title: Therapeutic use of R-spondins to augment the cerebrovascular and neuronal Wnt signaling and improve stroke outcome in mice [scRNA-Seq]

first: YINZHONG

last: MA

address: 1068 Xueyuan Avenue

department: Research Center for Protein and Cell-based Drugs

institute: Shenzhen Institutes of Advanced Technology，Chinese Academy of Sciences

summary: Wnt signaling is critical for blood-brain barrier function, neuronal survival and adult neurogenesis, yet Wnt proteins are poorly suited as therapeutics for stroke due to production and pharmacokinetic challenges. Here, we show that R-spondins (RSPOs), a family of easily produced and secreted proteins capable of robustly augmenting Wnt signaling, are widely expressed in adult mouse brain and upregulated upon ischemia and reperfusion injury. Neutralizing endogenous RSPOs with the soluble ectodomains of their membrane receptors LGR5, ZNRF3 and RNF43 increased cerebral infarction in a murine stroke model. Conversely, systemic administration of RSPOs substantially reduced cerebral infarction and improved neurological outcomes. The neuroprotective effects of RSPOs were dependent on LGR4/ZNRF3-mediated augmentation of canonical Wnt/-catenin signaling in endothelial and neuronal cells, which in turn promoted blood-brain barrier integrity, neuronal PDGF-CC expression and survival. Further, RSPOs promotes the proliferation and expansion of neural stem/progenitor cells and post-stroke neurogenesis. Thus, we identify a previously unknown neuroprotective and pro-neurogenic mechanism and describe the therapeutic potential of recombinant RSPOs in ischemic stroke.

overall_design: Examination of gene regulation by Wnt3a plus Rspondin 1 in Neural stem cells.

first: Yinzhong

last: Ma

first: Michael

last: Mancuso

first: Carolina

last: Maier-Albers

first: Xibin

last: Liang

first: Kelley

middle: S

last: Yan

last: Madl

first: Jingjing

last: Liu

first: Feng

first: Meifang

last: Yin

first: Mario

last: Vallon

first: Kanako

last: Yuki

first: Jenny

last: Yuan

first: Qianyan

last: He

first: Zhen-Ni

last: Guo

first: Fang

first: Fuyou

first: Sarah

last: Heilshorn

first: Katrin

last: Andreasson

first: Calvin

middle: J

last: Kuo

first: Junlei

last: Chang


title: Mouse methylation array of glioblastoma mGB2 cells

status: Public on Oct 06 2023

city: Saint Louis

first: Pavle

last: Boskovic

state: MO

address: 4515 McKinley Ave

country: USA

institute: Washington University in Saint Louis

summary: Glioblastoma is the most common malignant brain tumor in adults. Cellular plasticity and the poorly differentiated features result in a fast relapse of the tumors following treatment. Moreover, the immunosuppressive microenvironment proved to be a major obstacle to immunotherapeutic approaches. Branched-chain amino acid transaminase 1 (BCAT1) is a metabolic enzyme that converts branched-chain amino acids into branched-chain keto acids, depleting cellular α-ketoglutarate and producing glutamate. BCAT1 was shown to drive the growth of glioblastoma and other cancers; however, its oncogenic mechanism remains poorly understood. Here, we show that BCAT1 is crucial for maintaining the poorly differentiated state of glioblastoma cells and that its low expression correlates with a more differentiated glioblastoma phenotype. Furthermore, orthotopic tumor injection into immunocompetent mice demonstrated that the brain microenvironment is sufficient to induce differentiation of Bcat1-KO tumors in vivo. We link the transition to a differentiated cell state to the increased activity of TET demethylases and the hypomethylation and activation of neuronal differentiation genes. In addition, the knockout of Bcat1 attenuated immunosuppression, allowing for an extensive infiltration of CD8 + cytotoxic T-cells and complete abrogation of tumor growth. Further analysis in immunodeficient mice revealed that both tumor cell differentiation and immunomodulation following BCAT1-KO contribute to the long-term suppression of tumor growth. In summary, our study unveils BCAT1's pivotal role in promoting glioblastoma growth by inhibiting tumor cell differentiation and sustaining an immunosuppressive milieu. These findings offer a novel therapeutic avenue for targeting glioblastoma through the inhibition of BCAT1.

overall_design: DNA was extracted from cultured mGB2 cells. Samples unclude the control cells (NT), Bcat1-knockout cells (BKO) and Bcat1-KO cells expressing shRNA targeting Tet1 (shTet1) or Tet2 (shTet2). Each sample was present in triplicates

first: Nathalie

last: Wilke

first: Ka-Hou

last: Man

first: Peter

last: Lichter

first: Liliana

last: Francois

first: Bernhard

last: Radlwimmer


title: In vitro cell-line model to evaluate oncogenic functions associated with the HOXB13 protein with X285K variant

city: San Antonio

first: Yidong

last: Chen

state: Texas

address: 8403 Floyd Curl Drive, MSC 7784

department: Population Health Sciences

institute: UT Health Science Center at San Antonio

type: Expression profiling by high throughput sequencing

summary: A few recent reports uncovered a HOXB13 variant (X285K) predisposing to prostate cancer in men of West-African ancestry. The protein function associated with this inherited variant is unknown. To elucidate the oncogenic mechanisms of the X285K protein, we designed an in vitro cell-line model to evaluate oncogenic functions associated with the X285K protein. Replacement of the wild-type HOXB13 protein with the X285K protein resulted in a gain of the E2F/MYC signature, validated by a gain in the expression of Cyclin B1 and c-MYC, without affecting the androgen response signature.  In conclusion, Functional studies revealed a unique gain-of-function oncogenic mechanism of X285K protein in regulating E2F/MYC signatures.

overall_design: To study the functions mediated by X285K, we devised a strategy to replace the wild-type (WT) HOXB13 with X285K in LNCaP95, a castration-resistant prostate cancer (CRPC) cell line. Treatment with doxycycline (Dox) will displace the endogenous WT HOXB13 with exogenous WT or X285K HOXB13. A total of 11 stable clones, including five LN95WT (exogenous WT would replace endogenous WT after DOX), three LN95X285K (exogenous X285K would replace endogenous  WT after Dox), and three LN95NT (non-targeting vector) were generated. Each of the 11 clones was subjected to 4 different treatment conditions, with (Dox+) or without (Dox-) Dox (sample named are annotated as DoxP or DoxN), and in the absence (R1881-) or presence (R1881+) of synthetic androgen R1881 (sample names with R if R1881 is added). We generated RNA-sequencing (RNA-Seq) data from these 44 cell line samples.

first: Mayuko

last: Kanayama

first: Jun

last: Luo

first: Daniel

last: Rabizadeh

first: Zhao

last: Lai


title: Therapeutic use of R-spondins to augment the cerebrovascular and neuronal Wnt signaling and improve stroke outcome in mice

status: Public on Oct 07 2023

city: Shenzhen

first: YINZHONG

last: MA

state: Guangdong

country: China

summary: This SuperSeries is composed of the SubSeries listed below.

sample_organism:
Mus musculus
Rattus norvegicus

platform_organism:
Mus musculus
Rattus norvegicus

overall_design: Refer to individual Series


title: Therapeutic use of R-spondins to augment the cerebrovascular and neuronal Wnt signaling and improve stroke outcome in mice [neuron RNA-Seq]

summary: Although Wnt signaling is critical for blood-brain barrier function, neuronal survival and adult neurogenesis, Wnt proteins are poorly suited as therapeutics for stroke given production and pharmacokinetic challenges. Here, we show that R-spondins (RSPOs), a family of easily produced secreted proteins that robustly augment Wnt signaling, were widely expressed in adult mouse brain and upregulated upon ischemia and reperfusion injury. Neutralizing endogenous RSPOs with their membrane receptor LGR5 and ZNRF3/RNF43 soluble ectodomains increased cerebral infarction in a murine stroke model. Conversely, systemic administration of RSPOs substantially reduced cerebral infarction and improved neurological outcomes. The neuroprotective effects of RSPOs were dependent on LGR4/ZNRF3-mediated canonical Wnt/-catenin signaling in the endothelia, neuronal cells and neural stem/progenitor cells, all of which contributed synergistically to reduce cerebral ischemia/reperfusion injury. Thus, we identified a previously unknown neuroprotective mechanism and the therapeutic potential of recombinant RSPOs in ischemic stroke.

overall_design: Examination of gene regulation by Wnt3a plus Rspondin 1 in rat primary neuron under oxygen glucose deprivation (OGD)

first: Yinzhong

last: Ma

first: Michael

middle: R

last: Mancuso

first: Carolina

last: Maier-Albers

first: Xibin

last: Liang

first: Kelley

last: Yan

first: Christopher

middle: M

last: Madl

first: Jingjing

last: Liu

first: Feng

last: Wang

first: Meifang

last: Yin

first: Mario

last: Vallon

first: Kanako

last: Yuki

first: Jenny

last: Yuan

first: Qianyan

last: He

first: Zhen-Ni

last: Guo

first: Fang

first: Fuyou

first: Yi

last: Yang

middle: C


title: RNA sequencing data from MCF10AT cells  expressing hPRLrL/hPRLrI or hPRLrL/hPRLrI I-tail removal mutant

city: RICHMOND

first: Shanwei

last: Shen

state: VA

address: 1101 E Marshall St

department: Pathology

institute: Virginia Commonwealth University

summary: The intermediate hPRLr (hPRLrI) is produced by alternative splicing which induces a frameshift, resulting in a novel 13 amino acid tail ("I-Tail") gain and a premature stop codon. hPRLrI induces significant proliferation and anchorage-independent growth of normal mammary epithelia when co-expressed with long form hPRLr (hPRLrL). hPRLrL and hPRLrI co-expression are necessary to induce the transformation of mammary epithelia. In studying the function of hPRLrI I-tail, the ubiquitin-like protein neural precursor cell expressed developmentally down-regulated protein 8 (NEDD8) was found to be interacting with the I-tail by yeast two-hybrid analysis. hPRLrI I-tail deletion results in attenuated ERK1/2 signaling, decreased anchorage-independent growth, and decreased cell motility. The goal of this study was to generate mRNA profiles for MCF10AT cells expressing hPRLrL/hPRLrI, or hPRLrL/hPRLrI I-tail removal mutant treated with or without prolactin (PRL).

overall_design: To examine role of hPRLrI I-tail in the pathogenesis of breast cancer, mRNA profiling of MCF10AT cells expressing either hPRLrL/hPRLrI, or  hPRLrL/hPRLrI I-tail removal mutant  treated  with or without prolactin (PRL) for 2 hours.

first: Christiane

last: Morecock


title: ERK signaling plays an essential role in the IFNg-mediated apoptosis of melanoma cells. [CRISPR screen]

city: Los Angeles

first: Ameya

last: Champhekar

state: California

address: 700 Tiverton Ave, 11-272 Factor Bldg

department: Medicine, HemOnc Division

institute: University of California, Los Angeles

summary: Interferon-gamma (IFNg) exerts potent growth inhibitory (antiproliferative/pro-apoptotic) effects on a wide range of tumors, including melanoma. While several terminal effectors of cell cycle arrest and apoptosis have been identified, a definitive account of the signaling pathway leading to these events is lacking. We set up a chemical genomics screen and a whole genome targeting CRISPR/Cas9 screen in a growth inhibition (GI)-sensitive patient-derived melanoma (PDM) cell line. Drug screening revealed that treatment with RAF and ERK inhibitors disrupted IFNg GI in PDM cells. For the CRISPR screen, the gene-level analysis showed that the magnitude of enrichment for guide RNAs targeting ERK2 in IFNg-treated cells was comparable to core IFNg signaling proteins like IFNGR2, JAK1, JAK2, and STAT1. We validated the involvement of ERK by detecting a sustained increase in phospho-ERK1/2 (p-ERK) levels following IFNg treatment. In live imaging experiments, we found that an ERK inhibitor (ERKi) blocks the induction of cell death in 17 of 23 (~74%) IFNg-sensitive PDM lines covering all the MAPK mutant and triple wildtype molecular subtypes. Through gene expression analysis, we found that IFNg-ERK signaling triggered the expression of stress response genes and subsequent upregulation of DR5 and NOXA, which were both critical for the induction of cell death. In summary, the IFNg-ERK signaling axis mediates cell death downstream of IFNg treatment in melanoma cells. Our results provide a new understanding of the IFNg-mediated GI pathway that will also be crucial to define mechanisms of GI resistance in tumor cells.

