 19024984

It is crucial to know whether stem cells retain its stemnness properties after advance in vitro manipulation. The objective of this study was to investigate the stemness gene expression of human adipose tissue derived stem cells (ADSCs) in long-term culture using quantitative RT-PCR technique. Our data showed that the expression level of Sox-2, Rex-1, FGF-4, Nanog, Nestin, BST-1, FZD-9 and Oct-4 were decreased gradually in long-term culture. This could mean that the ability of ADSCs to differentiate into other cell lineages reduce after extensive culture.

Matched MeSH terms: Gene Expression Profiling
Identification and analysis of a prepro-chicken gonadotropin releasing hormone II (preprocGnRH-II) precursor in the Asian seabass, Lates calcarifer, based on an EST-based assessment of its brain transcriptome

Tan SL, Mohd-Adnan A, Mohd-Yusof NY, Forstner MR, Wan KL

Gene, 2008 Mar 31;411(1-2):77-86.
PMID: 18280674 DOI: 10.1016/j.gene.2008.01.008

Using a novel library of 5637 expressed sequence tags (ESTs) from the brain tissue of the Asian seabass (Lates calcarifer), we first characterized the brain transcriptome for this economically important species. The ESTs generated from the brain of L. calcarifer yielded 2410 unique transcripts (UTs) which comprise of 982 consensi and 1428 singletons. Based on database similarity, 1005 UTs (41.7%) can be assigned putative functions and were grouped into 12 functional categories related to the brain function. Amongst others, we have identified genes that are putatively involved in energy metabolism, ion pumps and channels, synapse related genes, neurotransmitter and its receptors, stress induced genes and hormone related genes. Subsequently we selected a putative preprocGnRH-II precursor for further characterization. The complete cDNA sequence of the gene obtained was found to code for an 85-amino acid polypeptide that significantly matched preprocGnRH-II precursor sequences from other vertebrates, and possesses structural characteristics that are similar to that of other species, consisting of a signal peptide (23 residues), a GnRH decapeptide (10 residues), an amidation/proteolytic-processing signal (glycine-lysine-argine) and a GnRH associated peptide (GAP) (49 residues). Phylogenetic analysis showed that this putative L. calcarifer preprocGnRH-II sequence is a member of the subcohort Euteleostei and divergent from the sequences of the subcohort Otocephalan. These findings provide compelling evidence that the putative L. calcarifer preprocGnRH-II precursor obtained in this study is orthologous to that of other vertebrates. The functional prediction of this preprocGnRH-II precursor sequence through in silico analyses emphasizes the effectiveness of the EST approach in gene identification in L. calcarifer.

Matched MeSH terms: Gene Expression Profiling
Analysis and functional annotation of expressed sequence tags (ESTs) from multiple tissues of oil palm (Elaeis guineensis Jacq.)

Ho CL, Kwan YY, Choi MC, Tee SS, Ng WH, Lim KA, et al.

BMC Genomics, 2007;8:381.
PMID: 17953740

Oil palm is the second largest source of edible oil which contributes to approximately 20% of the world's production of oils and fats. In order to understand the molecular biology involved in in vitro propagation, flowering, efficient utilization of nitrogen sources and root diseases, we have initiated an expressed sequence tag (EST) analysis on oil palm.

Matched MeSH terms: Gene Expression Profiling
Identification, by gene expression profiling analysis, of novel gene targets in Staphylococcus aureus treated with betulinaldehyde

Chung PY, Chung LY, Navaratnam P

Res. Microbiol., 2013 May;164(4):319-26.
PMID: 23385141 DOI: 10.1016/j.resmic.2013.01.005

