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  1. Han F, Gulam MY, Zheng Y, Zulhaimi NS, Sia WR, He D, et al.
    Front Immunol, 2022;13:985385.
    PMID: 36341446 DOI: 10.3389/fimmu.2022.985385
    MAIT cells are persistently depleted and functionally exhausted in HIV-1-infected patients despite long-term combination antiretroviral therapy (cART). IL-7 treatment supports MAIT cell reconstitution in vivo HIV-1-infected individuals and rescues their functionality in vitro. Single-nucleotide polymorphisms (SNPs) of the IL-7RA gene modulate the levels of soluble(s)IL-7Rα (sCD127) levels and influence bioavailability of circulating IL-7. Here we evaluate the potential influence of IL-7RA polymorphisms on MAIT cell numbers and function in healthy control (HC) subjects and HIV-1-infected individuals on long-term cART. Our findings indicate that IL-7RA haplotype 2 (H2*T), defined as T-allele carriers at the tagging SNP rs6897932, affects the size of the peripheral blood MAIT cell pool, as well as their production of cytokines and cytolytic effector proteins in response to bacterial stimulation. H2*T carriers had lower sIL-7Rα levels and higher MAIT cell frequency with enhanced functionality linked to higher expression of MAIT cell-associated transcription factors. Despite an average of 7 years on suppressive cART, MAIT cell levels and function in HIV-1-infected individuals were still significantly lower than those of HC. Notably, we observed a significant correlation between MAIT cell levels and cART duration only in HIV-1-infected individuals carrying IL-7RA haplotype 2. Interestingly, treatment with sIL-7Rα in vitro suppressed IL-7-dependent MAIT cell proliferation and function following cognate stimulations. These observations suggest that sIL-7Rα levels may influence MAIT cell numbers and function in vivo by limiting IL-7 bioavailability to MAIT cells. Collectively, these observations suggest that IL-7RA polymorphisms may play a significant role in MAIT cell biology and influence MAIT cells recovery in HIV-1 infection. The potential links between IL7RA polymorphisms, MAIT cell immunobiology, and HIV-1 infection warrant further studies going forward.
    Matched MeSH terms: Interleukin-7/genetics
  2. Sumarli A, Grismer LL, Wood PL, Ahmad AB, Rizal S, Ismail LH, et al.
    Zootaxa, 2016 Oct 02;4173(1):29-44.
    PMID: 27701201 DOI: 10.11646/zootaxa.4173.1.3
    Recently discovered populations of skinks of the genus Sphenomorphus from central Peninsular Malaysia represent a new species, S. sungaicolus sp. nov., and the first riparian skink known from Peninsular Malaysia. Morphological analyses of an earlier specimen reported as S. tersus from the Forest Research Institute of Malaysia (FRIM), Selangor indicate that it too is the new riparian species S. sungaicolus sp. nov. Additionally, two specimens from the Tembat Forest Reserve, Hulu Terengganu, Kelantan and another from Ulu Gombak, Selangor have been diagnosed as new the species. The latter specimen remained unidentified in the Bernice Pauahi Bishop Museum, Honolulu, Hawaii since its collection in June 1962. Morphological and molecular analyses demonstrate that S. sungaicolus sp. nov. forms a clade with the Indochinese species S. maculatus, S. indicus, and S. tersus and is the sister species of the latter. Sphenomorphus sungaicolus sp. nov. can be differentiated from all other members of this clade by having a smaller SVL (66.5-89.6 mm); 39-44 midbody scale rows; 72-81 paravertebral scales; 74-86 ventral scales; a primitive plantar scale arrangement; and 20-22 scale rows around the tail at the position of the 10th subcaudal.
    Matched MeSH terms: Lizards/genetics
  3. Khoo SP, Muhammad Ridzuan Tan NA, Rajasuriar R, Nasir NH, Gravitt P, Ng CW, et al.
    PLoS One, 2022;17(12):e0278477.
    PMID: 36538522 DOI: 10.1371/journal.pone.0278477
    To increase the coverage of HPV vaccination, Malaysia implemented a national school-based vaccination program for all 13-year-old girls in 2010. Two years later, a clinic-based catch-up program was started for 16 to 21-year-old girls. We assessed the prevalence of a range of HPV genotypes, among a sample of urban women within the age groups of 18-24 and 35-45 years in 2019-2020, a decade into the national vaccination program. The HPV prevalence was then compared to that reported in an unvaccinated population in 2013-2015. We sampled a total of 1134 participants, comprising of 277 women aged 18-24 years and 857 women aged 35-45 years, from several urban clinics in the state of Selangor. Participants provided a self-acquired vaginal sample for HPV genotyping. Comprehensive sociodemographic and vaccination history were collected. The HPV vaccination coverage among women in the younger age group increased from 9.3% in 2013-2015 to 75.5% in 2019-2020. The prevalence of vaccine-targeted HPV16/18 decreased 91% (CI: 14.5%-99.0%) among the younger women, from 4.0% in 2013-2015 to 0.4% in 2019-2020. There was also an 87% (CI: 27.5%-97.5%) reduction in HPV6/11/16/18. There was no difference in the prevalence of non-vaccine targeted HPV genotypes among younger women. The HPV prevalence among older women, for both vaccine targeted and non-vaccine targeted genotypes in 2019-2020, did not differ from 2013-2015. The observed decline in prevalence of vaccine-targeted HPV genotype among younger women a decade after the national HPV vaccination program is an early indication of its effectiveness in reducing the burden of cervical cancer.