overall_design: Cas9-expressing M238 melanoma clonal line was transduced with either the full human GeCKO v2 or Brunello sgRNA libraries at an MOI ≤0.3. Transduced cells were selected with Puromycin for 7 days and treated with or without IFNg. Cells were harvested after 10-14 days and gDNA was isolated for library preparation. Human GeCKO library was used to perform one screen, while the Brunello library was used in two screens.

first: Egmidio

last: Medina

first: Katie

last: Campbell

first: Antoni

last: Ribas


title: MiR-146a-5p and miR-191-5p as novel diagnostic marker candidates for ovarian clear cell carcinoma

city: Shinjyuku

first: Tomohiro

last: Umezu

state: Tokyo

address: 6-1-1 Shinjyuku

department: Department of Molecular Pathology

country: Japan

institute: Tokyo Medical University

summary: Ovarian cancer is a malignant gynecologic disease rarely diagnosed in the early stages. Among ovarian cancers, clear cell carcinoma has a poor prognosis due to its malignant potential. MicroRNAs (miRNAs) regulate gene expression in cells by suppressing the translation of the target gene or by degrading the target mRNA. They are also secreted from the cells in the blood, binding to the proteins or lipids and assisting in cell-cell communication. Hence, serum miRNAs can also be diagnostic biomarkers for ovarian cancer. This study investigated and identified specific miRNAs for ovarian clear cell carcinoma and compared them to those of ovarian endometrioma in healthy patients. CA125, an ovarian tumor marker, did not differ between patients with ovarian clear cell carcinoma, endometriosis, or healthy controls. Four miRNAs (miR-146a-5p, miR-191-5p, miR-484, and miR-574-3p) were analyzed. The miR-146a-5p and miR-191-5p expression levels were significantly increased in the serum samples from the patients with ovarian clear cell carcinoma compared to the healthy controls but not in the patients with endometriosis (P < 0.05). Furthermore, the bioinformatics analysis showed that CCND2 and NOTCH2 were the candidate target genes of miR 146a-5p and miR-191-5p. In conclusion, our results showed that miR 146a-5p and miR-191-5p might be useful as early and non-invasive diagnostic tools in ovarian clear cell carcinoma. These miRNAs can help in distinguishing between ovarian clear cell carcinoma and ovarian endometrioma. To the best of our knowledge, no studies have screened any candidates specifically for clear cell carcinoma.

overall_design: The blood samples were collected from patients with ovarian clear cell carcinoma, as well as from the healthy controls. We measured the CA125 levels in patients with endometriosis and ovarian cancer before surgery. The blood serum was separated by centrifugation at 1800 rpm for 10 min and stored at –80 °C. The total RNA was extracted from the serum using the miRNeasy Serum/Plasma Advanced Kit (Qiagen, Hilden, Germany). We used TaqMan™ Array Human MicroRNA A Card Set v2.0 (Thermo Fisher Scientific, Inc.) to search for candidate miRNAs in 20 samples (16 samples of ovarian clear cell carcinoma and four healthy control samples).


title: ERK signaling plays an essential role in the IFNg-mediated apoptosis of melanoma cells. [RNAseq]

overall_design: We performed gene expression analysis in order to understand which pathways downstream of ERK activation were involved in inducing cell death. To do this, we stimulated M230 and M238 cells with IFNg in the presence or absence of ERKi for 24 hours resulting in 4 treatments per line: DMSO, DMSO + IFNg, ERKi, and ERKi + IFNg. Ulixertinib was used as the ERKi at 6 µM and IFNg treatment was at 100 U/ml. RNAseq data was generated from 2 experiments per line.


title: ERK signaling plays an essential role in the IFNg-mediated apoptosis of melanoma cells.


title: A common single nucleotide variant in the cytokine receptor-like factor-3 (CRLF3) gene causes neuronal deficits in human and mouse cells

first: David

last: Gutmann

address: 660 S. Euclid Ave

institute: Washington University in St. Louis School of Medicine

summary: Single nucleotide variants in the general population are common genomic alterations, where the majority are presumed to be silent polymorphisms without known clinical significance. Using human induced pluripotent stem cell (hiPSC) cerebral organoid modeling, we previously discovered that the cytokine receptor-like factor-3 (CRLF3) gene is a major regulator of neuronal maturation in the 1.4 megabase Neurofibromatosis type 1 (NF1) deletion syndrome. Moreover, children with NF1 and the CRLF3L389P variant have greater autism burden, suggesting that this gene might be important for neurologic function. To explore the functional consequences of this variant, we generated CRLF3L389P-mutant hiPSC lines and Crlf3L389P-mutant genetically engineered mice. While this variant does not impair protein stability, brain structure, or mouse behavior, CRLF3L389P-mutant human cerebral organoids and mouse brains exhibit impaired neuronal maturation and dendrite formation. In addition, Crlf3L389P-mutant mouse neurons have reduced dendrite lengths and branching, without any axonal deficits. Moreover, Crlf3L389P-mutant mouse hippocampal neurons have decreased firing rates and amplitudes relative to wild type controls. Taken together, these findings establish the CRLF3L389P variant as functionally deleterious and suggest that it may be a neurodevelopmental disease modifier.

overall_design: Crlf3L389P-mutant and WT hippocampi were collected from four 4-week-old mice (4 hippocampi/  2 mice per genotype) and pooled to prepare single-cell isolations for each region.

first: Anna

middle: F

last: Wilson

first: Rasha

last: Barakat

first: Rui

last: Mu

first: Leah

last: Karush

first: Yinqing

last: Gao

first: Kelly

middle: A

last: Hartigan

first: Ji-Kang

last: Chen

first: Hongjin

last: Shu

first: Tychele

middle: N

last: Turner

first: Susan

middle: E

last: Maloney

first: Steven

last: Mennerick

middle: H

first: Corina

last: Anastasaki


title: MAPK1 promotes the metastasis and invasion of gastric cancer as a bidirectional transcription factor (ChIP-Seq)

city: Changchun

first: yue

last: wang

address: 2699 Qianjin Street

institute: Jilin University

type: Genome binding/occupancy profiling by high throughput sequencing

summary: Background Mitogen-activated protein kinase 1 (MAPK1) has independent functions of phosphorylating histones as a kinase and directly binding the promoter regions of genes to regulate gene expression as a transcription factor. Previous studies identified elevated expression of MAPK1 in human gastric cancer, which is associated with its role as a kinase, facilitating gastric cancer cell migration and invasion. However, being a transcription factor, how MAPK1 binds its target genes and whether it modulated related gene expressions in gastric cancer remains unclear.   Results Here, we integrated biochemical assays (protein interactions and chromatin immunoprecipitation (ChIP)), cellular analysis assays (cell proliferation and migration), RNA sequencing, ChIP sequencing, and clinical analysis to investigate the potential genomic recognition patterns of MAPK1 in a human gastric adenocarcinoma cell-line (AGS) and to uncover its regulatory effect on gastric cancer progression. We confirmed that MAPK1 promotes AGS cells invasion and migration by regulating the target genes in controversial directions, up-regulating seven target genes (KRT13, KRT6A, KRT81, MYH15, STARD4, SYTL4, and TMEM267) and down-regulating one gene (FGG). Among them, five genes (FGG, MYH15, STARD4, SYTL4, and TMEM267) were first associated with cancer procession, while the other three (KRT81, KRT6A, and KRT13) have been previously confirmed to be related to cancer metastasis and migration.   Conclusion Our data showed that MAPK1 binds to the promoter regions of these target genes to control their transcription, hence encouraging AGS cell motility and invasion. Our research broadened the understanding of the regulatory roles of MAPK1, enriched the knowledge of transcription factors, and provided novel candidates for cancer therapeutics.

overall_design: Previous studies identified elevated expression of MAPK1 in human gastric cancer, which is associated with its role as a kinase, facilitating gastric cancer cell migration and invasion. However, being a transcription factor, how MAPK1 binds its target genes and whether it modulated related gene expressions in gastric cancer remains unclear. In the current study, we performed the integrated approaches of gene overexpression, gene knockdown, RNA sequencing (RNA-seq), and ChIP sequencing (ChIP-seq) to investigate the transcription regulatory function of MAPK1 and its effect on gastric cancer progress.

first: Yue

last: Wang

first: Zheng

last: Guo

first: Yueli

last: Tian

first: Liang

last: Cong

first: Yulu

last: Zheng

first: Zhiyuan

last: Wu

first: Guangle

last: Shan

first: Yao

last: Xia

first: Yahong

last: Zhu

first: Xingang

last: Li

first: Ying

last: Song


title: MAPK1 promotes the metastasis and invasion of gastric cancer as a bidirectional transcription factor (RNA-Seq)


title: Single cell gene expression analysis of mouse colon ΤCRδ+CD8α+ and TCRβ+CD8α+ intraepitehlial lymphocytes (IELs)

city: Clayton

first: Wei

last: Shi

state: VIC

address: 15 Innovation Walk

department: Department of Biochemistry and Molecular Biology

country: Australia

institute: Monash University

summary: TCF-1 is highly expressed in colon T- IELs.Tο understand the role of TCF-1 in regulating the gene expression of colon CD8+ T IELs, we isolated and sorted CD8α+TCRδ+ and CD8α+TCRβ+ from colons of  E8Ιcre-Transgentic Tcf7 floxed mice or control Tcf7 floxed mice.

overall_design: Single cell RNA sequencing of  colon ΤCRγδ+CD8α+ and TCRβ+CD8α+ IELs from mice with and without Tcf7 (E8ICre, Tcf7 floxed)

first: Dinesh

last: Raghu

first: Yang

last: Liao

first: Lisa

last: Mielke


title: Bulk RNA sequencing of epithelial cells from  AOM-DSS mouse colorectal cancer (CRC)

summary: Gamma-delta T cells prevent CRC. To understand the criticial role of Gamma-delta T cells in CRC,  AOM-DSS tumors from mice lacking TCRγδ and with TCRγδ cells were used to isolate epithelial cells  to study gene expression by bulk RNA sequencing.

overall_design: Bulk RNA sequencing of epithelial cells from  mouse CRC tumors induced by AOM-DSS.


title: Single cell gene expression analysis of mouse CD45.2+ intraepithelial lymphocyes (IELs) from stomach, small intestine, cecum and colon.

summary: To understand the diversity of IELs in the gastrointestinal tract, CD45.2+ IELs from stomach, small intestine, cecum and colon of C57BL/6 mice were isolated for single cell RNA sequencing.

overall_design: Single cell RNA sequencing of mouse CD45.2+ IELs from stomach, small intestine, cecum and colon.


