Probes for INS
ACD can configure probes for the various manual and automated assays for INS for RNAscope Assay, or for Basescope Assay compatible for your species of interest.
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Pediatric and developmental pathology : the official journal of the Society for Pediatric Pathology and the Paediatric Pathology Society
2022 Dec 26
Terry, J;
PMID: 36571293 | DOI: 10.1177/10935266221144083
The pathogenesis of chronic intervillositis of unknown etiology (CIUE) may involve IFNγ overexpression. This study assesses the extent of IFNγ expression in CIUE by immunohistochemistry and compares it to spontaneous pregnancy losses. C4d deposition is also assessed to see whether IFNγ and C4d might represent separate diagnostic categories. Placenta from first to early second trimester with high grade CIUE (CHG; 17 cases) and low grade CIUE (CLG; 12 cases) is compared to euploid (SPLN; 18 cases), aneuploid spontaneous pregnancy losses (SPLA, 17 cases), normal placenta (NP, 13 cases). Protein level expression of IFNγ and C4d is assessed on whole tissue sections by immunohistochemistry. 35% of CHG and 42% of CLG show some level of IFNγ expression localized to the luminal surface of syncytiotrophoblast. 12% of SPLA and no SPLN or NP cases are IFNγ positive. C4d deposition is seen in 100% of CIUE, 88% of SPLA, 83% of SPLN, and 46% of NP samples. IFNγ overexpression occurs in approximately 40% of CIUE-related pregnancy losses. IFNγ expression restricted to a subgroup of CIUE implies that IFNγ may define a distinct disease process. The non-discriminatory pattern of C4d deposition suggests it is a non-specific phenomenon possibly related to placental damage.
International journal of molecular sciences
2022 Oct 22
Oku, Y;Madia, F;Lau, P;Paparella, M;McGovern, T;Luijten, M;Jacobs, MN;
PMID: 36361516 | DOI: 10.3390/ijms232112718
With recent rapid advancement of methodological tools, mechanistic understanding of biological processes leading to carcinogenesis is expanding. New approach methodologies such as transcriptomics can inform on non-genotoxic mechanisms of chemical carcinogens and can be developed for regulatory applications. The Organisation for the Economic Cooperation and Development (OECD) expert group developing an Integrated Approach to the Testing and Assessment (IATA) of Non-Genotoxic Carcinogens (NGTxC) is reviewing the possible assays to be integrated therein. In this context, we review the application of transcriptomics approaches suitable for pre-screening gene expression changes associated with phenotypic alterations that underlie the carcinogenic processes for subsequent prioritisation of downstream test methods appropriate to specific key events of non-genotoxic carcinogenesis. Using case studies, we evaluate the potential of gene expression analyses especially in relation to breast cancer, to identify the most relevant approaches that could be utilised as (pre-) screening tools, for example Gene Set Enrichment Analysis (GSEA). We also consider how to address the challenges to integrate gene panels and transcriptomic assays into the IATA, highlighting the pivotal omics markers identified for assay measurement in the IATA key events of inflammation, immune response, mitogenic signalling and cell injury.
Mucosal immunology
2023 Jun 07
Cortez, V;Livingston, B;Sharp, B;Hargest, V;Papizan, JB;Pedicino, N;Lanning, S;Jordan, SV;Gulman, J;Vogel, P;DuBois, RM;Crawford, JC;Boyd, DF;Pruett-Miller, SM;Thomas, PG;Schultz-Cherry, S;
PMID: 37290501 | DOI: 10.1016/j.mucimm.2023.05.011
Astroviruses cause a spectrum of diseases spanning asymptomatic infections to severe diarrhea, but little is understood about their pathogenesis. We previously determined that small intestinal goblet cells were the main cell type infected by murine astrovirus-1. Here, we focused on the host immune response to infection and inadvertently discovered a role for indoleamine 2,3-dioxygenase 1 (Ido1), a host tryptophan catabolizing enzyme, in the cellular tropism of murine and human astroviruses. We identified that Ido1 expression was highly enriched among infected goblet cells, and spatially corresponded to the zonation of infection. Because Ido1 can act as a negative regulator of inflammation, we hypothesized it could dampen host antiviral responses. Despite robust interferon signaling in goblet cells, as well as tuft cell and enterocyte bystanders, we observed delayed cytokine induction and suppressed levels of fecal lipocalin-2. Although we found Ido-/- animals were more resistant to infection, this was not associated with fewer goblet cells nor could it be rescued by knocking out interferon responses, suggesting that IDO1 instead regulates cell permissivity. We characterized IDO1-/- Caco-2 cells and observed significantly reduced human astrovirus-1 infection. Together this study highlights a role for Ido1 in astrovirus infection and epithelial cell maturation.
