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Article ; Online: Computational workflow for investigating highly variable genes in single-cell RNA-seq across multiple time points and cell types

Jantarika Kumar Arora / Anunya Opasawatchai / Sarah A. Teichmann / Ponpan Matangkasombut / Varodom Charoensawan

STAR Protocols, Vol 4, Iss 3, Pp 102387- (2023)

2023

Abstract: Summary: Here, we present a computational approach for investigating highly variable genes (HVGs) associated with biological pathways of interest, across multiple time points and cell types in single-cell RNA-sequencing (scRNA-seq) data. Using public ... ...

Abstract	Summary: Here, we present a computational approach for investigating highly variable genes (HVGs) associated with biological pathways of interest, across multiple time points and cell types in single-cell RNA-sequencing (scRNA-seq) data. Using public dengue virus and COVID-19 datasets, we describe steps for using the framework to characterize the dynamic expression levels of HVGs related to common and cell-type-specific biological pathways over multiple immune cell types.For complete details on the use and execution of this protocol, please refer to Arora et al.1 : Publisher’s note: Undertaking any experimental protocol requires adherence to local institutional guidelines for laboratory safety and ethics.
Keywords	Bioinformatics ; Single Cell ; RNAseq ; Immunology ; Gene Expression ; Systems Biology ; Science (General) ; Q1-390
Language	English
Publishing date	2023-09-01T00:00:00Z
Publisher	Elsevier
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Genome Characterization and Comparison of Early Mortality Syndrome Causing Vibrio parahaemolyticus pirABvp− Mutant From Thailand With V. parahaemolyticus pirABvp+ AHPND Isolates

Nalumon Thadtapong / Marvin Bryan Segundo Salinas / Varodom Charoensawan / Vanvimon Saksmerprome / Soraya Chaturongakul

Frontiers in Marine Science, Vol

2020 Volume 7

Keywords	Vibrio parahaemolyticus ; non-acute hepatopancreatic necrosis disease ; early mortality syndrome ; shrimp disease ; comparative genomics ; Science ; Q ; General. Including nature conservation ; geographical distribution ; QH1-199.5
Language	English
Publishing date	2020-04-01T00:00:00Z
Publisher	Frontiers Media S.A.
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Antisense Oligonucleotide Induction of the hnRNPA1b Isoform Affects Pre-mRNA Splicing of SMN2 in SMA Type I Fibroblasts

Jarichad Toosaranont / Sukanya Ruschadaariyachat / Warasinee Mujchariyakul / Jantarika Kumar Arora / Varodom Charoensawan / Bhoom Suktitipat / Thomas N. Palmer / Sue Fletcher / Steve D. Wilton / Chalermchai Mitrpant

International Journal of Molecular Sciences, Vol 23, Iss 3937, p

2022 Volume 3937

Abstract: Spinal muscular atrophy (SMA) is a severe, debilitating neuromuscular condition characterised by loss of motor neurons and progressive muscle wasting. SMA is caused by a loss of expression of SMN1 that encodes the survival motor neuron (SMN) protein ... ...

