title: The efficacy of LCMV-based cancer vaccines is unleashed by intratumoral injections of polyI:C (II)

city: Pamplona

first: Jose

last: Gonzalez

state: Navarra

address: C/PIO XII s/n

institute: FIMA

summary: Background Lymphocytic choriomeningitis virus (LCMV) belongs to the Arenavirus family known for inducing strong cytotoxic T-cell responses in both mice and humans. LCMV has been engineered for the development of anti-tumor vaccines, currently undergoing evaluation in phase I/II clinical trials. Initial findings have demonstrated safety and an exceptional ability to induce and expand tumor-specific T lymphocytes. Combination strategies to maximize the anti-tumor effectiveness of LCMV-based vaccines are required. Methods We assessed the anti-tumor therapeutic effects of intratumoral administration of polyinosinic:polycytidylic acid (poly(I:C)) and systemic vaccination using an LCMV-vector expressing non-oncogenic versions of the E6 and E7 antigens of human papillomavirus 16 (artLCMV-E7E6) in a bilateral model engrafting TC-1/A9 cells. This cell line, derived from the parental TC-1, exhibits low MHC class I expression and is highly immune-resistant. The mechanisms underlying the combination's efficacy were investigated through bulk RNAseq, flow cytometry analyses of the tumor microenvironment, selective depletions using antibodies and clodronate liposomes, Batf3 deficient mice, and in vivo bioluminescence experiments. Finally, we assessed the anti-tumor effectiveness of the combining of LCMV-E6E7 with BO-112, a GMP-grade poly(I:C) formulated in polyethyleneimine, currently under evaluation in clinical trials. Results Intratumoral injection of poly(I:C) enhanced the anti-tumor efficacy of artLCMV-E7E6 in both injected and non-injected tumor lesions. The combined treatment resulted in a significant delay in tumor growth and often complete eradication of several tumor lesions, leading to significantly improved survival compared to monotherapies. While intratumoral administration of poly(I:C) did not impact LCMV vector biodistribution or transgene expression, it significantly modified leukocyte infiltrates within the tumor microenvironment and amplified systemic efficacy through proinflammatory cytokines/chemokines such as  CCL3, CCL5, CXCL10, TNF, IFNα, and IL12p70. Upregulation of MHC on tumor cells and a reconfiguration of the gene expression programs related to tumor vasculature, leukocyte migration, and the activation profile of tumor-infiltrating CD8+ T lymphocytes were observed. Indeed, the anti-tumor effect relied on the functions of CD8+ T lymphocytes and macrophages. The synergistic efficacy of the combination was further confirmed when BO-112 was included. Conclusion Intratumoral injection of poly(I:C) sensitizes MHClow tumors to the anti-tumor effects of artLCMV-E7E6, resulting in a potent therapeutic synergy

overall_design: TC1/A9 tumor-bearing mice received intravenous treatment with 1×105 RCV FFU artLCMV-E7E6 on day 7 and intratumoral injections of 50 μg of poly(I:C) or BO-112

first: Celia

last: Gomar

first: José

last: González-Gomariz

first: Pedro

last: Berraondo


title: Potential utility of L-carnitine for preventing liver tumors derived from metabolic dysfunction-associated steatohepatitis

status: Public on Apr 24 2024

city: Kanazawa

first: Masao

last: Honda

address: Takara-Machi 13-1

department: Gastroenterology

country: Japan

institute: Kanazawa University

summary:
We examined the potential utility of L-carnitine for alleviating metabolic dysfunction-associated steatohepatitis (MASH) and preventing the development of hepatocellular carcinoma.
Short-term L-carnitine administration ameliorated MASH through its anti-inflammatory effects.

overall_design:
L-carnitine (2 g/day) was administered to 11 MASH patients for 10 weeks, and blood liver function tests were performed. Five patients received a serial liver biopsy, and liver histology and hepatic gene expression were evaluated using this tissue. 10-weeks L-carnitine administration significantly improved serum alanine transaminase and aspartate transaminase levels along with a histological improvement of the nonalcoholic fatty liver disease activity score, while steatosis and fibrosis were not improved. Gene expression profiling revealed a significant improvement of the inflammation and pro-fibrotic gene signature as well as the recovery of lipid metabolism.
*** According to the submitter raw data are not available for this submission because the HDD was broken and we lost original CEL files. ***

first: Junyan

last: Lyu

first: Hikari

last: Okada

first: Hajime

last: Sunagozaka

first: Kazunori

last: Kawaguchi

first: Tetsuro

last: Shimakami

first: Kouki

last: Nio

first: Kazuhisa

last: Murai

first: Takayoshi

last: Shirasaki

first: Mika

last: Yoshida

first: Kuniaki

last: Arai

first: Tatsuya

last: Yamashita

first: Takuji

last: Tanaka

first: Kenichi

last: Harada

first: Toshinari

last: Takamura

first: Shuichi

last: Kaneko

first: Taro


title: Siglec-F+ neutrophils in the spleen induce immunosuppression following acute infection

city: Zhanjiang

first: Chaoxiong

last: Liao

address: 57 Renmin Avenue South

country: China

institute: Anesthesia

type: Expression profiling by high throughput sequencing

summary: The mechanisms underlying the increased mortality of secondary infections during the immunosuppressive phase of sepsis remain elusive. We established a mouse model of sepsis-induced immunosuppression followed by secondary infection. Compared to other organs, we observed a significant reduction in pro-inflammatory cytokines in the spleen, accompanied by a marked increase in IL-10 production, primarily by infiltrating neutrophils. Furthermore, we confirmed that these infiltrating neutrophils in the spleen during the immunosuppressive phase of sepsis undergo phenotypic change in the local microenvironment, exhibiting high expression of neutrophil biomarkers such as Siglec-F, Ly6G, and Siglec-E. These neutrophils subsequently produced IL-10 to suppress T lymphocytes. Depletion of neutrophils or specifically targeting Siglec-F leads to a notable improvement in the survival of mice with secondary infections. The identification of Siglec-F+ neutrophils as key regulators of immunosuppression following sepsis represents a novel finding with potential therapeutic implications.

overall_design: To investigate the mechanism underlying the increased mortality of secondary infections, we established a mouse model of sepsis-induced immunosuppression followed by secondary infection.

first: Shuhua

last: Luo

first: Xiaolei

last: Liu

first: Lina

last: Zhang


title: ZBTB16 inhibits DNA replication and induces cell cycle arrest by targeting WDHD1 transcription in lung adenocarcinoma [RNA-seq]

city: jinan

first: Deyu

last: Guo

state: Shandong Province

address: Science and Education Park

department: Shandong Provincial Hospital

institute: Shandong University

summary: Lung adenocarcinoma is a malignant tumor with high morbidity and mortality. ZBTB16 plays a double role in various tumors; however, the potential mechanism of ZBTB16 in the pathophysiology of lung adenocarcinoma has yet to be elucidated. We herein observed a decreased expression of ZBTB16 mRNA and protein in lung adenocarcinoma and a significantly increased DNA methylation level of ZBTB16 in patients with lung adenocarcinoma. Analysis of public databases and patients’ clinical data indicated a close association between ZBTB16 and patient survival. Ectopic expression of ZBTB16 in lung adenocarcinoma cells significantly inhibited cell proliferation, invasion, and migration. It also induced cell cycle arrest in the S phase. Meanwhile, mitotic catastrophe was induced, and DNA damage and apoptosis occurred. In line with these findings, the overexpression of ZBTB16 in xenograft mice resulted in the inhibition of tumor growth. Comprehensive analysis showed that WDHD1 was a potential target for ZBTB16. The overexpression of both isoforms of WDHD1 significantly reversed the ZBTB16-mediated inhibition of lung adenocarcinoma proliferation and cell cycle. These studies suggest that ZBTB16 impedes the progression of lung adenocarcinoma by interfering with WDHD1 transcription, making it a potential novel therapeutic target in the management of lung adenocarcinoma.

overall_design: We performed RNA sequencing on A549 cell lines transfected with pcDNA3.1 and ZBTB16 plasmids.

first: Jiajun

last: Du

first: Kai

last: Wang

first: Tao

last: Yan

first: Shijie

last: Sun

first: Yadong

first: Haotian

last: Zheng

first: Guanghui


title: Gene expression in PBMC treated with cilostazol,Ginkgo Biloba Extract and rosuvastatin

city: Taipei

first: Yi-Lin

last: Chiu

address: No.161, Sec. 6, Minquan E. Rd., Neihu Dist., Taipei City 11490, Taiwan

department: Department of Biochemistry, College of Biomedical Sciences

country: Taiwan

institute: National Defense Medical University

summary: The primary objective for collecting RNA-seq data in this study was to uncover the molecular mechanisms through which various drug  impacts cardiovascular health. Specifically, the study aimed to explore how these drugs affects monocyte-to-macrophage differentiation and endothelial cell functions, both of which are crucial in the pathogenesis of cardiovascular diseases.

overall_design: Healthy donors' Peripheral Blood Mononuclear Cells (PBMCs) were isolated and divided into two groups: one treated with drugs and the other with a vehicle control. After the treatment period, total RNA was extracted from these cells.

first: Chia-Ning

last: Fan


title: A Single-atom Manganese Nanozyme Mn-N/C Promotes Anti-tumor Immune Response via Eliciting Type I Interferon Signaling

city: Shanghai

first: Wen

last: Qiao

address: 1630 Dongfang Road, Pudong New Area, Shanghai

institute: 上海交通大学医学院

summary: Tumor microenvironment (TME)-induced nanocatalytic therapy is a promising strategy for cancer treatment, but the low catalytic efficiency limits its therapeutic efficacy. Single-atom catalysts (SACs) are a new type of nanozyme with incredible catalytic efficiency. Here we construct a single-atom manganese (Mn)-N/C nanozyme. Mn-N/C catalyzes the conversion of cellular H2O2 to ∙OH through a Fenton-like reaction and enables the sufficient generation of reactive oxygen species (ROS), which induces immunogenic cell death (ICD) of tumor cells and significantly promotes CD8+T anti-tumor immunity. Moreover, RNA sequencing reveals that Mn-N/C treatment activates type I interferon (IFN) signaling which is critical for Mn-N/C-mediated anti-tumor immune response. Mechanistically, Mn-N/C-triggered releasing of cytosolic DNA from ICD tumor cells activates cGAS-STING pathway, consequently stimulating type I IFN induction. We propose a new promising single-atom nanozyme with extraordinary catalytic activity, which enhances anti-tumor immune response and exhibits synergistic therapeutic effects when combined with anti-PD-L1 blockade.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for tumor tissues treated with saline or Mn-N/C

first: Jingqi

last: Chen

first: Huayuan

last: Zhou

first: Cegui

last: Hu

first: Sumiya

last: Dalangood

first: Hanjun

last: Li

first: Dandan

last: Yang

first: Yu

first: Gui

last: Jun


title: DNA Polymerase Delta Governs Parental Histone Transfer to DNA Replication Lagging Strand

city: Shenzhen

first: haiyun

last: gan

address: xueyuan lu 1068

institute: Shenzhen Institute of Advanced Technology

type: Genome binding/occupancy profiling by high throughput sequencing

summary: Chromatin replication is intricately intertwined with DNA replication, and the recycling of parental histones is essential for epigenetic inheritance. The transfer of parental histones to both the DNA replication leading and lagging strands involves two distinct pathways: the leading strand utilizes DNA polymerase ε subunits Dpb3/Dpb4, while the lagging strand is facilitated by the MCM helicase subunit Mcm2. However, the process by which Mcm2, moving along the leading strand, facilitates the transfer of parental histones to the lagging strand remains unclear. Our study reveals that the deletion of Pol32, a non-essential subunit of major lagging-strand DNA polymerase δ, results in a predominant transfer of parental histone H3-H4 to the replication leading strand. Biochemical analyses further demonstrate that Pol32 can bind histone H3-H4 both in vivo and in vitro. The interaction of Pol32 with parental histone H3-H4 is disrupted by the mutation of Mcm2's histone H3-H4 binding domain. In conclusion, our findings identify the DNA polymerase delta subunit Pol32 as a novel key histone chaperone downstream of Mcm2, mediating the transfer of parental histones to the lagging strand during DNA replication.

