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Sca-1+Lin−CD117− Mesenchymal Stem/Stromal Cells Induce the Generation of Novel IRF8-Controlled Regulatory Dendritic Cells through Notch−RBP-J Signaling

Xingxia Liu, Shaoda Ren, Chaozhuo Ge, Kai Cheng, Martin Zenke, Armand Keating and Robert C. H. Zhao
This information is current as of September 25, 2021.

J Immunol 2015; 194:4298-4308; Prepublished online 30 March 2015; doi: 10.4049/jimmunol.1402641

http://www.jimmunol.org/content/194/9/4298

Supplementary http://www.jimmunol.org/content/suppl/2015/03/28/jimmunol.140264
Material 1.DCSupplemental

References This article cites 59 articles, 19 of which you can access for free at:

http://www.jimmunol.org/content/194/9/4298.full#ref-list-1

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The Journal of Immunology

Sca-1+Lin2CD1172 Mesenchymal Stem/Stromal Cells Induce the Generation of Novel IRF8-Controlled Regulatory Dendritic Cells through Notch–RBP-J Signaling

Xingxia Liu,*,1 Shaoda Ren,*,1 Chaozhuo Ge,* Kai Cheng,* Martin Zenke,† Armand Keating,‡,x and Robert C. H. Zhao*

Mesenchymal stem/stromal cells (MSCs) can influence the destiny of hematopoietic stem/progenitor cells (HSCs) and exert broadly immunomodulatory effects on immune cells. However, how MSCs regulate the differentiation of regulatory dendritic cells (regDCs) from HSCs remains incompletely understood. In this study, we show that mouse bone marrow–derived Sca-1+Lin2CD1172 MSCs can drive HSCs to differentiate into a novel IFN regulatory factor (IRF)8–controlled regDC population (Sca+ BM-MSC–driven DC [sBM-DCs]) when cocultured without exogenous cytokines. The Notch pathway plays a critical role in the generation of the sBM-DCs by controlling IRF8 expression in an RBP-J–dependent way. We observed a high level of H3K27me3 methylation and a low level of H3K4me3 methylation at the Irf8 promoter during sBM-DC induction. Importantly, infusion of sBM-DCs could alleviate colitis in mice with inflammatory bowel disease by inhibiting lymphocyte proliferation and increasing the numbers of CD4+CD25+ regulatory T cells. Thus, these data infer a possible mechanism for the development of regDCs and further support the role of MSCs in treating immune disorders. The Journal of Immunology, 2015, 194: 4298–4308.

s an important component of the hematopoietic stem/ progenitor cell (HSC) microenvironment, mesenchymal

Astromal/stem cells (MSCs) are capable of self-renewal and

attractive because of their unique immunological characteristics, such as low immunogenicity and immunoregulatory properties (3, 4). The results from various studies have shown that MSCs are not able to stimulate T cell proliferation but can suppress T cell proliferation, and they also exert an inhibitory effect on the proliferation of B cells (5, 6). Additionally, MSCs might also act on dendritic cells (DCs) to regulate immune responses (7); however, relatively little is known about their effects on DC development and function. multilineage differentiation (1, 2). However, MSCs are particularly

*Center of Excellence in Tissue Engineering, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences, School of Basic Medicine, Peking Union Medical College, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences, Beijing 100005, People’s Republic of China; †Department of Cell Biology, Institute for Biomedical Engineering, Rhenish-Westphalian Technical University, Aachen University Medical School, 52074 Aachen, Germany; ‡Cell Therapy Program, Princess Margaret Hospital, Toronto, Ontario M5G 2M9, Canada; and xInstitute of Biomaterials and Biomedical Engineering, University of Toronto, Toronto, Ontario M5G 2M9, Canada