Staphylococcus aureus has become a serious concern in hospitals and community due to rapid adaptation to existing antimicrobial agents. Betulinaldehyde [3β-hydroxy-20(29)-lupen-28-al (BE)] belongs to pentacyclic triterpenoids that are based on a 30-carbon skeleton comprising four six-membered rings and one five-membered ring. In a preliminary study, BE exhibited antimicrobial activity against reference strains of methicillin-resistant and methicillin-sensitive S. aureus. However, the response mechanism of S. aureus to this compound is not known. In this study, the global gene expression patterns of both the reference strains in response to sub-inhibitory concentrations of BE were analyzed using DNA microarray to identify gene targets, particularly essential targets in novel pathways, i.e. not targeted by currently used antibiotics, or novel targets in existing pathways. The transcriptome analysis revealed repression of genes in the aminoacyl-tRNA synthetase and ribosome pathways in both the reference strains. Other pathways such as cell division, two-component systems, ABC transporters, fatty acid biosynthesis and peptidoglycan biosynthesis were affected only in the reference strain of methicillin-resistant S. aureus. The findings suggest that BE regulates multiple desirable targets which could be further explored in the development of therapeutic agents for the treatment of S. aureus infections.

Matched MeSH terms: Gene Expression Profiling
Fulltext Sequence comparison of six human microRNAs genes between tuberculosis patients and healthy individuals

Amila A, Acosta A, Sarmiento ME, Suraiya S, Zafarina Z, Panneerchelvam S, et al.

Int J Mycobacteriol, 2015 Dec;4(4):341-6.
PMID: 26964819 DOI: 10.1016/j.ijmyco.2015.06.009

MicroRNAs (miRNAs) play an important role in diseases development. Therefore, human miRNAs may be able to inhibit the survival of Mycobacterium tuberculosis (Mtb) in the human host by targeting critical genes of the pathogen. Mutations within miRNAs can alter their target selection, thereby preventing them from inhibiting Mtb genes, thus increasing host susceptibility to the disease.

Matched MeSH terms: Gene Expression Profiling
Fulltext Survival Rate and Transcriptional Response upon Infection with the Generalist Parasite Beauveria bassiana in a World-Wide Sample of Drosophila melanogaster

Paparazzo F, Tellier A, Stephan W, Hutter S

PLoS One, 2015;10(7):e0132129.
PMID: 26154519 DOI: 10.1371/journal.pone.0132129

The ability to cope with infection by a parasite is one of the major challenges for any host species and is a major driver of evolution. Parasite pressure differs between habitats. It is thought to be higher in tropical regions compared to temporal ones. We infected Drosophila melanogaster from two tropical (Malaysia and Zimbabwe) and two temperate populations (the Netherlands and North Carolina) with the generalist entomopathogenic fungus Beauveria bassiana to examine if adaptation to local parasite pressures led to differences in resistance. Contrary to previous findings we observed increased survival in temperate populations. This, however, is not due to increased resistance to infection per se, but rather the consequence of a higher general vigor of the temperate populations. We also assessed transcriptional response to infection within these flies eight and 24 hours after infection. Only few genes were induced at the earlier time point, most of which are involved in detoxification. In contrast, we identified more than 4,000 genes that changed their expression state after 24 hours. This response was generally conserved over all populations with only few genes being uniquely regulated in the temperate populations. We furthermore found that the American population was transcriptionally highly diverged from all other populations concerning basal levels of gene expression. This was particularly true for stress and immune response genes, which might be the genetic basis for their elevated vigor.

Matched MeSH terms: Gene Expression Profiling
In vitro modulation of probiotic bacteria on the biofilm of Candida glabrata

Chew SY, Cheah YK, Seow HF, Sandai D, Than LT

Anaerobe, 2015 Aug;34:132-8.
PMID: 26028405 DOI: 10.1016/j.anaerobe.2015.05.009

A conspicuous new concept of pathogens living as the microbial societies in the human host rather than free planktonic cells has raised considerable concerns among scientists and clinicians. Fungal biofilms are communities of cells that possess distinct characteristic such as increased resistance to the immune defence and antimycotic agents in comparison to their planktonic cells counterpart. Therefore, inhibition of the biofilm may represent a new paradigm for antifungal development. In this study, we aim to evaluate the in vitro modulation of vulvovaginal candidiasis (VVC)-causing Candida glabrata biofilms using probiotic lactobacilli strains. Probiotic Lactobacillus rhamnosus GR-1 and Lactobacillus reuteri RC-14 were shown to have completely inhibited C. glabrata biofilms and the results were corroborated by scanning electron microscopy (SEM), which revealed scanty structures of the mixed biofilms of C. glabrata and probiotic lactobacilli strains. In addition, biofilm-related C. glabrata genes EPA6 and YAK1 were downregulated in response to the probiotic lactobacilli challenges. The present study suggested that probiotic L. rhamnosus GR-1 and L. reuteri RC-14 strains inhibited C. glabrata biofilm by partially impeding the adherence of yeast cells and the effect might be contributed by the secretory compounds produced by these probiotic lactobacilli strains. Further investigations are required to examine and identify the biofilm inhibitory compounds and the mechanism of probiotic actions of these lactobacilli strains.

