CircFISH: A Novel Method for the Simultaneous Imaging of Linear and Circular RNAs

Cancers

2022 Jan 15

Koppula, A;Abdelgawad, A;Guarnerio, J;Batish, M;Parashar, V;
PMID: 35053590 | DOI: 10.3390/cancers14020428

Circular RNAs (circRNAs) are regulatory RNAs which have recently been shown to have clinical significance in several diseases, including, but not limited to, various cancers, neurological diseases and cardiovascular diseases. The function of such regulatory RNAs is largely dependent on their subcellular localization. Several circRNAs have been shown to conduct antagonistic roles compared to the products of the linear isoforms, and thus need to be characterized distinctly from the linear RNAs. However, conventional fluorescent in situ hybridization (FISH) techniques cannot be employed directly to distinguish the signals from linear and circular isoforms because most circRNAs share the same sequence with the linear RNAs. In order to address this unmet need, we adapted the well-established method of single-molecule FISH by designing two sets of probes to differentiate the linear and circular RNA isoforms by virtue of signal colocalization. We call this method 'circular fluorescent in situ hybridization' (circFISH). Linear and circular RNAs were successfully visualized and quantified at a single-molecule resolution in fixed cells. RNase R treatment during the circFISH reduced the levels of linear RNAs while the circRNA levels remain unaltered. Furthermore, cells with shRNAs specific to circRNA showed the loss of circRNA levels, whereas the linear RNA levels were unaffected. The optimization of the in-situ RNase R treatment allowed the multiplexing of circFISH to combine it with organelle staining. CircFISH was found to be compatible with multiple sample types, including cultured cells and fresh-frozen and formalin-fixed tissue sections. Thus, we present circFISH as a versatile method for the simultaneous visualization and quantification of the distribution and localization of linear and circular RNA in fixed cells and tissue samples.

The Gliopeptide ODN, a Ligand for the Benzodiazepine Site of GABAA Receptors, Boosts Functional Recovery after Stroke

The Journal of neuroscience : the official journal of the Society for Neuroscience

2021 Aug 18

Lamtahri, R;Hazime, M;Gowing, EK;Nagaraja, RY;Maucotel, J;Alasoadura, M;Quilichini, PP;Lehongre, K;Lefranc, B;Gach-Janczak, K;Marcher, AB;Mandrup, S;Vaudry, D;Clarkson, AN;Leprince, J;Chuquet, J;
PMID: 34210784 | DOI: 10.1523/JNEUROSCI.2255-20.2021

Following stroke, the survival of neurons and their ability to reestablish connections is critical to functional recovery. This is strongly influenced by the balance between neuronal excitation and inhibition. In the acute phase of experimental stroke, lethal hyperexcitability can be attenuated by positive allosteric modulation of GABAA receptors (GABAARs). Conversely, in the late phase, negative allosteric modulation of GABAAR can correct the suboptimal excitability and improves both sensory and motor recovery. Here, we hypothesized that octadecaneuropeptide (ODN), an endogenous allosteric modulator of the GABAAR synthesized by astrocytes, influences the outcome of ischemic brain tissue and subsequent functional recovery. We show that ODN boosts the excitability of cortical neurons, which makes it deleterious in the acute phase of stroke. However, if delivered after day 3, ODN is safe and improves motor recovery over the following month in two different paradigms of experimental stroke in mice. Furthermore, we bring evidence that, during the subacute period after stroke, the repairing cortex can be treated with ODN by means of a single hydrogel deposit into the stroke cavity.SIGNIFICANCE STATEMENT Stroke remains a devastating clinical challenge because there is no efficient therapy to either minimize neuronal death with neuroprotective drugs or to enhance spontaneous recovery with neurorepair drugs. Around the brain damage, the peri-infarct cortex can be viewed as a reservoir of plasticity. However, the potential of wiring new circuits in these areas is restrained by a chronic excess of GABAergic inhibition. Here we show that an astrocyte-derived peptide, can be used as a delayed treatment, to safely correct cortical excitability and facilitate sensorimotor recovery after stroke.