DCs not only play a role in the initiation of immunity but also are indispensable for the preservation of tolerance. They work as professional APCs in promoting Ag-specific immune responses and are likewise implicated in tuning the balance between immunity and tolerance induction (8, 9). DCs arise from HSCs and were initially identified by their potent activation of naive T cells (10). DCs can be divided into distinct subsets by anatomical location, and different subsets of classical DCs express a diversity of phenotype and function and favor alternative modules of immunity (11–13). Recent findings suggest that DC heterogeneity is developmentally determined, and it has been difficult to identify the relationships between these various cells based only on cell surface markers and functional responses. Consequently, understanding the molecular basis of DC development and diversification is important to better appreciate immune regulation. Currently, the basis for DC development into the recognized subsets/lineages is only partially understood, based on the requirements for several transcription factors, including PU.1, IFN regulatory factor (IRF)8, E2-2, IRF4, Batf3, Ikaros, GFi1, and ID2 (14-16). These transcription factors combine to form a transcriptional network that gives rise to the phenotypically and functionally distinct subsets under steady-state conditions. It is now becoming evident that DC development is guided by lineage-restricted transcription factors such as IRF8, E2-2, and Batf3 (17-19). However, little is known regarding how cytokines and lineage-restricted transcription factors operate at a molecular level to direct DC diversification and development. The Notch family provides an evolutionarily conserved signaling network that plays a key role in the development of a variety of immune cells. To date, four Notch receptor family members and five Notch ligands have been identified in mammalian cells (20,

1X.L. and S.R. contributed equally to this work. Received for publication October 21, 2014. Accepted for publication February 27, 2015.

This work was supported by the National Key Scientific Program of China Grant 2011CB964901, Program for International Science and Technology Cooperation Projects of China Grant 2013DFG30680, National Natural Science Foundation of China Grants 81370879 and 81370466, National Science and Technology Major Project of the Ministry of Science and Technology of China Grant 2014ZX09101042, and by Key Program for Beijing Municipal Natural Science Foundation Grant 7141006.

Address correspondence and reprint requests to Prof. Robert C.H. Zhao, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences, School of Basic Medicine, Peking Union Medical College, Peking Union Medical College Hospital, Center of Excellence in Tissue Engineering, Chinese Academy of Medical Sciences, 5 Dongdansantiao, Beijing 100005, People’s Republic of China. E-mail address: [email protected]

The online version of this article contains supplemental material. Abbreviations used in this article: BM, bone marrow; BM-HSC, BM-derived hematopoietic stem/progenitor cell; BM-MSC, BM-derived MSC; ChIP, chromatin immunoprecipitation; DAPT, N-[N-(3,5-difluorophenacetyl)-L-alanyl]-S-phenylglycine t-butyl ester; DC, dendritic cell; H3K4me3, trimethylation at lysine 4 of histone H3; H3K27me3, trimethylation at lysine 27 of histone H3; HSC, hematopoietic stem/progenitor cell; IBD, inflammatory bowel disease; imDC, immature DC; IRF, IFN regulatory factor; maDC, mature DC; MSC, mesenchymal stem/stromal cell; PRC, polycomb repressive complex; qRT-PCR, quantitative RT-PCR; regDC, regulatory DC; sBM-DC, Sca+ BM-MSC–driven DC; siRNA, small interfering RNA; TCF, T cell–specific factor; TNBS, 2,4,6-trinitrobenzene sulfonic acid; TRAF, TNFR-associated factor.

Copyright Ó 2015 by The American Association of Immunologists, Inc. 0022-1767/15/$25.00

www.jimmunol.org/cgi/doi/10.4049/jimmunol.1402641

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acetyl)-L-alanyl]-S-phenylglycine t-butyl ester (DAPT; the cells in the sBM-DCs plus DAPT group were treated with 20 mM DAPT that was dissolved in DMSO). DMSO or 20 mM DAPT (a Notch inhibitor, Tocris Bioscience) was added every 2 d; after coculture for 7 d, the remaining loosely adherent cell clusters were collected for the following experiment.

21). Notch receptors are activated following binding of appropriate ligands, which results in the nuclear translocation of the Notch intracellular domain. The Notch intracellular domain interacts with a number of cytoplasmic and nuclear proteins, permitting signal transduction through several pathways that include activation of the CBF-1/RBP-J transcription factor, which works as a negative regulator of lineage-specific gene expression (22, 23). Several studies suggest possible involvement of Notch in myeloid cell differentiation (13, 24–26). It seems that there is reciprocal regulation of Notch in DC development, but the detailed relationship and underlying mechanisms remain far from being understood.

Flow cytometric analysis

Flow cytometric analysis was performed as previously described (39). The fluorescent Abs used in the study included FITC-conjugated anti-mouse Sca-1, CD4, CD9, CD90, CD31, CD44, H-2Kd, Ia, CD11c, CD40, CD80, and CD86 and PE-conjugated anti-mouse CD25, CD45, CD73, and CD11b (BD Biosciences). For each Ab, IgG of the same isotype from the same species was used as the isotype control (BD Biosciences). Analysis was performed on Accuri C6 flow cytometers with CFlow software (Accuri Cytometers, Ann Arbor, MI).

