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Wnts produced by Osterix-expressing osteolineage cells regulate their proliferation and differentiation.

Proc Natl Acad Sci U S A. 2014 Dec 9;111(49):E5262-71.

Tan SH, Senarath-Yapa K, Chung MT, Longaker MT, Wu JY, Nusse R.

Wnt signaling is a critical regulator of bone development, but the identity and role of the Wnt-producing cells are still unclear. We addressed these questions through in situ hybridization, lineage tracing, and genetic experiments. First, we surveyed the expression of all 19 Wnt genes and Wnt target gene Axin2 in the neonatal mouse bone by in situ hybridization, and demonstrated--to our knowledge for the first time--that Osterix-expressing cells coexpress Wnt and Axin2. To track the behavior and cell fate of Axin2-expressing osteolineage cells, we performed lineage tracing and showed that they sustain bone formation over the long term. Finally, to examine the role of Wnts produced by Osterix-expressing cells, we inhibited Wnt secretion in vivo, and observed inappropriate differentiation, impaired proliferation, and diminished Wnt signaling response. Therefore, Osterix-expressing cells produce their own Wnts that in turn induce Wnt signaling response, thereby regulating their proliferation and differentiation.
A novel role for C–C motif chemokine receptor 2 during infection with hypervirulent Mycobacterium tuberculosis

Mucosal Immunol.

2018 Aug 16

Dunlap MD, Howard N, Das S, Scott N, Ahmed M, Prince O, Rangel-Moreno J, Rosa BA, Martin J, Kaushal D, Kaplan G, Mitreva M, Kim KW, Randolph GJ, Khader SA.
PMID: 30115997 | DOI: 10.1038/s41385-018-0071-y

C-C motif chemokine receptor 2 (CCR2) is a major chemokine axis that recruits myeloid cells including monocytes and macrophages. Thus far, CCR2-/- mice have not been found to be susceptible to infection with Mycobacterium tuberculosis (Mtb). Here, using a prototype W-Beijing family lineage 2 Mtb strain, HN878, we show that CCR2-/- mice exhibit increased susceptibility to tuberculosis (TB). Following exposure to Mtb HN878, alveolar macrophages (AMs) are amongst the earliest cells infected. We show that AMs accumulate early in the airways following infection and express CCR2. During disease progression, CCR2-expressing AMs exit the airways and localize within the TB granulomas. RNA-sequencing of sorted airway and non-airway AMs from infected mice show distinct gene expression profiles, suggesting that upon exit from airways and localization within granulomas, AMs become classically activated. The absence of CCR2+ cells specifically at the time of AM egress from the airways resulted in enhanced susceptibility to Mtb infection. Furthermore, infection with an Mtb HN878 mutant lacking phenolic glycolipid (PGL) expression still resulted in increased susceptibility in CCR2-/- mice. Together, these data show a novel rolefor CCR2 in protective immunity against clinically relevant Mtb infections.

Apoptotic tumor cell-derived microRNA-375 uses CD36 to alter the tumor-associated macrophage phenotype.

Nat Commun.

2019 Mar 08

Frank AC, Ebersberger S, Fink AF, Weigert A, Schmid T, Ebersberger I, Syed SN, Brüne B.
PMID: 30850595 | DOI: 10.1038/s41467-019-08989-2

Tumor-immune cell interactions shape the immune cell phenotype, with microRNAs (miRs) being crucial components of this crosstalk. How they are transferred and how they affect their target landscape, especially in tumor-associated macrophages (TAMs), is largely unknown. Here we report that breast cancer cells have a high constitutive expression of miR-375, which is released as a non-exosome entity during apoptosis. Deep sequencing of the miRome pointed to enhanced accumulation of miR-375 in TAMs, facilitated by the uptake of tumor-derived miR-375 via CD36. In macrophages, miR-375 directly targets TNS3 and PXN to enhance macrophage migration and infiltration into tumor spheroids and in tumors of a xenograft mouse model. In tumor cells, miR-375 regulates CCL2 expression to increase recruitment of macrophages. Our study provides evidence for miR transfer from tumor cells to TAMs and identifies miR-375 as a crucial regulator of phagocyte infiltration and the subsequent development of a tumor-promoting microenvironment.

