Distinct biogenesis pathways may have led to functional divergence of the human and Drosophila Arglu1 sisRNA

EMBO reports

2022 Dec 19

Chan, SN;Pek, JW;
PMID: 36533631 | DOI: 10.15252/embr.202154350

Stable intronic sequence RNAs (sisRNAs) are stable, long noncoding RNAs containing intronic sequences. While sisRNAs have been found across diverse species, their level of conservation remains poorly understood. Here we report that the biogenesis and functions of a sisRNA transcribed from the highly conserved Arglu1 locus are distinct in human and Drosophila melanogaster. The Arglu1 genes in both species show similar exon-intron structures where the intron 2 is orthologous and positionally conserved. In humans, Arglu1 sisRNA retains the entire intron 2 and promotes host gene splicing. Mechanistically, Arglu1 sisRNA represses the splicing-inhibitory activity of ARGLU1 protein by binding to ARGLU1 protein and promoting its localization to nuclear speckles, away from the Arglu1 gene locus. In contrast, Drosophila dArglu1 sisRNA forms via premature cleavage of intron 2 and represses host gene splicing. This repression occurs through a local accumulation of dARGLU1 protein and inhibition of telescripting by U1 snRNPs at the dArglu1 locus. We propose that distinct biogenesis of positionally conserved Arglu1 sisRNAs in both species may have led to functional divergence.

Somatosensory neurons express specific sets of lincRNAs, and lincRNA CLAP promotes itch sensation in mice

EMBO reports

2022 Dec 16

Wang, B;Jiang, B;Li, GW;Dong, F;Luo, Z;Cai, B;Wei, M;Huang, J;Wang, K;Feng, X;Tong, F;Wang, S;Wang, Q;Han, Q;Li, C;Zhang, X;Yang, L;Bao, L;
PMID: 36524339 | DOI: 10.15252/embr.202154313

Somatosensory neurons are highly heterogeneous with distinct types of neural cells responding to specific stimuli. However, the distribution and roles of cell-type-specific long intergenic noncoding RNAs (lincRNAs) in somatosensory neurons remain largely unexplored. Here, by utilizing droplet-based single-cell RNA-seq (scRNA-seq) and full-length Smart-seq2, we show that lincRNAs, but not coding mRNAs, are enriched in specific types of mouse somatosensory neurons. Profiling of lincRNAs from single neurons located in dorsal root ganglia (DRG) identifies 200 lincRNAs localized in specific types or subtypes of somatosensory neurons. Among them, the conserved cell-type-specific lincRNA CLAP associates with pruritus and is abundantly expressed in somatostatin (SST)-positive neurons. CLAP knockdown reduces histamine-induced Ca2+ influx in cultured SST-positive neurons and in vivo reduces histamine-induced scratching in mice. In vivo knockdown of CLAP also decreases the expression of neuron-type-specific and itch-related genes in somatosensory neurons, and this partially depends on the RNA binding protein MSI2. Our data reveal a cell-type-specific landscape of lincRNAs and a function for CLAP in somatosensory neurons in sensory transmission.

Far from home: the role of glial mRNA localization in synaptic plasticity

RNA (New York, N.Y.)

2022 Nov 28

Gala, DS;Titlow, JS;Teodoro, RO;Davis, I;
PMID: 36442969 | DOI: 10.1261/rna.079422.122

Neurons and glia are highly polarized cells, whose distal cytoplasmic functional subdomains require specific proteins. Neurons have axonal and dendritic cytoplasmic extensions containing synapses requiring mRNA transport and localized translation to regulate synaptic plasticity efficiently. The principles behind these mechanisms are equally attractive for explaining rapid local regulation of distal glial cytoplasmic projections, independent of their cell nucleus. However, in contrast to neurons, this topic has received little experimental attention in glia. Nevertheless, there are many functionally diverse glial sub-types, containing extensive networks of long cytoplasmic projections with likely localized regulation that influence neurons and their synapses. Moreover, glia have many other neuron-like properties, including electrical activity, secretion of gliotransmitters and calcium signaling, influencing for example synaptic transmission, plasticity and axon pruning. Here, we review previous studies concerning glial transcripts with important roles in influencing synaptic plasticity, focusing on a few cases involving localized translation. We discuss a variety of important questions about mRNA transport and localized translation in glia that remain to be addressed using cutting-edge tools already available for neurons.

