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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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Distinct uptake, amplification, and release of SARS-CoV-2 by M1 and M2 alveolar macrophages

Cell discovery

2021 Apr 13

Lv, J;Wang, Z;Qu, Y;Zhu, H;Zhu, Q;Tong, W;Bao, L;Lv, Q;Cong, J;Li, D;Deng, W;Yu, P;Song, J;Tong, WM;Liu, J;Liu, Y;Qin, C;Huang, B;
PMID: 33850112 | DOI: 10.1038/s41421-021-00258-1

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) invades the alveoli, where abundant alveolar macrophages (AMs) reside. How AMs respond to SARS-CoV-2 invasion remains elusive. Here, we show that classically activated M1 AMs facilitate viral spread; however, alternatively activated M2 AMs limit the spread. M1 AMs utilize cellular softness to efficiently take up SARS-CoV-2. Subsequently, the invaded viruses take over the endo-lysosomal system to escape. M1 AMs have a lower endosomal pH, favoring membrane fusion and allowing the entry of viral RNA from the endosomes into the cytoplasm, where the virus achieves replication and is packaged to be released. In contrast, M2 AMs have a higher endosomal pH but a lower lysosomal pH, thus delivering the virus to lysosomes for degradation. In hACE2 transgenic mouse model, M1 AMs are found to facilitate SARS-CoV-2 infection of the lungs. These findings provide insights into the complex roles of AMs during SARS-CoV-2 infection, along with potential therapeutic targets.
Basal forebrain projections to the lateral habenula modulate aggression reward.

Nature.

2016 Jun 29

Golden SA, Heshmati M, Flanigan M, Christoffel DJ, Guise K, Pfau ML, Aleyasin H, Menard C, Zhang H, Hodes GE, Bregman D, Khibnik L, Tai J, Rebusi N, Krawitz B, Chaudhury D, Walsh JJ, Han MH, Shapiro ML, Russo SJ.
PMID: 27357796 | DOI: 10.1038/nature18601

Maladaptive aggressive behaviour is associated with a number of neuropsychiatric disorders and is thought to result partly from the inappropriate activation of brain reward systems in response to aggressive or violent social stimuli. Nuclei within the ventromedial hypothalamus, extended amygdala and limbic circuits are known to encode initiation of aggression; however, little is known about the neural mechanisms that directlymodulate the motivational component of aggressive behaviour. Here we established a mouse model to measure the valence of aggressive inter-male social interaction with a smaller subordinate intruder as reinforcement for the development of conditioned place preference (CPP). Aggressors develop a CPP, whereas non-aggressors develop a conditioned place aversion to the intruder-paired context. Furthermore, we identify a functional GABAergic projection from the basal forebrain (BF) to the lateral habenula (lHb) that bi-directionally controls the valence of aggressive interactions. Circuit-specific silencing of GABAergic BF-lHb terminals of aggressors with halorhodopsin (NpHR3.0) increases lHb neuronal firing and abolishes CPP to the intruder-paired context. Activation of GABAergic BF-lHb terminals of non-aggressors with channelrhodopsin (ChR2) decreases lHb neuronal firing and promotes CPP to the intruder-paired context. Finally, we show that altering inhibitory transmission at BF-lHb terminals does not control the initiation of aggressive behaviour. These results demonstrate that the BF-lHb circuit has a critical role in regulating the valence of inter-male aggressive behaviour and provide novel mechanistic insight into the neural circuits modulatingaggression reward processing.