overall_design: We performed eSPAN according to the protocol in our previous studies with some modifications. Briefly, yeast cells were synchronized with alpha-factor and released in YPD medium with BrdU (400ug/ml) following the standard protocol. The cells were digested with MNase (NEB, Cat# M0247S), after saving 1% for BrdU-IP, the rest of digested chromatin was subjected to ChIP against H3K4me3 (ab8580), H3K56ac, HA-Tag (BETHYL,Cat#12CA5), or T7-Tag (BETHYL,Cat#A190-117A), individually. Then DNA extracted from the ChIP products was end-repaired and ligated with adapters using the VAHTS® Universal DNA Library Prep Kit for Illumina V3 (Vazyme, Cat#ND607). After saving 1% for ChIP-seq analysis, the products was subjected to BrdU-IP as previous reported, and the products was amplified with NEBNext High-Fidelity 2X PCR Master Mix (NEB, Cat# M0541L) and indexing primers. The obtained libraries were sequenced using the paired-end method by Illumina nova 6000.

first: Chuanhe

last: Yu

first: Haiyun

last: Gan

first: Congcong

last: Tian

first: Qin

last: Zhang

first: Jiaqi


title: Chemical manipulation of m1A mediates its detection in human tRNA

city: Chicago

first: Ruitu

last: Lyu

state: IL

address: 929 E 57th Street

department: Chemistry

country: USA

institute: The University of Chicago

type: Non-coding RNA profiling by high throughput sequencing

summary: N1-methyl adenosine (m1A) is a wide-spread RNA modification present in tRNA, rRNA and mRNA. m1A modification sites in tRNAs are evolutionary conserved and its formation on tRNA is catalyzed by methyltransferase TRMT61A and TRMT6 complex. m1A promotes translation initiation and elongation. Due to its positive charge under physiological conditions, m1A can notably modulate RNA structure. It also blocks Watson-Crick base pairing and causes mutation and truncation during reverse transcription. Several misincorporation-based high throughput sequencing methods have been developed to sequence m1A. In this study, we introduce a reduction-based m1A sequencing (red-m1A-seq). We report that NaBH4 reduction of m1A can improve the mutation and readthrough rates using commercially available RT enzymes to give better positive signature, while alkaline-catalyzed Dimroth rearrangement can efficiently convert m1A to m6A to provide good controls, allowing the detection of m1A with higher sensitivity and accuracy. We applied red‑m1A-seq to sequence human small RNA  and we not only detected all the previously reported tRNA m1A sites, but also new m1A sites in mt-tRNAAsn-ATT and 5.8S rRNA.

overall_design: Detect m1A sites on tRNA and rRNA in HeLa cells using new chemical manipulation method

first: Kinga

last: Pajdzik

first: Qing

last: Dai

first: Chuan

last: He


title: Conditionally Replicative Adenovirus as a Therapy for Malignant Peripheral Nerve Sheath Tumors

city: Minneapolis

first: David

last: Largaespada

state: MN

address: 515 Delaware St SE

department: Department of Pediatrics

institute: University of Minnesota

summary:
BACKGROUND: Conditionally replicative adenoviruses (CRAds) preferentially infect and lyse tumor cells. While CRAds have been clinically applied, their potential for neurofibromatosis type-1 associated malignant peripheral nerve sheath tumors (MPNSTs) remains unexplored. This study evaluates Cyclooxygenase 2 (COX2)-driven CRAds as a therapy for MPNST.
METHODS: Viruses with wild type (WT) and modified fiber-knob domains were assessed for binding efficiency to the MPNST models. Viral infectivity, spread, and susceptibility of MPNST cells to oncolytic adenoviruses were assessed using both WT viruses or engineered CRAd constructs, with cell viability quantification. Tumor growth rates and survival probability of mice bearing human tumor xenografts or syngeneic allografts were assessed using intratumoral injections of CRAds.
RESULTS: RGD-modified fibers exhibited improved binding to MPNST cells compared to non-cancer Schwann cells. vectors effectively replicated and lysed MPNST cells, displaying enhanced selectivity towards transformed cells. Tumor-bearing immunodeficient mice survived significantly longer when injected with CRAds compared to PBS controls, and immunocompetent models demonstrate robust infiltration of CD8+ T-cells.
CONCLUSIONS: CRAds demonstrate selective binding and efficient replication in MPNST cells, leading to tumor cell lysis while sparing non-cancerous cells. These results suggest that oncolytic adenoviruses may have the potential as novel agents for MPNST therapy and thus warrant further investigation.

overall_design:
Syngeneic mouse allografts were established in a to compare the impact of CRAds on tumor growth. RNAseq was performed on these samples to understand the transcriptomic effects of the CRAds within allografts. Additionally, mouse nerve and liver RNAseq samples were taken for comparison.
Whole Exome Sequencing was conducted on the cell lines of origin for the syngeneic allografts.

first: Julia

middle: A

last: Nikrad

first: Robert

middle: T

last: Galvin

first: Tyler

last: Jubenville


title: scRNA-seq of day 32 p.i. GC B cells induced by experimental Plasmodium infection following the inducible deletion of IL-21 from CD4 T cells on day 16-18

city: Iowa City

first: Noah

middle: S

last: Butler

state: IA

address: 4-350 BSB, 51 Newton Road

department: Department of Microbiology and Immunology

institute: University of Iowa

summary: IL-21 is critical for initiating humoral immune responses, but whether sustained IL-21 production by T follicular helper cells regulates the quality or output of memory B cells and plasma cells during an established germinal center response is unknown. Here, we applied scRNA and approaches to determine the heterogeneity of germinal center B cells from Plasmodium infected mice with or without truncated IL-21 expression.

overall_design: Mice were infected with 1 million Plasmodium yoelii parasitized red blood cells and subsequently treated with tamoxifen on days 16, 17 and 18 p.i. to induce the deletion of Il21 from the CD4 T cell compartment. Comparator cells derive from Plasmodium infected and tamoxifen treated mice bearing the conditional alleles of Il21 but lacking the Cd4-ERT2/Cre transgene. On day 32 p.i., CD95+ GL-7+CD19+B220+ cells were FACS-sorted from mice (4 donor mice/genotype) and loaded on the Chromium Controller (10x Genomics) Single-cell RNA-seq libraries were prepared using the Chromium Single Cell 3’ v2 Reagent Kit (10x Genomics) according to the manufacturer’s protocol.

first: Jordan

last: Johnson


title: The efficacy of LCMV-based cancer vaccines is unleashed by intratumoral injections of polyI:C

first: Jose

last: Gonzalez

country: Spain

overall_design: TC1/A9 tumor-bearing mice received intravenous treatment with 1×105 RCV FFU artLCMV-E7E6 on day 7 and intratumoral injections of 50 μg of poly(I:C) in the right tumor lesion on days 7, 10, and 13. On day 8 and day 14, mice were euthanized, and RNA from tumors was subjected to RNAseq analysis.

first: Celia

last: Gomar

first: José

last: González-Gomariz

first: Pedro

last: Berraondo


title: Analyses of lncRNA and mRNA profiles in the recurrent atrial fibrillation after Catheter Ablation

city: Qingdao

first: Xiaomeng

last: Chen

address: No. 17, Shandong Road

institute: Qingdao Municipal Hospital, University of Health and Rehabilitation Sciences

summary: Our study aims to elucidate the role of lncRNA-mRNA regulatory networks in AF recurrence after catheter ablation. We performed RNA sequencing to profile the transcriptomes of 5 samples from atrial fibrillation recurrence and 5 samples from sinus rhythm maintenance. 96 differentially expressed genes (DEGs) and 203 differentially expressed long non-coding RNAs (DE-lncRNAs) were identified between atrial fibrillation recurrence group and sinus rhythm maintenance group. Gene Ontology (GO) analysis showed that DEGs were enriched in “regulation of immune response”, and “regulation of immune system process” for biological processes (BP), enriched in “extracellular matrix”, “cell-cell junction” for cellular components (CC), and enriched in “signaling adaptor activity”, “protein-macromolecule adaptor activity” for molecular functions (MF). For KEGG analysis, DEGs are associated with “PI3K-Akt signaling pathway”, “MAPK signaling pathway”. 9 hub genes (MMP9, IGF2, FGFR1, HSPG2, GZMB, PEG10, GNLY, COL6A1, and KCNE3) were identified through the Protein-Protein Interaction network. LncRNA-TMEM51-AS1-201 was identified as a core regulator and may impact AF recurrence after catheter ablation by regulating “COL6A1, FGFR1, HSPG2, and IGF2.”

overall_design: To elucidate the potential mechanisms behind AF recurrence after catheter ablation, a long-term follow-up study was conducted on AF patients who had undergone catheter ablation. Patients were categorized into two groups based on whether AF recurred or was maintained in sinus rhythm after catheter ablation, with 5 individuals in each group. Fasting blood samples were collected for RNA-seq.

first: Huaiguang

last: Tang


title: Comparative transcriptional analysis identifies genes associated with the attenuation of Theileria parva infected cells after long-term in vitro culture

city: Edinburgh

first: Elisabeth

middle: Margaretha Diana Louise

last: van der Heijden

state: Midlothian

address: Easter Bush Campus

department: Division of Immunology

country: United Kingdom

institute: The Roslin Institute, The University of Edinburgh

summary: Administration of attenuated autologous Theileria parva infected cells can be used as an alternative to the infection-and-treatment method for inducing immunological protection against East Coast Fever. The mechanism of attenuation however has not been described. Using RNA sequencing, the transcriptomes of both host and parasite in uninfected (control), pathogenic (day 7 post-infection) and attenuated (day 69 post-infection) T. parva infected bovine CD4+ T-cells were characterized and compared. Our findings suggest that three major mechanisms are associated with attenuation of T. parva-infected cells – a decrease in proliferation, a partial restoration of the inflammatory profile, and a shift in metabolism. Several host genes (TRAIL, PD-1, TGF-β and granzymes) were identified as candidates for further exploration. Evaluation of the parasite transcriptomes in these cells also provided first insights into potential candidate T. parva genes involved in attenuation, but subsequent studies are required to further examine these.

sample_organism:
Theileria parva
Bos taurus

platform_organism:
Theileria parva
Bos taurus

overall_design: To investigate the mechanisms of attenuation Theileria parva infected bovine CD4 T-cell lines were established. RNA seq was then performed on cell lines from 6 animals at 3 time points (day 0 (uninfected), day 7 (pathogenic) and day 69 (attenuated). 2 cell lines could not be maintained in vitro until day 69 as such there are only 4 samples for day 69).