Matched MeSH terms: Gene Expression Profiling
Fulltext A hybrid-membrane migration method to isolate high-purity adipose-derived stem cells from fat tissues

Higuchi A, Wang CT, Ling QD, Lee HH, Kumar SS, Chang Y, et al.

Sci Rep, 2015;5:10217.
PMID: 25970301 DOI: 10.1038/srep10217

Human adipose-derived stem cells (hADSCs) exhibit heterogeneous characteristics, indicating various genotypes and differentiation abilities. The isolated hADSCs can possess different purity levels and divergent properties depending on the purification methods used. We developed a hybrid-membrane migration method that purifies hADSCs from a fat tissue solution with extremely high purity and pluripotency. A primary fat-tissue solution was permeated through the porous membranes with a pore size from 8 to 25 μm, and the membranes were incubated in cell culture medium for 15-18 days. The hADSCs that migrated from the membranes contained an extremely high percentage (e.g., >98%) of cells positive for mesenchymal stem cell markers and showed almost one order of magnitude higher expression of some pluripotency genes (Oct4, Sox2, Klf4 and Nanog) compared with cells isolated using the conventional culture method.

Matched MeSH terms: Gene Expression Profiling
Fulltext Control of Polyamine Biosynthesis by Antizyme Inhibitor 1 Is Important for Transcriptional Regulation of Arginine Vasopressin in the Male Rat Hypothalamus

Greenwood MP, Greenwood M, Paton JF, Murphy D

Endocrinology, 2015 Aug;156(8):2905-17.
PMID: 25961839 DOI: 10.1210/en.2015-1074

The polyamines spermidine and spermine are small cations present in all living cells. In the brain, these cations are particularly abundant in the neurons of the paraventricular (PVN) and supraoptic nuclei (SON) of the hypothalamus, which synthesize the neuropeptide hormones arginine vasopressin (AVP) and oxytocin. We recently reported increased mRNA expression of antizyme inhibitor 1 (Azin1), an important regulator of polyamine synthesis, in rat SON and PVN as a consequence of 3 days of dehydration. Here we show that AZIN1 protein is highly expressed in both AVP- and oxytocin-positive magnocellular neurons of the SON and PVN together with antizyme 1 (AZ1), ornithine decarboxylase, and polyamines. Azin1 mRNA expression increased in the SON and PVN as a consequence of dehydration, salt loading, and acute hypertonic stress. In organotypic hypothalamic cultures, addition of the irreversible ornithine decarboxylase inhibitor DL-2-(difluoromethyl)-ornithine hydrochloride significantly increased the abundance of heteronuclear AVP but not heteronuclear oxytocin. To identify the function of Azin1 in vivo, lentiviral vectors that either overexpress or knock down Azin1 were stereotaxically delivered into the SON and/or PVN. Azin1 short hairpin RNA delivery resulted in decreased plasma osmolality and had a significant effect on food intake. The expression of AVP mRNA was also significantly increased in the SON by Azin1 short hairpin RNA. In contrast, Azin1 overexpression in the SON decreased AVP mRNA expression. We have therefore identified AZIN1, and hence by inference, polyamines as novel regulators of the expression of the AVP gene.

