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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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NK Cells in Cancer Immunotherapy: Successes and Challenges
2023 Jan 19
Navin, I;Parihar, R;
| DOI: 10.1016/B978-0-12-822620-9.00011-2
The efficacy of natural killer (NK) cell-based therapies against solid tumors has been poor. Solid tumors generate a hostile tumor microenvironment (TME) comprising multiple cell types including inhibitory immune cells that play a key role in depressing the antitumor functions of therapeutic NK cells. Understanding how inhibitory immune effectors operate within the confines of the TME is critical to developing therapies to reverse this inhibition. In this chapter, we cover the suppressive mechanisms employed by TME-resident inhibitory immune cells and discuss methodologies to assess their composition and functionality within the TME. We also highlight novel therapeutic strategies that target inhibitory cells of the TME to improve the antitumor functions of endogenous or adoptively transferred NK cells. Multimodal approaches to overcome inhibitory immune cells within the TME will drive the development of personalized NK cell therapeutics with optimal activity, leading to improved clinical outcomes in patients with solid tumors.
Life Medicine
2022 Nov 14
Zhang, J;Yin, J;Heng, Y;Xie, K;Chen, A;Amit, I;Bian, X;Xu, X;
| DOI: 10.1093/lifemedi/lnac053
Current streamline of precision medicine uses histomorphological and molecular information to indicate individual phenotypes and genotypes to achieve optimal outcome of treatment. The knowledge of detected mutations and alteration can hardly describe molecular interaction and biological process which can finally be manifested as a disease. With molecular diagnosis revising the modalities of disease, there is a trend in precision medicine to apply multi-omic and multi-dimensional information to decode tumors, regarding heterogeneity, pathogenesis, prognosis, etc. Emerging state-of-art spatiotemporal omics provides a novel vision for in discovering clinicopathogenesis associated findings, some of which show a promising potential to be translated to facilitate clinical practice. Here, we summarize the available spatiotemporal omic technologies and algorithms, highlight the novel scientific findings and explore potential applications in the clinical scenario. Spatiotemporal omics present the ability to provide impetus to rewrite clinical pathology and to answer outstanding clinical questions. This review emphasizes the novel vision of spatiotemporal omics to refine the landscape of precision medicine in the clinic.
Preprint
2022 Oct 17
Luo, W;
| DOI: 10.20944/preprints202210.0226.v1
Nasopharyngeal carcinoma (NPC) is generally regarded as a genetic disease with diverse extent of intertumor and intratumor heterogeneity. Here we propose that, NPC is not only a genetic disease; it could be conceptualized as a multidimensional spatiotemporal “unity of ecology and evolution” pathological ecosystem. In the text, we first discuss NPC cells an invasive species and its metastasis as a multidirectional ecological dispersal, which consisting of four interdependent parts: primary ecosystem, circulating ecosystem, metastatic ecosystem and multidirectional ecosystem. We then interpreter the foundational ecological principles to understand NPC progression. The model of “mulberry-fish-ponds” can well illustrate the dynamic reciprocity of cancer ecosystem. Subsequently, we demonstrate that tumor-host interface is the ecological transition zone in cancers, and tumor buddings should be recognized as ecological islands separated from the mainland. Selection driving factors and ecological therapy including hyperthermia for NPC patients, and future perspectives of “ecological pathology”, “multidimensional spatiotemporal tumoriecology” and “integrated tumoriecology” are also pointed out. We advance that “nothing in cancer evolution or ecology makes sense except in the light of the other”. The essence of NPC and other human neoplasms should be pathological an “unity of ecology and evolution”. The establishment of “NPC ecology” might open up a new horizon, and provide a comprehensive framework for our understanding of the complex progression of this disease and development of potential preventive and therapeutic strategies for patients.
Journal of Diabetes and its Complications
2022 Sep 01
Schmidt, B;Holmes, C;Najarian, K;Gallagher, K;Haus, J;Shadiow, J;Ye, W;Ang, L;Burant, A;Baker, N;Katona, A;Martin, C;Pop-Busui, R;
| DOI: 10.1016/j.jdiacomp.2022.108317
Diabetic foot ulcers (DFUs) remain a very prevalent and challenging complication of diabetes worldwide due to high morbidity, high risks of lower extremity amputation and associated mortality. Despite major advances in diabetes treatment in general, there is a paucity of FDA approved technologies and therapies to promote successful healing. Furthermore, accurate biomarkers to identify patients at risk of non-healing and monitor response-to-therapy are significantly lacking. To date, research has been slowed by a lack of coordinated efforts among basic scientists and clinical researchers and confounded by non-standardized heterogenous collection of biospecimen and patient associated data. Novel technologies, especially those in the single and ‘multiomics’ arena, are being used to advance the study of diabetic foot ulcers but require pragmatic study design to ensure broad adoption following validation. These high throughput analyses offer promise to investigate potential biomarkers across wound trajectories and may support information on wound healing and pathophysiology not previously well understood. Additionally, these biomarkers may be used at the point-of-care. In combination with national scalable research efforts, which seek to address the limitations and better inform clinical practice, coordinated and integrative insights may lead to improved limb salvage rates.