Postnatal age-differential ASD-like transcriptomic, synaptic, and behavioral deficits in Myt1l-mutant mice

Cell reports

2022 Sep 20

Kim, S;Oh, H;Choi, SH;Yoo, YE;Noh, YW;Cho, Y;Im, GH;Lee, C;Oh, Y;Yang, E;Kim, G;Chung, WS;Kim, H;Kang, H;Bae, Y;Kim, SG;Kim, E;
PMID: 36130507 | DOI: 10.1016/j.celrep.2022.111398

Myelin transcription factor 1 like (Myt1l), a zinc-finger transcription factor, promotes neuronal differentiation and is implicated in autism spectrum disorder (ASD) and intellectual disability. However, it remains unclear whether Myt1l promotes neuronal differentiation in vivo and its deficiency in mice leads to disease-related phenotypes. Here, we report that Myt1l-heterozygous mutant (Myt1l-HT) mice display postnatal age-differential ASD-related phenotypes: newborn Myt1l-HT mice, with strong Myt1l expression, show ASD-like transcriptomic changes involving decreased synaptic gene expression and prefrontal excitatory synaptic transmission and altered righting reflex. Juvenile Myt1l-HT mice, with markedly decreased Myt1l expression, display reverse ASD-like transcriptomes, increased prefrontal excitatory transmission, and largely normal behaviors. Adult Myt1l-HT mice show ASD-like transcriptomes involving astrocytic and microglial gene upregulation, increased prefrontal inhibitory transmission, and behavioral deficits. Therefore, Myt1l haploinsufficiency leads to ASD-related phenotypes in newborn mice, which are temporarily normalized in juveniles but re-appear in adults, pointing to continuing phenotypic changes long after a marked decrease of Myt1l expression in juveniles.

The Role of Nerve Fibers in the Tumor Immune Microenvironment of Solid Tumors

Advanced biology

2022 Jun 25

Hernandez, S;Serrano, AG;Solis Soto, LM;
PMID: 35751462 | DOI: 10.1002/adbi.202200046

The importance of neurons and nerve fibers in the tumor microenvironment (TME) of solid tumors is now acknowledged after being unexplored for a long time; this is possible due to the development of new technologies that allow in situ characterization of the TME. Recent studies have shown that the density and types of nerves that innervate tumors can predict a patient's clinical outcome and drive several processes of tumor biology. Nowadays, several efforts in cancer research and neuroscience are taking place to elucidate the mechanisms that drive tumor-associated innervation and nerve-tumor and nerve-immune interaction. Assessment of neurons and nerves within the context of the TME can be performed in situ, in tumor tissue, using several pathology-based strategies that utilize histochemical and immunohistochemistry principles, hi-plex technologies, and computational pathology approaches to identify measurable histopathological characteristics of nerves. These features include the number and type of tumor associated nerves, topographical location and microenvironment of neural invasion of malignant cells, and investigation of neuro-related biomarker expression in nerves, tumor cells, and cells of the TME. A deeper understanding of these complex interactions and the impact of nerves in tumor biology will guide the design of better strategies for targeted therapy in clinical trials.

BS20 Dexamethasone inhibits opn-activation associated with intimal hyperplasia in vein grafts

Basic science

2022 Jun 01

McQueen, L;Ladak, S;Tavares, A;Murphy, G;Zakkar, M;
| DOI: 10.1136/heartjnl-2022-bcs.200

BACKGROUND The long saphenous vein (LSV) is commonly utilised in CABG surgery to facilitate revascularisation. However, over time these grafts develop intimal hyperplasia (IH) and accelerated atherosclerosis, leading to stenosis and occlusion. A common feature of IH is vascular calcification (VC) within the affected vessel. Recently, the matricellular protein osteopontin (OPN) has been implicated in this process at endothelial injury sites in porcine models, but this has not been expanded to humans. Consecutively, studies have implicated the arterial haemodynamic environment as a major driver of the pro-inflammatory conditions facilitating VC and IH. As such, treatment with a synthetic glucocorticoid, dexamethasone, which has proven beneficial in inhibiting IH in murine models, may beneficially modulate this process in humans. This work aims to assess the role of OPN on VC and IH in an ex vivo model, whether dexamethasone can modulate this process, and whether detection of VC in situ can act as a novel clinical monitoring approach to graft patency.

