Excitatory neuronal CHD8 in the regulation of neocortical development and sensory-motor behaviors

Cell reports

2021 Feb 23

Kweon, H;Jung, WB;Im, GH;Ryoo, J;Lee, JH;Do, H;Choi, Y;Song, YH;Jung, H;Park, H;Qiu, LR;Ellegood, J;Shim, HJ;Yang, E;Kim, H;Lerch, JP;Lee, SH;Chung, WS;Kim, D;Kim, SG;Kim, E;
PMID: 33626347 | DOI: 10.1016/j.celrep.2021.108780

CHD8 (chromodomain helicase DNA-binding protein 8) is a chromatin remodeler associated with autism spectrum disorders. Homozygous Chd8 deletion in mice leads to embryonic lethality, making it difficult to assess whether CHD8 regulates brain development and whether CHD8 haploinsufficiency-related macrocephaly reflects normal CHD8 functions. Here, we report that homozygous conditional knockout of Chd8 restricted to neocortical glutamatergic neurons causes apoptosis-dependent near-complete elimination of neocortical structures. These mice, however, display normal survival and hyperactivity, anxiolytic-like behavior, and increased social interaction. They also show largely normal auditory function and moderately impaired visual and motor functions but enhanced whisker-related somatosensory function. These changes accompany thalamic hyperactivity, revealed by 15.2-Tesla fMRI, and increased intrinsic excitability and decreased inhibitory synaptic transmission in thalamic ventral posterior medial (VPM) neurons involved in somatosensation. These results suggest that excitatory neuronal CHD8 critically regulates neocortical development through anti-apoptotic mechanisms, neocortical elimination distinctly affects cognitive behaviors and sensory-motor functions in mice, and Chd8 haploinsufficiency-related macrocephaly might represent compensatory responses.

AKT3 Expression in Mesenchymal Colorectal Cancer Cells Drives Growth and Is Associated with Epithelial-Mesenchymal Transition

Cancers

2021 Feb 14

Buikhuisen, JY;Gomez Barila, PM;Torang, A;Dekker, D;de Jong, JH;Cameron, K;Vitale, S;Stassi, G;van Hooff, SR;Castro, MAA;Vermeulen, L;Medema, JP;
PMID: 33673003 | DOI: 10.3390/cancers13040801

Colorectal cancer (CRC) is a heterogeneous disease that can currently be subdivided into four distinct consensus molecular subtypes (CMS) based on gene expression profiling. The CMS4 subtype is marked by high expression of mesenchymal genes and is associated with a worse overall prognosis compared to other CMSs. Importantly, this subtype responds poorly to the standard therapies currently used to treat CRC. We set out to explore what regulatory signalling networks underlie the CMS4 phenotype of cancer cells, specifically, by analysing which kinases were more highly expressed in this subtype compared to others. We found AKT3 to be expressed in the cancer cell epithelium of CRC specimens, patient derived xenograft (PDX) models and in (primary) cell cultures representing CMS4. Importantly, chemical inhibition or knockout of this gene hampers outgrowth of this subtype, as AKT3 controls expression of the cell cycle regulator p27KIP1. Furthermore, high AKT3 expression was associated with high expression of epithelial-mesenchymal transition (EMT) genes, and this observation could be expanded to cell lines representing other carcinoma types. More importantly, this association allowed for the identification of CRC patients with a high propensity to metastasise and an associated poor prognosis. High AKT3 expression in the tumour epithelial compartment may thus be used as a surrogate marker for EMT and may allow for a selection of CRC patients that could benefit from AKT3-targeted therapy.