    Matched MeSH terms: Papillomaviridae/genetics
  4. Vazifehmand R, Ali DS, Othman Z, Chau DM, Stanslas J, Shafa M, et al.
    J Neurovirol, 2022 Dec;28(4-6):566-582.
    PMID: 35951174 DOI: 10.1007/s13365-022-01089-w
    Glioblastoma multiforme is the most aggressive astrocytes brain tumor. Glioblastoma cancer stem cells and hypoxia conditions are well-known major obstacles in treatment. Studies have revealed that non-coding RNAs serve a critical role in glioblastoma progression, invasion, and resistance to chemo-radiotherapy. The present study examined the expression levels of microRNAs (in normoxic condition) and long non-coding RNAs (in normoxic and hypoxic conditions) in glioblastoma stem cells treated with the HSV-G47∆. The expression levels of 43 miRNAs and 8 lncRNAs isolated from U251-GBM-CSCs were analyzed using a miRCURY LNA custom PCR array and a quantitative PCR assay, respectively. The data revealed that out of 43 miRNAs that only were checked in normoxic condition, the only 8 miRNAs, including miR-7-1, miR-let-7b, miR-130a, miR-137, miR-200b, miR-221, miR-222, and miR-874, were markedly upregulated. The expression levels of lncRNAs, including LEF1 antisense RNA 1 (LEF1-AS1), metastasis-associated lung adenocarcinoma transcript 1 (MALAT1), long intergenic non-protein coding RNA 470 (LINC00470), tumor suppressor candidate 7 (TUSC7), HOX transcript antisense RNA (HOTAIR), nuclear paraspeckle assembly transcript 1 (NEAT1), and X inactive specific transcript (XIST), were markedly downregulated in the hypoxic microenvironment, and H19-imprinted maternally expressed transcript (H19) was not observed to be dysregulated in this environment. Under normoxic conditions, LEF1-AS1, MALAT1, LINC00470, H19, HOTAIR, NEAT1, and XIST were downregulated and TUSC7 was not targeted by HSV-G47∆. Overall, the present data shows HSVG47Δ treatment deregulates non-coding RNA expression in GBM-CSC tumor microenvironments.
    Matched MeSH terms: Tumor Microenvironment/genetics
  5. Qatrun Nada D, Masniza ML, Abdullah N, Marlini M, Elias MH, Pathmanathan SG, et al.
    Malays J Pathol, 2022 Dec;44(3):367-385.
    PMID: 36591707
    Breast cancer remains a significant cause of mortality in females worldwide, despite advances in technology and treatment. MicroRNA expression in breast cancer is studied both as potential biomarkers and for therapeutic purposes. Accumulated evidence revealed microRNA profile of various types of cancer cells following antineoplastic treatment. The progression of research in this area provides better understanding on the anti-cancer mechanism of various natural compounds and drugs specifically on the microRNA regulation. Hence, we aim to systematically review differentially expressed microRNA in MCF-7, a commonly studied breast cancer cell line, after treatment with anti-neoplastic agents. Relevant keywords were used to screen for research articles that reported on the differentially expressed microRNAs in experimental models of MCF-7 before and after anti-neoplastic treatment. Target genes of microRNAs were identified from MiRTarbase and further in silico functional analysis of the target genes were performed using DAVID bioinformatic resources. Two upregulated microRNAs (mir-200c and let-7d) and 3 downregulated microRNAs (mir-27a, mir-27b and mir-203) were identified by highest number of studies. Three microRNAs (let-7a, mir-23a and mir-7) showed inconsistent direction of expression. Genes functional analysis revealed the regulatory effect of microRNA on genes related to angiogenesis, hypoxia, P53, FoxO and PI3K-AKT signalling. Clusters of genes associated to the pathway of angiogenesis, cancers, cell proliferation and apoptosis were noted through protein-protein interaction analysis. MicroRNAs, especially the mir-200c, let-7d, mir-27a, mir-27b and mir-203 from this review could be further validated experimentally to serve as molecular target or biomarkers for anti-neoplastic therapy.
    Matched MeSH terms: Phosphatidylinositol 3-Kinases/genetics
  6. Mohd Rani F, Lean SS, A Rahman NI, Ismail S, Alattraqchi AG, Amonov M, et al.
    J Glob Antimicrob Resist, 2022 Dec;31:104-109.
    PMID: 36049733 DOI: 10.1016/j.jgar.2022.08.019
    OBJECTIVES: To analyse the genome sequences of four archival Acinetobacter nosocomialis clinical isolates (designated AC13, AC15, AC21 and AC25) obtained from Terengganu, Malaysia in 2011 to determine their genetic relatedness and basis of antimicrobial resistance.