Matched MeSH terms: Gene Expression Profiling
Fulltext Curcumin rescues Caenorhabditis elegans from a Burkholderia pseudomallei infection

Eng SA, Nathan S

Front Microbiol, 2015;6:290.
PMID: 25914690 DOI: 10.3389/fmicb.2015.00290

The tropical pathogen Burkholderia pseudomallei requires long-term parenteral antimicrobial treatment to eradicate the pathogen from an infected patient. However, the development of antibiotic resistance is emerging as a threat to this form of treatment. To meet the need for alternative therapeutics, we proposed a screen of natural products for compounds that do not kill the pathogen, but in turn, abrogate bacterial virulence. We suggest that the use of molecules or compounds that are non-bactericidal (bacteriostatic) will reduce or abolish the development of resistance by the pathogen. In this study, we adopted the established Caenorhabditis elegans-B. pseudomallei infection model to screen a collection of natural products for any that are able to extend the survival of B. pseudomallei infected worms. Of the 42 natural products screened, only curcumin significantly improved worm survival following infection whilst not affecting bacterial growth. This suggested that curcumin promoted B. pseudomallei-infected worm survival independent of pathogen killing. To validate that the protective effect of curcumin was directed toward the pathogen, bacteria were treated with curcumin prior to infection. Worms fed with curcumin-treated bacteria survived with a significantly extended mean-time-to-death (p < 0.0001) compared to the untreated control. In in vitro assays, curcumin reduced the activity of known virulence factors (lipase and protease) and biofilm formation. To determine if other bacterial genes were also regulated in the presence of curcumin, a genome-wide transcriptome analysis was performed on curcumin-treated pathogen. A number of genes involved in iron acquisition and transport as well as genes encoding hypothetical proteins were induced in the presence of curcumin. Thus, we propose that curcumin may attenuate B. pseudomallei by modulating the expression of a number of bacterial proteins including lipase and protease as well as biofilm formation whilst concomitantly regulating iron transport and other proteins of unknown function.

Matched MeSH terms: Gene Expression Profiling
Identification of immune response-related genes and signalling pathways in spleen of Vibrio parahaemolyticus-infected Epinephelus fuscoguttatus (Forskal) by next-generation sequencing

Low CF, Mariana NS, Maha A, Chee HY, Fatimah MY

J Fish Dis, 2016 Mar;39(3):389-94.
PMID: 25786532 DOI: 10.1111/jfd.12359
Matched MeSH terms: Gene Expression Profiling
Kernel-specific cDNA clones encoding three different isoforms of seed storage protein glutelin from oil palm Elaeis guineensis

Cha TS, Habib Shah F

Plant Sci, 2001 Apr;160(5):913-923.
PMID: 11297788

The mRNA differential display method was used to identify and isolate cDNAs corresponding to transcripts that accumulate during the period of lipid synthesis, 12-20 weeks after anthesis (WAA) in the kernel of Elaeis guineensis, var. Tenera. We successfully isolated two cDNA clones, KT7 (312 bp) and KT8 (266 bp). Interestingly, both clones show 79% nucleotide sequence identity to each other. This suggests that both clones encode the isoforms of the same protein. We screened the kernel (15 WAA) cDNA library and isolated the clone pKT7 (587 bp) using KT7 as probe, and isolated another isoform with KT8 probe, which designated as pKT9 (900 bp). Clone pKT9 has 93% nucleotide identity to KT8 and only 46% to pKT7 in their 3'-untranslated region. All three clones displayed significant amino acid sequence identity to seed storage protein glutelin from monocotyledon and globulin from dicotyledon plants. The coding sequence of KT8 (106 bp) shows 76 and 97% identity to pKT9 and pKT7, respectively. Therefore, we suggest that clones KT8 and pKT7 are members of the same subfamily (A), while pKT9 belongs to another subfamily (B) of glutelin multigene families. Southern analysis shows that there are at least four members for the subfamily B. Northern analysis shows that these three members of the glutelin family are co-ordinately expressed and developmentally regulated during the development of the kernel. The transcripts begin to accumulate at 12 WAA, increase in 15 WAA and show a significant reduction at 17 WAA.

Matched MeSH terms: Gene Expression Profiling
Fulltext Transcriptomic analysis of resistant and susceptible banana corms in response to infection by Fusarium oxysporum f. sp. cubense tropical race 4

Zhang L, Cenci A, Rouard M, Zhang D, Wang Y, Tang W, et al.