Recent data support the concept that specific gene expression patterns are under the control of epigenetic alterations (27, 28). Acetylation and methylation of specific lysine residues on N-terminal histone tails are fundamental for the formation of chromatin domains. Two canonical modifications are trimethylation at lysine 27 of histone H3 (H3K27me3) and trimethylation at lysine 4 of histone H3 (H3K4me3). It is known that H3K27me3 is a repressive mark catalyzed by polycomb repressive complex (PRC)2 and is associated with promoters of inactive genes. Conversely, H3K4me3, catalyzed by the trithorax family of proteins, is a hallmark of transcriptional start sites and generally associated with transcriptionally active genes (29–32). A growing body of evidence has shown that epigenetic alterations are involved in the regulation of various genes expression (33–36), but little is known about epigenetic alterations during the generation of DCs. Although several studies have demonstrated that MSCs can modulate the development and function of DCs, the underlying mechanisms remain to be determined. In this study, we report that Sca-1+ Lin2CD1172 bone marrow (BM)–derived MSCs (BM-MSCs) influenced the fate decision of BM-derived HSCs (BM-HSCs) and drove them to differentiate into distinct IRF8-controlled regulatory DCs (regDCs, Sca+ BM-MSC–driven DCs [sBM-DCs]). The Notch signaling pathway plays a critical role in the generation of the sBM-DCs by controlling IRF8 expression in an RBP-J–dependent way.

Endocytosis assay and MLCs

Endocytosis and MLCs were performed as previously described (39).

Cytokine analysis

The supernatant of the sBM-DCs was harvested in RPMI 1640 medium without FBS for 4 h. The supernatant of the MLCs was harvested after 3 d. All supernatants and sera from mice were analyzed using ELISA kits (BD Biosciences) according to the manufacturer’s instructions.

RNA isolation and quantitative RT-PCR analysis

Total RNA was extracted from cells with TRIzol reagent (Invitrogen) and then reverse transcribed using a Quantiscript RT kit (TaKaRa Bio). Quantitative RT-PCR (qRT-PCR) was performed on a StepOne system (Applied Biosystems) with a SYBR Green real-time PCR kit (TaKaRa Bio). Data were normalized to the reference gene b-actin. The primers used are listed in Supplemental Table I.

Western blot analysis

The protein expression level was analyzed by Western blot as previously described (38). Abs were obtained from Cell Signaling Technology.

Chromatin immunoprecipitation

Chromatin immunoprecipitation (ChIP) was performed using an EZ-Magna ChIP kit (Millipore) according to the manufacturer’s instructions. ChIP- grade Abs specific for H3K4me3, H3K27me3, and EED were obtained from Millipore; anti-SIRT1 and anti-IRF8 Abs were obtained from Cell Signaling Technology; anti-WDR5 and anti-SUZ12 Abs were obtained from Abcam; and anti-ASH2, anti-RbBP5, and anti-MLL1 Abs were obtained from Bethyl Laboratories. The primers used are listed in Supplemental Table I.

Materials and Methods

Animals

Five- to 6-wk-old BALB/C and C57BL/6 mice were purchased from the Laboratory Animal Center of the Chinese Academy of Medical Sciences (Beijing, China). All mice were bred and maintained under specific pathogen-free conditions. Animal handling and experimental procedures were approved by the Animal Care and Use Committee of the Chinese Academy of Medical Sciences.

Coimmunoprecipitation

Cells were harvested and lysed in RIPA buffer. The lysates were incubated with protein A/G agarose beads (Millipore); SIRT1 Ab (10 mg) was subsequently added, and the resulting mixture was incubated overnight at 4˚C. Beads conjugated with lysates and SIRT1 Abs were precipitated, washed three times with RIPA buffer, and then analyzed by Western blot.