Inhibitory CD161 receptor identified in glioma-infiltrating T cells by single-cell analysis

Cell

2021 Feb 10

Mathewson, ND;Ashenberg, O;Tirosh, I;Gritsch, S;Perez, EM;Marx, S;Jerby-Arnon, L;Chanoch-Myers, R;Hara, T;Richman, AR;Ito, Y;Pyrdol, J;Friedrich, M;Schumann, K;Poitras, MJ;Gokhale, PC;Gonzalez Castro, LN;Shore, ME;Hebert, CM;Shaw, B;Cahill, HL;Drummond, M;Zhang, W;Olawoyin, O;Wakimoto, H;Rozenblatt-Rosen, O;Brastianos, PK;Liu, XS;Jones, PS;Cahill, DP;Frosch, MP;Louis, DN;Freeman, GJ;Ligon, KL;Marson, A;Chiocca, EA;Reardon, DA;Regev, A;Suvà, ML;Wucherpfennig, KW;
PMID: 33592174 | DOI: 10.1016/j.cell.2021.01.022

T cells are critical effectors of cancer immunotherapies, but little is known about their gene expression programs in diffuse gliomas. Here, we leverage single-cell RNA sequencing (RNA-seq) to chart the gene expression and clonal landscape of tumor-infiltrating T cells across 31 patients with isocitrate dehydrogenase (IDH) wild-type glioblastoma and IDH mutant glioma. We identify potential effectors of anti-tumor immunity in subsets of T cells that co-express cytotoxic programs and several natural killer (NK) cell genes. Analysis of clonally expanded tumor-infiltrating T cells further identifies the NK gene KLRB1 (encoding CD161) as a candidate inhibitory receptor. Accordingly, genetic inactivation of KLRB1 or antibody-mediated CD161 blockade enhances T cell-mediated killing of glioma cells in vitro and their anti-tumor function in vivo. KLRB1 and its associated transcriptional program are also expressed by substantial T cell populations in other human cancers. Our work provides an atlas of T cells in gliomas and highlights CD161 and other NK cell receptors as immunotherapy targets.

TRPM4 mediates a subthreshold membrane potential oscillation in respiratory chemoreceptor neurons that drives pacemaker firing and breathing

Cell reports

2021 Feb 02

Li, K;Abbott, SBG;Shi, Y;Eggan, P;Gonye, EC;Bayliss, DA;
PMID: 33535052 | DOI: 10.1016/j.celrep.2021.108714

Brainstem networks that control regular tidal breathing depend on excitatory drive, including from tonically active, CO2/H+-sensitive neurons of the retrotrapezoid nucleus (RTN). Here, we examine intrinsic ionic mechanisms underlying the metronomic firing activity characteristic of RTN neurons. In mouse brainstem slices, large-amplitude membrane potential oscillations are evident in synaptically isolated RTN neurons after blocking action potentials. The voltage-dependent oscillations are abolished by sodium replacement; blocking calcium channels (primarily L-type); chelating intracellular Ca2+; and inhibiting TRPM4, a Ca2+-dependent cationic channel. Likewise, oscillation voltage waveform currents are sensitive to calcium and TRPM4 channel blockers. Extracellular acidification and serotonin (5-HT) evoke membrane depolarization that augments TRPM4-dependent oscillatory activity and action potential discharge. Finally, inhibition of TRPM4 channels in the RTN of anesthetized mice reduces central respiratory output. These data implicate TRPM4 in a subthreshold oscillation that supports the pacemaker-like firing of RTN neurons required for basal, CO2-stimulated, and state-dependent breathing.

Molecular characterization of the human kidney interstitium in health and disease

Science advances

2021 Feb 01

Barwinska, D;El-Achkar, TM;Ferreira, RM;Syed, F;Cheng, YH;Winfree, S;Ferkowicz, MJ;Hato, T;Collins, KS;Dunn, KW;Kelly, KJ;Sutton, TA;Rovin, BH;Parikh, SV;Phillips, CL;Dagher, PC;Eadon, MT;Kidney Precision Medicine Project, ;
PMID: 33568476 | DOI: 10.1126/sciadv.abd3359