Sci Rep, 2019 06 03;9(1):8199.
PMID: 31160634 DOI: 10.1038/s41598-019-44637-x

Fusarium wilt disease, caused by Fusarium oxysporum f. sp. cubense, especially by tropical race 4 (Foc TR4), is threatening the global banana industry. Musa acuminata Pahang, a wild diploid banana that displays strong resistance to Foc TR4, holds great potential to understand the underlying resistance mechanisms. Microscopic examination reports that, in a wounding inoculation system, the Foc TR4 infection processes in roots of Pahang (resistant) and a triploid cultivar Brazilian (susceptible) were similar by 7 days post inoculation (dpi), but significant differences were observed in corms of both genotypes at 14 dpi. We compare transcriptomic responses in the corms of Pahang and Brazilian, and show that Pahang exhibited constitutive defense responses before Foc TR4 infection and inducible defense responses prior to Brazilian at the initial Foc TR4 infection stage. Most key enzymatic genes in the phenylalanine metabolism pathway were up-regulated in Brazilian, suggesting that lignin and phytotoxin may be triggered during later stages of Foc TR4 infection. This study unravels a few potential resistance candidate genes whose expression patterns were assessed by RT-qPCR assay and improves our understanding the defense mechanisms of Pahang response to Foc TR4.

Matched MeSH terms: Gene Expression Profiling
Fulltext Comprehensive functional profiling of long non-coding RNAs through a novel pan-cancer integration approach and modular analysis of their protein-coding gene association networks

Walters K, Sarsenov R, Too WS, Hare RK, Paterson IC, Lambert DW, et al.

BMC Genomics, 2019 Jun 03;20(1):454.
PMID: 31159744 DOI: 10.1186/s12864-019-5850-7

BACKGROUND: Long non-coding RNAs (lncRNAs) are emerging as crucial regulators of cellular processes in diseases such as cancer, although the functions of most remain poorly understood. To address this, here we apply a novel strategy to integrate gene expression profiles across 32 cancer types, and cluster human lncRNAs based on their pan-cancer protein-coding gene associations. By doing so, we derive 16 lncRNA modules whose unique properties allow simultaneous inference of function, disease specificity and regulation for over 800 lncRNAs.
RESULTS: Remarkably, modules could be grouped into just four functional themes: transcription regulation, immunological, extracellular, and neurological, with module generation frequently driven by lncRNA tissue specificity. Notably, three modules associated with the extracellular matrix represented potential networks of lncRNAs regulating key events in tumour progression. These included a tumour-specific signature of 33 lncRNAs that may play a role in inducing epithelial-mesenchymal transition through modulation of TGFβ signalling, and two stromal-specific modules comprising 26 lncRNAs linked to a tumour suppressive microenvironment and 12 lncRNAs related to cancer-associated fibroblasts. One member of the 12-lncRNA signature was experimentally supported by siRNA knockdown, which resulted in attenuated differentiation of quiescent fibroblasts to a cancer-associated phenotype.
CONCLUSIONS: Overall, the study provides a unique pan-cancer perspective on the lncRNA functional landscape, acting as a global source of novel hypotheses on lncRNA contribution to tumour progression.

Matched MeSH terms: Gene Expression Profiling
Fulltext A systems biology approach towards the identification of candidate therapeutic genes and potential biomarkers for Parkinson's disease

Sakharkar MK, Kashmir Singh SK, Rajamanickam K, Mohamed Essa M, Yang J, Chidambaram SB

PLoS One, 2019;14(9):e0220995.
PMID: 31487305 DOI: 10.1371/journal.pone.0220995

Parkinson's disease (PD) is an irreversible and incurable multigenic neurodegenerative disorder. It involves progressive loss of mid brain dopaminergic neurons in the substantia nigra pars compacta (SN). We compared brain gene expression profiles with those from the peripheral blood cells of a separate sample of PD patients to identify disease-associated genes. Here, we demonstrate the use of gene expression profiling of brain and blood for detecting valid targets and identifying early PD biomarkers. Implementing this systematic approach, we discovered putative PD risk genes in brain, delineated biological processes and molecular functions that may be particularly disrupted in PD and also identified several putative PD biomarkers in blood. 20 of the differentially expressed genes in SN were also found to be differentially expressed in the blood. Further application of this methodology to other brain regions and neurological disorders should facilitate the discovery of highly reliable and reproducible candidate risk genes and biomarkers for PD. The identification of valid peripheral biomarkers for PD may ultimately facilitate early identification, intervention, and prevention efforts as well.