Pthlha and mechanical force control early patterning of growth zones in the zebrafish craniofacial skeleton

Development (Cambridge, England)

2022 Jan 15

Hoyle, DJ;Dranow, DB;Schilling, TF;
PMID: 34919126 | DOI: 10.1242/dev.199826

Secreted signals in patterning systems often induce repressive signals that shape their distributions in space and time. In developing growth plates (GPs) of endochondral long bones, Parathyroid hormone-like hormone (Pthlh) inhibits Indian hedgehog (Ihh) to form a negative-feedback loop that controls GP progression and bone size. Whether similar systems operate in other bones and how they arise during embryogenesis remain unclear. We show that Pthlha expression in the zebrafish craniofacial skeleton precedes chondrocyte differentiation and restricts where cells undergo hypertrophy, thereby initiating a future GP. Loss of Pthlha leads to an expansion of cells expressing a novel early marker of the hypertrophic zone (HZ), entpd5a, and later HZ markers, such as ihha, whereas local Pthlha misexpression induces ectopic entpd5a expression. Formation of this early pre-HZ correlates with onset of muscle contraction and requires mechanical force; paralysis leads to loss of entpd5a and ihha expression in the pre-HZ, mislocalized pthlha expression and no subsequent ossification. These results suggest that local Pthlh sources combined with force determine HZ locations, establishing the negative-feedback loop that later maintains GPs.

Senecavirus A: Frequently asked questions

Journal of Swine Health and Production

2022 May 02

Buckley, A;Lager, K;
| DOI: 10.54846/jshap/1270

Senecavirus A (SVA) has been demonstrated to be a causative agent for vesicular disease in swine. It is clinically indistinguishable from other agents that cause vesicular disease such as foot-and-mouth disease virus (FMDV), which is a reportable foreign animal disease (FAD). Thus, an investigation is initiated to rule out FMDV every time a vesicle is observed. Senecavirus A has now been reported across the Americas and Asia, and it appears the ecology of this virus has changed from sporadic infections to an endemic disease in some areas. In addition to vesicular disease, there have also been reports of increased neonatal mortality on affected sow farms. Knowledge about the pathogenesis of SVA in swine can provide many benefits to the swine industry. Understanding how long the virus can be detected in various sample types after infection can aide in choosing the correct samples to collect for diagnosis. In addition, the duration of virus shedding can help determine measures to control virus spread between animals. Prevention of SVA infection and disease with an efficacious vaccine could improve swine welfare, minimize SVA transmission, and reduce the burden of FAD investigations.

NMNAT2 is downregulated in glaucomatous RGCs, and RGC-specific gene therapy rescues neurodegeneration and visual function

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

2022 Jan 31

Fang, F;Zhuang, P;Feng, X;Liu, P;Liu, D;Huang, H;Li, L;Chen, W;Liu, L;Sun, Y;Jiang, H;Ye, J;Hu, Y;
PMID: 35114390 | DOI: 10.1016/j.ymthe.2022.01.035

The lack of neuroprotective treatments for retinal ganglion cells (RGCs) and optic nerve (ON) is a central challenge for glaucoma management. Emerging evidence suggests that redox factor NAD+ decline is a hallmark of aging and neurodegenerative diseases. Supplementation with NAD+ precursors and overexpression of NMNAT1, the key enzyme in the NAD+ biosynthetic process, have significant neuroprotective effects. We first profile the translatomes of RGCs in naive mice and mice with silicone oil-induced ocular hypertension (SOHU)/glaucoma by RiboTag mRNA sequencing. Intriguingly, only NMNAT2, but not NMNAT1 or NMNAT3, is significantly decreased in SOHU glaucomatous RGCs, which we confirm by in situ hybridization. We next demonstrate that AAV2 intravitreal injection-mediated overexpression of long half-life NMNAT2 mutant driven by RGC-specific mouse γ-synuclein (mSncg) promoter restores decreased NAD+ levels in glaucomatous RGCs and ONs. Moreover, this RGC-specific gene therapy strategy delivers significant neuroprotection of both RGC soma and axon and preservation of visual function in the traumatic ON crush model and the SOHU glaucoma model. Collectively, our studies suggest that the weakening of NMNAT2 expression in glaucomatous RGCs contributes to a deleterious NAD+ decline, and that modulating RGC-intrinsic NMNAT2 levels by AAV2-mSncg vector is a promising gene therapy for glaucomatous neurodegeneration.