Abstract	Spinal muscular atrophy (SMA) is a severe, debilitating neuromuscular condition characterised by loss of motor neurons and progressive muscle wasting. SMA is caused by a loss of expression of SMN1 that encodes the survival motor neuron (SMN) protein necessary for the survival of motor neurons. Restoration of SMN expression through increased inclusion of SMN2 exon 7 is known to ameliorate symptoms in SMA patients. As a consequence, regulation of pre-mRNA splicing of SMN2 could provide a potential molecular therapy for SMA. In this study, we explored if splice switching antisense oligonucleotides could redirect the splicing repressor hnRNPA1 to the hnRNPA1b isoform and restore SMN expression in fibroblasts from a type I SMA patient. Antisense oligonucleotides (AOs) were designed to promote exon 7b retention in the mature mRNA and induce the hnRNPA1b isoform. RT-PCR and western blot analysis were used to assess and monitor the efficiency of different AO combinations. A combination of AOs targeting multiple silencing motifs in hnRNPA1 pre-mRNA led to robust hnRNPA1b induction, which, in turn, significantly increased expression of full-length SMN (FL-SMN) protein. A combination of PMOs targeting the same motifs also strongly induced hnRNPA1b isoform, but surprisingly SMN2 exon 5 skipping was detected, and the PMO cocktail did not lead to a significant increase in expression of FL-SMN protein. We further performed RNA sequencing to assess the genome-wide effects of hnRNPA1b induction. Some 3244 genes were differentially expressed between the hnRNPA1b-induced and untreated SMA fibroblasts, which are functionally enriched in cell cycle and chromosome segregation processes. RT-PCR analysis demonstrated that expression of the master regulator of these enrichment pathways, MYBL2 and FOXM1B, were reduced in response to PMO treatment. These findings suggested that induction of hnRNPA1b can promote SMN protein expression, but not at sufficient levels to be clinically relevant.
Keywords	spinal muscular atrophy ; hnRNPA1 ; antisense oligonucleotide ; phosphorodiamidate morpholino oligomer ; transcriptome ; Biology (General) ; QH301-705.5 ; Chemistry ; QD1-999
Subject code	570
Language	English
Publishing date	2022-04-01T00:00:00Z
Publisher	MDPI AG
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Single-cell temporal analysis of natural dengue infection reveals skin-homing lymphocyte expansion one day before defervescence

Jantarika Kumar Arora / Anunya Opasawatchai / Tiraput Poonpanichakul / Natnicha Jiravejchakul / Waradon Sungnak / Oranart Matangkasombut / Sarah A. Teichmann / Ponpan Matangkasombut / Varodom Charoensawan / Anavaj Sakuntabhai / Pratap Singhasivanon / Swangjit Suraamornkul / Tawatchai Yingtaweesak / Khajohnpong Manopwisedjaroen / Nada Pitabut

iScience, Vol 25, Iss 4, Pp 104034- (2022)

2022

Abstract: Summary: Effective clinical management of acute dengue virus (DENV) infection relies on the timing of suitable treatments during the disease progression. We analyzed single-cell transcriptomic profiles of the peripheral blood mononuclear cell samples ... ...

Abstract	Summary: Effective clinical management of acute dengue virus (DENV) infection relies on the timing of suitable treatments during the disease progression. We analyzed single-cell transcriptomic profiles of the peripheral blood mononuclear cell samples from two DENV patients, collected daily during acute phase and also at convalescence. Key immune cell types demonstrated different dynamic responses over the course of the infection. On the day before defervescence (Day −1), we observed the peak expression of several prominent genes in the adaptive immunological pathways. We also characterized unique effector T cell clusters that expressed skin-homing signature genes at Day −1, whereas upregulation of skin and gut homing genes was also observed in plasma cells and plasmablasts during the febrile period. This work provides an overview of unique molecular dynamics that signify the entry of the critical phase, and the findings could improve the patient management of DENV infection.
Keywords	Single-cell Omics ; Systems biology ; Immunology ; Science ; Q
Language	English
Publishing date	2022-04-01T00:00:00Z
Publisher	Elsevier
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Emergence of Intrahepatic Cholangiocarcinoma

Meng-Shin Shiao / Khajeelak Chiablaem / Varodom Charoensawan / Nuttapong Ngamphaiboon / Natini Jinawath

Frontiers in Genetics, Vol

How High-Throughput Technologies Expedite the Solutions for a Rare Cancer Type

2018 Volume 9

Abstract: Intrahepatic cholangiocarcinoma (ICC) is the cancer of the intrahepatic bile ducts, and together with hepatocellular carcinoma (HCC), constitute the majority of primary liver cancers. ICC is a rare disorder as its overall incidence is < 1/100,000 in the ... ...