Current environmental health reports
2022 Aug 19
Kay, JE;Cardona, B;Rudel, RA;Vandenberg, LN;Soto, AM;Christiansen, S;Birnbaum, LS;Fenton, SE;
PMID: 35984634 | DOI: 10.1007/s40572-022-00376-2
Population studies show worrisome trends towards earlier breast development, difficulty in breastfeeding, and increasing rates of breast cancer in young women. Multiple epidemiological studies have linked these outcomes with chemical exposures, and experimental studies have shown that many of these chemicals generate similar effects in rodents, often by disrupting hormonal regulation. These endocrine-disrupting chemicals (EDCs) can alter the progression of mammary gland (MG) development, impair the ability to nourish offspring via lactation, increase mammary tissue density, and increase the propensity to develop cancer. However, current toxicological approaches to measuring the effects of chemical exposures on the MG are often inadequate to detect these effects, impairing our ability to identify exposures harmful to the breast and limiting opportunities for prevention. This paper describes key adverse outcomes for the MG, including impaired lactation, altered pubertal development, altered morphology (such as increased mammographic density), and cancer. It also summarizes evidence from humans and rodent models for exposures associated with these effects. We also review current toxicological practices for evaluating MG effects, highlight limitations of current methods, summarize debates related to how effects are interpreted in risk assessment, and make recommendations to strengthen assessment approaches. Increasing the rigor of MG assessment would improve our ability to identify chemicals of concern, regulate those chemicals based on their effects, and prevent exposures and associated adverse health effects.
Blood
2021 Nov 10
Olsen, EA;Whittaker, S;Willemze, R;Pinter-Brown, L;Foss, FM;Geskin, LJ;Schwartz, LH;Horwitz, SM;Guitart, J;Zic, J;Kim, YH;Wood, GS;Duvic, M;Ai, WZ;Girardi, M;Gru, A;Guenova, E;Hodak, E;Hoppe, RT;Kempf, W;Kim, EJ;Lechowicz, MJ;Ortiz-Romero, PL;Papadavid, E;Quaglino, P;Pittelkow, MR;Prince, HM;Sanches, JA;Sugaya, M;Vermeer, MH;Zain, J;Knobler, R;Stadler, R;Bagot, M;Scarisbrick, JJ;
PMID: 34758074 | DOI: 10.1182/blood.2021012057
The number of patients with primary cutaneous lymphoma (PCL) relative to other non-Hodgkin lymphomas (NHLs) is small and the number of subtypes large. Although clinical trial guidelines have been published for mycosis fungoides/Sézary syndrome (MF/SS), the most common type of PCL, none exist for the other PCLs. In addition, staging in the PCLs has been evolving based on new data on potential prognostic factors, diagnosis, and assessment methods of both skin and extracutaneous disease and a desire to align the latter with the Lugano guidelines for all NHLs. The International Society for Cutaneous Lymphomas (ISCL), the United States Cutaneous Lymphoma Consortium (USCLC), and the Cutaneous Lymphoma Task Force of the European Organization for the Research and Treatment of Cancer (EORTC) now propose updated staging and guidelines for the study design, assessment, endpoints and response criteria in clinical trials for all the PCLs in alignment with that of the Lugano guidelines. These recommendations provide standardized methodology that should facilitate planning and regulatory approval of new treatments for these lymphomas worldwide, encourage cooperative investigator-initiated trials, and help to assess the comparative efficacy of therapeutic agents tested across sites and studies.
Genome medicine
2022 Jun 27
Williams, CG;Lee, HJ;Asatsuma, T;Vento-Tormo, R;Haque, A;
PMID: 35761361 | DOI: 10.1186/s13073-022-01075-1
Single-cell transcriptomics (scRNA-seq) has become essential for biomedical research over the past decade, particularly in developmental biology, cancer, immunology, and neuroscience. Most commercially available scRNA-seq protocols require cells to be recovered intact and viable from tissue. This has precluded many cell types from study and largely destroys the spatial context that could otherwise inform analyses of cell identity and function. An increasing number of commercially available platforms now facilitate spatially resolved, high-dimensional assessment of gene transcription, known as 'spatial transcriptomics'. Here, we introduce different classes of method, which either record the locations of hybridized mRNA molecules in tissue, image the positions of cells themselves prior to assessment, or employ spatial arrays of mRNA probes of pre-determined location. We review sizes of tissue area that can be assessed, their spatial resolution, and the number and types of genes that can be profiled. We discuss if tissue preservation influences choice of platform, and provide guidance on whether specific platforms may be better suited to discovery screens or hypothesis testing. Finally, we introduce bioinformatic methods for analysing spatial transcriptomic data, including pre-processing, integration with existing scRNA-seq data, and inference of cell-cell interactions. Spatial -omics methods are already improving our understanding of human tissues in research, diagnostic, and therapeutic settings. To build upon these recent advancements, we provide entry-level guidance for those seeking to employ spatial transcriptomics in their own biomedical research.