    METHODS: Antimicrobial susceptibility profiles of the A. nosocomialis isolates were determined by disk diffusion. Genome sequencing was performed using the Illumina NextSeq platform.

    RESULTS: The four A. nosocomialis isolates were cefotaxime resistant whereas three isolates (namely, AC13, AC15 and AC25) were tetracycline resistant. The carriage of the blaADC-255-encoded cephalosporinase gene is likely responsible for cefotaxime resistance in all four isolates. Phylogenetic analysis indicated that the three tetracycline-resistant isolates were closely related, with an average nucleotide identity of 99.9%, suggestive of nosocomial spread, whereas AC21 had an average nucleotide identity of 97.9% when compared to these three isolates. The tetracycline-resistant isolates harboured two plasmids: a 13476 bp Rep3-family plasmid of the GR17 group designated pAC13-1, which encodes the tetA(39) tetracycline-resistance gene, and pAC13-2, a 4872 bp cryptic PriCT-1-family plasmid of a new Acinetobacter plasmid group, GR60. The tetA(39) gene was in a 2 001 bp fragment flanked by XerC/XerD recombination sites characteristic of a mobile pdif module. Both plasmids also harboured mobilisation/transfer-related genes.

    CONCLUSIONS: Genome sequencing of A. nosocomialis isolates led to the discovery of two novel plasmids, one of which encodes the tetA(39) tetracycline-resistant gene in a mobile pdif module. The high degree of genetic relatedness among the three tetracycline-resistant A. nosocomialis isolates is indicative of nosocomial transmission.

