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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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Presence of TRPA1 Modifies CD4+/CD8+ T Lymphocyte Ratio and Activation

Pharmaceuticals (Basel, Switzerland)

2022 Jan 01

Szabó, K;Kemény, Á;Balázs, N;Khanfar, E;Sándor, Z;Boldizsár, F;Gyulai, R;Najbauer, J;Pintér, E;Berki, T;
PMID: 35056114 | DOI: 10.3390/ph15010057

Transient Receptor Potential Ankyrin 1 (TRPA1) has been reported to influence neuroinflammation and lymphocyte function. We analysed the immune phenotype and activation characteristics of TRPA1-deficient mice (knockout-KO) generated by targeted deletion of the pore-loop domain of the ion channel. We compared TRPA1 mRNA and protein expression in monocyte and lymphocyte subpopulations isolated from primary and secondary lymphatic organs of wild type (WT) and KO mice. qRT-PCR and flow cytometric studies indicated a higher level of TRPA1 in monocytes than in lymphocytes, but both were orders of magnitude lower than in sensory neurons. We found lower CD4+/CD8+ thymocyte ratios, diminished CD4/CD8 rates, and B cell numbers in the KO mice. Early activation marker CD69 was lower in CD4+ T cells of KO, while the level of CD8+/CD25+ cells was higher. In vitro TcR-mediated activation did not result in significant differences in CD69 level between WT and KO splenocytes, but lower cytokine (IL-1β, IL-6, TNF-α, IL-17A, IL-22, and RANTES) secretion was observed in KO splenocytes. Basal intracellular Ca2+ level and TcR-induced Ca2+ signal in T lymphocytes did not differ significantly, but interestingly, imiquimod-induced Ca2+ level in KO thymocytes was higher. Our results support the role of TRPA1 in the regulation of activation, cytokine production, and T and B lymphocytes composition in mice.
PD-L1 expression in tumor cells is associated with a favorable prognosis in patients with high-risk endometrial cancer

Gynecologic oncology

2021 Jul 13

Zong, L;Sun, Z;Mo, S;Lu, Z;Yu, S;Xiang, Y;Chen, J;
PMID: 34272092 | DOI: 10.1016/j.ygyno.2021.07.009

To investigate programmed cell death ligand 1 (PD-L1) expression patterns and define the associations among PD-L1, molecular subtypes, pathological features, and survival in a cohort of 833 patients with endometrial cancer, of whom approximately half had high-risk disease.Using direct sequencing of the polymerase epsilon (POLE) exonuclease domain as well as immunohistochemistry for mismatch repair (MMR) proteins (MLH1, PMS2, MSH2, and MSH6) and p53, we stratified endometrial cancers into four molecular subtypes: POLE ultramutated, MMR-deficient, p53-mutant, and non-specific molecular profile (NSMP). PD-L1 was detected via immunohistochemistry and evaluated in tumor cells (TCs) and immune cells (ICs) individually and using the combined positive score (CPS).Positive PD-L1 staining in TCs (≥1%), ICs (≥1%), and in combination (CPS ≥1) was detected in 14.0%, 37.3%, and 45.1% of the samples, respectively. PD-L1 positivity in TCs was more frequent in high-grade than in low-grade tumors, while that in ICs was associated with lymphovascular space invasion, non-endometrioid histology, and deep myometrial invasion. PD-L1 expression in both TCs and ICs was more frequent in POLE ultramutated and MMR-deficient subtypes than in p53-mutant and NSMP subtypes. PD-L1 positivity in TCs, but not in ICs or combined (CPS), was associated with a favorable prognosis in patients with high-risk endometrial cancer.The distribution and prognostic significance of PD-L1 in TCs versus ICs differ in patients with endometrial cancer, indicating that the separate assessment of PD-L1 in these cells (rather than determining the CPS) may be more relevant to selecting patients eligible for endometrial cancer immunotherapy.
JAK1 Inhibition during CAR T-Cell Treatment Does Not Affect CAR T-Cell Proliferation, Persistence, or Function