Biochemical and biophysical research communications
2023 Mar 16
Yanagihara, T;Zhou, Q;Tsubouchi, K;Revill, S;Ayoub, A;Gholiof, M;Chong, SG;Dvorkin-Gheva, A;Ask, K;Shi, W;Kolb, MR;
PMID: 36958255 | DOI: 10.1016/j.bbrc.2023.03.020
Type 1 alveolar epithelial cells (AT1s) and type 2 alveolar epithelial cells (AT2s) regulate the structural integrity and function of alveoli. AT1s mediate gas exchange, whereas AT2s serve multiple functions, including surfactant secretion and alveolar repair through proliferation and differentiation into AT1s as progenitors. However, mechanisms regulating AT2 proliferation and differentiation remain unclear. Here we demonstrate that Gremlin, an intrinsic inhibitor of bone morphogenetic protein (BMP), induces AT2 proliferation and differentiation. Transient overexpression of Gremlin in rat lungs by adenovirus vector delivery suppressed BMP signaling, induced proliferation of AT2s and the production of Bmp2, which in turn led to the recovery of BMP signaling and induced AT2 differentiation into AT1s. Bleomycin-induced lung injury upregulated Gremlin and showed a similar time course of biomarker expression comparable to the adenovirus model. TGF-β and IL-1β induced Gremlin expression in fibroblasts. Taken together, our findings implicate that Gremlin expression during lung injury leads to precisely timed inhibition of BMP signaling and activates AT2s, leading to alveolar repair.
Anatomia, histologia, embryologia
2022 Sep 30
Yahya, I;Omer, EAM;Gellisch, M;Brand-Saberi, B;Morosan-Puopolo, G;
PMID: 36177714 | DOI: 10.1111/ahe.12868
Embryology belongs to the basic sciences and is usually an integral part of the anatomy. The subject is traditionally taught by visual inspection of embryonic tissue slides stained with Haematoxylin and Eosin (H&E) to expose the dynamics of tissue histology as development proceeds. While combining in situ hybridization for gene expression analysis and immunostaining for protein expression analysis is an established technique for embryology research, the implementation of this tool in embryology teaching has not been described. The present study was conducted to assess the use of an online multi-colour gene expression analysis technique, alongside histological sections and diagrams, to improve students' understanding of embryology. The participants of this study were bachelor's students of Veterinary Medicine at the University of Khartoum. The method was also evaluated by distributing questionnaire items to Veterinary students via Google forms; subsequently, their responses were analysed qualitatively. The majority of students stated that the new technique was beneficial for their learning of embryology. The multi-colour images proved a more effective means for learning embryology than the traditional H&E image. Results from the students strengthen the belief in applying the multi-colour technique for better embryology course learning.