Establishment of gastrointestinal assembloids to study the interplay between epithelial crypts and their mesenchymal niche

Nature communications

2023 May 25

Lin, M;Hartl, K;Heuberger, J;Beccaceci, G;Berger, H;Li, H;Liu, L;Müllerke, S;Conrad, T;Heymann, F;Woehler, A;Tacke, F;Rajewsky, N;Sigal, M;
PMID: 37230989 | DOI: 10.1038/s41467-023-38780-3

The cellular organization of gastrointestinal crypts is orchestrated by different cells of the stromal niche but available in vitro models fail to fully recapitulate the interplay between epithelium and stroma. Here, we establish a colon assembloid system comprising the epithelium and diverse stromal cell subtypes. These assembloids recapitulate the development of mature crypts resembling in vivo cellular diversity and organization, including maintenance of a stem/progenitor cell compartment in the base and their maturation into secretory/absorptive cell types. This process is supported by self-organizing stromal cells around the crypts that resemble in vivo organization, with cell types that support stem cell turnover adjacent to the stem cell compartment. Assembloids that lack BMP receptors either in epithelial or stromal cells fail to undergo proper crypt formation. Our data highlight the crucial role of bidirectional signaling between epithelium and stroma, with BMP as a central determinant of compartmentalization along the crypt axis.
Creb5 coordinates synovial joint formation with the genesis of articular cartilage

Nature communications

2022 Nov 26

Zhang, CH;Gao, Y;Hung, HH;Zhuo, Z;Grodzinsky, AJ;Lassar, AB;
PMID: 36435829 | DOI: 10.1038/s41467-022-35010-0

While prior work has established that articular cartilage arises from Prg4-expressing perichondrial cells, it is not clear how this process is specifically restricted to the perichondrium of synovial joints. We document that the transcription factor Creb5 is necessary to initiate the expression of signaling molecules that both direct the formation of synovial joints and guide perichondrial tissue to form articular cartilage instead of bone. Creb5 promotes the generation of articular chondrocytes from perichondrial precursors in part by inducing expression of signaling molecules that block a Wnt5a autoregulatory loop in the perichondrium. Postnatal deletion of Creb5 in the articular cartilage leads to loss of both flat superficial zone articular chondrocytes coupled with a loss of both Prg4 and Wif1 expression in the articular cartilage; and a non-cell autonomous up-regulation of Ctgf. Our findings indicate that Creb5 promotes joint formation and the subsequent development of articular chondrocytes by driving the expression of signaling molecules that both specify the joint interzone and simultaneously inhibit a Wnt5a positive-feedback loop in the perichondrium.
A cellular and spatial map of the choroid plexus across brain ventricles and ages

Cell

2021 Apr 27

Dani, N;Herbst, RH;McCabe, C;Green, GS;Kaiser, K;Head, JP;Cui, J;Shipley, FB;Jang, A;Dionne, D;Nguyen, L;Rodman, C;Riesenfeld, SJ;Prochazka, J;Prochazkova, M;Sedlacek, R;Zhang, F;Bryja, V;Rozenblatt-Rosen, O;Habib, N;Regev, A;Lehtinen, MK;
PMID: 33932339 | DOI: 10.1016/j.cell.2021.04.003

The choroid plexus (ChP) in each brain ventricle produces cerebrospinal fluid (CSF) and forms the blood-CSF barrier. Here, we construct a single-cell and spatial atlas of each ChP in the developing, adult, and aged mouse brain. We delineate diverse cell types, subtypes, cell states, and expression programs in epithelial and mesenchymal cells across ages and ventricles. In the developing ChP, we predict a common progenitor pool for epithelial and neuronal cells, validated by lineage tracing. Epithelial and fibroblast cells show regionalized expression by ventricle, starting at embryonic stages and persisting with age, with a dramatic transcriptional shift with maturation, and a smaller shift in each aged cell type. With aging, epithelial cells upregulate host-defense programs, and resident macrophages upregulate interleukin-1β (IL-1β) signaling genes. Our atlas reveals cellular diversity, architecture and signaling across ventricles during development, maturation, and aging of the ChP-brain barrier.
Early Pulmonary Lesions in Cattle Infected via Aerosolized Mycobacterium bovis