title: The gene expression profile of CD4 T-cells with STAT3 gain-of-function and loss-of-function mutations

city: Freiburg

first: Senthilkumar

last: Ramamoorthy

address: Mathildenstraße 1

country: Germany

institute: UNIVERSITAETSKLINIKUM FREIBURG

summary:
Purpose: Recently discovered activating Interleukin-6 receptor subunit beta (IL6ST, encoding glycoprotein 130 (gp130)) mutations, as well as germline Signal transducer and activator of transcription 3 (STAT3) gain-of-function mutations are associated with multi-organ autoimmunity, severe morbidity, and adverse prognosis, resulting in an unmet medical need.
Methods: To decipher the crucial cellular subsets and disease biology associated with STAT3 gain-of-function mutations, we examined the gene expression profile of STAT3 gain-of-function and loss-of-function mutations in unstimulated, IL10- or IL21-stimulated CD4 T cells and compared them to healthy donor cells.
Results: Activating gp130 signaling in vivo resulted in fatal early-onset multi-organ autoimmunity, resembling numerous clinical features of human STAT3 gain-of-function disease. We observed strong T-cell activation and effector differentiation, accompanied by TH17 expansion and interferon-gamma production.  Transcriptome profiling of murine CD4+ and CD8+ T-cells revealed commonly dysregulated genes and a STAT3 gain-of-function signature that was used to discriminate between STAT3 gain-of-function and healthy control patients.
Conclusions: Hyperactive gp130/STAT3 signaling leads to strong TH17-mediated autoimmunity phenotypically resembling human STAT3 gain-of-function disease and identify TH17-cells as a key cellular subset for initiation and maintenance of autoimmunity

first: Laura

last: Faletti

first: Francis

last: Baumgartner

first: Stefanos

last: Bamopoulos

first: Stephan

last: Ehl


title: The Transcription Factor IRF4 Determines the Anti-Tumor Immunity of CD8+ T cells

city: Houston

first: Yulin

last: Dai

state: TX

address: 7000 fannin, suite 600

department: School of Biomedical Informatics

institute: University of Texas health science center at Houston

summary: Four TIL populations from B16-F10 melanoma were analyzed by scRNA-seq, including adoptively transterred anti-tumor CD8+ Pmel-1 T cells that were transduced with IRF4 (sample 1, IRF4_Pmel) or GFP control (Sample 3, Ctrl_Pmel), and CD45+ endogenous TILs from either the IRF4 group (Sample 2, IRF4_TILs) or Ctrl group (Sample 4, Ctrl_TILS).

overall_design: scRNAseq analysis of TILs from B16-F10 melanoma was performed.

first: Yan

last: Hui

first: Dawei

last: Zou

first: Wenhao

last: Chen


title: Maternal blood transcriptome reflects fetal maturation at the end of the organogenesis in cattle.

city: Utrecht

first: Maria

middle: Belen

last: Rabaglino

address: Yalelaan 7

department: Population Health Science

country: Netherlands

institute: Utrecht University

summary: In cattle, harnessing information from the maternal blood to predict fetal health and development is attractive yet scarcely explored. We hypothesised that variations in fetal growth at the end of the organogenesis period impact on the molecular profile of fetal organs and is reflected in the maternal blood transcriptome. The objectives were to determine the transcriptomic modifications in maternal blood and in fetal liver, gonads, and heart according to fetal weight and to model a molecular signature based on the fetal organs allowing the prediction of fetal weight from the maternal blood transcriptome. In addition to a contemporaneous maternal blood sample, organ samples were collected from 10 male fetuses at day 42 day of gestation for RNA-sequencing. Fetal weight ranged from 1.25 to 1.69 gr (mean 1.44 ± 0.15 gr). Data were analysed through co-expression cluster analysis to identify biologically relevant genes dynamically changing according to fetal weight in each fetal organ and in maternal blood. Results revealed clusters of genes, the expression of which was positively correlated with fetal weight, and which enriched ontological terms involved in the organ functionality. For the heart, the 1346 co-expressed genes were involved in energy generation and protein synthesis. For the gonads, the 1042 co-expressed genes enriched seminiferous tubule development. The 459 co-expressed genes identified in the liver were associated with lipid synthesis and metabolism. Finally, the cluster of 571 co-expressed genes determined in maternal blood enriched oxidative phosphorylation and thermogenesis. The expression patterns of the common genes between the clusters in each fetal organ and the cluster in maternal blood were employed to construct a predictive regression model of fetal weight. The data from the fetal organs were used to train the model, and the data from the maternal blood were used to test it. The best prediction was achieved when the model was trained with the 35 common genes between heart and maternal blood (root mean square error=0.04, R-square=0.93). In conclusion, linking transcriptomic information from maternal blood with that from the fetal heart unveils maternal blood as a sensor of fetal development.

overall_design: We used an asynchronous embryo transfer model to stimulate fetal growth physiologically, as demonstrated in our previous study (PMID: 36739669). Heifers were randomly assigned to one of the two groups: those receiving a Day 7 embryo on Day 7 of the cycle (synchronous; ET_D7, n=23) and those transferred a Day 7 embryo on Day 9 of the cycle (asynchronous; ET_D9, n=33). The synchronisation protocol was started two days earlier for heifers in the ET_D9 group, such that ET was done on the same day for both groups. Blood samples were collected in Tempus Tubes (Thermofisher Scientific, Waltham, MA USA) from pregnant heifers (n=25) on Day 42 of gestation, following which they were slaughtered in a commercial abattoir. The reproductive tract was recovered and held on ice until processing for sample collection, which was done in the first 30 min after slaughter. The pregnant uterine horn was opened along the major curvature to expose and retrieve the fetal membranes. Once the fetus was isolated, the liver, heart and gonads were dissected, placed in individual RNAse-free tubes and snap-frozen in liquid nitrogen. Blood and fetal organ samples were stored at -80 °C until processing for RNAseq. Samples corresponding to 10 male fetuses (equally derived from heifers in the ET_D7 and ET_D9 groups) were employed in the current study.

middle: B

first: Sanchez

last: Jose

first: McDonald

last: Michael

first: O'Callaghan

last: Elena

first: Pat

last: Lonergan


title: Colorectal cancer

first: Wei

last: Shi


title: IL-33 priming and antigenic stimulation synergistically promote the transcription of proinflammatory cytokine and chemokine genes in human skin mast cells

city: Denver

first: HUA

last: HUANG

state: Colorado

address: 1400 Jackson street, K511

department: Immunology and Genomic Medicine

institute: National Jewish Health

summary: Antigenic stimulation through cross-linking the IgE receptor and epithelial cell-derived cytokine IL-33 are potent stimuli of mast cell (MC) activation. Moreover, IL-33 primes a variety of cell types, including MCs to respond more vigorously to external stimuli. However, target genes induced by the combined IL-33 priming and antigenic stimulation have not been investigated in human skin mast cells (HSMCs) in a genome-wide manner. Furthermore, epigenetic changes induced by the combined IL-33 priming and antigenic stimulation have not been evaluated. In this study, we found that IL-33 priming of HSMCs enhanced their capacity to promote transcriptional synergy of the IL1B and CXCL8 genes by 16- and 3-fold, respectively, in response to combined IL-33 and antigen stimulation compared to without IL-33 priming. We identified the target genes in IL-33-primed HSMCs in response to the combined IL-33 and antigenic stimulation using RNA sequencing (RNA-seq). We found that the majority of genes synergistically upregulated in the IL-33-primed HSMCs in response to the combined IL-33 and antigenic stimulation were predominantly proinflammatory cytokine and chemokine genes. Moreover, the combined IL-33 priming and antigenic stimulation increase chromatin accessibility in the synergy target genes but not synergistically. Transcription factor binding motif analysis revealed more binding sites for NF-κB, AP-1, GABPA, and RAP1 in the induced or increased chromatin accessible regions of the synergy target genes. Our study demonstrates that IL-33 priming greatly potentiates MCs’ ability to transcribe proinflammatory cytokine and chemokine genes in response to antigenic stimulation, shining light on how epithelial cell-derived cytokine IL-33 can cause exacerbation of skin MC-mediated allergic inflammation.


title: Integrome signatures of lentiviral gene therapy for SCID-X1 patients

city: Memphis

first: Jiyang

last: Yu

state: TN

address: 262 Danny Thomas Pl

department: Department of Computational Biology

institute: St Jude Children's Research Hospital

summary: Lentiviral vector (LV)-based gene therapy holds promise for a broad range of diseases. Analyzing more than 280,000 vector integration sites (VISs) in 273 samples from 10 patients with X-linked severe combined immunodeficiency (SCID-X1), we discovered shared LV integrome signatures in 9 out of 10 patients in relation to the genomics, epigenomics, and 3D structure of the human genome. VISs were enriched in the nuclear sub-compartment A1 and integrated into super-enhancers close to nuclear pore complexes. These signatures were validated in T cells transduced with an LV encoding a CD19-specific chimeric antigen receptor. Intriguingly, the one patient whose VISs deviated from the identified integrome signatures had a distinct clinical course. Comparison of LV and gamma retrovirus integromes regarding their 3D genome signatures, identified differences that might explain the lower risk of insertional mutagenesis in LV-based gene therapy. Our findings suggest that LV integrome signatures, shaped by common features such as genome organization, may impact the efficacy of LV-based cellular therapies.

overall_design: To confirm VIS signatures, we performed single-cell profilng for bone marrow samples of two SCID-X1 patients 18 months after gene transfusion.

first: Koon-Kiu

last: Yan

first: Stephen

last: Gottschalk


title: Gene expression profiles at the single cell levels of murine  airway T helper cells challenged with dog allergens

status: Public on Oct 05 2023

city: Solna

first: Chris

middle: Andrew

last: Tibbitt

state: non-US

address: Biomedicum C7,, Tomtebodavägen 16

country: Sweden

institute: KI

summary: We established a mouse model of dog allergy by repeatedly administering dog dander and epithelium extracts via the intranasal route. scRNA-Seq analysis of T helper cells in the airways pinpointed a unique gene signature for TH17 cells. Analysis of T-cell receptors depicted a high frequency of clones that were shared between TH17, TH2 and suppressive Treg cells, indicative of a common differentiation trajectory for these subsets.

overall_design: Using WT challenged with dog allergens we performed single cell RNA-sequencing (scRNA-SEQ) using the 10X platform on airway-infiltrating CD4+ T helper cells.

first: Christopher

first: Jonathan

last: Coquet


title: IL-33 priming and antigenic stimulation synergistically promote the transcription of proinflammatory cytokine and chemokine genes in human skin mast cells [ATAC-Seq]

overall_design: Omni-ATAC-seq in unstimulated or stimulated HSMCs, in duplicate, using Illumina NovaSEQ6000 platform.

first: Junfeng

last: Gao

first: Hua

last: Huang


title: miRNA expression profiles of  multiple myeloma

city: Wuhan

first: Han

address: Jiefang  Avenue

institute: Institute of Hematology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology

type: Non-coding RNA profiling by high throughput sequencing

summary: To further investigate the differential expression miRNA of multiple myeloma, three multiple myeloma samples and three normal samples were used for miRNA sequencing.

overall_design: Bone marrow CD138+ cells were sorted from multiple myeloma patients and normal individuals. Samples were treated with TRIzol and total RNA was extracted.miRNA expression profiling was carried out in three multiple myeloma patients and three controls.

first: Su


title: IL-33 priming and antigenic stimulation synergistically promote the transcription of proinflammatory cytokine and chemokine genes in human skin mast cells [RNA-Seq]

overall_design: mRNA profiles of unstimulated or stimulated HSMCs were generated by deep sequencing, in quadruplicate or duplicate, using Illumina NovaSEQ6000 platform.