Culture of mouse BM-MSCs and BM-DCs
Lentiviral vector preparation and infection and small interfering RNA knockdown assay

MSCs were prepared and purified from mouse BM cells as previously described (37, 38). Mouse immature DCs (imDCs) and mature DCs (maDCs) were generated according to previously published protocols (39). In brief, BM mononuclear cells were prepared from BALB/C mouse femur BM suspensions by depletion of red cells and then cultured at a density of 2 3 106 cells/ml in RPMI 1640 supplemented with 10% FBS, 10 ng/ml GM-CSF, and 5 ng/ml IL-4 (R&D Systems). For imDCs, nonadherent cells were gently washed out on day 4, and the remaining loosely adherent cell clusters were collected. imDCs cultured for a further 4 d under the stimulation of 10 ng/ml bacterial LPS (Sigma-Aldrich) were used as maDCs.
Lentivirus production was carried out according to protocols from GenePharma. The small interfering RNA (siRNA) sequences of RBP-J, IRF8, and negative control were 59-GGTTACGCTGTGCTCTGAACA-39, 59- GCTGACTTGTGCATTGCTTCA-39, and 59-TTCTCCGAACGTGTCA- CGTTTC-39, respectively. GFP+ and red fluorescent protein+ cells were sorted by a BD FACSCalibur flow cytometer.

In vivo allogeneic delayed-type hypersensitivity assay

The allogeneic delayed-type hypersensitivity assay was performed as previously described (39).

Coculture experiment

HSCs were enriched from BM cells using an EasySep mouse hematopoietic progenitor enrichment kit (StemCell Technologies). After HSCs were purified, they were seeded onto Sca-1+CD1172Lin2 BM-MSC monolayers at a density of 1 3 105 cells in 2 ml per well in six-well plates, and MSC culture medium was replaced with RPMI 1640 supplemented with 10% FBS. The ratio of MSCs/HSCs is 1:10. In some cases, the experiments were divided into two groups: sBM-DCs (the cells in the sBM-DC group were treated with DMSO) and sBM-DCs plus N-[N-(3,5-difluorophen-

Preparation and treatment of inflammatory bowel disease mouse model

sBM-DCs were i.p. injected (3 3 106 cells/mouse) into six BALB/C recipient mice on days 26, 24, and 0. On day 0, the pretreated mice were injected by an intrarectal instillation of 2,4,6-trinitrobenzene sulfonic acid (TNBS; Sigma-Aldrich) in 150 mg/kg 1:1 ethanol/PBS solution via a 4-cm

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catheter (TNBS plus sBM-DCs); six mice were injected with TNBS and used as inflammatory bowel disease (IBD) model control (TNBS); six mice were injected with normal saline as normal controls. On day 5, the colon was photographed and stained with H&E. The levels of IL-12, IL-10, and TNF-a in serum were assessed by ELISA. The proportion of CD4+ CD25+ regulatory T lymphocytes in spleen was assessed using FACS analysis. CD11b+ splenocytes were isolated and used for detection IRF8 expression by Western blot analysis.

Statistical analysis

All statistical analysis was performed with SPSS software version 17.0. The p values were calculated using a Student t test, and p values ,0.05 were considered to be statistically significant.

Results

Sca-1+CD1172Lin2 BM-MSCs induce the generation of a novel DC population
Histology

To investigate the influence of MSCs on the differentiation of HSCs, we isolated Sca-1+CD1172Lin2 MSCs from BM (Supplemental Fig. 1A, 1B) and then seeded BM-HSCs on MSC monolayers at a ratio of

Colons of mice from different groups were harvested, fixed in 4% formalin for 48 h, and embedded in paraffin. Histological sections were cut and stained with H&E.

FIGURE 1. Sca-1+CD1172Lin2 BM-MSCs induce the generation of regulatory sBM-DCs. (A) Morphology of sBM-DCs induced from BM-HSCs cocultured with Sca-1+CD1172Lin2 BM-MSCs for 7 d compared with imDCs and maDCs. Scale bars, 20 mm. (B) Expression of functional molecules on sBM-DCs, imDCs, and maDCs. Red lines represent cells stained with isotype-matched control Abs. (C) The expression of DC transcription factors of sBM- DCs, imDCs, and maDCs examined by Western blot. imDCs and maDCs were used as controls. Representative data from one of three independent experiments are shown. (D) Phagocytic ability of sBM-DCs and maDCs examined by flow cytometric analysis. The gray lines represent the controls (Ctrol). Representative data from one of three independent experiments are shown. (E) Different secretion of cytokines by sBM-DCs, imDCs, and maDCs. Cells (5 3 105) grown in RPMI 1640 without serum and the supernatants were collected after 4 h. The levels of IL-10, IL-12, and TNF-a were analyzed by ELISA. ★p , 0.05, ★★p , 0.01.