    Matched MeSH terms: Plasmids/genetics
  7. Subach OM, Vlaskina AV, Agapova YK, Korzhenevskiy DA, Nikolaeva AY, Varizhuk AM, et al.
    Int J Mol Sci, 2022 Nov 23;23(23).
    PMID: 36498942 DOI: 10.3390/ijms232314614
    NTnC-like green fluorescent genetically encoded calcium indicators (GECIs) with two calcium ion binding sites were constructed using the insertion of truncated troponin C (TnC) from Opsanus tau into green fluorescent proteins (GFPs). These GECIs are small proteins containing the N- and C-termini of GFP; they exert a limited effect on the cellular free calcium ion concentration; and in contrast to calmodulin-based calcium indicators they lack undesired interactions with intracellular proteins in neurons. The available TnC-based NTnC or YTnC GECIs had either an inverted response and high brightness but a limited dynamic range or a positive response and fast kinetics in neurons but lower brightness and an enhanced but still limited dF/F dynamic range. Here, we solved the crystal structure of NTnC at 2.5 Å resolution. Based on this structure, we developed positive NTnC2 and inverted iNTnC2 GECIs with a large dF/F dynamic range in vitro but very slow rise and decay kinetics in neurons. To overcome their slow responsiveness, we swapped TnC from O. tau in NTnC2 with truncated troponin C proteins from the muscles of fast animals, namely, the falcon, hummingbird, cheetah, bat, rattlesnake, and ant, and then optimized the resulting constructs using directed molecular evolution. Characterization of the engineered variants using purified proteins, mammalian cells, and neuronal cultures revealed cNTnC GECI with truncated TnC from Calypte anna (hummingbird) to have the largest dF/F fluorescence response and fast dissociation kinetics in neuronal cultures. In addition, based on the insertion of truncated TnCs from fast animals into YTnC2, we developed fYTnC2 GECI with TnC from Falco peregrinus (falcon). The purified proteins cNTnC and fYTnC2 had 8- and 6-fold higher molecular brightness and 7- and 6-fold larger dF/F responses to the increase in Ca2+ ion concentration than YTnC, respectively. cNTnC GECI was also 4-fold more photostable than YTnC and fYTnC2 GECIs. Finally, we assessed the developed GECIs in primary mouse neuronal cultures stimulated with an external electric field; in these conditions, cNTnC had a 2.4-fold higher dF/F fluorescence response than YTnC and fYTnC2 and was the same or slightly slower (1.4-fold) than fYTnC2 and YTnC in the rise and decay half-times, respectively.
    Matched MeSH terms: Green Fluorescent Proteins/genetics
  8. Ferdaos N, Lowell S, Mason JO
    PLoS One, 2022;17(11):e0278147.
    PMID: 36441708 DOI: 10.1371/journal.pone.0278147
    Cerebral organoids show great promise as tools to unravel the complex mechanisms by which the mammalian brain develops during embryogenesis. We generated mouse cerebral organoids harbouring constitutive or conditional mutations in Pax6, which encodes a transcription factor with multiple important roles in brain development. By comparing the phenotypes of mutant organoids with the well-described phenotypes of Pax6 mutant mouse embryos, we evaluated the extent to which cerebral organoids reproduce phenotypes previously described in vivo. Organoids lacking Pax6 showed multiple phenotypes associated with its activity in mice, including precocious neural differentiation, altered cell cycle and an increase in abventricular mitoses. Neural progenitors in both Pax6 mutant and wild type control organoids cycled more slowly than their in vivo counterparts, but nonetheless we were able to identify clear changes to cell cycle attributable to the absence of Pax6. Our findings support the value of cerebral organoids as tools to explore mechanisms of brain development, complementing the use of mouse models.
    Matched MeSH terms: PAX6 Transcription Factor/genetics
  9. Chin KL, Teoh BT, Sam SS, Loong SK, Tan KK, Azizan NS, et al.
    Trop Biomed, 2022 Dec 01;39(4):518-523.
    PMID: 36602210 DOI: 10.47665/tb.39.4.005
    Zika virus (ZIKV) infection has emerged as a global health concern following epidemic outbreaks of severe neurological disorders reported in Pacific and Americas since 2016. Therefore, a rapid, sensitive and specific diagnostic test for ZIKV infection is critical for the appropriate patient management and the control of disease spread. A TaqMan minor groove binding (MGB) probe-based quantitative reverse transcription-polymerase chain reaction (qRT-PCR) assay was developed based on the conserved sequence regions of 463 ZIKV NS2B genes. The designed ZIKV qRT-PCR assay was evaluated for its detection limit, strain coverage and cross-reactivity. We further assessed the clinical applicability of qRT-PCR assay for ZIKV RNA detection using a total 18 simulated clinical specimens. The detection limit of the qRT-PCR assay was 11.276 ZIKV RNA copies at the 95% probability level (probit analysis, p<= 0.05). Both Asian and African ZIKV strains were detected by the qRT-PCR assay without cross-reacting with DENV-1, DENV-2, DENV-3, DENV-4, CHIKV, JEV, LGTV, GETV and SINV. The qRT-PCR assay demonstrated a perfect agreement (k = 1.000, P < 0.001) with the reference assay; the sensitivity and specificity of the qRT-PCR assay were 100% (95% CI= 79.6-100) and 100% (95% CI= 43.9-100) respectively. The qRT-PCR assay developed in this study is a useful diagnostic tool for the broad coverage detection and quantification of both the Asian and African ZIKV strains.
    Matched MeSH terms: RNA, Viral/genetics
  10. Sharudin NA, Murtadha Noor Din AH, Azahar II, Mohd Azlan M, Yaacob NS, Sarmiento ME, et al.
    Asian Pac J Cancer Prev, 2022 Sep 01;23(9):2953-2964.
    PMID: 36172657 DOI: 10.31557/APJCP.2022.23.9.2953
    BACKGROUND: Detectable neonatal Nav1.5 (nNav1.5) expression in tumour breast tissue positive for lymph node metastasis and triple-negative subtype serves as a valid tumour-associated antigen to target and prevent breast cancer invasion and metastasis. Therapeutic antibodies against tumour antigens have become the predominant class of new drugs in cancer therapy because of their fewer adverse effects and high specificity.