Biology and Cellular Tropism of a Unique Astrovirus Strain: Murine Astrovirus 2

Comparative medicine

2021 Dec 01

Kelly, SP;Ricart Arbona, RJ;Michel, AO;Wang, C;Henderson, KS;Lipman, NS;
PMID: 34794533 | DOI: 10.30802/AALAS-CM-21-000039

Murine astrovirus 2 (MuAstV2) is a novel murine astrovirus recently identified in laboratory and wild mice. MuAstV2 readily transmits between immunocompetent mice yet fails to transmit to highly immunocompromised mouse strains-a unique characteristic when contrasted with other murine viruses including other astroviruses. We characterized the viral shedding kinetics and tissue tropism of MuAstV2 in immunocompetent C57BL/6NCrl mice and evaluated the apparent resistance of highly immunocompromised NOD- Prkdcem26Cd52Il2rgem26Cd22 /NjuCrl mice to MuAstV2 after oral inoculation. Temporal patterns of viral shedding were determined by serially measuring fecal viral RNA. Tissue tropism and viral load were characterized and quantified by using in-situ hybridization (ISH) targeting viral RNA. Cellular tropism was characterized by evaluating fluorescent colocalization of viral ISH with various immunohistochemical markers. We found a rapid increase of fecal viral RNA in B6 mice, which peaked at 5 d after inoculation (dpi) followed by cessation of shedding by 168 dpi. The small intestine had the highest percentage of hybridization (3.09% of tissue area) of all tissues in which hybridization occurred at 5 dpi. The thymus displayed the next highest degree of hybridization (2.3%) at 7 dpi, indicating extraintestinal viral spread. MuAstV2 RNA hybridization was found to colocalize with only 3 of the markers evaluated: CD3 (T cells), Iba1 (macrophages), and cytokeratin (enterocytes). A higher percentage of CD3 cells and Iba1 cells hybridized with MuAstV2 as compared with cytokeratin at 2 dpi (CD3, 59%; Iba1, 46%; cytokeratin, 6%) and 35 dpi (CD3, 14%; Iba1, 55%; cytokeratin, 3%). Neither fecal viral RNA nor viral hybridization was noted in NCG mice at the time points examined. In addition, mice of mixed genetic background were inoculated, and only those with a functioning Il2rg gene shed MuAstV2. Results from this study suggest that infection of, or interaction with, the immune system is required for infection by or replication of MuAstV2.

METASTATIC MEDULLOBLASTOMA TO THE MANDIBLE: A CASE REPORT

Oral Surgery, Oral Medicine, Oral Pathology and Oral Radiology

2021 Jul 01

Alotaiby, F;Bhattacharyya, I;Fatani, H;
| DOI: 10.1016/j.oooo.2021.03.037

Introduction Medulloblastoma is the most common tumor of the brain of neuroendocrine origin in children and typically demonstrates an aggressive, relentless clinical behavior and high recurrence rate. Extraneuraxial metastasis of medulloblastoma to the jaw is extremely rare, with fewer than 10 cases reported in the literature. Case Report A 10-year-old male patient presented with a swelling in the right side of the face for 15 days. The patient had a past history of medulloblastoma diagnosed a few years earlier. Clinical examination revealed a diffuse painless mass in the right mandible. Multiplanar reconstruction demonstrated a 1.5 × 1.5 cm well-defined round lesion with extensive necrosis involving mostly the ramus of right mandible with resultant bone erosion on the lingual aspect. The lesion involved the regional structures including maxillary sinus, pterygoid process, and carotid sheath. Microscopic examination of the biopsy specimen exhibited sheets of poorly differentiated malignant small round blue cells with extensive necrosis. The tumor cells revealed molding of nuclei with speckled chromatin and inconspicuous cytoplasm. Evidence of vascular and perineural invasion was noted. Immunohistochemical studies demonstrated weak granular positivity for synaptophysin, but staining for AE1/3, desmin, CD99, and LCA was negative in the lesion tissue. A diagnosis of round blue cell malignancy of neuroendocrine origin compatible with medulloblastoma metastatic to the jaw was rendered. Our case represents only the 10th such as case in the English-language literature. Owing to the rarity of this entity, a more accurate understanding of the prognosis and treatment of metastatic medulloblastoma is not well known.