title: Lung epithelial cell ATAC G9ai

city: Boston

first: Samuel

middle: P

last: Rowbotham

state: MA

address: 185 Cambridge Street

institute: Massachusetts General Hospital

summary: The goal of the experiment was to assess the changes in chromatin accessibility in different populations of lung epithelial cells after H3K9me2 depletion via G9a inhibition

overall_design: 3 populations of lung epithelial cells were collected each from lungs of 3 mice treated with G9a inhibitor and 3 mice treated with vehicle control and ATAC libraries were prepared from 10K cells

first: Rowbotham

last: Samuel

first: Joon

last: Yoon

first: HoSui

last: Shannan

first: Kim

last: Carla


title: Transcriptome analysis of transplanted vascular organoid grafts under cranial window at the time of thrombosis after SARS-CoV-2 spike-ECD infusion

city: Tokyo

first: Norikazu

last: Saiki

address: 1-5-45 Yushima, Bunkyo-ku

department: Institute of Research

institute: Tokyo Medical and Dental University

summary: We evaluated virus-induced damages in perfused human blood vessels from iPS-derived vascular organoid (iVO). By taking advantage of the cranial window model, iVOs were transplanted to develop human blood vessels by anastomosing the recipient mouse circulatory system. we infused SARS-CoV-2 spike protein (extracellular domain, ECD) in the mouse to determine the impact on chimeric human-mouse blood vessels formed under the cranial window. Our iVO transplantation studies indicated that Spike protein could specifically target human endothelial cells, but not murine endothelial cells, which leads to neutrophil migration by creating a coagulopathic milieu and therein generating microthrombi.

overall_design: Bulk RNA-seq of transplanted vascular organoid grafts under cranial window at day 1 after SARS-CoV-2 spike-ECD infusion.

first: Eri

last: Kawakami

first: Yosuke

last: Yoneyama

first: Chiharu

last: Moriya

first: Tamaki

last: Kono

first: Takanori

last: Takebe


title: Gene expression profile at single cell level of mononuclear cells from skeletal muscle (gastrocnemius) of non-PAD controls and PAD patients

city: Zurich

first: Genome

last: Informatics

address: Winterthurerstrasse 190

department: Functional Genomics Center Zurich (FGCZ)

country: Switzerland

institute: ETH ZURICH / University of Zurich

summary: The molecular and cellular mechanisms of skeletal muscle from peripheral artery disease (PAD) patients are not completely understood. We used single cell RNA sequencing (scRNA-seq) to characterize the skeletal muscle diversity between control and PAD patients.

overall_design: Live mononuclear cells (Calcein+) from human skeletal muscle were isolated by Fluorescence-activated cell sorting (FACS) and analyzed using scRNAseq.

first: Guillermo

last: Turiel

first: Thibaut

last: Desgeorges

first: Evi

last: Masschelein

first: Jing

last: Zhang

first: Stephan

last: Engelberger

first: Katrien

last: De Bock


title: CITE-seq reveals inhibition of NF-kB pathway in B cells from vitamin D-treated multiple sclerosis patients

city: Montpellier

first: Eric

last: Thouvenot

address: 141 rue de la Cardonille

country: France

institute: IGF

summary: Vitamin D deficiency is a risk factor for multiple sclerosis (MS) and is correlated with disease activity and progression. Vitamin D treatment has emerged as potentially protective, even though results from randomized controlled trials are conflicting. Here, we used single-cell RNA-seq (scRNA-seq) coupled with barcoded antibodies targeting surface markers (CITE-seq) to discover candidate genes and pathways regulated in PBMC subpopulations from MS patients treated with high-dose vitamin D (n=5) or placebo (n=5). Best candidates were combined with genes involved in immune function and vitamin D metabolism for validation in a new cohort (n=8 in each group) by high-throughput qPCR (HT-qPCR) in naive CD4, Th1, Th17, Treg, naive CD8, memory and naive B cells, and MAIT cells, sorted by FACS. CITE-seq showed no significant changes in the proportions of these subpopulations in vitamin D-treated patients. Of the 92 candidate genes revealed by CITE-seq, differential expression of five genes (UXT, SNRPN, SUB1, GNLY and KLF6) was validated by HT-qPCR. CITE-seq also revealed the regulation of several pathways by vitamin D in naive and memory B cells, including MAPK, TLR and interleukin pathways, that contribute to counteract EBV-induced resistance to apoptosis through inhibition of the NF-kB pathway.

overall_design: Five MS patients treated with high dose vitamin D (100,000 IU every 2 weeks for 3 months) and 5-matched MS patients treated with placebo were selected from the D-lay MS cohort (NCT01817166). Blood samples of study participants of the D-lay MS study had been previously collected in EDTA-containing tubes at D0 and M3 of treatment (placebo or vitamin D). PBMCs had been isolated by Ficoll® gradient and cryopreserved in liquid nitrogen using 4% human albumin solution + 10% DMSO medium in concentration of 5x106 cells per ml.  Cells were labeled with CITE-seq antibodies and live cells were isolated by fluorescence-activated cell sorting (FACS).

first: Manon

last: Galoppin

last: Rival

first: Anaïs

last: Louis

first: Saniya

last: Kari

first: Sasha

last: Soldati

first: Britta

last: Engelhardt

first: Anne

last: Astier

first: Philippe

last: Marin


title: Depletion of ADAM12+ MSCs normalizes the tumor stromal microenvironment

city: Paris

first: Lucie

last: Peduto

address: 25 rue du Docteur Roux

institute: Institut Pasteur

summary: This study investigates transcriptomic changes occurring in PDPN+PDGFRa+ stromal cells from murine B16-OVA melanomas (MO5) when ADAM12+ mesenchymal stromal cells (MSCs) are depleted.

overall_design: RNA sequencing was performed on PDPN+PDGFRa+ stromal cells isolated from MO5 melanomas that are WT (Samples C1-C3) or depleted of ADAM12+ cells (Samples D1-D3) in ADAM12-DTR mice.

first: Selene

last: Di Carlo

first: Rachel

last: Legendre

first: Hugo

last: Varet


title: CDK11 requires a critical activator SAP30BP to regulate pre-mRNA splicing

city: Shanghai

first: Hong

last: Cheng

state: State

address: 320 Yue Yang Road

institute: Shanghai Institute of Biochemistry and Cell Biology, CAS.

summary: CDK11 is an emerging druggable target for cancer therapy due to its prevalent roles in phosphorylating critical transcription and splicing factors and in facilitating cell cycle progression in cancer cells. Like other cyclin-dependent kinases, CDK11 requires its cognate cyclin, cyclin L1 or cyclin L2, for activation. However, little is known about how CDK11 activities might be modulated by other regulators. In this study, we show that CDK11 forms a tight complex with cyclins L1/L2 and SAP30BP, the latter of which is a poorly characterized factor. Acute degradation of SAP30BP mirrors that of CDK11 in causing widespread and strong defects in pre-mRNA splicing. Furthermore, we demonstrate that SAP30BP facilitates CDK11 kinase activities in vitro and in vivo, through ensuring the stabilities and the assembly of cyclins L1/L2 with CDK11. Together, these findings uncover SAP30BP as a critical CDK11 activator that regulates global pre-mRNA splicing.

overall_design: siSAP30BP-RNAseq, siU1C-RNAseq, time course RNA-seq in presence or absence of CDK11 or SAP30BP


title: RNA-sequence analysis of WT mice hearts and cardiomyocyte-specific deletion of STAT3 mice hearts

status: Public on Oct 12 2023

first: Wei

last: Jin

address: 197 Ruijin 2nd Road,

institute: Department of Cardiology, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine

summary: The RNA-sequence analysis of cardiomyocyte-specific deletion of STAT3 mice hearts showed that comparing with WT mice hearts, the STAT3cKO mice hearts showed reduced cardiac function by affecting some key pathways.

overall_design: STAT3 may affect cardiac fucntion,and RNA-sequence analysis was used to explore the key pathways that influnce cardiac funciton in STAT3cKO mice hearts.


title: Transcriptome analysis of induced vascular organoids at 4 dpi of SARS-CoV-2 infection to probe infected endothelial cell-specific signatures

first: Norikazu

last: Saiki

summary: we have successfully established an in vitro iPSC-derived vascular organoid (iVO) model that can reproduce the vascular injury and inflammatory phenotype associated with the viral infection. In particular, we identified a marked increase in the expression of a part of the membrane attack complex, an intermediate and final product of the complement pathway, and molecules that catalyze upstream reactions (classical; C1QA, C1QB, C1QC, and alternative; CFD)

overall_design: We developed an infection-competent human vascular organoid from pluripotent stem cells amenable for modeling endotheliopathy and performed transcriptome analysis at 4 days-post-infection of SARS-CoV-2 to probe infected endothelial cell-specific signatures.

first: Eri

last: Kawakami

first: Tamaki

last: Kono

first: Takanori

last: Takebe


title: Molecular profiling of ADAM12+ MSCs in B16-OVA melanomas

summary: This study investigates the transcriptome of ADAM12+ mesenchymal stromal cells (MSCs) in B16-OVA (MO5) melanomas

overall_design: RNA sequencing was performed on ADAM12+ (GFP+) and ADAM12- (GFP-) stromal cells isolated from MO5 melanoma in ADAM12-GFP mice


title: Effect of Hyperbaric Oxygen and Inflammation on Human Gingival Mesenchymal Stem/Progenitor Cells

city: Kiel

first: Kristina

last: Schlicht

address: Düsternbrooker Weg 17

institute: UKSH Kiel

summary: The present study explores for the first time the effect of hyperbaric oxygen (HBO) on gingival mesenchymal stem cells’ (G-MSCs) gene expression profile, intracellular pathways activation, pluripotency and differentiation potential under an experimental inflammatory setup. G-MSCs were isolated from five healthy individuals (n=5) and characterized. Single (24h) or double (72h) HBO stimulation (100%O2, 3bar, 90min) was performed under experimental in-flammatory [IL-1β(1ng/ml)/TNF-α(10ng/ml)/IFN-γ(100ng/ml)] and non-inflammatory mi-cro-environment. Next Generation Sequencing and KEGG pathway enrichment analysis, G-MSCs’ pluripotency gene expression, Wnt-/β-catenin pathway activation, proliferation, colo-ny-formation and differentiation were investigated. G-MSCs demonstrated all mesenchymal stem/progenitor cells’ characteristics. The benefi-cial effect of a single HBO stimulation was evident, with anti-inflammatory effects and induction of differentiation (TLL1, ID3, BHLHE40), proliferation/cell survival (BMF, ID3, TXNIP, PDK4, ABL2), migration (ABL2) and osteogenic differentiation (p<0.05). A second HBO stimulation at 72h had a detrimental effect, significantly increasing the inflammation-induced cellular stress and ROS accumulation through HMOX1, BHLHE40 and ARL4C amplification and pathway en-richment (p<0.05).  Results outline a positive short-term single HBO anti-inflammatory, regenerative and dif-ferentiation stimulatory effect on G-MSCs. A second (72h) stimulation is yet detrimental on the same properties. The current results could open new perspectives in the clinical application of short-termed HBO induction in G-MSCs-mediated periodontal reparative/regenerative mecha-nisms.

overall_design: The present study explores for the first time the effect of hyperbaric oxygen (HBO) on gingival mesenchymal stem cells’ (G-MSCs) gene expression profile. Single (24h) or double (72h) HBO stimulation (100%O2, 3bar, 90min) was performed under experimental inflammatory [IL-1β(1ng/ml)/TNF-α(10ng/ml)/IFN-γ(100ng/ml)] and non-inflammatory micro-environment.