Matched MeSH terms: Gene Expression Profiling
Changes of alternative splicing in Arabidopsis thaliana grown under different CO2 concentrations

Huang W, Chen X, Guan Q, Zhong Z, Ma J, Yang B, et al.

Gene, 2019 Mar 20;689:43-50.
PMID: 30528270 DOI: 10.1016/j.gene.2018.11.083

Atmospheric CO2 level is one of the most important factors which affect plant growth and crop production. Although many crucial genes and pathways have been identified in response to atmospheric CO2 changes, the integrated and precise mechanisms of plant CO2 response are not well understood. Alternative splicing (AS) is an important gene regulation process that affects many biological processes in plants. However, the AS pattern changes in plants in response to elevated CO2 levels have not yet been investigated. Here, we used RNA-Seq data of Arabidopsis thaliana grown under different CO2 concentration to analyze the global changes in AS. We found that AS increased with the rise in CO2 concentration. Additionally, we identified 345 differentially expressed (DE) genes and 251 differentially alternative splicing (DAS) genes under the elevated CO2 condition. Moreover, the results showed that the expression of most of the DAS genes did not change significantly, indicating that AS can serve as an independent mechanism for gene regulation in response to elevated CO2. Furthermore, our analysis of function categories revealed that the DAS genes were associated mainly with the stimulus response. Overall, this the first study to explore the changes of AS in plants in response to elevated CO2.

Matched MeSH terms: Gene Expression Profiling
Fruit characteristics, soluble sugar compositions and transcriptome analysis during the development of Citrus maxima "seedless", and identification of SUS and INV genes involved in sucrose degradation

Deng S, Mai Y, Niu J

Gene, 2019 Mar 20;689:131-140.
PMID: 30576805 DOI: 10.1016/j.gene.2018.12.016

Citrus maxima "seedless" is originally from Malaysia, and now is widely cultivated in Hainan province, China. The essential features of this cultivar are thin skin, green epicarp and seedless at the ripening stage. Here, using C. maxima "seedless" as experimental material, we investigated the physical and inclusion indicators, and found the accumulation of storage compounds during 120-210 DAF leading to inconsistent increase between volume and weight. Component analysis of soluble sugar indicated that arabinose and xylose have a high content in early development of pummelo juice sacs (PJS), whereas fructose, glucose and sucrose show a significant increase during PJS maturation. To clarify a global overview of the gene expressing profiles, the PJSs from four periods (60, 120, 180 and 240 DAF) were selected for comparative transcriptome analysis. The resulting 8275 unigenes showed differential expression during PJS development. Also, the stability of 11 housekeeping genes were evaluated by geNorm method, resulting in a set of five genes (UBC, ACT, OR23, DWA2 and CYP21D) used as control for normalization of gene expression. Based on transcriptome data, 5 sucrose synthases (SUSs) and 10 invertases (INVs) were identified to be involved in sucrose degradation. Importantly, SUS4 may be responsible for arabinose and xylose biosynthesis to form the cell wall in early development, while SUS3 and VIN2 may be important in the accumulation of soluble hexose leading to cell expansion through an osmotic-independent pathway in late development. The information provides valuable metabolite and genetic resources in C. maxima "seedless", and is important for achieving high fruit yield and quality.

Matched MeSH terms: Gene Expression Profiling
Fulltext Evaluation of female Aedes aegypti proteome via LC-ESI-MS/MS using two protein extraction methods