    OBJECTIVE: This study was designed to investigate the therapeutic and anti-metastatic potential of the two newly obtained anti-nNav1.5 antibodies, polyclonal anti-nNav1.5 (pAb-nNav1.5) and monoclonal anti-nNav1.5 (mAb-nNav1.5), on breast cancer invasion and metastasis.

    METHODS: MDA-MB-231 and 4T1 cells were used as in vitro models to study the effect of pAb-nNav1.5 (59.2 µg/ml) and mAb-nNav1.5 (10 µg/ml) (24 hours treatment) on cell invasion. 4T1-induced mammary tumours in BALB/c female mice were used as an in vivo model to study the effect of a single dose of intravenous pAb-nNav1.5 (1 mg/ml) and mAb-nNav1.5 (1 mg/ml) on the occurrence of metastasis. Real-time PCR and immunofluorescence staining were conducted to assess the effect of antibody treatment on nNav1.5 mRNA and protein expression, respectively. The animals' body weight, organs, lesions, and tumour mass were also measured and compared.

    RESULTS: pAb-nNav1.5 and mAb-nNav1.5 treatments effectively suppressed the invasion of MDA-MB-231 and 4T1 cells in the 3D spheroid invasion assay. Both antibodies significantly reduced nNav1.5 gene and protein expression in these cell lines. Treatment with pAb-nNav1.5 and mAb-nNav1.5 successfully reduced mammary tumour tissue size and mass and prevented lesions in vital organs of the mammary tumour animal model whilst maintaining the animal's healthy weight. mRNA expression of nNav1.5 in mammary tumour tissues was only reduced by mAb-nNav1.5.

    CONCLUSION: Overall, this work verifies the uniqueness of targeting nNav1.5 in breast cancer invasion and metastasis prevention, but more importantly, humanised versions of mAb-nNav1.5 may be valuable passive immunotherapeutic agents to target nNav1.5 in breast cancer.

    Matched MeSH terms: RNA, Messenger/genetics
  11. Zhang S, Chong LH, Woon JYX, Chua TX, Cheruba E, Yip AK, et al.
    Commun Biol, 2023 Jan 18;6(1):62.
    PMID: 36653484 DOI: 10.1038/s42003-023-04421-0
    Biochemical signaling and mechano-transduction are both critical in regulating stem cell fate. How crosstalk between mechanical and biochemical cues influences embryonic development, however, is not extensively investigated. Using a comparative study of focal adhesion constituents between mouse embryonic stem cell (mESC) and their differentiated counterparts, we find while zyxin is lowly expressed in mESCs, its levels increase dramatically during early differentiation. Interestingly, overexpression of zyxin in mESCs suppresses Oct4 and Nanog. Using an integrative biochemical and biophysical approach, we demonstrate involvement of zyxin in regulating pluripotency through actin stress fibres and focal adhesions which are known to modulate cellular traction stress and facilitate substrate rigidity-sensing. YAP signaling is identified as an important biochemical effector of zyxin-induced mechanotransduction. These results provide insights into the role of zyxin in the integration of mechanical and biochemical cues for the regulation of embryonic stem cell fate.
    Matched MeSH terms: Zyxin/genetics
  12. Al-Wrafy FA, Alariqi R, Noman EA, Al-Gheethi AA, Mutahar M
    Microbiol Res, 2023 Mar;268:127298.
    PMID: 36610273 DOI: 10.1016/j.micres.2022.127298
    Pseudomonas aeruginosa is mostly associated with persistent infections and antibiotic resistance as a result of several factors, biofilms one of them. Microorganisms within the polymicrobial biofilm (PMB) reveal various transcriptional profiles and affect each other which might influence their pathogenicity and antibiotic tolerance and subsequent worsening of the biofilm infection. P. aeruginosa within PMB exhibits various behaviours toward other microorganisms, which may enhance or repress the virulence of these microbes. Microbial neighbours, in turn, may affect P. aeruginosa's virulence either positively or negatively. Such interactions among microorganisms lead to emerging persistent and antibiotic-resistant infections. This review highlights the relationship between P. aeruginosa and its microbial neighbours within the PMB in an attempt to better understand the mechanisms of polymicrobial interaction and the correlation between increased exacerbations of infection and the P. aeruginosa-microbe interaction. Researching in the literature that was carried out in vitro either in co-cultures or in the models to simulate the environment at the site of infection suggested that the interplay between P. aeruginosa and other microorganisms is one main reason for the worsening of the infection and which in turn requires a treatment approach different from that followed with P. aeruginosa mono-infection.
    Matched MeSH terms: Pseudomonas aeruginosa/genetics
  13. Albela H, Leong KF
    Int J Dermatol, 2023 Jan;62(1):e27-e29.
    PMID: 35933655 DOI: 10.1111/ijd.16378
    Matched MeSH terms: ATP-Binding Cassette Transporters/genetics
  14. Ho PJ, Khng AJ, Tan BK, Tan EY, Tan SM, Tan VKM, et al.
    Breast Cancer, 2022 Sep;29(5):869-879.
    PMID: 35543923 DOI: 10.1007/s12282-022-01366-w
    BACKGROUND: Human leukocyte antigen (HLA) genes play critical roles in immune surveillance, an important defence against tumors. Imputing HLA genotypes from existing single-nucleotide polymorphism datasets is low-cost and efficient. We investigate the relevance of the major histocompatibility complex region in breast cancer susceptibility, using imputed class I and II HLA alleles, in 25,484 women of Asian ancestry.