Abstract	Intrahepatic cholangiocarcinoma (ICC) is the cancer of the intrahepatic bile ducts, and together with hepatocellular carcinoma (HCC), constitute the majority of primary liver cancers. ICC is a rare disorder as its overall incidence is < 1/100,000 in the United States and Europe. However, it shows much higher incidence in particular geographical regions, such as northeastern Thailand, where liver fluke infection is the most common risk factor of ICC. Since the early stages of ICC are often asymptomatic, the patients are usually diagnosed at advanced stages with no effective treatments available, leading to the high mortality rate. In addition, unclear genetic mechanisms, heterogeneous nature, and various etiologies complicate the development of new efficient treatments. Recently, a number of studies have employed high-throughput approaches, including next-generation sequencing and mass spectrometry, in order to understand ICC in different biological aspects. In general, the majority of recurrent genetic alterations identified in ICC are enriched in known tumor suppressor genes and oncogenes, such as mutations in TP53, KRAS, BAP1, ARID1A, IDH1, IDH2, and novel FGFR2 fusion genes. Yet, there are no major driver genes with immediate clinical solutions characterized. Interestingly, recent studies utilized multi-omics data to classify ICC into two main subgroups, one with immune response genes as the main driving factor, while another is enriched with driver mutations in the genes associated with epigenetic regulations, such as IDH1 and IDH2. The two subgroups also show different hypermethylation patterns in the promoter regions. Additionally, the immune response induced by host-pathogen interactions, i.e., liver fluke infection, may further stimulate tumor growth through alterations of the tumor microenvironment. For in-depth functional studies, although many ICC cell lines have been globally established, these homogeneous cell lines may not fully explain the highly heterogeneous genetic contents of this disorder. ...
Keywords	intrahepatic cholangiocarcinoma ; high-throughput technology ; integrative multi-omics analysis ; molecular biomarker ; disease model ; translational medicine ; Genetics ; QH426-470
Subject code	610 ; 616
Language	English
Publishing date	2018-08-01T00:00:00Z
Publisher	Frontiers Media S.A.
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article: MicroRNAs and oncogenic transcriptional regulatory networks controlling metabolic reprogramming in cancers

Pinweha, Pannapa / Khanti Rattanapornsompong / Sarawut Jitrapakdee / Varodom Charoensawan

Computational and Structural Biotechnology Journal. 2016, v. 14

2016

Abstract: Altered cellular metabolism is a fundamental adaptation of cancer during rapid proliferation as a result of growth factor overstimulation. We review different pathways involving metabolic alterations in cancers including aerobic glycolysis, pentose ... ...

Abstract	Altered cellular metabolism is a fundamental adaptation of cancer during rapid proliferation as a result of growth factor overstimulation. We review different pathways involving metabolic alterations in cancers including aerobic glycolysis, pentose phosphate pathway, de novo fatty acid synthesis, and serine and glycine metabolism. Although oncoproteins, c-MYC, HIF1α and p53 are the major drivers of this metabolic reprogramming, post-transcriptional regulation by microRNAs (miR) also plays an important role in finely adjusting the requirement of the key metabolic enzymes underlying this metabolic reprogramming. We also combine the literature data on the miRNAs that potentially regulate 40 metabolic enzymes responsible for metabolic reprogramming in cancers, with additional miRs from computational prediction. Our analyses show that: (1) a metabolic enzyme is frequently regulated by multiple miRs, (2) confidence scores from prediction algorithms might be useful to help narrow down functional miR-mRNA interaction, which might be worth further experimental validation. By combining known and predicted interactions of oncogenic transcription factors (TFs) (c-MYC, HIF1α and p53), sterol regulatory element binding protein 1 (SREBP1), 40 metabolic enzymes, and regulatory miRs we have established one of the first reference maps for miRs and oncogenic TFs that regulate metabolic reprogramming in cancers. The combined network shows that glycolytic enzymes are linked to miRs via p53, c-MYC, HIF1α, whereas the genes in serine, glycine and one carbon metabolism are regulated via the c-MYC, as well as other regulatory organization that cannot be observed by investigating individual miRs, TFs, and target genes.
Keywords	algorithms ; binding proteins ; biotechnology ; carbon metabolism ; enzymes ; fatty acids ; genes ; glycolysis ; microRNA ; neoplasms ; oncogene proteins ; pentose phosphate cycle ; prediction ; serine ; sterols ; transcription (genetics) ; transcription factors
Language	English
Size	p. 223-233.
Publishing place	Elsevier B.V.
Document type	Article
ISSN	2001-0370
DOI	10.1016/j.csbj.2016.05.005
Database	NAL-Catalogue (AGRICOLA)