Setting up a PDXO platform of pancreatic cancer with spatial-omics characterization

Pancreatology

2021 Jul 01

Michiels, E;Messaoudi, N;Heremans, Y;Giron, P;Janssens, T;Frederix, K;Aerts, S;Reynaert, H;Rooman, I;
| DOI: 10.1016/j.pan.2021.05.188

Introduction: Pancreatic ductal adenocarcinoma (PDAC) is known for its aggressive biology and lethality. Due to a low success rate of current diagnostic and therapeutic approaches in clinic, there is an urgent need for preclinical research studies to investigate the underlying biology of this malignancy. This knowledge is indispensable to facilitate the development and validation of potential new therapeutic compounds. Superior to conventional biomedical research models, the focus of this study is on the development and use of a well-established patient-derived 3D model, mimicking the tumor as it is present in a human body. Aims: The development and characterization of patient-derived organoids (PDO) and patient-derived xenografts (PDX) of PDAC. Materials and Methods: The models are extensively analysed using advanced histological methods such as BaseScope^®, 3D imaging and DNA hotspot sequencing. Results: 10 established PDAC-PDO and their corresponding parental tumors are already validated using immunostainings and DNA hotspot sequencing. The latter confirms presence of tumor cells in the organoids. In addition, this study is the first to show in situ detection of important driver mutations of pancreatic cancer, like KrasG12D, both in parental tumor and PDO. Thus far, 5 PDX have been generated that will undergo similar analysis. Conclusion: We have successfully started a pre-clinical screening platform for PDAC based on PDO and PDX. Altogether, spatial-omics analysis of both models can substantiate (1) resemblance to parental tissue and (2) spatial genomic characteristics associated with the type of model used. Ultimately, the screening platform can be used by pharmaceutical companies to facilitate oncological drug testing.

The persistent pain transcriptome: identification of cells and molecules activated by hyperalgesia

The journal of pain

2021 Apr 20

Sapio, MR;Kim, JJ;Loydpierson, AJ;Maric, D;Goto, T;Vazquez, FA;Dougherty, MK;Narasimhan, R;Muhly, WT;Iadarola, MJ;Mannes, AJ;
PMID: 33892151 | DOI: 10.1016/j.jpain.2021.03.155

During persistent pain, the dorsal spinal cord responds to painful inputs from the site of injury, but the molecular modulatory processes have not been comprehensively examined. Using transcriptomics and multiplex in situ hybridization, we identified the most highly regulated receptors and signaling molecules in rat dorsal spinal cord in peripheral inflammatory and post-surgical incisional pain models. We examined a time course of the response including acute (2 hrs) and longer term (2 day) time points after peripheral injury representing the early onset and instantiation of hyperalgesic processes. From this analysis, we identify a key population of superficial dorsal spinal cord neurons marked by somatotopic upregulation of the opioid neuropeptide precursor prodynorphin, and two receptors: the neurokinin 1 receptor, and anaplastic lymphoma kinase. These alterations occur specifically in the glutamatergic subpopulation of superficial dynorphinergic neurons. In addition to specific neuronal gene regulation, both models showed induction of broad transcriptional signatures for tissue remodeling, synaptic rearrangement, and immune signaling defined by complement and interferon induction. These signatures were predominantly induced ipsilateral to tissue injury, implying linkage to primary afferent drive. We present a comprehensive set of gene regulatory events across two models that can be targeted for the development of non-opioid analgesics. PERSPECTIVE: The deadly impact of the opioid crisis and the need to replace morphine and other opioids in clinical practice is well recognized. Embedded within this research is an overarching goal of obtaining foundational knowledge from transcriptomics to search for non-opioid analgesic targets. Developing such analgesics would address unmet clinical needs.

Mapping the regulatory landscape of auditory hair cells from single-cell multi-omics data

Genome research

2021 Apr 09

Wang, S;Lee, MP;Jones, S;Liu, J;Waldhaus, J;
PMID: 33837132 | DOI: 10.1101/gr.271080.120