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10:1 (HSCs/MSCs). During the coculture, the nonadherent HSCs gradually extended small and short processes from different points of the cell body to become DC-like cells, which we termed sBM-DCs (Fig. 1A). Phenotype analysis (Fig. 1B) showed that sBM-DCs, compared with maDCs, expressed a higher level of the myeloid lineage marker CD11b but lower levels of functional markers Ia, CD80, CD86, and CD40, similar to imDCs. In contrast to imDCs, addition of LPS to these cells could not increase the expression of the above markers (Supplemental Fig. 2A). To understand the molecular repertoires of sBM-DCs, based on the requirements for several transcription factors, we determined the expression of DC transcription factors as reported by Steinman and Idoyaga (40) by Western blot analysis (Fig. 1C). Interestingly, sBM-DCs expressed most of the aforementioned DC transcription factors such as IRF4, IRF8, PU.1, Ikaros, Batf3, Spib, and T cell–specific factor (TCF)4, but at lower levels compared with imDCs and maDCs, indicating that sBM-DCs represent a novel DC population with a similar phenotype but different transcription factor pattern to imDCs. We also found that sBM- DCs had a greater phagocytic capacity compared with maDCs (Fig. 1D). To further characterize sBM-DCs, we determined their cytokine expression patterns by ELISA (Fig. 1E). In contrast to maDCs, sBM- DCs secreted more IL-10 but less IL-12 and TNF-a, and this profile was not altered after LPS stimulation (Supplemental Fig. 2B), suggesting that sBM-DCs maybe be involved in immune regulation. These results demonstrate that mouse BM-derived Sca-1+CD1172Lin2 MSCs drive HSCs to differentiate into a unique population of DCs.
Fig. 1, sBM-DCs had a stable immature-like phenotype and secreted IL-10, an important inhibitory cytokine. We hypothesized that sBM- DCs may have immune regulatory functions. To confirm this hypothesis, we added sBM-DCs into an allogeneic lymphocyte coculture system and showed that they significantly suppressed lymphocyte proliferation (Fig. 2A). Meanwhile, we also observed that IFN-g and IL-2 levels in culture supernatant were greatly reduced in the presence of sBM-DCs (Fig. 2B). Thus, we have shown that sBM-DCs are a novel DC population with low immunogenicity and high immunoregulatory potential. Because sBM-DCs were potent inhibitors of the lymphocyte proliferation in vitro, we wondered whether sBM-DCs could also suppress allospecific immune reactions in vivo. An allogeneic delayed-type hypersensitivity experiment was performed. As shown in Fig. 2C, the footpad swelling of BALB/C mice receiving the alloantigen was suppressed significantly by infusion of sBM- DCs. Taken together, these results demonstrate that sBM-DCs might be used as a negative regulator of immune responses and have the potential to treat immune dysregulation diseases.

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  • Differential Expression of Vitamin D Binding Protein in Thyroid Cancer Health Disparities

    Differential Expression of Vitamin D Binding Protein in Thyroid Cancer Health Disparities

    www.oncotarget.com Oncotarget, 2021, Vol. 12, (No. 7), pp: 596-607 Research Paper Differential expression of Vitamin D binding protein in thyroid cancer health disparities Brittany Mull1, Ryan Davis2,3, Iqbal Munir4, Mia C. Perez5, Alfred A. Simental6 and Salma Khan2,3,6,7 1Harbor UCLA Medical Center, Torrance, CA 90502, USA 2Division of Biochemistry, Loma Linda, CA 92350, USA 3Center for Health Disparities & Molecular Medicine, Loma Linda, CA 92350, USA 4Riverside University Health System, Moreno Valley, CA 92555, USA 5Department of Pathology & Human Anatomy, Loma Linda University School of Medicine, Loma Linda, CA 92354, USA 6Department of Otolaryngology, Loma Linda University School of Medicine, Loma Linda, CA 92354, USA 7Department of Internal Medicine, Loma Linda University School of Medicine, Loma Linda, CA 92354, USA Correspondence to: Salma Khan, email: [email protected] Keywords: DBP; thyroid cancer; health disparities Received: November 16, 2020 Accepted: March 05, 2021 Published: March 30, 2021 Copyright: © 2021 Mull et al. This is an open access article distributed under the terms of the Creative Commons Attribution License (CC BY 3.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. ABSTRACT Thyroid cancer incidence, recurrence, and death rates are higher among Filipino Americans than European Americans. We propose that vitamin D binding protein (DBP) with multifunctionality with ethnic variability plays a key role within different ethnicities. In this study, we determined the correlation between differential DBP expression in tumor tissues and cancer staging in Filipino Americans versus European Americans. We assayed DBP expression by immunohistochemistry and analyzed the data with confocal microscopy on 200 thyroid cancer archival tissue samples obtained from both ethnicities.
  • Prox1regulates the Subtype-Specific Development of Caudal Ganglionic

