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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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A lncRNA-encoded mitochondrial micropeptide exacerbates microglia-mediated neuroinflammation in retinal ischemia/reperfusion injury

Cell death & disease

2023 Feb 15

Zheng, X;Wang, M;Liu, S;Chen, H;Li, Y;Yuan, F;Yang, L;Qiu, S;Wang, H;Xie, Z;Xiang, M;
PMID: 36792584 | DOI: 10.1038/s41419-023-05617-2

As a common pathology of many ocular disorders such as diabetic retinopathy and glaucoma, retinal ischemia/reperfusion (IR) triggers inflammation and microglia activation that lead to irreversible retinal damage. The detailed molecular mechanism underlying retinal IR injury, however, remains poorly understood at present. Here we report the bioinformatic identification of a lncRNA 1810058I24Rik (181-Rik) that was shown to encode a mitochondrion-located micropeptide Stmp1. Its deficiency in mice protected retinal ganglion cells from retinal IR injury by attenuating the activation of microglia and the Nlrp3 inflammasome pathway. Moreover, its genetic knockout in mice or knockdown in primary microglia promoted mitochondrial fusion, impaired mitochondrial membrane potential, and reactive oxygen species (ROS) production, diminished aerobic glycolysis, and ameliorated inflammation. It appears that 181-Rik may trigger the Nlrp3 inflammasome activation by controlling mitochondrial functions through inhibiting expression of the metabolic sensor uncoupling protein 2 (Ucp2) and activating expression of the Ca2+ sensors S100a8/a9. Together, our findings shed new light on the molecular pathogenesis of retinal IR injury and may provide a fresh therapeutic target for IR-associated neurodegenerative diseases.
A TRPV4-dependent neuro-immune axis in the spinal cord promotes neuropathic pain

The Journal of clinical investigation

2023 Jan 26

Hu, X;Du, L;Liu, S;Lan, Z;Zang, K;Feng, J;Zhao, Y;Yang, X;Xie, Z;Wang, PL;Ver Heul, AM;Chen, L;Samineni, VK;Wang, YQ;Lavine, KJ;Gereau, RW;Wu, GF;Hu, H;
PMID: 36701202 | DOI: 10.1172/JCI161507

Microglia, resident macrophages of the central nervous system (CNS), are essential to brain development, homeostasis, and disease. Microglial activation and proliferation are hallmarks of many CNS diseases including neuropathic pain. However, molecular mechanisms that govern the spinal neuro-immune axis in the setting of neuropathic pain remain incompletely understood. Here we show that genetic ablation or pharmacological blockade of transient receptor potential vanilloid type 4 (TRPV4) markedly attenuated neuropathic pain-like behaviors in a mouse model of spared nerve injury. Mechanistically, microglia-expressed TRPV4 mediated microglial activation and proliferation and promoted functional and structural plasticity of excitatory spinal neurons through releasing lipocalin-2. Our results suggest that microglial TRPV4 channels reside at the center of the neuro-immune axis in the spinal cord that transforms peripheral nerve injury into central sensitization and neuropathic pain, thereby identifying TRPV4 as a promising new target for the treatment of chronic pain.
Blood-brain barrier penetration of non-replicating SARS-CoV-2 and S1 Variants of Concern induce neuroinflammation which is accentuated in a mouse model of Alzheimer's disease

Brain, behavior, and immunity

2023 Jan 19

Erickson, MA;Logsdon, AF;Rhea, EM;Hansen, KM;Holden, SJ;Banks, WA;Smith, JL;German, C;Farr, SA;Morley, JE;Weaver, RR;Hirsch, AJ;Kovac, A;Kontsekova, E;Baumann, KK;Omer, MA;Raber, J;
PMID: 36682515 | DOI: 10.1016/j.bbi.2023.01.010

COVID-19 and especially Long COVID are associated with severe CNS symptoms and may place persons at risk to develop long-term cognitive impairments. Here, we show that two non-infective models of SARS-CoV-2 can cross the blood-brain barrier (BBB) and induce neuroinflammation, a major mechanism underpinning CNS and cognitive impairments, even in the absence of productive infection. The viral models cross the BBB by the mechanism of adsorptive transcytosis with the sugar N-acetylglucosamine being key. The delta and omicron variants cross the BBB faster than the other variants of concern, with peripheral tissue uptake rates also differing for the variants. Neuroinflammation induced by icv injection of S1 protein was greatly enhanced in young and especially in aged SAMP8 mice, a model of Alzheimer's disease, whereas sex and obesity had little effect.
Continuous cholinergic-dopaminergic updating in the nucleus accumbens underlies approaches to reward-predicting cues