Vet Pathol

2019 Mar 21

Palmer MV, Wiarda J, Kanipe C and Thacker TC
PMID: 30895908 | DOI: 10.1177/0300985819833454

Mycobacterium bovis is a serious zoonotic pathogen and the cause of tuberculosis in many mammalian species, most notably, cattle. The hallmark lesion of tuberculosis is the granuloma. It is within the developing granuloma where host and pathogen interact; therefore, it is critical to understand host-pathogen interactions at the granuloma level. Cytokines and chemokines drive cell recruitment, activity, and function and ultimately determine the success or failure of the host to control infection. In calves, early lesions (ie, 15 and 30 days) after experimental aerosol infection were examined microscopically using in situ hybridization and immunohistochemistry to demonstrate early infiltrates of CD68+ macrophages within alveoli and alveolar interstitium, as well as the presence of CD4, CD8, and gammadelta T cells. Unlike lesions at 15 days, lesions at 30 days after infection contained small foci of necrosis among infiltrates of macrophages, lymphocytes, neutrophils, and multinucleated giant cells and extracellular acid-fast bacilli within necrotic areas. At both time points, there was abundant expression of the chemokines CXCL9, MCP-1/CCL2, and the cytokine transforming growth factor (TGF)-beta. The proinflammatory cytokines tumor necrosis factor (TNF)-alpha and interleukin (IL)-1beta, as well as the anti-inflammatory cytokine IL-10, were expressed at moderate levels at both time points, while expression of IFN-gamma was limited. These findings document the early pulmonary lesions after M. bovis infection in calves and are in general agreement with the proposed pathogenesis of tuberculosis described in laboratory animal and nonhuman primate models of tuberculosis.
Single-nuclear transcriptomics reveals diversity of proximal tubule cell states in a dynamic response to acute kidney injury

Proceedings of the National Academy of Sciences of the United States of America

2021 Jul 06

Gerhardt, LMS;Liu, J;Koppitch, K;Cippà, PE;McMahon, AP;
PMID: 34183416 | DOI: 10.1073/pnas.2026684118

Acute kidney injury (AKI), commonly caused by ischemia, sepsis, or nephrotoxic insult, is associated with increased mortality and a heightened risk of chronic kidney disease (CKD). AKI results in the dysfunction or death of proximal tubule cells (PTCs), triggering a poorly understood autologous cellular repair program. Defective repair associates with a long-term transition to CKD. We performed a mild-to-moderate ischemia-reperfusion injury (IRI) to model injury responses reflective of kidney injury in a variety of clinical settings, including kidney transplant surgery. Single-nucleus RNA sequencing of genetically labeled injured PTCs at 7-d ("early") and 28-d ("late") time points post-IRI identified specific gene and pathway activity in the injury-repair transition. In particular, we identified Vcam1 +/Ccl2 + PTCs at a late injury stage distinguished by marked activation of NF-κB-, TNF-, and AP-1-signaling pathways. This population of PTCs showed features of a senescence-associated secretory phenotype but did not exhibit G2/M cell cycle arrest, distinct from other reports of maladaptive PTCs following kidney injury. Fate-mapping experiments identified spatially and temporally distinct origins for these cells. At the cortico-medullary boundary (CMB), where injury initiates, the majority of Vcam1 +/Ccl2 + PTCs arose from early replicating PTCs. In contrast, in cortical regions, only a subset of Vcam1 +/Ccl2 + PTCs could be traced to early repairing cells, suggesting late-arising sites of secondary PTC injury. Together, these data indicate even moderate IRI is associated with a lasting injury, which spreads from the CMB to cortical regions. Remaining failed-repair PTCs are likely triggers for chronic disease progression.
Intra-articular injection of phospholipid-based lubricant reduces shear-responsive inflammatory genes in the superficial layer of cartilage post murine joint destabilisation