Blood

2022 Nov 15

Pratta, M;Burke, L;DiPersio, J;Maziarz, R;Feldman, P;Brodeur, T;Timmers, C;Ivanova, O;Barbour, A;Morariu-Zamfir, R;Frigault, M;
| DOI: 10.1182/blood-2022-169382

PRATTA:_Incyte Corporation:_ Current Employment, Current equity holder in private company, Current holder of _stock options_ in a privately-held company. BURKE:_Incyte Corporation:_ Current Employment, Current equity holder in private company, Current holder of _stock options_ in a privately-held company. DIPERSIO:_BioLineRx, Ltd.:_ Research Funding; _Macrogenics:_ Research Funding; _NeoImmune Tech:_ Research Funding; _Amphivena Therapeutics:_ Research Funding; _hC Bioscience, Inc.:_ Membership on an entity's Board of Directors or advisory committees; _RiverVest Venture Partners:_ Consultancy, Membership on an entity's Board of Directors or advisory committees; _Incyte:_ Consultancy, Research Funding; _WUGEN:_ Current equity holder in private company, Research Funding; _CAR-T cell Product with Washington University and WUGEN:_ Patents & Royalties; _VLA-4 Inhibitor with Washington University and Magenta Therapeutics:_ Patents & Royalties; _Magenta Therapeutics:_ Current equity holder in private company, Membership on an entity's Board of Directors or advisory committees. MAZIARZ:_ASTCT:_ Membership on an entity's Board of Directors or advisory committees; _CRISPR Therapeutics:_ Consultancy, Honoraria; _Novartis:_ Other: Support for research on CART; _Allovir:_ Other: Support for research on Allo HCT costs of care of infectious related complications; _Orca Bio:_ Other: Support for research analysis and for medical writing. FELDMAN:_Incyte Corporation:_ Current Employment, Current equity holder in private company, Current holder of _stock options_ in a privately-held company. BRODEUR:_Incyte Corporation:_ Current Employment, Current equity holder in private company, Current holder of _stock options_ in a privately-held company. TIMMERS:_Incyte Corporation:_ Current Employment, Current equity holder in private company, Current holder of _stock options_ in a privately-held company. IVANOVA:_Incyte Corporation:_ Current Employment, Current equity holder in private company, Current holder of _stock options_ in a privately-held company. BARBOUR:_Incyte Corporation:_ Ended employment in the past 24 months; _Karyopharm:_ Current Employment, Current equity holder in publicly-traded company. MORARIU-ZAMFIR:_Incyte Corporation:_ Current Employment, Current equity holder in private company, Current holder of _stock options_ in a privately-held company. FRIGAULT:_Cytoagents:_ Consultancy; _Iovance:_ Consultancy; _Novartis:_ Consultancy, Research Funding; _Kite/Gilead:_ Consultancy, Research Funding; _Arcellx:_ Research Funding; _JnJ/Legend:_ Consultancy; _BMS:_ Consultancy.
Intercellular Arc Signaling Regulates Vasodilation

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

2021 Jul 29

de la Peña, JB;Barragan-Iglesias, P;Lou, TF;Kunder, N;Loerch, S;Shukla, T;Basavarajappa, L;Song, J;James, DN;Megat, S;Moy, JK;Wanghzou, A;Ray, PR;Hoyt, K;Steward, O;Price, TJ;Shepherd, J;Campbell, ZT;
PMID: 34326146 | DOI: 10.1523/JNEUROSCI.0440-21.2021