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Article: Gene expression and promoter characterization of heat-shock protein 90B gene (HSP90B) in the model unicellular green alga Chlamydomonas reinhardtii

Traewachiwiphak, Somchoke / Chotika Yokthongwattana / Kittisak Yokthongwattana / Parthompong Ves-Urai / Varodom Charoensawan

Plant science. 2018 July, v. 272

2018

Abstract: Molecular chaperones or heat shock proteins are a large protein family with important functions in every cellular organism. Among all types of the heat shock proteins, information on the ER-localized HSP90 protein (HSP90B) and its encoding gene is ... ...

Abstract	Molecular chaperones or heat shock proteins are a large protein family with important functions in every cellular organism. Among all types of the heat shock proteins, information on the ER-localized HSP90 protein (HSP90B) and its encoding gene is relatively scarce in the literature, especially in photosynthetic organisms. In this study, expression profiles as well as promoter sequence of the HSP90B gene were investigated in the model green alga Chlamydomonas reinhardtii. We have found that HSP90B is strongly induced by heat and ER stresses, while other short-term exposure to abiotic stresses, such as salinity, dark-to-light transition or light stress does not appear to affect the expression. Promoter truncation analysis as well as chromatin immunoprecipitation using the antibodies recognizing histone H3 and acetylated histone H3, revealed a putative core constitutive promoter sequence between −1 to −253 bp from the transcription start site. Our results also suggested that the nucleotides upstream of the core promoter may contain repressive elements such as putative repressor binding site(s).
Keywords	abiotic stress ; acute exposure ; antibodies ; autotrophs ; binding sites ; Chlamydomonas reinhardtii ; chromatin ; gene expression ; heat ; heat shock proteins ; histones ; models ; nucleotides ; precipitin tests ; promoter regions ; salinity ; transcription initiation site
Language	English
Dates of publication	2018-07
Size	p. 107-116.
Publishing place	Elsevier B.V.
Document type	Article
ZDB-ID	742010-9
ISSN	1873-2259 ; 0168-9452
ISSN (online)	1873-2259
ISSN	0168-9452
DOI	10.1016/j.plantsci.2018.04.010
Database	NAL-Catalogue (AGRICOLA)

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Article ; Online: Bridging the gap between clinicians and systems biologists

Natini Jinawath / Sacarin Bunbanjerdsuk / Maneerat Chayanupatkul / Nuttapong Ngamphaiboon / Nithi Asavapanumas / Jisnuson Svasti / Varodom Charoensawan

Journal of Translational Medicine, Vol 14, Iss 1, Pp 1-

from network biology to translational biomedical research

2016 Volume 13

Abstract: Abstract With the wealth of data accumulated from completely sequenced genomes and other high-throughput experiments, global studies of biological systems, by simultaneously investigating multiple biological entities (e.g. genes, transcripts, proteins), ... ...