    Prox1regulates the Subtype-Specific Development of Caudal Ganglionic

    The Journal of Neuroscience, September 16, 2015 • 35(37):12869–12889 • 12869 Development/Plasticity/Repair Prox1 Regulates the Subtype-Specific Development of Caudal Ganglionic Eminence-Derived GABAergic Cortical Interneurons X Goichi Miyoshi,1 Allison Young,1 Timothy Petros,1 Theofanis Karayannis,1 Melissa McKenzie Chang,1 Alfonso Lavado,2 Tomohiko Iwano,3 Miho Nakajima,4 Hiroki Taniguchi,5 Z. Josh Huang,5 XNathaniel Heintz,4 Guillermo Oliver,2 Fumio Matsuzaki,3 Robert P. Machold,1 and Gord Fishell1 1Department of Neuroscience and Physiology, NYU Neuroscience Institute, Smilow Research Center, New York University School of Medicine, New York, New York 10016, 2Department of Genetics & Tumor Cell Biology, St. Jude Children’s Research Hospital, Memphis, Tennessee 38105, 3Laboratory for Cell Asymmetry, RIKEN Center for Developmental Biology, Kobe 650-0047, Japan, 4Laboratory of Molecular Biology, Howard Hughes Medical Institute, GENSAT Project, The Rockefeller University, New York, New York 10065, and 5Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724 Neurogliaform (RELNϩ) and bipolar (VIPϩ) GABAergic interneurons of the mammalian cerebral cortex provide critical inhibition locally within the superficial layers. While these subtypes are known to originate from the embryonic caudal ganglionic eminence (CGE), the specific genetic programs that direct their positioning, maturation, and integration into the cortical network have not been eluci- dated. Here, we report that in mice expression of the transcription factor Prox1 is selectively maintained in postmitotic CGE-derived cortical interneuron precursors and that loss of Prox1 impairs the integration of these cells into superficial layers. Moreover, Prox1 differentially regulates the postnatal maturation of each specific subtype originating from the CGE (RELN, Calb2/VIP, and VIP).
  • Landscape of Transcriptional Deregulation in Lung Cancer Shu Zhang1,2,3,4, Mingfa Li1, Hongbin Ji2,3,4,5* and Zhaoyuan Fang2,3,4,6*

    Landscape of Transcriptional Deregulation in Lung Cancer Shu Zhang1,2,3,4, Mingfa Li1, Hongbin Ji2,3,4,5* and Zhaoyuan Fang2,3,4,6*

    Zhang et al. BMC Genomics (2018) 19:435 https://doi.org/10.1186/s12864-018-4828-1 RESEARCHARTICLE Open Access Landscape of transcriptional deregulation in lung cancer Shu Zhang1,2,3,4, Mingfa Li1, Hongbin Ji2,3,4,5* and Zhaoyuan Fang2,3,4,6* Abstract Background: Lung cancer is a very heterogeneous disease that can be pathologically classified into different subtypes including small-cell lung carcinoma (SCLC), lung adenocarcinoma (LUAD), lung squamous cell carcinoma (LUSC) and large-cell carcinoma (LCC). Although much progress has been made towards the oncogenic mechanism of each subtype, transcriptional circuits mediating the upstream signaling pathways and downstream functional consequences remain to be systematically studied. Results: Here we trained a one-class support vector machine (OC-SVM) model to establish a general transcription factor (TF) regulatory network containing 325 TFs and 18724 target genes. We then applied this network to lung cancer subtypes and identified those deregulated TFs and downstream targets. We found that the TP63/SOX2/ DMRT3 module was specific to LUSC, corresponding to squamous epithelial differentiation and/or survival. Moreover, the LEF1/MSC module was specifically activated in LUAD and likely to confer epithelial-to-mesenchymal transition, known important for cancer malignant progression and metastasis. The proneural factor, ASCL1, was specifically up-regulated in SCLC which is known to have a neuroendocrine phenotype. Also, ID2 was differentially regulated between SCLC and LUSC, with its up-regulation in SCLC linking to energy supply for fast mitosis and its down-regulation in LUSC linking to the attenuation of immune response. We further described the landscape of TF regulation among the three major subtypes of lung cancer, highlighting their functional commonalities and specificities.
  • Clinical Utility of Recently Identified Diagnostic, Prognostic, And