Nature communications

2022 Dec 24

Skirzewski, M;Princz-Lebel, O;German-Castelan, L;Crooks, AM;Kim, GK;Tarnow, SH;Reichelt, A;Memar, S;Palmer, D;Li, Y;Jane Rylett, R;Saksida, LM;Prado, VF;Prado, MAM;Bussey, TJ;
PMID: 36564387 | DOI: 10.1038/s41467-022-35601-x

The ability to learn Pavlovian associations from environmental cues predicting positive outcomes is critical for survival, motivating adaptive behaviours. This cued-motivated behaviour depends on the nucleus accumbens (NAc). NAc output activity mediated by spiny projecting neurons (SPNs) is regulated by dopamine, but also by cholinergic interneurons (CINs), which can release acetylcholine and glutamate via the activity of the vesicular acetylcholine transporter (VAChT) or the vesicular glutamate transporter (VGLUT3), respectively. Here we investigated behavioural and neurochemical changes in mice performing a touchscreen Pavlovian approach task by recording dopamine, acetylcholine, and calcium dynamics from D1- and D2-SPNs using fibre photometry in control, VAChT or VGLUT3 mutant mice to understand how these signals cooperate in the service of approach behaviours toward reward-predicting cues. We reveal that NAc acetylcholine-dopaminergic signalling is continuously updated to regulate striatal output underlying the acquisition of Pavlovian approach learning toward reward-predicting cues.
An opioid-gated thalamoaccumbal circuit for the suppression of reward seeking in mice

Nature communications

2022 Nov 11

Vollmer, KM;Green, LM;Grant, RI;Winston, KT;Doncheck, EM;Bowen, CW;Paniccia, JE;Clarke, RE;Tiller, A;Siegler, PN;Bordieanu, B;Siemsen, BM;Denton, AR;Westphal, AM;Jhou, TC;Rinker, JA;McGinty, JF;Scofield, MD;Otis, JM;
PMID: 36369508 | DOI: 10.1038/s41467-022-34517-w

Suppression of dangerous or inappropriate reward-motivated behaviors is critical for survival, whereas therapeutic or recreational opioid use can unleash detrimental behavioral actions and addiction. Nevertheless, the neuronal systems that suppress maladaptive motivated behaviors remain unclear, and whether opioids disengage those systems is unknown. In a mouse model using two-photon calcium imaging in vivo, we identify paraventricular thalamostriatal neuronal ensembles that are inhibited upon sucrose self-administration and seeking, yet these neurons are tonically active when behavior is suppressed by a fear-provoking predator odor, a pharmacological stressor, or inhibitory learning. Electrophysiological, optogenetic, and chemogenetic experiments reveal that thalamostriatal neurons innervate accumbal parvalbumin interneurons through synapses enriched with calcium permeable AMPA receptors, and activity within this circuit is necessary and sufficient for the suppression of sucrose seeking regardless of the behavioral suppressor administered. Furthermore, systemic or intra-accumbal opioid injections rapidly dysregulate thalamostriatal ensemble dynamics, weaken thalamostriatal synaptic innervation of downstream neurons, and unleash reward-seeking behaviors in a manner that is reversed by genetic deletion of thalamic µ-opioid receptors. Overall, our findings reveal a thalamostriatal to parvalbumin interneuron circuit that is both required for the suppression of reward seeking and rapidly disengaged by opioids.
IL-15 Blockade and Rapamycin Rescue Multifactorial Loss of Factor VIII from AAV-Transduced Hepatocytes in Hemophilia A Mice

Molecular therapy : the journal of the American Society of Gene Therapy

2022 Jul 12

Butterfield, JSS;Yamada, K;Bertolini, TB;Syed, F;Kumar, SRP;Li, X;Arisa, S;Piñeros, AR;Tapia, A;Rogers, CA;Li, N;Rana, J;Biswas, M;Terhorst, C;Kaufman, RJ;de Jong, YP;Herzog, RW;
PMID: 35821634 | DOI: 10.1016/j.ymthe.2022.07.005

Hepatic adeno-associated viral (AAV) gene transfer has the potential to cure the X-linked bleeding disorder hemophilia A. However, declining therapeutic coagulation factor VIII (FVIII) expression has plagued clinical trials. To assess the mechanistic underpinnings of this loss of FVIII expression, we developed a hemophilia A mouse model that shares key features observed in clinical trials. Following liver-directed AAV8 gene transfer in the presence of rapamycin, initial FVIII protein expression declines over time in the absence of antibody formation. Surprisingly, loss of FVIII protein production occurs despite persistence of transgene and mRNA, suggesting a translational shutdown rather than a loss of transduced hepatocytes. Some of the animals develop ER stress, which may be linked to hepatic inflammatory cytokine expression. FVIII protein expression is preserved by IL-15/IL-15R blockade, which suppresses CD8+ T and NK cell responses. Interestingly, mice with initial FVIII levels >100% of normal had diminishing expression while still under immune suppression. Taken together, our findings of inter-animal variability of the response, and the ability of the immune system to shut down transgene expression without utilizing cytolytic or antibody-mediated mechanisms illustrate the challenges associated with FVIII gene transfer. Our protocols based upon cytokine blockade should help maintaining efficient FVIII expression.
Mapping hormone-regulated cell-cell interaction networks in the human breast at single-cell resolution