Injury responses require communication between different cell types in the skin. Sensory neurons contribute to inflammation and can secrete signaling molecules that affect non-neuronal cells. Despite the pervasive role of translational regulation in nociception, the contribution of activity-dependent protein synthesis to inflammation is not well understood. To address this problem, we examined the landscape of nascent translation in murine dorsal root ganglion (DRG) neurons treated with inflammatory mediators using ribosome profiling. We identified the activity-dependent gene, Arc, as a target of translation in vitro and in vivo Inflammatory cues promote local translation of Arc in the skin. Arc-deficient male mice display exaggerated paw temperatures and vasodilation in response to an inflammatory challenge. Since Arc has recently been shown to be released from neurons in extracellular vesicles (EVs), we hypothesized that intercellular Arc signaling regulates the inflammatory response in skin. We found that the excessive thermal responses and vasodilation observed in Arc defective mice are rescued by injection of Arc-containing EVs into the skin. Our findings suggest that activity-dependent production of Arc in afferent fibers regulates neurogenic inflammation potentially through intercellular signaling.SIGNIFICANCE STATEMENTNociceptors play prominent roles in pain and inflammation. We examined rapid changes in the landscape of nascent translation in cultured dorsal root ganglia (DRGs) treated with a combination of inflammatory mediators using ribosome profiling. We identified several hundred transcripts subject to rapid preferential translation. Among them is the immediate early gene (IEG) Arc. We provide evidence that Arc is translated in afferent fibers in the skin. Arc-deficient mice display several signs of exaggerated inflammation which is normalized on injection of Arc containing extracellular vesicles (EVs). Our work suggests that noxious cues can trigger Arc production by nociceptors which in turn constrains neurogenic inflammation in the skin.
A03 Alternative processing of human HTT MRNA in YAC128 mice: implications for Huntington’s disease therapeutics

A: Pathogenic mechanisms

2022 Sep 01

Fienko, S;Landles, C;Sathasivam, K;Gomez-Paredes, C;McAteer, S;Milton, R;Osborne, G;Jones, S;Phillips, J;Kordasiewicz, H;Bates, G;
| DOI: 10.1136/jnnp-2022-ehdn.3

RESULTS Microscopic analysis revealed that the full-length _HTT_ mRNA (_FL-HTT_) was retained in RNA nuclear clusters together with the incompletely spliced _HTT1a_ transcript. These clusters were not observed in zQ175 HD mouse model where, instead, _FL-Htt_ and _Htt1a_ mRNAs were detected as mostly cytoplasmic molecules. Immunohistochemistry showed a progressive appearance of aggregated HTT in nuclei in the cortex, striatum, hippocampus and cerebellum. HTRF indicated that the level of exon 1 HTT was highest in the cerebellum. Soluble mutant exon 1 HTT decreased with age, with concomitant increase in aggregated HTT. In YAC128 MEFs, _HTT1a_ was detected and ASOs targeting _HTT_ were efficient in lowering _HTT_ levels in this model system.
Macrophage Identification In Situ

Biomedicines

2021 Oct 04

Nikovics, K;Favier, AL;
PMID: 34680510 | DOI: 10.3390/biomedicines9101393

Understanding the processes of inflammation and tissue regeneration after injury is of great importance. For a long time, macrophages have been known to play a central role during different stages of inflammation and tissue regeneration. However, the molecular and cellular mechanisms by which they exert their effects are as yet mostly unknown. While in vitro macrophages have been characterized, recent progress in macrophage biology studies revealed that macrophages in vivo exhibited distinctive features. Actually, the precise characterization of the macrophages in vivo is essential to develop new healing treatments and can be approached via in situ analyses. Nowadays, the characterization of macrophages in situ has improved significantly using antigen surface markers and cytokine secretion identification resulting in specific patterns. This review aims for a comprehensive overview of different tools used for in situ macrophage identification, reporter genes, immunolabeling and in situ hybridization, discussing their advantages and limitations.
Dysfunction of Trio GEF1 involves in excitatory/inhibitory imbalance and autism-like behaviors through regulation of interneuron migration

Molecular psychiatry

2021 May 07

Sun, X;Wang, L;Wei, C;Sun, M;Li, Q;Meng, H;Yue, W;Zhang, D;Li, J;
PMID: 33963279 | DOI: 10.1038/s41380-021-01109-x