Auditory hair cells transduce sound to the brain and in mammals these cells reside together with supporting cells in the sensory epithelium of the cochlea, called the organ of Corti. To establish the organ's delicate function during development and differentiation, spatiotemporal gene expression is strictly controlled by chromatin accessibility and cell type-specific transcription factors, jointly representing the regulatory landscape. Bulk-sequencing technology and cellular heterogeneity obscured investigations on the interplay between transcription factors and chromatin accessibility in inner ear development. To study the formation of the regulatory landscape in hair cells, we collected single-cell chromatin accessibility profiles accompanied by single-cell RNA data from genetically labeled murine hair cells and supporting cells after birth. Using an integrative approach, we predicted cell type-specific activating and repressing functions of developmental transcription factors. Furthermore, by integrating gene expression and chromatin accessibility datasets, we reconstructed gene regulatory networks. Then, using a comparative approach, 20 hair cell-specific activators and repressors, including putative downstream target genes, were identified. Clustering of target genes resolved groups of related transcription factors and was utilized to infer their developmental functions. Finally, the heterogeneity in the single-cell data allowed us to spatially reconstruct transcriptional as well as chromatin accessibility trajectories, indicating that gradual changes in the chromatin accessibility landscape were lagging behind the transcriptional identity of hair cells along the organ's longitudinal axis. Overall, this study provides a strategy to spatially reconstruct the formation of a lineage specific regulatory landscape using a single-cell multi-omics approach.

Myocardial Infarction Induces Cardiac Fibroblast Transformation within Injured and Noninjured Regions of the Mouse Heart

Journal of proteome research

2021 Mar 31

Shah, H;Hacker, A;Langburt, D;Dewar, M;McFadden, MJ;Zhang, H;Kuzmanov, U;Zhou, YQ;Hussain, B;Ehsan, F;Hinz, B;Gramolini, AO;Heximer, SP;
PMID: 33789425 | DOI: 10.1021/acs.jproteome.1c00098

Heart failure (HF) is associated with pathological remodeling of the myocardium, including the initiation of fibrosis and scar formation by activated cardiac fibroblasts (CFs). Although early CF-dependent scar formation helps prevent cardiac rupture by maintaining the heart's structural integrity, ongoing deposition of the extracellular matrix in the remote and infarct regions can reduce tissue compliance, impair cardiac function, and accelerate progression to HF. In our study, we conducted mass spectrometry (MS) analysis to identify differentially altered proteins and signaling pathways between CFs isolated from 7 day sham and infarcted murine hearts. Surprisingly, CFs from both the remote and infarct regions of injured hearts had a wide number of similarly altered proteins and signaling pathways that were consistent with fibrosis and activation into pathological myofibroblasts. Specifically, proteins enriched in CFs isolated from MI hearts were involved in pathways pertaining to cell-cell and cell-matrix adhesion, chaperone-mediated protein folding, and collagen fibril organization. These results, together with principal component analyses, provided evidence of global CF activation postinjury. Interestingly, however, direct comparisons between CFs from the remote and infarct regions of injured hearts identified 15 differentially expressed proteins between MI remote and MI infarct CFs. Eleven of these proteins (Gpc1, Cthrc1, Vmac, Nexn, Znf185, Sprr1a, Specc1, Emb, Limd2, Pawr, and Mcam) were higher in MI infarct CFs, whereas four proteins (Gstt1, Gstm1, Tceal3, and Inmt) were higher in MI remote CFs. Collectively, our study shows that MI injury induced global changes to the CF proteome, with the magnitude of change reflecting their relative proximity to the site of injury.

Shotgun transcriptome, spatial omics, and isothermal profiling of SARS-CoV-2 infection reveals unique host responses, viral diversification, and drug interactions

Nature communications

2021 Mar 12

Butler, D;Mozsary, C;Meydan, C;Foox, J;Rosiene, J;Shaiber, A;Danko, D;Afshinnekoo, E;MacKay, M;Sedlazeck, FJ;Ivanov, NA;Sierra, M;Pohle, D;Zietz, M;Gisladottir, U;Ramlall, V;Sholle, ET;Schenck, EJ;Westover, CD;Hassan, C;Ryon, K;Young, B;Bhattacharya, C;Ng, DL;Granados, AC;Santos, YA;Servellita, V;Federman, S;Ruggiero, P;Fungtammasan, A;Chin, CS;Pearson, NM;Langhorst, BW;Tanner, NA;Kim, Y;Reeves, JW;Hether, TD;Warren, SE;Bailey, M;Gawrys, J;Meleshko, D;Xu, D;Couto-Rodriguez, M;Nagy-Szakal, D;Barrows, J;Wells, H;O'Hara, NB;Rosenfeld, JA;Chen, Y;Steel, PAD;Shemesh, AJ;Xiang, J;Thierry-Mieg, J;Thierry-Mieg, D;Iftner, A;Bezdan, D;Sanchez, E;Campion, TR;Sipley, J;Cong, L;Craney, A;Velu, P;Melnick, AM;Shapira, S;Hajirasouliha, I;Borczuk, A;Iftner, T;Salvatore, M;Loda, M;Westblade, LF;Cushing, M;Wu, S;Levy, S;Chiu, C;Schwartz, RE;Tatonetti, N;Rennert, H;Imielinski, M;Mason, CE;
PMID: 33712587 | DOI: 10.1038/s41467-021-21361-7