Shettima A, Ishak IH, Abdul Rais SH, Abu Hasan H, Othman N

PeerJ, 2021;9:e10863.
PMID: 33717682 DOI: 10.7717/peerj.10863

Background: Proteomic analyses have broadened the horizons of vector control measures by identifying proteins associated with different biological and physiological processes and give further insight into the mosquitoes' biology, mechanism of insecticide resistance and pathogens-mosquitoes interaction. Female Ae. aegypti ingests human blood to acquire the requisite nutrients to make eggs. During blood ingestion, female mosquitoes transmit different pathogens. Therefore, this study aimed to determine the best protein extraction method for mass spectrometry analysis which will allow a better proteome profiling for female mosquitoes.
Methods: In this present study, two protein extractions methods were performed to analyze female Ae. aegyti proteome, via TCA acetone precipitation extraction method and a commercial protein extraction reagent CytoBusterTM. Then, protein identification was performed by LC-ESI-MS/MS and followed by functional protein annotation analysis.
Results: The CytoBusterTM reagent gave the highest protein yield with a mean of 475.90 µg compared to TCA acetone precipitation extraction showed 283.15 µg mean of protein. LC-ESI-MS/MS identified 1,290 and 890 proteins from the CytoBusterTM reagent and TCA acetone precipitation, respectively. When comparing the protein class categories in both methods, there were three additional categories for proteins identified using CytoBusterTM reagent. The proteins were related to scaffold/adaptor protein (PC00226), protein binding activity modulator (PC00095) and intercellular signal molecule (PC00207). In conclusion, the CytoBusterTM protein extraction reagent showed a better performance for the extraction of proteins in term of the protein yield, proteome coverage and extraction speed.

Matched MeSH terms: Gene Expression Profiling
Insight into delivery of dermal fibroblast by non-biodegradable bacterial nanocellulose composite hydrogel on wound healing

Loh EYX, Fauzi MB, Ng MH, Ng PY, Ng SF, Mohd Amin MCI

Int J Biol Macromol, 2020 Sep 15;159:497-509.
PMID: 32387606 DOI: 10.1016/j.ijbiomac.2020.05.011

In skin tissue engineering, a biodegradable scaffold is usually used where cells grow, produce its own cytokines, growth factors, and extracellular matrix, until the regenerated tissue gradually replaces the scaffold upon its degradation. However, the role of non-biodegradable scaffold remains unexplored. This study investigates the potential of a non-biodegradable bacterial nanocellulose/acrylic acid (BNC/AA) hydrogel to transfer human dermal fibroblasts (HDF) to the wound and the resulting healing effects of transferred HDF in athymic mice. Results demonstrated that the fabricated hydrogel successfully transferred >50% of HDF onto the wound site within 24 h, with evidence of HDF detected on day 7. The gene and protein study unveiled faster wound healing in the hydrogel with HDF group and characterized more mature newly formed skin microstructure on day 7, despite no visible differences. These findings give a new perspective regarding the role of non-biodegradable materials in skin tissue engineering, in the presence of exogenous cells, mainly at the molecular level.

Matched MeSH terms: Gene Expression Profiling
Extracellular Vesicles Derived From Colorectal Cancer Affects CD8 T Cells: An Analysis Based on Body Mass Index

Abu N, Othman N, Ab Razak NS, Bakarurraini NAAR, Nasir SN, Soh JEC, et al.

Front Cell Dev Biol, 2020;8:564648.
PMID: 33324632 DOI: 10.3389/fcell.2020.564648

Colorectal cancer (CRC) is one of the most widely diagnosed cancers worldwide. It has been shown that the body-mass index (BMI) of the patients could influence the tumor microenvironment, treatment response, and overall survival rates. Nevertheless, the mechanism on how BMI affects the tumorigenesis process, particularly the tumor microenvironment is still elusive. Herein, we postulate that extracellular vesicles (EVs) from CRC patients and non-CRC volunteers with different BMI could affect immune cells differently, in CD8 T cells particularly. We isolated the EVs from the archived serum of CRC patients with high and low BMI, as well as healthy controls with similar BMI status. The EVs were further characterized via electron microscopy, western blot and dynamic light scattering. Then, functional analysis was performed on CD8 T cells including apoptosis, cell proliferation, gene expression profiling and cytokine release upon co-incubation with the different EVs. Our results suggest that CRC-derived EVs were able to regulate the CD8 T cells. In some assays, low BMI EVs were functionally different than high BMI EVs. This study highlights the possible difference in the regulatory mechanism of cancer patients-derived EVs, especially on CD8 T cells.

Matched MeSH terms: Gene Expression Profiling

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