Autism spectrum disorders (ASDs) are a group of highly inheritable neurodevelopmental disorders. Functional mutations in TRIO, especially in the GEF1 domain, are strongly implicated in ASDs, whereas the underlying neurobiological pathogenesis and molecular mechanisms remain to be clarified. Here we characterize the abnormal morphology and behavior of embryonic migratory interneurons (INs) upon Trio deficiency or GEF1 mutation in mice, which are mediated by the Trio GEF1-Rac1 activation and involved in SDF1α/CXCR4 signaling. In addition, the migration deficits are specifically associated with altered neural microcircuit, decreased inhibitory neurotransmission, and autism-like behaviors, which are reminiscent of some features observed in patients with ASDs. Furthermore, restoring the excitatory/inhibitory (E/I) imbalance via activation of GABA signaling rescues autism-like deficits. Our findings demonstrate a critical role of Trio GEF1 mediated signaling in IN migration and E/I balance, which are related to autism-related behavioral phenotypes.
MYD88 L265P mutation and interleukin-10 detection in cerebrospinal fluid are highly specific discriminating markers in patients with primary central nervous system lymphoma: results from a prospective study

British journal of haematology

2021 Feb 23

Ferreri, AJM;Calimeri, T;Lopedote, P;Francaviglia, I;Daverio, R;Iacona, C;Belloni, C;Steffanoni, S;Gulino, A;Anghileri, E;Diffidenti, A;Finardi, A;Gagliardi, F;Anzalone, N;Nonis, A;Furlan, R;De Lorenzo, D;Terreni, MR;Martinelli, V;Sassone, M;Foppoli, M;Angelillo, P;Guggiari, E;Falini, A;Mortini, P;Filippi, M;Tarantino, V;Eoli, M;Ciceri, F;Doglioni, C;Tripodo, C;Locatelli, M;Cangi, MG;Ponzoni, M;
PMID: 33620087 | DOI: 10.1111/bjh.17357

Reliable biomarkers are needed to avoid diagnostic delay and its devastating effects in patients with primary central nervous system (CNS) lymphoma (PCNSL). We analysed the discriminating sensitivity and specificity of myeloid differentiation primary response (88) (MYD88) L265P mutation (mut-MYD88) and interleukin-10 (IL-10) in cerebrospinal fluid (CSF) of both patients with newly diagnosed (n = 36) and relapsed (n = 27) PCNSL and 162 controls (118 CNS disorders and 44 extra-CNS lymphomas). The concordance of MYD88 mutational status between tumour tissue and CSF sample and the source of ILs in PCNSL tissues were also investigated. Mut-MYD88 was assessed by TaqMan-based polymerase chain reaction. IL-6 and IL-10 messenger RNA (mRNA) was assessed on PCNSL biopsies using RNAscope technology. IL levels in CSF were assessed by enzyme-linked immunosorbent assay. Mut-MYD88 was detected in 15/17 (88%) PCNSL biopsies, with an 82% concordance in paired tissue-CSF samples. IL-10 mRNA was detected in lymphomatous B cells in most PCNSL; expression of IL-6 transcripts was negligible. In CSF samples, mut-MYD88 and high IL-10 levels were detected, respectively, in 72% and 88% of patients with newly diagnosed PCNSL and in 1% of controls; conversely, IL-6 showed a low discriminating sensitivity and specificity. Combined analysis of MYD88 and IL-10 exhibits a sensitivity and specificity to distinguish PCNSL of 94% and 98% respectively. Similar figures were recorded in patients with relapsed PCNSL. In conclusion, high detection rates of mut-MYD88 and IL-10 in CSF reflect, respectively, the MYD88 mutational status and synthesis of this IL in PCNSL tissue. These biomarkers exhibit a very high sensitivity and specificity in detecting PCNSL both at initial diagnosis and relapse. Implications of these findings in patients with lesions unsuitable for biopsy deserve to be investigated.
Quality Assessment of Proteins and RNA Following Storage in Archival Formalin-Fixed Paraffin-Embedded Human Breast Cancer Tissue Microarray Sections