Handbook of Genetic Diagnostic Technologies in Reproductive Medicine
2022 May 10
Lorenzi, V;Vento-Tormo, R;
| DOI: 10.1201/9781003024941-2
The Human Cell Atlas (HCA) is an international consortium established at the end of 2016 with the mission of mapping and characterizing all cells in the human body in terms of their distinctive patterns of gene expression, physiological states, and location (Rozenblatt-Rosen et al., 2017); (Regev et al., 2017) (http://www.humancellatlas.org" xmlns:xlink="http://www.w3.org/1999/xlink">www.humancellatlas.org). It is an open and collaborative initiative, bringing together experts across multiple disciplines, and is meant to progress in phases. Recently, the first maps focused on specific organs and tissues (Ordovas-Montanes et al., 2018; Vento-Tormo et al., 2018; Popescu et al., 2019; Ramachandran et al., 2019; Smillie et al., 2019; Stewart et al., 2019; Vieira Braga et al., 2019) have laid the foundations for further work aimed at completing the atlas to include at least ten billion cells that fully represent the world's diversity.
Plastic and reconstructive surgery
2023 May 24
Stanton, E;Feng, J;Kondra, K;Sanchez, J;Jimenez, C;Brown, KS;Skiles, ML;Urata, MM;Chai, Y;Hammoudeh, JA;
PMID: 37224290 | DOI: 10.1097/PRS.0000000000010754
The standard graft material for alveolar cleft repair (ACR) is autogenous iliac crest. However, a promising alternative potential graft adjunct - newborn human umbilical cord mesenchymal stem cells (h-UCMSC) - has yet to be explored in vivo. Their capacity for self-renewal, multipotent differentiation, and proliferation allows h-UCMSC to be harnessed for regenerative medicine. Our study seeks to evaluate the efficacy of using tissue-derived h-UCMSC and their osteogenic capabilities in a murine model to improve ACR.Foxn1 mice were separated into three groups with the following calvarial defects: (1) no-treatment (empty defect; n=6), (2) poly (D,L-lactide-co-glycolide) (PLGA) scaffold (n=6), and (3) h-UCMSC with PLGA (n=4). Bilateral 2-mm diameter parietal bone critical-sized defects were created using a dental drill. Micro-CT imaging occurred at 1, 2, 3, and 4 weeks postoperatively. The mice were euthanized 4 weeks postoperatively for RNAscope analysis, immunohistochemistry, and histology.No mice experienced complications during the follow-up period. Micro-CT and histology demonstrated that the no-treatment (1) and PLGA-only (2) defects remained patent without significant defect size differences across groups. In contrast, the h-UCMSC with PLGA group (3) had significantly greater bone fill on micro-CT and histology.We demonstrate a successful calvarial defect model for the investigation of h-UCMSC-mediated osteogenesis and bone repair. Furthermore, evidence reveals that PLGA alone has neither short-term effects on bone formation nor any unwanted side effects, making it an attractive scaffold. Further investigation using h-UCMSC with PLGA in larger animals is warranted to advance future translation to patients requiring ACR.Our results demonstrate a successful murine calvarial defect model for the investigation of h-UCMSC-mediated osteogenesis and bone repair and provide preliminary evidence for the safe and efficacious use of this graft adjunct in alveolar cleft repair.
Journal of Comparative Pathology
2022 Feb 01
Gaide, N;Crispo, M;Jbenyeni, A;Croville, G;Vergne, T;Bleuart, C;Delverdier, M;Guérin, J;
| DOI: 10.1016/j.jcpa.2021.11.125
Introduction: Avian influenza (AI) is a highly contagious disease that, during the last few years, has been occurring with increased frequency in Europe. Immunohistochemistry (IHC) is commonly used to demonstrate AI virus (AIV) antigens in affected tissues. Recent studies suggest that RNAscope in-situ hybridization outperforms IHC for viral detection in human tissues. This study aims to validate and compare RNAscope with IHC routinely used for the detection of AIV. Materials and Methods: RNAscope targeting the Influenza M gene and anti-influenza A virus nucleoprotein IHC were first performed on AIV positive (n=7) and negative tissues (n=6) collected between 2009 and 2021, including seven avian species (chicken, duck, guinea fowl, quail, turkey, goose and houbara bustard) and three different AIVs (H5N8, H5N9, H6N1). A Tissue Micro-Array (TMA) with 132 cores, including 44 triplicated organs (brain, lung, heart, spleen, pancreas) originating from nine mule ducks naturally infected with H5N8 (2020) was then used to compare techniques through computer-assisted quantitative analysis. Results: AIV nucleoprotein and M gene were detected in all positive tissues of all species and for all AIVs. All uninfected birds were negative. While IHC appeared affected by autolysis, the quality of the RNAscope signal remained unchanged. On the TMA, viral detection efficacy measurements revealed higher sensitivity with RNAscope compared with IHC, in particular for brain and heart tissues. Conclusions: These preliminary results indicate that RNAscope is a suitable and sensitive tool for the detection of AIV and encourage the development of additional probes for the detection of AIV subtypes.