The gene expression signature of the human kidney interstitium is incompletely understood. The cortical interstitium (excluding tubules, glomeruli, and vessels) in reference nephrectomies (N = 9) and diabetic kidney biopsy specimens (N = 6) was laser microdissected (LMD) and sequenced. Samples underwent RNA sequencing. Gene signatures were deconvolved using single nuclear RNA sequencing (snRNAseq) data derived from overlapping specimens. Interstitial LMD transcriptomics uncovered previously unidentified markers including KISS1, validated with in situ hybridization. LMD transcriptomics and snRNAseq revealed strong correlation of gene expression within corresponding kidney regions. Relevant enriched interstitial pathways included G-protein coupled receptor. binding and collagen biosynthesis. The diabetic interstitium was enriched for extracellular matrix organization and small-molecule catabolism. Cell type markers with unchanged expression (NOTCH3, EGFR, and HEG1) and those down-regulated in diabetic nephropathy (MYH11, LUM, and CCDC3) were identified. LMD transcriptomics complements snRNAseq; together, they facilitate mapping of interstitial marker genes to aid interpretation of pathophysiology in precision medicine studies.

Mesencephalic Electrical Stimulation Reduces Neuroinflammation after Photothrombotic Stroke in Rats by Targeting the Cholinergic Anti-Inflammatory Pathway

International journal of molecular sciences

2021 Jan 27

Schuhmann, MK;Papp, L;Stoll, G;Blum, R;Volkmann, J;Fluri, F;
PMID: 33514001 | DOI: 10.3390/ijms22031254

Inflammation is crucial in the pathophysiology of stroke and thus a promising therapeutic target. High-frequency stimulation (HFS) of the mesencephalic locomotor region (MLR) reduces perilesional inflammation after photothrombotic stroke (PTS). However, the underlying mechanism is not completely understood. Since distinct neural and immune cells respond to electrical stimulation by releasing acetylcholine, we hypothesize that HFS might trigger the cholinergic anti-inflammatory pathway via activation of the α7 nicotinic acetylcholine receptor (α7nAchR). To test this hypothesis, rats underwent PTS and implantation of a microelectrode into the MLR. Three hours after intervention, either HFS or sham-stimulation of the MLR was applied for 24 h. IFN-γ, TNF-α, and IL-1α were quantified by cytometric bead array. Choline acetyltransferase (ChAT)+ CD4+-cells and α7nAchR+-cells were quantified visually using immunohistochemistry. Phosphorylation of NFĸB, ERK1/2, Akt, and Stat3 was determined by Western blot analyses. IFN-γ, TNF-α, and IL-1α were decreased in the perilesional area of stimulated rats compared to controls. The number of ChAT+ CD4+-cells increased after MLR-HFS, whereas the amount of α7nAchR+-cells was similar in both groups. Phospho-ERK1/2 was reduced significantly in stimulated rats. The present study suggests that MLR-HFS may trigger anti-inflammatory processes within the perilesional area by modulating the cholinergic system, probably via activation of the α7nAchR.

Histamine H2 receptor negatively regulates oligodendrocyte differentiation in neonatal hypoxic-ischemic white matter injury

J Exp Med

2021 Jan 04

Jiang, L;Cheng, L;Chen, H;Dai, H;An, D;Ma, Q;Zheng, Y;Zhang, X;Hu, W;Chen, Z;
PMID: 32991666 | DOI: 10.1084/jem.20191365

Neonatal hypoxic-ischemic encephalopathy (HIE) with the pathological characteristic of white matter injury often leads to lifelong cognitive and neurobehavioral dysfunction, but relevant therapies to promote remyelination are still unavailable. We found that histamine H2 receptor (H2R) negatively regulated the oligodendrocyte differentiation rate without affecting the oligodendrocytes at the oligodendrocyte precursor cell stage or mature stage following oxygen-glucose deprivation in vitro. Notably, selective deletion of the H2R gene (Hrh2) in differentiating oligodendrocytes (Hrh2fl/fl;CNPase-Cre) improved their differentiation, remyelination, and functional recovery following neonatal hypoxia-ischemia in mice. The regulation of oligodendrocyte differentiation by H2R is mediated by binding with Axin2, which leads to up-regulation of the Wnt/β-catenin signaling pathway. Furthermore, H2R antagonists also promoted oligodendrocyte differentiation and remyelination and the recovery of cognition and motor functions following neonatal hypoxia-ischemia. Thus, histamine H2R in oligodendrocytes could serve as a novel and effective therapeutic target for the retard of oligodendrocyte differentiation and remyelination following neonatal hypoxia-ischemia. The H2R antagonists may have potential therapeutic value for neonatal HIE.