title: Boreal toad transcriptomic response to Bd infection

status: Public on Oct 04 2023

city: Las Vegas

first: Sarah

last: Corey-Rivas

state: New Mexico

address: PO BOX 9000

department: Biology

institute: New Mexico Highlands University

summary: Boreal toads (Anaxyrus boreas boreas) of the Southern Rocky Mountain population are declining due to the introduction of the chytrid fungus Batrachochytrium dendrobatidis (Bd). Boreal toads in Colorado are generally susceptible to Bd infection, but some Bd-tolerant populations persist in parts of the Southern Rocky Mountain and broader Eastern boreal toad population. We conducted a Bd challenge with lab-reared sibling toads from Bd-susceptible Colorado and purportedly Bd-tolerant Utah populations and report on transcriptomic responses to Bd during late infection in skin and liver tissue. Fewer immune genes were expressed in response to Bd in Colorado toads, but with greater upregulation compared to Utah toads, indicating a dysregulated immune response. Signatures of Bd-tolerance in Utah toads included more moderate upregulation in immune gene expression and a significantly enriched suite of gene functions related to innate and adaptive immune responses. Our transcriptomic results support the notion that Utah toads are tolerant to Bd, rather than resistant, carrying Bd loads similar to Colorado yet having a unique transcriptomic profile and presenting minimal clinical signs of chytridiomycosis. We conclude that closely related populations have divergent transcriptomic responses to Bd with a dysregulated immune response in Bd-susceptible toads.

overall_design: To investigate the transcriptomic responses to Bd infection in tolerant and susceptible boreal toads, we reared toads from both poulations in the lab from wild-caught eggs of the same clutch (sibling biological replicates). A 34 day Bd challenge was conducted with sibling replicates for each site (Colorado and Utah) using Bd isolate JEL 275 from Colorado. Skin and liver tissue was collected from sets of six sibling biological replicates (3 female, 3 male) at day 34 post-Bd innoculation for control and Bd challenge groups, for each source site (24 skin and 24 liver). RNA-seq generated 150 bp paired end reads which were then used in a differential gene expression analysis using an assembled de novo transcriptome.

first: W

middle: W

last: Lorenz

first: Casey

last: Taylor


title: Joint sequence and chromatin neural networks characterize the differential abilities of Forkhead transcription factors to engage inaccessible chromatin (ATAC-seq)

city: University Park

first: Shaun

last: Mahony

state: PA

address: 404 South Frear Bldg

department: Biochemistry & Molecular Biology

institute: Penn State University

summary: The DNA-binding activities of transcription factors (TFs) are influenced by both intrinsic sequence preferences and extrinsic interactions with cell-specific chromatin landscapes and other regulatory proteins. Disentangling the roles of these determinants in TF-DNA binding remains challenging. For instance, the FoxA subfamily of Forkhead domain TFs are known pioneer factors, yet their binding varies across cell types, pointing to a combination of intrinsic and extrinsic forces guiding their binding. How such sequence and chromatin influences vary across related Forkhead domain TFs remains mostly uncharacterized. Here, we present a principled approach to compare the relative contributions of intrinsic DNA sequence preference and cell-specific chromatin environments to a TF’s DNA-binding activities. We over-express a selection of Fox TFs in mouse embryonic stem (mES) cells, which offer a platform to contrast each TF's binding activity within the same preexisting chromatin background. By developing and applying a neural network that jointly models sequence and chromatin data, we can evaluate how sequence and preexisting chromatin features contribute to induced TF binding, both at individual sites and genome-wide. We demonstrate that Fox TFs bind different DNA targets, and drive differential gene expression patterns, even when induced in identical chromatin settings. Differential Fox binding activities can be attributed to distinct DNA-binding preferences coupled with differential abilities to engage relatively inaccessible chromatin. We propose that varying preferences for preexisting chromatin states enables the functional diversification of paralogous TFs.

overall_design: Genome-wide ATAC-seq profiling of chromatin accessibility after over-expression of selected Forkhead domain transcription factors in mouse embryonic stem cells

first: Sonny

last: Arora

first: Jianyu

last: Yang

first: Tomohiko

last: Akiyama

first: Daniela

last: James

first: Alexis

last: Morrissey

first: Thomas

last: Blanda

first: Nitika

last: Badjatia

first: William

middle: K

last: Lai

first: Minoru

last: Ko

first: B

last: Pugh


title: Joint sequence and chromatin neural networks characterize the differential abilities of Forkhead transcription factors to engage inaccessible chromatin (ChIP-exo)

overall_design: Genome-wide ChIP-exo profiling of high-resolution protein-DNA interactions for selected Forkhead domain transcription factors that have been over-expressed in mouse embryonic stem cells


title: Transcriptomic and Epigenetic Profile of Sorghum BTx623 Root Tissues

city: Cold Spring Harbor

first: Nicholas

last: Gladman

state: NY

address: 1 Bungtown Rd

department: ARS

institute: USDA

type: Methylation profiling by high throughput sequencing

summary: Identify the change in transcriptomic and epigenetic profiles within the sorghum root system of the cultivar BTx623 in response to limiting phosphorus conditions. This data is from the 2022 publication "Sorghum root epigenetic landscape during limiting phosphorus conditions".

overall_design:
For transcriptomic profiles, isolate replicates from three root areas (root apex, elongation zone, and lateral root region) from hydroponically-grown plants in sufficient and limiting phosphorus
Please note that the *csv *bw processed data files were generated from multiple samples as indicated in the corresponding sample description field.

first: Barbara

last: Hufnagel

first: Michael

last: Regulski

first: Zhigang

last: Liu

first: Xiaofei

last: Wang

first: Kapeel

last: Chougule

first: Leon

last: Kochian

first: Jurandir

last: Magalhães

first: Doreen

last: Ware


title: Joint sequence and chromatin neural networks characterize the differential abilities of Forkhead transcription factors to engage inaccessible chromatin (RNA-seq)

first: Shaun

last: Mahony

overall_design: RNA-seq analysis of transcriptome after over-expression of selected Forkhead domain transcription factors in mouse embryonic stem cells

first: Sonny

last: Arora

first: Jianyu

last: Yang

first: Tomohiko

last: Akiyama


title: Free bilirubin induces neuro-inflammation in an induced pluripotent stem cell-derived cortical organoid model of Crigler Najjar Syndrome

city: Düsseldorf

first: Wasco

last: Wruck

address: Moorenstr. 5

institute: Universitätsklinikum Düsseldorf

summary: Bilirubin-induced neurological damage (BIND), which might progress to kernicterus, occurs as a consequence of defects in the bilirubin conjugation machinery, thus enabling albumin-unbound free bilirubin (BF) to cross the blood–brain barrier and accumulate within. A defect in the UGT1A1 enzyme-encoding gene, which is directly responsible for bilirubin conjugation, can cause Crigler–Najjar syndrome (CNS) and Gilbert’s syndrome. We used human-induced plu-ripotent stem cell (hiPSC)-derived 3D brain organoids to model BIND in vitro and unveil the molecular basis of the detrimental effects of BF in the developing human brain. Healthy and pa-tient-derived iPSCs were differentiated into day-20 brain organoids, and then stimulated with 200 nM BF. Analyses at 24 and 72 h post-treatment point to BF-induced neuro-inflammation in both cell lines. Transcriptome, associated KEGG, and Gene Ontology analyses unveiled the acti-vation of distinct inflammatory pathways, such as cytokine–cytokine receptor interaction, MAPK signaling, and NFκB activation. Furthermore, the mRNA expression and secretome anal-ysis confirmed an upregulation of pro-inflammatory cytokines such as IL-6 and IL-8 upon BF stimulation. This novel study has provided insights into how a human iPSC-derived 3D brain organoid model can serve as a prospective platform for studying the etiology of BIND kernic-terus.

overall_design: The transcriptomes of brain organoids  with and without bilirubin were compared by microarray analysis (Clariom-S Human Gene Expression Array, Affymetrix, Thermo Fisher Scientific).

first: Abida

middle: I

last: Pranty

first: James

last: Adjaye


title: Joint sequence and chromatin neural networks characterize the differential abilities of Forkhead transcription factors to engage inaccessible chromatin

summary: This SuperSeries is composed of the SubSeries listed below.

overall_design: Refer to individual Series


title: The role of NLRP3 in regulation of antimicrobial peptides and estrogen signaling in UPEC-infected bladder epithelial cells

city: örebro

first: isak

last: demirel

address: campus usö

institute: örebro University

summary: The NLRP3 inflammasome, estrogen and antimicrobial peptides have all been emphasised to have a vital role in the protection of the bladder urothelium. However, the interdependence between these protective factors during a bladder infection is currently unknown. Our aim was to investigate the role of NLRP3 in regulation of antimicrobial peptides and estrogen signaling in bladder epithelial cells during a UPEC infection. Human bladder epithelial cells and CRISPR/Cas9 generated NLRP3-deficient cells were stimulated with the UPEC strain CFT073 and estradiol. The gene and protein expression were evaluated with microarray, qRT-PCR, western blot and ELISA. Microarray results showed that the expression of most antimicrobial peptides was reduced in CFT073-infected NLRP3-deficient cells compared to Cas9 control cells. Conditioned medium from NLRP3-deficient cells also lost the ability to suppress CFT073 growth. Moreover, NLRP3-deficient cells had lower basal release of Beta-defensin-1, Beta-defensin-2 and RNase7. The ability of estradiol to induce an increased expression of antimicrobial peptides was also abrogated in NLRP3-deficient cells. The decreased antimicrobial peptide expression might be linked to the observed reduced expression and activity of estradiol receptor beta in NLRP3-deficient cells. This study suggests that NLRP3 may regulate the release and expression of antimicrobial peptides and affect estrogen signaling in bladder epithelial cells.

overall_design: 5637 cells (Cas9 control and NLRP3-deficient) were stimulated with CFT073 MOI 10 for 6 h at 37 °C in 5% CO2 and the gene expression was evaluated.

first: Anna

last: Lindblad

first: Rongrong

last: Wu

first: Katarina

last: Persson

first: Isak

last: Demirel


title: Integrated characterization of cell types, states and molecular programs in disseinated appendiceal neoplasms

city: Phoenix

first: Nicholas

last: Banovich

state: AZ

address: 445 North Fifth Street

department: Integrated Cancer Genomics

institute: TGen - Translational Genomics Research Institute

summary: Appendiceal neoplasms include a heterogeneous group of epithelial and non-epithelial tumors with varying malignant potential. Despite the rise in incidence of appendiceal neoplasms in recent years, limited progress has been made in the understanding, management and therapeutic treatment. To comprehensively characterize the cell types and molecular mechanisms driving cellular remodeling in epithelial appendiceal neoplasms, we performed an integrated scRNA-seq study. We analyzed 126,998 cells from 16 appendix samples (11 peritoneal metastases samples, 5 healthy controls) and identified 33 distinct cell types/cell states with seven being cancer-specific. Highlights of our study include the characterization of tumor cells across the histologic spectrum, the identification of a novel cancer-associated-fibroblast (CAF) subtypes (fiCAFs) and the identification of pathologic-specific cellular crosstalks between tumor cells and the tumor microenvironment (TME). Together, our study provides a high-resolution insight into the complexity and heterogeneity of epithelial appendiceal neoplasms and a valuable resource for therapeutic strategies.