In less than nine months, the Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) killed over a million people, including >25,000 in New York City (NYC) alone. The COVID-19 pandemic caused by SARS-CoV-2 highlights clinical needs to detect infection, track strain evolution, and identify biomarkers of disease course. To address these challenges, we designed a fast (30-minute) colorimetric test (LAMP) for SARS-CoV-2 infection from naso/oropharyngeal swabs and a large-scale shotgun metatranscriptomics platform (total-RNA-seq) for host, viral, and microbial profiling. We applied these methods to clinical specimens gathered from 669 patients in New York City during the first two months of the outbreak, yielding a broad molecular portrait of the emerging COVID-19 disease. We find significant enrichment of a NYC-distinctive clade of the virus (20C), as well as host responses in interferon, ACE, hematological, and olfaction pathways. In addition, we use 50,821 patient records to find that renin-angiotensin-aldosterone system inhibitors have a protective effect for severe COVID-19 outcomes, unlike similar drugs. Finally, spatial transcriptomic data from COVID-19 patient autopsy tissues reveal distinct ACE2 expression loci, with macrophage and neutrophil infiltration in the lungs. These findings can inform public health and may help develop and drive SARS-CoV-2 diagnostic, prevention, and treatment strategies.

Targeted Single-Cell RNA-seq Identifies Minority Cell Types of Kidney Distal Nephron

Journal of the American Society of Nephrology : JASN

2021 Mar 04

Chen, L;Chou, CL;Knepper, MA;
PMID: 33769948 | DOI: 10.1681/ASN.2020101407

Proximal tubule cells dominate the kidney parenchyma numerically, although less abundant cell types of the distal nephron have disproportionate roles in water and electrolyte balance. Coupling of a FACS-based enrichment protocol with single-cell RNA-seq profiled the transcriptomes of 9099 cells from the thick ascending limb (CTAL)/distal convoluted tubule (DCT) region of the mouse nephron. Unsupervised clustering revealed Slc12a3+/Pvalb+ and Slc12a3+/Pvalb- cells, identified as DCT1 and DCT2 cells, respectively. DCT1 cells appear to be heterogeneous, with orthogonally variable expression of Slc8a1, Calb1, and Ckb. An additional DCT1 subcluster showed marked enrichment of cell cycle-/cell proliferation-associated mRNAs (e.g., Mki67, Stmn1, and Top2a), which fit with the known plasticity of DCT cells. No DCT2-specific transcripts were found. DCT2 cells contrast with DCT1 cells by expression of epithelial sodium channel β- and γ-subunits and much stronger expression of transcripts associated with calcium transport (Trpv5, Calb1, S100g, and Slc8a1). Additionally, scRNA-seq identified three distinct CTAL (Slc12a1+) cell subtypes. One of these expressed Nos1 and Avpr1a, consistent with macula densa cells. The other two CTAL clusters were distinguished by Cldn10 and Ptger3 in one and Cldn16 and Foxq1 in the other. These two CTAL cell types were also distinguished by expression of alternative Iroquois homeobox transcription factors, with Irx1 and Irx2 in the Cldn10+ CTAL cells and Irx3 in the Cldn16+ CTAL cells. Single-cell transcriptomics revealed unexpected diversity among the cells of the distal nephron in mouse. Web-based data resources are provided for the single-cell data.