Osteoarthritis and Cartilage

2021 Apr 01

Zhu, L;Miotla Zarebska, J;Batchelor, V;Lin, W;Goldberg, R;Klein, J;Vincent, T;
| DOI: 10.1016/j.joca.2021.02.239

Purpose: The synovial joint exhibits extraordinary biotribological properties allowing the articular cartilage layers to slide past each other at very low friction even under local pressures of up to 18 MPa (~180 atm). Articular cartilage is exquisitely mechanical sensitive. Compressive mechanical load contributes to articular cartilage homeostasis; however, overuse or destabilizing the joint increases surface shear stress, which promotes cartilage degradation. Our previous Results show that shear stress, induced by joint destabilization, regulates a number of inflammatory genes 6h post surgery, including Mmp3, Il1b, Arg1, Ccl2, and Il6. Immobilizing the joint by prolonged anesthesia or sciatic neurectomy abrogates the regulation of inflammatory genes and prevents development of OA. In this study, we use RNA Scope to identify which cells of the cartilage are activated by surface shear after joint destabilisation, and test whether this is modifiable by injection of a biocompatible phospholipid-based lubricant. Methods: Destabilization of the medial meniscus (DMM) or sham surgery was performed on the right knee of 10-week-old male C57BL/6 mice. 30 ml of lubricant (PMPC: poly(methacryloylphosphsphorylcholine)-functionalized lipid vesicles) or vehicle control (PBS) solution was injected in the joint two days before and at the time of surgery. Cartilage from naïve (no surgery) and DMM-operated knees of four mice per data point was collected by microdissection for bulk mRNA extraction. Expression levels of selected genes including shear-responsive genes Il1b and Mmp3 were tested by RT-PCR using TaqMan Low Density Arrays (TLDA) microfluidic cards. In addition, whole joints were collected and processed following the standard protocol for RNAscope (Advanced Cell Diagnostics). Coronal sections in the middle of the joints were sliced by a cryostat. Consecutive sections were used for Safranin O staining and RNAscope to identify anatomical tissues and detect the expression of genes of interest. Gene expression signals were collated from 11 stacks by confocal microscopy (Zeiss Confocal 880) focusing on the medial tibia cartilage, and were quantified by counting individual mRNA dots in the sham, DMM, vehicle and lubricant groups. Results: We observed the upregulation of injury-responsive genes Il1b, Mmp3, Ccl2, Adamts 4, Nos2, and Timp1 in the articular cartilage of DMM operated joints compared to Naïve (non-operated) animals. The injection of the lubricant in the joint significantly suppressed the expression of shear-responsive genes Il1b and Mmp3 after DMM, but did not influence the increase of other injury-induced inflammatory genes, such as Timp1, Adamts 4, Ccl2, Nos2. For RNAscope, focusing on Mmp3 expression, the number of Mmp3 positive cells increased two-fold in the DMM-vehicle group compared with the sham-vehicle group. Most of Mmp3 signal was expressed in the superficial region of the cartilage. DMM-PMPC groups showed a reduced number of Mmp3 positive cells compared with DMM-vehicle, with levels similar to sham-vehicle and sham-PMPC groups. Conclusions: Our data demonstrate that shear stress-induced inflammatory genes are regulated in the superficial layer of cartilage after joint destabilisation and can be suppressed by joint injection of a biocompatible engineered lubricant. As these lubricants have long retention times in the joint (data not presented), we believe that they may provide a potential novel therapeutic strategy for preventing the development of post-trauma OA. These studies are underway
Structural Remodeling of the Human Colonic Mesenchyme in Inflammatory Bowel Disease