    METHODS: A total of 12,901 breast cancer cases and 12,583 controls from 12 case-control studies were included in our pooled analysis. HLA imputation was performed using SNP2HLA on 10,886 quality-controlled variants within the 15-55 Mb region on chromosome 6. HLA alleles (n = 175) with info scores greater than 0.8 and frequencies greater than 0.01 were included (resolution at two-digit level: 71; four-digit level: 104). We studied the associations between HLA alleles and breast cancer risk using logistic regression, adjusting for population structure and age. Associations between HLA alleles and the risk of subtypes of breast cancer (ER-positive, ER-negative, HER2-positive, HER2-negative, early-stage, and late-stage) were examined.

    RESULTS: We did not observe associations between any HLA allele and breast cancer risk at P 

    Matched MeSH terms: Asian Continental Ancestry Group/genetics
  15. Tee KK, Chan PQ, Loh AM, Singh S, Teo CH, Iyadorai T, et al.
    J Med Virol, 2023 Feb;95(2):e28520.
    PMID: 36691929 DOI: 10.1002/jmv.28520
    Pteropine orthoreovirus (PRV), an emerging bat-borne virus, has been linked to cases of acute respiratory infections (ARI) in humans. The prevalence, epidemiology and genomic diversity of PRV among ARI of unknown origin were studied. Among 632 urban outpatients tested negative for all known respiratory viruses, 2.2% were PRV-positive. Patients mainly presented with moderate to severe forms of cough, sore throat and muscle ache, but rarely with fever. Phylogenetic analysis revealed that over 90% of patients infected with the Melaka virus (MelV)-like PRV, while one patient infected with the Pulau virus previously found only in fruit bats. Human oral keratinocytes and nasopharyngeal epithelial cells were susceptible to clinical isolates of PRV, including the newly isolated MelV-like 12MYKLU1034. Whole genome sequence of 12MYKLU1034 using Nanopore technique revealed a novel reassortant strain. Evolutionary analysis of the global PRV strains suggests the continuous evolution of PRV through genetic reassortment among PRV strains circulating in human, bats and non-human primate hosts, creating a spectrum of reassortant lineages with complex evolutionary characteristics. In summary, the role of PRV as a common etiologic agent of ARI is evident. Continuous monitoring of PRV prevalence, pathogenicity and diversity among human and animal hosts is important to trace the emergence of novel reassortants.
    Matched MeSH terms: RNA, Viral/genetics
  16. Liaqat Ali Khan N, Nafee T, Shao T, Hart AR, Elliott S, Ola B, et al.
    Int J Mol Sci, 2022 Dec 16;23(24).
    PMID: 36555686 DOI: 10.3390/ijms232416051
    Overlapping disease aetiologies associated with multiple altered biological processes have been identified that change the endometrial function leading to recurrent implantation failure (RIF) and recurrent early pregnancy loss (REPL). We aimed to provide a detailed insight into the nature of the biological malfunction and related pathways of differentially expressed genes in RIF and REPL. Endometrial biopsies were obtained from 9 women experiencing RIF, REPL and control groups. Affymetrix microarray analysis was performed to measure the gene expression level of the endometrial biopsies. Unsupervised clustering of endometrial samples shows scattered distribution of gene expression between the RIF, REPL and control groups. 