middle: M

first: Lucas

last: Lefevre

first: Anton

last: Gossner

first: Thomas

last: Tzelos

first: Tim

last: Connelley

first: Musa

last: Hassan


title: Circulating monocyte counts coupled with a 4-gene signature at leukapheresis predict survival of lymphoma patients treated with CAR T

city: MILAN

first: Luca

last: Agnelli

address: Venezian 1

department: Department of Advanced Diagnostics

country: Italy

institute: IRCCS Istituto Nazionale dei Tumori

summary: CD19-directed chimeric antigen receptor (CAR) T cells can induce durable remissions in relapsed/refractory large B-cell lymphomas (R/R LBCL), but 60% of patients still relapse. Biological mechanisms explaining lack of disease-response  are largely unknown. To identify mechanisms of response and survival before CAR T manufacturing in 95 R/R LBCL receiving tisagenlecleucel or axicabtagene ciloleucel, we performed phenotypic, transcriptomic and functional evaluations of leukapheresis products (LK).  Transcriptomic profiling of T cells in LK, revealed a signature composed of 4 myeloid genes able to identify patients with very short progression-free survival, highlighting the role of monocytes in CAR T therapy response. Accordingly, response and survival were negatively influenced by high circulating absolute monocyte counts at the time of leukapheresis, and the combined evaluation of peripheral blood monocytes and the four-gene signature in LK, identifies LBCL patients at very high risk of progression after CAR T.

overall_design: The transcriptomic analysis was performed on a cohort of 77 relapsed/refractory large B-cell lymphoma patients. CD3+ T cells selected from 77 patient leukapheresis and 8 leftover lymphocytes from donor lymphocyte infusions (healthy controls) were profiled using the nCounter 780 gene CAR-T characterization panel.

first: Cristiana

last: Carniti

first: Nicole

last: Caldarelli

first: Tommaso

last: Torelli

first: Silva

last: Ljevar

first: Sadhana

last: Jonnalagadda

first: Giada

last: Zanirato

first: Eugenio

last: Fardella

first: Daniele

last: Lorenzini

first: Silvia

last: Brich

first: Anna

last: Dodero

first: Annalisa

last: Chiappella

first: Martina

last: Magni

first: Paolo

last: Corradini


title: Systematic identification of transcriptional activation domains from non-transcription factor proteins in plants and yeast

city: Berkeley

first: Niklas

last: Hummel

address: 1 Cycloton Road

institute: Lawrence Berkeley National Laboratory

summary: Transcription factors can promote gene expression through activation domains. Whole-genome screens have systematically mapped activation domains in transcription factors, but not in non-transcription factor proteins (e.g., chromatin regulators, coactivators). To fill this knowledge gap, we employed the activation domain predictor PADDLE to analyze the proteomes of Arabidopsis thaliana and Saccharomyces cerevisiae. We screened 18,000 predicted activation domains from >800 non-transcription factor genes in both species, confirming that 89% of candidate proteins contain active fragments. Our work enables the annotation of hundreds of nuclear proteins as putative coactivators, many of which have never been ascribed any function in plants. Analysis of peptide sequence compositions reveals how the distribution of key amino acids dictates activity. Finally, we validated short, 'universal' activation domains with comparable performance to state-of-the-art activation domains used for genome engineering. Our approach enables the genome-wide discovery and annotation of activation domains that can function across diverse eukaryotes.

overall_design: To measure transcriptional activation domain activity, we used FACS to separate cells with different GFP levels of a reporter construct. We sequenced the barcodes attached to each activation domain in each sorted population.

middle: F

first: Jordan

last: Stefani

first: Max

middle: V

last: Staller

first: Patrick

last: Shih


title: GDF-15 is a biomarker of aggressiveness and is down-regulated by the mTOR inhibitor sirolimus through ATF4 and ATF5 suppression in epithelioid hemangioendothelioma.

city: Milano

first: Stefano

last: Percio

address: VIa Amadeo 42

institute: Istituto Nazionale dei Tumori

summary: Growth and differentiation factor-15 (GDF-15), a member of the TGF-β superfamily, exhibits elevated expression in various tumor types, often linked to disease aggressiveness. In this study, which used patient-derived xenografts and paired cell lines of epithelioid hemangioendothelioma (EHE), it was found that EHE cells produce and release GDF-15. Furthermore, the mTOR inhibitor sirolimus was observed to inhibit GDF-15 expression and release by down-regulating ATF4 and ATF5 transcription factors. To assess the clinical relevance of GDF-15 in EHE, which can manifest as both relatively indolent and exceptionally aggressive forms, circulating GDF-15 levels were assessed in two independent cohorts of EHE patients, one retrospective and one prospective. The results provided evidence of an association between circulating GDF-15 levels and the aggressiveness of EHE. In summary, these findings suggest that GDF-15 can serve as a biomarker for EHE aggressiveness and may have implications for monitoring the effectiveness of sirolimus in EHE patients.

overall_design: mRNA profiles of treated and untreated EHE cell lines on an Illumina NovaSeq sequencer.

first: Alessia

last: Beretta


title: Skeletal muscle methylation signatures of obese high- and low- responders to   endurance exercise training

city: Nuthetal

first: Heike

last: Vogel

state: BRB

address: Arthur-Scheunert-Allee 114-116

department: Department of Experimental Diabetology

country: Germany

institute: German Institute of Human Nutrition Potsdam-Rehbruecke

summary: The participants performed 8 weeks of superised aerobic endurance exercise. Skeletal muscle biopsise were taken at rest before and after intervention and matched analysis was performed.

overall_design: We performed DNA methylation array on skeletal muscle biopsies before and after exercise training intervention.

first: Annette

last: Schürmann

first: Cora

last: Weigert

first: Andreas

last: Birkenfeld

last: Peter

first: Martin

last: Hrabe de Angelis

first: Johannes

last: Beckers

first: Markus

last: Jähnert

last: Irmler

first: Meriem

last: Ouni

first: Thomas

last: Goj

first: Leona

last: Kovac


title: Fasting upregulates the monocarboxylate transporter Mct1 at the rat blood-brain barrier through Ppar δ activation

city: PARIS

first: Stephane

last: Le Crom

address: 46 rue Ulm

department: Genomic Core Facility

country: France

institute: IBENS

summary: Fasting is increasingly recognized as a potential therapeutic intervention in the field of neurology and psychiatry. However, its impact upon the blood-brain barrier (BBB), which strictly regulates the cerebral uptake of a wide range of endogenous compounds and drugs, is unknown. In this study we used a combination of in vivo and in vitro experiments to assess the response of the brain endothelium in rats that were fed ad libitum or fasted for one to three days. Fasting did not change the expression of the main drug efflux ATP-binding cassette transporters or P-glycoprotein activity at the BBB but modulated a restrictive set of solute carrier transporters. These included the monocarboxylate transporter Mct1, which is pivotal for the cerebral uptake of ketone bodies and thus for brain adaptation to fasting. Transcriptional profiling of freshly isolated brain endothelial cells showed that Ppar δ, a major lipid sensor, was selectively activated in response to fasting. In primary cultured rat brain endothelial cells, pharmacological agonists and free fatty acids selectively activated Ppar δ, resulting in the upregulation of Mct1 expression at the transcriptional and protein level. This was confirmed in vivo, by showing that dosing rats with a specific Ppar δ antagonist blocked the upregulation of Mct1 expression and activity induced by fasting. Altogether, our study describes for the first time a selective adaptive response of the brain vasculature to fasting and opens new perspectives for the metabolic manipulation of the BBB in the healthy or diseased brain.

overall_design: Comparison of gene expression in endothelial cells from the cerebral cortex of Wistar-Han rats fed ad libitum or fasted for one, two, or three days

first: Stéphanie

last: Chasseigneaux

first: Véronique

last: Cochois-Guégan

first: Lucas

last: Lecorgne

first: Murielle

last: Lochus

first: Sophie

last: Nicolic

first: Corinne

last: Blugeon

first: Laurent

last: Jourdren

first: David

last: Gomez-Zepeda

first: Stefan

last: Tenzer

first: Sylvia

last: Sanquer

first: Valérie

last: Nivet-Antoine

first: Marie-Claude

last: Menet

first: Jean-Louis

last: Laplanche

first: Xavier

last: Declèves

first: Salvatore

last: Cisternino

first: Bruno

last: Saubaméa


title: Cationic amphiphilic drug induced phospholipidosis and lysosomal dysgenesis during in vitro adipogenesis

city: Utrecht

first: Jorke

last: Kamstra

state: Non United States Or Canada

address: PO Box 80177

department: Faculty of Veterinary Medicine

country: Netherlands

institute: Utrecht University

summary: Selective Serotonin Reuptake Inhibitors (SSRIs) are widely used medications for the treatment of major depressive disorder. However, long-term SSRI use has been associated with weight gain and altered lipid profiles. These findings suggest that SSRIs may have negative effects on metabolism. Exposure to certain chemicals called 'obesogens' are known to promote lipid accumulation and obesity by modulating adipogenesis. Here, we investigated whether citalopram (CIT) and sertraline (SER) interfere with the process of adipogenesis, using human mesenchymal stem cells (MSCs) in a 2D and a 3D model. Assessment of intracellular lipid accumulation by fluorescence staining was used as a measure for enhanced adipogenesis. To explore possible mechanisms behind SSRIs' effects, receptor mediated activity was studied using responsive cell lines for various nuclear receptors. Furthermore, RNA sequencing was performed in the 3D model, followed by differential gene expression and pathway analysis. A dose dependent increase in lipid accumulation was observed in both models with CIT and SER. For the 3D model, the effect was seen in a range close to reported steady-state plasma concentrations (0,065-0,65 μM for SER and 0,12-0,92 μM for CIT). Pathway analysis revealed unexpected results of downregulation in adipogenesis-related pathways and upregulation in phospholipids and lysosomal pathways. This was confirmed by an observed increase in lysosomes in the 2D model. Our findings suggest lysosomal dysfunction and disrupted lipid metabolism in mature adipocytes, leading to excessive phospholipid synthesis. Moreover, important adipogenic processes are inhibited, potentially leading to dysfunctional adipocytes, which might have implications in maintenance of a healthy metabolic balance.

overall_design: For transcriptomics profiling, cells were differentiated in parallel via 2D or 3D protocols, with and without the positive control ROSI at 0.1 µM, CIT or SER where 0.1% DMSO was used as a vehicle control. These exposures were repeated in 3 independent biological experiments.

first: Deniz

last: Bozdag

first: Hande

middle: G

last: Orhan

first: Jeroen

last: van Voorthuizen

middle: H

first: Sander

last: Lentz


title: Gene expression profiling in dendritic cell progenitors and dendritic cells

city: Yokohama

first: Tomohiko

last: Tamura

address: 3-9 Fukuura, Kanazawa-ku

department: Department of Immunology

institute: Yokohama City University

summary: To understand the roles of Irf8 3’ enhancers on Irf8 expression during cDC1 differentiation, we performed RNA-seq analysis of bone marrow cells and splenocytes from wild-type, and the Irf8 enhancer-deficient mice. Phenotypic analysis and integrated analysis of transcriptome data with genome-wide CUT&Tag data analysis for H3K27ac revealed that the +56 kb enhancer acts on other 3′ enhancers via an IRF8-dependent TF program and the +32 kb enhancer acts in cis to activate other 3′ enhancers.

overall_design: Murine type1 classical dendritic cells (cDC1s), cDC1 subset-committed progenitors (pre-cDC1s), common DC progenitors (CDPs), and monocyte-DC progenitors (MDPs) were isolated from WT, +56 kb enhancer-heterozygous deficient (d+56het), or +32 kb enhancer-heterozygous deficient (d+32het). The IRF8-rescued cDC1s were prepared from Lin– cells from WT, +56 kb enhancer-deficient (d+56), or +32 kb enhancer-deficient (d+32). These cells were subjected to RNA-seq analysis (biological duplicates for each cell type).