Cell systems

2022 Jul 15

Murrow, LM;Weber, RJ;Caruso, JA;McGinnis, CS;Phong, K;Gascard, P;Rabadam, G;Borowsky, AD;Desai, TA;Thomson, M;Tlsty, T;Gartner, ZJ;
PMID: 35863345 | DOI: 10.1016/j.cels.2022.06.005

The rise and fall of estrogen and progesterone across menstrual cycles and during pregnancy regulates breast development and modifies cancer risk. How these hormones impact each cell type in the breast remains poorly understood because they act indirectly through paracrine networks. Using single-cell analysis of premenopausal breast tissue, we reveal a network of coordinated transcriptional programs representing the tissue-level response to changing hormone levels. Our computational approach, DECIPHER-seq, leverages person-to-person variability in breast composition and cell state to uncover programs that co-vary across individuals. We use differences in cell-type proportions to infer a subset of programs that arise from direct cell-cell interactions regulated by hormones. Further, we demonstrate that prior pregnancy and obesity modify hormone responsiveness through distinct mechanisms: obesity reduces the proportion of hormone-responsive cells, whereas pregnancy dampens the direct response of these cells to hormones. Together, these results provide a comprehensive map of the cycling human breast.
An atlas of transcriptionally defined cell populations in the rat ventral tegmental area

Cell reports

2022 Apr 05

Phillips, RA;Tuscher, JJ;Black, SL;Andraka, E;Fitzgerald, ND;Ianov, L;Day, JJ;
PMID: 35385745 | DOI: 10.1016/j.celrep.2022.110616

The ventral tegmental area (VTA) is a complex brain region that is essential for reward function and frequently implicated in neuropsychiatric disease. While decades of research on VTA function have focused on dopamine neurons, recent evidence has identified critical roles for GABAergic and glutamatergic neurons in reward processes. Additionally, although subsets of VTA neurons express genes involved in the synthesis and transport of multiple neurotransmitters, characterization of these combinatorial populations has largely relied on low-throughput methods. To comprehensively define the molecular architecture of the VTA, we performed single-nucleus RNA sequencing on 21,600 cells from the rat VTA. Analysis of neuronal subclusters identifies selective markers for dopamine and combinatorial neurons, reveals expression profiles for receptors targeted by drugs of abuse, and demonstrates population-specific enrichment of gene sets linked to brain disorders. These results highlight the heterogeneity of the VTA and provide a resource for further exploration of VTA gene expression.
Lymphocyte infiltration and thyrocyte destruction are driven by stromal and immune cell components in Hashimoto's thyroiditis

Nature communications

2022 Feb 09

Zhang, QY;Ye, XP;Zhou, Z;Zhu, CF;Li, R;Fang, Y;Zhang, RJ;Li, L;Liu, W;Wang, Z;Song, SY;Lu, SY;Zhao, SX;Lin, JN;Song, HD;
PMID: 35140214 | DOI: 10.1038/s41467-022-28120-2

Hashimoto's thyroiditis (HT) is the most common autoimmune disease characterized by lymphocytic infiltration and thyrocyte destruction. Dissection of the interaction between the thyroidal stromal microenvironment and the infiltrating immune cells might lead to a better understanding of HT pathogenesis. Here we show, using single-cell RNA-sequencing, that three thyroidal stromal cell subsets, ACKR1+ endothelial cells and CCL21+ myofibroblasts and CCL21+ fibroblasts, contribute to the thyroidal tissue microenvironment in HT. These cell types occupy distinct histological locations within the thyroid gland. Our experiments suggest that they might facilitate lymphocyte trafficking from the blood to thyroid tissues, and T cell zone CCL21+ fibroblasts may also promote the formation of tertiary lymphoid organs characteristic to HT. Our study also demonstrates the presence of inflammatory macrophages and dendritic cells expressing high levels of IL-1β in the thyroid, which may contribute to thyrocyte destruction in HT patients. Our findings thus provide a deeper insight into the cellular interactions that might prompt the pathogenesis of HT.
Topographic connectivity and cellular profiling reveal detailed input pathways and functionally distinct cell types in the subthalamic nucleus