Cell

2018 Sep 27

Kinchen J, Chen HH, Parikh K, Antanaviciute A, Jagielowicz M, Fawkner-Corbett D, Ashley N, Cubitt L, Mellado-Gomez E, Attar M, Sharma E, Wills Q, Bowden R, Richter FC, Ahern D, Puri KD, Henault J, Gervais F, Koohy H, Simmons A.
PMID: - | DOI: 10.1016/j.cell.2018.08.067

Intestinal mesenchymal cells play essential roles in epithelial homeostasis, matrix remodeling, immunity, and inflammation. But the extent of heterogeneity within the colonic mesenchyme in these processes remains unknown. Using unbiased single-cell profiling of over 16,500 colonic mesenchymal cells, we reveal four subsets of fibroblasts expressing divergent transcriptional regulators and functional pathways, in addition to pericytes and myofibroblasts. We identified a niche population located in proximity to epithelial crypts expressing SOX6, F3 (CD142), and WNT genes essential for colonic epithelial stem cellfunction. In colitis, we observed dysregulation of this niche and emergence of an activated mesenchymal population. This subset expressed TNF superfamily member 14 (TNFSF14), fibroblastic reticular cell-associated genes, IL-33, and Lysyl oxidases. Further, it induced factors that impaired epithelial proliferation and maturation and contributed to oxidative stress and disease severity in vivo. Our work defines how the colonic mesenchyme remodels to fuel inflammation and barrier dysfunction in IBD.

Deciphering the origins and fates of steroidogenic lineages in the mouse testis

Cell reports

2022 Jun 14

Ademi, H;Djari, C;Mayère, C;Neirijnck, Y;Sararols, P;Rands, CM;Stévant, I;Conne, B;Nef, S;
PMID: 35705036 | DOI: 10.1016/j.celrep.2022.110935

Leydig cells (LCs) are the major androgen-producing cells in the testis. They arise from steroidogenic progenitors (SPs), whose origins, maintenance, and differentiation dynamics remain largely unknown. Single-cell transcriptomics reveal that the mouse steroidogenic lineage is specified as early as embryonic day 12.5 (E12.5) and has a dual mesonephric and coelomic origin. SPs specifically express the Wnt5a gene and evolve rapidly. At E12.5 and E13.5, they give rise first to an intermediate population of pre-LCs, and finally to fetal LCs. At E16.5, SPs possess the characteristics of the dormant progenitors at the origin of adult LCs and are also transcriptionally closely related to peritubular myoid cells (PMCs). In agreement with our in silico analysis, in vivo lineage tracing indicates that Wnt5a-expressing cells are bona fide progenitors of PMCs as well as fetal and adult LCs, contributing to most of the LCs present in the fetal and adult testis.
Axin2 marks quiescent hair follicle bulge stem cells that are maintained by autocrine Wnt/β-catenin signaling.

Proc Natl Acad Sci U S A.

2016 Feb 22

Lim X, Tan SH, Yu KL, Lim SB, Nusse R.
PMID: 26903625 | DOI: -

How stem cells maintain their identity and potency as tissues change during growth is not well understood. In mammalian hair, it is unclear how hair follicle stem cells can enter an extended period of quiescence during the resting phase but retain stem cell potential and be subsequently activated for growth. Here, we use lineage tracing and gene expression mapping to show that the Wnt target gene Axin2 is constantly expressed throughout the hair cycle quiescent phase in outer bulge stem cells that produce their own Wnt signals. Ablating Wnt signaling in the bulge cells causes them to lose their stem cell potency to contribute to hair growth and undergo premature differentiation instead. Bulge cells express secreted Wnt inhibitors, including Dickkopf (Dkk) and secreted frizzled-related protein 1 (Sfrp1). However, the Dickkopf 3 (Dkk3) protein becomes localized to the Wnt-inactive inner bulge that contains differentiated cells. We find that Axin2 expression remains confined to the outer bulge, whereas Dkk3 continues to be localized to the inner bulge during the hair cycle growth phase. Our data suggest that autocrine Wnt signaling in the outer bulge maintains stem cell potency throughout hair cycle quiescence and growth, whereas paracrine Wnt inhibition of inner bulge cells reinforces differentiation.

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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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