first: Takaya

last: Yamasaki

first: Akira

last: Nishiyama


title: Off target expression data from iPSC derived microglia treated with APOE/TREM2 ASOs for 24h/48h. The iPSC cells are from a wild type donor (BIONi10C).

city: Beerse

first: Lina

last: Vandermeulen

address: Turnhoutseweg 30

department: Neuroscience

country: Belgium

institute: Johnson & Johnson

summary:
Microglia play important roles in maintaining brain homeostasis and neurodegeneration. The discovery of genetic variants in genes predominately or exclusively expressed in myeloid cells,  factors for Alzheimer’s disease (AD) highlights the importance of microglial biology in the brain.
such as Apolipoprotein E (APOE) and triggering receptor expressed on myeloid cells 2 (TREM2), as the strongest risk factors for Alzheimer’s disease (AD) highlights the importance of microglial biology in the brain.
The sequence, structure and function of several microglial proteins are poorly conserved across species, which has hampered the development of strategies aiming to modulate the expression of specific microglial genes.
One way to target APOE and TREM2 is to modulate their expression using antisense oligonucleotides (ASOs). In this study, we identified selective and potent ASOs for human APOE and TREM2.
We proved their efficacy in human iPSC microglia in vitro, as well as their pharmacological activity in vivo in a xenografted microglia model. We demonstrate ASOs targeting human microglia can modify
their transcriptional profile and their response to amyloid-b plaques in vivo in a model of AD. This study is the first proof-of-concept that human microglial can be modulated using ASOs in a dose-dependent manner to manipulate microglia phenotypes in vivo.
Since ASOs can have off-target effects, besides the expected decrease of APOE and TREM2 mRNA, this microarray was performed to determine the off-target profiles of the ASOs.
iPSC derived microglia were treated with the ASOs with 1.25uM and 20uM dosages, and the compounds were incubated either 24hours or 48hours.

overall_design: Cell lysates were collected upon 24 and 48hours of treatment with the ASOs. RNA was extracted and hybridization was done on Affymetrix microarrays.

first: Constantin

last: d'Ydewalle

first: Ilse

last: Van Den Wyngaert

first: An

last: De Bondt


first: Stefano

last: Percio

overall_design: mRNA profiles of PDX and clinical sample were generated on an Illumina NextSeq500 sequencer.

first: Valentina

last: Zuco


title: Inflammatory conversion of normal hematopoietic stem and progenitor cells by acute myeloid leukemia derived extracellular vesicles in vivo

city: Philadelphia

first: Peter

last: Kurre

state: PA

address: 3615 Civic Center Blvd

department: Pediatrics

institute: Children's Hospital of Philadelphia

summary: Inflammation in the bone marrow (BM) microenvironment is a constitutive component of acute myeloid leukemia (AML) pathogenesis. Studies have demonstrated that leukemic blasts propagate acute inflammation in the AML niche. Our recent studies in a congenic AML model suggest residual healthy hematopoietic stem and progenitor cells (HSPCs) participate in the inflammatory crosstalk. However, the underlying mechanism that drives the inflammatory conversion of HSPCs remains unclear. Here, we ask whether AML-derived extracellular vesicles (EV-AML) can convert HSPCs into an inflammatory active state in vivo. Using EV-AML purified from inducible (i)MLL-AF9 AML blasts (AF9-EV-AML), we challenged healthy C57BL/6J mice with serial injections of AF9-EVAML and analyzed HSPCs transcriptome. We show that HSPC transcriptome corroborates the enrichment of inflammatory and innate immune responses in EVAML-challenged BM HSPCs compared to controls. Our findings suggest that AML converts HSPCs into an inflammatory hub via EVAML in the AML niche.

overall_design: Healthy C57BL/6J mice (CD45.1; 8-12 weeks; female; Jacksons Laboratory) were challenged with either inducible(i)MLL-AF9 blasts-derived extracellular vesicles (AF9-EV), healthy peripheral blood extracellular vesicles (PB-EV), phosphat buffered saline (PBS), or lipopolysaccharides (LPS). AF9-EV (1-2E9 particles per injection), PB-EV (1-2E9 particles per injection), and PBS were administered every 24 hours for 3 days via intravenous (for the first two injections) and intraosseous (third injection). LPS (3mg/kg) were injected via single-dose (intraperitoneal) and serve as a positive control. Mice were sacrificed 24 hours the last injection and bone marrow HSPCs (Lin- cKit+ Sca1+)  were fluorescent-activated cell sorting (FACS)-sorted for gene expression assay.

first: Ding-Wen

last: Chen

first: Julie

last: Schrey

first: Jian-Meng

last: Fan

first: Dana

last: Mitchell

first: Deanne

last: Taylor


title: Physical and functional interaction among Irf8 enhancers during dendritic cell differentiation

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

overall_design: Refer to individual Series


title: Kinetic chromatin openin profiles in mouse ApcDHep or wt hepatocytes

city: Paris

first: Angelique

last: Gougelet

address: 15 rue de l'école de médecine

institute: INSERM U1138

summary: We analyzed  chromatin opening  in hepatocytes isolated from  Apclox/loxlivers, after injection of adenovirus Ad5 -Cre-GFP and sorting on the basis of GFP signal at day 6, 15 and 21 post-injection. Our aims was to study the impact of an aberrant beta-catenin activation on chromatin opening in hepatocytes during the early steps of liver tumorigenesis.

overall_design: ATAC-seq profiles from GFP+ ApcDHep hepatocytes  isolated from  ApcDHep livers versus GFP- Apcwt hepatocytes

first: Angélique


title: Rapid and synchronous chemical induction of replicative-like senescence via a small molecule inhibitor [scRNA-seq]

city: Göttingen

first: Argyris

last: Papantonis

state: Goettingen

address: Robert-Koch-Str. 40

department: Institute of Pathology

institute: University Medical Center Göttingen

summary: Cellular senescence is now acknowledged as a key contributor to organismal ageing and late-life disease. Although popular, the study of senescence in vitro can be complicated by the prolonged and asynchronous timing of cells committing to it and its paracrine effects. To address these issues, we repurposed the small molecule inhibitor inflachromene (ICM) to induce senescence to human primary cells. Within six days of treatment with ICM, senescence hallmarks, including the nuclear eviction of HMGB1 and -B2, are uniformly induced across the cell population. By comparing various high throughput datasets from ICM-induced and replicative senescence, we uncovered significant similarities between the two states. Notably, ICM suppresses the proinflammatory secretome associated with senescence, thus alleviating most paracrine effects. In summary, ICM rapidly and synchronously induces a senescence-like phenotype that allows us to study its core regulatory program without any confounding heterogeneity.

overall_design: Micro-C is applied to 4 low passage IMR90 wild type samples and 4 low passage ICM-treated samples. RNA-seq and Ribo-Seq are applied to  4 low passage IMR90 wild type samples, 4 high passage IMR90 senescent samples and to 2 low passage ICM-treated samples.  scRNA-seq is applied to 1 low passage IMR90 wild type samples, 1 high passage IMR90 senescent sample and to 1 low passage ICM-treated sample. FactoryRNA-seq is applied to 2 low passage IMR90 wild type samples, 2 low passage 3 days ICM-treated samples, 2 low passage 6 days ICM-treated samples and 2 low passage metaICM-treated samples.  Cut&tag for CTCF and SMC1 are applied to 1 low passage IMR90 wild type sample, 1 high passage IMR90 senescent sample and to 1 low passage ICM-treated sample.

first: Spyridon

last: Palikyras

first: Konstantinos

last: Sofiadis

first: Athanasia

last: Stavropoulou

first: Vassiliki

last: Varamogianni-Mamatsi

first: Adi

last: Danieli-Mackay

first: Yajie

last: Zhu

first: Natasa

last: Josipovic


title: Rapid and synchronous chemical induction of replicative-like senescence via a small molecule inhibitor [factory RNA-seq]


title: Rapid and synchronous chemical induction of replicative-like senescence via a small molecule inhibitor [CUT&TAG]


title: Histone modification in dendritic cell progenitors and dendritic cells

first: Tomohiko

last: Tamura

summary: To understand the roles of Irf8 3’ enhancers on Irf8 expression during cDC1 differentiation, we performed Cleavage Under Targets and Tagmentation (CUT&Tag) analysis for H3K27ac of bone marrow cells and splenocytes from wild-type, and the Irf8 enhancer-deficient mice. Phenotypic analysis and integrated analysis of CUT&Tag data with transcriptome data of these mouse mononuclear phagocytic lineage cells revealed that the +56 kb enhancer acts on other 3′ enhancers via an IRF8-dependent TF program and the +32 kb enhancer acts in cis to activate other 3′ enhancers.

overall_design: Murine type1 classical dendritic cells (cDC1s), cDC1 subset-committed progenitors (pre-cDC1s), common DC progenitors (CDPs), and monocyte-DC progenitors (MDPs) were isolated from WT, +56 kb enhancer-heterozygous deficient (d+56het), or +32 kb enhancer-heterozygous deficient (d+32het). The IRF8-rescued cDC1s were prepared from Lin– cells from WT, +56 kb enhancer-deficient (d+56), or +32 kb enhancer-deficient (d+32). These cells were subjected to CUT&Tag analysis (biological triplicates for each cell type).

first: Takaya

last: Yamasaki

first: Akira

last: Nishiyama


title: Rapid and synchronous chemical induction of replicative-like senescence via a small molecule inhibitor


title: Rapid and synchronous chemical induction of replicative-like senescence via a small molecule inhibitor [microC]


title: Rapid and synchronous chemical induction of replicative-like senescence via a small molecule inhibitor [Ribo-seq]


title: Rapid and synchronous chemical induction of replicative-like senescence via a small molecule inhibitor [bulk RNA-seq]


title: Identification of skewed X chromosome inactivation using exome and transcriptome sequencing in patients with suspected rare genetic disease

city: Rochester

first: Numrah

last: Fadra

institute: Mayo clinic

summary:
Purpose: Evaluation of XCI status in a cohot of female patients with suspected rare genetic diseases using exome and RNA sequencing
Results: We developed a method for estimating X inactivation status, using exome and transcriptome sequencing data from 112 female samples. We built a reference model for evaluation of XCI in 135 females from the GTEx consortium. We tested and validated the model on 14 female individuals with different types of undiagnosed rare genetic disorders who were clinically tested for X-skew using the AR gene assay and compared results to our outlier-based analysis technique. In comparison to the AR clinical test for identification of X inactivation, our method was concordant with AR method in 9 samples, discordant in 3, and provided measures of X inactivation in 2 samples with uninformative clinical results. We applied this method on an additional 98 females presenting to the clinic with phenotypes consistent with different hereditary disorders without a known genetic diagnosis. Here we show the use of transcriptome sequencing data to provide an accurate and complete estimation of X-inactivation and skew status in female patients.

overall_design: RNA from whole blood for all patients was extracted in a PAXgene Tube following manufacturer’s instructions (Qiagen). The miRNeasy Mini kit from Qiagen was used for isolation of RNA and 101 base pair paired libraries were prepared using capture probes from the TruSeq®RNA Access Library Prep Kit (Illumina). Samples were sequenced at Mayo Clinic Medical Genome Facility (MGF) using Illumina Hiseq 4000 generating on average greater than 100 million reads per sample.