Giant Cell Tumor of Bone Versus Tenosynovial Giant Cell Tumor- Similarities and Differences

International journal of surgical pathology

2022 Jan 31

Kropivšek, L;Pižem, J;Mavčič, B;
PMID: 35098753 | DOI: 10.1177/10668969221076545

Giant cell tumor of bone (GCTB) and tenosynovial giant cell tumor (TGCT) share misleadingly similar names, soft texture and brown color macroscopically, osteoclast-like multinucleated giant cells microscopically and localisation in the musculoskeletal system. However, these two tumor types are biologically and clinically two distinct entities with different natural courses of progression and considerably different modes of surgical and medical treatment. In this article, we provide a detailed update on the similarities and the differences between both tumor types.GCTB is a locally aggressive osteolytic bone tumor, commonly seen in patients in their third decade of life. It usually occurs as a solitary lesion in the meta-epiphyseal region of long bones. It can be diagnosed using plain radiographic imaging, CT radiography or MRI to estimate the tumor extent, soft tissue and joint involvement. GCTB is usually treated with intralesional excision by curettage. Systemically, it can be treated with bisphosphonates and denosumab or radiotherapy.TGCT is a rare, slowly progressing tumor of synovial tissue, affecting the joint, tendon sheath or bursa, mostly seen in middle-aged patients. TGCT is usually not visible on radiographs and MRI is mostly used to enable assessment of potential bone involvement and distinguishing between two TGCT types. Localised TGCT is mostly treated with marginal surgical resection, while diffuse TGCT is optimally treated with total synovectomy and is more difficult to remove. Additionally, radiotherapy, intraarticular injection of radioactive isotopes, anti-TNF-α antibodies and targeted medications may be used.

Vision-dependent specification of cell types and function in the developing cortex

Cell

2022 Jan 20

Cheng, S;Butrus, S;Tan, L;Xu, R;Sagireddy, S;Trachtenberg, JT;Shekhar, K;Zipursky, SL;
PMID: 35063073 | DOI: 10.1016/j.cell.2021.12.022

The role of postnatal experience in sculpting cortical circuitry, while long appreciated, is poorly understood at the level of cell types. We explore this in the mouse primary visual cortex (V1) using single-nucleus RNA sequencing, visual deprivation, genetics, and functional imaging. We find that vision selectively drives the specification of glutamatergic cell types in upper layers (L) (L2/3/4), while deeper-layer glutamatergic, GABAergic, and non-neuronal cell types are established prior to eye opening. L2/3 cell types form an experience-dependent spatial continuum defined by the graded expression of ∼200 genes, including regulators of cell adhesion and synapse formation. One of these genes, Igsf9b, a vision-dependent gene encoding an inhibitory synaptic cell adhesion molecule, is required for the normal development of binocular responses in L2/3. In summary, vision preferentially regulates the development of upper-layer glutamatergic cell types through the regulation of cell-type-specific gene expression programs.

Persistent Ebola Virus Infection within the Male Reproductive Tract is Related to Both Viral Replication Kinetics and Host Response at the Blood-Testis Barrier

SSRN Electronic Journal

2022 Jan 11

Webb, A;Schindell, B;Griffin, B;Soule, G;Siddik, A;Abrenica, B;Memon, H;Su, R;Kobasa, D;Safronetz, D;Kindrachuk, J;
| DOI: 10.2139/ssrn.4000892

Recent outbreaks of Ebola virus linked to chains of transmission from the 2014-2016 West African Ebola virus epidemic suggest a new paradigm for persistent Ebola virus infections as a lasting concern to public health. Cases of Ebola virus disease linked to sexual transmission and detection of Ebola virus in the male reproductive tract long after patients have recovered suggests that Ebola virus persistence occurs in this immune privileged area. However, little is known about Ebola virus cell tropism, viral kinetics, and host response to infection in the testis. In this study, we challenged immunocompromised mice and testicular tissue cultures with wild type Ebola virus. We utilized RT-qPCR and ISH to detect and quantify Ebola virus in the testis. We also employed RNAseq analysis to measure the transcriptomic response of specific testicular cell types to Ebola virus infection. Our results indicate that Ebola virus productively infects the cells at the blood-testis barrier, and that the interstitial space is more susceptible to infection compared to blood-testis barrier itself. In addition, the Sertoli cells that make up the physical structure of the blood-testis barrier maintain greater viability during Ebola virus infection, and this results from nonstandard immune response that prioritizes inhibited viral entry/replication and increased cell homeostatic activity. Our findings reinforce the need to further investigate viral persistence in the male reproductive tract as a reservoir for ongoing and future outbreaks of Ebola virus disease.

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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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