first: Linh

middle: T

last: Bui

first: Xu

last: Cao

first: Jinhui

last: Wang

first: Fan

last: Meng

first: Mingye

last: Feng

first: Leonidas

last: Arvanitis

first: Rifat

last: Mannan

first: Yanghee

last: Woo

first: Kamran

last: Idrees

first: Mustafa

last: Raoof


title: Pro-tumor Tfh2 cells induce detrimental IgG4 production and PGE2-dependent IgE inhibition in pancreatic cancer (tfh)

city: Milan,

first: Raffaella

last: Pini

address: Via Olgettina 58

department: Center for Omics Sciences

country: Italy

institute: IRCCS San Raffaele Scientific Institute

summary: Background: Pancreatic ductal adenocarcinoma (PDAC) has a dismal prognosis and it is characterized by predominant pro-tumor Th2-type inflammation. T follicular helper (Tfh) cells are relevant immunoregulators in cancer, and often correlate with better survival. How the Th2-skewed microenvironment in PDAC modulates the differentiation of Tfh cells and their immunoregulatory function is unknown. Methods: We carried out high-dimensional flow cytometry and T-cell receptor- and RNA-sequencing, as well as bioinformatics, immunohistochemistry and in vitro mechanistic studies. Findings: We identified Tfh1-, Tfh2-, and Tfh17-like cell clusters in the blood, tumors and tumor draining lymph-nodes (TDLNs) of chemo-naïve PDAC patients and showed that high percentages of Tfh2 cells within the tumor tissue and TDLNs correlated with reduced patient survival. Moreover, only Tfh2 cells were highly activated and were reduced in frequency in patients who responded to neoadjuvant chemotherapy. RNA-sequencing analysis of immunoglobulin expression showed that tumor and TDLN samples expressed all immunoglobulin (IGH) isotypes apart from IGHE. Consistent with these findings, Tfh2 cells differentiated in vitro by tumor microenvironment-conditioned dendritic cells promoted the production of anti-inflammatory IgG4 antibodies by co-cultured B cells, dependent on IL-13. Moreover, unexpectedly, Tfh2 cells inhibited the secretion of pro-inflammatory IgE, dependent on prostaglandin E2.  Interpretation: Our results indicate that in PDAC, highly activated pro-tumor Tfh2 favor anti-inflammatory IgG4 production, while inhibit pro-inflammatory IgE. Thus, targeting the circuits that drive Tfh2 cells, in combination with chemotherapy, may re-establish beneficial anti-tumor Tfh–B cell interactions and facilitate more effective treatment.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for Tfh cell subsets (Tfh1, Tfh2, Tfh17) isolated by flow cytometry cell sorting from peripheral blood mononuclear cells of healthy donors and pancreatic cancer patients with primary tumor at surgery or after neoadjuvant chemotherapy

first: Lucia

last: De Monte

first: Francesca

last: Clemente

first: Maria

last: Protti


title: Pro-tumor Tfh2 cells induce detrimental IgG4 production and PGE2-dependent IgE inhibition in pancreatic cancer


title: Pro-tumor Tfh2 cells induce detrimental IgG4 production and PGE2-dependent IgE inhibition in pancreatic cancer (tumor)

overall_design: Comparative gene expression profiling analysis of RNA-seq data for pancreatic cancer tissues from patiennts with primary tumors or treated with neoadjuvant chemotherapy, and gene expression profiling analysis of RNA-seq data of tumor draining lymphnpde tissue from chemonaive patients


title: miR-29a is downregulated in progenies derived from chronically stressed males

city: Barcelona

first: Marc

last: Dabad

address: Baldiri i Reixac, 4-8

country: Spain

institute: CNAG

summary: To investigate the potential vertical transmission of chronic stress to the unexposed larvae, to report novel consequences of paternally inherited chronic stress at molecular level

overall_design: We then performed small RNA seq profiling in the stress-derived group and the control one.

first: Marta

last: Riesco

first: David

middle: G

last: Valcarce

first: Alba

last: Sellés-Egea

first: Anna

last: Esteve-Codina

first: María

last: Paz Herráez

first: Vanesa

last: Robles


title: Response of osteoblasts on amine-based polymer coatings cor-relates with the amino group density

city: Rostock

first: Dirk

last: Koczan

address: Schillingallee 70

department: Institute for Immunology

institute: University of Rostock

summary: The integration of implants can be improved by physical but mainly by chemical modifications of the implant surface. It has already been shown that amine-based coatings improve cell attachment, cell migration, and intracellular signaling. The aim of this study was to determine the role of the amino group density in this positive cell response by developing controlled amino-rich nano-layers. Using Clariom S microarrays to perform genome-wide expression profilng, changes in adhesion related genes after cultivation of osteoblast-like cells on an amino group-rich coating could be seen.

overall_design: Human MG-63 osteoblast-like cells (ATCC® CRL-1427™, United States) were grown for 4 hours, respectively for 24 hours on amine-based polymer coating Ti-TMS-PEI (trimethoxysilylpropyl modified poly(ethyleneimine)) surface dishes in comparison with uncoated titanium surface controls (Ti-Ref). The cell culture samples were processed in quatruplicate. In the 24 hour control group one array was suspended becauese of quality issues.

first: Susanne

last: Seemann

first: Manuela

last: Dubs

first: Hernando

middle: S

last: Salapare

first: Arnaud

last: Ponche

first: Laurent

last: Pieuchot

first: Tatiana

last: Petithory

first: Annika

last: Wartenberg

last: Staehlke

first: Matthias

last: Schnabelrauch

first: Karine

last: Anselme

first: J

last: Nebe


title: A phase I trial of the IL1-receptor antagonist anakinra in previously untreated CLL patients at risk for progression

city: Toronto

first: YU XUAN

last: LUO

state: ON

address: 2075 Bayview Avenue

department: Biological sciences

country: Canada

institute: Sunnybrook research institute

summary: Inflammatory factors that activate NFkB play an important role in the pathogenesis of chronic lymphocytic leukemia (CLL) but are not addressed specifically by current therapies. Interleukin-1 (IL-1) is a master-regulator of inflammation that is inhibited safely in humans by the IL-1 receptor antagonist anakinra. Anakinra was found to inhibit NFkB activity in CLL cells in an IL-1 receptor independent manner and had properties of an intracellular anti-oxidant in vitro. A phase I dose-escalation trial in 11 previously untreated CLL patients (NCT04691765) indicated anakinra was safe at doses up to 400 mg daily and produced transient clinical responses associated with down-regulation of NFkB and oxidative stress in circulating CLL cells in vivo. However, type 1 interferon (IFN)-signaling and c-MYC-regulated genes and proteins were induced at the same time.

overall_design: CLL cells were  purified before starting anakinra (C1D1) and after 2 weeks on treatment with anakinra (C1D14).  Bulk RNA seqeuencing was performed to compare gene expression at the two time-points.

last: Spaner

first: Yonghong

last: Shi

first: YuXuan

last: Luo


title: PI3K-AKT activation resculpts integrin signaling to drive filamentous tau-induced proinflammatory astrogliosis [Tau with inhibitors]

city: Bethesda

first: Yihong

last: Ye

state: MD

address: 5 Center Drive

institute: NIH

summary: Microtubule-binding protein tau is a misfolding-prone protein associated with tauopathies. As tau undergoes cell-to-cell transmission, extracellular tau aggregates convert astrocytes into a pro- inflammatory state via integrin activation, causing them to release unknown neurotoxic factors. Here we combine transcriptomics with isotope labeling-based quantitative mass spectrometry analysis of mouse primary astrocyte secretome to establish PI3K-AKT as a critical differentiator between pathogenic and physiological integrin activation; simultaneous activation of PI3K-AKT and focal adhesion kinase (FAK) in tau fibril-treated astrocytes changes the output of integrin signaling, causing pro-inflammatory gene upregulation, trans-Golgi network restructuring, and altered secretory flow. Furthermore, NCAM1, as a proximal signaling component in tau-stimulated integrin and PI3K-AKT activation, facilitates the secretion of complement C3 as a main neurotoxic factor. Significantly, tau fibrils-associated astrogliosis and C3 secretion can be mitigated by FAK or PI3K inhibitors. These findings reveal an unexpected function for PI3K-AKT in tauopathy-associated astrogliosis and a target for anti-inflammation-based Alzheimer’s therapy.

overall_design: Primary astrocytes isolated from wild type C57BL/6J mice were treated with Tau PFF together with FAK inhibitor PF-562271, AKT inhibitor MK2202, PI3K inhibitor PI103, Nfkb inhibitor PDTC or FAK inhibitor PF271 for 6 hours. Cells were then collected and total RNA was extracted for RNA sequencing.

first: Peng

last: Wang

first: D

last: Anderson


title: Increased pro-inflammatory phenotype of peripheral blood monocytes and monocyte-derived macrophages among patients with excessive ethanol intake

city: Salamanca

first: Juan

middle: Luis

last: Garcia

state: Type Below

address: Campus Miguel de Unamuno Centro de Investigacion del Cancer, IBSAL

institute: CIC/IBSAL

summary:
Excessive alcohol consumption adversely affects the immune system and triggers the activation of peripheral blood (PB) monocytes and tissue macrophages, contributing to alcohol-  related organ damage. This study aimed to analyze the M1/M2 and inflammatory phenotypes of circulating monocytes and macrophage-derived monocytes (MDMs). This single-center cross-  sectional study included 20 excessive alcohol drinkers (EADs) and 22 healthy controls. PB samples were collected under fasting conditions for isolation of CD14+ monocytes and short-term  culture without stimulation, LPS/IFNγ, or IL4/IL13. These conditions were also used to polarize monocyte-derived macrophages (MDMs) into M0, M1, or M2 phenotypes. Cytokine production was  assessed in the blood samples and supernatants.
M1/M2 related markers in PB monocytes and MDMs were analyzed using mRNA expression and surface marker analyses. In addition, the miRNA profile was analyzed in CD14+ monocytes. PB samples from EADs exhibited increased levels of pro-inflammatory cytokines.

platform_organism:
Homo sapiens
Mus musculus
Rattus norvegicus
Human alphaherpesvirus 1
Human alphaherpesvirus 2
Human betaherpesvirus 5
Murid betaherpesvirus 1
human gammaherpesvirus 4
JC polyomavirus
Human immunodeficiency virus 1
Murid gammaherpesvirus 4
Human gammaherpesvirus 8
Merkel cell polyomavirus
Mus musculus cytomegalovirus 2
Betapolyomavirus hominis
Betapolyomavirus macacae

overall_design: In the present study, 22 samples are included, of which 8 samples are control samples from peripheral blood CD14+ monocytes, healthy controls, and 14 samples from CD14+ monocytes from patients with excessive alcohol intake.

first: María

last: Fernández-Regueras

first: Cristina

last: Carbonell

first: Daniel

last: Salete-Granado

first: Juan-Luis

last: García

first: Marcos

last: Gragera-Cabezudo

first: María-Ángeles

last: Pérez-Nieto

first: Andrea

last: Mayado

first: Jorge-Luis

last: Torres

first: Ricardo

last: Usategui-Martín

first: Maura

last: Rojas-Pirela

first: Guadalupe

last: Sabio

first: Alberto

last: Orfao

first: Rogelio

last: González-Sarmiento

first: Francisco

middle: J

last: Laso

first: Julia

last: Almeida

first: Miguel

last: Marcos


title: Recombinant IL-1 RA in human Chronic lymphocytic leukemia cells in vitro

first: YU XUAN

last: LUO

summary: Inflammatory factors that activate NFkB play an important role in the pathogenesis of chronic lymphocytic leukemia (CLL) but are not addressed specifically by current therapies. Interleukin-1 (IL-1) is a master-regulator of inflammation that is inhibited safely in humans by the IL-1 receptor antagonist anakinra. Anakinra (K) was found to inhibit NFkB activity in CLL cells in an IL-1 receptor independent manner and had properties of an intracellular anti-oxidant in vitro.

overall_design: Purified human CLL B cells were cultured with or without 300 microg/ml of anakinra for 48h before RNA was extracted and total RNA sequencing performed.

first: David

last: Spaner

first: YuXuan

last: Luo


title: PI3K-AKT activation resculpts integrin signaling to drive filamentous tau-induced proinflammatory astrogliosis

first: Yihong

last: Ye


title: Effect of small molecule inhibitors on transcriptome of B6.Sst1S bone marrow derived macrophages stimulated with TNF and infected with virulent Mycobacterium tuberculosis

city: Boston

first: Alexander

last: Gimelbrant

address: 31A Iroquois St

institute: Altius Institute

summary: We investigated  candidate host-directed therapies for tuberculosis in vitro. BMDMs from tuberculosis  susceptible mice B6.Sst1S were stimulated with TNF and infected with Mtb.  The infected macrophage were treated with Rocaglamide A, ISRIB and JNK inhibitor SP600125 alone or in combinations to asses the inhibitors' effectas on macrophage transcriptome.