Cell reports

2022 Mar 01

Jeon, H;Lee, H;Kwon, DH;Kim, J;Tanaka-Yamamoto, K;Yook, JS;Feng, L;Park, HR;Lim, YH;Cho, ZH;Paek, SH;Kim, J;
PMID: 35235786 | DOI: 10.1016/j.celrep.2022.110439

The subthalamic nucleus (STN) controls psychomotor activity and is an efficient therapeutic deep brain stimulation target in individuals with Parkinson's disease. Despite evidence indicating position-dependent therapeutic effects and distinct functions within the STN, the input circuit and cellular profile in the STN remain largely unclear. Using neuroanatomical techniques, we construct a comprehensive connectivity map of the indirect and hyperdirect pathways in the mouse STN. Our circuit- and cellular-level connectivities reveal a topographically graded organization with three types of indirect and hyperdirect pathways (external globus pallidus only, STN only, and collateral). We confirm consistent pathways into the human STN by 7 T MRI-based tractography. We identify two functional types of topographically distinct glutamatergic STN neurons (parvalbumin [PV+/-]) with synaptic connectivity from indirect and hyperdirect pathways. Glutamatergic PV+ STN neurons contribute to burst firing. These data suggest a complex interplay of information integration within the basal ganglia underlying coordinated movement control and therapeutic effects.
The role of epithelial Progesterone Receptor Isoforms in embryo implantation

iScience

2021 Nov 01

Li, R;Wang, X;Huang, Z;Balaji, J;Kim, T;Wang, T;Zhou, L;Deleon, A;Cook, M;Marbrey, M;Wu, S;Jeong, J;Arora, R;DeMayo, F;
| DOI: 10.1016/j.isci.2021.103487

The loss of uterine epithelial progesterone receptor (PGR) is crucial for successful embryo implantation in both humans and mice. The two major isoforms PGRA and PGRB have divergent functions under both physiological and pathological conditions. The present study compares phenotypes and gene signatures of PGRA and PGRB in uterine epithelium using uterine epithelial-specific constitutively expressed PGRA or PGRB mouse models. The cistrome and transcriptome analysis reveals substantial overlap between epithelial PGRA and PGRB, and both disrupt embryo implantation through FOXO1 pathways. Constitutive epithelial PGRA and PGRB expression impairs ESR1 occupancy at the promoter of Lif leading to reduced Lif transcription and further exaggerates SGK1 expression leading to enhanced PI3K-SGK1 activities, and both contribute to the decline of nuclear FOXO1 expression. Our study demonstrates that PGRA and PGRB in the uterine epithelium act on a similar set of target genes and commonly regulate the LIF-SGK1-FOXO1 signaling pathway for embryo implantation.
Potent anti-viral activity of a trispecific HIV neutralizing antibody in SHIV-infected monkeys

Cell reports

2022 Jan 04

Pegu, A;Xu, L;DeMouth, ME;Fabozzi, G;March, K;Almasri, CG;Cully, MD;Wang, K;Yang, ES;Dias, J;Fennessey, CM;Hataye, J;Wei, RR;Rao, E;Casazza, JP;Promsote, W;Asokan, M;McKee, K;Schmidt, SD;Chen, X;Liu, C;Shi, W;Geng, H;Foulds, KE;Kao, SF;Noe, A;Li, H;Shaw, GM;Zhou, T;Petrovas, C;Todd, JP;Keele, BF;Lifson, JD;Doria-Rose, NA;Koup, RA;Yang, ZY;Nabel, GJ;Mascola, JR;
PMID: 34986348 | DOI: 10.1016/j.celrep.2021.110199

Broadly neutralizing antibodies (bNAbs) represent an alternative to drug therapy for the treatment of HIV-1 infection. Immunotherapy with single bNAbs often leads to emergence of escape variants, suggesting a potential benefit of combination bNAb therapy. Here, a trispecific bNAb reduces viremia 100- to 1000-fold in viremic SHIV-infected macaques. After treatment discontinuation, viremia rebounds transiently and returns to low levels, through CD8-mediated immune control. These viruses remain sensitive to the trispecific antibody, despite loss of sensitivity to one of the parental bNAbs. Similarly, the trispecific bNAb suppresses the emergence of resistance in viruses derived from HIV-1-infected subjects, in contrast to parental bNAbs. Trispecific HIV-1 neutralizing antibodies, therefore, mediate potent antiviral activity in vivo and may minimize the potential for immune escape.

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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
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Example: Hs-CD3-pool (Hs-CD3D, Hs-CD3E, Hs-CD3G)
A mixture of multiple probe sets targeting multiple genes or transcripts
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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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