    Clinical Utility of Recently Identified Diagnostic, Prognostic, And

    Modern Pathology (2017) 30, 1338–1366 1338 © 2017 USCAP, Inc All rights reserved 0893-3952/17 $32.00 Clinical utility of recently identified diagnostic, prognostic, and predictive molecular biomarkers in mature B-cell neoplasms Arantza Onaindia1, L Jeffrey Medeiros2 and Keyur P Patel2 1Instituto de Investigacion Marques de Valdecilla (IDIVAL)/Hospital Universitario Marques de Valdecilla, Santander, Spain and 2Department of Hematopathology, MD Anderson Cancer Center, Houston, TX, USA Genomic profiling studies have provided new insights into the pathogenesis of mature B-cell neoplasms and have identified markers with prognostic impact. Recurrent mutations in tumor-suppressor genes (TP53, BIRC3, ATM), and common signaling pathways, such as the B-cell receptor (CD79A, CD79B, CARD11, TCF3, ID3), Toll- like receptor (MYD88), NOTCH (NOTCH1/2), nuclear factor-κB, and mitogen activated kinase signaling, have been identified in B-cell neoplasms. Chronic lymphocytic leukemia/small lymphocytic lymphoma, diffuse large B-cell lymphoma, follicular lymphoma, mantle cell lymphoma, Burkitt lymphoma, Waldenström macroglobulinemia, hairy cell leukemia, and marginal zone lymphomas of splenic, nodal, and extranodal types represent examples of B-cell neoplasms in which novel molecular biomarkers have been discovered in recent years. In addition, ongoing retrospective correlative and prospective outcome studies have resulted in an enhanced understanding of the clinical utility of novel biomarkers. This progress is reflected in the 2016 update of the World Health Organization classification of lymphoid neoplasms, which lists as many as 41 mature B-cell neoplasms (including provisional categories). Consequently, molecular genetic studies are increasingly being applied for the clinical workup of many of these neoplasms. In this review, we focus on the diagnostic, prognostic, and/or therapeutic utility of molecular biomarkers in mature B-cell neoplasms.
  • The E–Id Protein Axis Modulates the Activities of the PI3K–AKT–Mtorc1

    The E–Id Protein Axis Modulates the Activities of the PI3K–AKT–Mtorc1

    Downloaded from genesdev.cshlp.org on October 6, 2021 - Published by Cold Spring Harbor Laboratory Press The E–Id protein axis modulates the activities of the PI3K–AKT–mTORC1– Hif1a and c-myc/p19Arf pathways to suppress innate variant TFH cell development, thymocyte expansion, and lymphomagenesis Masaki Miyazaki,1,8 Kazuko Miyazaki,1,8 Shuwen Chen,1 Vivek Chandra,1 Keisuke Wagatsuma,2 Yasutoshi Agata,2 Hans-Reimer Rodewald,3 Rintaro Saito,4 Aaron N. Chang,5 Nissi Varki,6 Hiroshi Kawamoto,7 and Cornelis Murre1 1Department of Molecular Biology, University of California at San Diego, La Jolla, California 92093, USA; 2Department of Biochemistry and Molecular Biology, Shiga University of Medical School, Shiga 520-2192, Japan; 3Division of Cellular Immunology, German Cancer Research Center, D-69120 Heidelberg, Germany; 4Department of Medicine, University of California at San Diego, La Jolla, California 92093, USA; 5Center for Computational Biology, Institute for Genomic Medicine, University of California at San Diego, La Jolla, California 92093, USA; 6Department of Pathology, University of California at San Diego, La Jolla, California 92093, USA; 7Department of Immunology, Institute for Frontier Medical Sciences, Kyoto University, Kyoto 606-8507, Japan It is now well established that the E and Id protein axis regulates multiple steps in lymphocyte development. However, it remains unknown how E and Id proteins mechanistically enforce and maintain the naı¨ve T-cell fate. Here we show that Id2 and Id3 suppressed the development and expansion of innate variant follicular helper T (TFH) cells. Innate variant TFH cells required major histocompatibility complex (MHC) class I-like signaling and were associated with germinal center B cells.
  • Targeting Iron Homeostasis Induces Cellular Differentiation and Synergizes with Differentiating Agents in Acute Myeloid Leukemia

    Targeting Iron Homeostasis Induces Cellular Differentiation and Synergizes with Differentiating Agents in Acute Myeloid Leukemia