2556 and 1174 genes (p value < 0.05, Fold change > 1.2) were significantly altered in the endometria of RIF and REPL patients’ group, respectively compared to the control group. Downregulation in Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways of the differentially expressed genes (DEGs) in RIF and REPL including ribosome and oxidative phosphorylation pathways. Gene Ontology (GO) analysis revealed ribosomes and mitochondria inner membrane as the most significantly downregulated cellular component (CC) affected in RIF and REPL. Determination of the dysregulated genes and related biological pathways in RIF and REPL will be key in understanding their molecular pathology and of major importance in addressing diagnosis, prognosis, and treatment issues
    Matched MeSH terms: Embryo Implantation/genetics
  17. Munisamy S, Radhakrishnan AK, Ramdas P, Samuel PJ, Singh VA
    Curr Oncol, 2022 Aug 05;29(8):5585-5603.
    PMID: 36005179 DOI: 10.3390/curroncol29080441
    The main role of the host immune system is to identify and eliminate cancer cells, which is a complex process, but it is not a fail-safe mechanism. Many sarcoma patients succumb to this disease despite treatments rendered. The aim of this pilot study was to compare the levels of CD4+ T-cells, T-regulatory (Treg) cells, and cytokines such as tumor necrosis factor-alpha (TNF-α), interferon-gamma (IFN-γ), interleukin-17A (IL-17A), and transforming growth factor-beta-1 (TGF-β1) in peripheral blood leukocytes of sarcoma patients and healthy controls. For gene expression studies, total ribonucleic acid (RNA) was extracted from peripheral blood leukocytes and genes that were differentially regulated in peripheral blood leukocytes of sarcoma patients compared with healthy controls were determined using a commercial T-helper cell differentiation quantitative polymerase chain reaction (qPCR) array. Flow cytometer analysis was performed on blood samples from 26 sarcoma patients and 10 healthy controls to identify the levels of CD4+ T-cells and T-reg cells. The level of cytokines in plasma and culture supernatant were quantified using commercial enzyme-linked immunosorbent assay (ELISA) kits. A marked reduction in the percentage of CD4+ T-cells (p = 0.037) and levels of TNF-α (p = 0.004) and IFN-γ (0.010) was observed in sarcoma patients. Gene expression analysis showed five genes (homeobox A10 (HOXA10), GATA binding protein 3 (GATA3), prostaglandin D2 receptor 2 (PTGDR2), thymocyte selection associated high mobility group box (TOX), and C-C motif chemokine receptor 3 (CCR3)) were dysregulated (p < 0.05) in sarcoma patients. This study suggests that T-helper-1 immune responses are reduced in sarcoma patients.
    Matched MeSH terms: Interferon-gamma/genetics
  18. Jalanka J, Gunn D, Singh G, Krishnasamy S, Lingaya M, Crispie F, et al.
    Gut, 2023 Mar;72(3):451-459.
    PMID: 36171082 DOI: 10.1136/gutjnl-2021-326828
    OBJECTIVES: Persistent bowel dysfunction following gastroenteritis (postinfectious (PI)-BD) is well recognised, but the associated changes in microbiota remain unclear. Our aim was to define these changes after gastroenteritis caused by a single organism, Campylobacter jejuni, examining the dynamic changes in the microbiota and the impact of antibiotics.

    DESIGN: A single-centre cohort study of 155 patients infected with Campylobacter jejuni. Features of the initial illness as well as current bowel symptoms and the intestinal microbiota composition were recorded soon after infection (visit 1, <40 days) as well as 40-60 days and >80 days later (visits 2 and 3). Microbiota were assessed using 16S rRNA sequencing.