Science translational medicine
2022 Feb 16
Tavares-Ferreira, D;Shiers, S;Ray, PR;Wangzhou, A;Jeevakumar, V;Sankaranarayanan, I;Cervantes, AM;Reese, JC;Chamessian, A;Copits, BA;Dougherty, PM;Gereau, RW;Burton, MD;Dussor, G;Price, TJ;
PMID: 35171654 | DOI: 10.1126/scitranslmed.abj8186
Nociceptors are specialized sensory neurons that detect damaging or potentially damaging stimuli and are found in the dorsal root ganglia (DRG) and trigeminal ganglia. These neurons are critical for the generation of neuronal signals that ultimately create the perception of pain. Nociceptors are also primary targets for treating acute and chronic pain. Single-cell transcriptomics on mouse nociceptors has transformed our understanding of pain mechanisms. We sought to generate equivalent information for human nociceptors with the goal of identifying transcriptomic signatures of nociceptors, identifying species differences and potential drug targets. We used spatial transcriptomics to molecularly characterize transcriptomes of single DRG neurons from eight organ donors. We identified 12 clusters of human sensory neurons, 5 of which are C nociceptors, as well as 1 C low-threshold mechanoreceptors (LTMRs), 1 Aβ nociceptor, 2 Aδ, 2 Aβ, and 1 proprioceptor subtypes. By focusing on expression profiles for ion channels, G protein-coupled receptors (GPCRs), and other pharmacological targets, we provided a rich map of potential drug targets in the human DRG with direct comparison to mouse sensory neuron transcriptomes. We also compared human DRG neuronal subtypes to nonhuman primates showing conserved patterns of gene expression among many cell types but divergence among specific nociceptor subsets. Last, we identified sex differences in human DRG subpopulation transcriptomes, including a marked increase in calcitonin-related polypeptide alpha (CALCA) expression in female pruritogen receptor-enriched nociceptors. This comprehensive spatial characterization of human nociceptors might open the door to development of better treatments for acute and chronic pain disorders.
Journal of immunological methods
2023 May 16
Schafer, C;Young, D;Singh, H;Jayakrishnan, R;Banerjee, S;Song, Y;Dobi, A;Petrovics, G;Srivastava, S;Srivastava, S;Sesterhenn, IA;Chesnut, GT;Tan, SH;
PMID: 37196930 | DOI: 10.1016/j.jim.2023.113493
Aberrant ETV1 overexpression arising from gene rearrangements or mutations occur frequently in prostate cancer, round cell sarcomas, gastrointestinal stromal tumors, gliomas, and other malignancies. The absence of specific monoclonal antibodies (mAb) has limited its detection and our understanding of its oncogenic function.An ETV1 specific rabbit mAb (29E4) was raised using an immunogenic peptide. Key residues essential for its binding were probed by ELISA and its binding kinetics were measured by surface plasmon resonance imaging (SPRi). Its selective binding to ETV1 was assessed by immunoblots and immunofluorescence assays (IFA), and by both single and double-immuno-histochemistry (IHC) assays on prostate cancer tissue specimens.Immunoblot results showed that the mAb is highly specific and lacked cross-reactivity with other ETS factors. A minimal epitope with two phenylalanine residues at its core was found to be required for effective mAb binding. SPRi measurements revealed an equilibrium dissociation constant in the picomolar range, confirming its high affinity. ETV1 (+) tumors were detected in prostate cancer tissue microarray cases evaluated. IHC staining of whole-mounted sections revealed glands with a mosaic staining pattern of cells that are partly ETV1 (+) and interspersed with ETV1 (-) cells. Duplex IHC, using ETV1 and ERG mAbs, detected collision tumors containing glands with distinct ETV1 (+) and ERG (+) cells.The selective detection of ETV1 by the 29E4 mAb in immunoblots, IFA, and IHC assays using human prostate tissue specimens reveals a potential utility for the diagnosis, the prognosis of prostate adenocarcinoma and other cancers, and the stratification of patients for treatment by ETV1 inhibitors.
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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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