overall_design: B6.Ssts1S BMDMs were stimulated with 10 ng/ml of TNF for 16h and infected with Mtb H37Rv at MOI=1. At 72h post infection total RNA was isolated and processed for RNA-seq

first: Shivraj

middle: M

last: Yabaji

first: Oleksii

last: Rukhlenko

first: Igor

last: Kramnik


title: Effects of vortioxetine on cognitive impairment induced in rats by androgen deprivation as a model of prostate cancer treatment

city: San Antonio

first: Yidong

last: Chen

state: Texas

address: 8403 Floyd Curl Drive, MSC 7784

department: Population Health Sciences

institute: UT Health Science Center at San Antonio

summary: Androgen deprivation therapy (ADT) is a foundational treatment for advanced prostate cancer, but more than half of patients treated with ADT experience debilitating cognitive impairments in domains known to be mediated by the hippocampus and prefrontal cortex. Unfortunately, there are few treatments to prevent or reverse these changes from occuring, thus severely decreasing quality of life in patients. To begin studying these deficits, surgically castrated rats were used to model cognitive impairments associated with the spatial learning and executive function, then chronically treated with the multimodal antidepressant, vortioxetine, as in intervention to reverse these impairments. Vortioxetine effectively rescued cognitive deficits in after surgical castration, and increased resposivity in in vivo evoked local field potentials within the Schaeffer Collateral-CA1 pathway and the ventral hippocampus-mPFC pathway. Surgical castration also induced significant changes in gene expression within the mPFC and the dorsal hippcampus, whereas vortioxetine had little effect. Pathway analysis revealed that androgen depletion altered pathways related to synaptic plasticity. These results suggest that these two regions may be vulnerable to ADT, contributing to cognitive impairment in prostate cancer patients. Further, vortioxetine may be a candidate to improve cognition in patients that experience cognitive decline after androgen deprivation therapy for prostate cancer and may do so by restoring molecular and circuit level plasticity-related mechanisms compromised by ADT.

overall_design: Whole genome microarray in tissue collected from the dorsal hippocampus (dHipp) or medial prefrontal cortex (mPFC) of surgically castrated rats after chronic dietary drug treatment with the antidepressant vortioxetine (40 mg/kg/day at free-feeding or 28 mg/kg/day at food restriction for 17 days), compared to sham controls and animals receiving control diet (n=2-6/group, 4 groups total x two brain regions)

first: Alexandra

last: Vaiana

middle: A

last: Morilak

first: Jonathan

last: Gelfond

first: Teresa

middle: L

last: Johnson-Pais

first: Robin

last: Leach

first: Chethan

last: Ramamurthy

first: Ian

last: Thompson

first: Suphada

last: Lertphinyowong

first: Samantha

last: Yee

first: Denisse

last: Paredes

first: Michael

last: Liss

first: April

last: Risinger

first: Anna

middle: C

last: Sullivan


title: PI3K-AKT activation resculpts integrin signaling to drive filamentous tau-induced proinflammatory astrogliosis [Tau vs OPN]

first: Yihong

last: Ye

first: Peng

last: Wang

first: D

middle: E

last: Anderson


title: Meta-analysis of Single-cell RNA-seq Data Reveals the Formation of Tertiary Lymphoid Organ and Mechanism Heterogeneity in Vascular Disease

city: Changsha

first: Xuejing

last: Sun

state: Hunan

address: Ton-zi po road

department: Department of Cardiology

institute: Third Xinagya Hospital

summary: The role of different cells in intimal hyperplasia remains unintelligible. To characterize the cells in intimal hyperplasia, we performed single-cell RNA sequencing of whole remodeled vessel cells from C57BL/6J mice with a murine model of intimal hyperplasia at an early (IH 2w) or late stage (IH 4w). The single-cell RNA-seq analyses revealed the heterogeneity of cells in vascular remodeling.

overall_design:
Single-cell RNA sequencing of whole vessel cells from the remodeled carotid artery of a murine model of intimal hyperplasia at 2-week time point (n=18, eight weeks-age).
Single-cell RNA sequencing of whole vessel cells from the remodeled carotid artery of a murine model of intimal hyperplasia at 4-week time point (n=18, eight weeks-age).

first: Yao

last: Lu

first: Junru

last: Wu

first: Qing

last: Wen

first: Zhengxin

last: Li

first: Yan

last: Tang

first: Yunmin

last: Shi

first: Tian

last: He

first: Lun

last: Liu

first: Wei

last: Huang

first: Chunyan

last: Weng

first: Qingzhong

last: Xiao

first: Hong

last: Yuan

first: Qingbo

last: Xu

first: Jingjing

last: Cai


title: Gene expression data from 1 year and 16 weeks old SAMP8 and SAMR1 mice brain cortex.

city: つくば市

first: ミチタカ

last: フジワラ

state: 茨城県

institute: University of Tsukuba

summary:
Gene expression profiling reveals age dependent functional alternation in SAMP8 mice brain.
We evaluated the effects of aging on SAMP8 mice brain. We performed an untargeted whole-genome transcriptome analysis to explore functionality age dependent changes of brain in SAMP8 mice.

overall_design: According to the manufacturer's guide, the RNA was extracted using Isogen kit (Nip-pon Gene Co. Ltd., Japan). Then, RNA quantity and quality were determined using the NanoDrop 2000 spectrophotometer (ThermoScientific, USA). RNA samples from cortices were amplified and labeled with the Affymetrix 3' IVT PLUS Reagent Kit, following the manufacturer's instructions. The labeled RNA was then hybridized onto Affymetrix Mouse Genome 430 PM array strips for 16 hours at 45°C using a hybridization station. After hybridization, the arrays were washed, stained, and scanned using the GeneAtlas Fluidics and Imaging Station. The probe intensity files (CEL files) were then processed using the robust multichip analysis (RMA) summarization algorithm in the Expression Console software (Affymetrix) to obtain gene-level information (CHP files). Further analysis of the data was conducted using Transcriptome Analysis Console (TAC) ver.4 software (Thermo Fisher Scientific). Finally, genes that passed the filter criteria of p value < 0.05 (one-way between-subjects ANOVA) and fold change > 1.1 (in linear space) were considered as differentially expressed genes (DEGs).

first: Michitaka

last: Fujiwara


title: A laboratory-based model ecosystem reveals genetic determinants of methanotroph phenotypic heterogeneity in a methane-oxygen counter gradient

city: Salt Lake City

first: Aaron

last: Puri

state: UT

address: 1390 Presidents Circle

institute: University of Utah

summary: Connecting genes to phenotypic traits in bacteria is often challenging because of a lack of environmental cues in laboratory settings. However, laboratory-based model ecosystems offer a means to better account for natural conditions compared to standard planktonic cultures, aiding in the linking of genotypes and phenotypes. Here, we present a simple, cost-effective, laboratory-based model ecosystem to study aerobic methane-oxidizing bacteria (methanotrophs). This system, referred to as the gradient syringe, is made by inoculating bacteria into semi-solid agarose held within a disposable syringe. Empty space at one end of the syringe is flushed with methane gas, while the other end is open to the atmosphere through a sterile filter. We show this system replicates the methane-oxygen counter gradient typically found in the natural soil environment of methanotrophs. Culturing the methanotroph Methylomonas sp. strain LW13 in this system produced a distinct horizontal band at the intersection of the counter gradient, which we discovered was due not to increased cell growth at this location but instead to an increased amount of extracellular polymeric substances (EPS). We also discovered that different methanotrophic taxa formed EPS bands with distinct locations and morphologies when grown in the methane-oxygen counter gradient. By comparing transcriptomic data from LW13 growing within and surrounding this EPS band, we identified genes implicated in cell growth and EPS formation within the gradient syringe, and validated the involvement of these genes with knockout strains. This work highlights the use of a laboratory-based model ecosystem that more closely mimics the natural environment to uncover methanotroph phenotypes missing from standard planktonic cultures, and link these phenotypes their genetic determinants.

overall_design: To investigate the cellular functions underlying the extracellular polymeric substance (EPS) phenotype observed at the midpoint of the methane-oxygen counter gradient within a semi-solid agarose matrix, we compared transcriptomes of the aerobic methanotroph Methylomonas sp. LW13 isolated from increasing depths. Late exponential/early stationary phase gradient syringes inoculated with LW13 were divided into three 2 mL segments, with the middle segment centered around the EPS band. These segments were designated “above”, “band”,  and “below”, representing oxygen-exposed, band-centered, and methane-flushed regions. For each of three independent replicates, RNA from eight LW13-inoculated syringes were pooled.

first: Delaney

last: Beals


title: Targeting RBPMS selectively eliminates leukemia initiating cells via the USP1/m6A/FOXO1 axis

city: Shanghai

first: Jiaying

last: Zhang

state: Shanghai

address: 320 Yue Yang Road

department: CAS Key Laboratory of Tissue Microenvironment and Tumor, Shanghai Institute of Nutrition and Health

institute: Shanghai Institutes for Biological Sciences, University of Chinese Academy of Sciences, Chinese Academy of Sciences

summary: Acute myeloid leukemia (AML) is a malignant tumor with high recurrence rate and poor prognosis. RNA-binding proteins (RBPs) are essential modulators of transcription and translation played critical roles and frequently dysregulated in AML. Here we show that RBPMS (RNA binding protein with multiple splicing) which is highly expressed in AML and associated with poor prognosis of AML, plays critical roles in leukemogenesis. Our study shows that inhibition of RBPMS abrogates self-renewal of leukemia initiating cells (LICs) and AML development but has little effect on normal hematopoiesis. Mechanistically, RBPMS maintains the stability of the m6A reader IGF2BP3 by USP1-mediated deubiquitination, which promotes the translation of the FOXO1 mRNA in an m6A-dependent manner. Moreover, RBPMS contributes to the progression of leukemia by promoting FOXO1/ENO2/ALDOC regulated glycolysis. Overexpression of FOXO1 has been shown to rescue RBPMS inhibition-induced phenotypes in both leukemia cells and mouse models. We have also designed a specific inhibitor of RBPMS that has therapeutic effects in the AML patient derived xenograft model (PDX) model. We, therefore, we highlight RBPMS as a promising drug target for AML therapy.

overall_design: Suppression of RBPMS by shRNA in Kasumi-1 cells, as well as the control cells were subjected  to RNA-seq.Treatment with RB98# in Kasumi-1 cells, as well as the control cells were subjected  to RNA-seq. RIP-seq of HA RBPMS was performed with HA antibody in Kasumi-1 cells , and rabbit IgG as the control. m6A-seq of Kasumi-1 cells was performed with m6A antibody.