Fibronectin extra domain A (FN-EDA) causes glaucomatous trabecular meshwork and optic nerve head damage in mice

Investigative Ophthalmology & Visual Science

2021 Jan 01

McDowell, CM;Mavlyutov, T;

Purpose : Elevated intraocular pressure (IOP) is a major risk factor for the development and progression of primary open angle glaucoma and is due to trabecular meshwork (TM) damage. We investigated the role of an endogenous Toll-like receptor 4 (TLR4) ligand, FN-EDA, in the development of glaucoma utilizing a transgenic mouse strain (B6.EDA+/+) that constitutively expresses only FN containing the EDA isoform. Methods : Eyes (n=3/strain) were processed for electron microscopy, polymerized in EPON, ultrathin sections (80 nm) were cut and placed on formvar coated slot grids, and poststained with uranyl acetate and lead citrate. Consecutive images of the entire TM area spanning from anterior to posterior parts of Schlemm’s canal (SC) were collected at 2500x and montaged into a single image. ECM accumulation and basement membrane thickness were quantified by ImageJ analysis. TLR4 expression in ONH cells was conducted using RNAscope in situ hybridization and immunohistochemistry protocols (n=3 eyes/strain). IOP was measured using a rebound tonometer and ON damage assessed by PPD stain (n=20-22 eyes/strain). Results : Ultrastructure analyses show the TM of B6.EDA+/+ mice have significantly increased accumulation of ECM between the TM beams with few empty spaces compared to C57BL/6J control mice (P

Sensory specializations drive octopus and squid behaviour

Nature

2023 Apr 01

Kang, G;Allard, CAH;Valencia-Montoya, WA;van Giesen, L;Kim, JJ;Kilian, PB;Bai, X;Bellono, NW;Hibbs, RE;
PMID: 37045917 | DOI: 10.1038/s41586-023-05808-z

The evolution of new traits enables expansion into new ecological and behavioural niches. Nonetheless, demonstrated connections between divergence in protein structure, function and lineage-specific behaviours remain rare. Here we show that both octopus and squid use cephalopod-specific chemotactile receptors (CRs) to sense their respective marine environments, but structural adaptations in these receptors support the sensation of specific molecules suited to distinct physiological roles. We find that squid express ancient CRs that more closely resemble related nicotinic acetylcholine receptors, whereas octopuses exhibit a more recent expansion in CRs consistent with their elaborated 'taste by touch' sensory system. Using a combination of genetic profiling, physiology and behavioural analyses, we identify the founding member of squid CRs that detects soluble bitter molecules that are relevant in ambush predation. We present the cryo-electron microscopy structure of a squid CR and compare this with octopus CRs1 and nicotinic receptors2. These analyses demonstrate an evolutionary transition from an ancestral aromatic 'cage' that coordinates soluble neurotransmitters or tastants to a more recent octopus CR hydrophobic binding pocket that traps insoluble molecules to mediate contact-dependent chemosensation. Thus, our study provides a foundation for understanding how adaptation of protein structure drives the diversification of organismal traits and behaviour.

On the use of Earth Observation to support estimates of national greenhouse gas emissions and sinks for the Global stocktake process: lessons learned from ESA-CCI RECCAP2

Carbon balance and management

2022 Oct 01

Bastos, A;Ciais, P;Sitch, S;Aragão, LEOC;Chevallier, F;Fawcett, D;Rosan, TM;Saunois, M;Günther, D;Perugini, L;Robert, C;Deng, Z;Pongratz, J;Ganzenmüller, R;Fuchs, R;Winkler, K;Zaehle, S;Albergel, C;
PMID: 36183029 | DOI: 10.1186/s13021-022-00214-w