Direct mechanisms of SARS-CoV-2-induced cardiomyocyte damage: an update

Virology journal

2022 Jun 25

Yang, Y;Wei, Z;Xiong, C;Qian, H;
PMID: 35752810 | DOI: 10.1186/s12985-022-01833-y

Myocardial injury induced by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is reportedly related to disease severity and mortality, attracting attention to exploring relevant pathogenic mechanisms. Limited by insufficient evidence, myocardial injury caused by direct viral invasion of cardiomyocytes (CMs) is not fully understood. Based on recent studies, endosomal dependence can compensate for S protein priming to mediate SARS-CoV-2 infection of CMs, damage the contractile function of CMs, trigger electrical dysfunction, and tip the balance of the renin-angiotensin-aldosterone system to exert a myocardial injury effect. In this review, we shed light on the direct injury caused by SARS-CoV-2 to provide a comprehensive understanding of the cardiac manifestations of coronavirus disease 2019 (COVID-19).
SARS-CoV-2 replication in airway epithelia requires motile cilia and microvillar reprogramming

Cell

2022 Dec 02

Wu, CT;Lidsky, PV;Xiao, Y;Cheng, R;Lee, IT;Nakayama, T;Jiang, S;He, W;Demeter, J;Knight, MG;Turn, RE;Rojas-Hernandez, LS;Ye, C;Chiem, K;Shon, J;Martinez-Sobrido, L;Bertozzi, CR;Nolan, GP;Nayak, JV;Milla, C;Andino, R;Jackson, PK;
PMID: 36580912 | DOI: 10.1016/j.cell.2022.11.030

How SARS-CoV-2 penetrates the airway barrier of mucus and periciliary mucins to infect nasal epithelium remains unclear. Using primary nasal epithelial organoid cultures, we found that the virus attaches to motile cilia via the ACE2 receptor. SARS-CoV-2 traverses the mucus layer, using motile cilia as tracks to access the cell body. Depleting cilia blocks infection for SARS-CoV-2 and other respiratory viruses. SARS-CoV-2 progeny attach to airway microvilli 24 h post-infection and trigger formation of apically extended and highly branched microvilli that organize viral egress from the microvilli back into the mucus layer, supporting a model of virus dispersion throughout airway tissue via mucociliary transport. Phosphoproteomics and kinase inhibition reveal that microvillar remodeling is regulated by p21-activated kinases (PAK). Importantly, Omicron variants bind with higher affinity to motile cilia and show accelerated viral entry. Our work suggests that motile cilia, microvilli, and mucociliary-dependent mucus flow are critical for efficient virus replication in nasal epithelia.
Exposure Route Influences Disease Severity in the COVID-19 Cynomolgus Macaque Model

Viruses

2022 May 10

Bixler, SL;Stefan, CP;Jay, AN;Rossi, FD;Ricks, KM;Shoemaker, CJ;Moreau, AM;Zeng, X;Hooper, JW;Dyer, DN;Frick, OM;Koehler, JW;Kearney, BJ;DiPinto, N;Liu, J;Tostenson, SD;Clements, TL;Smith, JM;Johnson, JA;Berrier, KL;Esham, HL;Delp, KL;Coyne, SR;Bloomfield, HA;Kuehnert, PA;Akers, K;Gibson, KM;Minogue, TD;Nalca, A;Pitt, MLM;
PMID: 35632755 | DOI: 10.3390/v14051013

The emergence of SARS-CoV-2 and the subsequent pandemic has highlighted the need for animal models that faithfully replicate the salient features of COVID-19 disease in humans. These models are necessary for the rapid selection, testing, and evaluation of potential medical countermeasures. Here, we performed a direct comparison of two distinct routes of SARS-CoV-2 exposure-combined intratracheal/intranasal and small particle aerosol-in two nonhuman primate species, rhesus and cynomolgus macaques. While all four experimental groups displayed very few outward clinical signs, evidence of mild to moderate respiratory disease was present on radiographs and at necropsy. Cynomolgus macaques exposed via the aerosol route also developed the most consistent fever responses and had the most severe respiratory disease and pathology. This study demonstrates that while all four models produced suitable representations of mild COVID-like illness, aerosol exposure of cynomolgus macaques to SARS-CoV-2 produced the most severe disease, which may provide additional clinical endpoints for evaluating therapeutics and vaccines.
Repulsive cues combined with physical barriers and cell-cell adhesion determine progenitor cell positioning during organogenesis.

Nat Commun.