Abstract	Abstract With the wealth of data accumulated from completely sequenced genomes and other high-throughput experiments, global studies of biological systems, by simultaneously investigating multiple biological entities (e.g. genes, transcripts, proteins), has become a routine. Network representation is frequently used to capture the presence of these molecules as well as their relationship. Network biology has been widely used in molecular biology and genetics, where several network properties have been shown to be functionally important. Here, we discuss how such methodology can be useful to translational biomedical research, where scientists traditionally focus on one or a small set of genes, diseases, and drug candidates at any one time. We first give an overview of network representation frequently used in biology: what nodes and edges represent, and review its application in preclinical research to date. Using cancer as an example, we review how network biology can facilitate system-wide approaches to identify targeted small molecule inhibitors. These types of inhibitors have the potential to be more specific, resulting in high efficacy treatments with less side effects, compared to the conventional treatments such as chemotherapy. Global analysis may provide better insight into the overall picture of human diseases, as well as identify previously overlooked problems, leading to rapid advances in medicine. From the clinicians’ point of view, it is necessary to bridge the gap between theoretical network biology and practical biomedical research, in order to improve the diagnosis, prevention, and treatment of the world’s major diseases.
Keywords	Network biology ; Systems biology ; Biomedical research ; Cancers ; Personalized therapy ; Medicine ; R
Subject code	006
Language	English
Publishing date	2016-11-01T00:00:00Z
Publisher	BMC
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article: Dysregulated microRNA expression profiles in cholangiocarcinoma cell-derived exosomes

Kitdumrongthum, Sarunya / Chanatip Metheetrairut / Varodom Charoensawan / Puey Ounjai / Keatdamrong Janpipatkul / Wittaya Panvongsa / Jittima Weerachayaphorn / Pawinee Piyachaturawat / Arthit Chairoungdua

Life sciences. 2018 Oct. 01, v. 210

2018

Abstract: Cholangiocarcinoma (CCA) is a malignant tumor of bile duct epithelial cells. The prognosis of CCA is poor due to lack of effective therapeutic targets and detection at an advanced stage. Exosomes are secreted nano-sized vesicles and contribute to the ... ...

Abstract	Cholangiocarcinoma (CCA) is a malignant tumor of bile duct epithelial cells. The prognosis of CCA is poor due to lack of effective therapeutic targets and detection at an advanced stage. Exosomes are secreted nano-sized vesicles and contribute to the malignancy of several cancers via transferring their miRNAs between cells. Thus, exosomal miRNAs may serve as new therapeutic targets and potential biomarkers for CCA.Exosomes were isolated from three different CCA cell lines and normal human cholangiocyte cells, followed by miRNA profiling analysis. Potential role of dysregulated miRNA was investigated by knockdown experiment.We found that 38 and 460 miRNAs in CCA exosomes were significantly up- and down-regulated, respectively. Of these differentially expressed miRNAs, the hsa-miR-205-5p and miR-200 family members were markedly up-regulated for 600–1500 folds, whereas the miR-199 family members and their clustered miRNA, hsa-miR-214-3p, were down-regulated for 1000–2000 folds. The expression patterns of these representative exosomal miRNAs were similar to those observed in all types of CCA cells. The target genes of the top ten most up- and down-regulated miRNAs are significantly associated with well-characterized cancer-related pathways. Consistently, knockdown of the most up-regulated miRNA, miR-205-5p, reduced KKU-M213 cell invasion and migration.We have demonstrated the distinct miRNA signatures in exosomes released from CCA cells, compared to normal human cholangiocyte cells. These exosomal miRNAs may have the potential to be novel therapeutic targets and biomarkers for CCA.
Keywords	bile ducts ; biomarkers ; cell lines ; epithelial cells ; exosomes ; gene expression regulation ; humans ; microRNA ; neoplasms ; prognosis ; therapeutics
Language	English
Dates of publication	2018-1001
Size	p. 65-75.
Publishing place	Elsevier Inc.
Document type	Article
ZDB-ID	3378-9
ISSN	1879-0631 ; 0024-3205
ISSN (online)	1879-0631
ISSN	0024-3205
DOI	10.1016/j.lfs.2018.08.058
Database	NAL-Catalogue (AGRICOLA)

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Article ; Online: High-Throughput Screening for Biomarker Discovery

Tavan Janvilisri / Haruo Suzuki / Joy Scaria / Jenn-Wei Chen / Varodom Charoensawan

Disease Markers, Vol

2015 Volume 2015

Keywords	Medicine ; R ; Medicine (General) ; R5-920
Publishing date	2015-01-01T00:00:00Z
Publisher	Hindawi Publishing Corporation
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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