Biopreservation and biobanking

2022 Oct 19

Kim, K;Ylaya, K;Perry, C;Lee, MY;Kim, JW;Chung, JY;Hewitt, SM;
PMID: 36264172 | DOI: 10.1089/bio.2022.0090

Although the immunogenicity of formalin-fixed paraffin-embedded tissue sections can decrease during storage and transport, the exact mechanism of antigenic loss and how to prevent it are not clear. Herein, we investigated changes in the expression of estrogen receptor (ER), progesterone receptor (PR), human epidermal growth factor receptor 2 (HER-2), E-cadherin, and Ki-67 in human breast tissue microarray (TMA) tissue sections stored for up to 3 months in dry and wet conditions. The positive rates of ER and PR expression were minimally changed after 3 months of storage, but the Allred scores of ER and PR stored in humid conditions decreased remarkably in comparison to fresh-cut tissue. The HER-2 antigenicity and RNA integrity of breast TMA sections stored in dry conditions diminished gradually with storage time, whereas the immunoreactivity and RNA quality of HER-2 in humid conditions decreased sharply as storage length increased. The area and intensity of E-cadherin staining in tissue sections stored in dry conditions did not change significantly and were minimally changed after 3 months, respectively. In contrast, the area and intensity of E-cadherin staining in tissue sections stored in humid conditions decreased significantly as storage length increased. Finally, the Ki-67 labeling index of tissue sections stored for 3 months in dry (9% decrease) and wet (31.9% decrease) conditions was decreased in comparison to fresh sections. In conclusion, these results indicate that water is a crucial factor for protein and RNA degradation in stored tissue sections, and detailed guidelines are required in the clinic.
Repeated cocaine or methamphetamine treatment alters astrocytic CRF2 and GLAST expression in the ventral midbrain

Addiction biology

2021 Nov 25

Sharpe, AL;Trzeciak, M;Eliason, NL;Blankenship, HE;Byrd, BAM;Douglas, PD;Freeman, WM;Beckstead, MJ;
PMID: 34825430 | DOI: 10.1111/adb.13120

Dopamine neurons in the substantia nigra (SN) and ventral tegmental area (VTA) play a central role in the reinforcing properties of abused drugs including methamphetamine and cocaine. Chronic effects of psychostimulants in the SN/VTA also involve non-dopaminergic transmitters, including glutamate and the stress-related peptide corticotropin-releasing factor (CRF). In the SN/VTA, astrocytes express a variety of membrane-bound neurotransmitter receptors and transporters that influence neurotransmission. CRF receptor type 2 (CRF2) activity in the VTA is important for stress-induced relapse and drug-seeking behaviour, but the localization of its effects is incompletely understood. Here, we first identified CRF2 transcript in astrocytes of the SN/VTA using RNA-Seq in Aldh1l1;NuTRAP mice and confirmed it using in situ hybridization (RNAscope) in wild-type mice. We then used immunofluorescence to quantify the astrocytic marker protein S100β, glial-specific glutamate/aspartate transporter GLAST, and CRF2 in the SN/VTA following 12 days of treatment (i.p.) with methamphetamine (3 mg/kg), cocaine (10 mg/kg), or saline. We observed a significant decrease in GLAST immunofluorescence in brains of psychostimulant treated mice compared with saline controls. In addition, we observed increased labelling of CRF2 in drug treated groups, a decrease in the number of S100β positive cells, and an increase of co-staining of CRF2 with both S100β and tyrosine hydroxylase (dopamine neurons). Our results suggest a significant interaction between CRF2, GLAST, and astrocytes in the midbrain that emerges with repeated exposure to psychostimulants. These findings provide rationale for future investigation of astrocyte-based strategies for altering cellular and circuit function in response to stress and drug exposure.
Sex differences in the rodent hippocampal opioid system following stress and oxycodone associated learning processes