Canadian Journal of Pain
2022 Aug 15
Abou-Assalya, E;Timmersb, I;Simonsc, L;
| DOI: 10.1080/24740527.2022.2088027
RESULTS: Searches returned 10,055 unique titles/abstracts. Of these, 248 were screened at full-text, resulting in the inclusion of 14 studies. Health care providers (HCP) (N = 1622) participated in 11 studies. From the 614 parents included in 7 studies, 203 were reported as birthing mothers and 39 as partners. Studies described suboptimal practices, despite parents’ and HCPs’ intentions to use/advocate for analgesic strategies. Participants positively evaluated the use of parent-targeted interventions including breastfeeding, skin-to-skin care, and sweet solutions during painful procedures. Two studies evaluating the effectiveness of parent-targeted educational interventions on NPM practices found no improvement. Parental involvement facilitators comprised parents’ and HCPs’ knowledge, skills, positive beliefs about their capabilities and consequences of NPM, intentions to use/advocate for analgesic strategies, social influences, and environmental context and resources. Barriers were: parents’ and HCPs’ lack of knowledge; HCPs’ lack of skills, negative beliefs about their capabilities and consequences of NPM, social influences, and inadequate environmental context and resources.
The FASEB Journal
2022 May 01
Scaria, S;Frumm, S;Sheth, A;Tward, A;
| DOI: 10.1096/fasebj.2022.36.S1.R3190
RNA expression data from all timepoints of perforation were merged and analyzed, revealing 8 distinct major populations of cells and revealing time-dependent transcriptional shifts in each layer of the TM. From both cross-sectional and whole-mount views, the TM shows a rapid, proliferative response to injury by 18 hours post-injury, predominantly in the KCs. 3 days after perforation, there are large transcriptional shifts in the immune, mesenchymal, and mucosal populations. The multi-layered tissue shows a large volumetric increase by day 7 but quickly remodels and restores the original volume of the TM by day 14. At slightly longer timepoints, the radial and circular collagen patterning of the TM is also restored, creating a scar-free structure. We identified a regeneration-induced “wounded epithelial” population, characterized by a combination of distinct marker genes. A _K5Cre-ERT2;Confetti_ mouse model shows that the population migrates from known stem cell regions of the organ to the site of injury. Based on expression values and immunostaining, EGFR signaling is upregulated during regeneration, corresponding with increased expression of EGFR ligands and processing co-factors. When EGFR is deleted _in vivo_, using a _K5-CreERT2_;_Egfrfl/fl; R26mTmG/mTmG_ mouse model, TMs no longer display proliferation post-injury and cannot repair perforations.
nature.com
2023 Mar 01
Jensen, BEO;Kobbe, G;
| DOI: 10.1038/s41591-023-02215-9
We describe a 53-year-old man with HIV-1 who received allogeneic CCR5Δ32/Δ32 hematopoietic stem cell transplantation (HSCT) in 2013 to treat acute myeloid leukemia. Four years after analytic treatment interruption (ATI), the absence of viral rebound and the lack of immunological correlates of HIV-1 antigen persistence provide convincing evidence for HIV-1 cure.
NPJ vaccines
2023 May 17
den Hartog, Y;Malahe, SRK;Rietdijk, WJR;Dieterich, M;Gommers, L;Geers, D;Bogers, S;van Baarle, D;Diavatopoulos, DA;Messchendorp, AL;van der Molen, RG;Remmerswaal, EBM;Bemelman, FJ;Gansevoort, RT;Hilbrands, LB;Sanders, JS;GeurtsvanKessel, CH;Kho, MML;Reinders, MEJ;de Vries, RD;Baan, CC;RECOVAC Consortium, ;
PMID: 37198189 | DOI: 10.1038/s41541-023-00664-4
Cytokines are regulators of the immune response against severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2). However, the contribution of cytokine-secreting CD4+ and CD8+ memory T cells to the SARS-CoV-2-specific humoral immune response in immunocompromised kidney patients is unknown. Here, we profiled 12 cytokines after stimulation of whole blood obtained 28 days post second 100 μg mRNA-1273 vaccination with peptides covering the SARS-CoV-2 spike (S)-protein from patients with chronic kidney disease (CKD) stage 4/5, on dialysis, kidney transplant recipients (KTR), and healthy controls. Unsupervised hierarchical clustering analysis revealed two distinct vaccine-induced cytokine profiles. The first profile was characterized by high levels of T-helper (Th)1 (IL-2, TNF-α, and IFN-γ) and Th2 (IL-4, IL-5, IL-13) cytokines, and low levels of Th17 (IL-17A, IL-22) and Th9 (IL-9) cytokines. This cluster was dominated by patients with CKD, on dialysis, and healthy controls. In contrast, the second cytokine profile contained predominantly KTRs producing mainly Th1 cytokines upon re-stimulation, with lower levels or absence of Th2, Th17, and Th9 cytokines. Multivariate analyses indicated that a balanced memory T cell response with the production of Th1 and Th2 cytokines was associated with high levels of S1-specific binding and neutralizing antibodies mainly at 6 months after second vaccination. In conclusion, seroconversion is associated with the balanced production of cytokines by memory T cells. This emphasizes the importance of measuring multiple T cell cytokines to understand their influence on seroconversion and potentially gain more information about the protection induced by vaccine-induced memory T cells.