    Article Targeting iron homeostasis induces cellular differentiation and synergizes with differentiating agents in acute myeloid leukemia Celine Callens,1,2 Séverine Coulon,1,2 Jerome Naudin,1,2,3,4 Isabelle Radford-Weiss,2,5 Nicolas Boissel,4,9 Emmanuel Raffoux,4,9 Pamella Huey Mei Wang,3,4 Saurabh Agarwal,3,4 Houda Tamouza,3,4 Etienne Paubelle,1,2 Vahid Asnafi,1,2,6 Jean-Antoine Ribeil,1,2 Philippe Dessen,10 Danielle Canioni,2,7 Olivia Chandesris,2,8 Marie Therese Rubio,2,8 Carole Beaumont,4,11 Marc Benhamou,3,4 Hervé Dombret,4,9 Elizabeth Macintyre,1,2,6 Renato C. Monteiro,3,4 Ivan C. Moura,3,4 and Olivier Hermine1,2,8 1Centre National de la Recherche Scientifique UMR 8147, Paris 75015, France 2Faculté de Médecine, Université René Descartes Paris V, Institut Fédératif Necker, Paris 75015, France 3Institut National de la Santé et de la Recherche Médicale (INSERM), U699, Paris 75018, France 4Faculté de Médecine, Université Denis Diderot Paris VII, Paris 75018, France 5Laboratoire de cytogénétique, 6Laboratoire d’Hématologie, 7Service d’Anatomo-Pathologie, and 8Service d’Hématologie, Hôpital Necker-Enfants Malades, Assistance Publique Hôpitaux de Paris (AP-HP), Paris 75015, France 9Service d’Hématologie, Hôpital Saint-Louis, AP-HP, Paris 75010, France 10Unité de Génomique Fonctionnelle, Institut Gustave Roussy, Villejuif 94800, France 11INSERM U773, Centre de Recherche Biomédicale Bichat Beaujon CRB3, Paris 75018, France Differentiating agents have been proposed to overcome the impaired cellular differentia- tion in acute myeloid leukemia (AML). However, only the combinations of all-trans retinoic acid or arsenic trioxide with chemotherapy have been successful, and only in treating acute promyelocytic leukemia (also called AML3).
  • CDC2 Mediates Progestin Initiated Endometrial Stromal Cell Proliferation: a PR Signaling to Gene Expression Independently of Its Binding to Chromatin

    CDC2 Mediates Progestin Initiated Endometrial Stromal Cell Proliferation: a PR Signaling to Gene Expression Independently of Its Binding to Chromatin

    CDC2 Mediates Progestin Initiated Endometrial Stromal Cell Proliferation: A PR Signaling to Gene Expression Independently of Its Binding to Chromatin Griselda Vallejo1, Alejandro D. La Greca1., Inti C. Tarifa-Reischle1., Ana C. Mestre-Citrinovitz1, Cecilia Ballare´ 2, Miguel Beato2,3, Patricia Saragu¨ eta1* 1 Instituto de Biologı´a y Medicina Experimental, IByME-Conicet, Buenos Aires, Argentina, 2 Centre de Regulacio´ Geno`mica, (CRG), Barcelona, Spain, 3 University Pompeu Fabra (UPF), Barcelona, Spain Abstract Although non-genomic steroid receptor pathways have been studied over the past decade, little is known about the direct gene expression changes that take place as a consequence of their activation. Progesterone controls proliferation of rat endometrial stromal cells during the peri-implantation phase of pregnancy. We showed that picomolar concentration of progestin R5020 mimics this control in UIII endometrial stromal cells via ERK1-2 and AKT activation mediated by interaction of Progesterone Receptor (PR) with Estrogen Receptor beta (ERb) and without transcriptional activity of endogenous PR and ER. Here we identify early downstream targets of cytoplasmic PR signaling and their possible role in endometrial stromal cell proliferation. Microarray analysis of global gene expression changes in UIII cells treated for 45 min with progestin identified 97 up- and 341 down-regulated genes. The most over-represented molecular functions were transcription factors and regulatory factors associated with cell proliferation and cell cycle, a large fraction of which were repressors down-regulated by hormone. Further analysis verified that progestins regulate Ccnd1, JunD, Usf1, Gfi1, Cyr61, and Cdkn1b through PR- mediated activation of ligand-free ER, ERK1-2 or AKT, in the absence of genomic PR binding.