Neuropathology of the 21th century for the Latin American epilepsy community

Seizure

2021 Feb 08

Peixoto-Santos, JE;Blumcke, I;
PMID: 33602567 | DOI: 10.1016/j.seizure.2021.02.003

Many people with epilepsy remain drug-resistant, despite continuous efforts and advances in research and treatment. It is mandatory to understand the epilepsy's underlying etiology, whether it is structural, genetic, infectious, metabolic, immune or (currently) unknown, as it contains major information about the clinical phenotype, cognitive comorbidities, (new) drug targets and also help to predict postsurgical outcome. A multimodal approach, including digital slides and multichannel immunofluorescence labelling can increase the diagnostic yield of subtle pathologies, while DNA methylation arrays could helps in the diagnosis of difficult-to-classify lesions. Such techniques are not always available, however, in low-income countries. Even without access to expensive molecular techniques, automated analysis scripts and machine learning algorithms can be developed by Latin American researchers to improve our diagnostic yield from routine Hematoxylin & Eosin stained tissue sections. The pathology community of Latin America contributed substantially to our current knowledge of etiologies related to human epilepsies and experimental epilepsy models. To further boost the impact of Latin American research, local centers should adhere to modern, multimodal neuropathology techniques, integrate different levels of knowledge, and strengthen their scientific collaborations. Dedicated teaching courses in Epileptology, such as the Latin American Summer Schools of Epilepsy (LASSE) or International Summer School for Neuropathology and Epilepsy Surgery (INES) addressing young researcher and neurologists, are most successful to promote this endeavor. In this review, we will describe the state of neuropathology at the 21st century and also highlight Latin American researchers' contributions to the current knowledge in neuropathology of epilepsy.

EOSINOPHIL DEPLETION PARTIALLY PROTECTS FROM INTESTINAL INFLAMMATION, BUT RESULTS IN INCREASED COLLAGEN DEPOSITION IN A DSS COLITIS MODEL

Acta Gastro

2022 Jan 01

Sabino, J;Cremer, J;Guedelha, ;

Introduction: The role of eosinophils in intestinal inflammation and fibrosis in inflammatory bowel disease (IBD) is largely unknown. Aim: Therefore, we assessed the functional role of eosinophils in a chronic murine model of colitis and associated fibrosis via anti-CCR3 mediated eosinophil depletion. Methods: 6-8-week-old C57BL/6 RAG-/- mice received three cycles of dextran sodium sulphate (DSS) (1.75% - 2.25% - 2.25%) each interspersed with 14 days of recovery. Twice weekly, anti-CCR3 antibody (n=8), isotype (n=8) or saline injections (n=8) were given intraperitoneally. At the same timepoints, the disease activity index (DAI; mouse weight, stool consistency and presence of blood) was determined. At sacrifice, colonic damage was scored macroscopically (presence of hyperaemia, adhesions and length and degree of colon affected by inflammation). Colonic single cells were isolated and stained for flow cytometry, where eosinophils were characterized as CD45+ CD11b+ Siglec-F+ CD117- cells. Intestinal fibrosis was scored via colon weight/length, collagen deposition, using a colorimetric hydroxyproline assay and Martius Scarlet Blue staining (MSB), and COL1A1 expression by PCR.Results: Anti-CCR3 mediated eosinophil depletion resulted in decreased disease activity compared to the other DSS treated groups injected with saline or isotype, determined by the area under the curve of the DAI (74.6±18.4 vs. 127.5±42.9 and 136.9±33.6, p=0.01 and p=0.0008 respectively). The macroscopic damage score also suggested eosinophil depleted mice to be partially protected from colonic inflammation compared to the saline and isotype injected mice that received DSS (1.1±1.0 vs. 2.1±1.2 and 3.0±0.7, p=0.09 and p=0.001 respectively). Colon weight/length and hydroxyproline assay showed a trend towards increased fibrosis in the anti-CCR3 injected group compared to saline (p=0.03 and 0.07, respectively) but not isotype (p=0.3 and 0.1, respectively) injected groups. However, COL1A1 expression levels were significantly increased in the eosinophil depleted mice compared to the saline and isotype injected mice receiving DSS (43.2±11.4 vs. 23.3±8.7 and 30.1±11.0, p=0.002 and 0.04 respectively), indicating increased collagen expression. Moreover, MSB staining showed increased collagen deposition in the anti-CCR3 treated group compared to the isotype (p=0.0008), but not the saline (p=0.09) injected group exposed to DSS. Conclusions: Eosinophil depletion via intraperitoneal anti-CCR3 injections resulted in partial protection against colonic inflammation, but was associated with increased collagen expression and deposition. Caution is therefore needed when designing therapeutic interventions targeting eosinophils

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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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