2016 Apr 18

Paksa A, Bandemer J, Hoeckendorf B, Razin N, Tarbashevich K, Minina S, Meyen D, Biundo A, Leidel SA, Peyrieras N, Gov NS, Keller PJ, Raz E.
PMID: 27088892 | DOI: 10.1038/ncomms11288

The precise positioning of organ progenitor cells constitutes an essential, yet poorly understood step during organogenesis. Using primordial germ cells that participate in gonad formation, we present the developmental mechanisms maintaining a motile progenitor cell population at the site where the organ develops. Employing high-resolution live-cell microscopy, we find that repulsive cues coupled with physical barriers confine the cells to the correct bilateral positions. This analysis revealed that cell polarity changes on interaction with the physical barrier and that the establishment of compact clusters involves increased cell-cell interaction time. Using particle-based simulations, we demonstrate the role of reflecting barriers, from which cells turn away on contact, and the importance of proper cell-cell adhesion level for maintaining the tight cell clusters and their correct positioning at the target region. The combination of these developmental and cellular mechanisms prevents organ fusion, controls organ positioning and is thus critical for its proper function.

SARS-CoV-2 infection induces DNA damage, through CHK1 degradation and impaired 53BP1 recruitment, and cellular senescence

Nature cell biology

2023 Mar 09

Gioia, U;Tavella, S;Martínez-Orellana, P;Cicio, G;Colliva, A;Ceccon, M;Cabrini, M;Henriques, AC;Fumagalli, V;Paldino, A;Presot, E;Rajasekharan, S;Iacomino, N;Pisati, F;Matti, V;Sepe, S;Conte, MI;Barozzi, S;Lavagnino, Z;Carletti, T;Volpe, MC;Cavalcante, P;Iannacone, M;Rampazzo, C;Bussani, R;Tripodo, C;Zacchigna, S;Marcello, A;d'Adda di Fagagna, F;
PMID: 36894671 | DOI: 10.1038/s41556-023-01096-x

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is the RNA virus responsible for the coronavirus disease 2019 (COVID-19) pandemic. Although SARS-CoV-2 was reported to alter several cellular pathways, its impact on DNA integrity and the mechanisms involved remain unknown. Here we show that SARS-CoV-2 causes DNA damage and elicits an altered DNA damage response. Mechanistically, SARS-CoV-2 proteins ORF6 and NSP13 cause degradation of the DNA damage response kinase CHK1 through proteasome and autophagy, respectively. CHK1 loss leads to deoxynucleoside triphosphate (dNTP) shortage, causing impaired S-phase progression, DNA damage, pro-inflammatory pathways activation and cellular senescence. Supplementation of deoxynucleosides reduces that. Furthermore, SARS-CoV-2 N-protein impairs 53BP1 focal recruitment by interfering with damage-induced long non-coding RNAs, thus reducing DNA repair. Key observations are recapitulated in SARS-CoV-2-infected mice and patients with COVID-19. We propose that SARS-CoV-2, by boosting ribonucleoside triphosphate levels to promote its replication at the expense of dNTPs and by hijacking damage-induced long non-coding RNAs' biology, threatens genome integrity and causes altered DNA damage response activation, induction of inflammation and cellular senescence.
An Engineered IgG-VHH Bispecific Antibody against SARS-CoV-2 and Its Variants

Small methods

2022 Oct 27

Chi, H;Wang, L;Liu, C;Cheng, X;Zheng, H;Lv, L;Tan, Y;Zhang, N;Zhao, S;Wu, M;Luo, D;Qiu, H;Feng, R;Fu, W;Zhang, J;Xiong, X;Zhang, Y;Zu, S;Chen, Q;Ye, Q;Yan, X;Hu, Y;Zhang, Z;Yan, R;Yin, J;Lei, P;Wang, W;Lang, G;Shao, J;Deng, Y;Wang, X;Qin, C;
PMID: 36300882 | DOI: 10.1002/smtd.202200932