first: Eric

last: Klee

first: Garrett

last: Jenkinson

first: Laura

last: Rogers

first: Pritha

last: Chanana

first: Margot

last: Cousin

first: Erica

middle: L

last: Macke

first: Alejandro

last: Ferrer

first: Fillippo

middle: E

last: Vairo

first: Rory

last: Olson

first: Gavin

middle: R

last: Oliver

first: Lindsay

last: Mulvihill


title: Trophectoderm biopsies of blastocysts for preimplantation genetic testing following in vitro fertilization and embryo culture increases epigenetic dysregulation in a mouse model

middle: Alejandro

last: Rhon Calderon

state: Pennsylvania

address: 3400 Civic Center Blvd, Bldg 421, Floor 9-175

department: Cell and Developmental Biology

institute: University of Pennsylvania

type: Methylation profiling by genome tiling array


title: Trophectoderm biopsies of blastocysts for preimplantation genetic testing following in vitro fertilization and embryo culture increases epigenetic dysregulation in a mouse model [array]

summary:
Trophectoderm biopsy for preimplantation genetic testing (TEBx) impacts placental and embryonic health during early development, with some alterations resolving while others worsening later in development.
We observed that at E12.5, IVF + TEBx had a worse outcome in terms of changes in DNA methylation and differential gene expression in placentas and whole embryos compared with IVF alone. These changes were reflected in alterations in placental morphology and blood vessel density. At E18.5, early changes in embryos were maintained or worsened, while molecular and morphological changes in the placenta were not different from the IVF group, except for changes in blood vessel density, which persisted. Of note is that most differences were sex specific. We conclude that TEBx has more detrimental effects in both mid-gestation placental and embryonic tissues, with changes in embryonic tissues persisting or worsening in later developmental stages compared to IVF alone. Additionally, consistent with previous work, we report sex differences in the observed effects. Finally, we identified that the addition of vitrification after TEBx has a more pronounced detrimental effect on placental and fetal health. Our findings provide additional support that more studies should be done to assess the impact of new procedures during ART to ensure healthy pregnancies and offspring outcomes.

overall_design: Bisulfite converted DNA from 48 mouse E12.5 placenta samples from 3 different groups (Natural N=16, IVF N=16 and IVF+TEBx N=16) and two different sexes (Females N=24 and Males N=24) were hybridized to the Illumina Mouse Methylation285 12v1-0 BeadChip Array

last: Rhon-Calderon

first: Lisa

last: Vrooman

first: Casey

last: Rosier

first: Teri

last: Ord

first: Monica

last: Manigi

first: Richard

last: Schultz

first: Marisa

last: Bartolomei


title: Gene expression difference in cells expressing high and low FoxA2-Venus protein levels from mouse neural tube organoids.

city: Vienna

first: Maria

last: Novatchkova

address: Dr Bohrgasse

country: Austria

institute: IMP/IMBA

summary: We describe the transcriptomic differences in FoxA2-Venus high and low cell populations in neural tube organoids.

overall_design: Organoids were grown via clonal growth from R1 mouse ES cells of FoxA2-Venus genotype seeded in Matrigel and cultured in N2B27 medium at 37C, 5% CO2 as described (Meinhardt et al. Stem Cell Reports 2014, Ishihara et al. Methods in Mol. Bio. 2017). At Day 2 (=48 hrs post seeding), organoids were treated with or without 250 nM all trans retinoic acid. Organoids were extracted from the Matrigel at 66 hrs post Day 2 and FACS sorted based on high and low fluorescence signal using a GFP filter set, yielding the categories GFP+ and GFP-. Three biological replicates were prepared for each cell population, yielding 9 independent samples for RNA extraction.

first: Elena

last: Gromberg

first: Elly

last: Tanaka


title: Effect of cardiomyocyte-specific deletion of Gch1 on gene expression

city: Oxford

first: Sandy

last: Chu

address: Wellcome Trust Centre for Human Genetics, Roosevelt Drive

institute: University of Oxford

summary:
To investigate the physiological role of BH4 in cardiac function, we developed mice with cardiomyocyte-specific deletion of (cm)Gch1, the gene that encodes for GTPCH, which responsible for de novo synthesis of BH4.
We performed RNA sequencing in heart tissues from cmGch1 KO and WT mice.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for cmGch1 KO and WT mice

first: Benjamin

last: Wright

first: Matthieu

last: Miossec

first: Helene

last: Lockstone

first: Gillian

last: Douglas

first: Keith

last: Channon


title: SLC7A5 is critical for Paneth cell integrity and function

city: Bethesda

first: Ryan

last: Dale

state: MD

address: Rm 10D39, 10 Center Drive

department: National Institute of Child Health and Human Development

institute: National Institutes of Health

summary: The intestine is the critical organ not only for processing and resorbing nutrients from ingested food but also for defending the organism from external stresses such as pathogens.  These functions are mainly carried out by the epithelium which is constantly being self-renewed throughout adult life. Intestinal epithelial homeostasis is maintained through well-controlled cell proliferation of the stem cells and transient amplifying cells and the apoptotic degeneration of epithelial cells, mostly at or near the tip of the villi. Many genes and pathways have been found to influence intestinal epithelial cell proliferation. Among them is the mTORC1 signaling pathway, whose activation is known to increase cell proliferation. Here, we report the first intestinal epithelial specific knockout (IEC-KO) of an amino acid transporter capable of activating mTORC1. We show that the transporter, slc7a5, is highly expressed in the intestinal crypt and slc7a5 IEC-KO leads to expected reduction in mTORC1 signal in the crypt or even in intestinal organoids in vitro.  Surprisingly, slc7a5 IEC-KO leads to increased proliferation of both transit amplifying cells and crypt base stem cells but a reduction in the secretory cells, particularly mature Paneth cells in the crypt base. Our scRNA-seq and electron microscopic analyses reveals that slc7a5 IEC-KO causes dedifferentiation of the Paneth cells, leading to drastically reduced secretory granules and lysozyme expression without affecting the overall Paneth cell number. We further show that slc7a5 IEC-KO mice are prone to induced colitis due to this loss of Paneth cell differentiation.  We propose a model where slc7a5 regulates secretory cell differentiation to affect stem cell niche and/or inflammatory response to regulate cell proliferation in the crypts.

overall_design: Comparison of slc7a5 fl/flwith slc7a5 IEC-KO enriched intestinal crypts

first: Lingyu

last: Bao

first: Liezhen

last: Fu

first: Jia

last: Zuo


title: SUMOylation inhibitor TAK-981 potentiates rituximab activity by Type I IFN-dependent macrophage and NK cell stimulation

city: Cambridge

first: Min Young

last: Lee

state: MA

address: 40 Landsdowne St

institute: Takeda Pharmaceutical Company Limited

summary: SUMOylation is a reversible post-translational modification that has been implicated in the regulation of various cellular processes including inflammatory responses and expression of Type I interferons (IFN1). In this report, we have explored the activity of the selective small molecule SUMOylation inhibitor TAK-981 in promoting antitumor innate immune responses. We demonstrate that treatment with TAK-981 results in IFN1-dependent macrophage and NK cell activation, promoting macrophage phagocytosis and NK cell cytotoxicity in ex vivo assays. Furthermore, pre-treatment with TAK-981 enhanced macrophage phagocytosis or NK cell cytotoxicity against CD20-positive target cells in combination with the anti-CD20 antibody rituximab. In vivo studies demonstrated synergistic antitumor activity of TAK-981 and rituximab in CD20-positive lymphoma xenograft models. TAK-981 is currently being studied in phase 1 clinical trials (NCT03648372, NCT04074330, NCT04776018, and NCT04381650) for the treatment of patients with lymphomas and solid tumors.

overall_design: RNA sequencing of human monocyte-derived macrophages treated with control (DMSO) and 1 uM TAK-981 for 24 h, with 2 donors in 3 biological replicates

first: Akito

last: Nakamura

first: Stephen

last: Grossman

first: Keli

last: Song

first: Kristina

last: Xega

first: Yuhong

last: Zhang

first: Donna

last: Cvet

first: Allison

last: Berger

first: Gary

last: Shapiro

first: Dennis

last: Huszar


title: Acute stress transiently activates macrophages and chemokines in cervical lymph nodes

city: Simotsuke-si

first: Akihiro

last: Dohi

state: Tochigi

address: 3311-1 Yakushiji

department: Oral, Maxillofacial Surgery

institute: Jichi Medical University

summary: Lymph nodes are vital for optimizing immune responses. Stress can induce several cellular and humoral immune responses. Acute restraint stress (RS) is a routinely used experimental procedure for studying psychological and/or physiological stress effects. Here, we determined the impact of RS on cervical lymph nodes in rats at the molecular and cellular levels. Stress was induced in male Sprague-Dawley rats by immobilization for 30, 60, and 120 min (RS30, RS60, and RS120, respectively) relative to a no-stress control (C) group. Expression of genes encoding chemokines CXCL1/CXCL2 (Cxcl1 and Cxcl2) and their receptor CXCR2 (Cxcr2) was analyzed at the mRNA level by reverse transcription-quantitative PCR (RT-qPCR) and microarray analyses. Immunohistochemistry and in situ hybridization were performed to determine the expression of these moieties along with the macrophage biomarker, CD68. Microarray analysis revealed that expression of 514 and 496 genes was upregulated and downregulated, respectively, in RS30. Cxcl1 and Cxcl2 expression showed a 23- and 13-fold increase, respectively, in RS30 relative to the C group. Expression of Cxcr2 was upregulated by approximately 1.6-fold in RS30 relative to the C group. Gene ontology analysis of three upregulated genes induced by RS30 suggested that they may be responsible for the cytokine network, inflammation, as well as leukocyte chemotaxis and migration. RT-qPCR analysis indicated that the mRNA levels of Cxcl1 and Cxcl2 significantly increased in RS30 but reverted to normal levels in RS60 and RS120. Cxcr2 mRNA level also increased significantly in RS30 and RS120 relative to the C group. RS-induced CXCL1-immunopositive cells corresponded to B/plasma cells, while CXCL2-immunopositive cells corresponded to endothelial cells of the high endothelial venules. Stress-induced CXCR2-immunopositive cells corresponded to macrophages. Psychological and/or physiological stress induces acute stress response and immunoreactive microenvironment in cervical lymph nodes, and the CXCL1/CXCL2-CXCR2 axis is pivotal in acute stress response.

overall_design: In this study, we aimed to elucidate the effects of acute stress using our experimental model, on the cervical lymph nodes, as a representative secondary lymphatic organ, with respect to changes in expression levels and immunochemical characteristics of macrophages, erythrocytes, CXCL1, CXCL2, and CXCR2 in rats.

first: Kenichi

last: Sasaguri

first: Toshiharu

last: Yamamoto


title: A shared temporal chromatin program for ventral spinal cord progenitors [CaTS-ATAC]

status: Public on Apr 23 2024

city: London

first: M Joaquina

last: Delas

address: 1 Midland Road

department: Briscoe Lab

institute: The Francis Crick Institute

summary: The vertebrate neural tube generates a large diversity of molecularly and functionally distinct neurons and glia from a small progenitor pool. While the role of spatial patterning in organising cell fate specification has been extensively studied, temporal patterning, which controls the timing of cell type generation, is equally important. Here we define a global temporal programme in the spinal cord. This governs cell fate choices by regulating chromatin accessibility in neural progenitors. Perturbation of this cis-regulatory programme affects sequential transitions in spinal cord progenitors and the identity of progeny. The temporal programme operates in parallel to spatial patterning, ensuring the timely availability of regulatory elements for spatial determinants to direct cell-type specific gene expression. These findings identify a chronotopic spatiotemporal integration strategy in which a global temporal chromatin programme determines the output of a spatial gene regulatory network resulting in the temporally and spatially ordered allocation of cell type identity.