    RESULTS: PI-BD was found in 22 of the 99 patients who completed the trial. The cases reported significantly looser stools, with more somatic and gastrointestinal symptoms. Microbiota were assessed in 22 cases who had significantly lower diversity and altered microbiota composition compared with the 44 age-matched and sex-matched controls. Moreover 60 days after infection, cases showed a significantly lower abundance of 23 taxa including phylum Firmicutes, particularly in the order Clostridiales and the family Ruminoccocaceae, increased Proteobacteria abundance and increased levels of Fusobacteria and Gammaproteobacteria. The microbiota changes were linked with diet; higher fibre consumption being associated with lower levels of Gammaproteobacteria.

    CONCLUSION: The microbiota of PI-BD patients appeared more disturbed by the initial infection compared with the microbiota of those who recovered. The prebiotic effect of high fibre diets may inhibit some of the disturbances seen in PI-BD.

    TRIAL REGISTRATION NUMBER: NCT02040922.

    Matched MeSH terms: RNA, Ribosomal, 16S/genetics
  19. Padmanabhan H, Mariapun S, Lee SY, Hassan NT, Lee DS, Meiser B, et al.
    J Genet Couns, 2023 Feb;32(1):43-56.
    PMID: 35913122 DOI: 10.1002/jgc4.1619
    Cascade testing for families with BRCA pathogenic variants is important to identify relatives who are carriers. These relatives can benefit from appropriate risk management and preventative strategies arising from an inherited increased risk of breast, ovarian, prostate, melanoma, and pancreatic cancers. Cascade testing has the potential to enable cost-effective cancer control even in low- and middle-income settings, but few studies have hitherto evaluated the psychosocial impact of cascade testing in an Asian population, where the cultural and religious beliefs around inheritance and destiny have previously been shown to influence perception and attitudes toward screening. In this study, we evaluated the short- and long-term psychosocial impact of genetic testing among unaffected relatives of probands identified through the Malaysian Breast Cancer Genetics Study and the Malaysian Ovarian Cancer Study, using validated questionnaires (Hospital Anxiety and Depression Scale and Cancer Worry Scale) administered at baseline, and 1-month and 2-year post-disclosure of results. Of the 305 unaffected relatives from 98 independent families who were offered cascade testing, 256 (84%) completed predictive testing and family history of cancers was the only factor significantly associated with uptake of predictive testing. We found that the levels of anxiety, depression, and cancer worry among unaffected relatives decreased significantly after result disclosure and remained low 2-year post-result disclosure. Younger relatives and relatives of Malay descent had higher cancer worry at both baseline and after result disclosure compared to those of Chinese and Indian descent, whereas relatives of Indian descent and those with family history of cancers had higher anxiety and depression levels post-result disclosure. Taken together, the results from this Asian cohort highlight the differences in psychosocial needs in different communities and inform the development of culture-specific genetic counseling strategies.
    Matched MeSH terms: BRCA1 Protein/genetics
  20. Ealam Selvan M, Lim KS, Teo CH, Lim YY
    J Vis Exp, 2022 Oct 21.
    PMID: 36342167 DOI: 10.3791/64565
    Circular RNAs (circRNAs) are a class of non-coding RNAs that are formed via back-splicing. These circRNAs are predominantly studied for their roles as regulators of various biological processes. Notably, emerging evidence demonstrates that host circRNAs can be differentially expressed (DE) upon infection with pathogens (e.g., influenza and coronaviruses), suggesting a role for circRNAs in regulating host innate immune responses. However, investigations on the role of circRNAs during pathogenic infections are limited by the knowledge and skills required to carry out the necessary bioinformatic analysis to identify DE circRNAs from RNA sequencing (RNA-seq) data. Bioinformatics prediction and identification of circRNAs is crucial before any verification, and functional studies using costly and time-consuming wet-lab techniques. To solve this issue, a step-by-step protocol of in silico prediction and characterization of circRNAs using RNA-seq data is provided in this manuscript. The protocol can be divided into four steps: 1) Prediction and quantification of DE circRNAs via the CIRIquant pipeline; 2) Annotation via circBase and characterization of DE circRNAs; 3) CircRNA-miRNA interaction prediction through Circr pipeline; 4) functional enrichment analysis of circRNA parental genes using Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG). This pipeline will be useful in driving future in vitro and in vivo research to further unravel the role of circRNAs in host-pathogen interactions.
    Matched MeSH terms: Host-Pathogen Interactions/genetics
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