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) neutralizing antibodies are shown to be effective therapeutics for providing coronavirus disease 2019 (COVID-19) protection. However, recurrent variants arise and facilitate significant escape from current antibody therapeutics. Bispecific antibodies (bsAbs) represent a unique platform to increase antibody breadth and to reduce neutralization escape. Herein, a novel immunoglobulin G-variable domains of heavy-chain-only antibody (IgG-VHH) format bsAb derived from a potent human antibody R15-F7 and a humanized nanobody P14-F8-35 are rationally engineered. The resulting bsAb SYZJ001 efficiently neutralizes wild-type SARS-CoV-2 as well as the alpha, beta, gamma, and delta variants, with superior efficacy to its parental antibodies. Cryo-electron microscopy structural analysis reveals that R15-F7 and P14-F8-35 bind to nonoverlapping epitopes within the RBD and sterically hindered ACE2 receptor binding. Most importantly, SYZJ001 shows potent prophylactic and therapeutic efficacy against SARS-CoV-2 in three established mouse models. Collectively, the current results demonstrate that the novel bsAb format is feasible and effective, suggesting great potential as an inspiring antiviral strategy.
Rational development of a combined mRNA vaccine against COVID-19 and influenza

NPJ vaccines

2022 Jul 26

Ye, Q;Wu, M;Zhou, C;Lu, X;Huang, B;Zhang, N;Zhao, H;Chi, H;Zhang, X;Ling, D;Zhang, RR;Li, Z;Luo, D;Huang, YJ;Qiu, HY;Song, H;Tan, W;Xu, K;Ying, B;Qin, CF;
PMID: 35882870 | DOI: 10.1038/s41541-022-00478-w

As the world continues to experience the COVID-19 pandemic, seasonal influenza remain a cause of severe morbidity and mortality globally. Worse yet, coinfection with SARS-CoV-2 and influenza A virus (IAV) leads to more severe clinical outcomes. The development of a combined vaccine against both COVID-19 and influenza is thus of high priority. Based on our established lipid nanoparticle (LNP)-encapsulated mRNA vaccine platform, we developed and characterized a novel mRNA vaccine encoding the HA antigen of influenza A (H1N1) virus, termed ARIAV. Then, ARIAV was combined with our COVID-19 mRNA vaccine ARCoV, which encodes the receptor-binding domain (RBD) of the SARS-CoV-2 S protein, to formulate the final combined vaccine, AR-CoV/IAV. Further characterization demonstrated that immunization with two doses of AR-CoV/IAV elicited robust protective antibodies as well as antigen-specific cellular immune responses against SARS-CoV-2 and IAV. More importantly, AR-CoV/IAV immunization protected mice from coinfection with IAV and the SARS-CoV-2 Alpha and Delta variants. Our results highlight the potential of the LNP-mRNA vaccine platform in preventing COVID-19 and influenza, as well as other respiratory diseases.
In situ detection of vaccine mRNA in the cytoplasm of hepatocytes during COVID19 vaccine-related hepatitis

Journal of hepatology

2022 Sep 15

Martin-Navarro, L;de Andrea, C;Sangro, B;Argemi, J;
PMID: 36116717 | DOI: 10.1016/j.jhep.2022.08.039

Spike Protein-independent Attenuation of SARS-CoV-2 Omicron Variant in Laboratory Mice

Cell Reports

2022 Aug 01

Liu, S;Selvaraj, P;Sangare, K;Luan, B;Wang, T;
| DOI: 10.1016/j.celrep.2022.111359

Division of Viral Products, Center for Biologics Evaluation and Research, Food and Drug Administration; Silver Spring, Maryland, USA, 20993
HISTOLOGICAL FINDINGS IN TRANSBRONCHIAL CRYOBIOPSIES OBTAINED FROM PATIENTS AFTER COVID-19

Chest

2021 Sep 25

Culebras, M;Loor, K;Sansano, I;Persiva, Ó;Clofent, D;Polverino, E;Felipe, A;Osorio, J;Muñoz, X;Álvarez, A;Se-COVID-19 team, ;
PMID: 34582842 | DOI: 10.1016/j.chest.2021.09.016

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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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