overall_design: Mouse ES cell differentiation to spinal cord progenitors was sampled every two days from day 5 to day 11. Specific progenitors (p0-p1, p2 and pMN) were isolated and their chromatin accessibility or transcirption examined.

first: M

middle: J

first: James

last: Briscoe

first: Isabel


title: Trophectoderm biopsies of blastocysts for preimplantation genetic testing following in vitro fertilization and embryo culture increases epigenetic dysregulation in a mouse model [RNA-seq]

first: Eric

last: Rhon Calderon

summary: Trophectoderm biopsy for preimplantation genetic testing (TEBx) impacts placental and embryonic health during early development, with some alterations resolving while others worsening later in development. We observed that at E12.5, IVF + TEBx had a worse outcome in terms of changes in DNA methylation and differential gene expression in placentas and whole embryos compared with IVF alone. These changes were reflected in alterations in placental morphology and blood vessel density. At E18.5, early changes in embryos were maintained or worsened, while molecular and morphological changes in the placenta were not different from the IVF group, except for changes in blood vessel density, which persisted. Of note is that most differences were sex specific. We conclude that TEBx has more detrimental effects in both mid-gestation placental and embryonic tissues, with changes in embryonic tissues persisting or worsening in later developmental stages compared to IVF alone. Additionally, consistent with previous work, we report sex differences in the observed effects. Finally, we identified that the addition of vitrification after TEBx has a more pronounced detrimental effect on placental and fetal health. Our findings provide additional support that more studies should be done to assess the impact of new procedures during ART to ensure healthy pregnancies and offspring outcomes.

overall_design: Gene expression analysis using Total RNA extracted from E12.5 placenta n=30 (F=15 and M=15), E12.5 whole fetus n=30 (F=15 and M=15), E18.5 placentas (F=15 and M=15) and E18.5 fetal livers (F=15 and M=15) from 3 different groups Natural, IVF and IVF+TEBx were sequenced using Illumina NovaSeq6000

last: Rhon-Calderon

first: Lisa

last: Vrooman

first: Casey

last: Rosier

first: Teri

last: Ord

first: Monica

last: Mainigi

first: Richard

last: Schultz

first: Marisa

last: Bartolomei


title: RNA-Seq of MDA-MB-231 human triple-negative breast cancer cells treated with a copper chelator

city: Bologna

first: Daniele

last: Mercatelli

address: Via Irnerio 45

department: Pharmacy and Biotechnology

institute: University of Bologna

summary: We report the application of RNA-sequencing of MDA-MB-231 human triple-negative breast cancer cells treated with copper chelator Tetraethylenepentamine (TEPA) for 8 and 24 hours. We show transcriptome changes following copper chelation vs. control untreated cells.vs. control samples

overall_design: MDA-MB-231 human triple-negative breast cancer cells treated with copper chelator TEPA (8 mM) for 8 and 24 hours in vitro

first: Federica

last: Saletta

first: Federico

last: Giorgi

first: Orazio

last: Vittorio


title: Whole-Genome Methylation Profiling Reveals Regions Associated with Painful Temporomandibular Disorders and Active Recovery Processes

city: Montreal

first: Luda

last: Diatchenko

state: Quebec

address: 3775 University Street

department: Faculty of Dental Medicine and Oral Health Sciences

country: Canada

institute: McGill University

summary: Genome wide DNA methylation profiling of samples with/without chronic or acute Temporomandibular Disorders (TMD). The Illumina Infinium Human methylationEPIC Beadchip was used to obtain DNA methylation profiles across 1,051,943 CpGs in TMD samples. Samples included 452 non-TMD and 496 chronic TMD from OPPERA I, 36 healthy and 123 acute TMD from OPPERA II.

overall_design: Bisulphite converted DNA from the 1107 samples were hybridised to the Illumina Infinium Human MethylationEPIC Beadchip

first: Shad

last: Smith

first: Xiang

last: Ao

first: Marc

last: Parisien


title: Principles of chromosome organization for meiotic recombination

city: Washington

first: Mathilde

last: Biot

address: 800 22nd St NW

institute: George Washington University

summary: In meiotic cells, chromosomes are organized as chromatin loop arrays anchored to a protein axis. This organization is essential to regulate meiotic recombination, from DNA double-strand break (DSB) formation to their repair. In mammals, it is unknown how chromatin loops are organized along the genome and how proteins participating in DSB formation are tethered to the chromosome axes. Here, we identified three categories of axis-associated genomic sites: PRDM9 binding sites, where DSBs form, binding sites of the insulator protein CTCF, and H3K4me3-enriched sites. We demonstrated that PRDM9 promotes the recruitment of MEI4 and IHO1, two proteins essential for DSB formation. In turn, IHO1 anchors DSB sites to the axis components HORMAD1 and SYCP3. We discovered that IHO1, HORMAD1 and SYCP3 are associated at the DSB ends during DSB repair. Our results highlight how interactions of proteins with specific genomic elements shape the meiotic chromosome organization for recombination.

overall_design:
Chromatin immunoprecipitation DNA-sequencing (ChIP-seq) for PRDM9, MEI4, IHO1, HORMAD1, SYCP3 and CTCF proteins in differents genetic backgrounds in testes enriched in Leptotene-Zygotene spematocytes
Please note that no processed data is provided for the following knockout samples as all processed data have been subtracted by its corresponding knockout (as detailed in the sample data processing field):
Prdm9 ChIP-seq of the Prdm9KO mouse
MEI4 ChIP-seq of the Mei4KO mouse
IHO1 ChIP-seq of the Iho1KO mouse
HORMAD1 ChIP-seq of the Hormad1KO mouse
SYCP3 ChIP-seq of the Sycp3KO mouse


title: The effect of CRISPLD2 on  TGFβ-induced fibroblast fibrosis

city: changsha

first: Liqing

last: Ding

address: xiangya street

institute: Central South University

summary: Systemic sclerosis (SSc) is an autoimmune connective tissue disease involving multiple organs. The most common clinical symptom of SSc is progressive fibrosis of the skin, and the pathologically manifestations of skin were activation and proliferation of fibroblasts and continuous proliferation of extracellular matrix. Transforming growth factor β (TGFβ) can promote the proliferation and activation of fibroblasts, causing excessive deposition of collagen and structural proteins, and thereby causing fibrosis and dysfunction of tissues and organs. In this study, human cysteine-rich secreted protein LCCL domain protein 2 (CRISPLD2) was found increased reactivity in TGFβ induced fibroblasts, and we further confirmed that CRISPLD2 can participate in TGFβ induced fibroblast fibrosis from multiple perspectives and levels, and investigated the mechanism of CRISPLD2 in fibrosis, providing evidence for CRISPLD2 to become a clinical potential therapeutic target and a new biomarker.

overall_design: We examined the effect of CRISPLD2 on fibrosis genes by knocking down the expression of CRISPLD2 or up-regulating CRISPLD2 expression in human fibroblasts.


title: Effect of umbilical cord mesenchymal stem cells on preadipocyte differentiation

city: Taiyuan

first: Jingyi

last: Feng

address: Xinghualing

institute: The Second Hospital of Shanxi Medical University

summary: Umbilical cord mesenchymal stem cells (ucMSCs), being multipotent stem cells located within Wharton's jelly, have garnered substantial interest in the medical field due to their low immunogenicity and proven capabilities in inflammation attenuation, immune modulation, and regenerative applications. Multiple studies have evidenced that ucMSCs not only contribute to disease treatment but also exert an effect on adipose tissue, hinting at a potential relationship between these entities. It is widely acknowledged that adipose tissue predominantly originates from mesenchymal stem cells (MSCs), and that MSCs within a lipogenic milieu show increased commitment towards the adipogenic lineage. Consequently, we speculate that a complex interplay might exist between hucMSCs and adipose tissue during adipocyte differentiation. This study aims to investigate the specific nature of this influence and elucidate the underlying mechanisms involved.

overall_design: We performed transcriptomic profiling through RNA-seq analysis on 3T3-L1 cells cultivated in a co-culture setting, wherein 3T3-L1 cells were seeded in the lower chamber, while human umbilical cord mesenchymal stem cells (hucMSCs) were either present or absent in the upper chamber of a 0.4 μm Transwell insert. The cells were subjected to adipogenic differentiation medium (HG-DMEM supplemented with 10% FBS, 2 μmol/L rosiglitazone, 1 μmol/L dexamethasone, 0.5 mmol/L IBMX, and 10 mg/L insulin) for 72 hours, allowing us to compare gene expression patterns between 3T3-L1 cells co-cultured with and without hucMSCs.

first: Hongwei

last: Wang


title: RNA sequencing of sort-purified ILC3s from IBD patients

city: New York

first: Veronika

last: Horn

address: 413 East 69th Street

institute: Weill Cornell Medicine

summary: Group 3 innate lymphoid cells (ILC3s) are abundant in the developing or healthy intestine to critically support tissue homeostasis in response to microbial cues and other environmental signals. However, during gastrointestinal disease including infections, colorectal cancer, or inflammatory bowel disease (IBD), intestinal ILC3 numbers are dramatically reduced and the remaining ILC3s become dysfunctional which fuels disease and barrier breakdown. To define the underlying transcriptomic changes, we employed RNA sequencing of ILC3s from IBD patients. This may help to gain a deeper understanding of the mechanisms driving these alterations and ultimately lead to novel preventive, diagnostic, or therapeutic opportunities in IBD.

overall_design: Human ILC3s (CD45+CD3-CD4-CD8-CD19-CD94-CD14-CD123-FcεRIa-CD34-CD11c-CRTH2-CD127+CD117+) were sort-purified from surgical-resection samples from the colon of patients with Ulcerative Colitis or Crohn’s Disease. Sorted cells were used to prepare RNA sequencing libraries by the Epigenomics Core at Weill Cornell Medicine, using the Clontech SMARTer Ultra Low Input RNA Kit V4 (Clontech Laboratories). Sequencing was performed on an Illumina HiSeq 4000, yielding 50-bp single-end reads. Raw sequencing reads were demultiplexed with Illumina CASAVA (v.1.8.2). Adapters were trimmed from reads using FLEXBAR (v.2.4) (Dodt et al., 2012) and reads were aligned to the NCBI GRCh37/hg19 human genome using the STAR aligner (v.2.3.0) (Dobin et al., 2013) with default settings. Reads per gene were counted using Rsubread (Liao et al., 2019). Prior to differential expression analysis, genes were prefiltered, keeping only those genes with 50 or more counts in at least two samples. Differential expression analysis was performed using DESeq2 version 1.20.0 (Love et al., 2014) using both site (inflamed/adjacent tissue) and patient ID as factors in the design. A false discovery rate of 0.1 was taken to indicate significance. Principal components analysis (PCA) was performed using the top 500 highest variance genes after applying DESeq2′s variance stabilizing transformation. The degree to which samples clustered by site (inflamed versus adjacent tissue) in the PCA was assessed using PERMANOVA (Anderson, 2001) as implemented by the adonis function of the vegan R package (Oksanen et al., 2019) using the Euclidean metric and 20,000 permutations.