The Global Stocktake (GST), implemented by the Paris Agreement, requires rapid developments in the capabilities to quantify annual greenhouse gas (GHG) emissions and removals consistently from the global to the national scale and improvements to national GHG inventories. In particular, new capabilities are needed for accurate attribution of sources and sinks and their trends to natural and anthropogenic processes. On the one hand, this is still a major challenge as national GHG inventories follow globally harmonized methodologies based on the guidelines established by the Intergovernmental Panel on Climate Change, but these can be implemented differently for individual countries. Moreover, in many countries the capability to systematically produce detailed and annually updated GHG inventories is still lacking. On the other hand, spatially-explicit datasets quantifying sources and sinks of carbon dioxide, methane and nitrous oxide emissions from Earth Observations (EO) are still limited by many sources of uncertainty. While national GHG inventories follow diverse methodologies depending on the availability of activity data in the different countries, the proposed comparison with EO-based estimates can help improve our understanding of the comparability of the estimates

Current HIV/SIV Reservoir Assays for Preclinical and Clinical Applications: Recommendations from the Experts 2022 NIAID Workshop Summary

AIDS research and human retroviruses

2023 Apr 26

Sanders-Beer, BE;Archin, NM;Brumme, ZL;Busch, M;Deleage, C;O'Doherty, U;Hughes, SH;Jerome, K;Jones, RB;Karn, J;Kearney, MF;Keele, B;Kulpa, D;Laird, G;Li, JZ;Lichterfeld, M;Nussenzweig, MC;Persaud, D;Yukl, S;Siliciano, RF;Mellors, JW;
PMID: 37126090 | DOI: 10.1089/AID.2022.0188

Since the first HIV-cured person was reported in 2009, a strong interest in developing highly sensitive HIV and SIV reservoir assays has emerged. In particular, the question arose about the comparative value of state-of-the-art assays to measure and characterize the HIV reservoir, and how these assays can be applied to accurately detect changes in the reservoir during efforts to develop a cure for HIV infection. Secondly, it is important to consider the impact on the outcome of clinical trials if these relatively new HIV reservoir assays are incorporated into clinical trial endpoints and/or used for clinical decision-making. To understand the advantages and limitations and the regulatory implications of HIV reservoir assays, the National Institute of Allergy and Infectious Diseases (NIAID) sponsored and convened a meeting on September 16, 2022, to discuss the state of knowledge concerning these questions and best practices for selecting HIV reservoir assays for a particular research question or clinical trial protocol.

Inhibin-Positive "Cholangioblastic" Variant of Intrahepatic Cholangiocarcinoma: Report of 3 New Patients With Review of the Literature

International journal of surgical pathology

2023 Apr 18

Bakhshwin, A;Lai, KK;Ammoun, A;Friedman, K;El Hag, M;
PMID: 37073447 | DOI: 10.1177/10668969231157775

Cholangiocarcinoma is the second most common primary liver malignant neoplasm. It usually affects older individuals in their seventh decade of life with no gender predilection. Recently, a distinct subtype of cholangiocarcinoma has emerged with 2 proposed names: "cholangioblastic" and "solid tubulocystic." This variant predominantly occurs in younger women who lack the common risk factors for patients diagnosed with cholangiocarcinomas, such as older age and chronic liver disease or cirrhosis. We describe 3 new patients with a cholangioblastic variant of intrahepatic cholangiocarcinoma. At the time of diagnosis, the patients were aged 19-, 46-, and 28-year-old; 2 females and 1 male (the 46-year-old). None of our patients had a history of chronic liver disease or known predisposing factors for liver tumors. Tumor size ranged from 2.3 to 23 cm in greatest dimension. Histological examination of these tumors demonstrated reproducible morphology characterized by trabecular, nested, and multicystic patterns with micro and macro follicles filled with eosinophilic material. The immunohistochemical profile showed that the tumor cells were positive for keratin 7, inhibin, synaptophysin, and albumin in situ hybridization, while negative for HepPar1, arginase, and INSM1. All tumors lacked conventional intrahepatic cholangiocarcinoma/adenocarcinoma morphology. We also review the literature and emphasize that neuroendocrine tumors should be recognized as a major diagnostic pitfall of this variant.

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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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