Pharmacology, biochemistry, and behavior

2021 Nov 06

Chalangal, J;Mazid, S;Windisch, K;Milner, TA;
PMID: 34752798 | DOI: 10.1016/j.pbb.2021.173294

Over the past two decades, opioid abuse has risen especially among women. In both sexes hippocampal neural circuits involved in associative memory formation and encoding of motivational incentives are critically important in the transition from initial drug use to drug abuse/dependence. The opioid circuit particularly the mossy fiber pathway, are crucial for associative memory processes important for addiction. Our anatomical studies, especially those utilizing electron microscopic immunocytochemistry, have provided unique insight into sex differences in the distribution of opioid peptides and receptors in specific hippocampal circuits and how these distributions are altered following stress and oxycodone-associative learning processes. Here we review the hippocampal opioid system in rodents with respect to ovarian hormones effects and baseline sex differences then sex differences following acute and chronic stress. Next, we review sex differences in the hippocampal opioid system in unstressed and chronically stressed rats following oxycodone conditioned place preference. We show that opioid peptides and receptors are distributed within hippocampal circuits in females with elevated estrogen states in a manner that would enhance sensitivity to endogenous and exogenous opioids. Moreover, chronic stress primes the opioid system in females in a manner that would promote opioid-associative learning processes. In contrast, chronic stress has limited effects on the opioid system in males and reduces its capacity to support opioid-mediated learning processes. Interestingly, acute stress appears to prime males for opioid associative learning. On a broader scale the findings highlighted in this review have important implications in understanding sex differences in opioid drug use and abuse.
The spectrum of histopathological findings after SVR to DAA for recurrent HCV infection in liver transplant recipients

Virchows Archiv : an international journal of pathology

2021 Sep 08

Sanghi, V;Romero-Marrero, C;Flocco, G;Graham, RP;Abduljawad, B;Niyazi, F;Asfari, MM;Hashimoto, K;Eghtesad, B;Menon, KVN;Aucejo, FN;Lopez, R;Yerian, LM;Allende, DS;
PMID: 34498114 | DOI: 10.1007/s00428-021-03191-6

Sustained virological response (SVR) to the treatment of recurrent HCV in liver transplant recipients has excellent clinical outcomes; however, little is known about the effects on allograft histology. The study aimed to assess the histology of the allograft liver. In this single-center, retrospective cohort study, patients with recurrent hepatitis C (HCV) in allograft liver who were cured with antiviral therapy between 2010 and 2016 were identified. Biopsies were reviewed by two liver pathologists blinded to the treatment and SVR status. Paired analysis was performed to compare pre- and post-treatment histological features. Of the 62 patients analyzed, 22 patients received PEGylated interferon/ribavirin (IFN) therapy, while 40 patients received direct-acting antiviral agents (DAA). The mean age was 57 years, 24% were female, and 79% were Caucasian. RNA in situ hybridization testing for HCV and HEV was negative in all the tested patients. Significant reduction in the inflammatory grade of post-treatment biopsy specimens was noted in all subjects (n = 57; p < 0.001) and in the IFN group (n = 21; p = 0.001) but not in the DAA group (p = 0.093). Of all subjects, 21% had worsening stage, 31% had improvement, and 48% had no change in stage. Of the treatment groups, 27% in the IFN and 17% in the DAA groups had worsening stage; however, the results were not statistically significant in all subjects or by treatment modality. Persistent inflammatory infiltrates and fibrosis was noted in allograft tissue of patients cured with DAA. Significant improvement in grade was noted in the IFN group, without a significant change in stage.

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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
EnEmProbe targets exons n and m
En-EmProbe 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

Enabling research, drug development (CDx) and diagnostics

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