first: Jeremy

last: Goc

first: Anees

last: Ahmed

first: Gregory

last: Sonnenberg


title: Alternate high fat diet aggravates atherosclerosis through an IL1B- 2 dependent reprogramming of neutrophil progenitors

first: Hafid

last: Ait-Oufella

address: 56, Rue Leblanc

institute: Inserm

summary: Systemic immune responses induced by chronic hypercholesterolemia contribute to the initiation, progression and complications of atherosclerosis. However, it is common for individuals to change dietary habits over time. The consequences of an alternating high fat diet and the associated variations in plasma cholesterol levels on atherosclerosis are unknown. To address this relevant issue, we developed a novel protocol in atherosclerosis-prone mice that allowed us to compare the effects of alternate versus continuous high fat diet (HFD) on atherosclerosis, while keeping the overall period of exposure to HFD similar between groups. We showed that an alternate HFD lead to accelerated atherosclerosis in Ldlr-/- and Apoe 55 -/- mice compared to continuous HFD. This pro-atherogenic effect of alternate HFD was also observed in Apoe-/-Rag2 57 -/- mice lacking T, B, and NKT cells, ruling out the role of the adaptive immune system in the observed phenotype. Employing various complementary in vivo approaches, we discovered that discontinuing HFD in the alternate group downregulated Runx1, a negative regulator of inflammatory signaling pathways in the myeloid lineage. Consequently, after re61 exposure to HFD, myeloid progenitors were primed to respond to HFD re-exposure by differentiating into IL-1-producing immature neutrophils, and inducing a state of emergency myelopoiesis. Subsequently, neutrophils markedly increased in the peripheral blood, infiltrated atherosclerotic lesions and locally released neutrophil extracellular traps. Anti-Ly6G neutrophil depletion abolished the pro-atherogenic effects of alternate HFD. Specific deletion of Il1b and Il1 receptor confirmed that the IL-1 signaling pathway was a major driver of the pro67 inflammatory and pro-atherogenic neutrophil signature. Finally, treatment with anti-IL-1 neutralizing antibody or an inflammasome inhibitor during re-exposure to HFD reversed the pro-atherogenic effects of alternate HFD. In summary, we showed that alternate HFD accelerates atherosclerosis through IL-1-dependent neutrophil progenitor reprogramming.

overall_design: To investigate the impact of hypercholesterolemia re-exposure on atherosclerosis, we developed a protocol with 2 different diet regimens. One group of 6-week old female Ldlr-/- 360 mice was put on a so-called “alternate” HFD consisting of a first period of 4 weeks of HFD, followed by 8 weeks of regular chow diet, and then a final 4-weeks of HFD. The control group was fed a so-called “continuous” HFD during the last 8 weeks of the protocol

first: Jean-Rémi

last: Lavillegrand

last: Diedisheim


title: Leveraging Single-Cell Sequencing to Classify and Characterize Tumor Subgroups in Bulk RNA-Sequencing Data

city: Houston

first: Akdes

last: Serin Harmanci

state: TX

address: One Baylor Plaza

institute: Baylor College of Medicine

summary: We develop an algorithm for the integration of single-cell sequencing, RNA-inferred CNVs, and bulk transcriptomic sequencing to improve molecular classification of tumor sub-groups.

overall_design: Human meningioma

first: Akash

last: Patel


title: Identifying STRN3-RARA as a new fusion gene for acute promyelocytic leukemia [RNA-seq 2]

city: Chengdu, Cihna

first: Xaingyu

last: Pan

state: Sichuan

address: No.17 Renming road section3

department: State Key Laboratory of Biotherapy, West China Hospital, Sihcuan University.

institute: Sichuan University

summary: Acute promyelocytic leukemia (APL) is a distinct subtype of acute myeloid leukemia, that is generally driven by PML-RARA, resulting from a balanced chromosomal translocation t(15;17) (q24.1;q21.2). However, approximately 2% of APL patients carry other variants of RARA-fusions, which pose challenges for diagnosis and treatment. Here, we report a novel t(14;17) translocation in an APL patient that gave rise to a new fusion gene, STRN3-RARA. STRN3 forms a complex called the striatin-interacting phosphatase and kinase (STRIPAK), which couples kinases to protein phosphatase 2A and regulates their activities. Like other APL patients with RARA-variants, this patient quickly relapsed after the initial response to all-trans retinoic acid (ATRA) treatment. Mechanistically, we demonstrated that STRN3-RARA, in cooperating with UTX deficiency, which was mutated in the patient, drove APL formation in mice. Additionally, we found that STRN3-RARA cells were specifically susceptible to the TNFα pathway. Inhibition of this pathway by cepharanthine, an FDA-approved drug, effectively suppressed the growth of U937 cells with STRN3-RARA expression, as well as relapsed APL cells from the patient. Taken together, our study identified a new APL fusion gene, STRN3-RARA, and validated it as a functional APL driver, providing insight into the diagnosis and treatment of non-classic APL patients.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: Bulk RNAseq of murine sgUtx;SR APL cells treated with 200nM ATRA or vehicle in vitro. Bulk RNAseq of APL patient's bone marrow (BM) cells with STRN3-RARA(SR) fusion before treatment and treatment relapse.

first: Xuelan

last: Chen

first: Qi

last: Zhang

first: Chong

first: Yu

last: Liu


title: Multiomic profiling of medulloblastoma reveals subtype-specific targetable alterations at the proteome and N-glycan level [RNA-Seq]

city: Hamburg

first: Julia

middle: Elisabeth

last: Neumann

address: Martinistrasse 52

department: ZMNH

institute: University Hospital Hamburg Eppendorf

summary: Medulloblastomas (MBs) are malignant pediatric brain tumors that are molecularly and clinically very heterogenous. To unravel phenotypically relevant MB subtypes, we compiled a harmonized proteome dataset of 167 MBs and integrated findings with DNA methylation and N-glycome data. Six proteome MB subtypes emerged, that could be assigned to two main molecular programs: transcription/translation (pSHHt, pWNT and pGroup3-Myc), and synapses/immunological processes (pSHHs, pGroup3 and pGroup4). Multiomic analysis revealed different conservation levels of proteome features across MB subtypes at the DNA-methylation level. Aggressive pGroup3-Myc MBs and favorable pWNT MBs were most similar in cluster hierarchies concerning overall proteome patterns but showed different protein abundances of the vincristine resistance associated multiprotein complex TriC/CCT and of N-glycan turnover associated factors. The N-glycome reflected proteome subtypes and complex-bisecting N-glycans characterized pGroup3-Myc tumors. Our results shed light on new targetable alterations in MB and set a foundation for potential immunotherapies targeting glycan structures

overall_design: 21 human MB samples were analyzed using RNA Seq. Data was integrated with DNA Methylome and Proteome data

first: Shweta

last: Godbole

first: Hannah

last: Voss


title: Patient-Derived Organoids Recapitulate Pathological Intrinsic and Phenotypic Features of Fibrous Dysplasia

city: Seongnam-si

first: Chan Yeong

last: Heo

state: Gyeonggi-do

address: 82, Gumi-ro 173 Beon-gil, Bundang-gu

country: South Korea

institute: Seoul National University Bundang Hospital

summary: Fibrous dysplasia (FD) is a rare bone disorder characterized by the replacement of normal bone with benign fibro-osseous tissue. Developments in our understanding of the pathophysiology and treatment options are impeded by the lack of suitable research models. In this study, we developed an in vitro organotypic model capable of recapitulating key intrinsic and phenotypic properties of FD. Transcriptomic profiling of individual cells isolated from patient lesional tissues revealed extensive intralesional molecular and cellular heterogeneity, indicative of pathogenic fibrotic processes.

overall_design: A total of 3 craniofacial fibrous dysplasia tissue samples were collected from each patient (n=3) and analyzed using scRNA-seq.

first: Ha-Young

last: Kim

first: Clementine

last: Charton

first: Jung

last: Shim

first: So

middle: Y

last: Lim

first: Jinho

first: Sejoon

last: Lee

last: Ohn

first: Baek

middle: K

first: Chan


title: Identifying STRN3-RARA as a new fusion gene for acute promyelocytic leukemia [RNA-seq]

first: Xaingyu

overall_design: Bulk RNAseq of U937 cells transduced with pMIG; sgUTX-pMIG; SR and sgUTX-SR.


title: Identifying STRN3-RARA as a new fusion gene for acute promyelocytic leukemia [CUT&TAG]

overall_design: CUT&Tag of Flag-STRN3-RARA(SR) in U937 cells transduced with SR.

first: Xuelan


title: Adaptive Structural Variants Contributing to Human Brain Development Revealed by 1,026 Rhesus Macaque Genomes

city: Beijing

first: Ying

address: 5 Summer Palace Road, Haidian District, Beijing

department: College of Future Technology

institute: Peking University

summary: Clarifying structural variants (SV) profiles in nonhuman primates could provide insights into the genetic background underlying human-specific traits, but such resources are largely lacking. Here, we report the largest SV atlas generated to date from a population of 1,026 macaques, verified by genome assembly for one of them. This accurate, quantitative map indicates stronger purifying selection on inversions located in regulatory regions, suggesting a strategy for prioritizing those with the most important functions. We then identified 75 human-specific inversions and prioritized them. Notably, the top-ranked inversions have substantially shaped the transcriptome through their dual-effects of reconfiguring the ancestral genomic architecture and introducing regional mutation hotspots. As a proof-of-concept, the overexpression of APCDD1, located on one of these inversions and downregulated during human evolution, significantly accelerated neuronal maturation, while its depletion in mice delays the neuronal maturation and subsequently improved their cognitive ability. This study thus provides a valuable resource to explore human evolution and diseases,and broaden the understanding of the contribution of SVs in shaping the distinct features in human brain development.

overall_design: scRNA-seq of wild type and Apcdd1+/- mouse embryonic brain at E10.5

first: Wanqiu

last: Ding

first: Xiangshang

last: Li

first: Jie

first: Jiaxin

last: Wang

first: Li

first: Chuan-Yun


title: COP1 SUPPRESSOR 6 promotes photomorphogenesis by repressing the transcription and activity of PIF4 and PIF5

first: Xuncheng

address: 5 Yiheyuan Road

institute: Peiking University

summary: Light signaling precisely controls the photomorphogenic development in plants. In this study, we report COP1 SUPPRESSOR 6 (CSU6) function as positive regulator of light signaling. Loss of CSU6 function largely rescued the cop1-6 constitutively photomorphogenic phenotype. The hypocotyl length of csu6 mutant seedlings was shorter in the dark, but longer than that of wide-type in the light. CSU6 not only associated with the promoter regions of PIF4 and PIF5 to inhibit their expression during the day, but also directly interacts with both PIF4 and PIF5 to repress their transcriptional activity. CSU6 negatively controls a large group of PIF4- and PIF5-mediated genes' expression. Mutations in PIF4 and/or PIF5 are epistatic to the loss of CSU6, suggesting that CSU6 acts upstream of PIF4 and PIF5. Taken together, CSU6 promotes photomorphogenesis by negatively regulating PIF4 and PIF5 transcription and biochemical activity.

overall_design: Col-0 and csu6-2 mutant seedlings were grown in white light for 5 d. The samples were harvested and used to isolate total RNA with an RNeasy Plant Mini Kit (Qiagen).

first: Dongqing

last: Xu


title: Identifying STRN3-RARA as a new fusion gene for acute promyelocytic leukemia

last: Pan

summary: Here we report a new fusion gene, STRN3-RARA, in acute promyelocytic leukemia (APL). It cooperates with UTX deficiency to drive full-blown APL in mice. Although STRN3-RARA leukemia quickly relapses after all-trans retinoic acid treatment, it can be restrained by cepharanthine.