Annals of Oncology
2022 Oct 01
Okoli, U;Akman, G;Thavarajah, V;Carmona Echeverria, L;Griffin, J;Ohayi, R;Freeman, A;Haider, A;Shaw, G;Sridhar, A;Kelly, J;Simpson, B;Pye, H;Crompton, J;Whitaker, H;Cheema, U;Heavey, S;
| DOI: 10.1016/j.annonc.2022.09.100
Background PIM 1 and PI3K/mTOR pathways are frequently dysregulated in prostate cancer and may lead to decreased survival invasion and metastasis. Moreover, anti-tumour drug resistance has been associated with the interconnection of these pathways. Furthermore, current treatments exhibit issues with toxicity. Hence, these pathways were co-targeted with novel preclinical multikinase PIM/PI3K/mTOR inhibitor- AUM302, PI3K/mTOR inhibitor BEZ235 (Dactolisib) and PIM inhibitor, AZD-1208 in our laboratory using a cohort of cancer explants emanating from our PEOPLE: PatiEnt prOstate samPLes for rEsea ch study and our current SCREEN study. This cohort has a high Gleason grade score of ≥ 8. Therefore, this study aims to assess the effect of the combination therapy on the transcriptional landscape of ex vivo prostate cancer models derived from prostate cancer patients. Methods Using the Nanostring GeoMX DSP technology, we aim to analyse the spatial transcriptomic profile of the co-targeted therapy treated ex vivo models to decipher the effects of heterogeneity on the co-targeted therapies' efficacy. Tissue microarrays of co-targeted treated twenty-five ex vivo 3mm cores derived from 4 patients will be analysed. Following RNA Scope analysis, morphology markers, including PAN CK positive and PAN CK negative, will be used to guide the selection of 270 regions of interest (ROI). ROI will be segmented and profiled using immunofluorescence. The morphological markers will define these segments into areas of illumination (AOIs) using a combination of the absence or presence of CD45 and pSTAT3. The AOIs will generate multiple expression profiles for the related ROI. We intend to use this flexible, high-dimensional spatial profiling to identify the spatial transcriptomic signatures and explore phosphorylation sites in cancer-targeted therapies. Results The spatial transcriptomics analysis of this study is in view. Conclusions Our findings will contribute to understanding how the spatial landscape of the tumour microenvironment enhances the efficacy of anti-tumour drugs and what subset of patients are more likely to benefit from such therapy.