first: Ping

first: Bing

middle: Y

last: Chen

last: Jiang

first: Xi

first: Lan

last: Wang


title: Class I HDAC inhibition reduces DNA damage repair capacity of MYC-amplified medulloblastoma cells

city: Heidelberg

first: Jonas

last: Ecker

address: Im Neuenheimer Feld 430

institute: Hopp Children's Cancer Center

summary: MYC-driven Group 3 medulloblastoma (MB) (subtype II) is a highly aggressive childhood brain tumor. Sensitivity of MYC-driven MBs to class I histone deacetylase inhibitors (HDACi) has been previously demonstrated in vitro and in vivo. We here characterize the transcriptional effects of class I HDAC inhibition in MYC-driven MB and explore beneficial drug combinations. MYC-amplified Group 3 MB cells (HD-MB03) were treated with class I HDACi entinostat. Changes in the gene expression profile compared to untreated control were quantified on a microarray. Gene set enrichment analysis, cytoscape enrichment mapping and ingenuity pathway analysis led to the identification of pathways affected by entinostat treatment. Five drugs interfering with these pathways (olaparib, idasanutlin, ribociclib, selinexor, vinblastine) were tested as single agents in metabolic activity assays in three MYC-amplified and two non-MYC-amplified MB cell lines. Synergy with entinostat was evaluated by dose response curve shift, combination index and zero interaction potency synergy model and validated in cell count and flow cytometry experiments in two MYC-amplified and one non-MYC-amplified MB cell line. The effect of the most promising drug combination (entinostat and olaparib) on DNA damage was evaluated by γH2A.X quantification in immunoblotting, fluorescence microscopy and flow cytometry. Entinostat treatment changed the expression of genes involved in 22 pathways, including downregulation of DNA damage response. The PARP1 inhibitors olaparib and pamiparib showed synergy with entinostat. The combination of entinostat and olaparib led to increased cell death, decreased viability and increased formation of double strand breaks selectively in MYC-amplified MB cells. MYC-amplified MB cells treated with entinostat and olaparib were particularly vulnerable to additional induction of DNA damage by doxorubicin. Non-MYC-amplified MB cells and normal human fibroblasts were not susceptible to this triple treatment. Our study identifies the combination of entinostat with olaparib and doxorubicin as a new potential therapeutic approach for MYC-driven Group 3 MB.

overall_design: MYC amplified MB cells (HD-MB03) were treated with 1µM entinostat for 24h and 48h with respective DMSO treated samples, experiments were performed in triplicates, RNA was extracted and hybridized on the Human Genome U133 Plus 2.0 Affymetrix microarray


title: A novel irreversible TEAD inhibitor, SWTX-143, blocks the Hippo pathway and causes tumor regression in preclinical mesothelioma models [Invitro]

city: Leuven

first: Georg

last: Halder

address: Herestraat 49

department: VIB-KU Leuven Center for Cancer Biology

country: Belgium

institute: VIB-KU Leuven

summary: The Hippo pathway and its downstream effectors, the YAP and TAZ transcriptional coactivators, are deregulated in multiple different types of human cancer and are required for cancer cell phenotypes in vitro and in vivo, while largely dispensable for tissue homeostasis in adult mice. YAP/TAZ and their partner transcription factors, the TEAD1-4 factors, are therefore promising anti-cancer targets. Due to frequent YAP/TAZ hyperactivation caused by mutations in the Hippo pathway components NF2 and Lats2, mesothelioma is one of the prime cancer types predicted to be responsive to YAP/TAZ-TEAD inhibitor treatment. Mesothelioma is a devastating disease for which currently no effective treatment options exist. Here, we describe a novel covalent YAP/TAZ-TEAD inhibitor, SWTX-143, that binds to the palmitoylation pocket of all TEAD isoforms. SWTX-143 caused irreversible and specific inhibition of the transcriptional activity of YAP/TAZ-TEAD in Hippo-mutant tumor cell lines. More importantly, YAP/TAZ-TEAD inhibitor treatment caused strong mesothelioma regression in human subcutaneous xenograft models and in an orthotopic mesothelioma mouse model. Finally, SWTX-143 also selectively impaired the growth of NF2-mutant kidney cancer cell lines, suggesting that the exquisite sensitivity of mesothelioma to these YAP/TAZ-TEAD inhibitors can be extended to other tumor  types with aberrations in Hippo signaling. In brief, we describe a novel and specific YAP/TAZ-TEAD inhibitor that has great potential to treat multiple Hippo-mutant solid  tumor types.

overall_design: We measured the impact of 100nM SWTX-143 on the transcriptome of the Hippo pathway inactivated (NF2-deficient) mesothelioma cell line NCI-H226 and NF2-deficient kidney cancer cell line ACHN. In control conditions cells were treated with DMSO.

first: Weronika

last: Kowalczyk

first: Hanne

last: Hillen

first: Aurelie

last: Candi


title: A novel irreversible TEAD inhibitor, SWTX-143, blocks the Hippo pathway and causes tumor regression in preclinical mesothelioma models

summary: This SuperSeries is composed of the SubSeries listed below.

overall_design: Refer to individual Series


title: A novel irreversible TEAD inhibitor, SWTX-143, blocks the Hippo pathway and causes tumor regression in preclinical mesothelioma models [SubQ]

overall_design: NCI-H226 cells were injected subcutaneously into BALB/c nude mice. When tumors reached about 170mm3, mice were randomized into groups and treated once daily with SWTX-143 (10, 25 and 50mg/kg) or vehicle for control group. Samples were extracted either 4h or 24h after the last dose of treatment.


title: An Anterior Second Heart Field Enhancer Regulates the Gene Regulatory Network of the Cardiac Outflow Tract

city: New York City

first: Alireza

last: Khodadadi-Jamayran

address: 550 1st Ave, MSB 304

department: Division of Advanced Research Technologies (DART)

institute: New York University, NYU Langone Medical Center

summary:
To identify a functional gene regulatory network that orchestrate transcriptional programs to direct proper outflow tract development, we generated transgenic mice harboring a 226bp-deletion within a GATA-dependent, highly conserved cardiac enhancer region.
We then performed gene expression profiling analysis using data obtained from RNA-seq of outflow tract in wildtype and homozygous mutant littermates at embryonic day 12.5.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for Nkx2-5 anterior second heart field enhancer mutants and wildtype littermates.

first: Naoko

last: Yamaguchi

first: Ernest

last: Chang

first: Akshay

last: Shekhar

first: Lei

last: Bu

first: Ziyan

last: Lin

first: David

last: Park


title: The role of ABL kinases in medulloblastoma

city: 5841 S Maryland Ave. MC3026

first: Eric

last: Thompson

state: IL

institute: The University of Chicago

summary: Medulloblastoma is the most common malignant pediatric brain tumor, and leptomeningeal dissemination (LMD) of medulloblastoma portends a poorer prognosis at diagnosis and is incurable at recurrence. The biological mechanisms underlying LMD in medulloblastoma are largely unclear. The Abelson (ABL) family of non-receptor tyrosine kinases has been implicated in cancer cell migration, invasion, adhesion, and chemotherapy resistance, and these kinases are upstream mediators of the oncogene c-MYC in fibroblasts. However, their role in medulloblastoma has not yet been explored. Therefore, the purpose of this work is to elucidate the role of the ABL kinases, ABL1 and ABL2, in medulloblastoma LMD. We show here that ABL1/2 mRNA is highly expressed in human medulloblastoma tumor samples and cell lines and that pharmacologic inhibition of ABL kinases results in medulloblastoma cell death. Knockdown of the ABL kinase genes ABL1 and ABL2 results in decreased adhesion to the extracellular matrix protein, vitronectin, and decreased medulloblastoma proliferation in a mouse model of medulloblastoma LMD (resulting in decreased tumor burden with subsequent increased overall survival. Further, both pharmacologic inhibition of ABL1/2 and ABL1/2 knockdown resulted in decreased c-myc expression, revealing a putative signaling pathway. In summary, this work highlights the potential role of ABL kinases in medulloblastoma LMD via c-myc expression.

overall_design: Genetic inactivation of ABL1 and ABL2 vs. scrambled controls in D283 medulloblastoma cells.

first: Jill

last: Jones

first: Kevin

last: Stevenson


title: SMARCA5 deficiency reprograms AKR1B1-mediated endogenous fructose metabolism to eradicate leukemia stem cells in acute myeloid leukemia

first: Jiaying

last: Zhang

summary: A significant variation in chromatin accessibility is an epigenetic feature in leukemia cells. However, the regulators and consequences of the chromatin accessibility variations in leukemia remain elusive. Here we identified SMARCA5, a core ATPase of the ISWI chromatin remodeling complex, as the primary regulator of chromatin accessibility in acute myeloid leukemia (AML) by CRISPR-Cas9 library screening. We found that SMARCA5 is required for self-renewal of leukemia stem cells and myeloid leukemogenesis. Mechanistically, SMARCA5 promotes the transcriptional activation of AKR1B1, an aldo/keto reductase, by recruiting transcription co-activator DDX5 and transcription factor SP1 to its promoter. Clinical sample analysis has shown that high expression of AKR1B1 predicts a poor prognosis in AML patients. Interestingly, AKR1B1-mediated endogenous fructose metabolism is reprogrammed by Smarca5 in AML. Overexpression of AKR1B1 rescued the leukemogenesis impaired by Smarca5 deficiency. Moreover, pharmacological inhibition of AKR1B1 displayed significant therapeutic effects in the AML patient-derived xenograft (PDX) mouse model. Thus, our findings link chromatin state dynamics regulated by SMARCA5 to AKR1B1-mediated endogenous fructose metabolism reprogramming, and uncover an essential role of AKR1B1 in AML, which may provide a therapeutic target for AML patients.

overall_design: Suppression of SMARCA5 by shRNA in Kasumi-1 cells, as well as the control cells were subjected  to RNA-seq, ATAC-seq. Cut & Tag of SMARCA5 was performed with SMARCA5 antibody in Kasumi-1 cells and THP-1 cells, and rabbit IgG as the control.

first: Peng-cheng

last: Yu

first: Dan

last: Hou

first: Binhe

first: Chun-Hui

last: Xu


title: Differential gene expression in activated microglia treated with adenosine A2A antagonists and A3 receptor agonists. A transcriptomics study.

first: Rafael

last: Franco

address: Avinguda Diagonal, 643

institute: Universitat de Barcelona

summary: Microglial activation often accompanies the plastic changes occurring in the brain of patients with neurodegenerative diseases. A2A and A3 adenosine receptors have been proposed as therapeutic targets to combat neurodegeneration. RNAseq was performed using samples isolated from lipopolysaccharide/interferon-γ activated microglia treated with SCH 58261, a selective A2A receptor antagonist and 2-Cl-IB-MECA, a selective A3 receptor agonist.

overall_design: Cells were maintained in a humid atmosphere of 5% CO2 at 37ºC and were used for RNA extraction after 15 days of culture. Cells were activated for 48 h with 0.01% (v/v) LPS and 0.002% (v/v) IFN-γ in Dulbecco's modified Eagle medium and, at 24, 32 and 40 h, vehicle or 200 nM 2-Cl-IB-MECA was added.

first: Alejandro

last: Lillo

first: Joan

last: Serrano-Marín

first: Jaume

first: Lu

last: Raïch

first: Gemma

last: Navarro


title: A retrospective clinical study to explore diagnostically significant markers in circulating exosomes of patients with cerebral small vessels disease (CSVD)

city: QingDao

first: Kejin

last: Gao

state: Shan Dong

address: NO.59 hai er Rd, Qingdao, China

institute: The Affiliated Hospital of Qingdao University

summary: Often characterized by insidious onset, CSVD is the leading cause of vascular dementia.Nonetheless, early screening and diagnosis of CSVD remain challenging. Exosomal miRNAs in circulation have been found to be diagnostic markers for many diseases and to play an essential role in neurological disorders. The research will use peripheral blood samples from CSVD patients hospitalized and relatively healthy outpatients in our neurology department from 2018 to 2020. Specifically, microarray results from patients with CSVD will be obtained and then validated in peripheral blood samples, aiming to investigate abnormal expression indicators in circulating exosomes of patients with CSVD, for further mechanism exploration and diagnosis of CSVD.

overall_design: To obtain a general profile of differential miRNAs from the plasm exosomes of CSVD patients, 16 CSVD patients and 16 controls were chosen randomly to create 4 CSVD pools and 4 control pools (each pool contained 4 serum samples). Differential expression of miRNAs between CSVD and control cohorts was examined by using miRNA microarray: Affymetrix GeneChip miRNA 4.0 Array. Raw data was normalized using RMA algorithm (affy package). Differential expression analysis of microarray data was performed with the limma package. The Shanghai GeneChem company (GeneChem, China) performed hybridization, scanning, and data analysis of the microarrays.

first: Aijun

last: Ma

first: Xudong

last: Pan