overall_design: Refer to individual Series


title: Multi-tissue transcriptomic and metabolomic profile of ozone exposure in male WKY rats

city: Research Triangle Park

first: Thomas

last: Jackson

state: NC

address: 109 TW Alexander Dr

department: CPHEA

institute: United States Environmental Protection Agency

summary: Air pollutant exposures have been linked to systemic disease; however, underlying mechanisms between single-tissue exposures and systemic responses are poorly understood. A prototypic inducer of stress, ozone causes respiratory and systemic, multiorgan effects through neuroendocrine stress response activation. The goal of the presented study was to assess transcriptomic signatures of multiple tissues and serum metabolomics to understand how neuroendocrine and adrenal-derived stress hormones contribute to multiorgan health outcomes. Male Wistar Kyoto rats (12-13 weeks old) were exposed to filtered air or 0.8 ppm ozone for 4-hours, and blood/tissues were collected immediately post-exposure. Each tissue had distinct expression profile at baseline. Ozone changed (adjusted p-value < .1, absolute fold-change > 50%) 5,102 genes in muscle, 2,516 in adrenals, 1,640 in lung, 1,333 in liver, 1,242 in adrenals and 274 in hypothalamus. Serum metabolomic analysis identified 863 metabolites, of which 447 were significantly altered in ozone-exposed rats (adjusted p-value < .1, absolute fold change > 20%). Although overall hypoxia, GPCR signaling and glucocorticoid signaling pathways were commonly changed in most tissues, gene signatures within overrepresented pathways showed limited overlap between tissues. This pattern suggested the distribution of receptors and transcriptional mechanisms for stress hormones are likely tissue-specific and involve induction of different gene sets with shared initiating triggers. Metabolomic analysis suggested major changes in lipids, amino acids and metabolites linked to gut microbiome, which correlated with transcriptional changes identified through pathway analysis within liver, muscle, and adipose tissues. Systems-level examination of tissue-specific biological mechanisms could further understanding of air pollution-related health consequences.

overall_design: Examination of transcriptomic data from tissues (lung, hypothalamus, adrenals, liver, adipose, and muscle) from male WKY rats exposed to either air or 0.8ppm ozone for 4 hours

first: John

last: House

first: Andres

last: Henriquez

first: Mette

last: Schladweiler

first: Kimberly

first: Anna

last: Fisher

first: Sam

last: Snow

first: Devin

last: Alewel

first: Allison

last: Motsinger-Reif

first: Urmila

last: Kodavanti


title: Gene expression analysis in the presence or absence of N-terminal tag (9myc) of Swd2 in Saccharomyces cerevisiae

city: Chuncheon

first: Seho

last: Kim

address: 강원 춘천시 우석로79번길 15-5

department: Department of biomedical science

institute: Kangwon National Unversity

summary: project abstract : H3K4 methylation is a well-conserved histone modification from yeast to human. Because H3K4 methylase Set1 and its complex, COMPASS (Complex of proteins associated with Set1), are conserved from yeast to humans, budding yeast has been studied as an acceptable model organism. Since COMPASS components affect Set1 protein stability and H3K4 methylation activity variously, it is important to study how Set1 is regulated by complex components. However, deletion mutant of Swd2 component of COMPASS is not viable, although overexpression of Sen1 fragment enables the construction of Swd2 deletion mutant. This study found that positioning epitope tag to the N-terminal of Swd2 did not decrease interaction between Swd2 and Set1, but reduced the stability of both proteins, Swd2 and Set1, and global H3K4 methylation. Also, we observed that overexpression of N-terminal tagged Swd2 caused increased Set1 protein level and bulk H3K4 methylation. Therefore, Set1 protein can maintain its protein level only when enough Swd2 exist to cover the protein amount of Set1. Also, by comparing RNA sequencing analysis of N-terminal tagged Swd2 and Swd2 deletion mutant with Sen1 fragment overexpression, we isolated genes regulated by Swd2. In conclusion, we suggest that the abundance of Swd2 is important to regulate the protein stability of Set1 and the regulation of gene expression.

overall_design: mRNA profiles of 9myc-Swd2 strain and isogenic WT strain in S.cerevisiae, duplicate, by illumina HiSeq2500

first: Jung-Shin

first: Junsoo

last: Oh

first: Jueun

first: Soojin

last: Yeom


title: Transcriptome profiling of oxidase knockout mice response to gingival inflammation using RNA-seq

city: Louisville

first: Eric

middle: Christian

last: Rouchka

state: Kentucky

address: 522 East Gray Street

department: Biochemistry and Molecular Genetics

institute: University of Louisville

summary: Genetic defects in neutrophil function or trafficking are highly associated with oral inflammation and periodontitis. The leukocyte NADPH oxidase enzymes complex is a multi-subunit enzyme that has been described to play important immunomodulatory roles in limiting the inflammatory responses of neutrophils and macrophages. Here, we determined the impact of loss of NADPH oxidase dependent reactive oxygen species (ROS) generation in gingival inflammatory responses using a model of ligature induced murine periodontitis.

overall_design: Total RNA was isolated from inflamed gingival tissues (tissue surrounding the second maxillary ligated molar) as well as gingival tissues of naïve mice. 3 age and sex matched mice were used per group.  Libraries were prepared using the TruSeq Stranded mRNA Library Prep Kit along with TruSeq RNA CD Index Plate from Illumina. Sequencing runs were performed on the Illumina NextSeq 500 using the NextSeq 500/550 75 cycle High Output Kit v2.5.

first: Juhi

last: Bagaitkar

middle: C


title: AOS10-FMT could rescure the adverse effects induced by high fat diet on the Spleen

city: Qingdao

first: Yong

last: Zhao

state: Shandong

address: 700 Changcheng Road

department: College of Life Sciences

institute: Qingdao Agricultural University

summary: We report the side-effects of High fat diet on the spleen, and foud that the AOS10-FMT could rescure the side-effect of High fat diet in many factors,such as inflammation

overall_design: Exploration of the FMT effects on the damaged spleen induced by High fat diet

first: Yanan

last: Hao


title: AOS10-FMT could rescure the adverse effects induced by high fat diet on the Colon

summary: We report the side-effects of High fat diet on the colon, and foud that the AOS10-FMT could rescure the side-effect of High fat diet in many factors

overall_design: Exploration of the FMT effects on the damaged colon induced by High fat diet


title: AOS10-FMT could rescure the adverse effects induced by high fat diet on the testis

summary: We report the side-effects of High fat diet on the testis, and foud that the AOS10-FMT could rescure the side-effect of High fat diet in many factors,such as spermatogenesis,lipid metabolism and oxidative stress

overall_design: Exploration of the FMT effects on the damaged testis induced by High fat diet


title: Human Clariom S Array in OVCAR8 cells after silencing HSD17B14

first: Shaolin

last: Ma

state: Tx

address: 1881 East Road

institute: MD Anderson Cancer Center

summary:
We used a functional small interfering RNA (siRNA) screen in ovarian cancer cells to identify 17β-hydroxysteroid dehydrogenase type 14 (HSD17B14) as a novel regulator of small EV secretion.
We showed that the knockdown of HSD17B14 altered multiple gene expression in OVCAR8 cells.

overall_design: OVCAR8 cells were transfected with siControl and siHD17B14 for 48 hours. Total RNA was isolated using TRizol reagent (Thermo Fisher Scientific) and Direct-zol column kit (Genesee Scientific).

first: Karem

middle: A

last: Court

first: Anil

last: Sood

first: Cristina

last: Ivan


title: AOS10-FMT could rescure the adverse effects induced by high fat diet on the kidney

summary: We report the side-effects of High fat diet on the liver, and foud that the AOS10-FMT could rescure the side-effect of High fat diet in many factors,such as lipid metabolism and oxidative stress

overall_design: Exploration of the FMT effects on the damaged kidney induced by High fat diet


title: Differences in gene expression among AMD and non-AMD patients arise after initial fibroblasts are reprogrammed to iPSC and differentiation into RPE

city: New Haven

first: Hui

middle: Cong

last: Cai

state: CT

address: 300 George St, Suite 8100

institute: Yale University

summary:
Comparing fibroblasts and derived -iPSC and - RPE cells from human AMD and non-AMD donors
Retinal pigment epithelium (RPE) generated from skin biopsies of donors with age-related macular degeneration (AMD) exhibit a disease phenotype and a distinct transcriptome compared to age-matched controls. We investigated whether similar differences existed in the skin fibroblasts and induced pluripotent stem cells (iPSCs) derived from them. Hierarchical cluster and principal component analyses revealed significant overlap in the transcriptome of fibroblasts of AMD and non-AMD donors. After reprogramming, iPSCs exhibited slight differences. In contrast, the transcriptome of RPE derived from AMD and normal donors segregated into two distinct clusters. Differences in the expression of specific genes that were evident between normal and AMD-derived RPE were not observed in fibroblasts or iPSCs. Mitochondrial respiration was reduced in RPE from AMD patients but not in fibroblast or iPSCs. RPE derived from AMD patients have a distinct transcriptome and phenotype compared to controls that is not observed in their corresponding skin fibroblasts or iPSCs.

overall_design: Fibroblasts, iPSC and derived RPE cells, from patients with four (4) advanced AMD and age matched three (3) non-AMD  donors  were used to survey the transcriptons of these samples  with Affymetrix human Gene chips. Affymetrix Transcriptome Analysis Console software (Thermo Fisher Scientific) were used to process and analyze the data.

first: Jie

last: Gong

first: Lucian

last: DelPriore

first: Mark

last: Fields


title: Prognostic classifier for predicting biochemical recurrence in localized prostate cancer patients after radical prostatectomy

city: Barcelona

first: Juanjo

last: Lozano

address: C/ Rosselló 153

department: Plataforma de Bioinformatica

institute: CIBEREHD

summary: Accurate estimation of recurrence risk is needed for optimal treatment of clinically localized prostate cancer (PCa) patients. We combined classical clinicopathological predictors of biochemical recurrence (BCR) and molecular markers into a new risk score for predicting BCR after radical prostatectomy (RP). A retrospective study which included 122 PCa patients who attended our department between 2000 and 2007 was conducted. Total RNA was isolated from formalin-fixed paraffin embedded PCa tissue. Gene expression patterns were analyzed in 21 selected samples from 7 localized, 6 locally advanced, and 8 metastatic PCa patients using Illumina microarrays. Expression levels of 41 genes were validated by quantitative PCR in an independent retrospective series of 101 patients with ≥ 10 years follow-up who underwent RP for clinically localized PCa. Univariate and multivariate logistic regression analysis were used to identify individual predictors of BCR. A risk score (RS) for predicting BCR including clinicopathological and gene expression data was developed and Kaplan-Meier curves were generated. Interaction networks between the genes of the model were built by GeneMANIA Cytoscape plugin. In a median follow-up of 120 months (range 3-190), 37 patients developed BCR (36.6%). Expression levels of 7,930 transcripts differed between clinically localized and locally advanced-metastatic PCa groups (FDR<0.1). A set of 41 genes were validated by quantitative PCR. Regression analysis showed that expression of ASF1B and MCL1 as well as Gleason score, extracapsular extension, seminal vesicle invasion and positive margins were independent prognostic factors of BCR. A RS generated using these gene expression and clinicopathological variables was able to discriminate between two groups of patients with a significantly different probability of BCR (HR 6.24; CI 3.23-12.4, p<0.01), improving the individual discriminative performance of each of these variables on their own. Direct interactions between the two genes of the model were not found. In conclusion, identification of new gene expression patterns associated with a high probability of BCR in clinically localized PCa patients treated with RP, and their combination with clinicopathological variables in a robust, easy-to-use and reliable classifier may contribute to improve PCa risk stratification and, consequently, to tailor treatment and surveillance strategies in these patients.

overall_design: Trasncriptomic whole genome using formalin-fixed paraffin-embedded prostate tissue from 7 localized, 6 locally advanced, and 8 metastatic PCa patients using Illumina microarrays

first: L

last: Mengual

first: J

first: A

last: Alcaraz