Archives of pathology & laboratory medicine
2023 May 23
Haqshenas, G;Molano, M;Phillips, S;Balgovind, P;Garland, SM;Hawkes, D;Brotherton, JM;Machalek, DA;Murray, G;
PMID: 37226838 | DOI: 10.5858/arpa.2022-0317-OA
Detection of human papillomavirus (HPV) in formalin-fixed, paraffin-embedded (FFPE) tissues may identify the cause of lesions and has value for the development of new diagnostic assays and epidemiologic studies. Seegene Anyplex II assays are widely used for HPV screening, but their performance using FFPE samples has not been fully explored.To validate Anyplex II HPV HR Detection (Anyplex II, Seegene) using FFPE samples.We used 248 stored DNA extracts from cervical cancer FFPE samples collected during 2005-2015 and that tested HPV positive using the RHA kit HPV SPF10-LiPA25, v1 (SPF10, Labo Biomedical Products) HPV genotyping assay, manufacturer-validated for FFPE samples.Of the selected 248 samples, 243 were used in our analysis. Consistent with SPF10 genotyping results, Anyplex II detected all 12 oncogenic types and had an overall HPV detection rate of 86.4% (210 of 243 samples). Anyplex II and SPF10 showed very high agreement for the detection of the 2 most important oncogenic genotypes: HPV 16 (219 of 226; 96.9%; 95% CI, 93.7-98.75) and HPV 18 (221 of 226; 97.8%; 95% CI, 94.9-99.3).Overall results showed that both platforms produced comparable HPV genotyping results, indicating the suitability of Anyplex II for FFPE samples. The Anyplex II assay has the added convenience of being an efficient, single-well semiquantitative polymerase chain reaction assay. Further optimization of Anyplex II may enhance its performance using FFPE samples by improving the detection limit.
iScience
2023 May 01
Shan, D;Wang, Y;Chang, Y;Cui, H;Tao, M;Sheng, Y;Kang, H;Jia, P;Song, J;
| DOI: 10.1016/j.isci.2023.106646
Ischemia reperfusion injury (IRI), often related to surgical procedures, is one of the important causes of acute kidney injury (AKI). To decipher the dynamic process of AKI caused by IRI (with prolonged ischemia phase), we performed single-cell RNA sequencing (scRNA-seq) of clinically relevant IRI murine model with different ischemic intervals. We discovered that Slc5a2hi proximal tubular cells were susceptible to AKI and highly expressed neutral amino acid transporter gene Slc6a19, which was dramatically decreased over the time course. With the usage of mass spectrometry-based metabolomic analysis, we detected that the level of neutral amino acid isoleucine dropped off in AKI mouse plasma metabolites. And the reduction of plasma isoleucine was also verified in patients with cardiac surgery-associated acute kidney injury (CSA-AKI). The findings advanced the understanding of dynamic process of AKI and introduced reduction of isoleucine as a potential biomarker for CSA-AKI.
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| Description | ||
|---|---|---|
| sense Example: Hs-LAG3-sense | Standard probes for RNA detection are in antisense. Sense probe is reverse complent to the corresponding antisense probe. | |
| Intron# Example: Mm-Htt-intron2 | Probe targets the indicated intron in the target gene, commonly used for pre-mRNA detection | |
| Pool/Pan Example: Hs-CD3-pool (Hs-CD3D, Hs-CD3E, Hs-CD3G) | A mixture of multiple probe sets targeting multiple genes or transcripts | |
| No-XSp Example: Hs-PDGFB-No-XMm | Does not cross detect with the species (Sp) | |
| XSp Example: Rn-Pde9a-XMm | designed to cross detect with the species (Sp) | |
| O# Example: Mm-Islr-O1 | Alternative design targeting different regions of the same transcript or isoforms | |
| CDS Example: Hs-SLC31A-CDS | Probe targets the protein-coding sequence only | |
| EnEm | Probe targets exons n and m | |
| En-Em | Probe targets region from exon n to exon m | |
| Retired Nomenclature | ||
| tvn Example: Hs-LEPR-tv1 | Designed to target transcript variant n | |
| ORF Example: Hs-ACVRL1-ORF | Probe targets open reading frame | |
| UTR Example: Hs-HTT-UTR-C3 | Probe targets the untranslated region (non-protein-coding region) only | |
| 5UTR Example: Hs-GNRHR-5UTR | Probe targets the 5' untranslated region only | |
| 3UTR Example: Rn-Npy1r-3UTR | Probe targets the 3' untranslated region only | |
| Pan Example: Pool | A mixture of multiple probe sets targeting multiple genes or transcripts | |
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